Items where Community is "Publications"

Tang, Ziqi, Koo, Peter K (March 2024) Evaluating the representational power of pre-trained DNA language models for regulatory genomics. bioRxiv. (Public Dataset) (Submitted)

Satterlee, James W, Alonso, David, Gramazio, Pietro, Jenike, Katharine M, He, Jia, Arrones, Andrea, Villanueva, Gloria, Plazas, Mariola, Ramakrishnan, Srividya, Benoit, Matthias, Gentile, Iacopo, Hendelman, Anat, Shohat, Hagai, Fitzgerald, Blaine, Robitaille, Gina M, Green, Yumi, Swartwood, Kerry, Passalacqua, Michael J, Gagnon, Edeline, Hilgenhof, Rebecca, Huggins, Trevis D, Eizenga, Georgia C, Gur, Amit, Rutten, Twan, Stein, Nils, Yao, Shengrui, Bellot, Clement, Bendahmane, Mohammed, Frary, Amy, Knapp, Sandra, Särkinen, Tiina, Gillis, Jesse, Van Eck, Joyce, Schatz, Michael C, Eshed, Yuval, Prohens, Jaime, Vilanova, Santiago, Lippman, Zachary B (February 2024) Convergent evolution of plant prickles is driven by repeated gene co-option over deep time. bioRxiv. (Submitted)

Ortiz, Jenelys Ruiz, Lewis, Steven M, Ciccone, Michael, Chatterjee, Deeptiman, Henry, Samantha, Siepel, Adam, Dos Santos, Camila O (January 2024) Single-Cell Transcription Mapping of Murine and Human Mammary Organoids Responses to Female Hormones. Journal of Mammary Gland Biology and Neoplasia, 29 (1). p. 3. ISSN 1083-3021 (Public Dataset)

Amor, Corina, Fernández-Maestre, Inés, Chowdhury, Saria, Ho, Yu-Jui, Nadella, Sandeep, Graham, Courtenay, Carrasco, Sebastian E, Nnuji-John, Emmanuella, Feucht, Judith, Hinterleitner, Clemens, Barthet, Valentin JA, Boyer, Jacob A, Mezzadra, Riccardo, Wereski, Matthew G, Tuveson, David A, Levine, Ross L, Jones, Lee W, Sadelain, Michel, Lowe, Scott W (January 2024) Prophylactic and long-lasting efficacy of senolytic CAR T cells against age-related metabolic dysfunction. Nature Aging. ISSN 2662-8465 (Public Dataset)

Tonelli, Claudia, Yordanov, Georgi N, Hao, Yuan, Deschênes, Astrid, Hinds, Juliene, Belleau, Pascal, Klingbeil, Olaf, Brosnan, Erin, Doshi, Abhishek, Park, Youngkyu, Hruban, Ralph H, Vakoc, Christopher R, Dobin, Alexander, Preall, Jonathan, Tuveson, David A (January 2024) A mucus production programme promotes classical pancreatic ductal adenocarcinoma. Gut. ISSN 0017-5749

Kotagama, Kasuen, Grimme, Acadia L, Braviner, Leah, Yang, Bing, Sakhawala, Rima M, Yu, Guoyun, Benner, Lars Kristian, Joshua-Tor, Leemor, McJunkin, Katherine (January 2024) The catalytic activity of microRNA Argonautes plays a modest role in microRNA star strand destabilization in C. elegans. bioRxiv. (Submitted)

Wang, Julia H, Tsin, Dexter, Engel, Tatiana A (December 2023) Predictive variational autoencoder for learning robust representations of time-series data. arXiv. (Submitted)

Wang, Julia Huiming, Tsin, Dexter, Engel, Tatiana (December 2023) Predictive variational autoencoder for learning robust representations of time-series data. arXiv. (Submitted)

Loh, Liyen, Carcy, Salomé, Krovi, Harsha S, Domenico, Joanne, Spengler, Andrea, Lin, Yong, Torres, Joshua, Palmer, William, Norman, Paul J, Stone, Matthew, Brunetti, Tonya, Meyer, Hannah V, Gapin, Laurent (December 2023) Unraveling the Phenotypic States of Human innate-like T Cells: Comparative Insights with Conventional T Cells and Mouse Models. bioRxiv. (Submitted)

Tang, Ziqi, Toneyan, Shushan, Koo, Peter K (December 2023) Current approaches to genomic deep learning struggle to fully capture human genetic variation. Nature Genetics, 55 (12). pp. 2021-2022. ISSN 1061-4036

Zhang, Anqi, Zador, Anthony M (December 2023) Neurons in the primary visual cortex of freely moving rats encode both sensory and non-sensory task variables. PLoS Biology, 21 (12). e3002384. ISSN 1545-7885

Passalacqua, Michael John, Gillis, Jesse (November 2023) Coexpression enhances cross-species integration of scRNA-seq across diverse plant species. bioRxiv. (Submitted)

Staklinski, Stephen J, Scheben, Armin, Siepel, Adam, Kilberg, Michael S (November 2023) Utility of AlphaMissense predictions in Asparagine Synthetase deficiency variant classification. bioRxiv. (Submitted)

Maia-Silva, Diogo, Schier, Allison C, Skopelitis, Damianos, Kechejian, Vahag, Alpsoy, Aktan, Liverpool, Jynelle, Taatjes, Dylan J, Vakoc, Christopher R (October 2023) Marker-based CRISPR screening reveals a MED12-p63 interaction that activates basal identity in pancreatic ductal adenocarcinoma. bioRxiv. (Submitted)

Funamizu, A, Marbach, F, Zador, AM (October 2023) Stable sound decoding despite modulated sound representation in the auditory cortex. Current Biology, 33 (20). 4470-4483.e7. ISSN 0960-9822

Aguirre, Lyndsey, Hendelman, Anat, Hutton, Samuel F, McCandlish, David M, Lippman, Zachary B (October 2023) Idiosyncratic and dose-dependent epistasis drives variation in tomato fruit size. Science, 382 (6668). pp. 315-320. ISSN 0036-8075

Ortiz, Jenelys Ruiz, Lewis, Steven M, Ciccone, Michael F, Chatterjee, Deeptiman, Henry, Samantha, Siepel, Adam, Dos Santos, Camila O (September 2023) Single-cell transcription mapping of murine and human mammary organoids responses to female hormones. bioRxiv. (Public Dataset) (Submitted)

Amor, Corina, Fernández-Maestre, Inés, Chowdhury, Saria, Ho, Yu-Jui, Nadella, Sandeep, Graham, Courtenay, Carrasco, Sebastian E, Nnuji-John, Emmanuella, Feucht, Judith, Hinterleitner, Clemens, Barthet, Valentin JA, Boyer, Jacob A, Mezzadra, Riccardo, Wereski, Matthew G, Tuveson, David A, Levine, Ross L, Jones, Lee W, Sadelain, Michel, Lowe, Scott W (September 2023) Prophylactic and long-lasting efficacy of senolytic CAR T cells against age-related metabolic dysfunction. Research Square. (Submitted)

Iohannes, Sessen Daniel, Jackson, David (September 2023) Tackling redundancy: genetic mechanisms underlying paralog compensation in plants. New Phytologist. ISSN 0028-646X

Funamizu, Akihiro, Marbach, Fred, Zador, Anthony M (September 2023) Stable sound decoding despite modulated sound representation in the auditory cortex. bioRxiv. (Submitted)

Sroka, Martyna W, Skopelitis, Damianos, Vermunt, Marit W, Preall, Jonathan B, El Demerdash, Osama, de Almeida, Larissa MN, Chang, Kenneth, Utama, Raditya, Gryder, Berkley, Caligiuri, Giuseppina, Ren, Diqiu, Nalbant, Benan, Milazzo, Joseph P, Tuveson, David A, Dobin, Alexander, Hiebert, Scott W, Stengel, Kristy R, Mantovani, Roberto, Khan, Javed, Kohli, Rahul M, Shi, Junwei, Blobel, Gerd A, Vakoc, Christopher R (September 2023) Myo-differentiation reporter screen reveals NF-Y as an activator of PAX3-FOXO1 in rhabdomyosarcoma. Proceedings of the National Academy of Sciences of USA, 120 (36). e2303859120. ISSN 0027-8424 (Public Dataset)

Lei, Pin-Ji, Pereira, Ethel R, Andersson, Patrik, Amoozgar, Zohreh, Van Wijnbergen, Jan Willem, O'Melia, Meghan J, Zhou, Hengbo, Chatterjee, Sampurna, Ho, William W, Posada, Jessica M, Kumar, Ashwin S, Morita, Satoru, Menzel, Lutz, Chung, Charlie, Ergin, Ilgin, Jones, Dennis, Huang, Peigen, Beyaz, Semir, Padera, Timothy P (September 2023) Cancer cell plasticity and MHC-II-mediated immune tolerance promote breast cancer metastasis to lymph nodes. Journal of Experimental Medicine, 220 (9). e20221847. ISSN 0022-1007 (Public Dataset)

de Ruiter Swain, Jed, Michalopoulou, Evdokia, Noch, Evan K, Lukey, Michael J, Van Aelst, Linda (August 2023) Metabolic partitioning in the brain and its hijacking by glioblastoma. Genes and Development, 37. pp. 681-702. ISSN 0890-9369

Kahng, Jessica A, Xavier, Andre M, Ferro, Austin, Auguste, Yohan SS, Cheadle, Lucas (August 2023) Integrated high-confidence and high-throughput approaches for quantifying synapse engulfment by oligodendrocyte precursor cells. bioRxiv. (Submitted)

Girish, Vishruth, Lakhani, Asad A, Thompson, Sarah L, Scaduto, Christine M, Brown, Leanne M, Hagenson, Ryan A, Sausville, Erin L, Mendelson, Brianna E, Kandikuppa, Pranav K, Lukow, Devon A, Yuan, Monet Lou, Stevens, Eric C, Lee, Sophia N, Schukken, Klaske M, Akalu, Saron M, Vasudevan, Anand, Zou, Charles, Salovska, Barbora, Li, Wenxue, Smith, Joan C, Taylor, Alison M, Martienssen, Robert A, Liu, Yansheng, Sun, Ruping, Sheltzer, Jason M (August 2023) Oncogene-like addiction to aneuploidy in human cancers. Science, 381 (6660). eadg4521. ISSN 0036-8075 (Public Dataset)

Lee, Seung Cho, Adams, Dexter W, Ipsaro, Jonathan J, Cahn, Jonathan, Lynn, Jason, Kim, Hyun-Soo, Berube, Benjamin, Major, Viktoria, Calarco, Joseph P, LeBlanc, Chantal, Bhattacharjee, Sonali, Ramu, Umamaheswari, Grimanelli, Daniel, Jacob, Yannick, Voigt, Philipp, Joshua-Tor, Leemor, Martienssen, Robert A (August 2023) Chromatin remodeling of histone H3 variants by DDM1 underlies epigenetic inheritance of DNA methylation. Cell, 186 (19). 4100-4116.e15. ISSN 0092-8674 (Public Dataset)

Rupert, Deborah D, Pagliaro, Alexa, Choe, Jane, Shea, Stephen D (August 2023) Selective deletion of Methyl CpG binding protein 2 from parvalbumin interneurons in the auditory cortex delays the onset of maternal retrieval in mice. The Journal of Neuroscience. JN-RM-0838-23. ISSN 0270-6474

Wiberg, Akira, Lucey, Maria A, Kleeman, Sam, Kang, Youngjoo, Ng, Mike, Furniss, Dominic (August 2023) Genetic correlations between migraine and carpal tunnel syndrome. Plastic and Reconstructive Surgery. ISSN 0032-1052

Kleeman, Sam O, Thakir, Tuba Mansoor, Demestichas, Breanna, Mourikis, Nicholas, Loiero, Dominik, Ferrer, Miriam, Bankier, Sean, Riazat-Kesh, Yosef JRA, Lee, Hassal, Chantzichristos, Dimitrios, Regan, Claire, Preall, Jonathan, Sinha, Sarthak, Rosin, Nicole, Yipp, Bryan, de Almeida, Luiz GN, Biernaskie, Jeff, Dufour, Antoine, Tober-Lau, Pinkus, Ruusalepp, Arno, Bjorkegren, Johan LM, Ralser, Markus, Kurth, Florian, Demichev, Vadim, Heywood, Todd, Gao, Qing, Johannsson, Gudmundur, Koelzer, Viktor H, Walker, Brian R, Meyer, Hannah V, Janowitz, Tobias (August 2023) Cystatin C is glucocorticoid responsive, directs recruitment of Trem2+ macrophages, and predicts failure of cancer immunotherapy. Cell Genomics, 3 (8). p. 100347. ISSN 2666-979X

Berube, Benjamin, Ernst, Evan, Cahn, Jonathan, Roche, Benjamin, de Santis Alves, Cristiane, Lynn, Jason, Scheben, Armin, Siepel, Adam, Ross-Ibarra, Jeffrey, Kermicle, Jerry, Martienssen, Robert A (August 2023) Teosinte Pollen Drive guides maize domestication and evolution by RNAi. bioRxiv. (Public Dataset) (Submitted)

Lee, Seung Cho, Adams, Dexter W, Ipsaro, Jonathan J, Cahn, Jonathan, Lynn, Jason, Kim, Hyun-Soo, Berube, Benjamin, Major, Viktoria, Calarco, Joseph P, LeBlanc, Chantal, Bhattacharjee, Sonali, Ramu, Umamaheswari, Grimanelli, Daniel, Jacob, Yannick, Voigt, Philipp, Joshua-Tor, Leemor, Martienssen, Robert A (August 2023) Chromatin remodeling of histone H3 variants underlies epigenetic inheritance of DNA methylation. bioRxiv. (Submitted)

Corona, Alberto, Choe, Jane, Muñoz-Castañeda, Rodrigo, Osten, Pavel, Shea, Stephen D (July 2023) A circuit from the locus coeruleus to the anterior cingulate cortex modulates offspring interactions in mice. Cell Reports, 42 (7). p. 112771. ISSN 2211-1247

Ferrer, Miriam, Mourikis, Nicholas, Davidson, Emma E, Kleeman, Sam O, Zaccaria, Marta, Habel, Jill, Rubino, Rachel, Gao, Qing, Flint, Thomas R, Young, Lisa, Connell, Claire M, Lukey, Michael J, Goncalves, Marcus D, White, Eileen P, Venkitaraman, Ashok R, Janowitz, Tobias (July 2023) Ketogenic diet promotes tumor ferroptosis but induces relative corticosterone deficiency that accelerates cachexia. Cell Metabolism, 35 (7). 1147-1162.e7. ISSN 1550-4131

Findling, Charles, Hubert, Felix, Acerbi, Luigi, Benson, Brandon, Benson, Julius, Birman, Daniel, Bonacchi, Niccolò, Carandini, Matteo, Catarino, Joana A, Chapuis, Gaelle A, Churchland, Anne K, Dan, Yang, DeWitt, Eric EJ, Engel, Tatiana A, Fabbri, Michele, Faulkner, Mayo, Fiete, Ila Rani, Freitas-Silva, Laura, Gerçek, Berk, Harris, Kenneth D, Häusser, Michael, Hofer, Sonja B, Hu, Fei, Huntenburg, Julia M, Khanal, Anup, Krasniak, Chris, Langdon, Christopher, Latham, Peter E, P Lau, Petrina Y, Mainen, Zach, Meijer, Guido T, Miska, Nathaniel J, Mrsic-Flogel, Thomas D, Noel, Jean-Paul, Nylund, Kai, Pan-Vazquez, Alejandro, Paninski, Liam, Pillow, Jonathan, Rossant, Cyrille, Roth, Noam, Schaeffer, Rylan, Schartner, Michael, Shi, Yanliang, Socha, Karolina Z, Steinmetz, Nicholas A, Svoboda, Karel, Tessereau, Charline, Urai, Anne E, Wells, Miles J, West, Steven Jon, Whiteway, Matthew R, Winter, Olivier, Witten, Ilana B, Zador, Anthony, Dayan, Peter, Pouget, Alexandre (July 2023) Brain-wide representations of prior information in mouse decision-making. bioRxiv. (Submitted)

Toneyan, Shushan, Koo, Peter K (July 2023) Interpreting Cis -Regulatory Interactions from Large-Scale Deep Neural Networks for Genomics. bioRxiv. (Submitted)

Yan, Ran, Moresco, Philip, Gegenhuber, Bruno, Fearon, Douglas T (June 2023) T cell-Mediated Development of Stromal Fibroblasts with an Immune-Enhancing Chemokine Profile. Cancer Immunology Research. OF1-OF11. ISSN 2326-6066

Lee, Nicholas Keone, Tang, Ziqi, Toneyan, Shushan, Koo, Peter K (May 2023) EvoAug: improving generalization and interpretability of genomic deep neural networks with evolution-inspired data augmentations. Genome Biology, 24 (1). p. 105. ISSN 1474-760X

Guillotin, Bruno, Rahni, Ramin, Passalacqua, Michael, Mohammed, Mohammed Ateequr, Xu, Xiaosa, Raju, Sunil Kenchanmane, Ramírez, Carlos Ortiz, Jackson, David, Groen, Simon C, Gillis, Jesse, Birnbaum, Kenneth D (May 2023) A pan-grass transcriptome reveals patterns of cellular divergence in crops. Nature, 617 (7962). pp. 785-791. ISSN 0028-0836

Hur, Stella K, Somerville, Tim DD, Wu, Xiaoli S, Maia-Silva, Diogo, Demerdash, Osama E, Tuveson, David A, Notta, Faiyaz, Vakoc, Christopher R (April 2023) p73 activates transcriptional signatures of basal lineage identity and ciliogenesis in pancreatic ductal adenocarcinoma. bioRxiv. (Submitted)

Chang, Mario C, Staklinski, Stephen J, Malut, Vinay R, Pierre, Geraldine L, Kilberg, Michael S, Merritt, Matthew E (April 2023) Metabolomic Profiling of Asparagine Deprivation in Asparagine Synthetase Deficiency Patient-Derived Cells. Nutrients, 15 (8). p. 1938. ISSN 2072-6643

Staklinski, Stephen J, Chang, Mario C, Ahrens-Nicklas, Rebecca C, Kaur, Shagun, Stefanatos, Arianna K, Dudenhausen, Elizabeth E, Merritt, Matthew E, Kilberg, Michael S (March 2023) Characterizing asparagine synthetase deficiency variants in lymphoblastoid cell lines. JIMD Reports, 64 (2). pp. 167-179. ISSN 2192-8304

Meze, Katarina, Axhemi, Armend, Thomas, Dennis R, Doymaz, Ahmet, Joshua-Tor, Leemor (February 2023) A shape-shifting nuclease unravels structured RNA. Nature Structural and Molecular Biology. ISSN 1545-9993 (Public Dataset)

Ferrer, Miriam, Mourikis, Nicholas, Davidson, Emma E, Kleeman, Sam O, Zaccaria, Marta, Habel, Jill, Rubino, Rachel, Flint, Thomas R, Connell, Claire M, Lukey, Michael J, White, Eileen P, Coll, Anthony P, Venkitaraman, Ashok R, Janowitz, Tobias (February 2023) Ketogenic diet promotes tumor ferroptosis but induces relative corticosterone deficiency that accelerates cachexia. bioRxiv. (Submitted)

Gao, Yuan, He, Xue-Yan, Wu, Xiaoli S, Huang, Yu-Han, Toneyan, Shushan, Ha, Taehoon, Ipsaro, Jonathan J, Koo, Peter K, Joshua-Tor, Leemor, Bailey, Kelly M, Egeblad, Mikala, Vakoc, Christopher R (January 2023) ETV6 dependency in Ewing sarcoma by antagonism of EWS-FLI1-mediated enhancer activation. Nature Cell Biology. ISSN 1465-7392 (Public Dataset)

Girish, Vishruth, Lakhani, Asad A, Scaduto, Christine M, Thompson, Sarah L, Brown, Leanne M, Hagenson, Ryan A, Sausville, Erin L, Mendelson, Brianna E, Lukow, Devon A, Yuan, Monet Lou, Kandikuppa, Pranav K, Stevens, Eric C, Lee, Sophia N, Salovska, Barbora, Li, Wenxue, Smith, Joan C, Taylor, Alison M, Martienssen, Robert A, Liu, Yansheng, Sun, Ruping, Sheltzer, Jason M (January 2023) Oncogene-like addiction to aneuploidy in human cancers. bioRxiv. (Public Dataset) (Submitted)

Acerbi, L, Aguillon-Rodriguez, V, Ahmadi, M, Amjad, J, Angelaki, D, Arlandis, J, Ashwood, ZC, Banga, K, Barrell, H, Bayer, HM, Benson, J, Benson, B, Bhagat, J, Birman, D, Bougrova, K, Boussard, J, Bruijns, SA, Carandini, M, Catarino, J, Cazettes, F, Dan, Y, Davatolagh, F, Dayan, P, Denève, S, Dong, LL, Engel, T, Fabbri, M, Fiete, I, Findling, C, Freitas-Silva, L, Ganguli, S, Gercek, B, Ghani, N, Gordeliy, I, Haetzel, LM, Hausser, M, Hiratani, N, Hofer, S, Hu, F, Huber, F, Hurwitz, C, Khanal, A, Krasniak, CS, Krishnagopal, S, Krumin, M, Langdon, C, Latham, P, Lau, P, Lee, H, Liu, A, Mainen, ZF, Vergara, HM, Mcgrory, C, McMannon, B, Meijer, GT, Melin, M, Meshulam, L, Miska, NJ, Mitelut, C, Mohammadi, Z, Mrsic-Flogel, T, Murakami, M, Noel, JP, Nylund, K, Vazquez, AP, Paninski, L, Pezzotta, A, Picard, S, Pillow, JW, Pouget, A, Roth, N, Roy, NA, Saniee, K, Schaeffer, R, Shi, Y, Socha, KZ, Soitu, C, Svoboda, K, Taheri, M, Tessereau, C, Urai, AE, Varol, E, Wells, MJ, Whiteway, MR, Windolf, C, Witten, I, Wool, LE, Zador, AM, Bonacchi, N, Chapuis, GA, Churchland, AK, DeWitt, EEJ, Faulkner, M, Harris, KD, Huntenburg, JM, Hunter, M, Laranjeira, IC, Rossant, C, Sasaki, M, Schartner, MM (January 2023) A modular architecture for organizing, processing and sharing neurophysiology data. Nature Methods, 20 (3). pp. 403-407. ISSN 1548-7091 (Public Dataset)

Chang, Mario C, Staklinski, Stephen J, Merritt, Matthew E, Kilberg, Michael S (2023) A method for measurement of human asparagine synthetase (ASNS) activity and application to ASNS protein variants associated with ASNS deficiency. Biology Methods and Protocols, 8 (1). bpad026. ISSN 2396-8923

Karakida Kawaguchi, Risa, Tang, Ziqi, Fischer, Stephan, Rajesh, Chandana, Tripathy, Rohit, Koo, Peter K, Gillis, Jesse (December 2022) Learning single-cell chromatin accessibility profiles using meta-analytic marker genes. Briefings in Bioinformatics. bbac541. ISSN 1467-5463

Xie, Yunyao, Huang, Longwen, Corona, Alberto, Pagliaro, Alexa H, Shea, Stephen D (December 2022) A dopaminergic reward prediction error signal shapes maternal behavior in mice. Neuron. S0896-6273(22)01073. ISSN 0896-6273

Toneyan, Shushan, Tang, Ziqi, Koo, Peter K (December 2022) Evaluating deep learning for predicting epigenomic profiles. Nature Machine Intelligence, 4 (12). pp. 1088-1100. ISSN 2522-5839

Majdandzic, Antonio, Rajesh, Chandana, Tang, Amber, Toneyan, Shushan, Labelson, Ethan, Tripathy, Rohit, Koo, Peter K (November 2022) Selecting deep neural networks that yield consistent attribution-based interpretations for genomics. Proc Mach Learn Res, 200. pp. 131-149. ISSN 2640-3498

Hashimoto, Taiki, Takayanagi, Daisuke, Yonemaru, Junpei, Naka, Tomoaki, Nagashima, Kengo, Yatabe, Yasushi, Shida, Dai, Hamamoto, Ryuji, Kleeman, Sam O, Leedham, Simon J, Maughan, Timothy, Takashima, Atsuo, Shiraishi, Kouya, Sekine, Shigeki (October 2022) Clinicopathological and molecular characteristics of RSPO fusion-positive colorectal cancer. British Journal of Cancer, 127 (6). pp. 1043-1050. ISSN 0007-0920

Kleeman, Sam O, Cordioli, Mattia, Timmers, Paul RHJ, Khan, Atlas, Tober-Lau, Pinkus, Kurth, Florian, Demichev, Vadim, Meyer, Hannah V, Wilson, James F, Ralser, Markus, Kiryluk, Krzysztof, Ganna, Andrea, Baillie, Kenneth, Janowitz, Tobias (October 2022) Cystatin C is associated with adverse COVID-19 outcomes in diverse populations. iScience, 25 (10). p. 105040. ISSN 2589-0042 (In Press)

Auguste, Yohan SS, Ferro, Austin, Kahng, Jessica A, Xavier, Andre M, Dixon, Jessica R, Vrudhula, Uma, Nichitiu, Anne-Sarah, Rosado, Daniele, Wee, Tse-Luen, Pedmale, Ullas V, Cheadle, Lucas (September 2022) Oligodendrocyte precursor cells engulf synapses during circuit remodeling in mice. Nature Neuroscience. ISSN 1097-6256

Chae, Honggoo, Banerjee, Arkarup, Dussauze, Marie, Albeanu, Dinu F (September 2022) Long-range functional loops in the mouse olfactory system and their roles in computing odor identity. Neuron. S0896-6273(22)00810. ISSN 0896-6273

Carter, Jason A, Strömich, Léonie, Peacey, Matthew, Chapin, Sarah R, Velten, Lars, Steinmetz, Lars M, Brors, Benedikt, Pinto, Sheena, Meyer, Hannah V (August 2022) Transcriptomic diversity in human medullary thymic epithelial cells. Nature Communications, 13 (1). p. 4296. ISSN 2041-1723

Patel, B, Kleeman, SO, Neavin, D, Powell, J, Baskozos, G, Ng, M, Ahmed, WUR, Bennett, DL, Schmid, AB, Furniss, D, Wiberg, A (August 2022) Shared genetic susceptibility between trigger finger and carpal tunnel syndrome: a genome-wide association study. The Lancet Rheumatology, 4 (8). e556-e565. ISSN 2665-9913

Gegenhuber, Bruno, Tollkuhn, Jessica (July 2022) Epigenetic Mechanisms of Brain Sexual Differentiation. Cold Spring Harbor Perspectives in Biology. a039099. ISSN 1943-0264

Zhang, Anqi, Zador, Anthony M (July 2022) Diversity and task-dependence of task representations in V1 during freely-moving decisions. bioRxiv. (Submitted)

Ahmed, Waheed-Ul-Rahman, Kleeman, Sam, Ng, Michael, Wang, Wei, Auton, Adam, 23andMe Research Team, Lee, Regent, Handa, Ashok, Zondervan, Krina T, Wiberg, Akira, Furniss, Dominic (June 2022) Genome-wide association analysis and replication in 810,625 individuals with varicose veins. Nature Communications, 13 (1). p. 3065. ISSN 2041-1723

Bibel, Brianna, Elkayam, Elad, Silletti, Steve, Komives, Elizabeth A, Joshua-Tor, Leemor (May 2022) Target binding triggers hierarchical phosphorylation of human Argonaute-2 to promote target release. eLife, 11. ISSN 2050-084X

Luo, Pei X, Zakharenkov, Hannah Cortez, Torres, Lisette Y, Rios, Roberto A, Gegenhuber, Bruno, Black, Alexis M, Xu, Christine K, Minie, Vanessa A, Tran, Amy M, Tollkuhn, Jessica, Trainor, Brian C (May 2022) Oxytocin receptor behavioral effects and cell types in the bed nucleus of the stria terminalis. Hormones and Behaviour, 143. p. 105203. ISSN 0018-506X

Gegenhuber, B, Wu, MV, Bronstein, R, Tollkuhn, J (May 2022) Gene regulation by gonadal hormone receptors underlies brain sex differences. Nature. ISSN 0028-0836

Toneyan, Shushan, Tang, Ziqi, Koo, Peter K (May 2022) Evaluating deep learning for predicting epigenomic profiles. bioRxiv. (Unpublished)

Kwon, Choon-Tak, Tang, Lingli, Wang, Xingang, Gentile, Iacopo, Hendelman, Anat, Robitaille, Gina, Van Eck, Joyce, Xu, Cao, Lippman, Zachary B (March 2022) Dynamic evolution of small signalling peptide compensation in plant stem cell control. Nature Plants. ISSN 2055-0278

Xie, Yunyao, Huang, Longwen, Corona, Alberto, Pagliaro, Alexa H, Shea, Stephen D (March 2022) A reinforcement learning algorithm shapes maternal care in mice. bioRxiv. (Unpublished)

Czégel, Dániel, Giaffar, Hamza, Tenenbaum, Joshua B, Szathmáry, Eörs (February 2022) Bayes and Darwin: How replicator populations implement Bayesian computations. BioEssays : news and reviews in molecular, cellular and developmental biology. e2100255. ISSN 1521-1878

