Items where Community is "CSHL Cancer Center Program"

Paper

Chen, Wei-Chia, Zhou, Juannan, McCandlish, David M (October 2024) Density estimation for ordinal biological sequences and its applications. Physical Review E, 110 (4). ISSN 2470-0045

Swamynathan, Manojit M, Kuang, Shan, Watrud, Kaitlin E, Doherty, Mary R, Gineste, Charlotte, Mathew, Grinu, Gong, Grace Q, Cox, Hilary, Cheng, Eileen, Reiss, David, Kendall, Jude, Ghosh, Diya, Reczek, Colleen R, Zhao, Xiang, Herzka, Tali, Špokaitė, Saulė, Dessus, Antoine N, Kim, Seung Tea, Klingbeil, Olaf, Liu, Juan, Nowak, Dawid G, Alsudani, Habeeb, Wee, Tse-Luen, Park, Youngkyu, Minicozzi, Francesca, Rivera, Keith, Almeida, Ana S, Chang, Kenneth, Chakrabarty, Ram P, Wilkinson, John E, Gimotty, Phyllis A, Diermeier, Sarah D, Egeblad, Mikala, Vakoc, Christopher R, Locasale, Jason W, Chandel, Navdeep S, Janowitz, Tobias, Hicks, James B, Wigler, Michael, Pappin, Darryl J, Williams, Roger L, Cifani, Paolo, Tuveson, David A, Laporte, Jocelyn, Trotman, Lloyd C (October 2024) Dietary pro-oxidant therapy by a vitamin K precursor targets PI 3-kinase VPS34 function. Science, 386 (6720). eadk9167. ISSN 0036-8075

Homer, Joshua A, Johnson, Robert M, Koelln, Rebecca A, Moorhouse, Adam D, Moses, John E (October 2024) Strategic re-engineering of antibiotics. Nature Reviews Bioengineering. ISSN 2731-6092

Romero, Rodrigo, Chu, Tinyi, González Robles, Tania J, Smith, Perianne, Xie, Yubin, Kaur, Harmanpreet, Yoder, Sara, Zhao, Huiyong, Mao, Chenyi, Kang, Wenfei, Pulina, Maria V, Lawrence, Kayla E, Gopalan, Anuradha, Zaidi, Samir, Yoo, Kwangmin, Choi, Jungmin, Fan, Ning, Gerstner, Olivia, Karthaus, Wouter R, DeStanchina, Elisa, Ruggles, Kelly V, Westcott, Peter MK, Chaligné, Ronan, Pe'er, Dana, Sawyers, Charles L (October 2024) The neuroendocrine transition in prostate cancer is dynamic and dependent on ASCL1. Nature Cancer. ISSN 2662-1347 (Public Dataset)

Zubiete-Franco, Imanol, Tonks, Nicholas K (September 2024) Famotidine increases cellular phospho-tyrosine levels. Biochemical and Biophysical Research Communications, 734. p. 150763. ISSN 0006-291X

Murga, Matilde, Lopez-Pernas, Gema, Soliva, Robert, Fueyo-Marcos, Elena, Amor, Corina, Faustino, Ignacio, Serna, Marina, Serrano, Alicia G, Díaz, Lucía, Martínez, Sonia, Blanco-Aparicio, Carmen, Antón, Marta Elena, Seashore-Ludlow, Brinton, Pastor, Joaquín, Jafari, Rozbeh, Lafarga, Miguel, Llorca, Oscar, Orozco, Modesto, Fernández-Capetillo, Oscar (September 2024) SETD8 inhibition targets cancer cells with increased rates of ribosome biogenesis. Cell Death and Disease, 15 (9). p. 694. ISSN 2041-4889 (Public Dataset)

Wu, B, Koehler, AN, Westcott, PMK (September 2024) New opportunities to overcome T cell dysfunction: the role of transcription factors and how to target them. Trends in Biochemical Sciences. ISSN 0968-0004

Loh, Liyen, Carcy, Salomé, Krovi, Harsha S, Domenico, Joanne, Spengler, Andrea, Lin, Yong, Torres, Joshua, Prabakar, Rishvanth K, Palmer, William, Norman, Paul J, Stone, Matthew, Brunetti, Tonya, Meyer, Hannah V, Gapin, Laurent (September 2024) Unraveling the phenotypic states of human innate-like T cells: Comparative insights with conventional T cells and mouse models. Cell Reports, 43 (9). p. 114705. ISSN 2211-1247 (Public Dataset)

Herridge, Rowan P, Dolata, Jakub, Migliori, Valentina, de Santis Alves, Cristiane, Borges, Filipe, Schorn, Andrea J, van Ex, Frédéric, Lin, Ann, Bajczyk, Mateusz, Parent, Jean-Sebastien, Leonardi, Tommaso, Hendrick, Alan, Kouzarides, Tony, Martienssen, Robert A (September 2024) Pseudouridine guides germline small RNA transport and epigenetic inheritance. Nature Structural & Molecular Biology. ISSN 1545-9993 (Public Dataset)

Soula, Mariluz, Unlu, Gokhan, Welch, Rachel, Chudnovskiy, Aleksey, Uygur, Beste, Shah, Vyom, Alwaseem, Hanan, Bunk, Paul, Subramanyam, Vishvak, Yeh, Hsi-Wen, Khan, Artem, Heissel, Søren, Goodarzi, Hani, Victora, Gabriel D, Beyaz, Semir, Birsoy, Kıvanç (August 2024) Glycosphingolipid synthesis mediates immune evasion in KRAS-driven cancer. Nature. ISSN 0028-0836 (Public Dataset)

Berube, Benjamin, Ernst, Evan, Cahn, Jonathan, Roche, Benjamin, de Santis Alves, Cristiane, Lynn, Jason, Scheben, Armin, Grimanelli, Daniel, Siepel, Adam, Ross-Ibarra, Jeffrey, Kermicle, Jerry, Martienssen, Robert A (August 2024) Teosinte Pollen Drive guides maize diversification and domestication by RNAi. Nature. ISSN 0028-0836 (Public Dataset)

