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BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets (vol 20, pg 824, 2023) Manubens-Gil, Linus; Zhou, Zhi; Chen, Hanbo; Ramanathan, Arvind; Liu, Xiaoxiao; Liu, Yufeng; Bria, Alessandro; Gillette, Todd; Ruan, Zongcai; Yang, Jian; Radojevic, Miroslav; Zhao, Ting; Cheng, Li; Qu, Lei; Liu, Siqi; Bouchard, Kristofer E.; Gu, Lin; Cai, Weidong; Ji, Shuiwang; Roysam, Badrinath; Wang, Ching-Wei; Yu, Hongchuan; Sironi, Amos; Iascone, Daniel Maxim; Zhou, Jie; Bas, Erhan; Conde-Sousa, Eduardo; Aguiar, Paulo; Li, Xiang; Li, Yujie; Nanda, Sumit; Wang, Yuan; Muresan, Leila; Fua, Pascal; Ye, Bing; He, Hai-yan; Staiger, Jochen F.; Peter, Manuel; Cox, Daniel N.; Simonneau, Michel; Oberlaender, Marcel; Jefferis, Gregory; Ito, Kei; Gonzalez-Bellido, Paloma; Kim, Jinhyun; Rubel, Edwin; Cline, Hollis T.; Zeng, Hongkui; Nern, Aljoscha; Chiang, Ann-Shyn; Yao, Jianhua; Roskams, Jane; Livesey, Rick; Stevens, Janine; Liu, Tianming; Dang, Chinh; Guo, Yike; Zhong, Ning; Tourassi, Georgia; Hill, Sean; Hawrylycz, Michael; Koch, Christof; Meijering, Erik; Ascoli, Giorgio A.; Peng, Hanchuan 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
Machine Learning-Driven Multiscale Modeling: Bridging the Scales with a Next-Generation Simulation Infrastructure Ingolfsson, Helgi I.; Bhatia, Harsh; Aydin, Fikret; Oppelstrup, Tomas; Lopez, Cesar A.; Stanton, Liam G.; Carpenter, Timothy S.; Wong, Sergio; Di Natale, Francesco; Zhang, Xiaohua; Moon, Joseph Y.; Stanley, Christopher B.; Chavez, Joseph R.; Nguyen, Kien; Dharuman, Gautham; Burns, Violetta; Shrestha, Rebika; Goswami, Debanjan; Gulten, Gulcin; Van, Que N.; Ramanathan, Arvind; Van Essen, Brian; Hengartner, Nicolas W.; Stephen, Andrew G.; Turbyville, Thomas; Bremer, Peer-Timo; Gnanakaran, S.; Glosli, James N.; Lightstone, Felice C.; Nissley, Dwight V.; Streitz, Frederick H. Share Save
BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets Manubens-Gil, Linus; Zhou, Zhi; Chen, Hanbo; Ramanathan, Arvind; Liu, Xiaoxiao; Liu, Yufeng; Bria, Alessandro; Gillette, Todd; Ruan, Zongcai; Yang, Jian; Radojevic, Miroslav; Zhao, Ting; Cheng, Li; Qu, Lei; Liu, Siqi; Bouchard, Kristofer E.; Gu, Lin; Cai, Weidong; Ji, Shuiwang; Roysam, Badrinath; Wang, Ching-Wei; Yu, Hongchuan; Sironi, Amos; Iascone, Daniel Maxim; Zhou, Jie; Bas, Erhan; Conde-Sousa, Eduardo; Aguiar, Paulo; Li, Xiang; Li, Yujie; Nanda, Sumit; Wang, Yuan; Muresan, Leila; Fua, Pascal; Ye, Bing; He, Hai-yan; Staiger, Jochen F.; Peter, Manuel; Cox, Daniel N.; Simonneau, Michel; Oberlaender, Marcel; Jefferis, Gregory; Ito, Kei; Gonzalez-Bellido, Paloma; Kim, Jinhyun; Rubel, Edwin; Cline, Hollis T.; Zeng, Hongkui; Nern, Aljoscha; Chiang, Ann-Shyn; Yao, Jianhua; Roskams, Jane; Livesey, Rick; Stevens, Janine; Liu, Tianming; Dang, Chinh; Guo, Yike; Zhong, Ning; Tourassi, Georgia; Hill, Sean; Hawrylycz, Michael; Koch, Christof; Meijering, Erik; Ascoli, Giorgio A.; Peng, Hanchuan Share Save
