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Wang, Bo, Chougule, Kapeel, Jiao, Yinping, Olson, Andrew, Kumar, Vivek, Gladman, Nicholas, Huang, Jian, Llaca, Victor, Fengler, Kevin, Wei, Xuehong, Wang, Liya, Wang, Xiaofei, Regulski, Michael, Drenkow, Jorg, Gingeras, Thomas, Hayes, Chad, Armstrong, J Scott, Huang, Yinghua, Xin, Zhanguo, Ware, Doreen (September 2024) High-quality chromosome scale genome assemblies of two important Sorghum inbred lines, Tx2783 and RTx436. NAR Genomics and Bioinformatics, 6 (3). lqae097. ISSN 2631-9268 (Public Dataset)

Amaral, Paulo, Carbonell-Sala, Silvia, De La Vega, Francisco M, Faial, Tiago, Frankish, Adam, Gingeras, Thomas, Guigo, Roderic, Harrow, Jennifer L, Hatzigeorgiou, Artemis G, Johnson, Rory, Murphy, Terence D, Pertea, Mihaela, Pruitt, Kim D, Pujar, Shashikant, Takahashi, Hazuki, Ulitsky, Igor, Varabyou, Ales, Wells, Christine A, Yandell, Mark, Carninci, Piero, Salzberg, Steven L (October 2023) The status of the human gene catalogue. Nature, 622 (7981). pp. 41-47. ISSN 0028-0836

Hitz, Benjamin, Lee, Jin-Wook, Jolanki, Otto, Kagda, Meenakshi, Graham, Keenan, Sud, Paul, Gabdank, Idan, Strattan, J Seth, Sloan, Cricket, Dreszer, Timothy, Rowe, Laurence, Podduturi, Nikhil, Malladi, Venkat, Chan, Esther, Davidson, Jean, Ho, Marcus, Miyasato, Stuart, Simison, Matt, Tanaka, Forrest, Luo, Yunhai, Wahling, Ian, Lin, Khine Zin, Jou, Jennifer, Hong, Eurie, Lee, Brian, Sandstrom, Richard, Rynes, Eric, Nelson, Jemma, Nishida, Andrew, Ingersoll, Alyssa, Buckley, Michael, Frerker, Mark, Kim, Daniel, Boley, Nathan, Trout, Diane, Dobin, Alexander, Rahmanian, Sorena, Wyman, Dana, Balderrama-Gutierrez, Gabriela, Reese, Fairlie, Durand, Neva, Dudchenko, Olga, Weisz, David, Rao, Suhas, Blackburn, Alyssa, Gkountaroulis, Dimos, Sadr, Mahdi, Olshansky, Moshe, Eliaz, Yossi, Nguyen, Dat, Bochkov, Ivan, Shamim, Muhammad, Mahajan, Ragini, Aiden, Erez, Gingeras, Thomas, Heath, Simon, Hirst, Martin, Kent, W James, Kundaje, Anshul, Mortazavi, Ali, Wold, Barbara, Cherry, J (July 2023) The ENCODE Uniform Analysis Pipelines. Res Sq. (Submitted)

Hitz, Benjamin C, Lee, Jin-Wook, Jolanki, Otto, Kagda, Meenakshi S, Graham, Keenan, Sud, Paul, Gabdank, Idan, Seth Strattan, J, Sloan, Cricket A, Dreszer, Timothy, Rowe, Laurence D, Podduturi, Nikhil R, Malladi, Venkat S, Chan, Esther T, Davidson, Jean M, Ho, Marcus, Miyasato, Stuart, Simison, Matt, Tanaka, Forrest, Luo, Yunhai, Whaling, Ian, Hong, Eurie L, Lee, Brian T, Sandstrom, Richard, Rynes, Eric, Nelson, Jemma, Nishida, Andrew, Ingersoll, Alyssa, Buckley, Michael, Frerker, Mark, Kim, Daniel S, Boley, Nathan, Trout, Diane, Dobin, Alex, Rahmanian, Sorena, Wyman, Dana, Balderrama-Gutierrez, Gabriela, Reese, Fairlie, Durand, Neva C, Dudchenko, Olga, Weisz, David, Rao, Suhas SP, Blackburn, Alyssa, Gkountaroulis, Dimos, Sadr, Mahdi, Olshansky, Moshe, Eliaz, Yossi, Nguyen, Dat, Bochkov, Ivan, Shamim, Muhammad Saad, Mahajan, Ragini, Aiden, Erez, Gingeras, Tom, Heath, Simon, Hirst, Martin, James Kent, W, Kundaje, Anshul, Mortazavi, Ali, Wold, Barbara, Cherry, J Michael (April 2023) The ENCODE Uniform Analysis Pipelines. (Submitted)

Rozowsky, Joel, Gao, Jiahao, Borsari, Beatrice, Yang, Yucheng T, Galeev, Timur, Gürsoy, Gamze, Epstein, Charles B, Xiong, Kun, Xu, Jinrui, Li, Tianxiao, Liu, Jason, Yu, Keyang, Berthel, Ana, Chen, Zhanlin, Navarro, Fabio, Sun, Maxwell S, Wright, James, Chang, Justin, Cameron, Christopher JF, Shoresh, Noam, Gaskell, Elizabeth, Drenkow, Jorg, Adrian, Jessika, Aganezov, Sergey, Aguet, François, Balderrama-Gutierrez, Gabriela, Banskota, Samridhi, Corona, Guillermo Barreto, Chee, Sora, Chhetri, Surya B, Cortez Martins, Gabriel Conte, Danyko, Cassidy, Davis, Carrie A, Farid, Daniel, Farrell, Nina P, Gabdank, Idan, Gofin, Yoel, Gorkin, David U, Gu, Mengting, Hecht, Vivian, Hitz, Benjamin C, Issner, Robbyn, Jiang, Yunzhe, Kirsche, Melanie, Kong, Xiangmeng, Lam, Bonita R, Li, Shantao, Li, Bian, Li, Xiqi, Lin, Khine Zin, Luo, Ruibang, Mackiewicz, Mark, Meng, Ran, Moore, Jill E, Mudge, Jonathan, Nelson, Nicholas, Nusbaum, Chad, Popov, Ioann, Pratt, Henry E, Qiu, Yunjiang, Ramakrishnan, Srividya, Raymond, Joe, Salichos, Leonidas, Scavelli, Alexandra, Schreiber, Jacob M, Sedlazeck, Fritz J, See, Lei Hoon, Sherman, Rachel M, Shi, Xu, Shi, Minyi, Sloan, Cricket Alicia, Strattan, J Seth, Tan, Zhen, Tanaka, Forrest Y, Vlasova, Anna, Wang, Jun, Werner, Jonathan, Williams, Brian, Xu, Min, Yan, Chengfei, Yu, Lu, Zaleski, Christopher, Zhang, Jing, Ardlie, Kristin, Cherry, J Michael, Mendenhall, Eric M, Noble, William S, Weng, Zhiping, Levine, Morgan E, Dobin, Alexander, Wold, Barbara, Mortazavi, Ali, Ren, Bing, Gillis, Jesse, Myers, Richard M, Snyder, Michael P, Choudhary, Jyoti, Milosavljevic, Aleksandar, Schatz, Michael C, Bernstein, Bradley E, Guigó, Roderic, Gingeras, Thomas R, Gerstein, Mark (March 2023) The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models. Cell, 186 (7). 1493-1511.e40. ISSN 0092-8674

Amaral, Paulo, Carbonell-Sala, Silvia, De La Vega, Francisco M, Faial, Tiago, Frankish, Adam, Gingeras, Thomas, Guigo, Roderic, Harrow, Jennifer L, Hatzigeorgiou, Artemis G, Johnson, Rory, Murphy, Terence D, Pertea, Mihaela, Pruitt, Kim D, Pujar, Shashikant, Takahashi, Hazuki, Ulitsky, Igor, Varabyou, Ales, Wells, Christine A, Yandell, Mark, Carninci, Piero, Salzberg, Steven L (March 2023) The status of the human gene catalogue. (Submitted)

Mattick, John S, Amaral, Paulo P, Carninci, Piero, Carpenter, Susan, Chang, Howard Y, Chen, Ling-Ling, Chen, Runsheng, Dean, Caroline, Dinger, Marcel E, Fitzgerald, Katherine A, Gingeras, Thomas R, Guttman, Mitchell, Hirose, Tetsuro, Huarte, Maite, Johnson, Rory, Kanduri, Chandrasekhar, Kapranov, Philipp, Lawrence, Jeanne B, Lee, Jeannie T, Mendell, Joshua T, Mercer, Timothy R, Moore, Kathryn J, Nakagawa, Shinichi, Rinn, John L, Spector, David L, Ulitsky, Igor, Wan, Yue, Wilusz, Jeremy E, Wu, Mian (January 2023) Long non-coding RNAs: definitions, functions, challenges and recommendations. Nature Reviews Molecular Cell Biology. ISSN 1471-0072

ENCODE Project Consortium, Moore, Jill E, Purcaro, Michael J, Pratt, Henry E, Epstein, Charles B, Shoresh, Noam, Adrian, Jessika, Kawli, Trupti, Davis, Carrie A, Dobin, Alexander, Kaul, Rajinder, Halow, Jessica, Van Nostrand, Eric L, Freese, Peter, Gorkin, David U, Shen, Yin, He, Yupeng, Mackiewicz, Mark, Pauli-Behn, Florencia, Williams, Brian A, Mortazavi, Ali, Keller, Cheryl A, Zhang, Xiao-Ou, Elhajjajy, Shaimae I, Huey, Jack, Dickel, Diane E, Snetkova, Valentina, Wei, Xintao, Wang, Xiaofeng, Rivera-Mulia, Juan Carlos, Rozowsky, Joel, Zhang, Jing, Chhetri, Surya B, Zhang, Jialing, Victorsen, Alec, White, Kevin P, Visel, Axel, Yeo, Gene W, Burge, Christopher B, Lécuyer, Eric, Gilbert, David M, Dekker, Job, Rinn, John, Mendenhall, Eric M, Ecker, Joseph R, Kellis, Manolis, Klein, Robert J, Noble, William S, Kundaje, Anshul, Guigó, Roderic, Farnham, Peggy J, Cherry, J Michael, Myers, Richard M, Ren, Bing, Graveley, Brenton R, Gerstein, Mark B, Pennacchio, Len A, Snyder, Michael P, Bernstein, Bradley E, Wold, Barbara, Hardison, Ross C, Gingeras, Thomas R, Stamatoyannopoulos, John A, Weng, Zhiping (May 2022) Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature, 605 (7909). E3. ISSN 0028-0836

ENCODE Project Consortium, Snyder, Michael P, Gingeras, Thomas R, Moore, Jill E, Weng, Zhiping, Gerstein, Mark B, Ren, Bing, Hardison, Ross C, Stamatoyannopoulos, John A, Graveley, Brenton R, Feingold, Elise A, Pazin, Michael J, Pagan, Michael, Gilchrist, Daniel A, Hitz, Benjamin C, Cherry, J Michael, Bernstein, Bradley E, Mendenhall, Eric M, Zerbino, Daniel R, Frankish, Adam, Flicek, Paul, Myers, Richard M (May 2022) Author Correction: Perspectives on ENCODE. Nature, 605 (7909). E4. ISSN 0028-0836

Grapotte, Mathys, Saraswat, Manu, Bessière, Chloé, Menichelli, Christophe, Ramilowski, Jordan A, Severin, Jessica, Hayashizaki, Yoshihide, Itoh, Masayoshi, Tagami, Michihira, Murata, Mitsuyoshi, Kojima-Ishiyama, Miki, Noma, Shohei, Noguchi, Shuhei, Kasukawa, Takeya, Hasegawa, Akira, Suzuki, Harukazu, Nishiyori-Sueki, Hiromi, Frith, Martin C, FANTOM consortium, Chatelain, Clément, Carninci, Piero, de Hoon, Michiel JL, Wasserman, Wyeth W, Bréhélin, Laurent, Lecellier, Charles-Henri (March 2022) Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nature Communications, 13 (1). p. 1200. ISSN 2041-1723

Ortiz-Ramírez, Carlos, Guillotin, Bruno, Xu, Xiaosa, Rahni, Ramin, Zhang, Sanqiang, Yan, Zhe, Coqueiro Dias Araujo, Poliana, Demesa-Arevalo, Edgar, Lee, Laura, Van Eck, Joyce, Gingeras, Thomas R, Jackson, David, Gallagher, Kimberly L, Birnbaum, Kenneth D (December 2021) Ground tissue circuitry regulates organ complexity in maize and Setaria. Science, 374 (6572). pp. 1247-1252. ISSN 0036-8075