Qiu, Yijian, Stamatatos, Olivia T, Hu, Qingting, Ruiter Swain, Jed, Russo, Suzanne, Sann, Ava, Costa, Ana SH, Violante, Sara, Spector, David L, Cross, Justin R, Lukey, Michael J (August 2024) The unique catalytic properties of PSAT1 mediate metabolic adaptation to glutamine blockade. Nature Metabolism, 6 (8). pp. 1529-1548. ISSN 2522-5812 (Public Dataset)

Klingbeil, Olaf, Skopelitis, Damianos, Tonelli, Claudia, Yoshimoto, Toyoki, Alpsoy, Aktan, Panepinto, Maria C, Minicozzi, Francesca, Merrill, Joseph R, Cafiero, Amanda M, Aggarwal, Disha, Russo, Suzanne, Ha, Taehoon, Demerdash, Osama E, Wee, Tse-Luen, Spector, David L, Lyons, Scott K, Tuveson, David A, Cifani, Paolo, Vakoc, Christopher R (July 2024) MARK2/MARK3 kinases are catalytic co-dependencies of YAP/TAZ in human cancer. Cancer Discovery. ISSN 2159-8274 (Public Dataset)

Bermejo-Rodriguez, Camino, Araos Henríquez, Joaquín, Caligiuri, Giuseppina, Pinto Teles, Sara, Park, Youngkyu, Evans, Anthony, Barrera, Lawrence N, Neesse, Albrecht, Grutzmann, Robert, Aust, Daniela, Rümmele, Petra, Knösel, Thomas, Narita, Masako, Narita, Masashi, Campbell, Fiona, Öhlund, Daniel, Pilarsky, Christian, Dow, Lukas E, Humbert, Patrick O, Biffi, Giulia, Tuveson, David A, Perez-Mancera, Pedro A (July 2024) Scribble Deficiency Promotes Pancreatic Ductal Adenocarcinoma Development and Metastasis. Cancer Research. ISSN 0008-5472 (Public Dataset)

Duplaquet, Leslie, So, Kevin, Ying, Alexander W, Pal Choudhuri, Shreoshi, Li, Xinyue, Xu, Grace D, Li, Yixiang, Qiu, Xintao, Li, Rong, Singh, Shilpa, Wu, Xiaoli S, Hamilton, Seth, Chien, Victor D, Liu, Qi, Qi, Jun, Somerville, Tim DD, Heiling, Hillary M, Mazzola, Emanuele, Lee, Yenarae, Zoller, Thomas, Vakoc, Christopher R, Doench, John G, Forrester, William C, Abrams, Tinya, Long, Henry W, Niederst, Matthew J, Drapkin, Benjamin J, Kadoch, Cigall, Oser, Matthew G (July 2024) Mammalian SWI/SNF complex activity regulates POU2F3 and constitutes a targetable dependency in small cell lung cancer. Cancer Cell. S1535-6108(24)00237. ISSN 1535-6108 (Public Dataset)

Li, Jiayun, Moresco, Philip, Fearon, Douglas T (July 2024) Intratumoral NKT cell accumulation promotes antitumor immunity in pancreatic cancer. Proceedings of the National Academy of Sciences of the United States of America, 121 (29). e2403917121. ISSN 0027-8424 (Public Dataset)

Benitz, Simone, Steep, Alec, Nasser, Malak M, Preall, Jonathan, Mahajan, Ujjwal Mukund, McQuithey, Holly, Loveless, Ian, Davis, Erick T, Wen, Hui-Ju, Long, Daniel W, Metzler, Thomas, Zwernik, Samuel, Louw, Michaela, Rempinski, Donald, Salas-Escabillas, Daniel J, Brender, Sydney M, Song, Linghao, Huang, Ling, Theisen, Brian K, Zhang, Zhenyu, Steele, Nina G, Regel, Ivonne, Bednar, Filip, Crawford, Howard C (July 2024) ROR2 Regulates Cellular Plasticity in Pancreatic Neoplasia and Adenocarcinoma. Cancer Discovery. ISSN 2159-8274 (Public Dataset)

Serio, Ryan N, Scheben, Armin, Lu, Billy, Gargiulo, Domenic V, Patruno, Lucrezia, Buckholtz, Caroline L, Chaffee, Ryan J, Jibilian, Megan C, Persaud, Steven G, Staklinski, Stephen J, Hassett, Rebecca, Brault, Lise M, Ramazzotti, Daniele, Barbieri, Christopher E, Siepel, Adam C, Nowak, Dawid G (July 2024) Clonal Lineage Tracing with Somatic Delivery of Recordable Barcodes Reveals Migration Histories of Metastatic Prostate Cancer. Cancer Discovery. ISSN 2159-8274

Bojmar, Linda, Zambirinis, Constantinos P, Hernandez, Jonathan M, Chakraborty, Jayasree, Shaashua, Lee, Kim, Junbum, Johnson, Kofi Ennu, Hanna, Samer, Askan, Gokce, Burman, Jonas, Ravichandran, Hiranmayi, Zheng, Jian, Jolissaint, Joshua S, Srouji, Rami, Song, Yi, Choubey, Ankur, Kim, Han Sang, Cioffi, Michele, van Beek, Elke, Sigel, Carlie, Jessurun, Jose, Velasco Riestra, Paulina, Blomstrand, Hakon, Jönsson, Carolin, Jönsson, Anette, Lauritzen, Pernille, Buehring, Weston, Ararso, Yonathan, Hernandez, Dylanne, Vinagolu-Baur, Jessica P, Friedman, Madison, Glidden, Caroline, Firmenich, Laetitia, Lieberman, Grace, Mejia, Dianna L, Nasar, Naaz, Mutvei, Anders P, Paul, Doru M, Bram, Yaron, Costa-Silva, Bruno, Basturk, Olca, Boudreau, Nancy, Zhang, Haiying, Matei, Irina R, Hoshino, Ayuko, Kelsen, David, Sagi, Irit, Scherz, Avigdor, Scherz-Shouval, Ruth, Yarden, Yosef, Oren, Moshe, Egeblad, Mikala, Lewis, Jason S, Keshari, Kayvan, Grandgenett, Paul M, Hollingsworth, Michael A, Rajasekhar, Vinagolu K, Healey, John H, Björnsson, Bergthor, Simeone, Diane M, Tuveson, David A, Iacobuzio-Donahue, Christine A, Bromberg, Jaqueline, Vincent, C Theresa, O'Reilly, Eileen M, DeMatteo, Ronald P, Balachandran, Vinod P, D'Angelica, Michael I, Kingham, T Peter, Allen, Peter J, Simpson, Amber L, Elemento, Olivier, Sandström, Per, Schwartz, Robert E, Jarnagin, William R, Lyden, David (June 2024) Multi-parametric atlas of the pre-metastatic liver for prediction of metastatic outcome in early-stage pancreatic cancer. Nature Medicine. ISSN 1078-8956 (Public Dataset)

