Thomas S. Brettin

Publication Activity (10 Years)

Years Active: 2001-2024
Publications (10 Years): 30

Top Topics

Medical Image Analysis

Chemical Compounds

Top Venues

Briefings Bioinform.

Nucleic Acids Res.

Publications

Archit Vasan, Ozan Gökdemir, Alexander Brace, Arvind Ramanathan, Thomas S. Brettin, Rick Stevens, Venkatram Vishwanath
High Performance Binding Affinity Prediction with a Transformer-Based Surrogate Model. IPDPS (Workshops) (2024)
Oleksandr Narykov, Yitan Zhu, Thomas S. Brettin, Yvonne A. Evrard, Alexander Partin, Maulik Shukla, Priyanka Vasanthakumari, James H. Doroshow, Rick Stevens
Entropy-Based Regularization on Deep Learning Models for Anti-Cancer Drug Response Prediction. SC Workshops (2023)
Maxim Zvyagin, Alexander Brace, Kyle Hippe, Yuntian Deng, Bin Zhang, Cindy Orozco Bohorquez, Austin Clyde, Bharat Kale, Danilo Perez-Rivera, Heng Ma, Carla M. Mann, Michael W. Irvin, Defne G. Ozgulbas, Natalia Vassilieva, J. Gregory Pauloski, Logan Ward, Valerie Hayot-Sasson, Murali Emani, Sam Foreman, Zhen Xie, Diangen Lin, Maulik Shukla, Weili Nie, Josh Romero, Christian Dallago, Arash Vahdat, Chaowei Xiao, Thomas Gibbs, Ian T. Foster, James J. Davis, Michael E. Papka, Thomas S. Brettin, Rick Stevens, Anima Anandkumar, Venkatram Vishwanath, Arvind Ramanathan
GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics. Int. J. High Perform. Comput. Appl. 37 (6) (2023)
Robert D. Olson, Rida Assaf, Thomas S. Brettin, Neal Conrad, Clark Cucinell, James J. Davis, Donald M. Dempsey, Allan Dickerman, Emily M. Dietrich, Ronald W. Kenyon, Mehmet Kuscuoglu, Elliot J. Lefkowitz, Jian Lu, Dustin Machi, Catherine Macken, Chunhong Mao, Anna Maria Niewiadomska, Marcus Nguyen, Gary J. Olsen, Jamie C. Overbeek, Bruce D. Parrello, Victoria Parrello, Jacob s Porter, Gordon D. Pusch, Maulik Shukla, Indresh Singh, Lucy Stewart, Gene Tan, Chris Thomas, Margo VanOeffelen, Veronika Vonstein, Zachary S. Wallace, Andrew S. Warren, Alice R. Wattam, Fangfang Xia, Hyun Seung Yoo, Yun Zhang, Christian M. Zmasek, Richard H. Scheuermann, Rick L. Stevens
Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR. Nucleic Acids Res. 51 (D1) (2023)
Justin M. Wozniak, Rajeev Jain, Andreas Wilke, Rylie Weaver, Alexander Partin, Thomas S. Brettin, Rick Stevens
An Automation Framework for Comparison of Cancer Response Models Across Configurations. e-Science (2023)
Archit Vasan, Thomas S. Brettin, Rick Stevens, Arvind Ramanathan, Venkatram Vishwanath
Scalable Lead Prediction with Transformers using HPC resources. SC Workshops (2023)