Grapotte, M, Saraswat, M, Bessière, C, Menichelli, C, Ramilowski, JA, Severin, J, Hayashizaki, Y, Itoh, M, Tagami, M, Murata, M, Kojima-Ishiyama, M, Noma, S, Noguchi, S, Kasukawa, T, Hasegawa, A, Suzuki, H, Nishiyori-Sueki, H, Frith, MC, Abugessaisa, I, Aitken, S, Aken, BL, Alam, I, Alam, T, Alasiri, R, Alhendi, AMN, Alinejad-Rokny, H, Alvarez, MJ, Andersson, R, Arakawa, T, Araki, M, Arbel, T, Archer, J, Archibald, AL, Arner, E, Arner, P, Asai, K, Ashoor, H, Astrom, G, Babina, M, Baillie, JK, Bajic, VB, Bajpai, A, Baker, S, Baldarelli, RM, Balic, A, Bansal, M, Batagov, AO, Batzoglou, S, Beckhouse, AG, Beltrami, AP, Beltrami, CA, Bertin, N, Bhattacharya, S, Bickel, PJ, Blake, JA, Blanchette, M, Bodega, B, Bonetti, A, Bono, H, Bornholdt, J, Bttcher, M, Bougouffa, S, Boyd, M, Breda, J, Brombacher, F, Brown, JB, Bult, CJ, Burroughs, AM, Burt, DW, Busch, A, Caglio, G, Califano, A, Cameron, CJ, Cannistraci, CV, Carbone, A, Carlisle, AJ, Carninci, P, Carter, KW, Cesselli, D, Chang, JC, Chen, JC, Chen, Y, Chierici, M, Christodoulou, J, Ciani, Y, Clark, EL, Coskun, M, Dalby, M, Dalla, E, Daub, CO, Davis, CA, de Hoon, MJL, de Rie, D, Denisenko, E, Deplancke, B, Detmar, M, Deviatiiarov, R, Di Bernardo, D, Diehl, AD, Dieterich, LC (June 2021) Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nature Communications, 12 (1). ISSN 2041-1723 (In Press)

Rozowsky, Joel, Drenkow, Jorg, Yang, Yucheng, Gursoy, Gamze, Galeev, Timur, Borsari, Beatrice, Epstein, Charles, Xiong, Kun, Xu, Jinrui, Gao, Jiahao, Yu, Keyang, Berthel, Ana, Chen, Zhanlin, Navarro, Fabio, Liu, Jason, Sun, Maxwell, Wright, James, Chang, Justin, Cameron, Christopher, Shoresh, Noam, Gaskell, Elizabeth, Adrian, Jessika, Aganezov, Sergey, Balderrama-Gutierrez, Gabriela, Banskota, Samridhi, Corona, Guillermo, Chee, Sora, Chhetri, Surya, Martins, Gabriel, Danyko, Cassidy, Davis, Carrie, Farid, Daniel, Farrell, Nina, Gabdank, Idan, Gofin, Yoel, Gorkin, David, Gu, Mengting, Hecht, Vivian, Hitz, Benjamin, Issner, Robbyn, Kirsche, Melanie, Kong, Xiangmeng, Lam, Bonita, Li, Shantao, Li, Bian, Li, Tianxiao, Li, Xiqi, Lin, Khine, Luo, Ruibang, Mackiewicz, Mark, Moore, Jill, Mudge, Jonathan, Nelson, Nicholas, Nusbaum, Chad, Popov, Ioann, Pratt, Henry, Qiu, Yunjiang, Ramakrishnan, Srividya, Raymond, Joe, Salichos, Leonidas, Scavelli, Alexandra, Schreiber, Jacob, Sedlazeck, Fritz, See, Lei, Sherman, Rachel, Shi, Xu, Shi, Minyi, Sloan, Cricket, Strattan, Seth, Tan, Zhen, Tanaka, Forrest, Vlasova, Anna, Wang, Jun, Werner, Jonathan, Williams, Brian, Xu, Min, Yan, Chengfei, Yu, Lu, Zaleski, Christopher, Zhang, Jing, Cherry, Michael, Mendenhall, Eric, Noble, William, Weng, Zhiping, Levine, Morgan, Dobin, Alexander, Wold, Barbara, Mortazavi, Ali, Ren, Bing, Gillis, Jesse, Myers, Richard, Snyder, Michael, Choudhary, Jyoti, Milosavljevic, Aleksandar, Schatz, Michael, Guigo, Roderic, Bernstein, Bradley, Gingeras, Thomas, Gerstein, Mark (April 2021) Multi-tissue integrative analysis of personal epigenomes. bioRxiv. (Unpublished)

Dachet, Fabien, Brown, James B, Valyi-Nagy, Tibor, Narayan, Kunwar D, Serafini, Anna, Boley, Nathan, Gingeras, Thomas R, Celniker, Susan E, Mohapatra, Gayatry, Loeb, Jeffrey A (March 2021) Selective time-dependent changes in activity and cell-specific gene expression in human postmortem brain. Scientific Reports, 11 (1). p. 6078. ISSN 2045-2322

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

Nechooshtan, G., Yunusov, D., Chang, K., Gingeras, T. R. (August 2020) Processing by RNase 1 forms tRNA halves and distinct Y RNA fragments in the extracellular environment. Nucleic Acids Res, 48 (14). pp. 8035-8049. ISSN 0305-1048 (Print)0305-1048

Moore, J. E., Purcaro, M. J., Pratt, H. E., Epstein, C. B., Shoresh, N., Adrian, J., Kawli, T., Davis, C. A., Dobin, A., Kaul, R., Halow, J., Van Nostrand, E. L., Freese, P., Gorkin, D. U., Shen, Y., He, Y., Mackiewicz, M., Pauli-Behn, F., Williams, B. A., Mortazavi, A., Keller, C. A., Zhang, X. O., Elhajjajy, S. I., Huey, J., Dickel, D. E., Snetkova, V., Wei, X., Wang, X., Rivera-Mulia, J. C., Rozowsky, J., Zhang, J., Chhetri, S. B., Zhang, J., Victorsen, A., White, K. P., Visel, A., Yeo, G. W., Burge, C. B., Lécuyer, E., Gilbert, D. M., Dekker, J., Rinn, J., Mendenhall, E. M., Ecker, J. R., Kellis, M., Klein, R. J., Noble, W. S., Kundaje, A., Guigó, R., Farnham, P. J., Cherry, J. M., Myers, R. M., Ren, B., Graveley, B. R., Gerstein, M. B., Pennacchio, L. A., Snyder, M. P., Bernstein, B. E., Wold, B., Hardison, R. C., Gingeras, T. R., Stamatoyannopoulos, J. A., Weng, Z. (July 2020) Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature, 583 (7818). pp. 699-710. ISSN 0028-0836 (Print)0028-0836

Snyder, M. P., Gingeras, T. R., Moore, J. E., Weng, Z., Gerstein, M. B., Ren, B., Hardison, R. C., Stamatoyannopoulos, J. A., Graveley, B. R., Feingold, E. A., Pazin, M. J., Pagan, M., Gilchrist, D. A., Hitz, B. C., Cherry, J. M., Bernstein, B. E., Mendenhall, E. M., Zerbino, D. R., Frankish, A., Flicek, P., Myers, R. M. (July 2020) Perspectives on ENCODE. Nature, 583 (7818). pp. 693-698. ISSN 0028-0836 (Print)0028-0836

Breschi, A., Muñoz-Aguirre, M., Wucher, V., Davis, C. A., Garrido-Martín, D., Djebali, S., Gillis, J., Pervouchine, D. D., Vlasova, A., Dobin, A., Zaleski, C., Drenkow, J., Danyko, C., Scavelli, A., Reverter, F., Snyder, M. P., Gingeras, T. R., Guigó, R. (July 2020) A limited set of transcriptional programs define major cell types. Genome Res, 30 (7). pp. 1047-1059. ISSN 1088-9051 (Print)1088-9051

Wang, L., Lu, Z., Delabastide, M., Van Buren, P., Wang, X., Ghiban, C., Regulski, M., Drenkow, J., Xu, X., Ortiz-Ramirez, C., Marco, C.F., Goodwin, S., Dobin, A., Birnbaum, K. D., Jackson, D. P., Martienssen, R. A., McCombie, W. R., Micklos, D. A., Schatz, M. C., Ware, D. H., Gingeras, T. R. (March 2020) Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud. Frontiers in Plant Science, 11 (289). ISSN 1664-462X (Public Dataset)

Wang, Liya, Lu, Zhenyuan, delaBastide, Melissa, Van Buren, Peter, Wang, Xiaofei, Ghiban, Cornel, Regulski, Michael, Drenkow, Jorg, Xu, Xiaosa, Ortiz-Ramirez, Carlos, Fernandez-Marco, Cristina, Goodwin, Sara, Dobin, Alexander, Birnbaum, Kenneth, Jackson, David, Martienssen, Robert, McCombie, William, Micklos, David, Schatz, Michael, Ware, Doreen, Gingeras, Thomas (November 2019) Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud. BioRxiv. (Unpublished)

Rahmanian, S., Murad, R., Breschi, A., Zeng, W., Mackiewicz, M., Williams, B., Davis, C. A., Roberts, B., Meadows, S., Moore, D., Trout, D., Zaleski, C., Dobin, A., Sei, L. H., Drenkow, J., Scavelli, A., Gingeras, T. R., Wold, B. J., Myers, R. M., Guigo, R., Mortazavi, A. (November 2019) Dynamics of microRNA expression during mouse prenatal development. Genome Res, 29 (11). pp. 1900-1909. ISSN 1088-9051

Zhang, X. O., Gingeras, T. R., Weng, Z. (August 2019) Genome-wide analysis of polymerase III-transcribed Alu elements suggests cell-type-specific enhancer function. Genome Res, 29 (9). pp. 1402-1414. ISSN 1088-9051

Zhang, Q., Chao, T. C., Patil, V. S., Qin, Y., Tiwari, S. K., Chiou, J., Dobin, A., Tsai, C. M., Li, Z., Dang, J., Gupta, S., Urdahl, K., Nizet, V., Gingeras, T. R., Gaulton, K. J., Rana, T. M. (March 2019) The long noncoding RNA ROCKI regulates inflammatory gene expression. Embo j, 38 (8). Article number e100041. ISSN 0261-4189

Rahmanian, Sorena, Murad, Rabi, Breschi, Alessandra, Zeng, Weihua, Mackiewicz, Mark, Williams, Brian, Davis, Carrie, Roberts, Brian, Meadows, Sarah, Moore, Dianna, Trout, Diane, Zaleski, Chris, Dobin, Alex, Sei, Lei-Hoon, Drenkow, Jorg, Scavelli, Alex, Gingeras, Thomas, Wold, Barbara, Myers, Richard, Guigó, Roderic, Mortazavi, Ali (December 2018) Dynamics of microRNA expression during mouse prenatal development. BioRxiv. (Unpublished)

Ballouz, S., Dobin, A., Gingeras, T. R., Gillis, J. (May 2018) The fractured landscape of RNA-seq alignment: the default in our STARs. Nucleic Acids Res. ISSN 0305-1048

Li, K., Rodosthenous, R. S., Kashanchi, F., Gingeras, T., Gould, S. J., Kuo, L. S., Kurre, P., Lee, H., Leonard, J. N., Liu, H., Lombo, T. B., Momma, S., Nolan, J. P., Ochocinska, M. J., Pegtel, D. M., Sadovsky, Y., Sanchez-Madrid, F., Valdes, K. M., Vickers, K. C., Weaver, A. M., Witwer, K. W., Zeng, Y., Das, S., Raffai, R. L., Howcroft, T. K. (April 2018) Advances, challenges, and opportunities in extracellular RNA biology: insights from the NIH exRNA Strategic Workshop. JCI Insight, 3 (7). ISSN 2379-3708

Breschi, A., Davis, C., Djebali, S., Gillis, J., Pervouchine, D. D., Vlasova, A., Dobin, A., Zaleski, C., Drenkow, J., Danyko, C., Scavelli, A., Munoz, M., Garrido, D., Reverter, F., Gingeras, T. R., Guigo, R. (March 2018) The molecular basis of the cellular taxonomy of the human body. Human Genomics, 12 (Supple). Meeting Abstract A107. ISSN 1473-9542

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

Lagarde, J., Uszczynska-Ratajczak, B., Carbonell, S., Perez-Lluch, S., Abad, A., Davis, C., Gingeras, T. R., Frankish, A., Harrow, J., Guigo, R., Johnson, R. (December 2017) High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing. Nat Genet, 49 (12). pp. 1731-1740. ISSN 1061-4036

Noguchi, S., Arakawa, T., Fukuda, S., Furuno, M., Hasegawa, A., Hori, F., Ishikawa-Kato, S., Kaida, K., Kaiho, A., Kanamori-Katayama, M., Kawashima, T., Kojima, M., Kubosaki, A., Manabe, R. I., Murata, M., Nagao-Sato, S., Nakazato, K., Ninomiya, N., Nishiyori-Sueki, H., Noma, S., Saijyo, E., Saka, A., Sakai, M., Simon, C., Suzuki, N., Tagami, M., Watanabe, S., Yoshida, S., Arner, P., Axton, R. A., Babina, M., Baillie, J. K., Barnett, T. C., Beckhouse, A. G., Blumenthal, A., Bodega, B., Bonetti, A., Briggs, J., Brombacher, F., Carlisle, A. J., Clevers, H. C., Davis, C. A., Detmar, M., Dohi, T., Edge, A. S. B., Edinger, M., Ehrlund, A., Ekwall, K., Endoh, M., Enomoto, H., Eslami, A., Fagiolini, M., Fairbairn, L., Farach-Carson, M. C., Faulkner, G. J., Ferrai, C., Fisher, M. E., Forrester, L. M., Fujita, R., Furusawa, J. I., Geijtenbeek, T. B., Gingeras, T., Goldowitz, D., Guhl, S., Guler, R., Gustincich, S., Ha, T. J., Hamaguchi, M., Hara, M., Hasegawa, Y., Herlyn, M., Heutink, P., Hitchens, K. J., Hume, D. A., Ikawa, T., Ishizu, Y., Kai, C., Kawamoto, H., Kawamura, Y. I., Kempfle, J. S., Kenna, T. J., Kere, J., Khachigian, L. M., Kitamura, T., Klein, S., Klinken, S. P., Knox, A. J., Kojima, S., Koseki, H., Koyasu, S., Lee, W., Lennartsson, A., Mackay-Sim, A., Mejhert, N., Mizuno, Y., Morikawa, H., Morimoto, M., Moro, K., Morris, K. J., Motohashi, H. (August 2017) FANTOM5 CAGE profiles of human and mouse samples. Sci Data, 4. p. 170112. ISSN 2052-4463