He, Tongchen, Xiao, Lanbo, Qiao, Yuanyuan, Klingbeil, Olaf, Young, Eleanor, Wu, Xiaoli S, Mannan, Rahul, Mahapatra, Somnath, Redin, Esther, Cho, Hanbyul, Bao, Yi, Kandarpa, Malathi, Ching-Yi Tien, Jean, Wang, Xiaoju, Eyunni, Sanjana, Zheng, Yang, Kim, NamHoon, Zheng, Heng, Hou, Siyu, Su, Fengyun, Miner, Stephanie J, Mehra, Rohit, Cao, Xuhong, Abbineni, Chandrasekhar, Samajdar, Susanta, Ramachandra, Murali, Dhanasekaran, Saravana M, Talpaz, Moshe, Parolia, Abhijit, Rudin, Charles M, Vakoc, Christopher R, Chinnaiyan, Arul M (June 2024) Targeting the mSWI/SNF complex in POU2F-POU2AF transcription factor-driven malignancies. Cancer Cell. S1535-6108(24)00231. ISSN 1535-6108 (Public Dataset)

Boire, Adrienne, Burke, Katy, Cox, Thomas R, Guise, Theresa, Jamal-Hanjani, Mariam, Janowitz, Tobias, Kaplan, Rosandra, Lee, Rebecca, Swanton, Charles, Vander Heiden, Matthew G, Sahai, Erik (June 2024) Why do patients with cancer die? Nature Reviews Cancer. ISSN 1474-175X

Maia-Silva, Diogo, Cunniff, Patrick J, Schier, Allison C, Skopelitis, Damianos, Trousdell, Marygrace C, Moresco, Philip, Gao, Yuan, Kechejian, Vahag, He, Xue-Yan, Sahin, Yunus, Wan, Ledong, Alpsoy, Aktan, Liverpool, Jynelle, Krainer, Adrian R, Egeblad, Mikala, Spector, David L, Fearon, Douglas T, Dos Santos, Camila O, Taatjes, Dylan J, Vakoc, Christopher R (June 2024) Interaction between MED12 and ΔNp63 activates basal identity in pancreatic ductal adenocarcinoma. Nature Genetics. ISSN 1061-4036

Zhang, Jialin, Westcott, Peter MK (June 2024) Claudin 18 turns up the heat in cancer. Immunity, 57 (6). pp. 1187-1189. ISSN 1074-7613

Guo, Guangran, Amor, Corina (June 2024) SGLT2 regulates immune-mediated senolysis. Nature Aging. ISSN 2662-8465

Langer, Henning Tim, Ramsamooj, Shakti, Dantas, Ezequiel, Murthy, Anirudh, Ahmed, Mujmmail, Ahmed, Tanvir, Hwang, Seo-Kyoung, Grover, Rahul, Pozovskiy, Rita, Liang, Roger J, Queiroz, Andre Lima, Brown, Justin C, White, Eileen P, Janowitz, Tobias, Goncalves, Marcus D (May 2024) Restoring adiponectin via rosiglitazone ameliorates tissue wasting in mice with lung cancer. Acta Physiologica. e14167. ISSN 1748-1708

Aguzzoli Heberle, Bernardo, Brandon, J Anthony, Page, Madeline L, Nations, Kayla A, Dikobe, Ketsile I, White, Brendan J, Gordon, Lacey A, Fox, Grant A, Wadsworth, Mark E, Doyle, Patricia H, Williams, Brittney A, Fox, Edward J, Shantaraman, Anantharaman, Ryten, Mina, Goodwin, Sara, Ghiban, Elena, Wappel, Robert, Mavruk-Eskipehlivan, Senem, Miller, Justin B, Seyfried, Nicholas T, Nelson, Peter T, Fryer, John D, Ebbert, Mark TW (May 2024) Mapping medically relevant RNA isoform diversity in the aged human frontal cortex with deep long-read RNA-seq. Nature Biotechnology. ISSN 1087-0156 (Public Dataset)

Tollkuhn, Jessica (May 2024) Nuclear receptors - studying genes to understand hormones. Nature Reviews Genetics. ISSN 1471-0056

Segovia, Danilo, Adams, Dexter W, Hoffman, Nickolas, Safaric Tepes, Polona, Wee, Tse-Luen, Cifani, Paolo, Joshua-Tor, Leemor, Krainer, Adrian R (May 2024) SRSF1 interactome determined by proximity labeling reveals direct interaction with spliceosomal RNA helicase DDX23. Proceedings of the National Academy of Sciences of the United States of America, 121 (21). e2322974121. ISSN 0027-8424 (Public Dataset)

Wan, Ledong, Kral, Alexander J, Voss, Dillon, Schäfer, Balázs, Sudheendran, Kavitha, Danielsen, Mathias, Caruthers, Marvin H, Krainer, Adrian R (May 2024) Screening Splice-Switching Antisense Oligonucleotides in Pancreas-Cancer Organoids. Nucleic Acid Therapeutics. ISSN 2159-3337

