BioNeMo Framework: a modular, high-performance library for AI model development in drug discovery

Autor: John, Peter St., Lin, Dejun, Binder, Polina, Greaves, Malcolm, Shah, Vega, John, John St., Lange, Adrian, Hsu, Patrick, Illango, Rajesh, Ramanathan, Arvind, Anandkumar, Anima, Brookes, David H, Busia, Akosua, Mahajan, Abhishaike, Malina, Stephen, Prasad, Neha, Sinai, Sam, Edwards, Lindsay, Gaudelet, Thomas, Regep, Cristian, Steinegger, Martin, Rost, Burkhard, Brace, Alexander, Hippe, Kyle, Naef, Luca, Kamata, Keisuke, Armstrong, George, Boyd, Kevin, Cao, Zhonglin, Chou, Han-Yi, Chu, Simon, Costa, Allan dos Santos, Darabi, Sajad, Dawson, Eric, Didi, Kieran, Fu, Cong, Geiger, Mario, Gill, Michelle, Hsu, Darren, Kaushik, Gagan, Korshunova, Maria, Kothen-Hill, Steven, Lee, Youhan, Liu, Meng, Livne, Micha, McClure, Zachary, Mitchell, Jonathan, Moradzadeh, Alireza, Mosafi, Ohad, Nashed, Youssef, Paliwal, Saee, Peng, Yuxing, Rabhi, Sara, Ramezanghorbani, Farhad, Reidenbach, Danny, Ricketts, Camir, Roland, Brian, Shah, Kushal, Shimko, Tyler, Sirelkhatim, Hassan, Srinivasan, Savitha, Stern, Abraham C, Toczydlowska, Dorota, Veccham, Srimukh Prasad, Venanzi, Niccolò Alberto Elia, Vorontsov, Anton, Wilber, Jared, Wilkinson, Isabel, Wong, Wei Jing, Xue, Eva, Ye, Cory, Yu, Xin, Zhang, Yang, Zhou, Guoqing, Zandstein, Becca, Dallago, Christian, Trentini, Bruno, Kucukbenli, Emine, Rvachov, Timur, Calleja, Eddie, Israeli, Johnny, Clifford, Harry, Haukioja, Risto, Haemel, Nicholas, Tretina, Kyle, Tadimeti, Neha, Costa, Anthony B

Artificial Intelligence models encoding biology and chemistry are opening new routes to high-throughput and high-quality in-silico drug development. However, their training increasingly relies on computational scale, with recent protein language mode

Externí odkaz: http://arxiv.org/abs/2411.10548

Comprehensive, high-resolution binding energy landscapes reveal context dependencies of transcription factor binding

Autor: Le, Daniel D., Shimko, Tyler C., Aditham, Arjun K., Keys, Allison M., Longwell, Scott A., Orenstein, Yaron, Fordyce, Polly M.

Publikováno v: Proceedings of the National Academy of Sciences of the United States of America, 2018 Apr . 115(16), E3702-E3711.

Externí odkaz: https://www.jstor.org/stable/26508871

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Genetic effects on gene expression across human tissues

