Not logged in BV-BRC: a unified bacterial and viral bioinformatics resource with expanded functionality and AI integration Shukla, Maulik; Wattam, Alice R.; Aleman, Antonio; Bhattacharya, Roshni; Bowers, Nicole; Brettin, Thomas; Capria, Anna; Chia, Nicholas; Cucinell, Clark; Davis, James j; Dempsey, Donald M.; Dickerman, Allan; Dietrich, Emily M.; Gokdemir, Ozan; Hendrickson, R. curtis; Kenyon, Ronald W.; Klahn, Brian; Kuscuoglu, Mehmet; Lefkowitz, Elliot J.; Ma, Heng; Machi, Dustin; Macken, Catherine; Mann, Carla m; Mao, Chunhong; Nguyen, Marcus; Olsen, Gary J.; Olson, Robert D.; Overbeek, Ross; Owens, Sarah M.; Parrello, Bruce; Poretsky, Rachel; Pusch, Gordon D.; Ramanathan, Arvind; Sheriff, Jamal tyrone; Singh, Indresh; Stewart, Lucy; Vanoeffelen, Margo; Vonstein, Veronika; Warren, Andrew S.; Wilke, Andreas; Zmasek, Christian m; Zuniga, Abril; Stevens, Rick L. Share Save
Data imbalance in drug response prediction: multi-objective optimization approach in deep learning setting Narykov, Oleksandr; Zhu, Yitan; Brettin, Thomas; Evrard, Yvonne A.; Partin, Alexander; Xia, Fangfang; Shukla, Maulik; Vasanthakumari, Priyanka; Doroshow, James H.; Stevens, Rick L. Share Save
GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics Zvyagin, Maxim; Brace, Alexander; Hippe, Kyle; Deng, Yuntian; Zhang, Bin; Bohorquez, Cindy Orozco; Clyde, Austin; Kale, Bharat; Perez-Rivera, Danilo; Ma, Heng; Mann, Carla M.; Irvin, Michael; Ozgulbas, Defne G.; Vassilieva, Natalia; Pauloski, James Gregory; Ward, Logan; Hayot-Sasson, Valerie; Emani, Murali; Foreman, Sam; Xie, Zhen; Lin, Diangen; Shukla, Maulik; Nie, Weili; Romero, Josh; Dallago, Christian; Vahdat, Arash; Xiao, Chaowei; Gibbs, Thomas; Foster, Ian; Davis, James J.; Papka, Michael E.; Brettin, Thomas; Stevens, Rick; Anandkumar, Anima; Vishwanath, Venkatram; Ramanathan, Arvind Share Save
US National Institutes of Health Prioritization of SARS-CoV-2 Variants Turner, Sam; Alisoltani, Arghavan; Bratt, Debbie; Cohen-Lavi, Liel; Dearlove, Bethany L.; Drosten, Christian; Fischer, Will M.; Fouchier, Ron A. M.; Gonzalez-Reiche, Ana Silvia; Jaroszewski, Lukasz; Khalil, Zain; LeGresley, Eric; Johnson, Marc; Jones, Terry C.; Muehlemann, Barbara; O'Connor, David; Sedova, Mayya; Shukla, Maulik; Theiler, James; Wallace, Zachary S.; Yoon, Hyejin; Zhang, Yun; van Bakel, Harm; Degrace, Marciela M.; Ghedin, Elodie; Godzik, Adam; Hertz, Tomer; Korber, Bette; Lemieux, Jacob; Niewiadomska, Anna M.; Post, Diane J.; Rolland, Morgane; Scheuermann, Richard; Smith, Derek J. Share Save
Data augmentation and multimodal learning for predicting drug response in patient-derived xenografts from gene expressions and histology images Partin, Alexander; Brettin, Thomas; Zhu, Yitan; Dolezal, James M. M.; Kochanny, Sara; Pearson, Alexander T. T.; Shukla, Maulik; Evrard, Yvonne A. A.; Doroshow, James H. H.; Stevens, Rick L. L. Share Save
Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR Olson, Robert D.; Assaf, Rida; Brettin, Thomas; Conrad, Neal; Cucinell, Clark; Davis, James J.; Dempsey, Donald M.; Dickerman, Allan; Dietrich, Emily M.; Kenyon, Ronald W.; Kuscuoglu, Mehmet; Lefkowitz, Elliot J.; Lu, Jian; Machi, Dustin; Macken, Catherine; Mao, Chunhong; Niewiadomska, Anna; Nguyen, Marcus; Olsen, Gary J.; Overbeek, Jamie C.; Parrello, Bruce; Parrello, Victoria; Porter, Jacob S.; Pusch, Gordon D.; Shukla, Maulik; Singh, Indresh; Stewart, Lucy; Tan, Gene; Thomas, Chris; VanOeffelen, Margo; Vonstein, Veronika; Wallace, Zachary S.; Warren, Andrew S.; Wattam, Alice R.; Xia, Fangfang; Yoo, Hyunseung; Zhang, Yun; Zmasek, Christian M.; Scheuermann, Richard H.; Stevens, Rick L. Share Save
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A cross-study analysis of drug response prediction in cancer cell lines Xia, Fangfang; Allen, Jonathan; Balaprakash, Prasanna; Brettin, Thomas; Garcia-Cardona, Cristina; Clyde, Austin; Cohn, Judith; Doroshow, James; Duan, Xiaotian; Dubinkina, Veronika; Evrard, Yvonne; Fan, Ya Ju; Gans, Jason; He, Stewart; Lu, Pinyi; Maslov, Sergei; Partin, Alexander; Shukla, Maulik; Stahlberg, Eric; Wozniak, Justin M.; Yoo, Hyunseung; Zaki, George; Zhu, Yitan; Stevens, Rick Share Save
A genomic data resource for predicting antimicrobial resistance from laboratory-derived antimicrobial susceptibility phenotypes VanOeffelen, Margo; Nguyen, Marcus; Aytan-Aktug, Derya; Brettin, Thomas; Dietrich, Emily M.; Kenyon, Ronald W.; Machi, Dustin; Mao, Chunhong; Olson, Robert; Pusch, Gordon D.; Shukla, Maulik; Stevens, Rick; Vonstein, Veronika; Warren, Andrew S.; Wattam, Alice R.; Yoo, Hyunseung; Davis, James J. Share Save
Converting tabular data into images for deep learning with convolutional neural networks (vol 11, 11325, 2021) Zhu, Yitan; Brettin, Thomas; Xia, Fangfang; Partin, Alexander; Shukla, Maulik; Yoo, Hyunseung; Evrard, Yvonne A.; Doroshow, James H.; Stevens, Rick L. Share Save
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Molecular Architecture of Early Dissemination and Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area Long, S. Wesley; Olsen, Randall J.; Christensen, Paul A.; Bernard, David W.; Davis, James J.; Shukla, Maulik; Nguyen, Marcus; Saavedra, Matthew Ojeda; Yerramilli, Prasanti; Pruitt, Layne; Subedi, Sishir; Kuo, Hung-Che; Hendrickson, Heather; Eskandari, Ghazaleh; Nguyen, Hoang A. T.; Long, J. Hunter; Kumaraswami, Muthiah; Goike, Jule; Boutz, Daniel; Gollihar, Jimmy; McLellan, Jason S.; Chou, Chia-Wei; Javanmardi, Kamyab; Finkelstein, Ilya J.; Musser, James M. Share Save
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The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities Davis, James J.; Wattam, Alice R.; Aziz, Ramy K.; Brettin, Thomas; Butler, Ralph; Butler, Rory M.; Chlenski, Philippe; Conrad, Neal; Dickerman, Allan; Dietrich, Emily M.; Gabbard, Joseph L.; Gerdes, Svetlana; Guard, Andrew; Kenyon, Ronald W.; Machi, Dustin; Mao, Chunhong; Murphy-Olson, Dan; Nguyen, Marcus; Nordberg, Eric K.; Olsen, Gary J.; Olson, Robert D.; Overbeek, Jamie C.; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D.; Shukla, Maulik; Thomas, Chris; VanOeffelen, Margo; Vonstein, Veronika; Warren, Andrew S.; Xia, Fangfang; Xie, Dawen; Yoo, Hyunseung; Stevens, Rick Share Save