Breschi, A., Gingeras, T. R., Guigo, R. (July 2017) Comparative transcriptomics in human and mouse. Nat Rev Genet, 18 (7). pp. 425-440. ISSN 1471-0056

Haas, Brian, Dobin, Alex, Stransky, Nicolas, Li, Bo, Yang, Xiao, Tickle, Timothy, Bankapur, Asma, Ganote, Carrie, Doak, Thomas, Pochet, Nathalie, Sun, Jing, Wu, Catherine, Gingeras, Thomas, Regev, Aviv (March 2017) STAR-Fusion: Fast and Accurate Fusion Transcript Detection from RNA-Seq. BioRxiv. (Unpublished)

Dobin, A., Gingeras, T. R. (April 2016) Optimizing RNA-Seq Mapping with STAR. Methods Mol Biol, 1415. pp. 245-262. ISSN 1940-6029 (Electronic)1064-3745 (Linking)

Breschi, A., Djebali, S., Gillis, J., Pervouchine, D. D., Dobin, A., Davis, C. A., Gingeras, T. R., Guigo, R. (2016) Gene-specific patterns of expression variation across organs and species. Genome Biol, 17 (1). p. 151. ISSN 1474-760X (Electronic)1474-7596 (Linking)

Hurst, Laurence D, Ghanbarian, Avazeh T, Forrest, Alistair RR, FANTOM consortium, Huminiecki, Lukasz (December 2015) The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome. PLoS Biology, 13 (12). e1002315. ISSN 1544-9173

Chakrabortty, S. K., Prakash, A., Nechooshtan, G., Hearn, S., Gingeras, T. R. (November 2015) Extracellular vesicle-mediated transfer of processed and functional RNY5 RNA. RNA, 21 (11). pp. 1966-1979. ISSN 1469-9001 (Electronic)1355-8382 (Linking)

Dobin, A., Gingeras, T. R. (September 2015) Mapping RNA-seq Reads with STAR. Curr Protoc Bioinformatics, 51. 11.14.1-11.14.19. ISSN 1934-340X (Electronic)1934-3396 (Linking)

Pervouchine, D. D., Djebali, S., Breschi, A., Davis, C. A., Barja, P. P., Dobin, A., Tanzer, A., Lagarde, J., Zaleski, C., See, L. H., Fastuca, M., Drenkow, J., Wang, H., Bussotti, G., Pei, B., Balasubramanian, S., Monlong, J., Harmanci, A., Gerstein, M., Beer, M. A., Notredame, C., Guigo, R., Gingeras, T. R. (January 2015) Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression. Nat Commun, 6. p. 5903. ISSN 2041-1723

Lin, S., Lin, Y., Nery, J. R., Urich, M. A., Breschi, A., Davis, C. A., Dobin, A., Zaleski, C., Beer, M. A., Chapman, W. C., Gingeras, T. R., Ecker, J. R., Snyder, M. P. (November 2014) Comparison of the transcriptional landscapes between human and mouse tissues. Proceedings of the National Academy of Sciences of the United States of America, 111 (48). pp. 17224-17229. ISSN 0027-8424

Cheng, Y., Ma, Z., Kim, B. H., Wu, W., Cayting, P., Boyle, A. P., Sundaram, V., Xing, X., Dogan, N., Li, J., Euskirchen, G., Lin, S., Lin, Y., Visel, A., Kawli, T., Yang, X., Patacsil, D., Keller, C. A., Giardine, B., Kundaje, A., Wang, T., Pennacchio, L. A., Weng, Z., Hardison, R. C., Snyder, M. P., Consortium, Mouse ENCODE (November 2014) Principles of regulatory information conservation between mouse and human. Nature, 515 (7527). pp. 371-5. ISSN 0028-0836

Yue, F., Cheng, Y., Breschi, A., Vierstra, J., Wu, W., Ryba, T., Sandstrom, R., Ma, Z., Davis, C., Pope, B. D., Shen, Y., Pervouchine, D. D., Djebali, S., Thurman, R. E., Kaul, R., Rynes, E., Kirilusha, A., Marinov, G. K., Williams, B. A., Trout, D., Amrhein, H., Fisher-Aylor, K., Antoshechkin, I., DeSalvo, G., See, L. H., Fastuca, M., Drenkow, J., Zaleski, C., Dobin, A., Prieto, P., Lagarde, J., Bussotti, G., Tanzer, A., Denas, O., Li, K., Bender, M. A., Zhang, M., Byron, R., Groudine, M. T., McCleary, D., Pham, L., Ye, Z., Kuan, S., Edsall, L., Wu, Y. C., Rasmussen, M. D., Bansal, M. S., Kellis, M., Keller, C. A., Morrissey, C. S., Mishra, T., Jain, D., Dogan, N., Harris, R. S., Cayting, P., Kawli, T., Boyle, A. P., Euskirchen, G., Kundaje, A., Lin, S., Lin, Y., Jansen, C., Malladi, V. S., Cline, M. S., Erickson, D. T., Kirkup, V. M., Learned, K., Sloan, C. A., Rosenbloom, K. R., Lacerda de Sousa, B., Beal, K., Pignatelli, M., Flicek, P., Lian, J., Kahveci, T., Lee, D., Kent, W. J., Ramalho Santos, M., Herrero, J., Notredame, C., Johnson, A., Vong, S., Lee, K., Bates, D., Neri, F., Diegel, M., Canfield, T., Sabo, P. J., Wilken, M. S., Reh, T. A., Giste, E., Shafer, A., Kutyavin, T., Haugen, E., Dunn, D., Reynolds, A. P., Neph, S., Humbert, R., Hansen, R. S., De Bruijn, M. (November 2014) A comparative encyclopedia of DNA elements in the mouse genome. Nature, 515 (7527). pp. 355-64. ISSN 0028-0836

Pervouchine, Dmitri, Djebali, Sarah, Breschi, Alessandra, Davis, Carrie, Prieto Barja, Pablo, Dobin, Alex, Tanzer, Andrea, Lagarde, Julien, Zaleski, Chris, See, Lei-Hoon, Fastuca, Meagan, Drenkow, Jorg, Wang, Huaien, Bussotti, Giovanni, Pei, Baikang, Balasubramanian, Suganthi, Monlong, Jean, Harmanci, Arif, Gerstein, Mark, Beer, Michael, Notredame, Cedric, Guigo, Roderic, Gingeras, Thomas (October 2014) Enhanced Transcriptome Maps from Multiple Mouse Tissues Reveal Evolutionary Constraint in Gene Expression for Thousands of Genes. BioRxiv. (Unpublished)

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

Kellis, M., Wold, B., Snyder, M. P., Bernstein, B. E., Kundaje, A., Marinov, G. K., Ward, L. D., Birney, E., Crawford, G. E., Dekker, J., Dunham, I., Elnitski, L. L., Farnham, P. J., Feingold, E. A., Gerstein, M., Giddings, M. C., Gilbert, D. M., Gingeras, T. R., Green, E. D., Guigo, R., Hubbard, T., Kent, J., Lieb, J. D., Myers, R. M., Pazin, M. J., Ren, B., Stamatoyannopoulos, J., Weng, Z., White, K. P., Hardison, R. C. (August 2014) Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease. Proceedings of the National Academy of Sciences of the United States of America, 111 (33). E3366-E3366. ISSN 10916490 (ISSN)

Bassett, A. R., Akhtar, A., Barlow, D. P., Bird, A. P., Brockdorff, N., Duboule, D., Ephrussi, A., Ferguson-Smith, A. C., Gingeras, T. R., Haerty, W., Higgs, D. R., Miska, E. A., Ponting, C. P. (August 2014) Considerations when investigating IncRNA function in vivo. Elife, 3. ISSN 2050-084X

Fagegaltier, D., Konig, A., Gordon, A., Lai, E. C., Gingeras, T. R., Hannon, G. J., Shcherbata, H. R. (July 2014) A Genome-Wide Survey of Sexually Dimorphic Expression of Drosophila miRNAs Identifies the Steroid Hormone-Induced miRNA let-7 as a Regulator of Sexual Identity. Genetics, 198 (2). pp. 647-668. ISSN 0016-6731

Abdelhamid, R. F., Plessy, C., Yamauchi, Y., Taoka, M., de Hoon, M., Gingeras, T. R., Isobe, T., Carninci, P. (July 2014) Multiplicity of 5' Cap Structures Present on Short RNAs. PLoS One, 9 (7). e102895. ISSN 1932-6203

Morikawa, H., Ohkura, N., Vandenbon, A., Itoh, M., Nagao-Sato, S., Kawaji, H., Lassmann, T., Carninci, P., Hayashizaki, Y., Forrest, A. R., Standley, D. M., Date, H., Sakaguchi, S., FANTOM Consortium (April 2014) Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation. Proceedings of the National Academy of Sciences of the United States of America, 111 (14). pp. 5289-94. ISSN 0027-8424

Gingeras, T. R. (April 2014) Conservation and novel functions of non-coding RNAs. Prion, 8 (Supple). pp. 8-9. ISSN 1933-68961933-690X

Kellis, M., Wold, B., Snyder, M. P., Bernstein, B. E., Kundaje, A., Marinov, G. K., Ward, L. D., Birney, E., Crawford, G. E., Dekker, J., Dunham, I., Elnitski, L. L., Farnham, P. J., Feingold, E. A., Gerstein, M., Giddings, M. C., Gilbert, D. M., Gingeras, T. R., Green, E. D., Guigo, R., Hubbard, T., Kent, J., Lieb, J. D., Myers, R. M., Pazin, M. J., Ren, B., Stamatoyannopoulos, J. A., Weng, Z. P., White, K. P., Hardison, R. C. (April 2014) Defining functional DNA elements in the human genome. Proceedings of the National Academy of Sciences of the United States of America, 111 (17). pp. 6131-6138. ISSN 0027-8424

Andersson, R., Gebhard, C., Miguel-Escalada, I., Hoof, I., Bornholdt, J., Boyd, M., Chen, Y., Zhao, X., Schmidl, C., Suzuki, T., Ntini, E., Arner, E., Valen, E., Li, K., Schwarzfischer, L., Glatz, D., Raithel, J., Lilje, B., Rapin, N., Bagger, F. O., Jorgensen, M., Andersen, P. R., Bertin, N., Rackham, O., Burroughs, A. M., Baillie, J. K., Ishizu, Y., Shimizu, Y., Furuhata, E., Maeda, S., Negishi, Y., Mungall, C. J., Meehan, T. F., Lassmann, T., Itoh, M., Kawaji, H., Kondo, N., Kawai, J., Lennartsson, A., Daub, C. O., Heutink, P., Hume, D. A., Jensen, T. H., Suzuki, H., Hayashizaki, Y., Muller, F., Forrest, A. R., Carninci, P., Rehli, M., Sandelin, A., FANTOM Consortium (March 2014) An atlas of active enhancers across human cell types and tissues. Nature, 507 (7493). pp. 455-61. ISSN 0028-0836

Forest, A. R. R., Kawaji, H., Rehli, M., Baillie, J. K., De Hoon, M. J. L., Haberle, V., Lassmann, T., Kulakovskiy, I. V., Lizio, M., Itoh, M., Andersson, R., Mungall, C. J., Meehan, T. F., Schmeier, S., Bertin, N., Jørgensen, M., Dimont, E., Arner, E., Schmidl, C., Schaefer, U., Medvedeva, Y. A., Plessy, C., Vitezic, M., Severin, J., Semple, C. A., Ishizu, Y., Young, R. S., Francescatto, M., Altschuler, I. A., Albanese, D., Altschule, G. M., Arakawa, T., Archer, J. A. C., Arner, P., Babina, M., Rennie, S., Balwierz, P. J., Beckhouse, A. G., Pradhan-Bhatt, S., Blake, J. A., Blumenthal, A., Bodega, B., Bonetti, A., Briggs, J., Brombacher, F., Burroughs, A. M., Califano, A., Cannistraci, C. V., Carbajo, D., Chen, Y., Chierici, M., Ciani, Y., Clevers, H. C., Dalla, E., Davis, C. A., Detmar, M., Diehl, A. D., Dohi, T., Drabløs, F., Edge, A. S. B., Edinger, M., Ekwall, K., Endoh, M., Enomoto, H., Fagiolini, M., Fairbairn, L., Fang, H., Farach-Carson, M. C., Faulkner, G. J., Favorov, A. V., Fisher, M. E., Frith, M. C., Fujita, R., Fukuda, S., Furlanello, C., Furuno, M., Furusawa, J. I., Geijtenbeek, T. B., Gibson, A. P., Gingeras, T., Goldowitz, D., Gough, J., Guhl, S., Guler, R., Gustincich, S., Ha, T. J., Hamaguchi, M., Hara, M., Harbers, M., Harshbarger, J., Hasegawa, A., Hasegawa, Y., Hashimoto, T., Herlyn, M., Hitchens, K. J., Sui, S. J. H., Hofmann, O. M., Hoof, I., Hori, F., Huminiecki, L. (March 2014) A promoter-level mammalian expression atlas. Nature, 507 (7493). pp. 462-470. ISSN 14764687