Gutbrod, MJ, Roche, B, Steinberg, JI, Lakhani, AA, Chang, K, Schorn, AJ, Martienssen, RA (February 2022) Dicer promotes genome stability via the bromodomain transcriptional co-activator BRD4. Nature Communications, 13 (1). p. 1001. ISSN 2041-1723

Nowlan, Alexandra C, Kelahan, Clancy, Shea, Stephen D (February 2022) Multisensory integration of social signals by a pathway from the basal amygdala to the auditory cortex in maternal mice. bioRxiv. (Unpublished)

Brennan, Christina M, Nadella, Sandeep, Zhao, Xiang, Dima, Richard J, Jordan-Martin, Nicole, Demestichas, Breanna R, Kleeman, Sam O, Ferrer, Miriam, von Gablenz, Eva Carlotta, Mourikis, Nicholas, Rubin, Michael E, Adnani, Harsha, Lee, Hassal, Ha, Taehoon, Prum, Soma, Schleicher, Cheryl B, Fox, Sharon S, Ryan, Michael G, Pili, Christina, Goldberg, Gary, Crawford, James M, Goodwin, Sara, Zhang, Xiaoyue, Preall, Jonathan B, Costa, Ana SH, Conigliaro, Joseph, Masci, Joseph R, Yang, Jie, Tuveson, David A, Tracey, Kevin J, Janowitz, Tobias (February 2022) Oral famotidine versus placebo in non-hospitalised patients with COVID-19: a randomised, double-blind, data-intense, phase 2 clinical trial. Gut. ISSN 0017-5749

Petruzzelli, M, Ferrer, M, Schuijs, MJ, Kleeman, SO, Mourikis, N, Hall, Z, Perera, D, Raghunathan, S, Vacca, M, Gaude, E, Lukey, MJ, Jodrell, DI, Frezza, C, Wagner, EF, Venkitaraman, AR, Halim, TYF, Janowitz, T (February 2022) Early Neutrophilia Marked by Aerobic Glycolysis Sustains Host Metabolism and Delays Cancer Cachexia. Cancers, 14 (4). p. 963. ISSN 2072-6694

Wang, Zhikai, Moresco, Philip, Yan, Ran, Li, Jiayun, Gao, Ya, Biasci, Daniele, Yao, Min, Pearson, Jordan, Hechtman, Jaclyn F, Janowitz, Tobias, Zaidi, Raza M, Weiss, Matthew J, Fearon, Douglas T (January 2022) Carcinomas assemble a filamentous CXCL12-keratin-19 coating that suppresses T cell-mediated immune attack. Proceedings of the National Academy of Sciences of USA, 119 (4). e2119463119-e2119463119. ISSN 0027-8424

Kitagawa, Munenori, Wu, Peipei, Balkunde, Rachappa, Cunniff, Patrick, Jackson, David (January 2022) An RNA exosome subunit mediates cell-to-cell trafficking of a homeobox mRNA via plasmodesmata. Science, 375 (6577). pp. 177-182. ISSN 0036-8075

Polyanskaya, Sofya A, Moreno, Rosamaria Y, Lu, Bin, Feng, Ruopeng, Yao, Yu, Irani, Seema, Klingbeil, Olaf, Yang, Zhaolin, Wei, Yiliang, Demerdash, Osama E, Benjamin, Lukas A, Weiss, Mitchell J, Zhang, Yan Jessie, Vakoc, Christopher R (January 2022) SCP4-STK35/PDIK1L complex is a dual phospho-catalytic signaling dependency in acute myeloid leukemia. Cell Reports, 38 (2). p. 110233. ISSN 2211-1247

Bibel, Brianna, Elkayam, Elad, Silletti, Steve, Komives, Elizabeth, Joshua-Tor, Leemor (January 2022) Target binding triggers hierarchical phosphorylation of human Argonaute-2 to promote target release. Elife, 11 (e76908). ISSN 2050-084x

Maiorino, Laura, Shevik, Margaret, Adrover, José M, Han, Xiao, Georgas, Elias, Wilkinson, John Erby, Seidner, Harrison, Foerschner, Leonie, Tuveson, David A, Qin, Yi-Xian, Egeblad, Mikala (January 2022) Longitudinal Intravital Imaging Through Clear Silicone Windows. Journal of Visualized Experiments (179). ISSN 1940-087X

Shu, Daisy Y, Frank, Scott I, Fitch, Tessa C, Karg, Margarete M, Butcher, Erik R, Nnuji-John, Emmanuella, Kim, Leo A, Saint-Geniez, Magali (2022) Dimethyl Fumarate Blocks Tumor Necrosis Factor-Alpha-Driven Inflammation and Metabolic Rewiring in the Retinal Pigment Epithelium. Frontiers in Molecular Neuroscience, 15. p. 896786. ISSN 1662-5099

Kwon, Choon-Tak, Tang, Lingli, Wang, Xingang, Gentile, Iacopo, Hendelman, Anat, Robitaille, Gina, Van Eck, Joyce, Xu, Cao, Lippman, Zachary (2022) Dynamic evolution of small signaling peptide compensation in plant stem cell control. bioRxiv. (Submitted)

Lee, Nicholas Keone, Tang, Ziqi, Toneyan, Shushan, Koo, Peter (2022) EvoAug: improving generalization and interpretability of genomic deep neural networks with evolution-inspired data augmentations. bioRxiv. (Submitted)

López-Borrego, Silvia, Campos-Silva, Carmen, Sandúa, Amaia, Camino, Tamara, Téllez-Pérez, Lucía, Alegre, Estibaliz, Beneitez, Alexandra, Jara-Acevedo, Ricardo, Paschen, Annette, Pardo, María, González, Álvaro, Valés-Gómez, Mar (2022) MAPK inhibitors dynamically affect melanoma release of immune NKG2D-ligands, as soluble protein and extracellular vesicle-associated. Frontiers in Cell and Developmental Biology, 10. p. 1055288. ISSN 2296-634X

Corona, Alberto, Choe, Jane, Muñoz-Castañeda, Rodrigo, Osten, Pavel, Shea, Stephen (2022) A circuit from the locus coeruleus to the anterior cingulate cortex modulates offspring interactions in mice. bioRxiv. (Submitted)

Hanasoge Somasundara, Amritha Varshini, Moss, Matthew A, Feigman, Mary J, Chen, Chen, Cyrill, Samantha L, Ciccone, Michael F, Trousdell, Marygrace C, Vollbrecht, Macy, Li, Siran, Kendall, Jude, Beyaz, Semir, Wilkinson, John E, Dos Santos, Camila O (December 2021) Parity-induced changes to mammary epithelial cells control NKT cell expansion and mammary oncogenesis. Cell Reports, 37 (10). p. 110099. ISSN 2211-1247

Maiorino, Laura, Daßler-Plenker, Juliane, Sun, Lijuan, Egeblad, Mikala (November 2021) Innate Immunity and Cancer Pathophysiology. Annual Review of Pathology: Mechanisms of Disease, 17 (1). ISSN 1553-4006

Taranda, Julian, Mathew, Grinu, Watrud, Kaitlin, El-Amine, Nour, Lee, Matthew F, Elowsky, Corey, Bludova, Anastasiia, Escobar Avelar, Sintia, Nowak, Dawid G, Wee, Tse-Luen, Wilkinson, John E, Trotman, Lloyd C, Osten, Pavel (November 2021) Combined whole-organ imaging at single-cell resolution and immunohistochemical analysis of prostate cancer and its liver and brain metastases. Cell Reports, 37 (7). p. 110027. ISSN 2211-1247

Barth, Nicole, Mendive-Tapia, Lorena, Subiros-Funosas, Ramon, Ghashghaie, Ouldouz, Lavilla, Rodolfo, Maiorino, Laura, He, Xue-Yan, Dransfield, Ian, Egeblad, Mikala, Vendrell, Marc (November 2021) A Bivalent Activatable Fluorescent Probe for Screening and Intravital Imaging of Chemotherapy-induced Cancer Cell Death. Angewandte Chemie International Edition. ISSN 1433-7851

Carlston, Colleen, Weinmann, Robin, Stec, Natalia, Abbatemarco, Simona, Schwager, Francoise, Wang, Jing, Ouyang, Huiwu, Ewald, Collin Y, Gotta, Monica, Hammell, Christopher M (November 2021) PQN-59 antagonizes microRNA-mediated repression during post-embryonic temporal patterning and modulates translation and stress granule formation in C. elegans. PLoS Genetics, 17 (11). e1009599. ISSN 1553-7390

Lu, Shaina, Fürth, Daniel, Gillis, Jesse (October 2021) Integrative analysis methods for spatial transcriptomics. Nature Methods. ISSN 1548-7091

Rosado, Daniele, Ackermann, Amanda, Spassibojko, Olya, Rossi, Magdalena, Pedmale, Ullas V (October 2021) WRKY transcription factors and ethylene signaling modify root growth during the shade avoidance response. Plant Physiology. ISSN 1532-2548

Krause, William C, Rodriguez, Ruben, Gegenhuber, Bruno, Matharu, Navneet, Rodriguez, Andreas N, Padilla-Roger, Adriana M, Toma, Kenichi, Herber, Candice B, Correa, Stephanie M, Duan, Xin, Ahituv, Nadav, Tollkuhn, Jessica, Ingraham, Holly A (October 2021) Oestrogen engages brain MC4R signalling to drive physical activity in female mice. Nature. ISSN 0028-0836

Hutton, Elizabeth R, Vakoc, Christopher R, Siepel, Adam (September 2021) ACE: a probabilistic model for characterizing gene-level essentiality in CRISPR screens. Genome Biology, 22 (1). p. 278. ISSN 1474-760X

Wei, Yiliang, Huang, Yu-Han, Skopelitis, Damianos S, Iyer, Shruti V, Costa, Ana SH, Yang, Zhaolin, Kramer, Melissa, Adelman, Emmalee R, Klingbeil, Olaf, Demerdash, Osama E, Polyanskaya, Sofya A, Chang, Kenneth, Goodwin, Sara, Hodges, Emily, McCombie, W Richard, Figueroa, Maria E, Vakoc, Christopher R (September 2021) SLC5A3-dependent myo-inositol auxotrophy in acute myeloid leukemia. Cancer Discovery. candisc.1849.2020-candisc.1849.2020. ISSN 2159-8274

Beyaz, Semir, Chung, Charlie, Mou, Haiwei, Bauer-Rowe, Khristian E, Xifaras, Michael E, Ergin, Ilgin, Dohnalova, Lenka, Biton, Moshe, Shekhar, Karthik, Eskiocak, Onur, Papciak, Katherine, Ozler, Kadir, Almeqdadi, Mohammad, Yueh, Brian, Fein, Miriam, Annamalai, Damodaran, Valle-Encinas, Eider, Erdemir, Aysegul, Dogum, Karoline, Shah, Vyom, Alici-Garipcan, Aybuke, Meyer, Hannah V, Özata, Deniz M, Elinav, Eran, Kucukural, Alper, Kumar, Pawan, McAleer, Jeremy P, Fox, James G, Thaiss, Christoph A, Regev, Aviv, Roper, Jatin, Orkin, Stuart H, Yilmaz, Ömer H (September 2021) Dietary suppression of MHC class II expression in intestinal epithelial cells enhances intestinal tumorigenesis. Cell Stem Cell. ISSN 1934-5909

Shen, Yang, Wang, Julia, Navlakha, Saket (August 2021) A Correspondence between Normalization Strategies in Artificial and Biological Neural Networks. Neural Computation. pp. 1-25. ISSN 0899-7667

Harris, Benjamin, Lee, John, Gillis, Jesse (August 2021) A Meta-Analytic Single-Cell Atlas of Mouse Bone Marrow Hematopoietic Development. bioRxiv. (Unpublished)

Zhao, Yixin, Dukler, Noah, Barshad, Gilad, Toneyan, Shushan, Danko, Charles G, Siepel, Adam (August 2021) Deconvolution of Expression for Nascent RNA sequencing data (DENR) highlights pre-RNA isoform diversity in human cells. Bioinformatics. ISSN 1367-4803

Furlan, Alessandro, Corona, Alberto, Boyle, Sara, Sharma, Radhashree, Rubino, Rachel, Habel, Jill, Gablenz, Eva Carlotta, Giovanniello, Jacqueline, Beyaz, Semir, Janowitz, Tobias, Shea, Stephen D, Li, Bo (August 2021) Neurotensin neurons in the central extended amygdala control energy balance. bioRxiv. (Unpublished)

Lu, Shaina, Ortiz, Cantin, Fürth, Daniel, Fischer, Stephan, Meletis, Konstantinos, Zador, Anthony, Gillis, Jesse (July 2021) Assessing the replicability of spatial gene expression using atlas data from the adult mouse brain. PLoS Biology, 19 (7). e3001341. ISSN 1545-7885

Safaric Tepes, Polona, Pal, Debjani, Lindsted, Trine, Ibarra, Ingrid, Lujambio, Amaia, Jimenez Sabinina, Vilma, Senturk, Serif, Miller, Madison, Korimerla, Navya, Huang, Jiahao, Glassman, Lawrence, Lee, Paul, Zeltsman, David, Hyman, Kevin, Esposito, Michael, Hannon, Greg, Sordella, Raffaella (July 2021) An epigenetic switch regulates the ontogeny of AXL positive/EGFR-TKI resistant cells by modulating miR-335 expression. eLife, 10. ISSN 2050-084X

Fischer, Stephan, Crow, Megan, Harris, Benjamin D, Gillis, Jesse (July 2021) Scaling up reproducible research for single-cell transcriptomics using MetaNeighbor. Nature Protocols. ISSN 1754-2189

Czégel, Dániel, Giaffar, Hamza, Csillag, Márton, Futó, Bálint, Szathmáry, Eörs (June 2021) Novelty and imitation within the brain: a Darwinian neurodynamic approach to combinatorial problems. Scientific reports, 11 (1). p. 12513. ISSN 2045-2322

Hulse-Kemp, Amanda M, Bostan, Hamed, Chen, Shiyu, Ashrafi, Hamid, Stoffel, Kevin, Sanseverino, Walter, Li, Linzhou, Cheng, Shifeng, Schatz, Michael C, Garvin, Tyler, du Toit, Lindsey J, Tseng, Elizabeth, Chin, Jason, Iorizzo, Massimo, Van Deynze, Allen (June 2021) An anchored chromosome-scale genome assembly of spinach improves annotation and reveals extensive gene rearrangements in euasterids. The Plant Genome. e20101. ISSN 1940-3372

Giovanniello, Jacqueline, Ahrens, Sandra, Yu, Kai, Li, Bo (June 2021) Sex-Specific Stress-Related Behavioral Phenotypes and Central Amygdala Dysfunction in a Mouse Model of 16p11.2 Microdeletion. Biological Psychiatry Global Open Science, 1 (1). pp. 59-69. ISSN 2667-1743

International Brain Laboratory, Aguillon-Rodriguez, Valeria, Angelaki, Dora, Bayer, Hannah, Bonacchi, Niccolo, Carandini, Matteo, Cazettes, Fanny, Chapuis, Gaelle, Churchland, Anne K, Dan, Yang, Dewitt, Eric, Faulkner, Mayo, Forrest, Hamish, Haetzel, Laura, Häusser, Michael, Hofer, Sonja B, Hu, Fei, Khanal, Anup, Krasniak, Christopher, Laranjeira, Ines, Mainen, Zachary F, Meijer, Guido, Miska, Nathaniel J, Mrsic-Flogel, Thomas D, Murakami, Masayoshi, Noel, Jean-Paul, Pan-Vazquez, Alejandro, Rossant, Cyrille, Sanders, Joshua, Socha, Karolina, Terry, Rebecca, Urai, Anne E, Vergara, Hernando, Wells, Miles, Wilson, Christian J, Witten, Ilana B, Wool, Lauren E, Zador, Anthony M (May 2021) Standardized and reproducible measurement of decision-making in mice. eLife, 10. ISSN 2050-084X

Sun, Yu-Chi, Chen, Xiaoyin, Fischer, Stephan, Lu, Shaina, Zhan, Huiqing, Gillis, Jesse, Zador, Anthony M (May 2021) Integrating barcoded neuroanatomy with spatial transcriptional profiling enables identification of gene correlates of projections. Nature Neuroscience. ISSN 1097-6256

Harris, Benjamin D, Crow, Megan, Fischer, Stephan, Gillis, Jesse (May 2021) Single-cell co-expression analysis reveals that transcriptional modules are shared across cell types in the brain. Cell Systems. ISSN 2405-4712

Yang, Zhaolin, Wu, Xiaoli S, Wei, Yiliang, Polyanskaya, Sofya A, Iyer, Shruti V, Jung, Moonjung, Lach, Francis P, Adelman, Emmalee R, Klingbeil, Olaf, Milazzo, Joseph P, Kramer, Melissa, Demerdash, Osama E, Chang, Kenneth, Goodwin, Sara, Hodges, Emily, McCombie, W Richard, Figueroa, Maria E, Smogorzewska, Agata, Vakoc, Christopher R (April 2021) Transcriptional silencing of ALDH2 confers a dependency on Fanconi anemia proteins in acute myeloid leukemia. Cancer Discovery. ISSN 2159-8274

Kawaguchi, Risa Karakida, Tang, Ziqi, Fischer, Stephan, Tripathy, Rohit, Koo, Peter, Gillis, Jesse (April 2021) Exploiting marker genes for robust classification and characterization of single-cell chromatin accessibility. bioRxiv. (Unpublished)

Wang, Xingang, Aguirre, Lyndsey, Rodríguez-Leal, Daniel, Hendelman, Anat, Benoit, Matthias, Lippman, Zachary B (April 2021) Dissecting cis-regulatory control of quantitative trait variation in a plant stem cell circuit. Nature Plants, 7 (4). pp. 419-427. ISSN 2055-026X

Janowitz, Tobias, Kleeman, Sam, Vonderheide, Robert H (April 2021) Reconsidering Dexamethasone for Antiemesis when Combining Chemotherapy and Immunotherapy. The Oncologist, 26 (4). pp. 269-273. ISSN 1083-7159

Zhao, Yixin, Dukler, Noah, Barshad, Gilad, Toneyan, Shushan, Danko, Charles, Siepel, Adam (March 2021) Deconvolution of Expression for Nascent RNA Sequencing Data (DENR) Highlights Pre-RNA Isoform Diversity in Human Cells. BioRxiv. (Unpublished)

Ghosh, Sanchari, Zador, Anthony M (March 2021) Corticostriatal Plasticity Established by Initial Learning Persists after Behavioral Reversal. eNeuro, 8 (2). pp. 1-10. ISSN 2373-2822

Sroka, Martyna W, Vakoc, Christopher R (February 2021) An epigenetic tipping point in cancer comes under the microscope. Nature, 590 (7846). pp. 399-400. ISSN 0028-0836

Pisupati, Sashank, Chartarifsky-Lynn, Lital, Khanal, Anup, Churchland, Anne K (January 2021) Lapses in perceptual decisions reflect exploration. eLife, 10. pp. 1-27. ISSN 2050-084X

Shuvaev, Sergey A, Tran, Ngoc B, Stephenson-Jones, Marcus, Li, Bo, Koulakov, Alexei A (January 2021) Neural Networks With Motivation. Frontiers in Systems Neuroscience, 14. p. 609316. ISSN 1662-5137

Rallis, KS, Kleeman, SO, Grant, M, Ordidge, KL, Sahdev, A, Powles, T (January 2021) Radiomics for Renal Cell Carcinoma: Predicting Outcomes from Immunotherapy and Targeted Therapies—A Narrative Review. European Urology Focus. ISSN 2405-4569

Ruiz-Ortiz, Jenelys, Tollkuhn, Jessica (January 2021) Specificity in sociogenomics: Identifying causal relationships between genes and behavior. Hormones and Behaviour, 127. p. 104882. ISSN 0018-506X

Meze, Katarina, Axhemi, Armend, Thomas, Dennis, Doymaz, Ahmet, Joshua-Tor, Leemor (2021) A shape-shifting nuclease unravels structured RNA. bioRxiv. (Submitted)

Xu, X., Crow, M., Rice, B. R., Li, F., Harris, B., Liu, L., Demesa-Arevalo, E., Lu, Z., Wang, L., Fox, N., Wang, X., Drenkow, J., Luo, A., Char, S. N., Yang, B., Sylvester, A. W., Gingeras, T. R., Schmitz, R. J., Ware, D., Lipka, A. E., Gillis, J., Jackson, D. (December 2020) Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery. Dev Cell, S1534- (20). pp. 31021-31022. ISSN 1534-5807

Borges, F., Donoghue, M. T. A., LeBlanc, C., Wear, E. E., Tanurdžić, M., Berube, B., Brooks, A., Thompson, W. F., Hanley-Bowdoin, L., Martienssen, R. A. (November 2020) Loss of Small-RNA-Directed DNA Methylation in the Plant Cell Cycle Promotes Germline Reprogramming and Somaclonal Variation. Curr Biol, 31 (3). pp. 591-600. ISSN 0960-9822

Giovanniello, J., Yu, K., Furlan, A., Nachtrab, G. T., Sharma, R., Chen, X., Li, B. (November 2020) A Central Amygdala-Globus Pallidus Circuit Conveys Unconditioned Stimulus-Related Information and Controls Fear Learning. J Neurosci, 40 (47). pp. 9043-9054. ISSN 0270-6474 (Print)0270-6474

Giovanniello, Jacqueline, Ahrens, Sandra, Yu, Kai, Li, Bo (November 2020) Sex-specific stress-related behavioral phenotypes and central amygdala dysfunction in a mouse model of 16p11.2 microdeletion. bioRxiv. (Unpublished)

Kleeman, Sam O, Leedham, Simon J (November 2020) Not All Wnt Activation Is Equal: Ligand-Dependent versus Ligand-Independent Wnt Activation in Colorectal Cancer. Cancers, 12 (11). pp. 1-16. ISSN 2072-6694

Lu, Shaina, Ortiz, Cantin, Fürth, Daniel, Fischer, Stephan, Meletis, Konstantinos, Zador, Anthony, Gillis, Jesse (October 2020) Replicability of spatial gene expression atlas data from the adult mouse brain. bioRxiv. (Unpublished)

Slepicka, P. F., Somasundara, A. V. H., Dos Santos, C. O. (October 2020) The molecular basis of mammary gland development and epithelial differentiation. Semin Cell Dev Biol. ISSN 1084-9521

Fein, Miriam R, He, Xue-Yan, Almeida, Ana S, Bružas, Emilis, Pommier, Arnaud, Yan, Ran, Eberhardt, Anaïs, Fearon, Douglas T, Van Aelst, Linda, Wilkinson, John Erby, Dos Santos, Camila O, Egeblad, Mikala (October 2020) Cancer cell CCR2 orchestrates suppression of the adaptive immune response. Journal of Experimental Medicine, 217 (10). ISSN 0022-1007

Beyaz, S., Roper, J., Bauer-Rowe, K. E., Xifaras, M. E., Ergin, I., Dohnalova, L., Biton, M., Shekar, K., Mou, H. W., Eskiocak, O., Ozata, D., Papciak, K., Chung, C., Almeqdadi, M., Fein, M., Valle-Encinas, E., Erdemir, A., Dogum, K, Garipcan, A., Meyer, H., Fox, J.G., Elinav, E., Kucukural, A., Kumar, P., McAleer, J., Thaiss, C.A., Regev, A., Orkin, S. H., Yilmaz, O. H. (September 2020) Dietary suppression of MHC-II expression in intestinal stem cells enhances intestinal tumorigenesis. bioRxiv. (Unpublished)

Wang, Zhikai, Yan, Ran, Li, Jiayun, Gao, Ya, Moresco, Philip, Yao, Min, Hechtman, Jaclyn F, Weiss, Matthew J, Janowitz, Tobias, Fearon, Douglas T (September 2020) Pancreatic cancer cells assemble a CXCL12-keratin 19 coating to resist immunotherapy. bioRxiv. (Unpublished)

Sun, Yu-Chi, Chen, Xiaoyin, Fischer, Stephan, Lu, Shaina, Gillis, Jesse, Zador, Anthony (August 2020) Integrating barcoded neuroanatomy with spatial transcriptional profiling reveals cadherin correlates of projections shared across the cortex. bioRxiv. (Unpublished)

Nattestad, M., Aboukhalil, R., Chin, C. S., Schatz, M. C. (August 2020) Ribbon: Intuitive visualization for complex genomic variation. Bioinformatics. ISSN 1367-4803

Chou, Tsung-Han, Tajima, Nami, Romero-Hernandez, Annabel, Furukawa, Hiro (July 2020) Structural Basis of Functional Transitions in Mammalian NMDA Receptors. Cell, 182 (2). 357-371.e13. ISSN 0092-8674

Huang, Longwen, Kebschull, Justus M, Fürth, Daniel, Musall, Simon, Kaufman, Matthew T, Churchland, Anne K, Zador, Anthony M (July 2020) BRICseq Bridges Brain-wide Interregional Connectivity to Neural Activity and Gene Expression in Single Animals. Cell, 182 (1). 177-188.e27. ISSN 0092-8674

Alonge, M., Wang, X., Benoit, M., Soyk, S., Pereira, L., Zhang, L., Suresh, H., Ramakrishnan, S., Maumus, F., Ciren, D., Levy, Y., Harel, T. H., Shalev-Schlosser, G., Amsellem, Z., Razifard, H., Caicedo, A. L., Tieman, D. M., Klee, H., Kirsche, M., Aganezov, S., Ranallo-Benavidez, T. R., Lemmon, Z. H., Kim, J., Robitaille, G., Kramer, M., Goodwin, S., McCombie, W. R., Hutton, S., Van Eck, J., Gillis, J., Eshed, Y., Sedlazeck, F. J., van der Knaap, E., Schatz, M. C., Lippman, Z. B. (July 2020) Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato. Cell, 182 (1). 145-161.e23. ISSN 0092-8674 (Print)0092-8674

Masset, P., Ott, T., Lak, A., Hirokawa, J., Kepecs, A. (June 2020) Behavior- And Modality-General Representation of Confidence in Orbitofrontal Cortex. Cell, 182. ISSN 0092-8674

Somerville, T. D. D., Xu, Y., Wu, X. S., Maia-Silva, D., Hur, S. K., de Almeida, L. M. N., Preall, J. B., Koo, P. K., Vakoc, C. R. (May 2020) ZBED2 is an antagonist of interferon regulatory factor 1 and modifies cell identity in pancreatic cancer. Proc Natl Acad Sci U S A, 117 (21). pp. 11471-11482. ISSN 0027-8424 (Print)0027-8424

Rupert, D.D., Nowlan, A.C., Tam, O. H., Hammell, M. G. (May 2020) Ten Simple Rules for Running a Successful women-in-STEM Organization on an Academic Campus. PLoS Comput Biol, 16 (5). e1007754. ISSN 1553-734x

Gutbrod, M. J., Martienssen, R. A. (May 2020) Conserved chromosomal functions of RNA interference. Nat Rev Genet, 21 (5). pp. 311-331. ISSN 1471-0056

Giovanniello, Jacqueline, Yu, Kai, Furlan, Alessandro, Nachtrab, Gregory Thomas, Sharma, Radhashree, Chen, Xiaoke, Li, Bo (April 2020) A central amygdala-globus pallidus circuit conveys unconditioned stimulus information and controls fear learning. bioRxiv. (Unpublished)

Somerville, T. D. D., Biffi, G., DaBler-Plenker, J., Hur, S.K., He, X.-Y., Vance, K.E., Miyabayashi, K., Xu, Y., Maia-Silva, D., Klingbeil, O., Demerdash, O. E., Preall, J. B., Hollingsworth, M. A., Egeblad, M., Tuveson, D. A., Vakoc, C. R. (April 2020) Squamous trans-differentiation of pancreatic cancer cells promotes stromal inflammation. Elife, 9. e53381. ISSN 2050-084x (Public Dataset)

Xu, M., Ergin, I., Beyaz, S. (April 2020) Advances in Diagnostic Procedures and Their Applications in the Era of Cancer Immunotherapy. In: Immunotherapy. Springer, pp. 37-50.