Shuaiwen Leon Song, Bonnie Kruft, Minjia Zhang, Conglong Li, Shiyang Chen, Chengming Zhang, Masahiro Tanaka, Xiaoxia Wu, Jeff Rasley, Ammar Ahmad Awan, Connor Holmes, Martin Cai, Adam Ghanem, Zhongzhu Zhou, Yuxiong He, Pete Luferenko, Divya Kumar, Jonathan A. Weyn, Ruixiong Zhang, Sylwester Klocek, Volodymyr Vragov, Mohammed AlQuraishi, Gustaf Ahdritz, Christina Floristean, Cristina Negri, Rao Kotamarthi, Venkatram Vishwanath, Arvind Ramanathan, Sam Foreman, Kyle Hippe, Troy Arcomano, Romit Maulik, Maxim Zvyagin, Alexander Brace, Bin Zhang, Cindy Orozco Bohorquez, Austin Clyde, Bharat Kale, Danilo Perez-Rivera, Heng Ma, Carla M. Mann, Michael W. Irvin, J. Gregory Pauloski, Logan T. Ward, Valérie Hayot-Sasson, Murali Emani, Zhen Xie, Diangen Lin, Maulik Shukla, Ian T. Foster, James J. Davis, Michael E. Papka, Thomas S. Brettin, Prasanna Balaprakash, Gina Tourassi, John Gounley, Heidi A. Hanson, Thomas E. Potok, Massimiliano Lupo Pasini, Kate Evans, Dan Lu, Dalton D. Lunga, Junqi Yin, Sajal Dash, Feiyi Wang, Mallikarjun Shankar, Isaac Lyngaas, Xiao Wang, Guojing Cong, Pei Zhang, Ming Fan, Siyan Liu, Adolfy Hoisie, Shinjae Yoo, Yihui Ren, William Tang, Kyle Felker, Alexey Svyatkovskiy, Hang Liu, Ashwin M. Aji, Angela Dalton, Michael J. Schulte, Karl Schulz, Yuntian Deng, Weili Nie, Josh Romero, Christian Dallago, Arash Vahdat, Chaowei Xiao, Thomas Gibbs, Anima Anandkumar, Rick Stevens
DeepSpeed4Science Initiative: Enabling Large-Scale Scientific Discovery through Sophisticated AI System Technologies. CoRR (2023)
Yulun Wu, Nicholas Choma, Andrew Deru Chen, Mikaela Cashman, Érica Teixeira Prates, Verónica G. Melesse Vergara, Manesh Shah, Austin Clyde, Thomas S. Brettin, Wibe Albert de Jong, Neeraj Kumar, Martha S. Head, Rick L. Stevens, Peter Nugent, Daniel A. Jacobson, James B. Brown
Spatial Graph Attention and Curiosity-driven Policy for Antiviral Drug Discovery. ICLR (2022)
Fangfang Xia, Jonathan E. Allen, Prasanna Balaprakash, Thomas S. Brettin, Cristina Garcia-Cardona, Austin Clyde, Judith D. Cohn, James H. Doroshow, Xiaotian Duan, Veronika Dubinkina, Yvonne A. Evrard, Ya Ju Fan, Jason Gans, Stewart He, Pinyi Lu, Sergei Maslov, Alexander Partin, Maulik Shukla, Eric A. Stahlberg, Justin M. Wozniak, Hyun Seung Yoo, George F. Zaki, Yitan Zhu, Rick Stevens
A cross-study analysis of drug response prediction in cancer cell lines. Briefings Bioinform. 23 (1) (2022)
Austin Clyde, Stephanie Galanie, Daniel W. Kneller, Heng Ma, Yadu N. Babuji, Ben Blaiszik, Alexander Brace, Thomas S. Brettin, Kyle Chard, Ryan Chard, Leighton Coates, Ian T. Foster, Darin Hauner, Vilmos Kertesz, Neeraj Kumar, Hyungro Lee, Zhuozhao Li, André Merzky, Jurgen G. Schmidt, Li Tan, Mikhail Titov, Anda Trifan, Matteo Turilli, Hubertus Van Dam, Srinivas C. Chennubhotla, Shantenu Jha, Andrey Kovalevsky, Arvind Ramanathan, Martha S. Head, Rick Stevens
High-Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Noncovalent Inhibitor. J. Chem. Inf. Model. 62 (1) (2022)
Alexander Partin, Thomas S. Brettin, Yitan Zhu, Oleksandr Narykov, Austin Clyde, Jamie Overbeek, Rick L. Stevens
