Machine learning uncovers the Pseudomonas syringae transcriptome in microbial communities and during infection by Heera Bajpe, Kevin Rychel, Cameron R. Lamoureux, Anand V. Sastry, Bernhard O. Palsson

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Independent component analysis recovers consistent regulatory signals from disparate datasets. by Anand V Sastry, Alyssa Hu, David Heckmann, Saugat Poudel, Erol Kavvas, Bernhard O Palsson

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Pan-Genome Analysis of Transcriptional Regulation in Six Salmonella enterica Serovar Typhimurium Strains Reveals Their Different Regulatory Structures by Yuan Yuan, Yara Seif, Kevin Rychel, Reo Yoo, Siddharth Chauhan, Saugat Poudel, Tahani Al-bulushi, Bernhard O. Palsson, Anand V. Sastry

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Machine Learning of Bacterial Transcriptomes Reveals Responses Underlying Differential Antibiotic Susceptibility by Anand V. Sastry, Nicholas Dillon, Amitesh Anand, Saugat Poudel, Ying Hefner, Sibei Xu, Richard Szubin, Adam M. Feist, Victor Nizet, Bernhard Palsson

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The Escherichia coli transcriptome mostly consists of independently regulated modules by Anand V. Sastry, Ye Gao, Richard Szubin, Ying Hefner, Sibei Xu, Donghyuk Kim, Kumari Sonal Choudhary, Laurence Yang, Zachary A. King, Bernhard O. Palsson

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Machine Learning Uncovers a Data-Driven Transcriptional Regulatory Network for the Crenarchaeal Thermoacidophile Sulfolobus acidocaldarius by Siddharth M. Chauhan, Saugat Poudel, Kevin Rychel, Cameron Lamoureux, Reo Yoo, Tahani Al Bulushi, Yuan Yuan, Bernhard O. Palsson, Bernhard O. Palsson, Anand V. Sastry

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Independent component analysis reveals 49 independently modulated gene sets within the global transcriptional regulatory architecture of multidrug-resistant Acinetobacter baumannii by Nitasha D. Menon, Saugat Poudel, Anand V. Sastry, Kevin Rychel, Richard Szubin, Nicholas Dillon, Hannah Tsunemoto, Yujiro Hirose, Bipin G. Nair, Geetha B. Kumar, Bernhard O. Palsson, Victor Nizet

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BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data. by Jean-Christophe Lachance, Colton J Lloyd, Jonathan M Monk, Laurence Yang, Anand V Sastry, Yara Seif, Bernhard O Palsson, Sébastien Rodrigue, Adam M Feist, Zachary A King, Pierre-Étienne Jacques

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Elucidation of independently modulated genes in Streptococcus pyogenes reveals carbon sources that control its expression of hemolytic toxins by Yujiro Hirose, Saugat Poudel, Anand V. Sastry, Kevin Rychel, Cameron R. Lamoureux, Richard Szubin, Daniel C. Zielinski, Hyun Gyu Lim, Nitasha D. Menon, Helena Bergsten, Satoshi Uchiyama, Tomoki Hanada, Shigetada Kawabata, Bernhard O. Palsson, Victor Nizet

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Laboratory evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance by Kevin Rychel, Justin Tan, Arjun Patel, Cameron Lamoureux, Ying Hefner, Richard Szubin, Josefin Johnsen, Elsayed Tharwat Tolba Mohamed, Patrick V. Phaneuf, Amitesh Anand, Connor A. Olson, Joon Ho Park, Anand V. Sastry, Laurence Yang, Adam M. Feist, Bernhard O. Palsson

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Mathematical models to study the biology of pathogens and the infectious diseases they cause by Joao B. Xavier, Jonathan M. Monk, Saugat Poudel, Charles J. Norsigian, Anand V. Sastry, Chen Liao, Jose Bento, Marc A. Suchard, Mario L. Arrieta-Ortiz, Eliza J.R. Peterson, Nitin S. Baliga, Thomas Stoeger, Felicia Ruffin, Reese A.K. Richardson, Catherine A. Gao, Thomas D. Horvath, Anthony M. Haag, Qinglong Wu, Tor Savidge, Michael R. Yeaman

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