Lee, S.C., Ernst, E., Berube, B., Borges, F., Parent, J. S., Ledon, P., Schorn, A., Martienssen, R. A. (April 2020) Arabidopsis Retrotransposon Virus-Like Particles and Their Regulation by Epigenetically Activated Small RNA. Genome Research, 30 (4). pp. 576-588. ISSN 1088-9051

Lak, A., Hueske, E., Hirokawa, J., Masset, P., Ott, T., Urai, A. E., Donner, T.H., Carandini, M., Tonegawa, S., Uchida, N., Kepecs, A. (April 2020) Reinforcement Biases Subsequent Perceptual Decisions When Confidence Is Low: A Widespread Behavioral Phenomenon. Elife, 9 (e49834). ISSN 2050-084X

O'Neill, K., Brocks, D., Hammell, M. G. (March 2020) Mobile Genomics: Tools and Techniques for Tackling Transposons. Philos Trans R Soc Lond B Biol Sci, 375 (1795). ISSN 0962-8436

Rupert, Deborah, Nowlan, Alexandra, Tam, Oliver, Hammell, Molly Gale (February 2020) Methods for Running a Successful Women-in-STEM Organization on an Academic Campus. bioRxiv. (Unpublished)

Pisupati, S., Chartarifsky, L., Khanal, A., Churchland, A. K. (February 2020) Dataset from: Lapses in perceptual decisions reflect exploration. [Dataset]

Delevich, K., Jaaro-Peled, H., Penzo, M., Sawa, A., Li, B. (February 2020) Parvalbumin interneuron dysfunction in a thalamo-prefrontal cortical circuit in Disc1 locus impairment mice. eNeuro. ISSN 2373-2822

Demir, E., Li, K., Bobrowski-Khoury, N., Sanders, J. I., Beynon, R. J., Hurst, J. L., Kepecs, A., Axel, R. (January 2020) The pheromone darcin drives a circuit for innate and reinforced behaviours. Nature, 578 (7793). pp. 137-141. ISSN 0028-0836

Dore, K., Pao, Y., Soria Lopez, J., Aronson, S., Zhan, H., Ghosh, S., Merrill, S., Zador, A. M., Malinow, R., Kebschull, J. M. (January 2020) SYNPLA, a method to identify synapses displaying plasticity after learning. Proc Natl Acad Sci U S A, 117 (6). pp. 3214-3219. ISSN 0027-8424 (Public Dataset)

Wang, J. X., Irvine, M. W., Burnell, E. S., Sapkota, K., Thatcher, R. J., Li, M., Simorowski, N., Volianskis, A., Collingridge, G. L., Monaghan, D. T., Jane, D. E., Furukawa, H. (January 2020) Structural basis of subtype-selective competitive antagonism for GluN2C/2D-containing NMDA receptors. Nat Commun, 11 (1). p. 423. ISSN 2041-1723 (Public Dataset)

The International Brain Laboratory, Aguillon-Rodriguez, Valeria, Angelaki, Dora, Bayer, Hannah, Bonacchi, Niccolò, Carandini, Matteo, Cazettes, Fanny, Chapuis, Gaelle, Churchland, Anne, Dan, Yang, Dewitt, Eric, Faulkner, Mayo, Forrest, Hamish, Haetzel, Laura, Hausser, Michael, Hofer, Sonja, Hu, Fei, Khanal, Anup, Krasniak, Christopher, Laranjeira, Inês, Mainen, Zachary, Meijer, Guido, Miska, Nathaniel, Mrsic-Flogel, Thomas, Murakami, Masayoshi, Noel, Jean-Paul, Pan-Vazquez, Alejandro, Sanders, Josh, Socha, Karolina, Terry, Rebecca, Urai, Anne, Vergara, Hernando, Wells, Miles, Wilson, Christian, Witten, Ilana, Wool, Lauren, Zador, Anthony (January 2020) A standardized and reproducible method to measure decision-making in mice. bioRxiv. (Unpublished)

Sindhwani, S., Syed, A.M., Ngai, J., Kingston, B.R., Maiorino, L., Rothschild, J., MacMillan, P., Zhang, Y., Rajesh, N.U., Hoang, T., Wu, J.L.Y., Wilhelm, S., Zilman, A., Gadde, S., Sulaiman, A., Ouyang, B., Lin, Z., Wang, L., Egeblad, M., Chan, W.C.W. (January 2020) The entry of nanoparticles into solid tumours. Nat Mater. ISSN 1476-1122 (Public Dataset)

Gegenhuber, B., Tollkuhn, J. (January 2020) Signatures of Sex: Sex Differences in Gene Expression in the Vertebrate Brain. Wiley Interdiscip Rev Dev Biol, 9 (1). e348.

Lee, M. F., Trotman, L. C. (December 2019) PTEN: Bridging Endocytosis and Signaling. Cold Spring Harb Perspect Med. ISSN 2157-1422

Hutton, Elizabeth, Vakoc, Christopher, Siepel, Adam (December 2019) ACE: A Probabilistic Model for Characterizing Gene-Level Essentiality in CRISPR Screens. bioRxiv.

Hirokawa, J., Vaughan, A., Masset, P., Ott, T., Kepecs, A. (December 2019) Frontal cortex neuron types categorically encode single decision variables. Nature, 576 (7787). pp. 446-451. ISSN 0028-0836 (Public Dataset)

Li, S., Kendall, J., Park, S., Wang, Z., Alexander, J., Moffitt, A., Ranade, N., Danyko, C., Gegenhuber, B., Fischer, S., Robinson, B. D., Lepor, H., Tollkuhn, J., Gillis, J., Brouzes, E., Krasnitz, A., Levy, D., Wigler, M. (November 2019) Copolymerization of single-cell nucleic acids into balls of acrylamide gel. Genome Res, 30 (1). pp. 49-61. ISSN 1088-9051 (Public Dataset)

Caiado, F., Maia-Silva, D., Jardim, C., Schmolka, N., Carvalho, T., Reforco, C., Faria, R., Kolundzija, B., Simoes, A. E., Baubec, T., Vakoc, C. R., da Silva, M. G., Manz, M. G., Schumacher, T. N., Norell, H., Silva-Santos, B. (November 2019) Lineage tracing of acute myeloid leukemia reveals the impact of hypomethylating agents on chemoresistance selection. Nat Commun, 10 (1). p. 4986. ISSN 2041-1723

Tarumoto, Y., Lin, S., Wang, J., Milazzo, J. P., Xu, Y., Lu, B., Yang, Z., Wei, Y., Polyanskaya, S., Wunderlich, M., Gray, N. S., Stegmaier, K., Vakoc, C. R. (November 2019) Salt-Inducible Kinase inhibition suppresses acute myeloid leukemia progression in vivo. Blood. ISSN 0006-4971

Chen, X., Sun, Y. C., Zhan, H., Kebschull, J. M., Fischer, S., Matho, K., Huang, Z. J., Gillis, J., Zador, A. M. (October 2019) High-Throughput Mapping of Long-Range Neuronal Projection Using In Situ Sequencing. Cell, 179 (3). 772-786.e19. ISSN 0092-8674 (Public Dataset)

Maiorino, L., Egeblad, M. (August 2019) Tumours pick the path to cancer inflammation. Nat Cell Biol, 21 (9). pp. 1055-1057. ISSN 1465-7392

Chae, H., Kepple, D. R., Bast, W. G., Murthy, V. N., Koulakov, A. A., Albeanu, D. F. (August 2019) Mosaic representations of odors in the input and output layers of the mouse olfactory bulb. Nat Neurosci, 22 (8). 1306-1317.. ISSN 1097-6256 (Public Dataset)

Carter, J. A., Preall, J. B., Grigaityte, K., Goldfless, S. J., Jeffery, E., Briggs, A. W., Vigneault, F., Atwal, G. S. (July 2019) Single T Cell Sequencing Demonstrates the Functional Role alpha beta TCR Pairing in Cell Lineage and Antigen Specificity. Frontiers in Immunology, 10. Article Number:1516. ISSN 1664-3224

Humpton, T. J., Alagesan, B., DeNicola, G. M., Lu, D., Yordanov, G. N., Leonhardt, C. S., Yao, M. A., Alagesan, P., Zaatari, M. N., Park, Y., Skepper, J. N., Macleod, K. F., Perez-Mancera, P. A., Murphy, M. P., Evan, G. I., Vousden, K. H., Tuveson, D. A. (July 2019) Oncogenic Kras induces Nix-mediated mitophagy to promote pancreatic cancer. Cancer Discov, 99 (9). pp. 1268-1298. ISSN 2159-8274

Gegenhuber, B., Tollkuhn, J. (June 2019) Sex Differences in the Epigenome: A Cause or Consequence of Sexual Differentiation of the Brain? Genes (Basel), 10 (6). E432. ISSN 2073-4425 (Print)2073-4425

Tran, Ngoc, Kepple, Daniel, Shuvaev, Sergey A., Koulakov, Alexei A. (June 2019) DeepNose: Using artificial neural networks to represent the space of odorants. Proceedings of the 36th International Conference on Machine Learning, 97. pp. 6305-6314.

Arrazola, M. S., Saquel, C., Catalan, R. J., Barrientos, S. A., Hernandez, D. E., Catenaccio, A., Court, F. A. (May 2019) Axonal degeneration is mediated by necroptosis activation Necroptosis mediates axonal degeneration. J Neurosci, 39 (20). pp. 3832-2844. ISSN 0270-6474

Nowak, D. G., Katsenelson, K. C., Watrud, K. E., Chen, M., Mathew, G., D'Andrea, V. D., Lee, M. F., Swamynathan, M. M., Casanova-Salas, I., Jibilian, M. C., Buckholtz, C. L., Ambrico, A. J., Pan, C. H., Wilkinson, J. E., Newton, A. C., Trotman, L. C. (May 2019) The PHLPP2 phosphatase is a druggable driver of prostate cancer progression. J Cell Biol, 218 (6). pp. 1943-1957. ISSN 0021-9525

Delas, M. J., Jackson, B. T., Kovacevic, T., Vangelisti, S., Munera Maravilla, E., Wild, S. A., Stork, E. M., Erard, N., Knott, S. R. V., Hannon, G. J. (April 2019) lncRNA Spehd Regulates Hematopoietic Stem and Progenitor Cells and Is Required for Multilineage Differentiation. Cell Rep, 27 (3). 719-729.e6.

Kepple, D. R., Giaffar, H., Rinberg, D., Koulakov, A. A. (February 2019) Deconstructing Odorant Identity via Primacy in Dual Networks. Neural Computation, 31 (4). pp. 710-737. ISSN 08997667 (ISSN)

Wang, J. X., Furukawa, H. (January 2019) Dissecting diverse functions of NMDA receptors by structural biology. Curr Opin Struct Biol, 54. pp. 34-42. ISSN 0959-440x

Anaparthy, N., Ho, Y. J., Martelotto, L., Hammell, M., Hicks, J. (January 2019) Single-Cell Applications of Next-Generation Sequencing. Cold Spring Harb Perspect Med, 9 (10). ISSN 2157-1422

Somerville, Tim DD, Biffi, Giulia, Daßler-Plenker, Juliane, Miyabayashi, Koji, Xu, Yali, Maia-Silva, Diogo, Klingbeil, Olaf, Demerdash, Osama, Egeblad, Mikala, Tuveson, David, Vakoc, Christopher (2019) Squamous trans-differentiation of pancreatic cancer cells promotes stromal inflammation. eLife. (Submitted)

Forcier, T. L., Ayaz, A., Gill, M. S., Jones, D., Phillips, R., Kinney, J. B. (December 2018) Measuring cis-regulatory energetics in living cells using allelic manifolds. eLife, 7. ISSN 2050084X (ISSN)

McCarter, A., Yan, R., Alarcon, A. S., Chang, C., Kim, E., Sha, C., Liu, Y. R., Wang, Q., Peterson, L. F., Kuick, R., Ryan, R., Talpaz, M., Samuelson, L., Ostrowski, M., Chiang, M. Y. (November 2018) Ets1 Enhances Context-Dependent Notch1 Activity in T-Cell Leukemia. Blood, 132 (Supple). Meeting Abstract 2595. ISSN 0006-4971

Somerville, T. D. D., Xu, Y., Miyabayashi, K., Tiriac, H., Cleary, C. R., Maia-Silva, D., Milazzo, J. P., Tuveson, D. A., Vakoc, C. R. (November 2018) TP63-Mediated Enhancer Reprogramming Drives the Squamous Subtype of Pancreatic Ductal Adenocarcinoma. Cell Rep, 25 (7). 1741-1755.e7. ISSN 2211-1247 (Public Dataset)

Kebschull, J. M., Zador, A. M. (November 2018) Cellular barcoding: lineage tracing, screening and beyond. Nat Methods, 15 (11). pp. 871-879. ISSN 1548-7091

Maharjan, D. M., Dai, Y. Y., Glantz, E. H., Jadhav, S. P. (November 2018) Disruption of dorsal hippocampal – prefrontal interactions using chemogenetic inactivation impairs spatial learning. Neurobiology of Learning and Memory, 155. pp. 351-360. ISSN 10747427 (ISSN)

Hernandez, D. E., Salvadores, N. A., Moya-Alvarado, G., Catalan, R. J., Bronfman, F. C., Court, F. A. (October 2018) Axonal degeneration induced by glutamate-excitotoxicity is mediated by necroptosis. J Cell Sci, 131 (22). ISSN 0021-9533

Odoemene, O., Pisupati, S., Nguyen, H., Churchland, A. K. (October 2018) Visual evidence accumulation guides decision-making in unrestrained mice. J Neurosci, 38 (47). pp. 10143-10155. ISSN 0270-6474 (Public Dataset)

O'Neill, K., Liao, W. W., Patel, A., Hammell, M. G. (October 2018) TEsmall Identifies Small RNAs Associated With Targeted Inhibitor Resistance in Melanoma. Frontiers in Genetics, 9. Article Number: 461 . ISSN 1664-8021

Kepple, D. R., Giaffar, H., Rinberg, D., Koulakov, A. A. (October 2018) Primacy coding in dual olfactory networks. 51st Asilomar Conference on Signals, Systems, and Computers, 2017-O. pp. 587-592.

Albrengues, J., Shields, M. A., Ng, D., Park, C. G., Ambrico, A., Poindexter, M. E., Upadhyay, P., Uyeminami, D. L., Pommier, A., Kuttner, V., Bruzas, E., Maiorino, L., Bautista, C., Carmona, E. M., Gimotty, P. A., Fearon, D. T., Chang, K., Lyons, S. K., Pinkerton, K. E., Trotman, L. C., Goldberg, M. S., Yeh, J. T., Egeblad, M. (September 2018) Neutrophil extracellular traps produced during inflammation awaken dormant cancer cells in mice. Science, 361 (6409). ISSN 0036-8075

Huang, Longwen, Kebschull, Justus, Furth, Daniel, Musall, Simon, Kaufman, Matthew T., Churchland, Anne K., Zador, Anthony (September 2018) High-throughput mapping of mesoscale connectomes in individual mice. bioRxiv.

Fein, Miriam, He, Xue-Yan, Almeida, Ana, Bružas, Emilis, Pommier, Arnaud, Yan, Ran, Eberhardt, Anaïs, Fearon, Douglas, Van Aelst, Linda, Wilkinson, John, dos Santos, Camila, Egeblad, Mikala (August 2018) Cancer cell CCR2 orchestrates suppression of the adaptive immune response. bioRxiv.

Skopelitis, D. S., Hill, K., Klesen, S., Marco, C. F., von Born, P., Chitwood, D. H., Timmermans, M. C. P. (August 2018) Gating of miRNA movement at defined cell-cell interfaces governs their impact as positional signals. Nat Commun, 9 (1). p. 3107. ISSN 2041-1723

Wang, Q., Yan, R., Pinnell, N., McCarter, A. C., Oh, Y., Liu, Y., Sha, C., Garber, N. F., Chen, Y., Wu, Q., Ku, C. J., Tran, I., Serna Alarcon, A., Kuick, R., Engel, J. D., Maillard, I., Cierpicki, T., Chiang, M. Y. (August 2018) Stage-specific roles for Zmiz1 in Notch-dependent steps of early T-cell development. Blood, 132 (12). pp. 1279-1292. ISSN 0006-4971

Nattestad, M., Goodwin, S., Ng, K., Baslan, T., Sedlazeck, F., Rescheneder, P., Garvin, T., Fang, H., Gurtowski, J., Hutton, E., Tseng, E., Chin, J., Beck, T., Sundaravadanam, Y., Kramer, M., Antoniou, E., McPherson, J., Hicks, J., McCombie, W. R., Schatz, M. C. (August 2018) Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line. Genome Res, 28 (8). pp. 1126-1135. ISSN 1088-9051

Ho, Y. J., Anaparthy, N., Molik, D., Mathew, G., Aicher, T., Patel, A., Hicks, J., Gale Hammell, M. (July 2018) Single-cell RNA-seq analysis identifies markers of resistance to targeted BRAF inhibitors in melanoma cell populations. Genome Res, 28 (9). pp. 1353-1363. ISSN 1088-9051

Ott, T., Masset, P., Kepecs, A. (July 2018) The Neurobiology of Confidence: From Beliefs to Neurons. Cold Spring Harb Symp Quant Biol, 83. pp. 9-16. ISSN 0091-7451

O’Neill, Kathryn, Liao, Wen-Wei, Patel, Ami, Hammell, Molly Gale (June 2018) TEsmall identifies small RNAs associated with targeted inhibitor resistance in melanoma. bioRxiv.

Sonzogni, O., Haynes, J., Seifried, L. A., Kamel, Y. M., Huang, K., BeGora, M. D., Yeung, F. A., Robert-Tissot, C., Heng, Y. J., Yuan, X., Wulf, G. M., Kron, K. J., Wagenblast, E., Lupien, M., Kislinger, T., Hannon, G. J., Muthuswamy, S. K. (June 2018) Reporters to mark and eliminate basal or luminal epithelial cells in culture and in vivo. PLoS Biol, 16 (6). e2004049. ISSN 1544-9173

Kepple, Daniel, Cazakoff, Brittany, Demmer, Heike, Eckmeier, Dennis, Shea, Stephen, Koulakov, Alexei (June 2018) Computational algorithms and neural circuitry for compressed sensing in the mammalian main olfactory bulb. bioRxiv. (Unpublished)

Sedlazeck, F. J., Rescheneder, P., Smolka, M., Fang, H., Nattestad, M., von Haeseler, A., Schatz, M. C. (June 2018) Accurate detection of complex structural variations using single-molecule sequencing. Nat Methods, 15 (6). pp. 461-468. ISSN 1548-7091

Pommier, A., Anaparthy, N., Memos, N., Kelley, Z. L., Gouronnec, A., Yan, R., Auffray, C., Albrengues, J., Egeblad, M., Iacobuzio-Donahue, C. A., Lyons, S. K., Fearon, D. T. (May 2018) Unresolved endoplasmic reticulum stress engenders immune-resistant, latent pancreatic cancer metastases. Science, 360 (394). ISSN 0036-8075

Aznarez, Isabel, Nomakuchi, Tomoki T., Tetenbaum-Novatt, Jaclyn, Rahman, Mohammad Alinoor, Fregoso, Oliver, Rees, Holly, Krainer, Adrian R. (May 2018) Mechanism of Nonsense-Mediated mRNA Decay Stimulation by Splicing Factor SRSF1. Cell Reports, 23 (7). pp. 2186-2198. ISSN 2211-1247

Fein, M. R., He, X. Y., Almeida, A. S., Pommier, A., Bruzas, E., Eberhardt, A., Wilkinson, J. E., dos Santos, C., Egeblad, M. (May 2018) Targeting cancer cell CCR2 enhances synergistic immune surveillance in breast cancer. Cancer Research, 78 (10 Sup). pp. 75-76. ISSN 0008-5472

Han, Y., Kebschull, J. M., Campbell, R. A. A., Cowan, D., Imhof, F., Zador, A. M., Mrsic-Flogel, T. D. (April 2018) The logic of single-cell projections from visual cortex. Nature, 556 (7699). pp. 51-56. ISSN 0028-0836

Naguib, A., Mathew, G., Reczek, C. R., Watrud, K., Ambrico, A., Herzka, T., Salas, I. C., Lee, M. F., El-Amine, N., Zheng, W., Di Francesco, M. E., Marszalek, J. R., Pappin, D. J., Chandel, N. S., Trotman, L. C. (April 2018) Mitochondrial Complex I Inhibitors Expose a Vulnerability for Selective Killing of Pten-Null Cells. Cell Rep, 23 (1). pp. 58-67. ISSN 2211-1247 (Electronic)

Underwood, C. J., Choi, K., Lambing, C., Zhao, X., Serra, H., Borges, F., Simorowski, J., Ernst, E., Jacob, Y., Henderson, I. R., Martienssen, R. A. (April 2018) Epigenetic activation of meiotic recombination near Arabidopsis thaliana centromeres via loss of H3K9me2 and non-CG DNA methylation. Genome Res, 28 (4). pp. 519-531. ISSN 1088-9051

Choi, K., Zhao, X., Tock, A. J., Lambing, C., Underwood, C. J., Hardcastle, T. J., Serra, H., Kim, J., Cho, H. S., Kim, J., Ziolkowski, P. A., Yelina, N. E., Hwang, I., Martienssen, R. A., Henderson, I. R. (April 2018) Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions. Genome Res, 28 (4). pp. 532-546. ISSN 1088-9051

Bružas, Emilis, Egeblad, Mikala (March 2018) Bone Talk: Activated Osteoblasts Promote Lung Cancer Growth. Trends in Molecular Medicine, 24 (3). pp. 237-239. ISSN 1471-4914

Knott, S. R. V., Wagenblast, E., Khan, S., Kim, S. Y., Soto, M., Wagner, M., Turgeon, M. O., Fish, L., Erard, N., Gable, A. L., Maceli, A. R., Dickopf, S., Papachristou, E. K., D'Santos, C. S., Carey, L. A., Wilkinson, J. E., Harrell, J. C., Perou, C. M., Goodarzi, H., Poulogiannis, G., Hannon, G. J. (February 2018) Asparagine bioavailability governs metastasis in a model of breast cancer. Nature, 554 (7692). pp. 378-381. ISSN 0028-0836

Kumar, V., Rosenbaum, J., Wang, Z., Forcier, T., Ronemus, M., Wigler, M., Levy, D. (January 2018) Partial bisulfite conversion for unique template sequencing. Nucleic Acids Res, 46 (2). e10. ISSN 0305-1048

Alexander, J., Kendall, J., McIndoo, J., Rodgers, L., Aboukhalil, R., Levy, D., Stepansky, A., Sun, G., Chobadjiev, L., Riggs, M., Cox, H., Hakker, I., Nowak, D. G., Laze, J., Llukani, E., Srivastava, A., Gruschow, S., Yadav, S. S., Robinson, B. D., Atwal, G., Trotman, L. C., Lepor, H., Hicks, J. B., Wigler, M., Krasnitz, A. (January 2018) Utility of single cell genomics in diagnostic evaluation of prostate cancer. Cancer Res, 78 (2). pp. 348-358. ISSN 0008-5472

Ho, Yu-Jui, Anaparthy, Naishitha, Molik, David, Aicher, Toby, Patel, Ami, Hicks, James, Hammell, Molly (December 2017) SAKE (Single-cell RNA-Seq Analysis and Klustering Evaluation) Identifies Markers of Resistance to Targeted BRAF Inhibitors in Melanoma Cell Populations. bioRxiv. (Unpublished)

Batut, P. J., Gingeras, T. R. (December 2017) Conserved noncoding transcription and core promoter regulatory code in early Drosophila development. Elife, 6. ISSN 2050-084x

Shuvaev, Sergey, Giaffar, Hamza, Koulakov, Alexei A (December 2017) Representations of Sound in Deep Learning of Audio Features from Music. arXiv. (Submitted)

Lee, M., Naguib, A., Trotman, L. C., El-Amine, N. (December 2017) Endocytosis and PTEN in Tumor Suppression. Molecular Biology of the Cell, 28 (26 ASC). Abstract M257. ISSN 1059-15241939-4586

Albrengues, J., Wysocki, R. W., Maiorino, L., Egeblad, M. (November 2017) Re-cyclin' Cell-Cycle Components to Make NETs. Dev Cell, 43 (4). pp. 379-380. ISSN 1534-5807

Delas, M. J., Sabin, L. R., Dolzhenko, E., Knott, S. R., Munera Maravilla, E., Jackson, B. T., Wild, S. A., Kovacevic, T., Stork, E. M., Zhou, M., Erard, N., Lee, E., Kelley, D. R., Roth, M., Barbosa, I. S. A., Zuber, J., Rinn, J. L., Smith, A. D., Hannon, G. J. (September 2017) lncRNA requirements for mouse acute myeloid leukemia and normal differentiation. Elife, 6. e25607. ISSN 2050-084x

Roe, J. S., Hwang, C. I., Somerville, T. D. D., Milazzo, J. P., Lee, E. J., Da Silva, B., Maiorino, L., Tiriac, H., Young, C. M., Miyabayashi, K., Filippini, D., Creighton, B., Burkhart, R. A., Buscaglia, J. M., Kim, E. J., Grem, J. L., Lazenby, A. J., Grunkemeyer, J. A., Hollingsworth, M. A., Grandgenett, P. M., Egeblad, M., Park, Y., Tuveson, D. A., Vakoc, C. R. (August 2017) Enhancer Reprogramming Promotes Pancreatic Cancer Metastasis. Cell, 170 (5). pp. 875-888. ISSN 0092-8674

Faehnle, C. R., Walleshauser, J., Joshua-Tor, L. (August 2017) Multi-domain utilization by TUT4 and TUT7 in control of let-7 biogenesis. Nat Struct Mol Biol, 24 (8). pp. 658-665. ISSN 1545-9985 (Public Dataset)

Vurture, G. W., Sedlazeck, F. J., Nattestad, M., Underwood, C. J., Fang, H., Gurtowski, J., Schatz, M. C. (July 2017) GenomeScope: Fast reference-free genome profiling from short reads. Bioinformatics, 33 (14). pp. 2202-2204. ISSN 1367-4803

Banerjee, Arkarup, Marbach, F., Anselmi, Francesca, Koh, Matthew S, Davis, Martin B, Garcia da Silva, P., Delevich, K., Oyibo, Hassana K., Gupta, Priyanka, Li, Bo, Albeanu, Dinu F (July 2017) Long-range interactions between short axon cells and external tufted cells gate glomerular output in the mouse olfactory bulb. Neuron, 87 (1). pp. 193-207. ISSN 0896-6273

Romero-Hernandez, A., Furukawa, H. (July 2017) Novel mode of antagonist binding in NMDA receptors revealed by the crystal structure of the GluN1-GluN2A ligand-binding domain complexed to NVP-AAM077. Mol Pharmacol, 92 (1). pp. 22-29. ISSN 0026-895x (Public Dataset)

Delas, M. J., Hannon, G. J. (July 2017) lncRNAs in development and disease: from functions to mechanisms. Open Biol, 7 (7). ISSN 2046-2441

Schorn, A. J., Gutbrod, M. J., LeBlanc, C., Martienssen, R. (June 2017) LTR-Retrotransposon Control by tRNA-Derived Small RNAs. Cell, 170 (1). pp. 61-71. ISSN 0092-8674 (Public Dataset)

Chang, An-Yun, Castel, Stephane E., Ernst, Evan, Kim, Hyun Soo, Martienssen, Robert A. (June 2017) The Conserved RNA Binding Cyclophilin, Rct1, Regulates Small RNA Biogenesis and Splicing Independent of Heterochromatin Assembly. Cell Reports, 19 (12). pp. 2477-2489. ISSN 2211-1247

Chalk, M., Masset, P., Gutkin, B., Deneve, S. (June 2017) Sensory noise predicts divisive reshaping of receptive fields. PLoS Comput Biol, 13 (6). e1005582. ISSN 1553-734x

Kumar, Vijay, Rosenbaum, Julie, Wang, Zihua, Forcier, Talitha, Ronemus, Michael, Wigler, Michael, Levy, Dan (June 2017) Mutational sequencing for accurate count and long-range assembly. bioRxiv.

