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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 (2023) The status of the human gene catalogue. Nature, 622(7981) pp. 41-47.

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 (2023) The ENCODE Uniform Analysis Pipelines. Res Sq,

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 (2023) The ENCODE Uniform Analysis Pipelines..

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 (2023) The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models. Cell, 186(7) pp. 1493-1511.e40.

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 (2023) The status of the human gene catalogue.

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 (2023) Long non-coding RNAs: definitions, functions, challenges and recommendations. Nature Reviews Molecular Cell Biology,

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 (2022) Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature, 605(7909) pp. E3.

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 (2022) Author Correction: Perspectives on ENCODE. Nature, 605(7909) pp. E4.

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 (2022) Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nature Communications, 13(1) pp. 1200.

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 (2021) Ground tissue circuitry regulates organ complexity in maize and Setaria. Science, 374(6572) pp. 1247-1252.

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 (2021) Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nature Communications, 12(1)

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 (2021) Multi-tissue integrative analysis of personal epigenomes. BioRxiv,

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 (2021) Selective time-dependent changes in activity and cell-specific gene expression in human postmortem brain.. Scientific Reports, 11(1) pp. 6078.

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. (2020) Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery. Dev Cell, S1534-(20) pp. 31021-31022.

Nechooshtan, G., Yunusov, D., Chang, K. , Gingeras, T. R. (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.

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. (2020) A limited set of transcriptional programs define major cell types. Genome Res, 30(7) pp. 1047-1059. https://pubmed.ncbi.nlm.nih.gov/32759341/.

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. (2020) Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature, 583(7818) pp. 699-710.

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. (2020) Perspectives on ENCODE. Nature, 583(7818) pp. 693-698.

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. (2020) Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud. Frontiers in Plant Science, 11(289)

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 (2019) Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud. BioRxiv,

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. (2019) Dynamics of microRNA expression during mouse prenatal development. Genome Res, 29(11) pp. 1900-1909.

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

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. (2019) The long noncoding RNA ROCKI regulates inflammatory gene expression. Embo j, 38(8) pp. Article number e100041.

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 (2018) Dynamics of microRNA expression during mouse prenatal development.. BioRxiv,

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

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. (2018) Advances, challenges, and opportunities in extracellular RNA biology: insights from the NIH exRNA Strategic Workshop. JCI Insight, 3(7)

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. (2018) The molecular basis of the cellular taxonomy of the human body. Human Genomics, 12(Supple) pp. Meeting Abstract A107.

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

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. (2017) High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing. Nat Genet, 49(12) pp. 1731-1740.

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. (2017) FANTOM5 CAGE profiles of human and mouse samples. Sci Data, 4 pp. 170112.

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

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 (2017) STAR-Fusion: Fast and Accurate Fusion Transcript Detection from RNA-Seq. BioRxiv,

Dobin, A. , Gingeras, T. R. (2016) Optimizing RNA-Seq Mapping with STAR. Methods Mol Biol, 1415 pp. 245-262.

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) pp. 151.

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

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

Dobin, A. , Gingeras, T. R. (2015) Mapping RNA-seq Reads with STAR. Curr Protoc Bioinformatics, 51 pp. 11.14.1-11.14.19.

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. (2015) Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression. Nat Commun, 6 pp. 5903.

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Fagegaltier, D., Konig, A., Gordon, A., Lai, E. C., Gingeras, T. R., Hannon, G. J. , Shcherbata, H. R. (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.

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

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

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

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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.

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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. (2012) Modeling gene expression using chromatin features in various cellular contexts. Genome Biology, 13(9)

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Tilgner, H., Knowles, D. G., Johnson, R., Davis, C. A., Chakrabortty, S., Djebali, S., Curado, J., Snyder, M., Gingeras, T. R. , Guigo, R. (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.

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

Kowalczyk, M. S., Higgs, D. R. , Gingeras, T. R. (2012) Molecular biology: RNA discrimination. Nature, 482(7385) pp. 310-1.

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

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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.

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.

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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. (2010) Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Nature Methods, 7(7) pp. 528-34.

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 )

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)

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) pp. R101.

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

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. (2009) Variation in novel exons (RACEfrags) of the MECP2 gene in Rett syndrome patients and controls. Human Mutation, 30(9) pp. E866-79.

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. (2009) Unlocking the secrets of the genome. Nature, 459(7249) pp. 927-30.

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

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

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. (2009) Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs. Nature, 457(7232) pp. 1028-1032.

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) pp. R101.

Rada-Iglesias, A., Ameur, A., Kapranov, P., Enroth, S., Komorowski, J., Gingeras, T. R. , Wadelius, C. (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.

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.

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.

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

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.

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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.

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.

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

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

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.

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.

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.

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.

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.

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.

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. (2006) Genome-wide analysis of estrogen receptor binding sites. Nature Genetics, 38(11) pp. 1289-1297.

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

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

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 pp. S2.1-31.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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. (2004) Global analysis of gene networks involved in hematopoiesis. Blood, 104(11) pp. 137B-137B.

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

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.

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

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.

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. (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) pp. 185-185.

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

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.

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.

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.

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

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.

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.

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.

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)

Belcher, C. E., Drenkow, J., Kehoe, B., Gingeras, T. R., McNamara, N., Lemjabbar, H., Basbaum, C. , Relman, D. A. (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.

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

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

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

Belcher, C., Drenkow, J., Gingeras, T. R., McNamara, N., Basbaum, C. , Relman, D. (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) pp. 257A-257A.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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)

Winters, M. A., Shafer, R. W., Jellinger, R. A., Mamtora, G., Gingeras, T. R. , Merigan, T. C. (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.

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.

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.

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) pp. 76-76.

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) pp. S83-S94.

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.

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

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

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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

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.

Kwoh, T. J., Kwoh, D. Y., McCue, A. W., Davis, G. R., Patrick, D. , Gingeras, T. R. (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.

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

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.

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.

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) pp. 2038-2038.

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.

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.

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., 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.

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.

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.

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.

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.

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

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

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.

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.

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.

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 pp. 58.

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