Lupo, Francesca, Pezzini, Francesco, Pasini, Davide, Fiorini, Elena, Adamo, Annalisa, Veghini, Lisa, Bevere, Michele, Frusteri, Cristina, Delfino, Pietro, D'agosto, Sabrina, Andreani, Silvia, Piro, Geny, Malinova, Antonia, Wang, Tian, De Sanctis, Francesco, Lawlor, Rita Teresa, Hwang, Chang-Il, Carbone, Carmine, Amelio, Ivano, Bailey, Peter, Bronte, Vincenzo, Tuveson, David, Scarpa, Aldo, Ugel, Stefano, Corbo, Vincenzo (April 2024) Axon guidance cue SEMA3A promotes the aggressive phenotype of basal-like PDAC. Gut. gutjnl-2023. ISSN 0017-5749

Henry, Samantha, Lewis, Steven Macauley, Cyrill, Samantha Leeanne, Callaway, Mackenzie Kate, Chatterjee, Deeptiman, Hanasoge Somasundara, Amritha Varshini, Jones, Gina, He, Xue-Yan, Caligiuri, Giuseppina, Ciccone, Michael Francis, Diaz, Isabella Andrea, Biswas, Amelia Aumalika, Hernandez, Evelyn, Ha, Taehoon, Wilkinson, John Erby, Egeblad, Mikala, Tuveson, David Arthur, Dos Santos, Camila Oresco (April 2024) Host response during unresolved urinary tract infection alters female mammary tissue homeostasis through collagen deposition and TIMP1. Nature Communications, 15 (1). p. 3282. ISSN 2041-1723 (Public Dataset)

Boelaars, Kelly, Rodriguez, Ernesto, Huinen, Zowi R, Liu, Chang, Wang, Di, Springer, Babet O, Olesek, Katarzyna, Goossens-Kruijssen, Laura, van Ee, Thomas, Lindijer, Dimitri, Tak, Willemijn, de Haas, Aram, Wehry, Laetitia, Nugteren-Boogaard, Joline P, Mikula, Aleksandra, de Winde, Charlotte M, Mebius, Reina E, Tuveson, David A, Giovannetti, Elisa, Bijlsma, Maarten F, Wuhrer, Manfred, van Vliet, Sandra J, van Kooyk, Yvette (April 2024) Pancreatic cancer-associated fibroblasts modulate macrophage differentiation via sialic acid-Siglec interactions. Communications Biology, 7 (1). p. 430. ISSN 2399-3642 (Public Dataset)

Amit, Moran, Anastasaki, Corina, Dantzer, Robert, Demir, Ihsan Ekin, Deneen, Benjamin, Dixon, Karen O, Egeblad, Mikala, Gibson, Erin M, Hervey-Jumper, Shawn L, Hondermarck, Hubert, Magnon, Claire, Monje, Michelle, Na'ara, Shorook, Pan, Yuan, Repasky, Elizabeth A, Scheff, Nicole N, Sloan, Erica K, Talbot, Sebastien, Tracey, Kevin J, Trotman, Lloyd C, Valiente, Manuel, Van Aelst, Linda, Venkataramani, Varun, Venkatesh, Humsa S, Vermeer, Paola D, Winkler, Frank, Wong, Richard J, Gutmann, David H, Borniger, Jeremy C (April 2024) Next Directions in the Neuroscience of Cancers Arising outside the CNS. Cancer Discovery, 14 (4). pp. 669-673. ISSN 2159-8274

Damoci, Chris B, Merrill, Joseph R, Sun, Yanping, Lyons, Scott K, Olive, Kenneth P (March 2024) Addressing Biological Questions with Preclinical Cancer Imaging. Cold Spring Harbor Perspectives in Medicine. a041378-a041378. ISSN 2157-1422

Yashaswini, Chittampalli N, Qin, Tianyue, Bhattacharya, Dipankar, Amor, Corina, Lowe, Scott, Lujambio, Amaia, Wang, Shuang, Friedman, Scott L (March 2024) Phenotypes and ontogeny of senescent hepatic stellate cells in metabolic dysfunction-associated steatotic liver disease. Journal of Hepatology. S0168-8278(24)00197. ISSN 0168-8278

Homer, Joshua A, Koelln, Rebecca A, Barrow, Andrew S, Gialelis, Timothy L, Boiarska, Zlata, Steinohrt, Nikita S, Lee, Erinna F, Yang, Wen-Hsuan, Johnson, Robert M, Chung, Taemoon, Habowski, Amber N, Vishwakarma, Dharmendra S, Bhunia, Debmalya, Avanzi, Charlotte, Moorhouse, Adam D, Jackson, Mary, Tuveson, David A, Lyons, Scott K, Lukey, Michael J, Fairlie, W Douglas, Haider, Shozeb M, Steinmetz, Michel O, Prota, Andrea E, Moses, John E (March 2024) Modular synthesis of functional libraries by accelerated SuFEx click chemistry. Chemical Science, 15 (11). pp. 3879-3892. ISSN 2041-6520 (Public Dataset)

Ubhi, Tajinder, Zaslaver, Olga, Quaile, Andrew T, Plenker, Dennis, Cao, Pinjiang, Pham, Nhu-An, Békési, Angéla, Jang, Gun-Ho, O'Kane, Grainne M, Notta, Faiyaz, Moffat, Jason, Wilson, Julie M, Gallinger, Steven, Vértessy, Beáta G, Tuveson, David A, Röst, Hannes L, Brown, Grant W (March 2024) Cytidine deaminases APOBEC3C and APOBEC3D promote DNA replication stress resistance in pancreatic cancer cells. Nature Cancer. ISSN 2662-1347 (Public Dataset)

Ishigami, Yuma, Wong, Mandy S, Martí-Gómez, Carlos, Ayaz, Andalus, Kooshkbaghi, Mahdi, Hanson, Sonya M, McCandlish, David M, Krainer, Adrian R, Kinney, Justin B (February 2024) Specificity, synergy, and mechanisms of splice-modifying drugs. Nature Communications, 15 (1). p. 1880. ISSN 2041-1723 (Public Dataset)