Autor: Haugen, Eric, He, Yuan, Chen, Lin S., Dermitzakis, Emmanouil T., Branton, Philip A., Nobel, Andrew B., Park, YoSon, McLean, Jeffrey A., Neri, Fidencio J., Tabor, David E., Saha, Ashis, Sobin, Leslie, Doherty, Jennifer A., Rosenbloom, Kate R., Quan, Jie, Strober, Benjamin J., Liu, Yaping, Valley, Dana, Basha, Omer, Barshir, Ruth, Trowbridge, Casandra A., Segrè, Ayellet V., Skol, Andrew, Karasik, Ellen, Bridge, Jason, Kent, W. James, Chiang, Colby, Damani, Farhan N., Karczewski, Konrad J., Barcus, Mary E., Oliva, Meritxell, Papasaikas, Panagiotis, Nelson, Jemma, Linke, Caroline, Paten, Benedict, Gelfand, Ellen T., Zhu, Jingchun, Wright, Fred A., Smith, Kevin S., Halow, Jessica, Kim-Hellmuth, Sarah, Salvatore, Michael, Hunter, Steven, Noble, Michael S., Goldman, Mary, Nguyen, Duyen Y., Singh, Shilpi, Rohrer, Daniel C., Cox, Nancy J., Hickey, Peter F., Battle, Alexis, Claussnitzer, Melina, Molinie, Benoit, Aguet, François, Balliu, Brunilda, Thomas, Jeffrey A., Hormozdiari, Farhad, Hou, Lei, Kaul, Rajinder, Peterson, Christine B., Lin, Jessica, Barker, Laura K., Brown, Christopher D., Guan, Ping, Lee, Kristen, Gloudemans, Michael J., Ripke, Stephan, Moser, Michael T., Muñoz-Aguirre, Manuel, Haeussler, Maximilian, Vatanian, Negin, Gewirtz, Ariel D.H., Castel, Stephane E., Monlong, Jean, Scott, Alexandra J., Stamatoyannopoulos, John, Ruffier, Magali, Zappala, Zachary, Li, Xiao, Ferreira, Pedro G., Nierras, Concepcion R., Yeger-Lotem, Esti, Wen, Xiaoquan, Struewing, Jeffery P., Delaneau, Olivier, Tukiainen, Taru, Tomaszewski, Maria M., Jo, Brian, Park, Yongjin, Martin, Casey, Bogu, Gireesh K., Pierce, Brandon L., Zhou, Yi-Hui, Eskin, Eleazar, Reverter, Ferran, Guigó, Roderic, Teran, Nicole A., Lek, Monkol, Leinweber, William F., Ardlie, Kristin G., Kopen, Gene, Ongen, Halit, Lonsdale, John T., Hall, Ira M., Bustamante, Carlos D., Quon, Gerald, Han, Buhm, Mohammadi, Pejman, Nicolae, Dan L., Kellis, Manolis, Vivian, John, Robinson, Karna L., Davis, David A., Washington, Michael, Montroy, Robert G., Craft, Brian, Wang, Gao, Garrido-Martín, Diego, Taylor, Kieron, Linder, Sandra, Hadley, Kane, Addington, Anjene M., Davis, Joe R., Siminoff, Laura A., Miklos, Mark, Tsang, Emily K., Diegel, Morgan, Mash, Deborah C., McDowell, Ian C., Lockhart, Nicole C., Payne, Anthony J., Abell, Nathan S., Cummings, Beryl B., Wheeler, Joseph, Matose, Takunda, Demanelis, Kathryn, Gliner, Genna, Stephens, Matthew, McDonald, Alisa, Rao, Abhi, Foster, Barbara A., Frésard, Laure, Brown, Andrew A., Zhang, Rui, Rinaldi, Nicola J., Gillard, Bryan M., Zerbino, Daniel R., Sabatti, Chiara, Moore, Helen M., Hasz, Richard, Brigham, Lori E., Zaugg, Judith B., Jian, Ruiqi, Conrad, Donald F., Snyder, Michael P., Im, Hae Kyung, Wu, Fan, MacArthur, Daniel G., Liu, Boxiang, Gamazon, Eric R., Jiang, Lihua, Sammeth, Michael, Johns, Christopher, Maurano, Matthew T., Hansen, Kasper D., Kang, Eun Yong, Myer, Kevin, Tang, Hua, Johnson, Mark, Fernando, Marian S., Smith, Anna M., Urbut, Sarah, Gould, Sarah E., Van Wittenberghe, Nicholas, Lee, Christopher M., Engelhardt, Barbara E., Panousis, Nikolaos, Palowitch, John J., Kibriya, Muhammad G., Sheppard, Dan, McCarthy, Mark I., Ndungu, Anne W., Valentino, Kimberly M., Sodaei, Reza, Sandstrom, Richard, Parsana, Princy, Kim, Yungil, Kumar, Rachna, Chan, Joanne, Little, A. Roger, Shimko, Tyler C., Volpi, Simona, Li, Qin, Akey, Joshua M., Walters, Gary, Roe, Bryan, Undale, Anita H., Van De Bunt, Martijn, Getz, Gad, Li, Jin Billy, Mangul, Serghei, Feinberg, Andrew P., Sul, Jae Hoon, Rizzardi, Lindsay F., Nguyen, Duyen T., Stranger, Barbara E., Um, Ki Sung, Flicek, Paul, Trevanion, Stephen J., Vaught, Jimmie B., Lockart, Nicole C., Nedzel, Jared L., Handsaker, Robert E., Hunter, Marcus, Xi, Hualin S., Bates, Daniel, Howald, Cedric, Roche, Nancy V., Koester, Susan, Huang, Katherine H., Sullivan, Timothy J., Wang, Meng, Shabalin, Andrey A., Shad, Saboor, Hariharan, Pushpa, He, Amy Z., Qi, Liqun, Lappalainen, Tuuli, Li, Xin, Carithers, Latarsha J., Mestichelli, Bernadette, Kashin, Seva, Li, Gen, Jasmine, Farzana, Juettemann, Thomas, Montgomery, Stephen B., Zhang, Hailei, Traino, Heather M., Mosavel, Maghboeba, Koester, Susan E., Lin, Shin, Jewell, Scott D., Johnson, Audra, Wang, Li

Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project ai

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::2cfa79776c13af314e0a635e5e0aac59

Local genetic effects on gene expression across 44 human tissues

Autor: Aguet, François, Brown, Andrew A., Castel, Stephane E., Davis, Joe R., Mohammadi, Pejman, Segrè, Ayellet V., Zappala, Zachary, Abell, Nathan S., Frésard, Laure, Gamazon, Eric R., Gelfand, Ellen, Gloudemans, Michael J., He, Yuan, Hormozdiari, Farhad, Li, Xiao, Li, Xin, Liu, Boxiang, Garrido-Martín, Diego, Ongen, Halit, Palowitch, John J., Park, YoSon, Peterson, Christine B., Quon, Gerald, Ripke, Stephan, Shabalin, Andrey A., Shimko, Tyler C., Strober, Benjamin J., Sullivan, Timothy J., Teran, Nicole A., Tsang, Emily K., Zhang, Hailei, Zhou, Yi-Hui, Battle, Alexis, Bustamonte, Carlos D., Cox, Nancy J., Engelhardt, Barbara E., Eskin, Eleazar, Getz, Gad, Kellis, Manolis, Li, Gen, MacArthur, Daniel G., Nobel, Andrew B., Sabbati, Chiara, Wen, Xiaoquan, Wright, Fred A., Lappalainen, Tuuli, Ardlie, Kristin G., Dermitzakis, Emmanouil T., Brown, Christopher D., Montgomery, Stephen B.

Expression quantitative trait locus (eQTL) mapping provides a powerful means to identify functional variants influencing gene expression and disease pathogenesis. We report the identification of cis-eQTLs from 7,051 post-mortem samples representing 4

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fe30f61858ae2858caa877f8d294d26f
https://doi.org/10.1101/074450