Brown, J. B., Boley, N., Eisman, R., May, G. E., Stoiber, M. H., Duff, M. O., Booth, B. W., Wen, J., Park, S., Suzuki, A. M., Wan, K. H., Yu, C., Zhang, D., Carlson, J. W., Cherbas, L., Eads, B. D., Miller, D., Mockaitis, K., Roberts, J., Davis, C. A., Frise, E., Hammonds, A. S., Olson, S., Shenker, S., Sturgill, D., Samsonova, A. A., Weiszmann, R., Robinson, G., Hernandez, J., Andrews, J., Bickel, P. J., Carninci, P., Cherbas, P., Gingeras, T. R., Hoskins, R. A., Kaufman, T. C., Lai, E. C., Oliver, B., Perrimon, N., Graveley, B. R., Celniker, S. E. (March 2014) Diversity and dynamics of the Drosophila transcriptome. Nature, 512 (7515). pp. 393-399. ISSN 0028-0836

Hasegawa, Y., Tang, D., Takahashi, N., Hayashizaki, Y., Forrest, A. R., Suzuki, H., FANTOM Consortium (2014) CCL2 enhances pluripotency of human induced pluripotent stem cells by activating hypoxia related genes. Sci Rep, 4. p. 5228. ISSN 2045-2322

Engström, P. G., Steijger, T., Sipos, B., Grant, G. R., Kahles, A., Rätsch, G., Goldman, N., Hubbard, T. J., Harrow, J., Guigó, R., Bertone, P., Alioto, T., Behr, J., Bohnert, R., Campagna, D., Davis, C. A., Dobin, A., Gingeras, T. R., Jean, G., Kosarev, P., Li, S., Liu, J., Mason, C. E., Molodtsov, V., Ning, Z., Ponstingl, H., Prins, J. F., Ribeca, P., Seledtsov, I., Solovyev, V., Valle, G., Vitulo, N., Wang, K., Wu, T. D., Zeller, G. (December 2013) Systematic evaluation of spliced alignment programs for RNA-seq data. Nature Methods, 10 (12). pp. 1185-1191. ISSN 15487091 (ISSN)

Dobin, Alexander, Gingeras, Thomas (November 2013) Comment on TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions by Kim et al. BioRxiv. (Unpublished)

Steijger, T., Abril, J. F., Engström, P. G., Kokocinski, F., Akerman, M., Alioto, T., Ambrosini, G., Antonarakis, S. E., Behr, J., Bertone, P., Bohnert, R., Bucher, P., Cloonan, N., Derrien, T., Djebali, S., Du, J., Dudoit, S., Gerstein, M., Gingeras, T. R., Gonzalez, D., Grimmond, S. M., Guigó, R., Habegger, L., Harrow, J., Hubbard, T. J., Iseli, C., Jean, G., Kahles, A., Lagarde, J., Leng, J., Lefebvre, G., Lewis, S., Mortazavi, A., Niermann, P., Rätsch, G., Reymond, A., Ribeca, P., Richard, H., Rougemont, J., Rozowsky, J., Sammeth, M., Sboner, A., Schulz, M. H., Searle, S. M. J., Solorzano, N. D., Solovyev, V., Stanke, M., Stevenson, B. J., Stockinger, H., Valsesia, A., Weese, D., White, S., Wold, B. J., Wu, J., Wu, T. D., Zeller, G., Zerbino, D., Zhang, M. Q. (November 2013) Assessment of transcript reconstruction methods for RNA-seq. Nature Methods, 10 (12). pp. 1177-1184. ISSN 15487091 (ISSN)

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)

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

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)

Livyatan, I., Harikumar, A., Nissim-Rafinia, M., Duttagupta, R., Gingeras, T. R., Meshorer, E. (2013) Non-polyadenylated transcription in embryonic stem cells reveals novel non-coding RNA related to pluripotency and differentiation. Nucleic Acids Research, 41 (12). pp. 6300-6315. ISSN 03051048 (ISSN)

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)

Cheng, C., Alexander, R., Min, R. Q., Leng, J., Yip, K. Y., Rozowsky, J., Yan, K. K., Dong, X. J., Djebali, S., Ruan, Y. J., Davis, C. A., Carninci, P., Lassman, T., Gingeras, T. R., Guigo, R., Birney, E., Weng, Z. P., Snyder, M., Gerstein, M. (September 2012) Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Research, 22 (9). pp. 1658-1667. ISSN 1088-9051

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

Dong, X., Greven, M. C., Kundaje, A., Djebali, S., Brown, J. B., Cheng, C., Gingeras, T. R., Gerstein, M., Guigó, R., Birney, E., Weng, Z. (September 2012) Modeling gene expression using chromatin features in various cellular contexts. Genome Biology, 13 (9).

Tilgner, H., Knowles, D. G., Johnson, R., Davis, C. A., Chakrabortty, S., Djebali, S., Curado, J., Snyder, M., Gingeras, T. R., Guigo, R. (September 2012) Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for IncRNAs. Genome Research, 22 (9). pp. 1616-1625. ISSN 1088-9051

Derrien, T., Johnson, R., Bussotti, G., Tanzer, A., Djebali, S., Tilgner, H., Guernec, G., Martin, D., Merkel, A., Knowles, D. G., Lagarde, J., Veeravalli, L., Ruan, X. A., Ruan, Y. J., Lassmann, T., Carninci, P., Brown, J. B., Lipovich, L., Gonzalez, J. M., Thomas, M., Davis, C. A., Shiekhattar, R., Gingeras, T. R., Hubbard, T. J., Notredame, C., Harrow, J., Guigo, R. (September 2012) The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression. Genome Research, 22 (9 Spe). pp. 1775-1789. ISSN 1088-9051

Stamatoyannopoulos, J. A., Snyder, M., Hardison, R., Ren, B., Gingeras, T., Gilbert, D. M., Groudine, M., Bender, M., Kaul, R., Canfield, T., Giste, E., Johnson, A., Zhang, M., Balasundaram, G., Byron, R., Roach, V., Sabo, P. J., Sandstrom, R., Stehling, A. S., Thurman, R. E., Weissman, S. M., Cayting, P., Hariharan, M., Lian, J., Cheng, Y., Landt, S. G., Ma, Z., Wold, B. J., Dekker, J., Crawford, G. E., Keller, C. A., Wu, W., Morrissey, C., Kumar, S. A., Mishra, T., Jain, D., Byrska-Bishop, M., Blankenberg, D., Lajoiel, B. R., Jain, G., Sanyal, A., Chen, K. B., Denas, O., Taylor, J., Blobel, G. A., Weiss, M. J., Pimkin, M., Deng, W., Marinov, G. K., Williams, B. A., Fisher-Aylor, K. I., Desalvo, G., Kiralusha, A., Trout, D., Amrhein, H., Mortazavi, A., Edsall, L., McCleary, D., Kuan, S., Shen, Y., Yue, F., Ye, Z., Davis, C. A., Zaleski, C., Jha, S., Xue, C., Dobin, A., Lin, W., Fastuca, M., Wang, H., Guigo, R., Djebali, S., Lagarde, J., Ryba, T., Sasaki, T., Malladi, V. S., Cline, M. S., Kirkup, V. M., Learned, K., Rosenbloom, K. R., Kent, W. J., Feingold, E. A., Good, P. J., Pazin, M., Lowdon, R. F., Adams, L. B. (August 2012) An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biology, 13 (8).

Lasa, I., Toledo-Arana, A., Gingeras, T. R. (August 2012) An effort to make sense of antisense transcription in bacteria. RNA Biology, 9 (8). pp. 1039-1044. ISSN 1547-6286

Kowalczyk, M. S., Higgs, D. R., Gingeras, T. R. (February 2012) Molecular biology: RNA discrimination. Nature, 482 (7385). pp. 310-1. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Gingeras, T. R. (February 2012) Patience is a virtue. Nature, 482 (7385). pp. 310-311. ISSN 0028-0836

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)

Li, G., Ruan, X. A., Auerbach, R. K., Sandhu, K. S., Zheng, M., Wang, P. C., Poh, H. M., Goh, Y., Lim, J., Zhang, J., Sim, H. S., Peh, S. Q., Mulawadi, F. H., Ong, C. T., Orlov, Y. L., Hong, S., Zhang, Z., Landt, S. G., Raha, D., Euskirchen, G., Wei, C-L., Ge, W., Wang, H., Davis, C. A., Fisher-Aylor, K. I., Mortazavi, A., Gerstein, M., Gingeras, T. R., Wold, B., Sun, Yi, Fullwood, M. J., Cheung, E., Liu, E., Sung, W.-K., Snyder, M., Ruan, Y. (2012) Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation. Cell, 148 (1–2). pp. 84-98. ISSN 0092-8674

Lasa, I., Toledo-Arana, A., Dobin, A., Villanueva, M., de los Mozos, I. R., Vergara-Irigaray, M., Segura, V., Fagegaltier, D., Penades, J. R., Valle, J., Solano, C., Gingeras, T. R. (December 2011) Genome-wide antisense transcription drives mRNA processing in bacteria. Proceedings of the National Academy of Sciences of the United States of America, 108 (50). pp. 20172-20177. ISSN 0027-8424

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)

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)

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)

Graveley, B. R., Brooks, A. N., Carlson, J., Duff, M. O., Landolin, J. M., Yang, L., Artieri, C. G., van Baren, M. J., Boley, N., Booth, B. W., Brown, J. B., Cherbas, L., Davis, C. A., Dobin, A., Li, R. H., Lin, W., Malone, J. H., Mattiuzzo, N. R., Miller, D., Sturgill, D., Tuch, B. B., Zaleski, C., Zhang, D. Y., Blanchette, M., Dudoit, S., Eads, B., Green, R. E., Hammonds, A., Jiang, L. C., Kapranov, P., Langton, L., Perrimon, N., Sandler, J. E., Wan, K. H., Willingham, A., Zhang, Y., Zou, Y., Andrews, J., Bickel, P. J., Brenner, S. E., Brent, M. R., Cherbas, P., Gingeras, T. R., Hoskins, R. A., Kaufman, T. C., Oliver, B., Celniker, S. E. (March 2011) The developmental transcriptome of Drosophila melanogaster. Nature, 471 (7339). pp. 473-479. ISSN 0028-0836

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)

Cherbas, L., Willingham, A., Zhang, D., Yang, L., Zou, Y., Eads, B. D., Carlson, J. W., Landolin, J. M., Kapranov, P., Dumais, J., Samsonova, A., Choi, J. H., Roberts, J., Davis, C. A., Tang, H., Van Baren, M. J., Ghosh, S., Dobin, A., Bell, K. G., Lin, W., Langton, L., Duff, M. O., Tenney, A. E., Zaleski, C., Brent, M. R., Hoskins, R. A., Kaufman, T. C., Andrews, J., Graveley, B. R., Perrimon, N., Celniker, S. E., Gingeras, T. R., Cherbas, P. (2011) The transcriptional diversity of 25 Drosophila cell lines. Genome Research, 21 (2). pp. 301-314. ISSN 10889051 (ISSN) (Public Dataset)

Roy, S., Ernst, J., Kharchenko, P. V., Kheradpour, P., Negre, N., Eaton, M. L., Landolin, J. M., Bristow, C. A., Ma, L. J., Lin, M. F., Washietl, S., Arshinoff, B. I., Ay, F., Meyer, P. E., Robine, N., Washington, N. L., Di Stefano, L., Berezikov, E., Brown, C. D., Candeias, R., Carlson, J. W., Carr, A., Jungreis, I., Marbach, D., Sealfon, R., Tolstorukov, M. Y., Will, S., Alekseyenko, A. A., Artieri, C., Booth, B. W., Brooks, A. N., Dai, Q., Davis, C. A., Duff, M. O., Feng, X., Gorchakov, A. A., Gu, T. T., Henikoff, J. G., Kapranov, P., Li, R. H., MacAlpine, H. K., Malone, J., Minoda, A., Nordman, J., Okamura, K., Perry, M., Powell, S. K., Riddle, N. C., Sakai, A., Samsonova, A., Sandler, J. E., Schwartz, Y. B., Sher, N., Spokony, R., Sturgill, D., van Baren, M., Wan, K. H., Yang, L., Yu, C., Feingold, E., Good, P., Guyer, M., Lowdon, R., Ahmad, K., Andrews, J., Berger, B., Brenner, S. E., Brent, M. R., Cherbas, L., Elgin, S. C. R., Gingeras, T. R., Grossman, R., Hoskins, R. A., Kaufman, T. C., Kent, W., Kuroda, M. I., Orr-Weaver, T., Perrimon, N., Pirrotta, V., Posakony, J. W., Ren, B., Russell, S., Cherbas, P., Graveley, B. R., Lewis, S., Micklem, G., Oliver, B., Park, P. J., Celniker, S. E., Henikoff, S., Karpen, G. H., Lai, E. C., MacAlpine, D. M., Stein, L. D., White, K. P., Kellis, M. (December 2010) Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE. Science, 330 (6012). pp. 1787-1797. ISSN 0036-8075