Soyk, Sebastian, Lemmon, Zachary H., Oved, Matan, Fisher, Josef, Liberatore, Katie L., Park, Soon Ju, Goren, Anna, Jiang, Ke, Ramos, Alexis, van der Knaap, Esther, Van Eck, Joyce, Zamir, Dani, Eshed, Yuval, Lippman, Zachary B. (June 2017) Bypassing Negative Epistasis on Yield in Tomato Imposed by a Domestication Gene. Cell, 169 (6). pp. 1142-1155. ISSN 0092-8674

Feigin, M. E., Garvin, T., Bailey, P., Waddell, N., Chang, D. K., Kelley, D. R., Shuai, S., Gallinger, S., McPherson, J. D., Grimmond, S. M., Khurana, E., Stein, L. D., Biankin, A. V., Schatz, M. C., Tuveson, D. A. (June 2017) Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma. Nat Genet, 49 (6). pp. 825-833. ISSN 1061-4036

Oberauer, K., Stoneking, C., Wabersich, D., Lin, H. Y. (May 2017) Hierarchical Bayesian measurement models for continuous reproduction of visual features from working memory. J Vis, 17 (5). p. 11. ISSN 1534-7362

Peikon, I. D., Kebschull, J. M., Vagin, V. V., Ravens, D. I., Sun, Y. C., Brouzes, E., Correa, I. R., Bressan, D., Zador, A. M. (April 2017) Using high-throughput barcode sequencing to efficiently map connectomes. Nucleic Acids Res. ISSN 0305-1048

Underwood, Charles J., Henderson, Ian R., Martienssen, Robert A. (April 2017) Genetic and epigenetic variation of transposable elements in Arabidopsis. Current Opinion in Plant Biology, 36. pp. 135-141. ISSN 1369-5266

Krug, L., Chatterjee, N., Borges-Monroy, R., Hearn, S., Liao, W. W., Morrill, K., Prazak, L., Rozhkov, N., Theodorou, D., Hammell, M., Dubnau, J. (March 2017) Retrotransposon activation contributes to neurodegeneration in a Drosophila TDP-43 model of ALS. PLoS Genet, 13 (3). e1006635. ISSN 1553-7390 (Public Dataset)

Ohlund, D., Handly-Santana, A., Biffi, G., Elyada, E., Almeida, A. S., Ponz-Sarvise, M., Corbo, V., Oni, T. E., Hearn, S. A., Lee, E. J., Chio, II, Hwang, C. I., Tiriac, H., Baker, L. A., Engle, D. D., Feig, C., Kultti, A., Egeblad, M., Fearon, D. T., Crawford, J. M., Clevers, H., Park, Y., Tuveson, D. A. (March 2017) Distinct populations of inflammatory fibroblasts and myofibroblasts in pancreatic cancer. J Exp Med, 214 (3). pp. 579-596. ISSN 0022-1007

Chen, M., Nowak, D. G., Narula, N., Robinson, B., Watrud, K., Ambrico, A., Herzka, T. M., Zeeman, M. E., Minderer, M., Zheng, W., Ebbesen, S. H., Plafker, K. S., Stahlhut, C., Wang, V. M., Wills, L., Nasar, A., Castillo-Martin, M., Cordon-Cardo, C., Wilkinson, J. E., Powers, S., Sordella, R., Altorki, N. K., Mittal, V., Stiles, B. M., Plafker, S. M., Trotman, L. C. (March 2017) The nuclear transport receptor Importin-11 is a tumor suppressor that maintains PTEN protein. J Cell Biol, 216 (3). pp. 641-656. ISSN 0021-9525

Pal, D., Pertot, A., Shirole, N. H., Yao, Z., Anaparthy, N., Garvin, T., Cox, H., Chang, K., Rollins, F., Kendall, J., Edwards, L., Singh, V. A., Stone, G. C., Schatz, M. C., Hicks, J., Hannon, G., Sordella, R. (January 2017) TGF-beta reduces DNA ds-break repair mechanisms to heighten genetic diversity and adaptability of CD44+/CD24- cancer cells. Elife, 6. ISSN 2050-084X (Electronic)2050-084X (Linking)

Manchado, E., Huang, C. H., Tasdemir, N., Tschaharganeh, D. F., Wilkinson, J. E., Lowe, S. W. (January 2017) A Pipeline for Drug Target Identification and Validation. Cold Spring Harb Symp Quant Biol, 81. pp. 257-267. ISSN 1943-4456 (Electronic)0091-7451 (Linking)

Romero-Hernandez, Annabel, Simorowski, Noriko, Karakas, Erkan, Furukawa, Hiro (December 2016) Molecular Basis for Subtype Specificity and High-Affinity Zinc Inhibition in the GluN1-GluN2A NMDA Receptor Amino-Terminal Domain. Neuron, 92 (6). pp. 1324-1336. ISSN 0896-6273 (Public Dataset)

Chin, C. S., Peluso, P., Sedlazeck, F. J., Nattestad, M., Concepcion, G. T., Clum, A., Dunn, C., O'Malley, R., Figueroa-Balderas, R., Morales-Cruz, A., Cramer, G. R., Delledonne, M., Luo, C., Ecker, J. R., Cantu, D., Rank, D. R., Schatz, M. C. (December 2016) Phased diploid genome assembly with single-molecule real-time sequencing. Nat Methods, 13 (12). pp. 1050-1054. ISSN 1548-7105 (Electronic)1548-7091 (Linking)

Delevich, K., Abi-Dargham, A., Hall, J., Sawa, A. (October 2016) Studying schizophrenia in the post-genomic era: perspectives from the 2016 summer Banbury Workshop at Cold Spring Harbor Laboratory. Mol Psychiatry. ISSN 1476-5578 (Electronic)1359-4184 (Linking)

Nattestad, Maria, Chin, Chen-Shan, Schatz, Michael (October 2016) Ribbon: Visualizing complex genome alignments and structural variation. bioRxiv. (Unpublished)

Park, J., Wysocki, R. W., Amoozgar, Z., Maiorino, L., Fein, M. R., Jorns, J., Schott, A. F., Kinugasa-Katayama, Y., Lee, Y., Won, N. H., Nakasone, E. S., Hearn, S. A., Kuttner, V., Qiu, J., Almeida, A. S., Perurena, N., Kessenbrock, K., Goldberg, M. S., Egeblad, M. (October 2016) Cancer cells induce metastasis-supporting neutrophil extracellular DNA traps. Sci Transl Med, 8 (361). 361ra138. ISSN 1946-6242 (Electronic)1946-6234 (Linking)

Nattestad, M., Schatz, M. C. (October 2016) Assemblytics: a web analytics tool for the detection of variants from an assembly. Bioinformatics, 32 (19). pp. 3021-3023. ISSN 1367-4811 (Electronic)1367-4803 (Linking)

Pisupati, S., Chartarifsky, L., Churchland, A. K. (September 2016) Decision Activity in Parietal Cortex - Leader or Follower? Trends Cogn Sci. ISSN 1879-307X (Electronic)1364-6613 (Linking)

Kepple, Daniel, Giaffar, Hamza, Rinberg, Dmitry, Koulakov, Alexei (September 2016) Deconstructing Odorant Identity via Primacy in Dual Networks. arXiv. (Submitted)

Kebschull, Justus M, Garcia da Silva, Pedro, Reid, Ashlan P, Peikon, Ian D, Albeanu, Dinu F, Zador, Anthony M (September 2016) High-Throughput Mapping of Single-Neuron Projections by Sequencing of Barcoded RNA. Neuron, 91 (5). pp. 975-987. ISSN 0896-6273 (Public Dataset)

Otazu, G. H., Masset, P. P., Albeanu, D. F. (September 2016) A Computational Role for Cortical Feedback in Odor Detection in Natural Scenes. Chemical Senses, 41 (7). E101-E102. ISSN 0379-864X

Hangya, B., Sanders, J. L., Kepecs, A. (September 2016) A Mathematical Framework for Statistical Decision Confidence. Neural Comput, 28 (9). pp. 1840-1858. ISSN 1530-888X (Electronic)0899-7667 (Linking)

Hohmann, A. F., Martin, L. J., Minder, J. L., Roe, J. S., Shi, J., Steurer, S., Bader, G., McConnell, D., Pearson, M., Gerstberger, T., Gottschamel, T., Thompson, D., Suzuki, Y., Koegl, M., Vakoc, C. R. (September 2016) Sensitivity and engineered resistance of myeloid leukemia cells to BRD9 inhibition. Nat Chem Biol, 12 (9). pp. 672-9. ISSN 1552-4469 (Electronic)1552-4450 (Linking) (Public Dataset)

Vembar, S. S., Seetin, M., Lambert, C., Nattestad, M., Schatz, M. C., Baybayan, P., Scherf, A., Smith, M. L. (August 2016) Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome through long-read (>11 kb), single molecule, real-time sequencing. DNA Res, 23 (4). pp. 339-351. ISSN 1756-1663 (Electronic)1340-2838 (Linking)

Fagegaltier, D., Falciatori, I., Czech, B., Castel, S., Perrimon, N., Simcox, A., Hannon, G. J. (July 2016) Oncogenic transformation of Drosophila somatic cells induces a functional piRNA pathway. Genes Dev, 30 (14). pp. 1623-35. ISSN 1549-5477 (Electronic)0890-9369 (Linking)

Choi, K., Reinhard, C., Serra, H., Ziolkowski, P. A., Underwood, C. J., Zhao, X., Hardcastle, T. J., Yelina, N. E., Griffin, C., Jackson, M., Mezard, C., McVean, G., Copenhaver, G. P., Henderson, I. R. (July 2016) Recombination Rate Heterogeneity within Arabidopsis Disease Resistance Genes. PLoS Genet, 12 (7). e1006179. ISSN 1553-7404 (Electronic)1553-7390 (Linking)

Manchado, E., Weissmueller, S., Morris, J. P., Chen, C. C., Wullenkord, R., Lujambio, A., de Stanchina, E., Poirier, J. T., Gainor, J. F., Corcoran, R. B., Engelman, J. A., Rudin, C. M., Rosen, N., Lowe, S. W. (June 2016) A combinatorial strategy for treating KRAS-mutant lung cancer. Nature, 534. pp. 647-51. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Tasdemir, N., Banito, A., Roe, J. S., Alonso-Curbelo, D., Camiolo, M., Tschaharganeh, D. F., Huang, C. H., Aksoy, O., Bolden, J. E., Chen, C. C., Fennell, M., Thapar, V., Chicas, A., Vakoc, C. R., Lowe, S. W. (June 2016) BRD4 connects enhancer remodeling to senescence immune surveillance. Cancer Discov, 6 (6). pp. 612-629. ISSN 2159-8290 (Electronic)2159-8274 (Linking)

Öhlund, Daniel, Handly-Santana, Abram, Elyada, Ela, Biffi, Giulia, Tuveson, David A. (June 2016) Pancreatic stellate cell heterogeneity in cancer. Pancreatology, 16 (3, Sup). S15. ISSN 1424-3903

Martin, L. J., Koegl, M., Bader, G., Cockcroft, X. L., Fedorov, O., Fiegen, D., Gerstberger, T., Hofmann, M. H., Hohmann, A. F., Kessler, D., Knapp, S., Knesl, P., Kornigg, S., Muller, S., Nar, H., Rogers, C., Rumpel, K., Schaaf, O., Steurer, S., Tallant, C., Vakoc, C. R., Zeeb, M., Zoephel, A., Pearson, M., Boehmelt, G., McConnell, D. (May 2016) Structure-Based Design of an in Vivo Active Selective BRD9 Inhibitor. J Med Chem, 59 (10). pp. 4462-75. ISSN 1520-4804 (Electronic)0022-2623 (Linking)

Kebschull, J. M., Garcia da Silva, P., Zador, A. M. (May 2016) A New Defective Helper RNA to Produce Recombinant Sindbis Virus that Infects Neurons but does not Propagate. Front Neuroanat, 10. p. 56. ISSN 1662-5129 (Electronic)1662-5129 (Linking)

Sanders, Joshua I, Hangya, Balázs, Kepecs, Adam (May 2016) Signatures of a Statistical Computation in the Human Sense of Confidence. Neuron, 90 (3). pp. 499-506. ISSN 0896-6273

Bhagwat, A. S., Roe, J. S., Mok, B. Y., Hohmann, A. F., Shi, J., Vakoc, C. R. (April 2016) BET Bromodomain Inhibition Releases the Mediator Complex from Select cis-Regulatory Elements. Cell Rep, 15 (3). pp. 519-30. ISSN 2211-1247 (Electronic)

Vij, S., Kuhl, H., Kuznetsova, I. S., Komissarov, A., Yurchenko, A. A., Van Heusden, P., Singh, S., Thevasagayam, N. M., Prakki, S. R., Purushothaman, K., Saju, J. M., Jiang, J., Mbandi, S. K., Jonas, M., Hin Yan Tong, A., Mwangi, S., Lau, D., Ngoh, S. Y., Liew, W. C., Shen, X., Hon, L. S., Drake, J. P., Boitano, M., Hall, R., Chin, C. S., Lachumanan, R., Korlach, J., Trifonov, V., Kabilov, M., Tupikin, A., Green, D., Moxon, S., Garvin, T., Sedlazeck, F. J., Vurture, G. W., Gopalapillai, G., Kumar Katneni, V., Noble, T. H., Scaria, V., Sivasubbu, S., Jerry, D. R., O'Brien, S. J., Schatz, M. C., Dalmay, T., Turner, S. W., Lok, S., Christoffels, A., Orban, L. (April 2016) Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding. PLoS Genet, 12 (4). e1005954. ISSN 1553-7404 (Electronic)1553-7390 (Linking)

Christov-Moore, L., Sugiyama, T., Grigaityte, K., Iacoboni, M. (April 2016) Increasing generosity by disrupting prefrontal cortex. Soc Neurosci, 12 (2). pp. 174-181. ISSN 1747-0927 (Electronic)1747-0919 (Linking)

Ebbesen, S. H., Scaltriti, M., Bialucha, C. U., Morse, N., Kastenhuber, E. R., Wen, H. Y., Dow, L. E., Baselga, J., Lowe, S. W. (March 2016) Pten loss promotes MAPK pathway dependency in HER2/neu breast carcinomas. Proc Natl Acad Sci U S A, 113 (11). pp. 3030-3035. ISSN 1091-6490 (Electronic)0027-8424 (Linking)

Plavskin, Yevgeniy, Nagashima, Akitomo, Perroud, Pierre-François, Hasebe, Mitsuyasu, Quatrano, Ralph S, Atwal, Gurinder S, Timmermans, Marja C P. (February 2016) Ancient trans-Acting siRNAs Confer Robustness and Sensitivity onto the Auxin Response. Developmental Cell, 36 (3). pp. 276-289. ISSN 1534-5807

Kim, Y., Perova, Z., Mirrione, M. M., Pradhan, K., Henn, F. A., Shea, S., Osten, P., Li, B. (February 2016) Whole-Brain Mapping of Neuronal Activity in the Learned Helplessness Model of Depression. Front Neural Circuits, 10. ISSN 1662-5110 (Electronic)1662-5110 (Linking)

Seshadri, S., Faust, T., Ishizuka, K., Delevich, K., Chung, Y., Kim, S. H., Cowles, M., Niwa, M., Jaaro-Peled, H., Tomoda, T., Lai, C., Anton, E. S., Li, B., Sawa, A. (December 2015) Interneuronal DISC1 regulates NRG1-ErbB4 signalling and excitatory-inhibitory synapse formation in the mature cortex. Nat Commun, 6. p. 10118. ISSN 2041-1723

Kebschull, J. M., Zador, A. M. (December 2015) Sources of PCR-induced distortions in high-throughput sequencing data sets. Nucleic Acids Res, 43 (21). e143. ISSN 1362-4962 (Electronic)0305-1048 (Linking)

Zepeda-Mendoza, C. J., Mukhopadhyay, S., Wong, E. S., Harder, N., Splinter, E., de Wit, E., Eckersley-Maslin, M. A., Ried, T., Eils, R., Rohr, K., Mills, A., de Laat, W., Flicek, P., Sengupta, A. M., Spector, D. L. (November 2015) Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2. BMC Genomics, 16 (1). p. 982. ISSN 1471-2164 (Electronic)1471-2164 (Linking)

Zhou, X., Battistoni, G., El Demerdash, O., Gurtowski, J., Wunderer, J., Falciatori, I., Ladurner, P., Schatz, M. C., Hannon, G. J., Wasik, K. A. (November 2015) Dual functions of Macpiwi1 in transposon silencing and stem cell maintenance in the flatworm Macrostomum lignano. RNA, 21 (11). pp. 1885-1897. ISSN 1469-9001 (Electronic)1355-8382 (Linking)

Garvin, T., Aboukhalil, R., Kendall, J., Baslan, T., Atwal, G. S., Hicks, J., Wigler, M., Schatz, M. C. (November 2015) Interactive analysis and assessment of single-cell copy-number variations. Nat Methods, 12. pp. 1058-1060. ISSN 1548-7105 (Electronic)1548-7091 (Linking) (Public Dataset)

Yu, Y., Gu, J., Jin, Y., Luo, Y., Preall, J. B., Ma, J., Czech, B., Hannon, G. J. (October 2015) Panoramix enforces piRNA-dependent cotranscriptional silencing. Science, 350 (6258). pp. 339-42. ISSN 1095-9203 (Electronic)0036-8075 (Linking)

Wasik, K., Gurtowski, J., Zhou, X., Ramos, O. M., Delas, M. J., Battistoni, G., El Demerdash, O., Falciatori, I., Vizoso, D. B., Smith, A. D., Ladurner, P., Scharer, L., McCombie, W. R., Hannon, G. J., Schatz, M. (September 2015) Genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignano. Proc Natl Acad Sci U S A, 112 (40). pp. 12462-12467. ISSN 1091-6490 (Electronic)0027-8424 (Linking)

Dong, J., Panchakshari, R. A., Zhang, T., Zhang, Y., Hu, J., Volpi, S. A., Meyers, R. M., Ho, Y. J., Du, Z., Robbiani, D. F., Meng, F., Gostissa, M., Nussenzweig, M. C., Manis, J. P., Alt, F. W. (September 2015) Orientation-specific joining of AID-initiated DNA breaks promotes antibody class switching. Nature, 525 (7567). pp. 134-9. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Chae, H. G., Kepple, D., Koulakov, A. A., Murthy, V. N., Albeanu, D. F. (September 2015) Mosaic representation of odors in the output layer of the mouse olfactory bulb. Chemical Senses, 40 (7). p. 564. ISSN 0379-864X

Bergmann, J. H., Li, J., Eckersley-Maslin, M. A., Rigo, F., Freier, S. M., Spector, D. L. (September 2015) Regulation of the ESC transcriptome by nuclear long non-coding RNAs. Genome Res, 25 (9). pp. 1336-1346. ISSN 1549-5469 (Electronic)1088-9051 (Linking)

Regan, Michael C., Romero-Hernandez, Annabel, Furukawa, Hiro (August 2015) A structural biology perspective on NMDA receptor pharmacology and function. Current Opinion in Structural Biology, 33. pp. 68-75. ISSN 0959-440X

Chakraborty, A. A., Scuoppo, C., Dey, S., Thomas, L. R., Lorey, S. L., Lowe, S. W., Tansey, W. P. (July 2015) A common functional consequence of tumor-derived mutations within c-MYC. Oncogene, 34. pp. 2406-2409. ISSN 0950-9232

Banerjee, A., Marbach, F., Anselmi, F., Koh, M. S., Davis, M. B., Garcia da Silva, P., Delevich, K., Oyibo, H. K., Gupta, P., Li, B., Albeanu, D. F. (July 2015) An Interglomerular Circuit Gates Glomerular Output and Implements Gain Control in the Mouse Olfactory Bulb. Neuron, 87 (1). pp. 193-207. ISSN 0896-6273

Ren, J., Castel, S. E., Martienssen, R. A. (July 2015) Dicer in action at replication-transcription collisions. Mol Cell Oncol, 2 (3). e991224. ISSN 2372-3556 (Electronic)2372-3556 (Linking)

Xu, C., Liberatore, K. L., MacAlister, C. A., Huang, Z., Chu, Y. H., Jiang, K., Brooks, C., Ogawa-Ohnishi, M., Xiong, G., Pauly, M., Van Eck, J., Matsubayashi, Y., van der Knaap, E., Lippman, Z. B. (July 2015) A cascade of arabinosyltransferases controls shoot meristem size in tomato. Nat Genet, 47 (7). pp. 784-792. ISSN 1546-1718 (Electronic)1061-4036 (Linking)

Wasik, K. A., Tam, O. H., Knott, S. R., Falciatori, I., Hammell, M., Vagin, V. V., Hannon, G. J. (June 2015) RNF17 blocks promiscuous activity of PIWI proteins in mouse testes. Genes Dev, 29 (13). pp. 1403-1415. ISSN 1549-5477 (Electronic)0890-9369 (Linking)

Akerman, M., Fregoso, O. I., Das, S., Ruse, C., Jensen, M. A., Pappin, D. J., Zhang, M. Q., Krainer, A. R. (June 2015) Differential connectivity of splicing activators and repressors to the human spliceosome. Genome Biol, 16 (1). p. 119. ISSN 1465-6914 (Electronic)1465-6906 (Linking)

Xiong, Q., Znamenskiy, P., Zador, A. M. (May 2015) Selective corticostriatal plasticity during acquisition of an auditory discrimination task. Nature, 521 (7552). pp. 348-351. ISSN 0028-0836

Vigilant, L., Roy, J., Bradley, B. J., Stoneking, C. J., Robbins, M. M., Stoinski, T. S. (May 2015) Reproductive competition and inbreeding avoidance in a primate species with habitual female dispersal. Behavioral Ecology and Sociobiology, 69 (7). pp. 1163-1172. ISSN 03405443

Goh, W. S., Falciatori, I., Tam, O. H., Burgess, R., Meikar, O., Kotaja, N., Hammell, M., Hannon, G. J. (May 2015) piRNA-directed cleavage of meiotic transcripts regulates spermatogenesis. Genes Dev, 29 (10). pp. 1032-44. ISSN 1549-5477 (Electronic)0890-9369 (Linking)

Wang, E., Kawaoka, S., Roe, J. S., Shi, J., Hohmann, A. F., Xu, Y., Bhagwat, A. S., Suzuki, Y., Kinney, J. B., Vakoc, C. R. (April 2015) The transcriptional cofactor TRIM33 prevents apoptosis in B lymphoblastic leukemia by deactivating a single enhancer. Elife, 4. ISSN 2050-084X (Electronic)2050-084X (Linking)

Delevich, K., Tucciarone, J., Huang, Z. J., Li, B. (April 2015) The Mediodorsal Thalamus Drives Feedforward Inhibition in the Anterior Cingulate Cortex via Parvalbumin Interneurons. Journal of Neuroscience , 35 (14). pp. 5743-53. ISSN 0270-6474

Wagenblast, E., Soto, M., Gutierrez-Angel, S., Hartl, C. A., Gable, A. L., Maceli, A. R., Erard, N., Williams, A. M., Kim, S. Y., Dickopf, S., Harrell, J. C., Smith, A. D., Perou, C. M., Wilkinson, J. E., Hannon, G. J., Knott, S. R. (April 2015) A model of breast cancer heterogeneity reveals vascular mimicry as a driver of metastasis. Nature, 520 (7547). pp. 358-362. ISSN 0028-0836

Hogan, Megan S, Parfitt, David-Emlyn, Zepeda-Mendoza, Cinthya J, Shen, Michael M, Spector, David L (March 2015) Transient Pairing of Homologous Oct4 Alleles Accompanies the Onset of Embryonic Stem Cell Differentiation. Cell Stem Cell, 16 (3). pp. 275-288. ISSN 1934-5909

Perova, Z., Delevich, K., Li, B. (February 2015) Depression of excitatory synapses onto parvalbumin interneurons in the medial prefrontal cortex in susceptibility to stress. Journal of Neuroscience, 35 (7). pp. 3201-3206. ISSN 02706474

Underwood, C. J., Martienssen, R. A. (January 2015) Argonautes team up to silence transposable elements in Arabidopsis. Embo Journal, 34 (5). pp. 579-580. ISSN 0261-4189

Pautler, M., Eveland, A. L., LaRue, T., Yang, F., Weeks, R., Lunde, C., Je, B. I., Meeley, R., Komatsu, M., Vollbrecht, E., Sakai, H., Jackson, D. (January 2015) FASCIATED EAR4 Encodes a bZIP Transcription Factor That Regulates Shoot Meristem Size in Maize. Plant Cell, 27 (1). pp. 104-120. ISSN 1040-4651

Yang, F., Bui, H. T., Pautler, M., Llaca, V., Johnston, R., Lee, B. H., Kolbe, A., Sakai, H., Jackson, D. (January 2015) A Maize Glutaredoxin Gene, Abphyl2, Regulates Shoot Meristem Size and Phyllotaxy. Plant Cell, 27 (1). pp. 121-131. ISSN 1040-4651

Ahrens, S., Jaramillo, S., Yu, K., Ghosh, S., Hwang, G., Paik, R., Lai, C., He, M., Huang, Z. J., Li, B. (January 2015) ErbB4 regulation of a thalamic reticular nucleus circuit for sensory selection. Nature Neuroscience, 18. pp. 104-111. ISSN 1097-6256

Boj, Sylvia F, Hwang, Chang-Il, Baker, Lindsey A, Chio, Iok In Christine, Engle, Dannielle D, Corbo, Vincenzo, Jager, Myrthe, Ponz-Sarvise, Mariano, Tiriac, Hervé, Spector, Mona S, Gracanin, Ana, Oni, Tobiloba, Yu, Kenneth H, van Boxtel, Ruben, Huch, Meritxell, Rivera, Keith D, Wilson, John P, Feigin, Michael E, Öhlund, Daniel, Handly-Santana, Abram, Ardito-Abraham, Christine M, Ludwig, Michael, Elyada, Ela, Alagesan, Brinda, Biffi, Giulia, Yordanov, Georgi N, Delcuze, Bethany, Creighton, Brianna, Wright, Kevin, Park, Youngkyu, Morsink, Folkert H M., Molenaar, I.  Quintus, Borel Rinkes, Inne H, Cuppen, Edwin, Hao, Yuan, Jin, Ying, Nijman, Isaac J, Iacobuzio-Donahue, Christine, Leach, Steven D, Pappin, Darryl J, Hammell, Molly, Klimstra, David S, Basturk, Olca, Hruban, Ralph H, Offerhaus, George Johan, Vries, Robert G J., Clevers, Hans, Tuveson, David A (January 2015) Organoid Models of Human and Mouse Ductal Pancreatic Cancer. Cell, 160 (1-2). pp. 324-338. ISSN 0092-8674

Scaife, M. A., Nguyen, G. T., Rico, J., Lambert, D., Helliwell, K. E., Smith, A. G. (2015) Establishing Chlamydomonas reinhardtii as an industrial biotechnology host. Plant Journal.

Garvin, Tyler, Aboukhalil, Robert, Kendall, Jude, Baslan, Timour, Atwal, Gurinder S, Hicks, James, Wigler, Michael, Schatz, Michael (2015) Interactive analysis and quality assessment of single-cell copy-number variations. Nature Methods, 12. pp. 1058-1060. ISSN 15487091 (ISSN)

Knott, S. R., Maceli, A. R., Erard, N., Chang, K., Marran, K., Zhou, X., Gordon, A., El Demerdash, O., Wagenblast, E., Kim, S., Fellmann, C., Hannon, G. J. (December 2014) A Computational Algorithm to Predict shRNA Potency. Mol Cell, 56 (6). pp. 796-807. ISSN 1097-2765

Sanders, J. I., Kepecs, A. (December 2014) A low-cost programmable pulse generator for physiology and behavior. Frontiers in Neuroengineering, 7 (43). ISSN 16626443

Chio, II, Yordanov, G., Tuveson, D. (November 2014) MAX-ing out MYC: a novel small molecule inhibitor against MYC-dependent tumors. Journal of the National Cancer Institute, 106 (12). ISSN 0027-8874

Egeblad, M., Nakasone, E., Askautrud, H., Wysocki, R., Fein, M., Kees, T., Park, J., Park, J. H. (November 2014) Understanding drug responses and resistance mechanisms using imaging in live mice. Molecular Cancer Research, 12 (Supple). ISSN 1541-7786

Ponz-Sarvise, M., Corbo, V., Ohlund, D., Oni, T., Handly-Santana, A., Engle, D., Tiriac, H., Chio, C., Feigin, M., Baker, L., Ardito-Abraham, C., Park, Y., Hwang, C., Elyada, E., Yu, K., Clevers, H., Tuveson, D. A. (November 2014) Pancreatic ductal organoids as a new platform for drug discovery. European Journal of Cancer, 50. p. 63. ISSN 0959-8049

Castel, Stephane E, Ren, Jie, Bhattacharjee, Sonali, Chang, An-Yun, Sánchez, Mar, Valbuena, Alberto, Antequera, Francisco, Martienssen, Robert A (October 2014) Dicer Promotes Transcription Termination at Sites of Replication Stress to Maintain Genome Stability. Cell, 159 (3). pp. 572-583. ISSN 0092-8674

Faehnle, C. R., Walleshauser, J., Joshua-Tor, L. (October 2014) Mechanism of Dis3l2 substrate recognition in the Lin28-let-7 pathway. Nature, 514 (7521). pp. 252-6. ISSN 0028-0836 (Public Dataset)

Sun, J., Ramos, A., Chapman, B., Johnnidis, J. B., Le, L., Ho, Y. J., Klein, A., Hofmann, O., Camargo, F. D. (October 2014) Clonal dynamics of native haematopoiesis. Nature, 514. pp. 322-327. ISSN 0028-0836

Bolden, J. E., Tasdemir, N., Dow, L. E., van Es, J. H., Wilkinson, J. E., Zhao, Z., Clevers, H., Lowe, S. W. (September 2014) Inducible In Vivo Silencing of Brd4 Identifies Potential Toxicities of Sustained BET Protein Inhibition. Cell Rep, 8 (6). pp. 1919-1929. ISSN 2211-1247

Rudalska, R., Dauch, D., Longerich, T., McJunkin, K., Wuestefeld, T., Kang, T. W., Hohmeyer, A., Pesic, M., Leibold, J., von Thun, A., Schirmacher, P., Zuber, J., Weiss, K. H., Powers, S., Malek, N.P., Eilers, M., Sipos, B., Lowe, S. W., Geffers, R., Laufer, S., Zender, L. (September 2014) In vivo RNAi screening identifies a mechanism of sorafenib resistance in liver cancer. Nature Medicine, 20 (10). pp. 1138-1146. ISSN 1078-8956

Oyibo, Hassana K., Znamenskiy, Petr, Oviedo, Hysell V., Zador, Anthony M. (September 2014) Long-term Cre-mediated retrograde tagging of neurons using a novel recombinant pseudorabies virus. Frontiers in Neuroanatomy, 8 (SEP). Art. no.86. ISSN 16625129