Dai, Enyong, Chen, Xin, Linkermann, Andreas, Jiang, Xuejun, Kang, Rui, Kagan, Valerian E, Bayir, Hülya, Yang, Wan Seok, Garcia-Saez, Ana J, Ioannou, Maria S, Janowitz, Tobias, Ran, Qitao, Gu, Wei, Gan, Boyi, Krysko, Dmitri V, Zhu, Xiaofeng, Wang, Jiayi, Krautwald, Stefan, Toyokuni, Shinya, Xie, Yangchun, Greten, Florian R, Yi, Qing, Schick, Joel, Liu, Jiao, Gabrilovich, Dmitry I, Liu, Jinbao, Zeh, Herbert J, Zhang, Donna D, Yang, Minghua, Iovanna, Juan, Kopf, Manfred, Adolph, Timon E, Chi, Jen-Tsan, Li, Changfeng, Ichijo, Hidenori, Karin, Michael, Sankaran, Vijay G, Zou, Weiping, Galluzzi, Lorenzo, Bush, Ashley I, Li, Binghui, Melino, Gerry, Baehrecke, Eric H, Lotze, Michael T, Klionsky, Daniel J, Stockwell, Brent R, Kroemer, Guido, Tang, Daolin (February 2024) A guideline on the molecular ecosystem regulating ferroptosis. Nature Cell Biology. ISSN 1465-7392

Goto, Norihiro, Westcott, Peter MK, Goto, Saori, Imada, Shinya, Taylor, Martin S, Eng, George, Braverman, Jonathan, Deshpande, Vikram, Jacks, Tyler, Agudo, Judith, Yilmaz, Ömer H (February 2024) SOX17 enables immune evasion of early colorectal adenomas and cancers. Nature. ISSN 0028-0836 (Public Dataset)

Colucci, Manuel, Zumerle, Sara, Bressan, Silvia, Gianfanti, Federico, Troiani, Martina, Valdata, Aurora, D'Ambrosio, Mariantonietta, Pasquini, Emiliano, Varesi, Angelica, Cogo, Francesca, Mosole, Simone, Dongilli, Cristina, Desbats, Maria Andrea, Contu, Liliana, Revankdar, Ajinkya, Chen, Jingjing, Kalathur, Madhuri, Perciato, Maria Luna, Basilotta, Rossella, Endre, Laczko, Schauer, Stefan, Othman, Alaa, Guccini, Ilaria, Saponaro, Miriam, Maraccani, Luisa, Bancaro, Nicolò, Lai, Ping, Liu, Lei, Pernigoni, Nicolò, Mele, Federico, Merler, Sara, Trotman, Lloyd C, Guarda, Greta, Calì, Bianca, Montopoli, Monica, Alimonti, Andrea (February 2024) Retinoic acid receptor activation reprograms senescence response and enhances anti-tumor activity of natural killer cells. Cancer Cell. S1535-6108(24)00048. ISSN 1535-6108 (Public Dataset)

Gao, Yuan, Vakoc, Christopher R (February 2024) Therapeutic index of targeting select chromatin complexes in human cancer patients. Current Opinion in Genetics and Development, 85. p. 102162. ISSN 0959-437X

Gaudino, Stephen J, Singh, Ankita, Huang, Huakang, Padiadpu, Jyothi, Jean-Pierre, Makheni, Kempen, Cody, Bahadur, Tej, Shiomitsu, Kiyoshi, Blumberg, Richard, Shroyer, Kenneth R, Beyaz, Semir, Shulzhenko, Natalia, Morgun, Andrey, Kumar, Pawan (February 2024) Intestinal IL-22RA1 signaling regulates intrinsic and systemic lipid and glucose metabolism to alleviate obesity-associated disorders. Nature Communications, 15 (1). p. 1597. ISSN 2041-1723 (Public Dataset)

He, Xue-Yan, Gao, Yuan, Ng, David, Michalopoulou, Evdokia, George, Shanu, Adrover, Jose M, Sun, Lijuan, Albrengues, Jean, Daßler-Plenker, Juliane, Han, Xiao, Wan, Ledong, Wu, Xiaoli Sky, Shui, Longling S, Huang, Yu-Han, Liu, Bodu, Su, Chang, Spector, David L, Vakoc, Christopher R, Van Aelst, Linda, Egeblad, Mikala (February 2024) Chronic stress increases metastasis via neutrophil-mediated changes to the microenvironment. Cancer Cell. ISSN 1535-6108

Karakaya, Eda, Oleinik, Natalia, Edwards, Jazlyn, Tomberlin, Jensen, Barker, Randy Bent, Berber, Burak, Ericsson, Maria, Alsudani, Habeeb, Ergul, Adviye, Beyaz, Semir, Lemasters, John J, Ogretmen, Besim, Albayram, Onder (February 2024) p17/C18-ceramide-mediated mitophagy is an endogenous neuroprotective response in preclinical and clinical brain injury. PNAS Nexus, 3 (2). ISSN 2752-6542

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)

Rogava, Meri, Aprati, Tyler J, Chi, Wei-Yu, Melms, Johannes C, Hug, Clemens, Davis, Stephanie H, Earlie, Ethan M, Chung, Charlie, Deshmukh, Sachin K, Wu, Sharon, Sledge, George, Tang, Stephen, Ho, Patricia, Amin, Amit Dipak, Caprio, Lindsay, Gurjao, Carino, Tagore, Somnath, Ngo, Bryan, Lee, Michael J, Zanetti, Giorgia, Wang, Yiping, Chen, Sean, Ge, William, Melo, Luiza Martins Nascentes, Allies, Gabriele, Rösler, Jonas, Gibney, Goeffrey T, Schmitz, Oliver J, Sykes, Megan, Creusot, Rémi J, Tüting, Thomas, Schadendorf, Dirk, Röcken, Martin, Eigentler, Thomas K, Molotkov, Andrei, Mintz, Akiva, Bakhoum, Samuel F, Beyaz, Semir, Cantley, Lewis C, Sorger, Peter K, Meckelmann, Sven W, Tasdogan, Alpaslan, Liu, David, Laughney, Ashley M, Izar, Benjamin (January 2024) Loss of Pip4k2c confers liver-metastatic organotropism through insulin-dependent PI3K-AKT pathway activation. Nature Cancer. ISSN 2662-1347 (Public Dataset)