Plessy, C., Bertin, N., Takahashi, H., Simone, R., Salimullah, Md, Lassmann, T., Vitezic, M., Severin, J., Olivarius, S., Lazarevic, D., Hornig, N., Orlando, V., Bell, I., Gao, H., Dumais, J., Kapranov, P., Wang, H., Davis, C. A., Gingeras, T. R., Kawai, J., Daub, C. O., Hayashizaki, Y., Gustincich, S., Carninci, P. (June 2010) Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Nature Methods, 7 (7). pp. 528-34. ISSN 15487091 (ISSN)

Amid, C., Frankish, A., Aken, B., Ezkurdia, I., Kokocinsk, F., Gilbert, J., White, S., Carninci, P., Gingeras, T. R., Guigo, R., Searle, S., Tress, M. L., Harrow, J., Hubbard, T. (2010) From identification to validation to gene count. Genome Biology, 11 (Suppl ). ISSN 1474-760X

Yang, A., Zhu, Z., Kettenbach, A., Kapranov, P., McKeon, F., Gingeras, T. R., Struhl, K. (2010) Genome-wide mapping indicates that p73 and p63 Co-occupy target sites and have similar DNA-binding profiles in vivo. PLoS ONE, 5 (7). ISSN 19326203 (ISSN)

Ramani, A. K., Nelson, A. C., Kapranov, P., Bell, I., Gingeras, T. R., Fraser, A. G. (September 2009) High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans. Genome Biology, 10 (9). R101. ISSN 1474-7596

Gingeras, T. R. (September 2009) Implications of chimaeric non-co-linear transcripts. Nature, 461 (7261). pp. 206-11. ISSN 1476-4687 (Electronic)

Makrythanasis, P., Kapranov, P., Bartoloni, L., Reymond, A., Deutsch, S., Guigo, R., Denoeud, F., Drenkow, J., Rossier, C., Ariani, F., Capra, V., Excoffier, L., Renieri, A., Gingeras, T. R., Antonarakis, S. E. (September 2009) Variation in novel exons (RACEfrags) of the MECP2 gene in Rett syndrome patients and controls. Human Mutation, 30 (9). E866-79. ISSN 1059-7794

Celniker, S. E., Dillon, L. A., Gerstein, M. B., Gunsalus, K. C., Henikoff, S., Karpen, G. H., Kellis, M., Lai, E. C., Lieb, J. D., MacAlpine, D. M., Micklem, G., Piano, F., Snyder, M., Stein, L. D., White, K. P., Waterston, R. H. (June 2009) Unlocking the secrets of the genome. Nature, 459 (7249). pp. 927-30. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Gingeras, T. R. (April 2009) Missing lincs in the transcriptome. Nature Biotechnology, 27 (4). pp. 346-347. ISSN 1087-0156

Zhang, X., Lian, Z., Padden, C., Gerstein, M. B., Rozowsky, J., Snyder, M., Gingeras, T. R., Kapranov, P., Weissman, S. M., Newburger, P. E. (March 2009) A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster. Blood, 113 (11). pp. 2526-34. ISSN 1528-0020 (Electronic)

Fejes-Toth, K., Sotirova, V., Sachidanandam, R., Assaf, G., Hannon, G. J., Kapranov, P., Foissac, S., Willingham, A. T., Duttagupta, R., Dumais, E., Gingeras, T. R. (February 2009) Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs. Nature, 457 (7232). pp. 1028-1032. ISSN 0028-0836

Ramani, A. K., Nelson, A. C., Kapranov, P., Bell, I., Gingeras, T. R., Fraser, A. G. (2009) High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans. Genome Biology, 10 (9). R101. ISSN 1465-6906

Rada-Iglesias, A., Ameur, A., Kapranov, P., Enroth, S., Komorowski, J., Gingeras, T. R., Wadelius, C. (March 2008) Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders. Genome Research, 18 (3). pp. 380-92. ISSN 10889051 (ISSN)

Djebali, S., Kapranov, P., Foissac, S., Lagarde, J., Reymond, A., Ucla, C., Wyss, C., Drenkow, J., Dumais, E., Murray, R. R., Lin, C., Szeto, D., Denoeud, F., Calvo, M., Frankish, A., Harrow, J., Makrythanasis, P., Vidal, M., Salehi-Ashtiani, K., Antonarakis, S. E., Gingeras, T. R., Guigo, R. (2008) Efficient targeted transcript discovery via array-based normalization of RACE libraries. Nature Methods, 5 (7). pp. 629-35. ISSN 15487091 (ISSN) (Public Dataset)

Efroni, S., Duttagupta, R., Cheng, J., Dehghani, H., Hoeppner, D. J., Dash, C., Bazett-Jones, D. P., Le Grice, S., McKay, R. D. G., Buetow, K. H., Gingeras, T. R., Misteli, T., Meshorer, E. (2008) Global Transcription in Pluripotent Embryonic Stem Cells. Cell Stem Cell, 2 (5). pp. 437-447. ISSN 19345909 (ISSN) (Public Dataset)

Gingeras, T. R. (2008) Mapping the strand-specific transcriptome of fission yeast. Nature Genetics, 40 (8). pp. 935-936. ISSN 1061-4036

Jones, P. A., Archer, T. K., Baylin, S. B., Beck, S., Berger, S., Bernstein, B. E., Carpten, J. D., Clark, S. J., Costello, J. F., Doerge, R. W., Esteller, M., Feinberg, A. P., Gingeras, T. R., Greally, J. M., Henikoff, S., Herman, J. G., Jackson-Grusby, L., Jenuwein, T., Jirtle, R. L., Kim, Y. J., Laird, P. W., Lim, B., Martienssen, R., Polyak, K., Stunnenberg, H., Tlsty, T. D., Tycko, B., Ushijima, T., Zhu, J., Pirrotta, V., Allis, C. D., Elgin, S. C., Rine, J., Wu, C. (2008) Moving AHEAD with an international human epigenome project. Nature, 454 (7205). pp. 711-715. ISSN 00280836 (ISSN)

Johnson, D. S., Li, W., Gordon, D. B., Bhattacharjee, A., Curry, B., Ghosh, J., Brizuela, L., Carroll, J. S., Brown, M., Flicek, P., Koch, C. M., Dunham, I., Bieda, M., Xu, X., Farnham, P. J., Kapranov, P., Nix, D. A., Gingeras, T. R., Zhang, X., Holster, H., Jiang, N., Green, R. D., Song, J. S., McCuine, S. A., Anton, E., Nguyen, L., Trinklein, N. D., Ye, Z., Ching, K., Hawkins, D., Ren, B., Scacheri, P. C., Rozowsky, J., Karpikov, A., Euskirchen, G., Weissman, S., Gerstein, M., Snyder, M., Yang, A., Moqtaderi, Z., Hirsch, H., Shulha, H. P., Fu, Y., Weng, Z., Struhl, K., Myers, R. M., Lieb, J. D., Liu, X. S. (2008) Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Research, 18 (3). pp. 393-403. ISSN 10889051 (ISSN) (Public Dataset)

Li, X. Y., MacArthur, S., Bourgon, R., Nix, D., Pollard, D. A., Iyer, V. N., Hechmer, A., Simirenko, L., Stapleton, M., Luengo Hendriks, C. L., Hou, C. C., Ogawa, N., Inwood, W., Sementchenko, V., Beaton, A., Weiszmann, R., Celniker, S. E., Knowles, D. W., Gingeras, T. R., Speed, T. P., Eisen, M. B., Biggin, M. D. (2008) Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biology, 6 (2). 0365-0388. ISSN 1544-9173

Sasaki, D., Kondo, S., Maeda, N., Gingeras, T. R., Hasegawa, Y., Hayashizaki, Y. (2007) Characteristics of oligonucleotide tiling arrays measured by hybridizing full-length cDNA clones: Causes of signal variation and false positive signals. Genomics, 89 (4). pp. 541-551. ISSN 08887543 (ISSN)

Rozowsky, J. S., Newburger, D., Sayward, F., Wu, J., Jordan, G., Korbel, J. O., Nagalakshmi, U., Yang, J., Zheng, D., Guigó, R., Gingeras, T. R., Weissman, S., Miller, P., Snyder, M., Gerstein, M. B. (2007) The DART classification of unannotated transcription within the ENCODE regions: Associating transcription with known and novel loci. Genome Research, 17 (6). pp. 732-745. ISSN 10889051 (ISSN)

Ghosh, S., Hirsch, H. A., Sekinger, E. A., Kapranov, P., Struhl, K., Gingeras, T. R. (2007) Differential analysis for high density tiling microarray data. BMC Bioinformatics, 8. ISSN 14712105 (ISSN)

Kapranov, P., Willingham, A. T., Gingeras, T. R. (2007) Genome-wide transcription and the implications for genomic organization. Nature Reviews Genetics, 8 (6). pp. 413-423. ISSN 14710056 (ISSN)

Birney, E., Stamatoyannopoulos, J. A., Dutta, A., Guigó, R., Gingeras, T. R., Margulies, E. H., Weng, Z., Snyder, M., Dermitzakis, E. T., Thurman, R. E., Kuehn, M. S., Taylor, C. M., Neph, S., Koch, C. M., Asthana, S., Malhotra, A., Adzhubei, I., Greenbaum, J. A., Andrews, R. M., Flicek, P., Boyle, P. J., Cao, H., Carter, N. P., Clelland, G. K., Davis, S., Day, N., Dhami, P., Dillon, S. C., Dorschner, M. O., Fiegler, H., Giresi, P. G., Goldy, J., Hawrylycz, M., Haydock, A., Humbert, R., James, K. D., Johnson, B. E., Johnson, E. M., Frum, T. T., Rosenzweig, E. R., Karnani, N., Lee, K., Lefebvre, G. C., Navas, P. A., Neri, F., Parker, S. C. J., Sabo, P. J., Sandstrom, R., Shafer, A., Vetrie, D., Weaver, M., Wilcox, S., Yu, M., Collins, F. S., Dekker, J., Lieb, J. D., Tullius, T. D., Crawford, G. E., Sunyaev, S., Noble, W. S., Dunham, I., Denoeud, F., Reymond, A., Kapranov, P., Rozowsky, J., Zheng, D., Castelo, R., Frankish, A., Harrow, J., Ghosh, S., Sandelin, A., Hofacker, I. L., Baertsch, R., Keefe, D., Dike, S., Cheng, J., Hirsch, H. A., Sekinger, E. A., Lagarde, J., Abril, J. F., Shahab, A., Flamm, C., Fried, C., Hackermüller, J., Hertel, J., Lindemeyer, M., Missal, K., Tanzer, A., Washietl, S., Korbel, J., Emanuelsson, O., Pedersen, J. S., Holroyd, N., Taylor, R., Swarbreck, D., Matthews, N., Dickson, M. C., Thomas, D. J., Weirauch, M. T., Gilbert, J., Siepel, A. C. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447 (7146). pp. 799-816. ISSN 00280836 (ISSN)

Gingeras, T. R. (2007) Origin of phenotypes: Genes and transcripts. Genome Research, 17 (6). pp. 682-690. ISSN 10889051 (ISSN)

Denoeud, F., Kapranov, P., Ucla, C., Frankish, A., Castelo, R., Drenkow, J., Lagarde, J., Alioto, T., Manzano, C., Chrast, J., Dike, S., Wyss, C., Henrichsen, C. N., Holroyd, N., Dickson, M. C., Taylor, R., Hance, Z., Foissac, S., Myers, R. M., Rogers, J., Hubbard, T., Harrow, J., Guigó, R., Gingeras, T. R., Antonarakis, S. E., Reymond, A. (2007) Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Research, 17 (6). pp. 746-759. ISSN 10889051 (ISSN) (Public Dataset)

Zheng, D., Frankish, A., Baertsch, R., Kapranov, P., Reymond, A., Siew, W. C., Lu, Y., Denoeud, F., Antonarakis, S. E., Snyder, M., Ruan, Y., Wei, C. L., Gingeras, T. R., Guigó, R., Harrow, J., Gerstein, M. B. (2007) Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution. Genome Research, 17 (6). pp. 839-851. ISSN 10889051 (ISSN)

Kapranov, P., Cheng, J., Dike, S., Nix, D. A., Duttagupta, R., Willingham, A. T., Stadler, P. F., Hertel, J., Hackermüller, J., Hofacker, I. L., Bell, I., Cheung, E., Drenkow, J., Dumais, E., Patel, S., Helt, G., Ganesh, M., Ghosh, S., Piccolboni, A., Sementchenko, V., Tammana, H., Gingeras, T. R. (2007) RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science, 316 (5830). pp. 1484-1488. ISSN 00368075 (ISSN)

Washietl, S., Pedersen, J. S., Korbel, J. O., Stocsits, C., Gruber, A. R., Hackermüller, J., Hertel, J., Lindemeyer, M., Reiche, K., Tanzer, A., Ucla, C., Wyss, C., Antonarakis, S. E., Denoeud, F., Lagarde, J., Drenkow, J., Kapranov, P., Gingeras, T. R., Guigó, R., Snyder, M., Gerstein, M. B., Reymond, A., Hofacker, I. L., Stadler, P. F. (2007) Structured RNAs in the ENCODE selected regions of the human genome. Genome Research, 17 (6). pp. 852-864. ISSN 10889051 (ISSN) (Public Dataset)