Gerstein, M. B., Rozowsky, J., Yan, K. K., Wang, D., Cheng, C., Brown, J. B., Davis, C. A., Hillier, L., Sisu, C., Li, J. J., Pei, B., Harmanci, A. O., Duff, M. O., Djebali, S., Alexander, R. P., Alver, B. H., Auerbach, R., Bell, K., Bickel, P. J., Boeck, M. E., Boley, N. P., Booth, B. W., Cherbas, L., Cherbas, P., Di, C., Dobin, A., Drenkow, J., Ewing, B., Fang, G., Fastuca, M., Feingold, E. A., Frankish, A., Gao, G., Good, P. J., Guigo, R., Hammonds, A., Harrow, J., Hoskins, R. A., Howald, C., Hu, L., Huang, H., Hubbard, T. J., Huynh, C., Jha, S., Kasper, D., Kato, M., Kaufman, T. C., Kitchen, R. R., Ladewig, E., Lagarde, J., Lai, E., Leng, J., Lu, Z., MacCoss, M., May, G., McWhirter, R., Merrihew, G., Miller, D. M., Mortazavi, A., Murad, R., Oliver, B., Olson, S., Park, P. J., Pazin, M. J., Perrimon, N., Pervouchine, D., Reinke, V., Reymond, A., Robinson, G., Samsonova, A., Saunders, G. I., Schlesinger, F., Sethi, A., Slack, F. J., Spencer, W. C., Stoiber, M. H., Strasbourger, P., Tanzer, A., Thompson, O. A., Wan, K. H., Wang, G., Wang, H., Watkins, K. L., Wen, J., Wen, K., Xue, C., Yang, L., Yip, K., Zaleski, C., Zhang, Y., Zheng, H., Brenner, S. E., Graveley, B. R., Celniker, S. E., Gingeras, T. R., Waterston, R. (August 2014) Comparative analysis of the transcriptome across distant species. Nature, 512 (7515). pp. 445-8. ISSN 0028-0836

Tschaharganeh, D. F., Xue, W., Calvisi, D. F., Evert, M., Michurina, T. V., Dow, L. E., Banito, A., Katz, S. F., Kastenhuber, E. R., Weissmueller, S., Huang, C. H., Lechel, A., Andersen, J. B., Capper, D., Zender, L., Longerich, T., Enikolopov, G., Lowe, S. W. (July 2014) p53-Dependent Nestin Regulation Links Tumor Suppression to Cellular Plasticity in Liver Cancer. Cell, 158 (3). pp. 579-92. ISSN 0092-8674

Peikon, I. D., Gizatullina, D. I., Zador, A. M. (July 2014) In vivo generation of DNA sequence diversity for cellular barcoding. Nucleic Acids Res, 42 (16). ISSN 0305-1048

Rechavi, Oded, Houri-Ze’evi, Leah, Anava, Sarit, Goh, Wee Siong Sho, Kerk, Sze Yen, Hannon, Gregory J, Hobert, Oliver (July 2014) Starvation-Induced Transgenerational Inheritance of Small RNAs in C. elegans. Cell, 158 (2). pp. 277-287. ISSN 0092-8674

Ganapathy, G., Howard, J. T., Ward, J. M., Li, J., Li, B., Li, Y., Xiong, Y., Zhang, Y., Zhou, S., Schwartz, D. C., Schatz, M., Aboukhalil, R., Fedrigo, O., Bukovnik, L., Wang, T., Wray, G., Rasolonjatovo, I., Winer, R., Knight, J. R., Koren, S., Warren, W. C., Zhang, G., Phillippy, A. M., Jarvis, E. D. (July 2014) High-coverage sequencing and annotated assemblies of the budgerigar genome. Gigascience, 3. p. 11. ISSN 2047-217x

Hohmann, A. F., Vakoc, C. R. (June 2014) A rationale to target the SWI/SNF complex for cancer therapy. Trends in Genetics, 30 (8). pp. 356-363. ISSN 01689525

Odoemene, O., Churchland, A.K. (June 2014) Listening for the Right Sounds. Neuron, 82 (5). pp. 944-945. ISSN 0896-6273

Eckersley-Maslin, M. A., Spector, D. L. (June 2014) Random monoallelic expression: Regulating gene expression one allele at a time. Trends in Genetics, 30 (6). pp. 237-244. ISSN 13624555

Cressy, M., Valente, D., Altick, A., Kockenmesiter, E., Honegger, K., Qin, H., Mitra, P. P., Dubnau, J. (May 2014) Laboratory evolution of adenylyl cyclase independent learning in Drosophila and missing heritability. Genes, Brain and Behavior, 13 (6). pp. 565-577. ISSN 16011848

Wang, M., Perova, Z., Arenkiel, B. R., Li, B. (May 2014) Synaptic modifications in the medial prefrontal cortex in susceptibility and resilience to stress. Journal of Neuroscience, 34 (22). pp. 7485-92. ISSN 0270-6474

Sarkar, Bidyut, Banerjee, Arkarup, Das, Anand Kant, Nag, Suman, Kaushalya, Sanjeev Kumar, Tripathy, Umakanta, Shameem, Mohammad, Shukla, Shubha, Maiti, Sudipta (May 2014) Label-free dopamine imaging in live rat brain slices. ACS Chemical Neuroscience, 5 (5). pp. 329-334. ISSN 1948-7193

Miething, C., Scuoppo, C., Bosbach, B., Appelmann, I., Nakitandwe, J., Ma, J., Wu, G., Lintault, L., Auer, M., Premsrirut, P. K., Teruya-Feldstein, J., Hicks, J., Benveniste, H., Speicher, M. R., Downing, J. R., Lowe, S. W. (May 2014) PTEN action in leukaemia dictated by the tissue microenvironment. Nature, 510 (7505). p. 402. ISSN 0028-0836

Chen, C., Liu, Y., Rappaport, A. R., Kitzing, T., Schultz, N., Zhao, Z., Shroff, A. S., Dickins, R. A., Vakoc, C. R., Bradner, J. E., Stock, W., Lebeau, M. M., Shannon, K. M., Kogan, S., Zuber, J., Lowe, S. W. (April 2014) MLL3 Is a Haploinsufficient 7q Tumor Suppressor in Acute Myeloid Leukemia. Cancer Cell, 25 (5). pp. 652-665. ISSN 1878-3686 (Electronic)1535-6108 (Linking)

Dow, L. E., Nasr, Z., Saborowski, M., Ebbesen, S. H., Manchado, E., Tasdemir, N., Lee, T., Pelletier, J., Lowe, S. W. (April 2014) Conditional Reverse Tet-Transactivator Mouse Strains for the Efficient Induction of TRE-Regulated Transgenes in Mice. PLoS ONE, 9 (4). e95236. ISSN 1932-6203 (Electronic)1932-6203 (Linking)

Weissmueller, S., Manchado, E., Saborowski, M., Morris, J. P. th, Wagenblast, E., Davis, C. A., Moon, S. H., Pfister, N. T., Tschaharganeh, D. F., Kitzing, T., Aust, D., Markert, E. K., Wu, J., Grimmond, S. M., Pilarsky, C., Prives, C., Biankin, A. V., Lowe, S. W. (April 2014) Mutant p53 Drives Pancreatic Cancer Metastasis through Cell-Autonomous PDGF Receptor beta Signaling. Cell, 157 (2). pp. 382-94. ISSN 1097-4172 (Electronic)0092-8674 (Linking)

Meikar, O., Vagin, V. V., Chalmel, F., Sostar, K., Lardenois, A., Hammell, M., Jin, Y., Da Ros, M., Wasik, K. A., Toppari, J., Hannon, G. J., Kotaja, N. (April 2014) An atlas of chromatoid body components. RNA, 20 (4). pp. 483-95. ISSN 1355-8382

Goh, W. S. S., Seah, J. W. E., Harrison, E. J., Chen, C., Hammell, C. M., Hannon, G. J. (April 2014) A genome-wide RNAi screen identifies factors required for distinct stages of C-elegans piRNA biogenesis. Genes & Development, 28 (7). pp. 797-807. ISSN 0890-9369

Jacob, Y., Bergamin, E., Donoghue, M. T., Mongeon, V., LeBlanc, C., Voigt, P., Underwood, C. J., Brunzelle, J. S., Michaels, S. D., Reinberg, D., Couture, J. F., Martienssen, R. A. (March 2014) Selective methylation of histone H3 variant H3.1 regulates heterochromatin replication. Science, 343 (6176). pp. 1249-53. ISSN 0036-8075

Cazakoff, B. N., Lau, B. Y., Crump, K. L., Demmer, H. S., Shea, S. D. (March 2014) Broadly tuned and respiration-independent inhibition in the olfactory bulb of awake mice. Nature Neuroscience. ISSN 1097-6256

Bots, M., Verbrugge, I., Martin, B. P., Salmon, J. M., Ghisi, M., Baker, A., Stanley, K., Shortt, J., Ossenkoppele, G. J., Zuber, J., Rappaport, A. R., Atadja, P., Lowe, S. W., Johnstone, R. W. (February 2014) Differentiation therapy for the treatment of t(8;21) acute myeloid leukemia using histone deacetylase inhibitors. Blood, 123 (9). pp. 1341-52. ISSN 0006-4971

Eckersley-Maslin, M. A., Thybert, D., Bergmann, J. H., Marioni, J. C., Flicek, P., Spector, D. L. (February 2014) Random Monoallelic Gene Expression Increases upon Embryonic Stem Cell Differentiation. Developmental Cell, 28 (4). pp. 351-65. ISSN 1534-5807

Eveland, A. L., Goldshmidt, A., Pautler, M., Morohashi, K., Liseron-Monfils, C., Lewis, M. W., Kumari, S., Hiraga, S., Yang, F., Unger-Wallace, E., Olson, A., Hake, S., Vollbrecht, E., Grotewold, E., Ware, D., Jackson, D. (2014) Regulatory modules controlling maize inflorescence architecture. Genome Research, 24 (3). pp. 431-443. ISSN 1088-9051

Jiang, K., Liberatore, K. L., Park, S. J., Alvarez, J. P., Lippman, Z. B. (December 2013) Tomato yield heterosis is triggered by a dosage sensitivity of the florigen pathway that fine-tunes shoot architecture. PLoS Genetics, 9 (12). e1004043. ISSN 1553-7390

Shi, J., Whyte, W. A., Zepeda-Mendoza, C. J., Milazzo, J. P., Shen, C., Roe, J. S., Minder, J. L., Mercan, F., Wang, E., Eckersley-Maslin, M. A., Campbell, A. E., Kawaoka, S., Shareef, S., Zhu, Z., Kendall, J., Muhar, M., Haslinger, C., Yu, M., Roeder, R. G., Wigler, M. A., Blobel, G. A., Zuber, J., Spector, D. L., Young, R. A., Vakoc, C. R. (November 2013) Role of SWI/SNF in acute leukemia maintenance and enhancer-mediated Myc regulation. Genes and Development, 27 (24). pp. 264-273. ISSN 08909369 (ISSN)

Pi, H. J., Hangya, B., Kvitsiani, D., Sanders, J. I., Huang, Z. J., Kepecs, A. (October 2013) Cortical interneurons that specialize in disinhibitory control. Nature, 503. pp. 521-24. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Gruntman, E., Turner, G. C. (October 2013) Integration of the olfactory code across dendritic claws of single mushroom body neurons. Nature Neuroscience, 16 (12). pp. 1821-1829. ISSN 10976256

Vu, T. M., Nakamura, M., Calarco, J. P., Susaki, D., Lim, P. Q., Kinoshita, T., Higashiyama, T., Martienssen, R. A., Berger, F. (July 2013) RNA-directed DNA methylation regulates parental genomic imprinting at several loci in Arabidopsis. Development, 140 (14). pp. 2953-2960. ISSN 0950-1991

Schlesinger, F., Smith, A. D., Gingeras, T. R., Hannon, G. J., Hodges, E. (June 2013) De novo DNA demethylation and non-coding transcription define active intergenic regulatory elements. Genome Research, 23 (10). pp. 1601-1614. ISSN 10889051 (ISSN)

Vagin, V. V., Yu, Y., Jankowska, A., Luo, Y., Wasik, K. A., Malone, C. D., Harrison, E., Rosebrock, A., Wakimoto, B. T., Fagegaltier, D., Muerdter, F., Hannon, G. J. (June 2013) Minotaur is critical for primary piRNA biogenesis. RNA, 19 (8). pp. 1064-1077. ISSN 1469-9001 (Electronic)1355-8382 (Linking)

Campbell, R. A., Honegger, K. S., Qin, H., Li, W., Demir, E., Turner, G. C. (June 2013) Imaging a population code for odor identity in the Drosophila mushroom body. Journal of Neuroscience, 33 (25). pp. 10568-81. ISSN 0270-6474

Tasdemir, N., Lowe, S. W. (June 2013) Senescent cells spread the word: non-cell autonomous propagation of cellular senescence. Embo Journal, 84 (1). pp. 114-127. ISSN 0261-4189

Bodnar, M. S., Spector, D. L. (June 2013) Chromatin Meets Its Organizers. Cell, 153 (6). pp. 1187-1189. ISSN 0092-8674

Raddatz, G., Guzzardo, P. M., Olova, N., Fantappié, M. R., Rampp, M., Schaefer, M., Reik, W., Hannon, G. J., Lyko, F. (May 2013) Dnmt2-dependent methylomes lack defined DNA methylation patterns. Proceedings of the National Academy of Sciences of the United States of America, 110 (21). pp. 8627-8631. ISSN 00278424

Muerdter, F., Guzzardo, P. M., Gillis, J., Luo, Y., Yu, Y., Chen, C., Fekete, R., Hannon, G.J. (May 2013) A Genome-wide RNAi Screen Draws a Genetic Framework for Transposon Control and Primary piRNA Biogenesis in Drosophila. Molecular Cell, 50 (5). pp. 736-748. ISSN 1097-4164

Znamenskiy, P., Zador, A. M. (May 2013) Corticostriatal neurons in auditory cortex drive decisions during auditory discrimination. Nature, 497. pp. 482-485. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Li, W., Prazak, L., Chatterjee, N., Gruninger, S., Krug, L., Theodorou, D., Dubnau, J. (April 2013) Activation of transposable elements during aging and neuronal decline in Drosophila. Nature Neuroscience, 16. pp. 529-531. ISSN 1546-1726 (Electronic)1097-6256 (Linking)

Hubner, M. R., Eckersley-Maslin, M. A., Spector, D. L. (April 2013) Chromatin organization and transcriptional regulation. Current Opinion in Genetics & Development, 23 (2). pp. 89-95. ISSN 0959-437X

Lu, X. W., Wontakal, S. N., Kavi, H., Kim, B. J., Guzzardo, P. M., Emelyanov, A. V., Xu, N., Hannon, G. J., Zavadil, J., Fyodorov, D. V., Skoultchi, A. I. (April 2013) Drosophila H1 Regulates the Genetic Activity of Heterochromatin by Recruitment of Su(var)3-9. Science, 340 (6128). pp. 78-81. ISSN 0036-8075

Sabin, L. R., Delas, M. J., Hannon, G. J. (March 2013) Dogma derailed: the many influences of RNA on the genome. Molecular Cell, 49 (5). pp. 783-94. ISSN 1097-2765

Fregoso, O. I., Das, S., Akerman, M., Krainer, A. R. (March 2013) Splicing-Factor Oncoprotein SRSF1 Stabilizes p53 via RPL5 and Induces Cellular Senescence. Molecular Cell, 50 (1). pp. 56-66. ISSN 1097-2765

Nowak, M., Kramer, B., Haupt, M., Papapanou, P. N., Kebschull, J., Hoffmann, P., Schmidt-Wolf, I. G., Jepsen, S., Brossart, P., Perner, S., Kebschull, M. (March 2013) Activation of Invariant NK T Cells in Periodontitis Lesions. Journal of Immunology, 190 (5). pp. 2282-2291. ISSN 0022-1767

Pautler, M., Tanaka, W., Hirano, H. Y., Jackson, D. (March 2013) Grass meristems I: Shoot apical meristem maintenance, axillary meristem determinacy and the floral transition. Plant and Cell Physiology, 54 (3). pp. 302-312. ISSN 00320781 (ISSN)

Tanaka, W., Pautler, M., Jackson, D., Hirano, H. Y. (March 2013) Grass meristems II: Inflorescence architecture, flower development and meristem fate. Plant and Cell Physiology, 54 (3). pp. 313-324. ISSN 00320781 (ISSN)

Castel, S. E., Martienssen, R. A. (February 2013) RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond. Nat Rev Genet, 14 (2). pp. 100-12. ISSN 1471-0064 (Electronic)1471-0056 (Linking)

Nakasone, E., Askautrud, H., Kees, T., Park, J., Fein, M., Egeblad, M. (February 2013) Imaging contributions of the microenvironment to chemoresistance. Journal of Nuclear Medicine, 54 (Supple). p. 31. ISSN 0161-5505

Guzzardo, P. M., Muerdter, F., Hannon, G. J. (January 2013) The piRNA pathway in flies: highlights and future directions. Curr Opin Genet Dev, 23 (1). pp. 44-52. ISSN 1879-0380 (Electronic)0959-437X (Linking)

Plavskin, Y., Timmermans, M. C. (January 2013) Small RNA-Regulated Networks and the Evolution of Novel Structures in Plants. Cold Spring Harbor Symposia on Quantitative Biology, 77. ISSN 00917451 (ISSN)

Eckersley-Maslin, M. A., Bergmann, J. H., Lazar, Z., Spector, D. L. (January 2013) Lamin A/C is Expressed in Pluripotent Mouse Embryonic Stem Cells. Nucleus, 4 (1). pp. 53-60. ISSN 1949-1042 (Electronic)1949-1042 (Linking)

Aboukhalil, R., Fendler, B., Atwal, G. S. (January 2013) Kerfuffle: a web tool for multi-species gene colocalization analysis. BMC Bioinformatics, 14. ISSN 1471-2105

Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., Gingeras, T. R. (January 2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics, 29 (1). pp. 15-21. ISSN 1367-4803

Sheppard, J. P., Raposo, D., Churchland, A. K. (2013) Dynamic weighting of multisensory stimuli shapes decision-making in rats and humans. Journal of Vision, 13 (6). ISSN 1534-7362 (Electronic)1534-7362 (Linking)

Batut, P. J., Dobin, A., Plessy, C., Carninci, P., Gingeras, T. R. (2013) High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Res, 23 (1). pp. 169-180. ISSN 1549-5469 (Electronic)1088-9051 (Linking)

Nakasone, E. S., Askautrud, H. A., Egeblad, M. (2013) Live imaging of drug responses in the tumor microenvironment in mouse models of breast cancer. Journal of Visualized Experiments (73). ISSN 1940-087X (Electronic)1940-087X (Linking)

Shi, J., Wang, E., Zuber, J., Rappaport, A., Taylor, M., Johns, C., Lowe, S. W., Vakoc, C. R. (2013) The Polycomb complex PRC2 supports aberrant self-renewal in a mouse model of MLL-AF9;Nras(G12D) acute myeloid leukemia. Oncogene, 32 (7). pp. 930-938. ISSN 1476-5594 (Electronic)0950-9232 (Linking)

Batut, P., Gingeras, T. R. (2013) RAMPAGE: Promoter activity profiling by paired-end sequencing of 5'-complete cDNAs. Current Protocols in Molecular Biology (SUPPL). Unit25B. ISSN 19343639 (ISSN)

Borges, F., Calarco, J. P., Martienssen, R. A. (2013) Reprogramming the Epigenome in Arabidopsis Pollen. Cold Spring Harbor Symposia on Quantitative Biology, 77. pp. 1-5. ISSN 00917451 (ISSN)

Hromadka, T., Zador, A. M., DeWeese, M. R. (2013) Up states are rare in awake auditory cortex. Journal of Neurophysiology, 109 (8). pp. 1989-1995. ISSN 0022-3077

Das, S., Fregoso, O. I., Krainer, A. R. (2013) A new path to oncogene-induced senescence: At the cross-roads of splicing and translation. Cell Cycle, 12 (10). ISSN 1551-4005 (Electronic)1551-4005 (Linking)

Sanders, J. I., Kepecs, A. (December 2012) Choice ball: A response interface for two-choice psychometric discrimination in head-fixed mice. Journal of Neurophysiology, 108 (12). pp. 3416-3423. ISSN 00223077

Honegger, K. S., Turner, G. C., Campbell, R. A. (December 2012) Functional imaging of population coding in olfaction: linking neural activity to perception. Journal of Neurogenetics, 26. p. 64. ISSN 0167-7063

Borges, F., Gardner, R., Lopes, T., Calarco, J. P., Boavida, L. C., Slotkin, R. K., Martienssen, R. A., Becker, J. D. (October 2012) FACS-based purification of Arabidopsis microspores, sperm cells and vegetative nuclei. Plant methods, 8 (1). p. 44. ISSN 1746-4811 (Electronic)1746-4811 (Linking)

Wang, Z., Jeon, H. Y., Rigo, F., Bennett, C. F., Krainer, A. R. (October 2012) Manipulation of PK-M mutually exclusive alternative splicing by antisense oligonucleotides. Open Biol, 2 (10). p. 120133. ISSN 2046-2441 (Electronic)2046-2441 (Linking)

Zador, A. M., Dubnau, J., Oyibo, H. K., Zhan, H., Cao, G., Peikon, I. D. (October 2012) Sequencing the Connectome. PLoS Biology, 10 (10). ISSN 1544-9173

Miething, C., Scuoppo, C., Lindqvist, L., Reyes, J., Ruse, C., Appelmann, I., Yoon, S., Krasnitz, A., Teruya-Feldstein, J., Pappin, D., Pelletier, J., Lowe, S. (October 2012) An oncogenome-based RNAi screen identifies a tumour suppressor network in B-cell lymphoma relying on the polyamine-hypusine axis. Onkologie, 35. p. 104. ISSN 0378-584X

Djebali, S., Davis, C. A., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A., Tanzer, A., Lagarde, J., Lin, W., Schlesinger, F., Xue, C., Marinov, G. K., Khatun, J., Williams, B. A., Zaleski, C., Rozowsky, J., Röder, M., Kokocinski, F., Abdelhamid, R. F., Alioto, T., Antoshechkin, I., Baer, M. T., Bar, N. S., Batut, P., Bell, K., Bell, I., Chakrabortty, S., Chen, X., Chrast, J., Curado, J., Derrien, T., Drenkow, J., Dumais, E., Dumais, J., Duttagupta, R., Falconnet, E., Fastuca, M., Fejes-Toth, K., Ferreira, P., Foissac, S., Fullwood, M. J., Gao, H., Gonzalez, D., Gordon, A., Gunawardena, H., Howald, C., Jha, S., Johnson, R., Kapranov, P., King, B., Kingswood, C., Luo, O. J., Park, E., Persaud, K., Preall, J. B., Ribeca, P., Risk, B., Robyr, D., Sammeth, M., Schaffer, L., See, L. H., Shahab, A., Skancke, J., Suzuki, A. M., Takahashi, H., Tilgner, H., Trout, D., Walters, N., Wang, H., Wrobel, J., Yu, Y., Ruan, X., Hayashizaki, Y., Harrow, J., Gerstein, M., Hubbard, T., Reymond, A., Antonarakis, S. E., Hannon, G., Giddings, M. C., Ruan, Y., Wold, B., Carninci, P., Guig, R., Gingeras, T. R. (September 2012) Landscape of transcription in human cells. Nature, 489 (7414). pp. 101-108. ISSN 0028-0836

Dunham, I., Kundaje, A., Aldred, S. F., Collins, P. J., Davis, C., Doyle, F., Epstein, C. B., Frietze, S., Harrow, J., Kaul, R., Khatun, J., Lajoie, B. R., Landt, S. G., Lee, B. K., Pauli, F., Rosenbloom, K. R., Sabo, P., Safi, A., Sanyal, A., Shoresh, N., Simon, J. M., Song, L., Trinklein, N. D., Altshuler, R. C., Birney, E., Brown, J. B., Cheng, C., Djebali, S., Dong, X. J., Ernst, J., Furey, T. S., Gerstein, M., Giardine, B., Greven, M., Hardison, R. C., Harris, R. S., Herrero, J., Hoffman, M. M., Iyer, S., Kellis, M., Kheradpour, P., Lassmann, T., Li, Q. H., Lin, X., Marinov, G. K., Merkel, A., Mortazavi, A., Parker, S. C. J., Reddy, T. E., Rozowsky, J., Schlesinger, F., Thurman, R. E., Wang, J., Ward, L. D., Whitfield, T. W., Wilder, S. P., Wu, W., Xi, H. L. S., Yip, K. Y., Zhuang, J. L., Bernstein, B. E., Green, E. D., Gunter, C., Snyder, M., Pazin, M. J., Lowdon, R. F., Dillon, L. A. L., Adams, L. B., Kelly, C. J., Zhang, J., Wexler, J. R., Good, P. J., Feingold, E. A., Crawford, G. E., Dekker, J., Elnitski, L., Farnham, P. J., Giddings, M. C., Gingeras, T. R., Guigo, R., Hubbard, T. J., Kent, W. J., Lieb, J. D., Margulies, E. H., Myers, R. M., Stamatoyannopoulos, J. A., Tenenbaum, S. A., Weng, Z. P., White, K. P., Wold, B., Yu, Y., Wrobel, J., Risk, B. A., Gunawardena, H. P., Kuiper, H. C., Maier, C. W., Xie, L., Chen, X., Mikkelsen, T. S., Gillespie, S. (September 2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489 (7414). pp. 57-74. ISSN 0028-0836

Nowak, M., Kramer, B., Haupt, M., Papapanou, P. N., Kebschull, J., Hoffmann, P., Jepsen, S., Perner, S., Schmidt-Wolf, I. G. H., Kebschull, M. (September 2012) Activation of invariant natural killer T-cells in periodontitis lesions. Immunology, 137 (S1). p. 465. ISSN 0019-2805

Aksoy, O., Chicas, A., Zeng, T., Zhao, Z., McCurrach, M., Wang, X., Lowe, S. W. (July 2012) The atypical E2F family member E2F7 couples the p53 and RB pathways during cellular senescence. Genes Dev, 26 (14). pp. 1546-57. ISSN 1549-5477 (Electronic)0890-9369 (Linking)

Scuoppo, C., Miething, C., Lindqvist, L., Reyes, J., Ruse, C., Appelmann, I., Yoon, S., Krasnitz, A., Teruya-Feldstein, J., Pappin, D., Pelletier, J., Lowe, S. W. (July 2012) A tumour suppressor network relying on the polyamine-hypusine axis. Nature, 487 (7406). pp. 244-8. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Chicas, A., Kapoor, A., Wang, X. W., Aksoy, O., Evertts, A. G., Zhang, M. Q., Garcia, B. A., Bernstein, E., Lowe, S. W. (June 2012) H3K4 demethylation by Jarid1a and Jarid1b contributes to retinoblastoma-mediated gene silencing during cellular senescence. Proceedings of the National Academy of Sciences of the United States of America, 109 (23). pp. 8971-8976. ISSN 0027-8424

Qiao, S., Odoemene, O., Yoshida, K. (June 2012) Determination of electrode to nerve fiber distance and nerve conduction velocity through spectral analysis of the extracellular action potentials recorded from earthworm giant fibers. Medical and Biological Engineering and Computing, 50 (8). pp. 867-875. ISSN 01400118

Bergerson, R. J., Collier, L. S., Sarver, A. L., Been, R. A., Lugthart, S., Diers, M. D., Zuber, J., Rappaport, A. R., Nixon, M. J., Silverstein, K. A. T., Fan, D. H., Lamblin, A. F. J., Wolff, L., Kersey, J. H., Delwel, R., Lowe, S. W., O'Sullivan, M. G., Kogan, S. C., Adams, D. J., Largaespada, D. A. (May 2012) An insertional mutagenesis screen identifies genes that cooperate with Mll-AF9 in a murine leukemogenesis model. Blood, 119 (19). pp. 4512-4523. ISSN 0006-4971

Hanson, T. L., Omarsson, B., O'Doherty, J. E., Peikon, I. D., Lebedev, M. A., Nicolelis, M. A. L. (May 2012) High-Side Digitally Current Controlled Biphasic Bipolar Microstimulator. IEEE Transactions on Neural Systems and Rehabilitation Engineering, 20 (3). pp. 331-340. ISSN 1534-4320

Sheppard, J. P., Wang, J. P., Wong, P. C. M. (May 2012) Large-scale cortical network properties predict future sound-to-word learning success. Journal of Cognitive Neuroscience, 24 (5). pp. 1087-1103. ISSN 0898-929X

Xue, W., Kitzing, T., Roessler, S., Zuber, J., Krasnitz, A., Schultz, N., Revill, K., Weissmueller, S., Rappaport, A. R., Simon, J., Zhang, J., Luo, W. J., Hicks, J., Zender, L., Wang, X. W., Powers, S., Wigler, M., Lowe, S. W. (May 2012) A cluster of cooperating tumor-suppressor gene candidates in chromosomal deletions. Proceedings of the National Academy of Sciences of the United States of America, 109 (21). pp. 8212-8217. ISSN 0027-8424

Iossifov, I., Ronemus, M., Levy, D., Wang, Z. H., Hakker, I., Rosenbaum, J., Yamrom, B., Lee, Y. H., Narzisi, G., Leotta, A., Kendall, J., Grabowska, E., Ma, B. C., Marks, S., Rodgers, L., Stepansky, A., Troge, J., Andrews, P., Bekritsky, M., Pradhan, K., Ghiban, E., Kramer, M., Parla, J., Demeter, R., Fulton, L. L., Fulton, R. S., Magrini, V. J., Ye, K., Darnell, J. C., Darnell, R. B., Mardis, E. R., Wilson, R. K., Schatz, M. C., McCombie, W. R., Wigler, M. (April 2012) De Novo Gene Disruptions in Children on the Autistic Spectrum. Neuron, 74 (2). pp. 285-299. ISSN 0896-6273

Chatterjee, S., Seifried, L., Feigin, M. E., Gibbons, D. L., Scuoppo, C., Lin, W., Rizvi, Z. H., Lind, E., Dissanayake, D., Kurie, J., Ohashi, P., Muthuswamy, S. K. (April 2012) Dysregulation of Cell Polarity Proteins Synergize with Oncogenes or the Microenvironment to Induce Invasive Behavior in Epithelial Cells. PLoS ONE, 7 (4). ISSN 1932-6203

Teta, M., Choi, Y. S., Okegbe, T., Wong, G., Tam, O. H., Chong, M. M. W., Seykora, J. T., Nagy, A., Littman, D. R., Andl, T., Millar, S. E. (April 2012) Inducible deletion of epidermal Dicer and Drosha reveals multiple functions for miRNAs in postnatal skin. Development, 139 (8). pp. 1405-1416. ISSN 09501991 (ISSN)

Nakasone, E. S., Askautrud, H. A., Kees, T., Park, J. H., Plaks, V., Ewald, A. J., Fein, M., Rasch, M. G., Tan, Y. X., Qiu, J., Park, J., Sinha, P., Bissell, M. J., Frengen, E., Werb, Z., Egeblad, M. (April 2012) Imaging Tumor-Stroma Interactions during Chemotherapy Reveals Contributions of the Microenvironment to Resistance. Cancer Cell, 21 (4). pp. 488-503. ISSN 1535-6108

Raposo, D., Sheppard, J. P., Schrater, P. R., Churchland, A. K. (March 2012) Multisensory decision-making in rats and humans. Journal of Neuroscience, 32 (11). pp. 3726-35. ISSN 0270-6474

Sun, S. Y., Zhang, Z., Fregoso, O., Krainer, A. R. (February 2012) Mechanisms of activation and repression by the alternative splicing factors RBFOX1/2. RNA, 18 (2). pp. 274-283. ISSN 1355-8382

Glaser, S. P., Lee, E. F., Trounson, E., Bouillet, P., Wei, A., Fairlie, W. D., Izon, D. J., Zuber, J., Rappaport, A. R., Herold, M. J., Alexander, W. S., Lowe, S. W., Robb, L., Strasser, A. (January 2012) Anti-apoptotic mcl-1 is essential for the development and sustained growth of acute myeloid leukemia. Genes and Development, 26 (2). pp. 120-125. ISSN 08909369 (ISSN)

Djebali, S., Lagarde, J., Kapranov, P., Lacroix, V., Borel, C., Mudge, J. M., Howald, C., Foissac, S., Ucla, C., Chrast, J., Ribeca, P., Martin, D., Murray, R. R., Yang, X., Ghamsari, L., Lin, C., Bell, I., Dumais, E., Drenkow, J., Tress, M. L., Gelpí, J. L., Orozco, M., Valencia, A., van Berkum, N. L., Lajoie, B. R., Vidal, M., Stamatoyannopoulos, J., Batut, P., Dobin, A., Harrow, J., Hubbard, T., Dekker, J., Frankish, A., Salehi-Ashtiani, K., Reymond, A., Antonarakis, S. E., Guigó, R., Gingeras, T. R. (January 2012) Evidence for transcript networks composed of chimeric RNA's in human cells. PLoS ONE, 7 (1). ISSN 19326203 (ISSN)

Wang, Z. X., Chatterjee, D., Jeon, H. Y., Akerman, M., Vander Heiden, M. G., Cantley, L. C., Krainer, A. R. (2012) Exon-centric regulation of pyruvate kinase M alternative splicing via mutually exclusive exons. Journal of Molecular Cell Biology, 4 (2). pp. 79-87.