Alpsoy, Aktan, Wu, Xiaoli S, Pal, Sujay, Klingbeil, Olaf, Kumar, Pramod, El Demerdash, Osama, Nalbant, Benan, Vakoc, Christopher R (January 2024) IκBζ is a dual-use coactivator of NF-κB and POU transcription factors. Molecular Cell. S1097-2765(24)00008. ISSN 1097-2765 (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)

Homer, Joshua A, Sun, Shoujun, Koelln, Rebecca A, Moses, John E (January 2024) Protocol for producing phosphoramidate using phosphorus fluoride exchange click chemistry. STAR Protocols, 5 (1). p. 102824. ISSN 2666-1667

Leibold, Josef, Tsanov, Kaloyan M, Amor, Corina, Ho, Yu-Jui, Sánchez-Rivera, Francisco J, Feucht, Judith, Baslan, Timour, Chen, Hsuan-An, Tian, Sha, Simon, Janelle, Wuest, Alexandra, Wilkinson, John E, Lowe, Scott W (January 2024) Somatic mouse models of gastric cancer reveal genotype-specific features of metastatic disease. Nature Cancer. ISSN 2662-1347

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Westcott, Peter MK, Muyas, Francesc, Hauck, Haley, Smith, Olivia C, Sacks, Nathan J, Ely, Zackery A, Jaeger, Alex M, Rideout, William M, Zhang, Daniel, Bhutkar, Arjun, Beytagh, Mary C, Canner, David A, Jaramillo, Grissel C, Bronson, Roderick T, Naranjo, Santiago, Jin, Abbey, Patten, JJ, Cruz, Amanda M, Shanahan, Sean-Luc, Cortes-Ciriano, Isidro, Jacks, Tyler (September 2023) Mismatch repair deficiency is not sufficient to elicit tumor immunogenicity. Nature Genetics. ISSN 1061-4036

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Scheben, Armin, Mendivil Ramos, Olivia, Kramer, Melissa, Goodwin, Sara, Oppenheim, Sara, Becker, Daniel J, Schatz, Michael C, Simmons, Nancy B, Siepel, Adam, McCombie, W Richard (September 2023) Long-Read Sequencing Reveals Rapid Evolution of Immunity- and Cancer-Related Genes in Bats. Genome Biology and Evolution, 15 (9). ISSN 1759-6653 (Public Dataset)

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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)

Fisher, Matthew L, Balinth, Seamus, Hwangbo, Yon, Wu, Caizhi, Ballon, Carlos, Goldberg, Gary L, Mills, Alea A (August 2023) Cancer-associated fibroblasts promote cancer stemness by inducing expression of the chromatin-modifying protein CBX4 in squamous cell carcinoma. Carcinogenesis, 44 (6). pp. 485-496. ISSN 0143-3334

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Brina, Daniela, Ponzoni, Adele, Troiani, Martina, Calì, Bianca, Pasquini, Emiliano, Attanasio, Giuseppe, Mosole, Simone, Mirenda, Michela, D'Ambrosio, Mariantonietta, Colucci, Manuel, Guccini, Ilaria, Revandkar, Ajinkya, Alajati, Abdullah, Tebaldi, Toma, Donzel, Deborah, Lauria, Fabio, Parhizgari, Nahjme, Valdata, Aurora, Maddalena, Martino, Calcinotto, Arianna, Bolis, Marco, Rinaldi, Andrea, Barry, Simon, Rüschoff, Jan Hendrik, Sabbadin, Marianna, Sumanasuriya, Semini, Crespo, Mateus, Sharp, Adam, Yuan, Wei, Grinu, Mathew, Boyle, Alexandra, Miller, Cynthia, Trotman, Lloyd, Delaleu, Nicolas, Fassan, Matteo, Moch, Holger, Viero, Gabriella, de Bono, Johann, Alimonti, Andrea (August 2023) The Akt/mTOR and MNK/eIF4E pathways rewire the prostate cancer translatome to secrete HGF, SPP1 and BGN and recruit suppressive myeloid cells. Nature Cancer, 4 (8). pp. 1102-1121. ISSN 2662-1347 (Public Dataset)

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Li, Bin E, Li, Grace Y, Cai, Wenqing, Zhu, Qian, Seruggia, Davide, Fujiwara, Yuko, Vakoc, Christopher R, Orkin, Stuart (July 2023) In vivo CRISPR/Cas9 Screening Identifies Pbrm1 as a Regulator of Mouse Myeloid Leukemia Development. Blood Advances, 7 (18). pp. 5281-5293. ISSN 2473-9529 (Public Dataset)

Costa, Iris Munhoz, Effer, Brian, Costa-Silva, Tales Alexandre, Chen, Chen, Ciccone, Michael F, Pessoa, Adalberto, Dos Santos, Camila O, Monteiro, Gisele (July 2023) Cathepsin B Is Not an Intrinsic Factor Related to Asparaginase Resistance of the Acute Lymphoblastic Leukemia REH Cell Line. International Journal of Molecular Sciences, 24 (13). p. 11215. ISSN 1661-6596

Wan, Ledong, Lin, Kuan-Ting, Rahman, Mohammad Alinoor, Ishigami, Yuma, Wang, Zhikai, Jensen, Mads A, Wilkinson, John E, Park, Youngkyu, Tuveson, David A, Krainer, Adrian R (July 2023) Splicing Factor SRSF1 Promotes Pancreatitis and KRASG12D-Mediated Pancreatic Cancer. Cancer Discovery, 13 (7). pp. 1678-1695. ISSN 2159-8274 (Public Dataset)