AI-Accelerated Design of Targeted Covalent Inhibitors for SARS-CoV-2 Joshi, Rajendra P.; Schultz, Katherine J.; Wilson, Jesse William; Kruel, Agustin; Varikoti, Rohith Anand; Kombala, Chathuri J.; Kneller, Daniel W.; Galanie, Stephanie; Phillips, Gwyndalyn; Zhang, Qiu; Coates, Leighton; Parvathareddy, Jyothi; Surendranathan, Surekha; Kong, Ying; Clyde, Austin; Ramanathan, Arvind; Jonsson, Colleen B.; Brandvold, Kristoffer R.; Zhou, Mowei; Head, Martha S.; Kovalevsky, Andrey; Kumar, Neeraj Share Save
AI-accelerated protein-ligand docking for SARS-CoV-2 is 100-fold faster with no significant change in detection Clyde, Austin; Liu, Xuefeng; Brettin, Thomas; Yoo, Hyunseung; Partin, Alexander; Babuji, Yadu; Blaiszik, Ben; Mohd-Yusof, Jamaludin; Merzky, Andre; Turilli, Matteo; Jha, Shantenu; Ramanathan, Arvind; Stevens, Rick Share Save
Towards a modular architecture for science factories Vescovi, Rafael; Ginsburg, Tobias; Hippe, Kyle; Ozgulbas, Doga; Stone, Casey; Stroka, Abraham; Butler, Rory; Blaiszik, Ben; Brettin, Tom; Chard, Kyle; Hereld, Mark; Ramanathan, Arvind; Stevens, Rick; Vriza, Aikaterini; Xu, Jie; Zhang, Qingteng; Foster, Ian Share Save
#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol Dommer, Abigail; Casalino, Lorenzo; Kearns, Fiona; Rosenfeld, Mia; Wauer, Nicholas; Ahn, Surl-Hee; Russo, John; Oliveira, Sofia; Morris, Clare; Bogetti, Anthony; Trifan, Anda; Brace, Alexander; Sztain, Terra; Clyde, Austin; Ma, Heng; Chennubhotla, Chakra; Lee, Hyungro; Turilli, Matteo; Khalid, Syma; Tamayo-Mendoza, Teresa; Welborn, Matthew; Christensen, Anders; Smith, Daniel Ga; Qiao, Zhuoran; Sirumalla, Sai K.; O'Connor, Michael; Manby, Frederick; Anandkumar, Anima; Hardy, David; Phillips, James; Stern, Abraham; Romero, Josh; Clark, David; Dorrell, Mitchell; Maiden, Tom; Huang, Lei; McCalpin, John; Woods, Christopher; Gray, Alan; Williams, Matt; Barker, Bryan; Rajapaksha, Harinda; Pitts, Richard; Gibbs, Tom; Stone, John; Zuckerman, Daniel M.; Mulholland, Adrian J.; Miller, Thomas, III; Jha, Shantenu; Ramanathan, Arvind; Chong, Lillian; Amaro, Rommie E. Share Save
Intelligent resolution: Integrating Cryo-EM with AI-driven multi-resolution simulations to observe the severe acute respiratory syndrome coronavirus-2 replication-transcription machinery in action Trifan, Anda; Gorgun, Defne; Salim, Michael; Li, Zongyi; Brace, Alexander; Zvyagin, Maxim; Ma, Heng; Clyde, Austin; Clark, David; Hardy, David J.; Burnley, Tom; Huang, Lei; McCalpin, John; Emani, Murali; Yoo, Hyenseung; Yin, Junqi; Tsaris, Aristeidis; Subbiah, Vishal; Raza, Tanveer; Liu, Jessica; Trebesch, Noah; Wells, Geoffrey; Mysore, Venkatesh; Gibbs, Thomas; Phillips, James; Chennubhotla, S. Chakra; Foster, Ian; Stevens, Rick; Anandkumar, Anima; Vishwanath, Venkatram; Stone, John E.; Tajkhorshid, Emad; Harris, Sarah A.; Ramanathan, Arvind Share Save