Deep learning methods for drug response prediction in cancer: predominant and emerging trends. CoRR (2022)
Yulun Wu, Nicholas Choma, Andrew Chen, Mikaela Cashman, Érica T. Prates, Manesh Shah, Verónica G. Melesse Vergara, Austin Clyde, Thomas S. Brettin, Wibe A. de Jong, Neeraj Kumar, Martha S. Head, Rick L. Stevens, Peter Nugent, Daniel A. Jacobson, James B. Brown
Spatial Graph Attention and Curiosity-driven Policy for Antiviral Drug Discovery. CoRR (2021)
Margo VanOeffelen, Marcus Nguyen, Derya Aytan-Aktug, Thomas S. Brettin, Emily M. Dietrich, Ronald W. Kenyon, Dustin Machi, Chunhong Mao, Robert Olson, Gordon D. Pusch, Maulik Shukla, Rick Stevens, Veronika Vonstein, Andrew S. Warren, Alice R. Wattam, Hyun Seung Yoo, James J. Davis
A genomic data resource for predicting antimicrobial resistance from laboratory-derived antimicrobial susceptibility phenotypes. Briefings Bioinform. 22 (6) (2021)
Alexander Partin, Thomas S. Brettin, Yvonne A. Evrard, Yitan Zhu, Hyun Seung Yoo, Fangfang Xia, Songhao Jiang, Austin Clyde, Maulik Shukla, Michael Fonstein, James H. Doroshow, Rick L. Stevens
Learning curves for drug response prediction in cancer cell lines. BMC Bioinform. 22 (1) (2021)
Austin Clyde, Thomas S. Brettin, Alexander Partin, Hyun Seung Yoo, Yadu N. Babuji, Ben Blaiszik, André Merzky, Matteo Turilli, Shantenu Jha, Arvind Ramanathan, Rick Stevens
Protein-Ligand Docking Surrogate Models: A SARS-CoV-2 Benchmark for Deep Learning Accelerated Virtual Screening. CoRR (2021)
Max Zvyagin, Thomas S. Brettin, Arvind Ramanathan, Sumit Kumar Jha
CrossedWires: A Dataset of Syntactically Equivalent but Semantically Disparate Deep Learning Models. CoRR (2021)
Aymen Al Saadi, Dario Alfè, Yadu N. Babuji, Agastya Bhati, Ben Blaiszik, Alexander Brace, Thomas S. Brettin, Kyle Chard, Ryan Chard, Austin Clyde, Peter V. Coveney, Ian T. Foster, Tom Gibbs, Shantenu Jha, Kristopher Keipert, Dieter Kranzlmüller, Thorsten Kurth, Hyungro Lee, Zhuozhao Li, Heng Ma, Gerald Mathias, André Merzky, Alexander Partin, Arvind Ramanathan, Ashka Shah, Abraham C. Stern, Rick Stevens, Li Tan, Mikhail Titov, Anda Trifan, Aristeidis Tsaris, Matteo Turilli, Huub J. J. Van Dam, Shunzhou Wan, David Wifling, Junqi Yin
IMPECCABLE: Integrated Modeling PipelinE for COVID Cure by Assessing Better LEads. ICPP (2021)
Yitan Zhu, Thomas S. Brettin, Yvonne A. Evrard, Alexander Partin, Fangfang Xia, Maulik Shukla, Hyun Seung Yoo, James H. Doroshow, Rick Stevens
Ensemble Transfer Learning for the Prediction of Anti-Cancer Drug Response. CoRR (2020)
Alexander Partin, Thomas S. Brettin, Yvonne A. Evrard, Yitan Zhu, Hyun Seung Yoo, Fangfang Xia, Songhao Jiang, Austin Clyde, Maulik Shukla, Michael Fonstein, James H. Doroshow, Rick Stevens
Learning Curves for Drug Response Prediction in Cancer Cell Lines. CoRR (2020)
