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
Published 2015-08-01

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
Published 2020-11-01

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
Published 2017-05-01

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
Published 2018-01-01

Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism

by Douglas McCloskey, Sibei Xu, Troy E. Sandberg, Elizabeth Brunk, Ying Hefner, Richard Szubin, Adam M. Feist, Bernhard O. Palsson
Published 2018-09-01

Restoration of fitness lost due to dysregulation of the pyruvate dehydrogenase complex is triggered by ribosomal binding site modifications

by Amitesh Anand, Connor A. Olson, Anand V. Sastry, Arjun Patel, Richard Szubin, Laurence Yang, Adam M. Feist, Bernhard O. Palsson
Published 2021-04-01

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
Published 2021-08-01

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
Published 2019-05-01

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
Published 2019-12-01

Genetic Determinants Enabling Medium-Dependent Adaptation to Nafcillin in Methicillin-Resistant Staphylococcus aureus

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
Published 2020-03-01

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
Published 2021-06-01

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
Published 2016-10-01

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
Published 2018-08-01

Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient

by Xin Fang, Jonathan M. Monk, Sergey Nurk, Margarita Akseshina, Qiyun Zhu, Christopher Gemmell, Connor Gianetto-Hill, Nelly Leung, Richard Szubin, Jon Sanders, Paul L. Beck, Weizhong Li, Weizhong Li, William J. Sandborn, William J. Sandborn, Scott D. Gray-Owen, Rob Knight, Rob Knight, Rob Knight, Emma Allen-Vercoe, Bernhard O. Palsson, Bernhard O. Palsson, Bernhard O. Palsson, Bernhard O. Palsson, Larry Smarr, Larry Smarr, Larry Smarr
Published 2018-10-01