Bender, H. S., Murchison, E. P., Pickett, H. A., Deakin, J. E., Strong, M. A., Conlan, C., McMillan, D. A., Neumann, A. A., Greider, C. W., Hannon, G. J., Reddel, R. R., Graves, J. A. M. (2012) Extreme Telomere Length Dimorphism in the Tasmanian Devil and Related Marsupials Suggests Parental Control of Telomere Length. PLoS One, 7 (9). ISSN 19326203 (ISSN)

Calarco, Joseph P., Martienssen, Robert A. (2012) Imprinting: DNA methyltransferases illuminate reprogramming. Current Biology, 22 (21). pp. 929-931. ISSN 0960-9822

Calarco, J. P., Borges, F., Donoghue, M, Van Ex, F., Jullien, P. E., Lopes, T., Gardner, R., Berger, F., Feijó, J. A, Becker, J. D., Martienssen, R. A. (2012) Reprogramming of DNA Methylation in Pollen Guides Epigenetic Inheritance via Small RNA. Cell, 151 (1). pp. 194-205. ISSN 0092-8674

Preall, J. B., Czech, B., Guzzardo, P. M., Muerdter, F., Hannon, G. J. (2012) Shutdown is a component of the Drosophila piRNA biogenesis machinery. RNA, 18 (8). pp. 1446-1457. ISSN 13558382 (ISSN)

Campbell, R. A. A., Honegger, K. S., Gruntman, E., Turner, G. C. (2012) Two-Photon Imaging of Population Activity with Genetically Encoded Calcium Indicators in Living Flies. In: Genetically Encoded Functional Indicators. Neuromethods, 72 . Humana Press, pp. 113-124. ISBN 978-1-62703-013-7

Sarkar, Bidyut, Das, Anand Kant, Arumugam, Senthil, Kaushalya, Sanjeev Kumar, Bandyopadhyay, Arkarup, Balaji, Jayaprakash, Maiti, Sudipta (2012) The dynamics of somatic exocytosis in monoaminergic neurons. Frontiers in Physiology, 3. p. 414. ISSN 1664-042X

Dow, L. E., Premsrirut, P. K., Zuber, J., Fellmann, C., McJunkin, K., Miething, C., Park, Y., Dickins, R. A., Hannon, G. J., Lowe, S. W. (2012) A pipeline for the generation of shRNA transgenic mice. Nature Protocols, 7 (2). pp. 374-393. ISSN 17542189 (ISSN)

Gymrek, M., Erlich, Y. (November 2011) Using DNA sequencers as stethoscopes. Genome Med, 3 (11). p. 73. ISSN 1756-994X (Electronic)

Zaratiegui, M., Castel, S. E., Irvine, D. V., Kloc, A., Ren, J., Li, F., de Castro, E., Marin, L., Chang, A. Y., Goto, D., Cande, W. Z., Antequera, F., Arcangioli, B., Martienssen, R. A. (November 2011) RNAi promotes heterochromatic silencing through replication-coupled release of RNA Pol II. Nature, 479 (7371). pp. 135-8. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Hein, N., Bywater, M. J., Stanley, K., Verbrugge, I., Cullinane, C., Baker, A., Zuber, H., Rappaport, A., Drygin, D., Huser, N., Bliesath, J., Ryckman, D. M., Rice, W. G., Lowe, S. W., Johnstone, R. W., Pearson, R. B., McArthur, G. A., Hannan, R. D. (November 2011) Inhibition of RNA Polymerase I Transcription by CX-5461 As a Therapeutic Strategy for the Cancer-Specific Activation of p53 in MLL-Rearranged Acute Myeloid Leukemias. Blood, 118 (21). p. 1548. ISSN 0006-4971

Herrmann, H., Blatt, K., Shi, J. W., Rappaport, A. R., Gleixner, K. V., Cerny-Reiterer, S., Peter, B., Wang, E., Sperr, W. R., Bradner, J. E., Lowe, S. W., Vakoc, C. R., Zuber, J., Valent, P. (November 2011) Small-Molecule Inhibition of BRD4 Is a Novel Promising Approach to Therapeutically Target Leukemia Stem Cells in AML. Blood, 118 (21). p. 3484. ISSN 0006-4971

Chien, Y., Scuoppo, C., Wang, X., Fang, X., Balgley, B., Bolden, J. E., Premsrirut, P., Luo, W., Chicas, A., Lee, C. S., Kogan, S. C., Lowe, S. W. (October 2011) Control of the senescence-associated secretory phenotype by NF-kappaB promotes senescence and enhances chemosensitivity. Genes Dev, 25 (20). pp. 2125-36. ISSN 1549-5477 (Electronic) 0890-9369 (Linking)

Wasik, K. A., Rebbeck, C. A. (October 2011) Keystone Symposia 40th Season: MicroRNAs and Noncoding RNAs in Cancer. Cancer Res, 71 (19). ISSN 0008-5472

Pai, S., Erlich, J. C., Kopec, C., Brody, C. D. (September 2011) Minimal impairment in a rat model of duration discrimination following excitotoxic lesions of primary auditory and prefrontal cortices. Front Syst Neurosci, 5 (74). ISSN 1662-5137

Jiang, L. C., Schlesinger, F. J., Davis, C. A., Zhang, Y., Li, R. H., Salit, M., Gingeras, T. R., Oliver, B. (September 2011) Synthetic spike-in standards for RNA-seq experiments. Genome Research, 21 (9). pp. 1543-1551. ISSN 1088-9051 (Public Dataset)

Rangan, P., Malone, Colin D. , Navarro, C., Newbold, S. P, Hayes, P. S, Sachidanandam, R., Hannon, G. J., Lehmann, R. (August 2011) piRNA Production Requires Heterochromatin Formation in Drosophila. Current Biology, 21 (16). pp. 1373-1379. ISSN 0960-9822

Honegger, K. S., Campbell, R. A. A., Turner, G. C. (August 2011) Cellular-Resolution Population Imaging Reveals Robust Sparse Coding in the Drosophila Mushroom Body. Journal of Neuroscience, 31 (33). pp. 11772-11785. ISSN 0270-6474

Zuber, J., Shi, J., Wang, E., Rappaport, A. R., Herrmann, H., Sison, E. A., Magoon, D., Qi, J., Blatt, K., Wunderlich, M., Taylor, M. J., Johns, C., Chicas, A., Mulloy, J. C., Kogan, S. C., Brown, P., Valent, P., Bradner, J. E., Lowe, S. W., Vakoc, C. R. (August 2011) RNAi screen identifies Brd4 as a therapeutic target in acute myeloid leukaemia. Nature, 478 (7370). pp. 524-528. ISSN 0028-0836

Leung, A., Cajigas, I., Jia, P., Ezhkova, E., Brickner, J. H., Zhao, Z., Geng, F., Tansey, W. P. (August 2011) Histone H2B ubiquitylation and H3 lysine 4 methylation prevent ectopic silencing of euchromatic loci important for the cellular response to heat. Mol Biol Cell, 22 (15). pp. 2741-2753. ISSN 1939-4586 (Electronic)1059-1524 (Linking)

Zuber, J., Rappaport, A. R., Luo, W., Wang, E., Chen, C., Vaseva, A. V., Shi, J., Weissmueller, S., Fellman, C., Taylor, M. J., Weissenboeck, M., Graeber, T. G., Kogan, S. C., Vakoc, C. R., Lowe, S. W. (August 2011) An integrated approach to dissecting oncogene addiction implicates a Myb-coordinated self-renewal program as essential for leukemia maintenance. Genes & Development, 25 (15). pp. 1628-1640. ISSN 0890-9369

Clark, M. B., Amaral, P. P., Schlesinger, F. J., Dinger, M. E., Taft, R. J., Rinn, J. L., Ponting, C. P., Stadler, P. F., Morris, K. V., Morillon, A., Rozowsky, J. S., Gerstein, M. B., Wahlestedt, C., Hayashizaki, Y., Carninci, P., Gingeras, T. R., Mattick, J. S. (July 2011) The reality of pervasive transcription. Plos Biology, 9 (7). ISSN 15449173 (Public Dataset)

Simpson, D. R., Yu, M., Zheng, S. Y., Zhao, Z. M., Muthuswamy, S. K., Tansey, W. P. (June 2011) Epithelial Cell Organization Suppresses Myc Function by Attenuating Myc Expression. Cancer Research, 71 (11). pp. 3822-3830. ISSN 0008-5472

McJunkin, K., Mazurek, A., Premsrirut, P. K., Zuber, J., Dow, L. E., Simon, J., Stillman, B., Lowe, S. W. (April 2011) Reversible suppression of an essential gene in adult mice using transgenic RNA interference. Proceedings of the National Academy of Sciences of the United States of America, 108 (17). pp. 7113-7118. ISSN 0027-8424

Nag, Suman, Sarkar, Bidyut, Banerjee, Arkarup, Sahoo, Bankanidhi, Sreenivasan, Varun K A, Kombrabail, Mamata, Mralidharan, Chandrakesan, Maiti, Sudipta (April 2011) Nature of the amyloid-beta monomer and the monomer-oligomer equilibrium. Journal of Biological Chemistry, 286 (16). pp. 13827-13833. ISSN 0021-9258

Myers, R. M., Stamatoyannopoulos, J., Snyder, M., Dunham, I., Hardison, R. C., Bernstein, B. E., Gingeras, T. R., Kent, W. J., Birney, E., Wold, B., Crawford, G. E., Epstein, C. B., Shoresh, N., Ernst, J., Mikkelsen, T. S., Kheradpour, P., Zhang, X. L., Wang, L., Issner, R., Coyne, M. J., Durham, T., Ku, M. C., Truong, T., Ward, L. D., Altshuler, R. C., Lin, M. F., Kellis, M., Davis, C. A., Kapranov, P., Dobin, A., Zaleski, C., Schlesinger, F., Batut, P., Chakrabortty, S., Jha, S., Lin, W., Drenkow, J., Wang, H. E., Bell, K. G., Gao, H., Bell, I., Dumais, E., Dumais, J., Antonarakis, S. E., Ucla, C., Borel, C., Guigo, R., Djebali, S., Lagarde, J., Kingswood, C., Ribeca, P., Sammeth, M., Alioto, T., Merkel, A., Tilgner, H., Carninci, P., Hayashizaki, Y., Lassmann, T., Takahashi, H., Abdelhamid, R. F., Hannon, G., Fejes-Toth, K., Preall, J., Gordon, A., Sotirova, V., Reymond, A., Howald, C., Graison, E. A. Y., Chrast, J., Ruan, Y. J., Ruan, X. A., Shahab, A., Poh, W. T., Wei, C. L., Furey, T. S., Boyle, A. P., Sheffield, N. C., Song, L. Y., Shibata, Y., Vales, T., Winter, D., Zhang, Z. C., London, D., Wang, T. Y., Keefe, D., Iyer, V. R., Lee, B. K., McDaniell, R. M., Liu, Z., Battenhouse, A., Bhinge, A. A., Lieb, J. D., Grasfeder, L. L., Showers, K. A., Giresi, P. G., Kim, S. K. C., Shestak, C., Pauli, F., Reddy, T. E., Gertz, J. (April 2011) A User's Guide to the Encyclopedia of DNA Elements (ENCODE). Plos Biology, 9 (4). ISSN 1544-9173 (Public Dataset)

Premsrirut, P. K., Dow, L. E., Kim, S. Y., Camiolo, M., Malone, C. D., Miething, C., Scuoppo, C. , Zuber, J., Dickins, R. A., Kogan, Scott C, Shroyer, Kenneth R, Sordella, R., Hannon, G. J., Lowe, S. W. (March 2011) A Rapid and Scalable System for Studying Gene Function in Mice Using Conditional RNA Interference. Cell, 145 (1). pp. 145-158. ISSN 0092-8674

Fellmann, C., Zuber, J., McJunkin, K., Chang, K. , Malone, C. D., Dickins, R. A., Xu, Q., Hengartner, M. O., Elledge, S. J., Hannon, G. J., Lowe, S. W. (March 2011) Functional Identification of Optimized RNAi Triggers Using a Massively Parallel Sensor Assay. Molecular Cell, 41 (6). pp. 733-746. ISSN 1097-2765

Kopec, C. D., Bowers, A. C., Pai, S. , Brody, C. D. (March 2011) Semi-automated atlas-based analysis of brain histological sections. Journal of Neuroscience Methods, 196 (1). ISSN 0165-0270

Calarco, J. P., Martienssen, R. A. (February 2011) Genome reprogramming and small interfering RNA in the Arabidopsis germline. Curr Opin Genet Dev, 21 (2). pp. 134-9. ISSN 1879-0380 (Electronic) 0959-437X (Linking)

Varshney, L. R., Chen, B. L., Paniagua, E., Hall, D. H., Chklovskii, D. B. (February 2011) Structural Properties of the Caenorhabditis elegans Neuronal Network. Plos Computational Biology, 7 (2). ISSN 1553-734X

Sheppard, J. P., Wang, J. P., Wong, P. C. M. (January 2011) Large-Scale Cortical Functional Organization and Speech Perception across the Lifespan. PLoS ONE, 6 (1). ISSN 1932-6203

Zuber, J., McJunkin, K., Fellmann, C., Dow, L. E., Taylor, M. J., Hannon, G. J., Lowe, S. W. (January 2011) Toolkit for evaluating genes required for proliferation and survival using tetracycline-regulated RNA. Nature Biotechnology, 29 (1). pp. 79-85.

Harder, N., Bodnar, M., Eils, R., Spector, D. L., Rohr, K. (2011) 3D segmentation and quantification of mouse embryonic stem cells in fluorescence microscopy images. 2011 IEEE International Symposium on Biomedical Imaging: From Nano to Macro. pp. 216-219.

Deng, X., Hiatt, J. B., Nguyen, D. K., Ercan, S., Sturgill, D., Hillier, L. W., Schlesinger, F., Davis, C. A., Reinke, V. J., Gingeras, T. R., Shendure, J., Waterston, R. H., Oliver, B., Lieb, J. D., Disteche, C. M. (2011) Balance of the x restored: evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster. Nature Genetics, 43 (12). pp. 1179-85. ISSN 10614036 (ISSN)

Makino, H., Malinow, R. (2011) Compartmentalized versus global synaptic plasticity on dendrites controlled by experience. Neuron, 72 (6). pp. 1001-1011. ISSN 08966273 (ISSN)

Lee, S., Paulson, K. G., Murchison, E. P., Afanasiev, O. K., Alkan, C., Leonard, J. H., Byrd, D. R., Hannon, G. J., Nghiem, P. (2011) Identification and validation of a novel mature microRNA encoded by the Merkel cell polyomavirus in human Merkel cell carcinomas. Journal of Clinical Virology, 52 (3). pp. 272-275. ISSN 13866532 (ISSN)

Spierings, D. C., McGoldrick, D., Hamilton-Easton, A. M., Neale, G., Murchison, E. P., Hannon, G. J., Green, D. R., Withoff, S. (2011) Ordered progression of stage-specific miRNA profiles in the mouse B2 B-cell lineage. Blood, 117 (20). pp. 5340-5349. ISSN 00064971 (ISSN)

Navin, N. E., Kendall, J. T., Troge, J. E., Andrews, P., Rodgers,  L., McIndoo, J., Cook, K., Stepansky,  A., Levy, D., Esposito, D., Muthuswamy, L., Krasnitz, A., McCombie, W. R., Hicks, J. B., Wigler, M. H. (2011) Tumour evolution inferred by single-cell sequencing. Nature, 472 (7341). pp. 90-94. ISSN 00280836 (ISSN)

Zamparini, A. L., Davis, M. Y., Malone, C. D., Vieira, E., Zavadil, J., Sachidanandam, R., Hannon, G. J., Lehmann, R. (2011) Vreteno, a gonad-specific protein, is essential for germline development and primary pirna biogenesis in Drosophila. Development, 138 (18). pp. 4039-4050. ISSN 09501991 (ISSN)

Collins, G. A., Gomez, T. A., Deshaies, R. J., Tansey, W. P. (November 2010) Combined chemical and genetic approach to inhibit proteolysis by the proteasome. Yeast, 27 (11). pp. 965-974. ISSN 1097-0061 (Electronic) 0749-503X (Linking)

Vakoc, C. R., Zuber, J., Lowe, S., Wang, E., Rappaport, A. R., Shi, J. W. (November 2010) An RNA1 Screen Reveals a Pattern of Addiction to Epigenetic Pathways That Distinguishes MLL AF9 Leukemia From Normal Hematopoietic Cells. Blood, 116 (21). p. 35. ISSN 0006-4971

Haase, A. D., Fenoglio, S., Muerdter, F., Guzzardo, P. M., Czech, B., Pappin, D. J., Chen, C., Gordon, A., Hannon, G. J. (October 2010) Probing the initiation and effector phases of the somatic piRNA pathway in Drosophila. Genes and Development, 24 (22). pp. 2499-2504. ISSN 08909369 (ISSN)

Chitwood, D. H., Timmermans, M. C. P. (September 2010) Small RNAs are on the move. Nature, 467 (7314). pp. 415-419. ISSN 0028-0836

Yao, Z., Fenoglio, S., Gao, D. C., Camiolo, M., Stiles, B., Lindsted, T., Schlederer, M., Johns, C., Altorki, N., Mittal, V., Kenner, L., Sordella, R. (August 2010) TGF-beta IL-6 axis mediates selective and adaptive mechanisms of resistance to molecular targeted therapy in lung cancer. Proceedings of the National Academy of Sciences of the United States of America, 107 (35). pp. 15535-40. ISSN 0027-8424

Bolduc, F. V., Valente, D., Nguyen, A. T., Mitra, P. P., Tully, T. (July 2010) An assay for social interaction in Drosophila fragile X mutants. Fly (Austin), 4 (3). ISSN 1933-6942 (Electronic) 1933-6934 (Linking)

Egeblad, M., Nakasone, E. S., Werb, Z. (June 2010) Tumors as Organs: Complex Tissues that Interface with the Entire Organism. Developmental Cell, 18 (6). pp. 884-901. ISSN 1534-5807

Malone, C. D., Hannon, G. J. (May 2010) Molecular Evolution of piRNA and Transposon Control Pathways in Drosophila. Cold Spring Harb Symp Quant Biol. pp. 225-234. ISSN 1943-4456 (Electronic) 0091-7451 (Linking)

Navin, N. E., Hicks, J. B. (May 2010) Tracing the tumor lineage. Molecular Oncology. ISSN 1878-0261 (Electronic) 1574-7891 (Linking)

Hicks, J. B., Navin, N. E., Kendall, J. T., Levy, D., Wigler, M. H. (May 2010) Tracing Tumor Lineage and Progression through Genomic Copy Number Profiling at the Single Cell Level. Annals of Oncology, 21 (S4). iv49. ISSN 0923-7534

Chicas, A., Wang, X., Zhang, C., McCurrach, M. E., Zhao, Z., Mert, O., Dickins, R. A., Narita, M., Zhang, M. Q., Lowe, S. W. (April 2010) Dissecting the Unique Role of the Retinoblastoma Tumor Suppressor during Cellular Senescence. Cancer Cell, 17 (4). pp. 376-387.

Teta, M., Choi, Y., Andl, T., Murchison, E. P., Nagy, A., Hannon, G. J., Millar, S. E. (April 2010) Dicer is required in adult skin for maintenance of rapidly proliferating hair follicle matrix cells, hair shaft formation, and catagen. Journal of Investigative Dermatology, 130 (S1). S106. ISSN 0022-202X

Mavrakis, K. J., Wolfe, A. L., Oricchio, E., Palomero, T., de Keersmaecker, K., McJunkin, K., Zuber, J., James, T., Chang, K., Khan, A. A., Leslie, C. S., Parker, J. S., Paddison, P. J., Tam, W., Ferrando, A., Wendel, H. G. (April 2010) Genome-wide RNA-mediated interference screen identifies miR-19 targets in Notch-induced T-cell acute lymphoblastic leukaemia. Nature Cell Biology, 12 (4). 372-U159. ISSN 1465-7392

Blum, A., Dubnau, J. T. (April 2010) Parallel processing of olfactory memories in Drosophila. Fly, 4 (2). pp. 163-166. ISSN 19336934

Choi, Y., Nagy, A., Tam, O. H., Hannon, G. J., Millar, S. E. (April 2010) The miRNA-processing enzyme Drosha is required for hair follicle regression, hair shaft differentiation, long-term maintenance of hair follicle stem cells, and epidermal homeostasis. Journal of Investigative Dermatology, 130 (S1). S108. ISSN 0022-202X

Clower, C. V., Chatterjee, D., Wang, Z. X., Cantley, L. C., Heiden, M. G. V., Krainer, A. R. (February 2010) The alternative splicing repressors hnRNP A1/A2 and PTB influence pyruvate kinase isoform expression and cell metabolism. Proceedings of the National Academy of Sciences of the United States of America, 107 (5). pp. 1894-1899. ISSN 0027-8424

Wei, W., Nguyen, L. N., Kessels, H. W., Hagiwara, H., Sisodia, S., Malinow, R. (February 2010) Amyloid beta from axons and dendrites reduces local spine number and plasticity. Nature Neuroscience, 13 (2). 190-U71. ISSN 1097-6256

Erlich, Y., Gordon, A., Brand, M., Hannon, G. J., Mitra, P. P. (February 2010) Compressed genotyping. IEEE Transactions on Information Theory, 56 (2). pp. 706-723.

Mangone, M., Myers, M. P., Herr, W. (February 2010) Role of the HCF-1 Basic Region in Sustaining Cell Proliferation. PLoS ONE, 5 (2). e9020. ISSN 1932-6203 (Electronic) 1932-6203 (Linking)

Bolduc, F. V., Bell, K. G., Rosenfelt, C., Cox, H., Tully, T. (January 2010) Fragile x mental retardation 1 and filamin a interact genetically in Drosophila long-term memory. Front Neural Circuits, 3. p. 22. ISSN 1662-5110 (Electronic) 1662-5110 (Linking)

Edvardson, S., Shaag, A., Zenvirt, S., Erlich, Y., Hannon, G. J., Shanske, A. L., Gomori, J. M., Ekstein, J., Elpeleg, O. (January 2010) Joubert Syndrome 2 (JBTS2) in Ashkenazi Jews Is Associated with a TMEM216 Mutation. American Journal of Human Genetics, 86 (1). pp. 93-97.

Pineau, P., Volinia, S., McJunkin, K., Marchio, A., Battiston, C., Terris, B., Mazzaferro, V., Lowe, S. W., Croce, C. M., Dejean, A. (January 2010) miR-221 overexpression contributes to liver tumorigenesis. Proceedings of the National Academy of Sciences of the United States of America, 107 (1). pp. 264-269. ISSN 0027-8424

Murchison, E. P., Tovar, C., Hsu, A., Bender, H. S., Kheradpour, P., Rebbeck, C. A., Obendorf, D., Conlan, C., Bahlo, M., Blizzard, C. A., Pyecroft, S., Kreiss, A., Kellis, M., Stark, A., Harkins, T. T., Marshall Graves, J. A., Woods, G. M., Hannon, G. J., Papenfuss, A. T. (January 2010) The Tasmanian devil transcriptome reveals Schwann cell origins of a clonally transmissible cancer. Science, 327 (5961). pp. 84-7. ISSN 1095-9203 (Electronic) 1095-9203 (Linking)

Navin, N. E., Krasnitz, A., Rodgers, L., Cook, K., Meth, J. L., Kendall, J. T., Riggs, M., Eberling, Y., Troge, J. E., Grubor, V., Levy, D., Lundin, P., Månér, S., Zetterberg, A., Hicks, J. B., Wigler, M. H. (January 2010) Inferring tumor progression from genomic heterogeneity. Genome Research, 20 (1). pp. 68-80.

Chiu, S. L., Cline, H. T. (2010) Insulin receptor signaling in the development of neuronal structure and function. Neural Dev, 5. p. 7. ISSN 1749-8104

Li, J., Wang, Y., Chiu, S. L., Cline, H. T. (2010) Membrane targeted horseradish peroxidase as a marker for correlative fluorescence and electron microscopy studies. Front Neural Circuits, 4. p. 6. ISSN 1662-5110

Wilusz, J. E., Spector, D. L. (2010) An unexpected ending: Noncanonical 3′ end processing mechanisms. RNA, 16 (2). pp. 259-266. ISSN 13558382 (ISSN)

Makino, H., Malinow, R. (November 2009) AMPA Receptor Incorporation into Synapses during LTP: The Role of Lateral Movement and Exocytosis. Neuron, 64 (3). pp. 381-390. ISSN 0896-6273

Quirk, M. C., Sosulski, D. L., Feierstein, C. E., Uchida, N., Mainen, Z. F. (November 2009) A defined network of fast-spiking interneurons in orbitofrontal cortex: responses to behavioral contingencies and ketamine administration. Frontiers in Systems Neuroscience, 3. p. 13. ISSN ISSN 1662-5137

Collins, G. A., Lipford, J. R., Deshaies, R. J., Tansey, W. P. (October 2009) Gal4 turnover and transcription activation. Nature, 461 (7265). E7-E7.

Bric, A., Miething, C., Bialucha, C. U., Scuoppo, C., Zender, L., Krasnitz, A., Xuan, Z., Zuber, J., Wigler, M. H., Hicks, J. B., McCombie, W. R., Hemann, M. T., Hannon, G. J., Powers, S., Lowe, S. W. (October 2009) Functional identification of tumor-suppressor genes through an in vivo RNA interference screen in a mouse lymphoma model. Cancer Cell, 16 (4). pp. 324-35. ISSN 1535-6108

Erlich, Yaniv, Gordon, Assaf, Brand, Michael, Hannon, Gregory J, Mitra, Partha P (September 2009) Compressed Genotyping. IEEE Transactions on Information Theory. (Submitted)

Ewald, R. C., Cline, H. T. (September 2009) Cloning and Phylogenetic Analysis of NMDA Receptor Subunits NR1, NR2A and NR2B in Xenopus laevis Tadpoles. Front Mol Neurosci, 2. p. 4.

