Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655 by Sang Woo Seo, Donghyuk Kim, Richard Szubin, Bernhard O. Palsson

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Global pathogenomic analysis identifies known and candidate genetic antimicrobial resistance determinants in twelve species by Jason C. Hyun, Jonathan M. Monk, Richard Szubin, Ying Hefner, Bernhard O. Palsson

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Comprehensive whole genome sequencing with hybrid assembly of multi-drug resistant Candida albicans isolate causing cerebral abscess by Monika Kumaraswamy, Alison Coady, Richard Szubin, Thomas CS Martin, Bernhard Palsson, Victor Nizet, Jonathan M. Monk

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High-Quality Genome-Scale Models From Error-Prone, Long-Read Assemblies by Jared T. Broddrick, Richard Szubin, Charles J. Norsigian, Jonathan M. Monk, Bernhard O. Palsson, Mary N. Parenteau

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Advancing the scale of synthetic biology via cross-species transfer of cellular functions enabled by iModulon engraftment by Donghui Choe, Connor A. Olson, Richard Szubin, Hannah Yang, Jaemin Sung, Adam M. Feist, Bernhard O. Palsson

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ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions. by Haythem Latif, Stephen Federowicz, Ali Ebrahim, Janna Tarasova, Richard Szubin, Jose Utrilla, Karsten Zengler, Bernhard O Palsson

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Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655 by Sang Woo Seo, Ye Gao, Donghyuk Kim, Richard Szubin, Jina Yang, Byung-Kwan Cho, Bernhard O. Palsson

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Adaptive evolution of a minimal organism with a synthetic genome by Troy E. Sandberg, Kim S. Wise, Christopher Dalldorf, Richard Szubin, Adam M. Feist, John I. Glass, Bernhard O. Palsson

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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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Comparative Genome-Scale Metabolic Modeling of Metallo-Beta-Lactamase–Producing Multidrug-Resistant Klebsiella pneumoniae Clinical Isolates by Charles J. Norsigian, Heba Attia, Richard Szubin, Aymen S. Yassin, Aymen S. Yassin, Bernhard Ø. Palsson, Ramy K. Aziz, Ramy K. Aziz, Jonathan M. Monk

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Laboratory evolution of synthetic electron transport system variants reveals a larger metabolic respiratory system and its plasticity by Amitesh Anand, Arjun Patel, Ke Chen, Connor A. Olson, Patrick V. Phaneuf, Cameron Lamoureux, Ying Hefner, Richard Szubin, Adam M. Feist, Bernhard O. 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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Reconstructing the transcriptional regulatory network of probiotic L. reuteri is enabled by transcriptomics and machine learning by Jonathan Josephs-Spaulding, Akanksha Rajput, Ying Hefner, Richard Szubin, Archana Balasubramanian, Gaoyuan Li, Daniel C. Zielinski, Leonie Jahn, Morten Sommer, Patrick Phaneuf, Bernhard O. Palsson

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Genetic Determinants Enabling Medium-Dependent Adaptation to Nafcillin in Methicillin-Resistant <named-content content-type="genus-species">Staphylococcus aureus</named-content> by Michael J. Salazar, Henrique Machado, Nicholas A. Dillon, Hannah Tsunemoto, Richard Szubin, Samira Dahesh, Joseph Pogliano, George Sakoulas, Bernhard O. Palsson, Victor Nizet, Adam M. Feist

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Environmental conditions dictate differential evolution of vancomycin resistance in Staphylococcus aureus by Henrique Machado, Yara Seif, George Sakoulas, Connor A. Olson, Ying Hefner, Amitesh Anand, Ying Z. Jones, Richard Szubin, Bernhard O. Palsson, Victor Nizet, Adam M. Feist

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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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A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli by Irina A. Rodionova, Ye Gao, Jonathan Monk, Ying Hefner, Nicholas Wong, Richard Szubin, Hyun Gyu Lim, Dmitry A. Rodionov, Zhongge Zhang, Milton H. Saier, Bernhard O. Palsson

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Multi-omic data integration enables discovery of hidden biological regularities by Ali Ebrahim, Elizabeth Brunk, Justin Tan, Edward J. O'Brien, Donghyuk Kim, Richard Szubin, Joshua A. Lerman, Anna Lechner, Anand Sastry, Aarash Bordbar, 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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Growth Adaptation of gnd and sdhCB Escherichia coli Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome by Douglas McCloskey, Douglas McCloskey, Sibei Xu, Troy E. Sandberg, Elizabeth Brunk, Ying Hefner, Richard Szubin, Adam M. Feist, Adam M. Feist, Bernhard O. Palsson, Bernhard O. Palsson

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