Functional and Proteomic Analysis of Streptococcus pyogenes Virulence Upon Loss of Its Native Cas9 Nuclease by Nina J. Gao, Nina J. Gao, Mahmoud M. Al-Bassam, Saugat Poudel, Saugat Poudel, Saugat Poudel, Jacob M. Wozniak, Jacob M. Wozniak, David J. Gonzalez, David J. Gonzalez, Joshua Olson, Karsten Zengler, Karsten Zengler, Victor Nizet, Victor Nizet, J. Andrés Valderrama

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Elucidating the CodY regulon in Staphylococcus aureus USA300 substrains TCH1516 and LAC by Ye Gao, Saugat Poudel, Yara Seif, Zeyang Shen, 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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Coordination of CcpA and CodY Regulators in Staphylococcus aureus USA300 Strains by Saugat Poudel, Ying Hefner, Richard Szubin, Anand Sastry, Ye Gao, Victor Nizet, Bernhard O. Palsson

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Optimal dimensionality selection for independent component analysis of transcriptomic data by John Luke McConn, Cameron R. Lamoureux, Saugat Poudel, Bernhard O. Palsson, Anand V. Sastry

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Pangenome Analytics Reveal Two-Component Systems as Conserved Targets in ESKAPEE Pathogens by Akanksha Rajput, Yara Seif, Kumari Sonal Choudhary, Christopher Dalldorf, Saugat Poudel, Jonathan M. Monk, Bernhard O. Palsson

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A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types. by Yara Seif, Jonathan M Monk, Nathan Mih, Hannah Tsunemoto, Saugat Poudel, Cristal Zuniga, Jared Broddrick, Karsten Zengler, Bernhard O Palsson

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Machine Learning of All Mycobacterium tuberculosis H37Rv RNA-seq Data Reveals a Structured Interplay between Metabolism, Stress Response, and Infection by Reo Yoo, Kevin Rychel, Saugat Poudel, Tahani Al-bulushi, Yuan Yuan, Siddharth Chauhan, Cameron Lamoureux, Bernhard O. Palsson, Anand Sastry

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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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Malnutrition among Cancer Patients in a Tertiary Care Centre: A Descriptive Cross-sectional Study by Anuj K.C., Bishnu Dutta Poudel, Ramila Shilpakar, Sudip Thapa, Rajiv Sharma, Bibek Acharya, Sandhya Chapagain, Ambuj Karn, Saugat Poudel, Bishal Paudel

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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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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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A genome-scale metabolic model of a globally disseminated hyperinvasive M1 strain of Streptococcus pyogenes by Yujiro Hirose, Daniel C. Zielinski, Saugat Poudel, Kevin Rychel, Jonathon L. Baker, Yoshihiro Toya, Masaya Yamaguchi, Almut Heinken, Ines Thiele, Shigetada Kawabata, Bernhard O. Palsson, Victor Nizet

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Experimental Evolution Reveals Unifying Systems-Level Adaptations but Diversity in Driving Genotypes by Erol S. Kavvas, Christopher P. Long, Anand Sastry, Saugat Poudel, Maciek R. Antoniewicz, Yang Ding, Elsayed T. Mohamed, Richard Szubin, Jonathan M. Monk, Adam M. Feist, Bernhard O. Palsson

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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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iModulonMiner and PyModulon: Software for unsupervised mining of gene expression compendia. by Anand V Sastry, Yuan Yuan, Saugat Poudel, Kevin Rychel, Reo Yoo, Cameron R Lamoureux, Gaoyuan Li, Joshua T Burrows, Siddharth Chauhan, Zachary B Haiman, Tahani Al Bulushi, Yara Seif, Bernhard O Palsson, Daniel C Zielinski

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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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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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