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Machine learning-driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins Ingolfsson, Helgi I.; Neale, Chris; Carpenter, Timothy S.; Shrestha, Rebika; Lopez, Cesar A.; Tran, Timothy H.; Oppelstrup, Tomas; Bhatia, Harsh; Stanton, Liam G.; Zhang, Xiaohua; Sundram, Shiv; Di Natale, Francesco; Agarwal, Animesh; Dharuman, Gautham; Schumacher, Sara I. L. Kokkila; Turbyville, Thomas; Gulten, Gulcin; Van, Que N.; Goswami, Debanjan; Jean-Francois, Frantz; Agamasu, Constance; Chen, De; Hettige, Jeevapani J.; Travers, Timothy; Sarkar, Sumantra; Surh, Michael P.; Yang, Yue; Moody, Adam; Liu, Shusen; Van Essen, Brian C.; Voter, Arthur F.; Ramanathan, Arvind; Hengartner, Nicolas W.; Simanshu, Dhirendra K.; Stephen, Andrew G.; Bremer, Peer-Timo; Gnanakaran, S.; Glosli, James N.; Lightstone, Felice C.; McCormick, Frank; Nissley, Dwight, V; Streitz, Frederick H. Share Save
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High-Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Noncovalent Inhibitor Clyde, Austin; Galanie, Stephanie; Kneller, Daniel W.; Ma, Heng; Babuji, Yadu; Blaiszik, Ben; Brace, Alexander; Brettin, Thomas; Chard, Kyle; Chard, Ryan; Coates, Leighton; Foster, Ian; Hauner, Darin; Kertesz, Vilmos; Kumar, Neeraj; Lee, Hyungro; Li, Zhuozhao; Merzky, Andre; Schmidt, Jurgen G.; Tan, Li; Titov, Mikhail; Trifan, Anda; Turilli, Matteo; Van Dam, Hubertus; Chennubhotla, Srinivas C.; Jha, Shantenu; Kovalevsky, Andrey; Ramanathan, Arvind; Head, Martha S.; Stevens, Rick Share Save
Structural, Electronic, and Electrostatic Determinants for Inhibitor Binding to Subsites S1 and S2 in SARS-CoV-2 Main Protease Kneller, Daniel W.; Li, Hui; Galanie, Stephanie; Phillips, Gwyndalyn; Labbe, Audrey; Weiss, Kevin L.; Zhang, Qiu; Arnould, Mark A.; Clyde, Austin; Ma, Heng; Ramanathan, Arvind; Jonsson, Colleen B.; Head, Martha S.; Coates, Leighton; Louis, John M.; Bonnesen, Peter, V; Kovalevsky, Andrey Share Save
Pandemic drugs at pandemic speed: infrastructure for accelerating COVID-19 drug discovery with hybrid machine learning- and physics-based simulations on high-performance computers Bhati, Agastya P.; Wan, Shunzhou; Alfe, Dario; Clyde, Austin R.; Bode, Mathis; Tan, Li; Titov, Mikhail; Merzky, Andre; Turilli, Matteo; Jha, Shantenu; Highfield, Roger R.; Rocchia, Walter; Scafuri, Nicola; Succi, Sauro; Kranzlmueller, Dieter; Mathias, Gerald; Wifling, David; Donon, Yann; Di Meglio, Alberto; Vallecorsa, Sofia; Ma, Heng; Trifan, Anda; Ramanathan, Arvind; Brettin, Tom; Partin, Alexander; Xia, Fangfang; Duan, Xiaotan; Stevens, Rick; Coveney, Peter V. Share Save
Dynamic Profiling of β-Coronavirus 3CL Mpro Protease Ligand-Binding Sites Cho, Eunice; Rosa, Margarida; Anjum, Ruhi; Mehmood, Saman; Soban, Mariya; Mujtaba, Moniza; Bux, Khair; Moin, Syed T.; Tanweer, Mohammad; Dantu, Sarath; Pandini, Alessandro; Yin, Junqi; Ma, Heng; Ramanathan, Arvind; Islam, Barira; Mey, Antonia S. J. S.; Bhowmik, Debsindhu; Haider, Shozeb Share Save
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