Machine learning uncovers independently regulated modules in the Bacillus subtilis transcriptome

by Kevin Rychel, Anand V. Sastry, Bernhard O. Palsson
Published 2020

Modeling genome-wide enzyme evolution predicts strong epistasis underlying catalytic turnover rates

by David Heckmann, Daniel C. Zielinski, Bernhard O. Palsson
Published 2018

Identification of potential pathway mediation targets in Toll-like receptor signaling.

by Fan Li, Ines Thiele, Neema Jamshidi, Bernhard Ø Palsson
Published 2009

The quantitative metabolome is shaped by abiotic constraints

by Amir Akbari, James T. Yurkovich, Daniel C. Zielinski, Bernhard O. Palsson
Published 2021

Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization.

by Ines Thiele, Neema Jamshidi, Ronan M T Fleming, Bernhard Ø Palsson
Published 2009

Systems Biology and Pangenome of <italic toggle="yes">Salmonella</italic> O-Antigens

by Yara Seif, Jonathan M. Monk, Henrique Machado, Erol Kavvas, Bernhard O. Palsson
Published 2019

A biochemically-interpretable machine learning classifier for microbial GWAS

by Erol S. Kavvas, Laurence Yang, Jonathan M. Monk, David Heckmann, Bernhard O. Palsson
Published 2020

Integrated Regulatory and Metabolic Networks of the Marine Diatom <italic toggle="yes">Phaeodactylum tricornutum</italic> Predict the Response to Rising CO₂ Levels

by Jennifer Levering, Christopher L. Dupont, Andrew E. Allen, Bernhard O. Palsson, Karsten Zengler
Published 2017

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
Published 2021

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

Genome-scale determination of 5´ and 3´ boundaries of RNA transcripts in Streptomyces genomes

by Yongjae Lee, Namil Lee, Soonkyu Hwang, Woori Kim, Yujin Jeong, Suhyung Cho, Bernhard O. Palsson, Byung-Kwan Cho
Published 2020

Elucidation of Regulatory Modes for Five Two-Component Systems in <named-content content-type="genus-species">Escherichia coli</named-content> Reveals Novel Relationships

by Kumari Sonal Choudhary, Julia A. Kleinmanns, Katherine Decker, Anand V. Sastry, Ye Gao, Richard Szubin, Yara Seif, Bernhard O. Palsson
Published 2020

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

Elucidating the Regulatory Elements for Transcription Termination and Posttranscriptional Processing in the Streptomyces clavuligerus Genome

by Soonkyu Hwang, Namil Lee, Donghui Choe, Yongjae Lee, Woori Kim, Yujin Jeong, Suhyung Cho, Bernhard O. Palsson, Byung-Kwan Cho
Published 2021

Biochemical characterization of human gluconokinase and the proposed metabolic impact of gluconic acid as determined by constraint based metabolic network analysis.

by Neha Rohatgi, Tine Kragh Nielsen, Sara Petersen Bjørn, Ivar Axelsson, Giuseppe Paglia, Bjørn Gunnar Voldborg, Bernhard O Palsson, Óttar Rolfsson
Published 2014

Identification of a transcription factor, PunR, that regulates the purine and purine nucleoside transporter punC in E. coli

by Irina A. Rodionova, Ye Gao, Anand Sastry, Ying Hefner, Hyun Gyu Lim, Dmitry A. Rodionov, Milton H. Saier, Bernhard O. Palsson
Published 2021

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

Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models

by David Heckmann, Colton J. Lloyd, Nathan Mih, Yuanchi Ha, Daniel C. Zielinski, Zachary B. Haiman, Abdelmoneim Amer Desouki, Martin J. Lercher, Bernhard O. Palsson
Published 2018

Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits

by Yara Seif, Erol Kavvas, Jean-Christophe Lachance, James T. Yurkovich, Sean-Paul Nuccio, Xin Fang, Edward Catoiu, Manuela Raffatellu, Bernhard O. Palsson, Jonathan M. Monk
Published 2018

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
Published 2020