Carroll, J. S., Meyer, C. A., Song, J., Li, W., Geistlinger, T. R., Eeckhoute, J., Brodsky, A. S., Keeton, E. K., Fertuck, K. C., Hall, G. F., Wang, Q., Bekiranov, S., Sementchenko, V., Fox, E. A., Silver, P. A., Gingeras, T. R., Liu, X. S., Brown, M. (November 2006) Genome-wide analysis of estrogen receptor binding sites. Nature Genetics, 38 (11). pp. 1289-1297. ISSN 1061-4036

Ghosh, S., Hirsch, H. A., Sekinger, E., Struhl, K., Gingeras, T. R. (October 2006) Rank-statistics based enrichment-site prediction algorithm developed for chromatin immunoprecipitation on chip experiments. BMC Bioinformatics, 7. ISSN 1471-2105

Manak, J. R., Dike, S., Sementchenko, V., Kapranov, P., Biemar, F., Long, J., Cheng, J., Bell, I., Ghosh, S., Piccolboni, A., Gingeras, T. R. (2006) Biological function of unannotated transcription during the early development of Drosophila melanogaster. Nature Genetics, 38 (10). pp. 1151-1158. ISSN 10614036 (ISSN) (Public Dataset)

Liu, W., Putnam, A. L., Xu-yu, Z., Szot, G. L., Lee, M. R., Zhu, S., Gottlieb, P. A., Kapranov, P., Gingeras, T. R., De St. Groth, B. F., Clayberger, C., Soper, D. M., Ziegler, S. F., Bluestone, J. A. (2006) CD127 expression inversely correlates with FoxP3 and suppressive function of human CD4+ T reg cells. Journal of Experimental Medicine, 203 (7). pp. 1701-1711. ISSN 00221007 (ISSN)

Guigó, R., Flicek, P., Abril, J. F., Reymond, A., Lagarde, J., Denoeud, F., Antonarakis, S., Ashburner, M., Bajic, V. B., Birney, E., Castelo, R., Eyras, E., Ucla, C., Gingeras, T. R., Harrow, J., Hubbard, T., Lewis, S. E., Reese, M. G. (2006) EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biology, 7 Supp. S2.1-31. ISSN 14656914 (ISSN)

Zhang, M., Drenkow, J., Lankford, C. S. R., Frucht, D. M., Rabin, R. L., Gingeras, T. R., Venkateshan, C., Schwartzkopff, F., Clouse, K. A., Dayton, A. I. (2006) HIV regulation of the IL-7R: A viral mechanism for enhancing HIV-1 replication in human macrophages in vitro. Journal of Leukocyte Biology, 79 (6). pp. 1328-1338. ISSN 07415400 (ISSN)

Schumacher, A., Kapranov, P., Kaminsky, Z., Flanagan, J., Assadzadeh, A., Yau, P., Virtanen, C., Winegarden, N., Cheng, J., Gingeras, T., Petronis, A. (2006) Microarray-based DNA methylation profiling: Technology and applications. Nucleic Acids Research, 34 (2). pp. 528-542. ISSN 03051048 (ISSN)

Rozowsky, J., Wu, J., Lian, Z., Nagalakshmi, U., Korbel, J. O., Kapranov, P., Zheng, D., Dyke, S., Newburger, P., Miller, P., Gingeras, T. R., Weissman, S., Gerstein, M., Snyder, M. (2006) Novel transcribed regions in the human genome. Cold Spring Harbor Symposia on Quantitative Biology, 71. pp. 111-116. ISSN 00917451 (ISSN)

Yang, A., Zhu, Z., Kapranov, P., McKeon, F., Church, G. M., Gingeras, T. R., Struhl, K. (2006) Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells. Molecular Cell, 24 (4). pp. 593-602. ISSN 10972765 (ISSN)

Willingham, A. T., Gingeras, T. R. (2006) TUF Love for "Junk" DNA. Cell, 125 (7). pp. 1215-1220. ISSN 00928674 (ISSN)

Willingham, A. T., Dike, S., Cheng, J., Manak, J. R., Bell, I., Cheung, E., Drenkow, J., Dumais, E., Duttagupta, R., Ganesh, M., Ghosh, S., Helt, G., Nix, D., Piccolboni, A., Sementchenko, V., Tammana, H., Kapranov, P., Gingeras, T. R. (2006) Transcriptional landscape of the human and fly genomes: Nonlinear and multifunctional modular model of transcriptomes. Cold Spring Harbor Symposia on Quantitative Biology, 71. pp. 101-110. ISSN 00917451 (ISSN)

Gingeras, T. R. (2006) The multitasking genome. Nature Genetics, 38 (6). pp. 608-609. ISSN 10614036 (ISSN)

Kapranov, P., Drenkow, J., Cheng, J., Long, J., Helt, G., Dike, S., Gingeras, T. R. (2005) Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome Research, 15 (7). pp. 987-997. ISSN 10889051 (ISSN) (Public Dataset)

Gingeras, T. R., Higuchi, R., Kricka, L. J., Lo, Y. M. D., Wittwer, C. T. (2005) Fifty years of molecular (DNA/RNA) diagnostics. Clinical Chemistry, 51 (3). pp. 661-671. ISSN 00099147 (ISSN)

Bernstein, Bradley E., Kamal, Michael, Lindblad-Toh, Kerstin, Bekiranov, Stefan, Bailey, Dione K., Huebert, Dana J., McMahon, Scott, Karlsson, Elinor K., Kulbokas Iii, Edward J., Gingeras, Thomas R., Schreiber, Stuart L., Lander, Eric S. (2005) Genomic Maps and Comparative Analysis of Histone Modifications in Human and Mouse. Cell, 120 (2). pp. 169-181. ISSN 0092-8674

Jeon, Y., Bekiranov, S., Karnani, N., Kapranov, P., Ghosh, S., MacAlpine, D., Lee, C., Deog, S. H., Gingeras, T. R., Dutta, A. (2005) Temporal profile of replication of human chromosomes. Proceedings of the National Academy of Sciences of the United States of America, 102 (18). pp. 6419-6424. ISSN 00278424 (ISSN)

Cheng, J., Kapranov, P., Drenkow, J., Dike, S., Brubaker, S., Patel, S., Long, J., Stern, D., Tammana, H., Helt, G., Sementchenko, V., Piccolboni, A., Bekiranov, S., Bailey, D. K., Ganesh, M., Ghosh, S., Bell, I., Gerhard, D. S., Gingeras, T. R. (2005) Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science, 308 (5725). pp. 1149-1154. ISSN 00368075 (ISSN) (Public Dataset)

Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M. C., Maeda, N., Oyama, R., Ravasi, T., Lenhard, B., Wells, C., Kodzius, R., Shimokawa, K., Bajic, V. B., Brenner, S. E., Batalov, S., Forrest, A. R. R., Zavolan, M., Davis, M. J., Wilming, L. G., Aidinis, V., Allen, J. E., Ambesi-Impiombato, A., Apweiler, R., Aturaliya, R. N., Bailey, T. L., Bansal, M., Baxter, L., Beisel, K. W., Bersano, T., Bono, H., Chalk, A. M., Chiu, K. P., Choudhary, V., Christoffels, A., Clutterbuck, D. R., Crowe, M. L., Dalla, E., Dalrymple, B. P., de Bono, B., della Gatta, G., di Bernardo, D., Down, T., Engstrom, P., Fagiolini, M., Faulkner, G., Fletcher, C. F., Fukushima, T., Furuno, M., Futaki, S., Gariboldi, M., Georgii-Hemming, P., Gingeras, T. R., Gojobori, T., Green, R. E., Gustincich, S., Harbers, M., Hayashi, Y., Hensch, T. K., Hirokawa, N., Hill, D., Huminiecki, L., Iacono, M., Ikeo, K., Iwama, A., Ishikawa, T., Jakt, M., Kanapin, A., Katoh, M., Kawasawa, Y., Kelso, J., Kitamura, H., Kitano, H., Kollias, G., Krishnan, S. P. T., Kruger, A. F., Kummerfeld, S. K., Kurochkin, I. V., Lareau, L. F., Lazarevic, D., Lipovich, L., Liu, J., Liuni, S., McWilliam, S., Madan Babu, M., Madera, M., Marchionni, L., Matsuda, H., Matsuzawa, S., Miki, H., Mignone, F., Miyake, S., Morris, K., Mottagui-Tabar, S., Mulder, N., Nakano, N., Nakauchi, H., Ng, P., Nilsson, R., Nishiguchi, S., Nishikawa, S. (2005) The transcriptional landscape of the mammalian genome. Science, 309 (5740). pp. 1559-1563. ISSN 10959203 (ISSN)

Lian, Z., Lian, J., Urban, A. E., Colangelo, C., Kluger, Y., Zhang, X. Q., Konpe, D., Snyder, M., Newburger, P., Gingeras, T. R., Weissman, S. S. (November 2004) Global analysis of gene networks involved in hematopoiesis. Blood, 104 (11). 137B-137B. ISSN 0006-4971

ENCODE Project Consortium (October 2004) The ENCODE (ENCyclopedia Of DNA Elements) Project. Science, 306 (5696). pp. 636-40. ISSN 0036-8075

Kampa, D., Cheng, J., Kapranov, P., Yamanaka, M., Brubaker, S., Cawley, S., Drenkow, J., Piccolboni, A., Bekiranov, S., Helt, G., Tammana, H., Gingeras, T. R. (2004) Novel RNAs identified from a in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Research, 14 (3). pp. 331-342. ISSN 10889051 (ISSN) (Public Dataset)

Gingeras, T. R. (2004) RNA reference materials for gene expression studies. Difficult first steps. Clinical Chemistry, 50 (8). pp. 1289-1290. ISSN 00099147 (ISSN)

Cawley, S., Bekiranov, S., Ng, H. H., Kapranov, P., Sekinger, E. A., Kampa, D., Piccolboni, A., Sementchenko, V., Cheng, J., Williams, A. J., Wheeler, R., Wong, B., Drenkow, J., Yamanaka, M., Patel, S., Brubaker, S., Tammana, H., Helt, G., Struhl, K., Gingeras, T. R. (2004) Unbiased Mapping of Transcription Factor Binding Sites along Human Chromosomes 21 and 22 Points to Widespread Regulation of Noncoding RNAs. Cell, 116 (4). pp. 499-509. ISSN 0092-8674

Kampa, D., Kapranov, P., Cawley, S., Bekiranov, S., Ng, H. H., Sekinger, E. A., Piccolboni, A., Sementchenko, V., Cheng, J., Drenkow, J., Yamanaka, M., Patel, S., Brubaker, S., Tammana, H., Narayanan, B., Helt, G., Struhl, K., Gingeras, T. R. (November 2003) Global mapping of functionally-important and regulatory regions on human chromosomes 21 and 22 reveal novel regulatory networks in the human genome. American Journal of Human Genetics, 73 (5). p. 185. ISSN 0002-9297

Kapranov, P., Sementchenko, V. I., Gingeras, T. R. (April 2003) Beyond expression profiling: next generation uses of high density oligonucleotide arrays. Briefings in Functional Genomics & Proteomics, 2 (1). pp. 47-56. ISSN 1473-9550 (Print)1473-9550

Shi, S., Nathan, C., Schnappinger, D., Drenkow, J., Fuortes, M., Block, E., Ding, A., Gingeras, T. R., Schoolnik, G., Akira, S., Takeda, K., Ehrt, S. (2003) MyD88 primes macrophages for full-scale activation by interferon-γ yet mediates few responses to Mycobacterium tuberculosis. Journal of Experimental Medicine, 198 (7). pp. 987-997. ISSN 00221007 (ISSN)

Kapranov, P., Cawley, S. E., Drenkow, J., Bekiranov, S., Strausberg, R. L., Fodor, S. P. A., Gingeras, T. R. (2002) Large-scale transcriptional activity in chromosomes 21 and 22. Science, 296 (5569). pp. 916-919. ISSN 00368075 (ISSN)

Dalma-Weiszhausz, D. D., Chicurel, M. E., Gingeras, T. R. (2002) Microarrays and genetic epidemiology: A multipurpose tool for a multifaceted field. Genetic Epidemiology, 23 (1). pp. 4-20. ISSN 07410395 (ISSN)

Dong, S. L., Wang, E., Hsie, L., Cao, Y. X., Chen, X. G., Gingeras, T. R. (August 2001) Flexible use of high-density oligonucleotide arrays for single-nucleotide polymorphism discovery and validation. Genome Research, 11 (8). pp. 1418-1424. ISSN 1088-9051

Kato-Maeda, M., Rhee, J. T., Gingeras, T. R., Salamon, H., Drenkow, J., Smittipat, N., Small, P. M. (2001) Comparing genomes within the species Mycobacterium tuberculosis. Genome Research, 11 (4). pp. 547-554. ISSN 10889051 (ISSN) (Public Dataset)

Rosenow, C., Saxena, R. M., Durst, M., Gingeras, T. R. (2001) Prokaryotic RNA preparation methods useful for high density array analysis: comparison of two approaches. Nucleic Acids Research, 29 (22). ISSN 13624962 (ISSN)