Husbands, A. Y., Chitwood, D. H., Plavskin, Y., Timmermans, M. C. P. (September 2009) Signals and prepatterns: new insights into organ polarity in plants. Genes and Development, 23 (17). pp. 1986-97. ISSN 08909369 (ISSN)

Blum, A. L., Li, W., Cressy, M., Dubnau, J. T. (August 2009) Short- and Long-Term Memory in Drosophila Require cAMP Signaling in Distinct Neuron Types. Current Biology, 19 (16). 1341-1350 . ISSN 0960-9822

Asari, H., Zador, A. M. (August 2009) Long-Lasting Context Dependence Constrains Neural Encoding Models in Rodent Auditory Cortex. J Neurophysiol, 102 (5). pp. 2638-56.

Hromadka, T., Zador, A. M. (August 2009) Representations in auditory cortex. Current Opinion in Neurobiology, 19 (4). 430-433 . ISSN 0959-4388

Gracheva, E., Dus, M., Elgin, S. C. (July 2009) Drosophila RISC Component VIG and Its Homolog Vig2 Impact Heterochromatin Formation. PLoS ONE, 4 (7). e6182.

Lima, S. Q., Hromadka, T., Znamenskiy, P., Zador, A. M. (July 2009) PINP: a new method of tagging neuronal populations for identification during in vivo electrophysiological recording. PLoS ONE, 4 (7). e6099. ISSN 1932-6203 (Electronic)

Wilusz, J. E., Sunwoo, H., Spector, D. L. (July 2009) Long noncoding RNAs: functional surprises from the RNA world. Genes & Development, 23 (13). pp. 1494-1504. ISSN 0890-9369

Kessels, H. W., Kopec, C. D., Klein, M. E., Malinow, R. (July 2009) Roles of stargazin and phosphorylation in the control of AMPA receptor subcellular distribution. Nat Neurosci, 12 (7). pp. 888-896.

Nag, Suman, Banerjee, Arkarup, Maiti, Sudipta (May 2009) Spatial pH-jump measures chemical kinetics in a steady state system. Journal of Physical Chemistry A, 113 (18). pp. 5269-5272. ISSN 1089-5639

Malone, C. D., Brennecke, J., Dus, M., Stark, A., McCombie, W. R., Sachidanandam, R., Hannon, G. J. (May 2009) Specialized piRNA Pathways Act in Germline and Somatic Tissues of the Drosophila Ovary. Cell, 137 (3). 522-535 . ISSN 0092-8674

Zuber, J., Radtke, I., Pardee, T. S., Zhao, Z., Rappaport, A. R., Luo, W., McCurrach, M. E., Yang, M. M., Dolan, M. E., Kogan, S. C., Downing, J. R., Lowe, S. W. (April 2009) Mouse models of human AML accurately predict chemotherapy response. Genes Dev, 23 (7). pp. 877-89.

Zhao, R., Bodnar, M. S., Spector, D. L. (April 2009) Nuclear neighborhoods and gene expression. Current Opinion in Genetics & Development, 19 (2). pp. 172-179. ISSN 0959-437X

Koulakov, A. A., Hromadka, T., Zador, A. M. (March 2009) Correlated Connectivity and the Distribution of Firing Rates in the Neocortex. J Neurosci, 29 (12). pp. 3685-3694. ISSN 0270-6474

Benitez-Alfonso, Y., Cilia, M., Roman, A. S., Thomas, C., Maule, A., Hearn, S., Jackson, D. P. (March 2009) Control of Arabidopsis meristem development by thioredoxin-dependent regulation of intercellular transport. Proc Natl Acad Sci U S A, 106 (9). pp. 3615-3620. ISSN 0027-8424

Sunwoo, H., Dinger, M. E., Wilusz, J. E., Amaral, P. P., Mattick, J. S., Spector, D. L. (March 2009) MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Research, 19 (3). pp. 347-359. ISSN 10889051 (ISSN)

Chitwood, D. H., Nogueira, F. T. S., Howell, M. D., Montgomery, T. A., Carrington, J. C., Timmermans, M. C. P. (March 2009) Pattern formation via small RNA mobility. Genes Dev, 23 (5). pp. 549-554. ISSN 0890-9369

Malone, C. D., Hannon, G. J. (February 2009) Small RNAs as Guardians of the Genome. Cell, 136 (4). pp. 656-668. ISSN 0092-8674

Grubor, V., Krasnitz, A., Troge, J. E., Meth, J. L., Lakshmi, B., Kendall, J. T., Yamrom, B., Alex, G., Pai, D., Navin, N. E., Hufnagel, L. A., Lee, Y. H., Cook, K., Allen, S. L., Rai, K. R., Damle, R. N., Calissano, C., Chiorazzi, N., Wigler, M. H., Esposito, D. (February 2009) Novel genomic alterations and clonal evolution in chronic lymphocytic leukemia revealed by representational oligonucleotide microarray analysis (ROMA). Blood, 113 (6). pp. 1294-1303. ISSN 0006-4971

Bolduc, F. V., Tully, T. (January 2009) Fruit flies and intellectual disability. Fly, 3 (1). pp. 91-104. ISSN 1933-6934

Nogueira, F. T. S., Chitwood, D. H., Madi, S., Ohtsu, K., Schnable, P. S., Scanlon, M. J., Timmermans, M. C. P. (January 2009) Regulation of Small RNA Accumulation in the Maize Shoot Apex. Plos Genetics, 5 (1). e1000320. ISSN 1553-7390

Rechavi, O., Erlich, Y., Amram, H., Flomenblit, L., Karginov, F. V., Goldstein, I., Hannon, G. J., Kloog, Y. (2009) Cell contact-dependent acquisition of cellular and viral nonautonomously encoded small RNAs. Genes and Development, 23 (16). pp. 1971-1979. ISSN 08909369 (ISSN)

Chen, C. M., Chiu, S. L., Shen, W., Cline, H. T. (2009) Co-expression of Argonaute2 Enhances Short Hairpin RNA-induced RNA Interference in Xenopus CNS Neurons In Vivo. Frontiers in Neuroscience, 3. p. 63.

Erlich, Y., Chang, K., Gordon, A., Ronen, R., Navon, O., Rooks, M., Hannon, G. J. (2009) DNA Sudoku - Harnessing high-throughput sequencing for multiplexed specimen analysis. Genome Research, 19 (7). pp. 1243-1253. ISSN 10889051 (ISSN)

Czech, B., Zhou, R., Erlich, Y., Brennecke, J., Binari, R., Villalta, C., Gordon, A., Perrimon, N., Hannon, G. J. (2009) Hierarchical Rules for Argonaute Loading in Drosophila. Molecular Cell, 36 (3). pp. 445-456. ISSN 10972765 (ISSN)

Vagin, V. V., Wohlschlegel, J., Qu, J., Jonsson, Z., Huang, X., Chuma, S., Girard, A., Sachidanandam, R., Hannon, G. J., Aravin, A. A. (2009) Proteomic analysis of murine Piwi proteins reveals a role for arginine methylation in specifying interaction with Tudor family members. Genes and Development, 23 (15). pp. 1749-1762. ISSN 08909369 (ISSN)

Couvillion, M. T., Lee, S. R., Hogstad, B., Malone, C. D., Tonkin, L. A., Sachidanandam, R., Hannon, G. J., Collins, K. (2009) Sequence, biogenesis, and function of diverse small RNA classes bound to the Piwi family proteins of Tetrahymena thermophila. Genes and Development, 23 (17). pp. 2016-2032. ISSN 08909369 (ISSN)

Pierce-Shimomura, J. T. , Chen, B. L. , Mun, J. J. , Ho, R., Sarkis, R., McIntire, S. L. (December 2008) Genetic analysis of crawling and swimming locomotory patterns in C. elegans. Proc Natl Acad Sci U S A, 105 (52). pp. 20982-20987.

Finigan, P., Martienssen, R. A. (December 2008) Nucleolar dominance and DNA methylation directed by small interfering RNA. Molecular Cell, 32 (6). pp. 753-4. ISSN 1097-2765

Harvey, C. D., Ehrhardt, A. G., Cellurale, C., Zhong, H., Yasuda, R., Davis, R. J., Svoboda, K. (December 2008) A genetically encoded fluorescent sensor of ERK activity. Proc Natl Acad Sci U S A, 105 (49). pp. 19264-9.

Humbey, O., Pimkina, J., Zilfou, J. T., Jarnik, M., Dominguez-Brauer, C., Burgess, D. J., Eischen, C. M., Murphy, M. E. (December 2008) The ARF Tumor Suppressor Can Promote the Progression of Some Tumors. Cancer Res, 68 (23). pp. 9608-9613.

Brennecke, J., Malone, C. D., Aravin, A. A., Sachidanandam, R., Stark, A., Hannon, G. J. (November 2008) An epigenetic role for maternally inherited piRNAs in transposon silencing. Science, 322 (5906). pp. 1387-92.

Wilusz, J. E., Freier, S. M., Spector, D. L. (November 2008) 3' End Processing of a Long Nuclear-Retained Noncoding RNA Yields a tRNA-like Cytoplasmic RNA. Cell, 135 (5). pp. 919-932. ISSN 0092-8674

Grubor, V., Krasnitz, A., Troge, J. E., Meth, J. L., Lakshmi, B., Kendall, J. T., Yamrom, B., Alex, G., Pai, D., Navin, N. E., Hufnagel, L. A., Lee, Y. H., Cook, K., Allen, S. L., Rai, K. R., Damle, R., Calissano, C., Chiorazzi, N., Wigler, M. H., Esposito, D. (November 2008) High-Resolution Array-Based Comparative Genome Hybridization (CGH) Identifies Novel and Recurrent Regions in CLL. Blood, 112 (11). p. 717. ISSN 0006-4971

Bolduc, F. V., Bell, K. G., Cox, H., Broadie, K. S., Tully, T. (October 2008) Excess protein synthesis in Drosophila Fragile X mutants impairs long-term memory. Nat Neurosci, 11 (10). 1143 - 1145 .

Gruntman, E., Qi, Y., Slotkin, R. K., Roeder, T., Martienssen, R. A., Sachidanandam, R. (September 2008) Kismeth: analyzer of plant methylation states through bisulfite sequencing. BMC bioinformatics, 9. p. 371. ISSN 1471-2105 (Electronic)1471-2105 (Linking)

Malone, C. D., Falkowska, K. A., Li, A. Y., Galanti, S. E., Kanuru, R. C., LaMont, E. G., Mazzarella, K. C., Micev, A. J., Osman, M. M., Piotrowski, N. K., Suszko, J. W., Timm, A. C., Xu, M.-M., Liu, L. F., Chalker, D. L. (September 2008) Nucleus-Specific Importin Alpha Proteins and Nucleoporins Regulate Protein Import and Nuclear Division in the Binucleate Tetrahymena thermophila. Eukaryotic Cell, 7 (9). pp. 1487-1499.

Burgess, R., Yang, Z. (September 2008) Estimation of hominoid ancestral population sizes under Bayesian coalescent models incorporating mutation rate variation and sequencing errors. Molecular Biology and Evolution, 25 (9). pp. 1979-1994. ISSN 0737-4038

Wu, Y., Bolduc, F. V., Bell, K. G., Tully, T., Fang, Y., Sehgal, A., Fischer, J. A. (August 2008) A Drosophila model for Angelman syndrome. Proc Natl Acad Sci U S A, 105 (34). pp. 12399-404.

Erlich, Y., Mitra, P. P., Delabastide, M., McCombie, W. R., Hannon, G. J. (August 2008) Alta-Cyclic: a self-optimizing base caller for next-generation sequencing. Nature Methods, 5 (8). 679 - 682.

Bish, R. A., Fregoso, O. I., Piccini, A., Myers, M. P. (August 2008) Conjugation of Complex Polyubiquitin Chains to WRNIP1. J Proteome Res, 7 (8). 3481-3489 .

Teta, M., Thomas, A., Okegbe, T., Murchison, E. P., Nagy, A., Hannon, G. J., Millar, S. E. (July 2008) Dicer is required for maintenance of hair follicle stem cells in adult skin. Developmental Biology, 319 (2). p. 556. ISSN 0012-1606

Timmermans, M. C. P., Chitwood, D., Nogueira, F., Madi, S. (July 2008) Pattern formation by small RNA signals. Developmental Biology, 319 (2). pp. 463-464. ISSN 0012-1606

Harvey, C. D., Yasuda, R., Zhong, H., Svoboda, K. (July 2008) The spread of ras activity triggered by activation of a single dendritic spine. Science, 321 (5885). pp. 136-40.

Burgess, D. J., Doles, J., Zender, L., Xue, W., Ma, B., McCombie, W. R., Hannon, G. J., Lowe, S. W., Hemann, M. T. (July 2008) Topoisomerase levels determine chemotherapy response in vitro and in vivo. Proc Natl Acad Sci U S A, 105 (25). pp. 9053-9058.

Chiu, S. L., Chen, C. M., Cline, H. T. (June 2008) Insulin receptor signaling regulates synapse number, dendritic plasticity, and circuit function in vivo. Neuron, 58 (5). pp. 708-719.

Murchison, E. P., Kheradpour, P., Sachidanandam, R., Smith, C., Hodges, E., Xuan, Z., Kellis, M., Grutzner, F., Stark, A., Hannon, G. J. (June 2008) Conservation of small RNA pathways in platypus. Genome Research, 18 (6). pp. 995-1004. ISSN 1088-9051

Timmermans, M. C., Chitwood, D., Nogueira, F., Madi, S. (April 2008) Small RNAs as Mobile Signals in Development. Faseb Journal, 22. p. 1. ISSN 0892-6638

Benetti, R., Gonzalo, S., Jaco, I., Munoz, P., Gonzalez, S., Schoeftner, S., Murchison, E. P., Andl, T., Chen, T. P., Klatt, P., Li, E., Serrano, M., Millar, S., Hannon, G. J., Blasco, M. A. (March 2008) A mammalian microRNA cluster controls DNA methylation and telomere recombination via Rbl2-dependent regulation of DNA methyltransferases. Nature Structural & Molecular Biology, 15 (3). pp. 268-279. ISSN 1545-998515459993 (ISSN)

Iijima, K., Chiang, H. C., Hearn, S. A., Hakker, I., Gatt, A., Shenton, C., Granger, L., Leung, A., Iijima-Ando, K., Zhong, Y. (February 2008) A beta 42 Mutants with Different Aggregation Profiles Induce Distinct Pathologies in Drosophila. PLoS ONE, 3 (2). e1703. ISSN 1932-6203 (Electronic)

Chen, J. F., Murchison, E. P., Tang, R., Callis, T. E., Tatsuguchi, M., Deng, Z., Rojas, M., Hammond, S. M., Schneider, M. D., Selzman, C. H., Meissner, G., Patterson, C., Hannon, G. J., Wang, D. Z. (February 2008) Targeted deletion of Dicer in the heart leads to dilated cardiomyopathy and heart failure. Proc Natl Acad Sci U S A, 105 (6). pp. 2111-2116. ISSN 0027-8424

Ewald, R. C., Van Keuren-Jensen, K. R., Aizenman, C. D., Cline, H. T. (January 2008) Roles of NR2A and NR2B in the development of dendritic arbor morphology in vivo. J Neurosci, 28 (4). pp. 850-861.

Huber, D., Petreanu, L., Ghitani, N., Ranade, S., Hromadka, T., Mainen, Z., Svoboda, K. (January 2008) Sparse optical microstimulation in barrel cortex drives learned behaviour in freely moving mice. Nature, 451 (7174). pp. 61-4.

Guo, M., Thomas, J., Collins, G. A., Timmermans, M. C. P. (January 2008) Direct Repression of KNOX Loci by the ASYMMETRIC LEAVES1 Complex of Arabidopsis. Plant Cell, 20 (1). pp. 48-58.

Hromádka, T., Deweese, M. R., Zador, A. M. (January 2008) Sparse representation of sounds in the unanesthetized auditory cortex. PLoS Biology, 6 (1). e16. ISSN 1545-7885 (Electronic)

Zhou, R., Hotta, I., Denli, A. M., Hong, P., Perrimon, N., Hannon, G. J. (2008) Comparative Analysis of Argonaute-Dependent Small RNA Pathways in Drosophila. Molecular Cell, 32 (4). pp. 592-599. ISSN 10972765 (ISSN)

Girard, A., Hannon, G. J. (2008) Conserved themes in small-RNA-mediated transposon control. Trends Cell Biol, 18 (3). pp. 136-148.

Warren, W. C., Hillier, L. W., Marshall Graves, J. A., Birney, E., Ponting, C. P., Grützner, F., Belov, K., Miller, W., Clarke, L., Chinwalla, A. T., Yang, S. P., Heger, A., Locke, D. P., Miethke, P., Waters, P. D., Veyrunes, F., Fulton, L., Fulton, B., Graves, T., Wallis, J., Puente, X. S., López-Otín, C., Ordóñez, G. R., Eichler, E. E., Chen, L., Cheng, Z., Deakin, J. E., Alsop, A., Thompson, K., Kirby, P., Papenfuss, A. T., Wakefield, M. J., Olender, T., Lancet, D., Huttley, G. A., Smit, A. F. A., Pask, A., Temple-Smith, P., Batzer, M. A., Walker, J. A., Konkel, M. K., Harris, R. S., Whittington, C. M., Wong, E. S. W., Gemmell, N. J., Buschiazzo, E., Vargas Jentzsch, I. M., Merkel, A., Schmitz, J., Zemann, A., Churakov, G., Ole Kriegs, J., Brosius, J., Murchison, E. P., Sachidanandam, R., Smith, C., Hannon, G. J., Tsend-Ayush, E., McMillan, D., Attenborough, R., Rens, W., Ferguson-Smith, M., Lefèvre, C. M., Sharp, J. A., Nicholas, K. R., Ray, D. A., Kube, M., Reinhardt, R., Pringle, T. H., Taylor, J., Jones, R. C., Nixon, B., Dacheux, J. L., Niwa, H., Sekita, Y., Huang, X., Stark, A., Kheradpour, P., Kellis, M., Flicek, P., Chen, Y., Webber, C., Hardison, R., Nelson, J., Hallsworth-Pepin, K., Delehaunty, K., Markovic, C., Minx, P., Feng, Y., Kremitzki, C., Mitreva, M., Glasscock, J., Wylie, T., Wohldmann, P., Thiru, P., Nhan, M. N., Pohl, C. S., Smith, S. M., Hou, S., Renfree, M. B. (2008) Genome analysis of the platypus reveals unique signatures of evolution. Nature, 453 (7192). pp. 175-183. ISSN 00280836 (ISSN)

Daulny, A., Geng, F., Muratani, M., Geisinger, J. M., Salghetti, S. E., Tansey, W. P. (2008) Modulation of RNA polymerase II subunit composition by ubiquitylation. Proc Natl Acad Sci U S A, 105 (50). 19649-19654 .

Chitwood, D. H., Nogueira, F. T., Howell, M. D., Montogmery, T. A., Carrington, J. C., Timmermans, M. C. (2008) Pattern formation in leaves via small RNA mobility. Developmental Biology, 319 (2). pp. 587-588. ISSN 0012-1606

Tam, O. H., Aravin, A. A., Stein, P., Girard, A., Murchison, E. P., Cheloufi, S., Hodges, E., Anger, M., Sachidanandam, R., Schultz, R. M., Hannon, G. J. (2008) Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature, 453 (7194). pp. 534-538. ISSN 00280836 (ISSN)

Leung, A., Geng, F., Daulny, A., Collins, G. A., Guzzardo, P. M., Tansey, W. P. (2008) Transcriptional control and the ubiquitin-proteasome system. Ernst Schering Found Symp Proc (1). pp. 75-97.

Czech, B., Malone, C. D., Zhou, R., Stark, A., Schlingeheyde, C., Dus, M., Perrimon, N., Kellis, M., Wohlschlegel, J. A., Sachidanandam, R., Hannon, G. J., Brennecke, J. (2008) An endogenous small interfering RNA pathway in Drosophila. Nature, 453 (7196). pp. 798-802. ISSN 0028-0836

De Pietri Tonelli, D., Pulvers, J. N., Haffner, C., Murchison, E. P., Hannon, G. J., Huttner, W. B. (2008) miRNAs are essential for survival and differentiation of newborn neurons but not for expansion of neural progenitors during early neurogenesis in the mouse embryonic neocortex. Development, 135 (23). pp. 3911-3921. ISSN 09501991 (ISSN)

Harvey, C. D., Svoboda, K. (December 2007) Locally dynamic synaptic learning rules in pyramidal neuron dendrites. Nature, 450 (7173). pp. 1195-1200. ISSN 0028-0836

Ibarra, I., Erlich, Y., Muthuswamy, S. K., Sachidanandam, R., Hannon, Gregory J. (December 2007) A role for microRNAs in maintenance of mouse mammary epithelial progenitor cells. Genes Dev, 21 (24). pp. 3238-43. ISSN 0890-9369 (Print)

Kopec, C. D., Real, E., Kessels, H. W., Malinow, R. (December 2007) GluR1 links structural and functional plasticity at excitatory synapses. J Neurosci, 27 (50). pp. 13706-18. ISSN 1529-2401 (Electronic)

Egan, C. M., Sridhar, S., Wigler, M. H., Hall, I. M. (November 2007) Recurrent DNA copy number variation in the laboratory mouse. Nat Genet, 39 (11). pp. 1384-9. ISSN 1061-4036 (Print)

Tervo, D. G. R., Karpova, A. Y. (October 2007) Rapidly inducible, genetically targeted inactivation of neural and synaptic activity in vivo. Current Opinion in Neurobiology, 17 (5). 581-586 .

Brower-Toland, B., Findley, S. D., Jiang, L., Liu, L., Yin, H., Dus, M., Zhou, P., Elgin, S. C., Lin, H. (September 2007) Drosophila PIWI associates with chromatin and interacts directly with HP1a. Genes Dev, 21 (18). pp. 2300-11. ISSN 0890-9369 (Print)0890-9369

Kim, J., Inoue, K., Ishii, J., Vanti, W. B., Voronov, S. V., Murchison, E., Hannon, G. J., Abeliovich, A. (August 2007) A MicroRNA feedback circuit in midbrain dopamine neurons. Science, 317 (5842). pp. 1220-4. ISSN 1095-9203 (Electronic) 1095-9203 (Linking)

Bish, Rebecca A., Myers, Michael P. (August 2007) Werner helicase interacting protein 1 (WRNIP1) binds polyubiquitin via its zinc finger domain. J Biol Chem, 282 (32). pp. 23184-23193. ISSN 0021-9258 (Print)

Chitwood, D. H., Timmermans, M. C. P. (August 2007) Target mimics modulate miRNAs. Nat Genet, 39 (8). pp. 935-6. ISSN 1061-4036 (Print)

Vaughn, M. W., Tanurdzic, M., Lippman, Z. B., Jiang, H., Carrasquillo, R., Rabinowicz, P. D., Dedhia, N., McCombie, W. R., Agier, N., Bulski, A., Colot, V., Doerge, R. W., Martienssen, R. A. (July 2007) Epigenetic natural variation in Arabidopsis thaliana. PLoS Biology, 5 (7). pp. 1617-1629. ISSN 1544-9173

Dickins, R. A., McJunkin, K., Hernando, E., Premsrirut, P. K., Krizhanovsky, V., Burgess, D. J., Kim, S. Y., Cordon-Cardo, C., Zender, L., Hannon, G. J., Lowe, S. W. (July 2007) Tissue-specific and reversible RNA interference in transgenic mice. Nat Genet, 39 (7). 914 - 921. ISSN 1061-4036 (Print)

Hromádka, T., Zador, A. M. (July 2007) Toward the mechanisms of auditory attention. Hear Res, 229 (1-2). pp. 180-5. ISSN 0378-5955 (Print)

Aravin, A. A., Sachidanandam, R., Girard, A., Fejes-Toth, K., Hannon, G. J. (May 2007) Developmentally regulated piRNA clusters implicate MILI in transposon control. Science, 316 (5825). pp. 744-7. ISSN 1095-9203 (Electronic)

Nogueira, F. T., Madi, S., Chitwood, D. H., Juarez, M. T., Timmermans, M. C. P. (April 2007) Two small regulatory RNAs establish opposing fates of a developmental axis. Genes Dev, 21 (7). pp. 750-5. ISSN 0890-9369 (Print)

Carmell, M. A., Girard, A., van de Kant, H. J. G., Bourc'his, D., Bestor, T. H., de Rooij, D. G., Hannon, G. J. (April 2007) MIWI2 Is Essential for Spermatogenesis and Repression of Transposons in the Mouse Male Germline. Developmental Cell, 12 (4). pp. 503-514.

Houwing, S., Kamminga, L. M., Berezikov, E., Cronembold, D., Girard, A., van den Elst, H., Filippov, D. V., Blaser, H., Raz, E., Moens, C. B., Plasterk, R. H. A., Hannon, G. J., Draper, B. W., Ketting, R. F. (April 2007) A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in zebrafish. Cell, 129 (1). pp. 69-82. ISSN 0092-8674

Brennecke, J., Aravin, A. A., Stark, A., Dus, M., Kellis, M., Sachidanandam, R., Hannon, G. J. (March 2007) Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell, 128 (6). pp. 1089-103. ISSN 0092-8674 (Print)

Murchison, E. P., Stein, P., Xuan, Z. Y., Pan, H., Zhang, M. Q., Schultz, R. M., Hannon, G. J. (March 2007) Critical roles for Dicer in the female germline. Genes Dev, 21 (6). pp. 682-93. ISSN 0890-9369 (Print)

Chitwood, D. H., Guo, M., Nogueira, F. T. S., Timmermans, M. C. P. (March 2007) Establishing leaf polarity: the role of small RNAs and positional signals in the shoot apex. Development, 134 (5). pp. 813-23. ISSN 0950-1991 (Print)

Maximov, A., Pang, Z. P. P., Tervo, D. G. R., Sudhof, T. C. (March 2007) Monitoring synaptic transmission in primary neuronal cultures using local extracellular stimulation. Journal of Neuroscience Methods, 161 (1). pp. 75-87. ISSN 0165-0270

Girard, A., Hannon, G. J. (March 2007) [The role of piRNAs in mouse spermatogenesis.]. J Soc Biol, 201 (4). pp. 411-8.

Tolia, N. H., Joshua-Tor, L. (January 2007) Slicer and the Argonautes. Nature Chemical Biology, 3 (1). pp. 36-43. ISSN 1552-4450

Kopec, C. D., Kessels, H. W., Bush, D. E., Cain, C. K., LeDoux, J. E., Malinow, R. (January 2007) A robust automated method to analyze rodent motion during fear conditioning. Neuropharmacology, 52 (1). pp. 228-33. ISSN 0028-3908 (Print)

Kopec, C. D., Malinow, R. (December 2006) Neuroscience. Matters of size. Science, 314 (5805). pp. 1554-5. ISSN 1095-9203 (Electronic)

Pelham, R. J., Rodgers, L., Hall, I. M., Lucito, R., Nguyen, K. C. Q., Navin, N. E., Hicks, J. B., Mu, D., Powers, S., Wigler, M. H., Botstein, D. (December 2006) Identification of alterations in DNA copy number in host stromal cells during tumor progression. Proc Natl Acad Sci U S A, 103 (52). pp. 19848-19853. ISSN 0027-8424

Hicks, J. B., Krasnitz, A., Lakshmi, B., Navin, N. E., Riggs, M., Leibu, E., Esposito, D., Alexander, J., Troge, J. E., Grubor, V., Yoon, S., Wigler, M. H., Ye, K., Borresen-Dale, A. L., Naume, B., Schlicting, E., Norton, L., Hagerstrom, T., Skoog, L., Auer, G., Månér, S., Lundin, P., Zetterberg, A. (December 2006) Novel patterns of genome rearrangement and their association with survival in breast cancer. Genome Research, 16 (12). pp. 1465-79. ISSN 1088-9051

Rial Verde, E. M. , Lee-Osbourne, J., Worley, P. F., Malinow, R., Cline, H. T. (November 2006) Increased expression of the immediate-early gene arc/arg3.1 reduces AMPA receptor-mediated synaptic transmission. Neuron, 52 (3). pp. 461-74. ISSN 0896-6273 (Print)

Aranda, V., Haire, T., Nolan, M. E., Calarco, J. P., Rosenberg, A. Z., Fawcett, J. P., Pawson, T., Muthuswamy, S. K. (November 2006) Par6-aPKC uncouples ErbB2 induced disruption of polarized epithelial organization from proliferation control. Nat Cell Biol, 8 (11). pp. 1235-45. ISSN 1465-7392 (Print)

Navin, N. E., Grubor, V., Hicks, J. B., Leibu, E., Thomas, E., Troge, J., Riggs, M., Lundin, P., Månér, S., Sebat, J., Zetterberg, A., Wigler, M. H. (October 2006) PROBER: oligonucleotide FISH probe design software. Bioinformatics, 22 (19). pp. 2437-8. ISSN 1460-2059 (Electronic)

Watabe-Uchida, M., John, K. A., Janas, J. A., Newey, S. E., Van Aelst, L. (September 2006) The Rac activator DOCK7 regulates neuronal polarity through local phosphorylation of stathmin/Op18. Neuron, 51 (6). pp. 727-39. ISSN 0896-6273 (Print)

Irvine, D. V., Zaratiegui, Mi., Tolia, N. H., Goto, D. B., Chitwood, D. H., Vaughn, M. W., Joshua-Tor, L., Martienssen, R. A. (August 2006) Argonaute slicing is required for heterochromatic silencing and spreading. Science, 313 (5790). pp. 1134-7. ISSN 1095-9203 (Electronic)

Feierstein, C. E. , Quirk, M. C., Uchida, N., Sosulski, D. L., Mainen, Z. F. (August 2006) Representation of spatial goals in rat orbitofrontal cortex. Neuron, 51 (4). pp. 495-507. ISSN 0896-6273 (Print)

Lakshmi, B., Hall, I. M., Egan, C., Alexander, J., Leotta, A., Healy, J., Zender, L., Spector, M. S., Xue, W., Lowe, S. W., Wigler, M. H., Lucito, R. (July 2006) Mouse genomic representational oligonucleotide microarray analysis: detection of copy number variations in normal and tumor specimens. Proc Natl Acad Sci U S A, 103 (30). pp. 11234-9. ISSN 0027-8424 (Print)

Asari, H., Pearlmutter, B. A., Zador, A. M. (July 2006) Sparse representations for the cocktail party problem. Journal of Neuroscience, 26 (28). pp. 7477-7490. ISSN 02706474

Andl, T., Murchison, E. P., Liu, Fei, Zhang, Yi, Yunta-Gonzalez, M., Tobias, J. W., Andl, C. D., Seykora, J. T., Hannon, G. J., Millar, S. E. (May 2006) The miRNA-Processing Enzyme Dicer Is Essential for the Morphogenesis and Maintenance of Hair Follicles. Current Biology, 16 (10). pp. 1041-1049. ISSN 09609822

Chen, B. L., Chklovskii, D. B. (April 2006) Placement and routing optimization in the brain. Proceedings of the 2006 international symposium on Physical design, 2006. pp. 136-141.