James J. Davis, Alice R. Wattam, Ramy K. Aziz, Thomas S. Brettin, Ralph Butler, Rory Butler, Philippe Chlenski, Neal Conrad, Allan Dickerman, Emily M. Dietrich, Joseph L. Gabbard, Svetlana Gerdes, Andrew Guard, Ronald W. Kenyon, Dustin Machi, Chunhong Mao, Daniel E. Murphy-Olson, Marcus Nguyen, Eric K. Nordberg, Gary J. Olsen, Robert Olson, Jamie C. Overbeek, Ross A. Overbeek, Bruce D. Parrello, Gordon D. Pusch, Maulik Shukla, Chris Thomas, Margo VanOeffelen, Veronika Vonstein, Andrew S. Warren, Fangfang Xia, Dawen Xie, Hyun Seung Yoo, Rick Stevens
The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities. Nucleic Acids Res. 48 (Database-Issue) (2020)
Aymen Al Saadi, Dario Alfè, Yadu N. Babuji, Agastya Bhati, Ben Blaiszik, Thomas S. Brettin, Kyle Chard, Ryan Chard, Peter V. Coveney, Anda Trifan, Alex Brace, Austin Clyde, Ian T. Foster, Tom Gibbs, Shantenu Jha, Kristopher Keipert, Thorsten Kurth, Dieter Kranzlmüller, Hyungro Lee, Zhuozhao Li, Heng Ma, André Merzky, Gerald Mathias, Alexander Partin, Junqi Yin, Arvind Ramanathan, Ashka Shah, Abraham C. Stern, Rick Stevens, Li Tan, Mikhail Titov, Aristeidis Tsaris, Matteo Turilli, Huub J. J. Van Dam, Shunzhou Wan, David Wifling
IMPECCABLE: Integrated Modeling PipelinE for COVID Cure by Assessing Better LEads. CoRR (2020)
Neil Getty, Thomas S. Brettin, Dong Jin, Rick Stevens, Fangfang Xia
Deep Medical Image Analysis with Representation Learning and Neuromorphic Computing. CoRR (2020)
Justin M. Wozniak, Hyun Seung Yoo, Jamaludin Mohd-Yusof, Bogdan Nicolae, Nicholson T. Collier, Jonathan Ozik, Thomas S. Brettin, Rick Stevens
High-bypass Learning: Automated Detection of Tumor Cells That Significantly Impact Drug Response. MLHPC/AI4S@SC (2020)
Xingfu Wu, Valerie E. Taylor, Justin M. Wozniak, Rick Stevens, Thomas S. Brettin, Fangfang Xia
Performance, Energy, and Scalability Analysis and Improvement of Parallel Cancer Deep Learning CANDLE Benchmarks. ICPP (2019)
Dionysios A. Antonopoulos, Rida Assaf, Ramy Karam Aziz, Thomas S. Brettin, Christopher Bun, Neal Conrad, James J. Davis, Emily M. Dietrich, Terry Disz, Svetlana Gerdes, Ronald W. Kenyon, Dustin Machi, Chunhong Mao, Daniel E. Murphy-Olson, Eric K. Nordberg, Gary J. Olsen, Robert Olson, Ross A. Overbeek, Bruce D. Parrello, Gordon D. Pusch, John Santerre, Maulik Shukla, Rick L. Stevens, Margo VanOeffelen, Veronika Vonstein, Andrew S. Warren, Alice R. Wattam, Fangfang Xia, Hyun Seung Yoo
PATRIC as a unique resource for studying antimicrobial resistance. Briefings Bioinform. 20 (4) (2019)
Justin M. Wozniak, Rajeev Jain, Prasanna Balaprakash, Jonathan Ozik, Nicholson T. Collier, John Bauer, Fangfang Xia, Thomas S. Brettin, Rick Stevens, Jamaludin Mohd-Yusof, Cristina Garcia-Cardona, Brian Van Essen, Matthew Baughman
CANDLE/Supervisor: a workflow framework for machine learning applied to cancer research. BMC Bioinform. (18) (2018)
George F. Zaki, Justin M. Wozniak, Jonathan Ozik, Nicholson T. Collier, Thomas S. Brettin, Rick Stevens