Ehrt, S., Schnappinger, D., Bekiranov, S., Drenkow, J., Shi, S., Gingeras, T. R., Gaasterland, T., Schoolnik, G., Nathan, C. (2001) Reprogramming of the macrophage transcriptome in response to interferon-γ and mycobacterium tuberculosis: Signaling roles of nitric oxide synthase-2 and phagocyte oxidase. Journal of Experimental Medicine, 194 (8). pp. 1123-1139. ISSN 00221007 (ISSN)

Corbeil, J., Sheeter, D., Genini, D., Rought, S., Leoni, L., Du, P., Ferguson, M., Masys, D. R., Welsh, J. B., Fink, J. L., Sasik, R., Huang, D., Drenkow, J., Richman, D. D., Gingeras, T. R. (2001) Temporal gene regulation during HIV-1 infection of human CD4+ T cells. Genome Research, 11 (7). pp. 1198-1204. ISSN 10889051 (ISSN)

Belcher, C. E., Drenkow, J., Kehoe, B., Gingeras, T. R., McNamara, N., Lemjabbar, H., Basbaum, C., Relman, D. A. (December 2000) The transcriptional responses of respiratory epithelial cells to Bordetella pertussis reveal host defensive and pathogen counter-defensive strategies. Proceedings of the National Academy of Sciences of the United States of America, 97 (25). pp. 13847-13852. ISSN 0027-8424

Hacker, C., Thomas, D., Doshi, J., Kimberly, R. P., Gingeras, T. R., Patil, N. (October 2000) Single nucleotide polymorphism discovery in candidate genes for rheumatoid arthritis. American Journal of Human Genetics, 67 (4). p. 335. ISSN 0002-9297

Gingeras, T. R., Rosenow, C. (August 2000) Studying microbial genomes with high-density oligonucleotide arrays. ASM News, 66 (8). pp. 463-469. ISSN 0044-7897

Gingeras, T. R. (May 2000) Using high-density oligonucleotide arrays in hypothesis- and discovery-driven studies of selected host-pathogen interactions. Faseb Journal, 14 (8). A1584-A1584. ISSN 0892-6638

Belcher, C., Drenkow, J., Gingeras, T. R., McNamara, N., Basbaum, C., Relman, D. (April 2000) A role for mucin in Bordetella pertussis pathogenesis is revealed in the transcriptional profile of infected human bronchial epithelial cells. Pediatric Research, 47 (4). 257A-257A. ISSN 0031-3998

Hu, J. S., Durst, M., Kerb, R., Truong, V., Ma, J. T., Khurgin, E., Balaban, D., Gingeras, T. R., Hoffman, B. B. (2000) Analysis of drug pharmacology towards predicting drug behavior by expression profiling using high-density oligonucleotide arrays. Annals of the New York Academy of Sciences, 919. pp. 9-15. ISSN 00778923 (ISSN)

Salamon, H., Kato-Maeda, M., Small, P. M., Drenkow, J., Gingeras, T. R. (2000) Detection of deleted genomic DNA using a semiautomated computational analysis of GeneChip data. Genome Research, 10 (12). pp. 2044-2054. ISSN 10889051 (ISSN)

Kuritzkes, D. R., Shugarts, D., Bakhtiari, M., Poticha, D., Johnson, J., Rubin, M., Gingeras, T. R., Kennedy, M., Eron, J. J. (2000) Emergence of dual resistance to zidovudine and lamivudine in HIV-1- infected patients treated with zidovudine plus lamivudine as initial therapy. Journal of Acquired Immune Deficiency Syndromes and Human Retrovirology, 23 (1). pp. 26-34. ISSN 10779450 (ISSN)

Lindblad-Toh, K., Winchester, E., Daly, M. J., Wang, D. G., Hirschhorn, J. N., Laviolette, J. P., Ardlie, K., Reich, D. E., Robinson, E., Sklar, P., Shah, N., Thomas, D., Fan, J. B., Gingeras, T. R., Warrington, J., Patil, N., Hudson, T. J., Lander, E. S. (2000) Large-scale discovery and genotyping of single-nucleotide polymorphisms in the mouse. Nature Genetics, 24 (4). pp. 381-386. ISSN 10614036 (ISSN)

Paxton, W. A., Kang, S., Liu, R., Landau, N. R., Gingeras, T. R., Wu, L., Mackay, C. R., Koup, R. A. (1999) HIV-1 infectability of CD4+ lymphocytes with relation to β-chemokines and the CCR5 coreceptor. Immunology Letters, 66 (1-3). pp. 71-75. ISSN 01652478 (ISSN)

Lipshutz, R. J., Fodor, S. P. A., Gingeras, T. R., Lockhart, D. J. (1999) High density synthetic oligonucleotide arrays. Nature Genetics, 21 (1 SUPP). pp. 20-24. ISSN 10614036 (ISSN)

Troesch, A., Nguyen, H., Miyada, C. G., Desvarenne, S., Gingeras, T. R., Kaplan, P. M., Cros, P., Mabilat, C. (1999) Mycobacterium species identification and rifampin resistance testing with high-density DNA probe arrays. Journal of Clinical Microbiology, 37 (1). pp. 49-55. ISSN 00951137 (ISSN)

Zhu, H., Cong, J. P., Mamtora, G., Gingeras, T. R., Shenk, T. (1998) Cellular gene expression altered by human cytomegalovirus: Global monitoring with oligonucleotide arrays. Proceedings of the National Academy of Sciences of the United States of America, 95 (24). pp. 14470-14475. ISSN 00278424 (ISSN) (Public Dataset)

Paxton, W. A., Liu, R., Kang, S., Wu, L., Gingeras, T. R., Landau, N. R., MacKay, C. R., Koup, R. A. (1998) Reduced HIV-1 infectability of CDd4+ lymphocytes from exposed- uninfected individuals: Association with low expression of CCR5 and high production of β-chemokines. Virology, 244 (1). pp. 66-73. ISSN 00426822 (ISSN)

Gingeras, T. R., Ghandour, G., Wang, E., Berno, A., Small, P. M., Drobniewski, F., Alland, D., Desmond, E., Holodniy, M., Drenkow, J. (1998) Simultaneous genotyping and species identification using hybridization pattern recognition analysis of generic Mycobacterium DNA arrays. Genome Research, 8 (5). pp. 435-448. ISSN 10889051 (ISSN) (Public Dataset)

Zhu, H., Cong, J. P., Mamtora, G., Gingeras, T. R., Shenk, T. (1998) Use of differential display and dna array technology to assess the effect of human cytomegalovirus infection on signal transduction pathways. Faseb Journal, 12 (8). ISSN 08926638 (ISSN)

Winters, M. A., Shafer, R. W., Jellinger, R. A., Mamtora, G., Gingeras, T. R., Merigan, T. C. (April 1997) Human immunodeficiency virus type 1 reverse transcriptase genotype and drug susceptibility changes in infected individuals receiving dideoxyinosine monotherapy for 1 to 2 years. Antimicrobial Agents and Chemotherapy, 41 (4). pp. 757-762. ISSN 0066-4804

Kozal, M. J., Shah, N., Shen, N., Yang, R., Fucini, R., Merigan, T. C., Richman, D. D., Morris, D., Hubbell, E., Chee, M., Gingeras, T. R. (1996) Extensive polymorphisms observed in HIV-1 clade B protease gene using high-density oligonucleotide arrays. Nature Medicine, 2 (7). pp. 753-759. ISSN 10788956 (ISSN)

Decker, D. J., Linton, P. J., Zaharevitz, S., Biery, M., Gingeras, T. R., Klinman, N. R. (1995) Defining subsets of naive and memory B cells based on the ability of their progeny to somatically mutate in vitro. Immunity, 2 (2). pp. 195-203. ISSN 10747613 (ISSN)

Kozal, M. J., Shah, N., Yang, R., Shen, N., Fucini, R., Merigan, T. C., Richman, D. D., Chee, M. S., Gingeras, T. R. (1995) Natural polymorphism of HIV-1 clade B protease gene and implications for therapy. Journal of Acquired Immune Deficiency Syndromes and Human Retrovirology, 10 (S3). p. 76. ISSN 1077-9450

Fahy, E., Biery, M., Goulden, M., Ghosh, S. S., Gingeras, T. R. (1994) Issues of variability, carryover contamination, and detection in 3SR-based assays. PCR Methods and Applications, 3 (5). S83-S94. ISSN 10549803 (ISSN)

Stillman, C. A., Linton, P. J., Koutz, P. J., Decker, D. J., Klinman, N. R., Gingeras, T. R. (1994) Specific immunoglobulin cDNA clones produced from hybridoma cell lines and murine spleen fragment cultures by 3SR amplification. PCR Methods and Applications, 3 (6). pp. 320-331. ISSN 10549803 (ISSN) (Public Dataset)

Gingeras, T. R., Ghosh, S., Blumeyer, K., Eis, P., Millar, D. (February 1993) A Spectrofluorometric Method for Measurement of Restriction Endonuclease activity based on Fluorescence Polarization. Journal of Cellular Biochemistry, 17C (Suppl). p. 173. ISSN 0730-2312

Decker, D. J., Linton, P. J., Gingeras, T. R., Klinman, N. R. (January 1993) In vitro analysis of somatically mutated B-cells. Journal of Cellular Biochemistry, 53 (S17B). p. 170. ISSN 0730-2312

Gingeras, T. R. (1993) Novel amplification targets for 3SR. Clinical Chemistry, 39 (4). pp. 726-727. ISSN 00099147 (ISSN)

Richman, D. D., Guatelli, J. C., Grimes, J., Tsiatis, A., Gingeras, T. R. (1991) Detection of mutations associated with zidovudine resistance in human immunodeficiency virus by use of the polymerase chain reaction. Journal of Infectious Diseases, 164 (6). pp. 1075-1081. ISSN 00221899 (ISSN)

Fahy, E., Kwoh, D. Y., Gingeras, T. R. (1991) Self-sustained sequence replication (3SR): An isothermal transcription-based amplification system alternative to PCR. Genome Research, 1 (1). pp. 25-33. ISSN 10889051 (ISSN)

Gingeras, T. R., Prodanovich, P., Latimer, T., Guatelli, J. C., Richman, D. D., Barringer, K. J. (1991) Use of self-sustained sequence replication amplification reaction to analyze and detect mutations in zidovudine-resistant human immunodeficiency virus. Journal of Infectious Diseases, 164 (6). pp. 1066-1074. ISSN 00221899 (ISSN)

Guatelli, J. C., Gingeras, T. R., Richman, D. D. (1990) Alternative splice acceptor utilization during human immunodeficiency virus type 1 infection of cultured cells. Journal of Virology, 64 (9). pp. 4093-4098. ISSN 0022538X (ISSN)

Ghosh, S. S., Obermiller, P. S., Kwoh, T. J., Gingeras, T. R. (1990) Analysis of substrate specificity of the PaeR7 endonuclease: Effect of base methylation on the kinetics of cleavage. Nucleic Acids Research, 18 (17). pp. 5063-5068. ISSN 03051048 (ISSN)

Barringer, K. J., Orgel, L., Wahl, G., Gingeras, T. R. (1990) Blunt-end and single-strand ligations by Escherichia coli ligase: influence on an in vitro amplication scheme. Gene, 89 (1). pp. 117-122. ISSN 0378-1119

Davis, G. R., Blumeyer, K., DiMichele, L. J., Whitfield, K. M., Chappelle, H., Riggs, N., Ghosh, S. S., Kao, P. M., Fahy, E., Kwoh, D. Y., Guatelli, J. C., Spector, S. A., Richman, D. D., Gingeras, T. R. (1990) Detection of human immunodeficiency virus type 1 in AIDS patients using amplification-mediated hybridization analyses: Reproducibility and quantitative limitations. Journal of Infectious Diseases, 162 (1). pp. 13-20. ISSN 00221899 (ISSN)

Guatelli, J. C., Whitfield, K. M., Kwoh, D. Y., Barringer, K. J., Richman, D. D., Gingeras, T. R. (1990) Isothermal, in vitro amplification of nucleic acids by a multienzyme reaction modeled after retroviral replication. Proceedings of the National Academy of Sciences of the United States of America, 87 (5). pp. 1874-1878. ISSN 00278424 (ISSN)

Gingeras, T. R., Richman, D. D., Kwoh, D. Y., Guatelli, J. C. (1990) Methodologies for in vitro nucleic acid amplification and their applications. Veterinary Microbiology, 24 (3-4). pp. 235-251. ISSN 03781135 (ISSN)

Gingeras, T. R., Whitfield, K. M., Kwoh, D. Y. (1990) Unique features of the self-sustained sequence replication (3SR) reaction in the in vitro amplification of nucleic acids. Annales de Biologie Clinique, 48 (7). pp. 498-501. ISSN 00033898 (ISSN)

Guatelli, J. C., Gingeras, T. R., Richman, D. D. (1989) Nucleic acid amplification in vitro: Detection of sequences with low copy numbers and application to diagnosis of human immunodeficiency virus type 1 infection. Clinical Microbiology Reviews, 2 (2). pp. 217-226. ISSN 08938512 (ISSN)

Kwoh, D. Y., Davis, G. R., Whitfield, K. M., Chappelle, H. L., DiMichelle, L. J., Gingeras, T. R. (1989) Transcription-based amplification system and detection of amplified human immunodeficiency virus type 1 with a bead-based sandwich hybridization format. Proceedings of the National Academy of Sciences of the United States of America, 86 (4). pp. 1173-1177. ISSN 00278424 (ISSN)