Yoo, Hye-Been, Moon, Jin Woo, Kim, Hwa-Ryeon, Lee, Hee Seung, Miyabayashi, Koji, Park, Chan Hee, Ge, Sabrina, Zhang, Amy, Tae, Yoo Keung, Sub, Yujin, Park, Hyun-Woo, Gee, Heon Yung, Notta, Faiyaz, Tuveson, David A, Bang, Seungmin, Kim, Mi-Young, Roe, Jae-Seok (July 2023) A TEAD2-Driven Endothelial-Like Program Shapes Basal-Like Differentiation and Metastasis of Pancreatic Cancer. Gastroenterology, 165 (1). 133-148.e17. ISSN 0016-5085

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

Haas, Brian J, Dobin, Alexander, Ghandi, Mahmoud, Van Arsdale, Anne, Tickle, Timothy, Robinson, James T, Gillani, Riaz, Kasif, Simon, Regev, Aviv (May 2023) Targeted in silico characterization of fusion transcripts in tumor and normal tissues via FusionInspector. Cell Reports: Methods, 3 (5). p. 100467. ISSN 2667-2375

Schwörer, Simon, Cimino, Francesco V, Ros, Manon, Tsanov, Kaloyan M, Ng, Charles, Lowe, Scott W, Carmona-Fontaine, Carlos, Thompson, Craig B (May 2023) Hypoxia Potentiates the Inflammatory Fibroblast Phenotype Promoted by Pancreatic Cancer Cell-Derived Cytokines. Cancer Research, 83 (10). pp. 1596-1610. ISSN 0008-5472

Wu, Xiaoli S, Vakoc, Christopher R (May 2023) Made to order tuft cells by an OCA-T1 isoform switch. Science Immunology, 8 (83). eadh3123. ISSN 2470-9468

Ely, Zackery A, Mathey-Andrews, Nicolas, Naranjo, Santiago, Gould, Samuel I, Mercer, Kim L, Newby, Gregory A, Cabana, Christina M, Rideout, William M, Jaramillo, Grissel Cervantes, Khirallah, Jennifer M, Holland, Katie, Randolph, Peyton B, Freed-Pastor, William A, Davis, Jessie R, Kulstad, Zachary, Westcott, Peter MK, Lin, Lin, Anzalone, Andrew V, Horton, Brendan L, Pattada, Nimisha B, Shanahan, Sean-Luc, Ye, Zhongfeng, Spranger, Stefani, Xu, Qiaobing, Sánchez-Rivera, Francisco J, Liu, David R, Jacks, Tyler (May 2023) A prime editor mouse to model a broad spectrum of somatic mutations in vivo. Nature Biotechnology. ISSN 1087-0156 (Public Dataset)

Majdandzic, Antonio, Rajesh, Chandana, Koo, Peter K (May 2023) Correcting gradient-based interpretations of deep neural networks for genomics. Genome Biology, 24 (1). p. 109. ISSN 1474-760X

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

Velt, Amandine, Frommer, Bianca, Blanc, Sophie, Holtgräwe, Daniela, Duchêne, Éric, Dumas, Vincent, Grimplet, Jérôme, Hugueney, Philippe, Kim, Catherine, Lahaye, Marie, Matus, José Tomás, Navarro-Payá, David, Orduña, Luis, Tello-Ruiz, Marcela K, Vitulo, Nicola, Ware, Doreen, Rustenholz, Camille (May 2023) An improved reference of the grapevine genome reasserts the origin of the PN40024 highly homozygous genotype. G3: Genes, Genomes, Genetics, 13 (5). jkad067. ISSN 2160-1836

Cable, Jennifer, Rathmell, Jeffrey C, Pearce, Erika L, Ho, Ping-Chih, Haigis, Marcia C, Mamedov, Murad R, Wu, Meng-Ju, Kaech, Susan M, Lynch, Lydia, Febbraio, Mark A, Bapat, Sagar P, Hong, Hanna S, Zou, Weiping, Belkaid, Yasmine, Sullivan, Zuri A, Keller, Andrea, Wculek, Stefanie K, Green, Douglas R, Postic, Catherine, Amit, Ido, Benitah, Salvador Aznar, Jones, Russell G, Reina-Campos, Miguel, Torres, Santiago Valle, Beyaz, Semir, Brennan, Donal, O'Neill, Luke AJ, Perry, Rachel J, Brenner, Dirk (May 2023) Immunometabolism at the crossroads of obesity and cancer-a Keystone Symposia report. Annals of the New York Academy of Sciences, 1523 (1). pp. 38-50. ISSN 0077-8923

Jbara, Amina, Lin, Kuan-Ting, Stossel, Chani, Siegfried, Zahava, Shqerat, Haya, Amar-Schwartz, Adi, Elyada, Ela, Mogilevsky, Maxim, Raitses-Gurevich, Maria, Johnson, Jared L, Yaron, Tomer M, Ovadia, Ofek, Jang, Gun Ho, Danan-Gotthold, Miri, Cantley, Lewis C, Levanon, Erez Y, Gallinger, Steven, Krainer, Adrian R, Golan, Talia, Karni, Rotem (May 2023) RBFOX2 modulates a metastatic signature of alternative splicing in pancreatic cancer. Nature, 617 (7959). pp. 147-153. ISSN 0028-0836 (Public Dataset)

Ferrer, Miriam, Anthony, Tracy G, Ayres, Janelle S, Biffi, Giulia, Brown, Justin C, Caan, Bette J, Cespedes Feliciano, Elizabeth M, Coll, Anthony P, Dunne, Richard F, Goncalves, Marcus D, Grethlein, Jonas, Heymsfield, Steven B, Hui, Sheng, Jamal-Hanjani, Mariam, Lam, Jie Min, Lewis, David Y, McCandlish, David, Mustian, Karen M, O'Rahilly, Stephen, Perrimon, Norbert, White, Eileen P, Janowitz, Tobias (April 2023) Cachexia: A systemic consequence of progressive, unresolved disease. Cell, 186 (9). pp. 1824-1845. ISSN 0092-8674

