An Evaluation of Information Visualization in Attention-Limited Environments. - Jacob P. Somervell; D. Scott McCrickard; Chris North 001; Maulik Shukla (VisSym, 2002)

Expresso and Chips: Creating a Next Generation Microarray Experiment Management System. - Allan A. Sioson; Jonathan I. Watkinson; Cecilia Vasquez-Robinet; Margaret Ellis 001; Maulik Shukla; Deept Kumar; Naren Ramakrishnan; Lenwood S. Heath; Ruth Grene; Boris I. Chevone; Karen Kafadar; Layne T. Watson (IPDPS, 2003)

PATRIC: The VBI PathoSystems Resource Integration Center. - E. E. Snyder; N. Kampanya; J. Lu; Eric K. Nordberg; H. R. Karur; Maulik Shukla; Jeetendra Soneja; Y. Tian; Tian Xue; Hyun Seung Yoo; Fengkai Zhang; C. Dharmanolla; et al. (Nucleic Acids Res., 2007)

Informatics-Driven Infectious Disease Research. - Bruno W. S. Sobral; Chunhong Mao; Maulik Shukla; Daniel E. Sullivan; Chengdong Zhang (BIOSTEC (Selected Papers), 2011)

Integration and visualization of host-pathogen data related to infectious diseases. - Timothy Driscoll; Joseph L. Gabbard; Chunhong Mao; Oral Dalay; Maulik Shukla; Clark C. Freifeld; Anne Gatewood Hoen; John S. Brownstein; Bruno W. S. Sobral (Bioinform., 2011)

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). - Ross A. Overbeek; Robert Olson; Gordon D. Pusch; Gary J. Olsen; James J. Davis 002; Terry Disz; Robert A. Edwards; Svetlana Gerdes; Bruce D. Parrello; Maulik Shukla; Veronika Vonstein; Alice R. Wattam; et al. (Nucleic Acids Res., 2014)

PATRIC, the bacterial bioinformatics database and analysis resource. - Alice R. Wattam; David Abraham; Oral Dalay; Terry Disz; Timothy Driscoll; Joseph L. Gabbard; Joseph J. Gillespie; Roger Gough; Deborah Hix; Ronald W. Kenyon; Dustin Machi; Chunhong Mao; et al. (Nucleic Acids Res., 2014)

Curation, integration and visualization of bacterial virulence factors in PATRIC. - Chunhong Mao; David Abraham; Alice R. Wattam; Meredith J. C. Wilson; Maulik Shukla; Hyun Seung Yoo; Bruno W. S. Sobral (Bioinform., 2015)

RNA-Rocket: an RNA-Seq analysis resource for infectious disease research. - Andrew S. Warren; Cristina Aurrecoechea; Brian P. Brunk; Prerak Desai; Scott J. Emrich; Gloria I. Giraldo-Calderón; Omar S. Harb; Deborah Hix; Daniel Lawson; Dustin Machi; Chunhong Mao; Michael McClelland; et al. (Bioinform., 2015)

Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. - Alice R. Wattam; James J. Davis 002; Rida Assaf; Sébastien Boisvert; Thomas S. Brettin; Christopher Bun; Neal Conrad; Emily M. Dietrich; Terry Disz; Joseph L. Gabbard; Svetlana Gerdes; Christopher S. Henry; et al. (Nucleic Acids Res., 2017)

Predicting tumor cell line response to drug pairs with deep learning. - 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 (BMC Bioinform., 2018)

PATRIC as a unique resource for studying antimicrobial resistance. - Dionysios A. Antonopoulos; Rida Assaf; Ramy Karam Aziz; Thomas S. Brettin; Christopher Bun; Neal Conrad; James J. Davis 002; Emily M. Dietrich; Terry Disz; Svetlana Gerdes; Ronald W. Kenyon; Dustin Machi; et al. (Briefings Bioinform., 2019)

Ensemble Transfer Learning for the Prediction of Anti-Cancer Drug Response. - Yitan Zhu; Thomas S. Brettin; Yvonne A. Evrard; Alexander Partin; Fangfang Xia; Maulik Shukla; Hyun Seung Yoo; James H. Doroshow; Rick Stevens (CoRR, 2020)

The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities. - James J. Davis 002; 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; et al. (Nucleic Acids Res., 2020)

Predicting antimicrobial resistance using conserved genes. - Marcus Nguyen; Robert Olson; Maulik Shukla; Margo VanOeffelen; James J. Davis 002 (PLoS Comput. Biol., 2020)

A genomic data resource for predicting antimicrobial resistance from laboratory-derived antimicrobial susceptibility phenotypes. - 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; et al. (Briefings Bioinform., 2021)

Learning curves for drug response prediction in cancer cell lines. - 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 (BMC Bioinform., 2021)

A cross-study analysis of drug response prediction in cancer cell lines. - 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; et al. (Briefings Bioinform., 2022)

Early detection of emerging SARS-CoV-2 variants of interest for experimental evaluation. - Zachary S. Wallace; James J. Davis 002; Anna Maria Niewiadomska; Robert D. Olson; Maulik Shukla; Rick Stevens; Yun Zhang 021; Christian M. Zmasek; Richard H. Scheuermann (Frontiers Bioinform., 2022)

Entropy-Based Regularization on Deep Learning Models for Anti-Cancer Drug Response Prediction. - Oleksandr Narykov; Yitan Zhu; Thomas S. Brettin; Yvonne A. Evrard; Alexander Partin; Maulik Shukla; Priyanka Vasanthakumari; James H. Doroshow; Rick Stevens (SC Workshops, 2023)

DeepSpeed4Science Initiative: Enabling Large-Scale Scientific Discovery through Sophisticated AI System Technologies. - Shuaiwen Leon Song; Bonnie Kruft; Minjia Zhang; Conglong Li; Shiyang Chen 004; Chengming Zhang 006; Masahiro Tanaka; Xiaoxia Wu; Jeff Rasley; Ammar Ahmad Awan; Connor Holmes; Martin Cai; et al. (CoRR, 2023)

Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR. - Robert D. Olson; Rida Assaf; Thomas S. Brettin; Neal Conrad; Clark Cucinell; James J. Davis 002; Donald M. Dempsey; Allan Dickerman; Emily M. Dietrich; Ronald W. Kenyon; Mehmet Kuscuoglu; Elliot J. Lefkowitz; et al. (Nucleic Acids Res., 2023)

GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics. - 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; et al. (Int. J. High Perform. Comput. Appl., 2023)

Data imbalance in drug response prediction: multi-objective optimization approach in deep learning setting. - Oleksandr Narykov; Yitan Zhu; Thomas S. Brettin; Yvonne A. Evrard; Alexander Partin; Fangfang Xia; Maulik Shukla; Priyanka Vasanthakumari; James H. Doroshow; Rick L. Stevens (Briefings Bioinform., 2025)