Kwoh, T. J., Obermiller, P. S., McCue, A. W., Kwoh, D. Y., Sullivan, S. A., Gingeras, T. R. (1988) Introduction and expression of the bacterial PaeR7 restriction endonuclease gene in mouse cells containing the PaeR7 methylase. Nucleic Acids Research, 16 (24). pp. 11489-11506. ISSN 03051048 (ISSN)

Ghosh, S. S., Gingeras, T. R., Davis, G. R., Musso, G. F., Kwoh, D. Y., Kao, P. M. (August 1987) Covalent attachment of nucleic acids to solid supports - chemistries of coupling and hybridization characteristics. Abstracts of Papers of the American Chemical Society, 194. 68-MBTD. ISSN 0065-7727

Tschopp, J. F., Brust, P. F., Cregg, J. M., Stillman, C. A., Gingeras, T. R. (1987) Expression of the lacZ gene from two methanol-regulated promoters in Pichia pastoris. Nucleic Acids Research, 15 (9). pp. 3859-3876. ISSN 03051048 (ISSN)

Gingeras, T. R., Kwoh, D. Y., Davis, G. R. (1987) Hybridization properties of immobilized nucleic acids. Nucleic Acids Research, 15 (13). pp. 5373-5390. ISSN 03051048 (ISSN)

Kwoh, T. J., Kwoh, D. Y., McCue, A. W., Davis, G. R., Patrick, D., Gingeras, T. R. (October 1986) Introduction and expression of the bacterial PaeR7 methylase gene in mammalian cells. Proc Natl Acad Sci U S A, 83 (20). pp. 7713-7. ISSN 0027-8424 (Print)0027-8424 (Linking)

Ellis, S. B., Brust, P. F., Koutz, P. J., Waters, A. F., Harpold, M. M., Gingeras, T. R. (May 1985) Isolation of alcohol oxidase and two other methanol regulatable genes from the yeast Pichia pastoris. Mol Cell Biol, 5 (5). pp. 1111-21. ISSN 0270-7306 (Print)0270-7306 (Linking)

Theriault, G., Roy, P. H., Howard, K. A., Benner, J. S., Brooks, J. E., Waters, A. F., Gingeras, T. R. (1985) Nucleotide sequence of the PaeR7 restriction/modification system and partial characterization of its protein products. Nucleic Acids Research, 13 (23). pp. 8441-8461. ISSN 03051048 (ISSN)

Gingeras, T. R., Brooks, J. E. (1983) Cloned restriction/modification system from Pseudomonas aeruginosa. Proceedings of the National Academy of Sciences of the United States of America, 80 (2). pp. 402-406. ISSN 00278424 (ISSN)

Brooks, J. E., Gingeras, T. R. (1983) The control of expression of a type-ll restriction modification system from Pseudomonas Aeroginosa. Federation Proceedings, 42 (7). p. 2038. ISSN 0014-9446

Brooks, J. E., Blumenthal, R. M., Gingeras, T. R. (1983) The isolation and characterization of the Esherichia Coli DNA adenine methylase (dam) gene. Nucleic Acids Research, 11 (3). pp. 837-851. ISSN 03051048 (ISSN)

Roberts, R. J., Sciaky, D., Gelinas, R. E., Jiang, B. D., Yen, C. E., Kelly, M. M., Bullock, P. A., Parsons, B. L., Oneill, K. E., Gingeras, T. R. (1982) Information-Content of the Adenovirus-2 Genome. Cold Spring Harbor Symposia on Quantitative Biology, 47. pp. 1025-1037. ISSN 0091-7451

Gingeras, T. R., Sciaky, D., Gelinas, R. E., Bing-Dong, J., Yen, C. E., Kelly, M. M., Bullock, P. A., Parsons, B. L., O'Neill, K., Roberts, R. J. (1982) Nucleotide sequences from the adenovirus-2 genome. Journal of Biological Chemistry, 257 (22). pp. 13475-13491. ISSN 00219258 (ISSN)

Fitzgerlad, G. F., Daly, C., Brown, L. R., Gingeras, T. R. (1982) ScrFi: A new sequence-specific endonuclease from Streptococcus cremoris. Nucleic Acids Research, 10 (24). pp. 8171-8179. ISSN 03051048 (ISSN)

Gingeras, T. R., Rice, P., Roberts, R. J. (1982) A semi-automated method for the reading of nucleic acid sequencing gels. Nucleic Acids Research, 10 (1). pp. 103-114. ISSN 03051048 (ISSN)

Gingeras, T. R., Rice, P., Roberts, R. J. (1982) A semi-automated method for the reading of nucleic acid sequencing gels. Nucleic Acids Research, 10 (1). pp. 103-114.

Gingeras, T. R., Greenough, L., Schildkraut, I., Roberts, R. J. (1981) Two new restriction endonucleases from Proteus vulgaris. Nucleic Acids Research, 9 (18). pp. 4525-4536. ISSN 03051048 (ISSN)

Garrels, J. I. (1980) Computer-Analyzed Two-Dimensional Gel-Electrophoresis of Proteins. Trends in Biochemical Sciences, 5 (11). pp. 281-283.

Gingeras, T. R. (1980) Restriction endonucleases and their recognition sequences. Biochemical Society Transactions, 8 (3). pp. 397-398. ISSN 03005127 (ISSN)

Gingeras, T. R., Roberts, R. J. (1980) Steps toward computer analysis of nucleotide sequences. Science, 209 (4463). pp. 1322-1328. ISSN 00368075 (ISSN)

Gingeras, T. R., Milazzo, J. P., Sciaky, D., Roberts, R. J. (September 1979) Computer programs for the assembly of DNA sequences. Nucleic Acids Research, 7 (2). pp. 529-45. ISSN 0305-1048 (Print)0305-1048

Zain, S., Gingeras, T. R., Bullock, P., Wong, G., Gelinas, R. E. (1979) Determination and analysis of adenovirus-2 DNA sequences which may include signals for late messenger RNA processing. Journal of Molecular Biology, 135 (2). pp. 413-433. ISSN 00222836 (ISSN)

Gingeras, T. R., Milazzo, J. P., Roberts, R. J. (1978) A computer assisted method for the determination of restriction enzyme recognition sites. Nucleic Acids Research, 5 (11). pp. 4105-4128. ISSN 03051048 (ISSN)

Gingeras, T. R., Myers, P. A., Olson, J. A., Hanberg, F. A., Roberts, R. J. (1978) A new specific endonuclease present in Xanthomonas holcicola, Xanthomonas papavericola and Brevibacterium luteum. Journal of Molecular Biology, 118 (1). pp. 113-122. ISSN 0022-2836

Gelti Douka, H., Gingeras, T. R., Kambysellis, M. P. (1974) Yolk proteins in Drosophila: identification and site of synthesis. Journal of Experimental Zoology, 187 (1). pp. 167-172.

Gelti Douka, H., Gingeras, T. R., Kambysellis, M. P. (1973) Site of the yolk protein synthesis in D. silvestris. Drosophila Information Service, 50. pp. 161-162.

Gelti Douka, H., Gingeras, T. R., Kambysellis, M. P. (1973) Site of the yolk protein synthesis in D. silvestris. Drosophila Information Service, 50. pp. 161-162.

Gingeras, T. R., Gelti Douka, H., Kambysellis, M. P. (1973) Yolk proteins in Drosophila. Drosophila Information Service, 50. p. 58.

Gingeras, T. R., Gelti Douka, H., Kambysellis, M. P. (1973) Yolk proteins in Drosophila. Drosophila Information Service, 50. p. 58.

Book Section

Mack, D. H., Tom, E. Y., Mahadev, M., Dong, H., Mittmann, M., Dee, S., Levine, A. J., Gingeras, T. R., Lockhart, D. L. (1998) Deciphering Molecular Circuitry using high-density DNA arrays. In: The Biology of Tumors. Springer, New York, pp. 85-108. ISBN 9780306459320

Fahy, E., Barringer, K. J., Kwoh, D. Y., Prodanovich, P., Gingeras, T. R. (1996) The self-sustained sequence replication (3SR) reaction and its application to the detection of mutations associated with Zidovudine resistance in HIV-1. In: PCR Protocols and Applications: Laboratory Manual. Academic Press, New York. ISBN 9780080886718

Ghosh, S. S., Fahy, E., Gingeras, T. R. (1995) 13 - The Self-Sustained Sequence Replication Reaction and Its Application in Clinical Diagnostics and Molecular Biology. In: Molecular Methods for Virus Detection. Academic Press, San Diego, pp. 287-314. ISBN 978-0-12-748920-9

Gingeras, T. R., Biery, M., Goulden, M., Ghosh, S. S., Fahy, E. (1995) Optimization and Characterization of 3SR-based Assays. In: PCR primer: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, pp. 653-666. ISBN 9780879694487

Ghosh, S. S., Fahy, E., Gingeras, T. R. (1995) The self-sustained sequence replication (3SR) reaction: Its practice and applications. In: Molecular Methods for Virus Detection. Academic Press, San Diego, pp. 287-313. ISBN 9780080536897

Gingeras, T. R., Koutz, P. J., Linton, P. J., Decker, D. J., Klinman, N. R., Stillman, C. A. (1994) Production of antibodies of monoclonal specificity without the use of hybridoma cell lines. In: Methods in DNA amplification. Plenum Press, New York. ISBN 9780306449086

Gingeras, T. R. (1991) Restriction-modification systems. Genetic sentries and useful systems in the study of molecular genetics. In: Modern Microbial Genetics. Wiley-Liss, New York, pp. 301-322. ISBN 9780471568452

Kwoh, D. Y., Kwoh, T. J., Gingeras, T. R. (1991) Transcription-based amplification system. In: Methods in Gene Technology. Jai Press, London, pp. 285-299. ISBN 9781559382632

Gingeras, T. R., Davis, G. R., Whitfield, K. M., Chappelle, H. L., DiMichele, L. J., Kwoh, D. Y. (1990) Transcription-based amplification system and the detection of its RNA products by the bead-based sandwich hybridization system. In: PCR Protocols and Applications: Laboratory Manual. Academic Press, New York, pp. 245-252.

Kwoh, D. Y., Gingeras, T. R. (1988) The use of transcription-based amplification systems in the diagnosis of HIV-1 infections. In: Applied virology research. Springer. ISBN 9780306446689

Roberts, R. J., Akusjarvi, G., Alestrom, P., Gelinas, R. E., Gingeras, T., Sciaky, D., Pettersson, U. (1986) A consensus sequence for the adenovirus-2 genome. In: Adenovirus DNA: The Viral Genome and Its Expression. Springer, pp. 1-51. ISBN 9780898387582

Gingeras, T. R. (1984) Organizational expression of a type II restriction-modified system from Pseudomonas aeruginosa. In: Metabolism and Enzymology of Nucleic Acids. Slovak Academy of Sciences, pp. 267-276.

Gingeras, T. R. (1983) Computers and DNA sequences: A natural combination. In: Statistical analysis of DNA sequence data. M. Dekker, New York, pp. 15-44. ISBN 9780824770327

Gingeras, T. R. (1982) The isolation and characterization of the E. coli dam methylase gene. In: Metabolism and Enzymology of Nucleic Acids. Slovak Academy of Sciences, pp. 320-340.

Gingeras, T. R., Roberts, R. J. (1981) Computer assisted methods for nucleic acid sequencing. In: Genetic Engineering: Principles and Methods. Plenum Press, pp. 319-338. ISBN 9780306439193

Gingeras, T. R. (1980) Restriction endonucleases and their role in genomic analysis. In: Gene structure and expression. Ohio State University Biosciences Colloquia. Ohio State University Press, pp. 3-20.

Conference or Workshop Item

Zhang, Qiong, Chao, Ti-chun, Patil, Veena S, Qin, Yue, Tiwari, Shashi Kant, Chiou, Joshua, Dobin, Alexander, Tsai, Chih-Ming, Li, Zhonghan, Dang, Jason, Gupta, Shagun, Urdahl, Kevin B, Nizet, Victor, Gingeras, Thomas R, Gaulton, Kyle J, Rana, Tariq M (May 2019) Genome-wide analysis identifies pairs of cis-acting lncRNAs and protein-coding genes involved in innate immunity. In: UNSPECIFIED. (Unpublished)

Djebali, S, Rodriguez Martin, B, Palumbo, E, Pervouchine, DD, Breschi, A, Davis, C, Dobin, A, Alonso, G, Rastrojo, A, Aguado, B, Gingeras, TR, Guigo, R (September 2016) Recurrent chimeric transcripts in human and mouse. In: Functional Annotation of Animal Genomes (FAANG) ASAS-ISAG Joint Symposium.

Gingeras, T. R. (2012) Important lessons from a complex genome. In: 22nd IUBMB & 37th FEBS Congress, Sept 4th-9th 2012, Seville, Spain.

GINGERAS, TR, GHOSH, S, BLUMEYER, K, EIS, P, MILLAR, D (February 1993) A SPECTROFLUOROMETRIC METHOD FOR MEASUREMENT OF RESTRICTION ENDONUCLEASE ACTIVITY BASED ON FLUORESCENCE POLARIZATION. In: UNSPECIFIED.

Patent

Thomas Gingeras (1999) Mycobacterial rpoB sequences. United States Patent 7108968. .

Thomas Gingeras (1991) Prenatal sex determination of bovine cells using male-specific oligonucleotides. United States Patent 5055393. .