Gialelis, Timothy L, Wang, Zifei, Homer, Joshua A, Yang, Wen-Hsuan, Chung, Taemoon, Hu, Qingting, Smedley, Christopher J, Pawar, Nitin J, Upadhyay, Nitinkumar S, Tuveson, David A, Lyons, Scott K, Lukey, Michael J, Moses, John E (April 2023) Inhibition of mitochondrial metabolism by (-)-jerantinine A: synthesis and biological studies in triple-negative breast cancer cells. MedChemComm, 14 (4). pp. 710-714. ISSN 2632-8682

Herrejon Chavez, Florisela, Luo, Hanzhi, Cifani, Paolo, Pine, Alli, Chu, Karen L, Joshi, Suhasini, Barin, Ersilia, Schurer, Alexandra, Chan, Mandy, Chang, Kathryn, Han, Grace YQ, Pierson, Aspen J, Xiao, Michael, Yang, Xuejing, Kuehm, Lindsey M, Hong, Yuning, Nguyen, Diu TT, Chiosis, Gabriela, Kentsis, Alex, Leslie, Christina, Vu, Ly P, Kharas, Michael G (April 2023) RNA binding protein SYNCRIP maintains proteostasis and self-renewal of hematopoietic stem and progenitor cells. Nature Communications, 14 (1). p. 2290. ISSN 2041-1723 (Public Dataset)

Fiskus, Warren, Mill, Christopher P, Birdwell, Christine, Davis, John A, Das, Kaberi, Boettcher, Steffen, Kadia, Tapan M, DiNardo, Courtney D, Takahashi, Koichi, Loghavi, Sanam, Soth, Michael J, Heffernan, Tim, McGeehan, Gerard M, Ruan, Xinjia, Su, Xiaoping, Vakoc, Christopher R, Daver, Naval, Bhalla, Kapil N (April 2023) Targeting of epigenetic co-dependencies enhances anti-AML efficacy of Menin inhibitor in AML with MLL1-r or mutant NPM1. Blood Cancer Journal, 13 (1). p. 53. ISSN 2044-5385 (Public Dataset)

Zhang, Qian, Yang, Lucia, Liu, Ying Hsiu, Wilkinson, John E, Krainer, Adrian R (April 2023) Antisense oligonucleotide therapy for H3.3K27M diffuse midline glioma. Science Translational Medicine, 15 (691). eadd8280. ISSN 1946-6234

Ottonello, Alessandra, Wyllie, Jessica A, Yahiaoui, Oussama, Sun, Shoujun, Koelln, Rebecca A, Homer, Joshua A, Johnson, Robert M, Murray, Ewan, Williams, Paul, Bolla, Jani R, Robinson, Carol V, Fallon, Thomas, Soares da Costa, Tatiana P, Moses, John E (April 2023) Shapeshifting bullvalene-linked vancomycin dimers as effective antibiotics against multidrug-resistant gram-positive bacteria. Proceedings of the National Academy of Sciences of USA, 120 (15). e2208737120. ISSN 0027-8424

Mousset, Alexandra, Lecorgne, Enora, Bourget, Isabelle, Lopez, Pascal, Jenovai, Kitti, Cherfils-Vicini, Julien, Dominici, Chloé, Rios, Géraldine, Girard-Riboulleau, Cédric, Liu, Bodu, Spector, David L, Ehmsen, Sidse, Renault, Shufang, Hego, Caroline, Mechta-Grigoriou, Fatima, Bidard, François-Clément, Terp, Mikkel Green, Egeblad, Mikala, Gaggioli, Cédric, Albrengues, Jean (April 2023) Neutrophil extracellular traps formed during chemotherapy confer treatment resistance via TGF-β activation. Cancer Cell, 41 (4). 757-775.e10. ISSN 1535-6108 (Public Dataset)

Abrams, Benjamin, Pengo, Thomas, Wee, Tse-Luen, Deagle, Rebecca C, Vuillemin, Nelly, Callahan, Linda M, Smith, Megan A, Kubow, Kristopher E, Girard, Anne-Marie, Rappoport, Joshua Z, Bayles, Carol J, Cameron, Lisa A, Cole, Richard, Brown, Claire M (April 2023) Tissue-Like 3D Standard and Protocols for Microscope Quality Management. Microscopy and Microanalysis, 29 (2). pp. 616-634. ISSN 1431-9276

Chung, Taemoon, Garcia, Libia, Swamynathan, Manojit M, Froeling, Fieke EM, Trotman, Lloyd C, Tuveson, David A, Lyons, Scott K (April 2023) Internally Controlled and Dynamic Optical Measures of Functional Tumor Biology. Analytical Chemistry, 95 (13). pp. 5661-5670. ISSN 0003-2700

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Book Section

Chung, Taemoon, Merrill, Joseph R, Lyons, Scott K (2024) CRISPR/Cas for PET Reporter Gene Engineering. In: Methods in Molecular Biology. UNSPECIFIED, pp. 285-301. ISBN 9781071634981

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Lei, Pin-Ji, Pereira, Ethel, Andersson, Patrik, Amoozgar, Zohreh, Van Wijnbergen, Jan Willem, O'Melia, Meghan J, Zhou, Hengbo, Chatterjee, Sampurna, Ho, William Wee, Posada, Jessica M, Kumar, Ashwin Srinivasan, Morita, Satoru, Chuang, Charlie, Ergin, Ilgin, Jones, Dennis, Huang, Peigen, Beyaz, Semir, Padera, Timothy P (2023) Single cell analysis of breast cancer progression and metastasis to lymph nodes reveals cancer cell plasticity and MHC class II-mediated immune regulation. In: 114th Annual Meeting of the American Association for Cancer Research (AACR), APR 14-19, 2023, Orlando, FL.

Book

Cifani, Paolo (2022) Automated Multidimensional Nanoscale Chromatography for Ultrasensitive Targeted Mass Spectrometry. Methods in Molecular Biology, 1 . Humana Press, New York, New York.