KBase: The United States Department of Energy Systems Biology Knowledgebase Arkin, Adam P.; Cottingham, Robert W.; Henry, Christopher S.; Harris, Nomi L.; Stevens, Rick L.; Maslov, Sergei; Dehal, Paramvir; Ware, Doreen; Perez, Fernando; Canon, Shane; Sneddon, Michael W.; Henderson, Matthew L.; Riehl, William J.; Murphy-Olson, Dan; Chan, Stephen Y.; Kamimura, Roy T.; Kumari, Sunita; Drake, Meghan M.; Brettin, Thomas S.; Glass, Elizabeth M.; Chivian, Dylan; Gunter, Dan; Weston, David J.; Allen, Benjamin H.; Baumohl, Jason; Best, Aaron A.; Bowen, Ben; Brenner, Steven E.; Bun, Christopher C.; Chandonia, John-Marc; Chia, Jer-Ming; Colasanti, Ric; Conrad, Neal; Davis, James J.; Davison, Brian H.; DeJongh, Matthew; Devoid, Scott; Dietrich, Emily; Dubchak, Inna; Edirisinghe, Janaka N.; Fang, Gang; Faria, Jose P.; Frybarger, Paul M.; Gerlach, Wolfgang; Gerstein, Mark; Greiner, Annette; Gurtowski, James; Haun, Holly L.; He, Fei; Jain, Rashmi; Joachimiak, Marcin P.; Keegan, Kevin P.; Kondo, Shinnosuke; Kumar, Vivek; Land, Miriam L.; Meyer, Folker; Mills, Marissa; Novichkov, Pavel S.; Oh, Taeyun; Olsen, Gary J.; Olson, Robert; Parrello, Bruce; Pasternak, Shiran; Pearson, Erik; Poon, Sarah S.; Price, Gavin A.; Ramakrishnan, Srividya; Ranjan, Priya; Ronald, Pamela C.; Schatz, Michael C.; Seaver, Samuel M. D.; Shukla, Maulik; Sutormin, Roman A.; Syed, Mustafa H.; Thomason, James; Tintle, Nathan L.; Wang, Daifeng; Xia, Fangfang; Yoo, Hyunseung; Yoo, Shinjae; Yu, Dantong Share Save
Developing an &ITin silico&IT minimum inhibitory concentration panel test for &ITKlebsiella pneumoniae &IT Nguyen, Marcus; Brettin, Thomas; Long, S. Wesley; Musser, James M.; Olsen, Randall J.; Olson, Robert; Shukla, Maulik; Stevens, Rick L.; Xia, Fangfang; Yoo, Hyunseung; Davis, James J. Share Save
PATRIC as a unique resource for studying antimicrobial resistance Antonopoulos, Dionysios A.; Assaf, Rida; Aziz, Ramy Karam; Brettin, Thomas; Bun, Christopher; Conrad, Neal; Davis, James J.; Dietrich, Emily M.; Disz, Terry; Gerdes, Svetlana; Kenyon, Ronald W.; Machi, Dustin; Mao, Chunhong; Murphy-Olson, Daniel E.; Nordberg, Eric K.; Olsen, Gary J.; Olson, Robert; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D.; Santerre, John; Shukla, Maulik; Stevens, Rick L.; VanOeffelen, Margo; Vonstein, Veronika; Warren, Andrew S.; Wattam, Alice R.; Xia, Fangfang; Yoo, Hyunseung Share Save
Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center Wattam, Alice R.; Davis, James J.; Assaf, Rida; Boisvert, Sebastien; Brettin, Thomas; Bun, Christopher; Conrad, Neal; Dietrich, Emily M.; Disz, Terry; Gabbard, Joseph L.; Gerdes, Svetlana; Henry, Christopher S.; Kenyon, Ronald W.; Machi, Dustin; Mao, Chunhong; Nordberg, Eric K.; Olsen, Gary J.; Murphy-Olson, Daniel E.; Olson, Robert; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D.; Shukla, Maulik; Vonstein, Veronika; Warren, Andrew; Xia, Fangfang; Yoo, Hyunseung; Stevens, Rick L. Share Save
Antimicrobial Resistance Prediction in PATRIC and RAST Davis, James J.; Boisvert, Sebastien; Brettin, Thomas; Kenyon, Ronald W.; Mao, Chunhong; Olson, Robert; Overbeek, Ross; Santerre, John; Shukla, Maulik; Wattam, Alice R.; Will, Rebecca; Xia, Fangfang; Stevens, Rick Share Save
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