Collins, G. A., Tansey, W. P. (April 2006) The proteasome: a utility tool for transcription? Curr Opin Genet Dev, 16 (2). pp. 197-202. ISSN 0959-437X (Print)

Chen, B. L., Hall, D. H., Chklovskii, D. B. (March 2006) Wiring optimization can relate neuronal structure and function. Proc Natl Acad Sci U S A, 103 (12). pp. 4723-8. ISSN 0027-8424 (Print)

Kopec, C. D., Li, B., Wei, W., Boehm, J., Malinow, R. (February 2006) Glutamate receptor exocytosis and spine enlargement during chemically induced long-term potentiation. J Neurosci, 26 (7). pp. 2000-9. ISSN 1529-2401 (Electronic)

Song, J. J., Joshua-Tor, L. (February 2006) Argonaute and RNA--getting into the groove. Curr Opin Struct Biol, 16 (1). pp. 5-11. ISSN 0959-440X (Print)

Tolia, N.H., Joshua-Tor, L. (January 2006) Strategies for protein coexpression in Escherichia coli. Nat Methods, 3 (1). pp. 55-64. ISSN 1548-7091 (Print)

Ezhkova, E., Tansey, William P. (2006) Chromatin immunoprecipitation to study protein-DNA interactions in budding yeast. Methods in Molecular Biology, 313. pp. 225-44. ISSN 1940-6029 (Electronic)1064-3745 (Linking)

Hannon, G. J., Rivas, F. V., Murchison, E. P., Steitz, J. A. (2006) The Expanding Universe of Noncoding RNAs. Cold Spring Harb Symp Quant Biol, 71. pp. 551-564. ISSN 1943-4456 (Electronic) 0091-7451 (Linking)

Bestman, J. E., Ewald, R. C., Chiu, S. L., Cline, H. T. (2006) In vivo single-cell electroporation for transfer of DNA and macromolecules. Nat Protoc, 1 (3). pp. 1267-72. ISSN 1750-2799 (Electronic)

Nogueira, F. T., Sarkar, A. K., Chitwood, D. H., Timmermans, M. C. (2006) Organ Polarity in Plants Is Specified through the Opposing Activity of Two Distinct Small Regulatory RNAs. Cold Spring Harbor Symposia on Quantitative Biology, 71. pp. 157-64. ISSN 00917451 (ISSN)

Locke, S. M., Martienssen, R. A. (2006) Slicing and spreading of heterochromatic silencing by RNA interference. Cold Spring Harbor Symposia on Quantitative Biology, 71. pp. 497-503. ISSN 00917451 (ISSN)

Yasuda, Ryohei, Harvey, Christopher D., Zhong, Haining, Sobczyk, Aleksander, Van Aelst, Linda, Svoboda, Karel (2006) Supersensitive Ras activation in dendrites and spines revealed by two-photon fluorescence lifetime imaging. Nature Neuroscience, 9 (2). pp. 283-291. ISSN 10976256

Dickins, R. A., Premsrirut, P., McJunkin, K., Kim, S. Y., Hannon, G. J., Lowe, S. W. (2006) Tetracycline-regulated p53 knockdown in cells and transgenic mice. Toxicologic Pathology, 34 (7). p. 1006. ISSN 0192-6233

Girard, A., Sachidanandam, R., Hannon, G. J., Carmell, M. A. (2006) A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature, 442 (7099). pp. 199-202. ISSN 00280836

Karpova, A. Y., Tervo, D. G., Gray, N. W., Svoboda, K. (December 2005) Rapid and reversible chemical inactivation of synaptic transmission in genetically targeted neurons. Neuron, 48 (5). pp. 727-35. ISSN 0896-6273 (Print)

May, B. P., Lippman, Z. B., Fang, Y., Spector, D. L., Martienssen, R. A. (December 2005) Differential regulation of strand-specific transcripts from Arabidopsis centromeric satellite repeats. PLoS Genet, 1 (6). e79. ISSN 1553-7404 (Electronic)

DeWeese, M. R., Hromádka, T., Zador, A. M. (November 2005) Reliability and representational bandwidth in the auditory cortex. Neuron, 48 (3). pp. 479-88. ISSN 0896-6273 (Print)

Bolduc, F. V., Shevell, M. I. (November 2005) Corrected head circumference centiles as a possible predictor of developmental performance in high-risk neonatal intensive care unit survivors. Dev Med Child Neurol, 47 (11). pp. 766-70. ISSN 0012-1622 (Print)

Dickins, R. A., Hemann, M. T., Zilfou, J. T., Simpson, D. R., Ibarra, I., Hannon, G. J., Lowe, S. W. (November 2005) Probing tumor phenotypes using stable and regulated synthetic microRNA precursors. Nat Genet, 37 (11). pp. 1289-95. ISSN 1061-4036 (Print)

Silva, J. M., Li, M. Z., Chang, K., Ge, W., Golding, M. C., Rickles, R. J., Siolas, D., Hu, G., Paddison, P. J., Schlabach, M. R., Sheth, N., Bradshaw, J., Burchard, J., Kulkarni, A., Cavet, G., Sachidanandam, R., McCombie, W. R., Cleary, M. A., Elledge, S. J., Hannon, G. J. (November 2005) Second-generation shRNA libraries covering the mouse and human genomes. Nat Genet, 37 (11). pp. 1281-8.

Lee, D. Y., Ezhkova, E., Li, B., Pattenden, S. G., Tansey, W. P., Workman, J. L. (November 2005) The proteasome regulatory particle alters the SAGA coactivator to enhance its interactions with transcriptional activators. Cell, 123 (3). pp. 423-436. ISSN 0092-8674

Murchison, E. P., Partridge, J. F., Tam, O. H., Cheloufi, S., Hannon, G. J. (August 2005) Characterization of Dicer-deficient murine embryonic stem cells. Proceedings of the National Academy of Sciences of the United States of America, 102 (34). pp. 12135-40. ISSN 0027-8424

Qi, Yijun, Denli, Ahmet M., Hannon, Gregory J. (August 2005) Biochemical specialization within Arabidopsis RNA silencing pathways. Mol Cell, 19 (3). pp. 421-8. ISSN 1097-2765 (Print)

Tolia, N. H., Enemark, E. J., Sim, B. K., Joshua-Tor, L. (July 2005) Structural basis for the EBA-175 erythrocyte invasion pathway of the malaria parasite Plasmodium falciparum. Cell, 122 (2). pp. 183-93. ISSN 0092-8674 (Print) (Public Dataset)

Forstemann, K., Tomari, Y., Du, T. T., Vagin, V. V., Denli, A. M., Bratu, D. P., Klattenhoff, C., Theurkauf, W. E., Zamore, P. D. (July 2005) Normal microRNA maturation and germ-line stem cell maintenance requires loquacious, a double-stranded RNA- binding domain protein. Plos Biology, 3 (7). pp. 1187-1201. ISSN 1544-9173

Schramke, V., Sheedy, D. M., Denli, A. M., Bonila, C., Ekwall, K., Hannon, G. J., Allshire, R. C. (June 2005) RNA-interference-directed chromatin modification coupled to RNA polymerase II transcription. Nature, 435 (7046). pp. 1275-1279. ISSN 0028-0836

Rivas, Fabiola V., Tolia, Nirja H., Song, Ji-Joon, Aragon, Juan P., Liu, Jidong, Hannon, Gregory J., Joshua-Tor, Leemor (April 2005) Purified Argonaute2 and an siRNA form recombinant human RISC. Nat Struct Mol Biol, 12 (4). pp. 340-9. ISSN 1545-9993 (Print) (Public Dataset)

Muratani, Masafumi, Kung, Charles, Shokat, Kevan M., Tansey, William P. (March 2005) The F box protein Dsg1/Mdm30 is a transcriptional coactivator that stimulates Gal4 turnover and cotranscriptional mRNA processing. Cell, 120 (6). pp. 887-899. ISSN 0092-8674

Lippman, Z. B., Gendrel, A. V., Colot, V., Martienssen, R. A. (March 2005) Profiling DNA methylation patterns using genomic tiling microarrays. Nat Methods, 2 (3). pp. 219-24. ISSN 1548-7091 (Print)

Gendrel, A. V., Lippman, Z. , Martienssen, R., Colot, V. (March 2005) Profiling histone modification patterns in plants using genomic tiling microarrays. Nature Methods, 2 (3). pp. 213-218. ISSN 1548-7091

Siolas, D., Lerner, C., Burchard, J., Ge, W., Linsley, P. S., Paddison, P. J., Hannon, G. J., Cleary, M. A. (February 2005) Synthetic shRNAs as potent RNAi triggers. Nat Biotechnol, 23 (2). pp. 227-31. ISSN 1087-0156 (Print)

Chen, N., Pai, S., Zhao, Z., Mah, A., Newbury, R., Johnsen, R. C., Altun, Z., Moerman, D. G., Baillie, D. L., Stein, L. D. (January 2005) Identification of a nematode chemosensory gene family. Proc Natl Acad Sci U S A, 102 (1). pp. 146-51. ISSN 0027-8424 (Print)

Chen, N., Harris, T. W., Antoshechkin, I., Bastiani, C., Bieri, T., Blasiar, D., Bradnam, K., Canaran, P., Chan, J., Chen, C.-K., Chen, W. J., Cunningham, F., Davis, P., Kenny, E., Kishore, Ra.., Lawson, D., Lee, R., Muller, H. M., Nakamura, Ce., Pai, S., Ozersky, P., Petcherski, A., Rogers, An., Sabo, A., Schwarz, Er. M., Van Auken, K., Wang, Q., Durbin, R., Spieth, J., Sternberg, P. W., Stein, L. D. (January 2005) WormBase: a comprehensive data resource for Caenorhabditis biology and genomics. Nucleic Acids Res, 33 (Databa). D383-9. ISSN 1362-4962 (Electronic)

Schramke, V., Sheedy, D. M., Denli, A. M., Bonila, C., Ekwall, K., Hannon, G. J., Allshire, R. C. (2005) Erratum (Retracted article): RNA-interference-directed chromatin modification coupled to RNA polymerase II transcription (Nature (2005) 435 (1275-1279)). Nature, 437 (7061). p. 1057. ISSN 00280836 (ISSN)

Hicks, J. B., Muthuswamy, L., Krasnitz, A., Navin, N. E., Riggs, M., Grubor, V., Esposito, D., Alexander, J., Troge, J. E., Wigler, M. H., Maner, S., Lundin, P., Zetterberg, A. (2005) High-resolution ROMA CGH and FISH analysis of aneuploid and diploid breast tumors. Cold Spring Harb Symp Quant Biol, 70. pp. 51-63. ISSN 1943-4456 (Electronic) 0091-7451 (Linking)

Bina, M., Wyss, P., Ren, W. H., Szpankowski, W., Thomas, E., Randhawa, R., Reddy, S., John, P. M., Pares-Matos, E. I., Stein, A., Xu, H., Lazarus, S. A. (December 2004) Exploring the characteristics of sequence elements in proximal promoters of human genes. Genomics, 84 (6). pp. 929-940. ISSN 0888-7543

Cleary, M. A., Kilian, K., Wang, Y., Bradshaw, J., Cavet, G., Ge, W., Kulkarni, A., Paddison, P. J., Chang, K., Sheth, N., Leproust, E., Coffey, E. M., Burchard, J., McCombie, W. R., Linsley, P., Hannon, G. J. (December 2004) Production of complex nucleic acid libraries using highly parallel in situ oligonucleotide synthesis. Nat Methods, 1 (3). pp. 241-8.

Denli, A. M., Tops, B. B., Plasterk, R. H., Ketting, R. F., Hannon, G. J. (November 2004) Processing of primary microRNAs by the Microprocessor complex. Nature, 432 (7014). pp. 231-5. ISSN 1476-4687 (Electronic)

Paddison, P. J., Cleary, M., Silva, J. M., Chang, K., Sheth, N., Sachidanandam, R., Hannon, G. J. (November 2004) Cloning of short hairpin RNAs for gene knockdown in mammalian cells. Nat Methods, 1 (2). pp. 163-7. ISSN 1548-7091 (Print)

Lippman, Z., Martienssen, R. A. (September 2004) The role of RNA interference in heterochromatic silencing. Nature, 431 (7006). pp. 364-70. ISSN 1476-4687 (Electronic)

Liu, J., Carmell, M. A., Rivas, F. V., Marsden, C. G., Thomson, J. M., Song, J. J., Hammond, S. M., Joshua-Tor, L., Hannon, G. J. (September 2004) Argonaute2 is the catalytic engine of mammalian RNAi. Science, 305 (5689). pp. 1437-41. ISSN 1095-9203 (Electronic)

Song, J. J., Smith, S. K., Hannon, G. J., Joshua-Tor, L. (September 2004) Crystal structure of argonaute and its implications for RISC slicer activity. Science, 305 (5689). pp. 1434-1437. ISSN 0036-8075 (Public Dataset)

Jeffrey Chen, Z., Wang, J., Tian, L., Lee, H. S., Wang, J. J., Chen, M., Lee, J. J., Josefsson, C., Madlung, A., Watson, B., Lippman, Z., Vaughn, M., Chris Pires, J., Colot, V., Doerge, R. W., Martienssen, R. A., Comai, L., Osborn, T. C. (August 2004) The development of an Arabidopsis model system for genome-wide analysis of polyploidy effects. Biological journal of the Linnean Society. Linnean Society of London, 82 (4). pp. 689-700. ISSN 0024-4066 (Print)0024-4066 (Linking)

Sebat, J., Lakshmi, B., Troge, J. E., Alexander, J., Young, J., Lundin, P., Maner, S., Massa, H., Walker, M., Chi, M., Navin, N. E., Lucito, R., Healy, J., Hicks, J. B., Ye, K., Reiner, A., Gilliam, T. C., Trask, B., Patterson, N., Zetterberg, A., Wigler, M. H. (July 2004) Large-scale copy number polymorphism in the human genome. Science, 305 (5683). pp. 525-8. ISSN 1095-9203 (Electronic)

Lippman, Z., Gendrel, A. V., Black, M., Vaughn, M. W., Dedhia, N., McCombie, W. R., Lavine, K., Mittal, V., May, B., Kasschau, K. D., Carrington, J. C., Doerge, R. W., Colot, V., Martienssen, R. (July 2004) Role of transposable elements in heterochromatin and epigenetic control. Nature, 430 (6998). pp. 471-6. ISSN 1476-4687 (Electronic)

Thomas, E. E., Srebro, N., Sebat, J., Navin, N., Healy, J., Mishra, B., Wigler, M. H. (July 2004) Distribution of short paired duplications in mammalian genomes. Proc Natl Acad Sci U S A, 101 (28). pp. 10349-54. ISSN 0027-8424 (Print)

Hemann, M. T., Zilfou, J. T., Zhao, Z., Burgess, D. J., Hannon, G. J., Lowe, S. W. (June 2004) Suppression of tumorigenesis by the p53 target PUMA. Proc Natl Acad Sci U S A, 101 (25). pp. 9333-8. ISSN 0027-8424 (Print)

Murchison, E. P., Hannon, G. J. (June 2004) miRNAs on the move: miRNA biogenesis and the RNAi machinery. Curr Opin Cell Biol, 16 (3). pp. 223-9. ISSN 0955-0674 (Print)

Tian, G. W., Mohanty, A., Chary, S. N., Li, S. J., Paap, B., Drakakaki, G., Kopec, C. D., Li, J. X., Ehrhardt, D., Jackson, D., Rhee, S. Y., Raikhel, N. V., Citovsky, V. (May 2004) High-throughput fluorescent tagging of full-length arabidopsis gene products in planta. Plant Physiology, 135 (1). pp. 25-38. ISSN 0032-0889

Tansey, W. P. , Ezhkova, E. (May 2004) Transcriptional control and the ubiquitin-proteasome system. Faseb Journal, 18 (8). C315-C315 Suppl S.. ISSN 0892-6638

Paddison, P. J., Silva, J. M., Conklin, D. S., Schlabach, M., Li, M., Aruleba, S., Balija, V., O'Shaughnessy, A., Gnoj, L., Scobie, K., Chang, K., Westbrook, T., Cleary, M., Sachidanandam, R., McCombie, W. R., Elledge, S. J., Hannon, G. J. (March 2004) A resource for large-scale RNA-interference-based screens in mammals. Nature, 428 (6981). pp. 427-31. ISSN 1476-4687 (Electronic)

Juarez, M. T., Kui, J. S., Thomas, J., Heller, B. A., Timmermans, M. C. (March 2004) microRNA-mediated repression of rolled leaf1 specifies maize leaf polarity. Nature, 428 (6978). pp. 84-8. ISSN 1476-4687 (Electronic)

Ezhkova, E., Tansey, W. P. (February 2004) Proteasomal ATPases link ubiquitylation of histone H2B to methylation of histone H3. Mol Cell, 13 (3). pp. 435-42. ISSN 1097-2765 (Print)

Chiang, A. S., Blum, A., Barditch, J., Chen, Y. H., Chiu, S. L., Regulski, M., Armstrong, J. D., Tully, T., Dubnau, J. T. (February 2004) radish encodes a phospholipase-A2 and defines a neural circuit involved in anesthesia-resistant memory. Current Biology, 14 (4). pp. 263-272. ISSN 0960-9822

Bastow, R., Mylne, J. S., Lister, C., Lippman, Z., Martienssen, R. A., Dean, C. (January 2004) Vernalization requires epigenetic silencing of FLC by histone methylation. Nature, 427 (6970). pp. 164-7. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Caudy, A. A., Hannon, G. J. (2004) Induction and biochemical purification of RNA-induced silencing complex from Drosophila S2 cells. Methods Mol Biol, 265. pp. 59-72. ISSN 1064-3745 (Print)

Cilia, M. L., Jackson, D. P. (2004) Plasmodesmata form and function. Current Opinion in Cell Biology, 16 (5). pp. 500-506. ISSN 09550674 (ISSN)

Paddison, P. J., Caudy, A. A., Sachidanandam, R., Hannon, G. J. (2004) Short hairpin activated gene silencing in mammalian cells. In: RNA Interference, Editing and Modification: methods and protocols. Methods Mol Biol, 265 . Springer, pp. 85-100.

Martienssen, R., Lippman, Z., May, B., Ronemus, M., Vaughn, M. (2004) Transposons, tandem repeats, and the silencing of imprinted genes. Cold Spring Harbor symposia on quantitative biology, 69. pp. 371-9. ISSN 0091-7451 (Print)0091-7451 (Linking)

Lippman, Z., May, B., Yordan, C., Singer, T., Martienssen, R. (December 2003) Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification. PLoS biology, 1 (3). pp. 420-428. ISSN 1545-7885 (Electronic)1544-9173 (Linking)

Song, J. J., Liu, J., Tolia, N. H., Schneiderman, J., Smith, S. K., Martienssen, R. A., Hannon, G. J., Joshua-Tor, L. (December 2003) The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes. Nat Struct Biol, 10 (12). pp. 1026-32. ISSN 1072-8368 (Print) (Public Dataset)

Healy, J., Thomas, E. E., Schwartz, J. T., Wigler, M. H. (October 2003) Annotating large genomes with exact word matches. Genome Research, 13 (10). pp. 2306-2315. ISSN 1088-9051

Hemann, M. T., Fridman, J. S., Zilfou, J. T., Hernando, E., Paddison, P. J., Cordon-Cardo, C., Hannon, G. J., Lowe, S. W. (March 2003) An epi-allelic series of p53 hypomorphs created by stable RNAi produces distinct tumor phenotypes in vivo. Nature Genetics, 33 (3). pp. 396-400. ISSN 1061-4036

Muratani, Masafumi, Tansey, William P. (March 2003) How the ubiquitin-proteasome system controls transcription. Nature Reviews Molecular Cell Biology, 4 (3). pp. 192-201. ISSN 1471-0072

Dubnau, J. T., Chiang, A. S., Grady, L., Barditch, J., Gossweiler, S., McNeil, J., Smith, P., Buldoc, F. V., Scott, R., Certa, U., Broger, C., Tully, T. (February 2003) The staufen/pumilio pathway is involved in Drosophila long-term memory. Current Biology, 13 (4). pp. 286-296. ISSN 0960-9822

Hall, I. M., Noma, K., Grewal, S. I. (January 2003) RNA interference machinery regulates chromosome dynamics during mitosis and meiosis in fission yeast. Proceedings of the National Academy of Sciences of the United States of America, 100 (1). pp. 193-8. ISSN 0027-8424 (Print)

Bernstein, E., Kim, S. Y., Carmell, M. A., Murchison, E. P., Alcorn, H., Li, M. Z., Mills, A. A., Elledge, S. J., Anderson, K. V., Hannon, G. J. (2003) Dicer is essential for mouse development. Nature Genetics, 35 (3). pp. 215-217. ISSN 10614036 (ISSN)

Denli, A. M., Hannon, G. J. (2003) RNAi: An ever-growing puzzle. Trends in Biochemical Sciences, 28 (4). pp. 196-201. ISSN 09680004 (ISSN)

Hall, I. M., Grewal, S. I. S. (2003) Structure and function of heterochromatin: implications for epigenetic gene silencing and genome organization. In: RNAi : a guide to gene silencing. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. , pp. 205-232. ISBN 978-087969641-2

Caudy, A. A., Ketting, R. F., Hammond, S. M., Denli, A. M., Bathoorn, A. M. P., Tops, B. B. J., Silva, J. M., Myers, M. M., Hannon, G. J., Plasterk, R. H. A. (2003) A micrococcal nuclease homologue in RNAi effector complexes. Nature, 425 (6956). pp. 411-414. ISSN 00280836 (ISSN)

Paddison, P. J., Hannon, G. J. (2003) siRNAs and shRNAs: Skeleton keys to the human genome. Current Opinion in Molecular Therapeutics, 5 (3). pp. 217-224. ISSN 14648431 (ISSN)

Stein, L. D., Mungall, C., Shu, S. Q., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J. E., Harris, T. W., Arva, A., Lewis, S. (October 2002) The Generic Genome Browser: A building block for a model organism system database. Genome Research, 12 (10). pp. 1599-1610. ISSN 1088-9051

Hall, I. M., Shankaranarayana, G. D., Noma, K. I., Ayoub, N., Cohen, A., Grewal, S. I. S. (September 2002) Establishment and maintenance of a heterochromatin domain. Science, 297 (5590). pp. 2232-2237. ISSN 0036-8075

Volpe, T. A., Kidner, C., Hall, I. M., Teng, G., Grewal, S. I., Martienssen, R. A. (September 2002) Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science, 297 (5588). pp. 1833-7. ISSN 1095-9203 (Electronic)0036-8075 (Linking)

Gendrel, A. V., Lippman, Z., Yordan, C., Colot, V., Martienssen, R. A. (September 2002) Dependence of heterochromatic histone H3 methylation patterns on the Arabidopsis gene DDM1. Science, 297 (5588). pp. 1871-1873. ISSN 0036-8075

Azumi, Y., Liu, D. H., Zhao, D. Z., Li, W. X., Wang, G. F., Hu, Y., Ma, H. (June 2002) Homolog interaction during meiotic prophase I in Arabidopsis requires the SOLO DANCERS gene encoding a novel cyclin-like protein. Embo Journal, 21 (12). pp. 3081-3095. ISSN 0261-4189

Bjerling, P., Silverstein, R. A., Thon, G., Caudy, A., Grewal, S., Ekwall, K. (April 2002) Functional divergence between histone deacetylases in fission yeast by distinct cellular localization and in vivo specificity. Molecular and Cellular Biology, 22 (7). pp. 2170-2181. ISSN 0270-7306

Kim, J. Y., Yuan, Z. A., Cilia, M., Khalfan-Jagani, Z., Jackson, D. P. (March 2002) Intercellular trafficking of a KNOTTED1 green fluorescent protein fusion in the leaf and shoot meristem of Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America, 99 (6). pp. 4103-4108. ISSN 0027-8424

Ejkova, Elena, Tansey, William P. (March 2002) Old dogs and new tricks: meeting on mechanisms of eukaryotic transcription. Embo Reports, 3 (3). pp. 219-23. ISSN 1469-221X

van der Knaap, E., Lippman, Z. B., Tanksley, S. D. (February 2002) Extremely elongated tomato fruit controlled by four quantitative trait loci with epistatic interactions. Theoretical and Applied Genetics, 104 (2-3). pp. 241-247. ISSN 0040-5752

Cilia, M., Cantrill, L., van Bel, A. (January 2002) Plasmodesma 2001: on safari through the symplast. Plant Cell, 14 (1). pp. 7-10. ISSN 1040-4651 (Print)

Caudy, A. A., Myers, M., Hannon, G. J., Hammond, S. M. (2002) Fragile X-related protein and VIG associate with the RNA interference machinery. Genes and Development, 16 (19). pp. 2491-2496. ISSN 08909369 (ISSN)

Muratani, M., Gerlich, D., Janicki, S. M., Gebhard, M., Eils, R., Spector, D. L. (2002) Metabolic-energy-dependent movement of PML bodies within the mammalian cell nucleus. Nature Cell Biology, 4. pp. 106-110. ISSN 1465-7392

Paddison, P. J., Hannon, G. J. (2002) RNA interference: The new somatic cell genetics? Cancer Cell, 2 (1). pp. 17-23. ISSN 15356108 (ISSN)

Paddison, P. J., Caudy, A. A., Bernstein, E., Hannon, G. J., Conklin, D. S. (2002) Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes and Development, 16 (8). pp. 948-958. ISSN 08909369 (ISSN)

Paddison, P. J., Caudy, A. A., Hannon, G. J. (2002) Stable suppression of gene expression by RNAi in mammalian cells. Proceedings of the National Academy of Sciences of the United States of America, 99 (3). pp. 1443-1448. ISSN 00278424 (ISSN)

Hammond, S. M., Boettcher, S., Caudy, A. A., Kobayashi, R., Hannon, G. J. (August 2001) Argonaute2, a link between genetic and biochemical analyses of RNAi. Science, 293 (5532). pp. 1146-1150. ISSN 0036-8075

Salghetti, S. E., Caudy, A. A., Chenoweth, J. G., Tansey, W. P. (August 2001) Regulation of transcriptional activation domain function by ubiquitin. Science, 293 (5535). pp. 1651-1653. ISSN 0036-8075

Hammond, S. M., Caudy, A. A., Hannon, G. J. (2001) Post-transcriptional gene silencing by double-stranded RNA. Nature Reviews Genetics, 2 (2). pp. 110-119. ISSN 14710056 (ISSN)

Bernstein, E., Caudy, A. A., Hammond, S. M., Hannon, G. J. (2001) Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature, 409 (6818). pp. 363-366. ISSN 00280836 (ISSN)

Bernstein, E., Denli, A. M., Hannon, G. J. (2001) The rest is silence. RNA, 7 (11). pp. 1509-1521. ISSN 13558382 (ISSN)

Piano, F., Schetter, A. J., Mangone, M., Stein, L., Kemphues, K. J. (December 2000) RNAi analysis of genes expressed in the ovary of Caenorhabditis elegans. Current Biology, 10 (24). pp. 1619-1622. ISSN 0960-9822

Gaasterland, T., Sczyrba, A., Thomas, E., Aytekin-Kurban, G., Gordon, P., Sensen, C. W. (April 2000) MAGPIE/EGRET annotation of the 2.9-Mb Drosophila melanogaster Adh region. Genome Research, 10 (4). pp. 502-510. ISSN 1088-9051

Salghetti, S. E., Muratani, M., Wijnen, H., Futcher, B., Tansey, W. P. (March 2000) Functional overlap of sequences that activate transcription and signal ubiquitin-mediated proteolysis. Proceedings of the National Academy of Sciences of the United States of America, 97 (7). pp. 3118-3123. ISSN 0027-8424