Portable and Reusable Deep Learning Infrastructure with Containers to Accelerate Cancer Studies. ESPM2@SC (2018)
Fangfang Xia, Maulik Shukla, Thomas S. Brettin, Cristina Garcia-Cardona, Judith D. Cohn, Jonathan E. Allen, Sergei Maslov, Susan L. Holbeck, James H. Doroshow, Yvonne A. Evrard, Eric A. Stahlberg, Rick L. Stevens
Predicting tumor cell line response to drug pairs with deep learning. BMC Bioinform. (18) (2018)
Alice R. Wattam, James J. Davis, Rida Assaf, Sébastien Boisvert, Thomas S. Brettin, Christopher Bun, Neal Conrad, Emily M. Dietrich, Terry Disz, Joseph L. Gabbard, Svetlana Gerdes, Christopher S. Henry, Ronald W. Kenyon, Dustin Machi, Chunhong Mao, Eric K. Nordberg, Gary J. Olsen, Daniel E. Murphy-Olson, Robert Olson, Ross A. Overbeek, Bruce D. Parrello, Gordon D. Pusch, Maulik Shukla, Veronika Vonstein, Andrew S. Warren, Fangfang Xia, Hyun Seung Yoo, Rick L. Stevens
Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. Nucleic Acids Res. 45 (Database-Issue) (2017)
Jessica A. Boten, Donna R. Rivera, Madhumita Myneni, Georgia D. Tourassi, Tanmoy Bhattacharya, Ana Paula de Oliveira Sales, Thomas S. Brettin, Paul A. Fearn, Lynne Penberthy
Leveraging Large-Scale Computing for Population Information Integration, Analysis, and Modeling. AMIA (2017)
Pavel S. Novichkov, Thomas S. Brettin, Elena S. Novichkova, Paramvir S. Dehal, Adam P. Arkin, Inna Dubchak, Dmitry A. Rodionov
RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics. Nucleic Acids Res. 40 (Web-Server-Issue) (2012)
Shelton D. Griffith, Daniel Quest, Thomas S. Brettin, Robert W. Cottingham
Scenario driven data modelling: a method for integrating diverse sources of data and data streams. BMC Bioinform. 12 (S-10) (2011)
Thomas S. Brettin, Laura Pullum, Daniel Quest, Xiaohui Cui, Songhua Xu, Richard Stouder
Poster: a novel architecture for biothreat situation awareness. SC Companion (2011)
Daniel Quest, Miriam L. Land, Thomas S. Brettin, Robert W. Cottingham
Next generation models for storage and representation of microbial biological annotation. BMC Bioinform. 11 (S-6) (2010)
Roxanne Tapia, Gary Xie, Ravi D. Barabote, Gerry Myers, Thomas S. Brettin
Streptococcus in Toto: A Species-specific Comparative Analysis Website Prototype. BIOCOMP (2008)
Avinash Kewalramani, Riley Arnaudville, Cliff Han, Olga Chertkov, Thomas S. Brettin
A novel approach to high throughput microbial genome finishing: Incorporation of 454 sequence data for gap closure in low quality Sanger data. BIOCOMP (2007)
Thomas S. Brettin, Avinash Kewalramani
BioFilter: An Architecture for Parallel Deployment and Dynamic Chaining of Standalone Bioinformatics Tools. IPDPS (2005)
Michael E. Wall, Patricia A. Dyck, Thomas S. Brettin
SVDMAN-singular value decomposition analysis of microarray data. Bioinform. 17 (6) (2001)