Machine learning uncovers independently regulated modules in the Bacillus subtilis transcriptome

por Kevin Rychel, Anand V. Sastry, Bernhard O. Palsson
Publicado 2020

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

por David Heckmann, Daniel C. Zielinski, Bernhard O. Palsson
Publicado 2018

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

por Fan Li, Ines Thiele, Neema Jamshidi, Bernhard Ø Palsson
Publicado 2009

The quantitative metabolome is shaped by abiotic constraints

por Amir Akbari, James T. Yurkovich, Daniel C. Zielinski, Bernhard O. Palsson
Publicado 2021

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

por Ines Thiele, Neema Jamshidi, Ronan M T Fleming, Bernhard Ø Palsson
Publicado 2009

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

por Yara Seif, Jonathan M. Monk, Henrique Machado, Erol Kavvas, Bernhard O. Palsson
Publicado 2019

A biochemically-interpretable machine learning classifier for microbial GWAS

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

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

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

Pangenome Analytics Reveal Two-Component Systems as Conserved Targets in ESKAPEE Pathogens

por Akanksha Rajput, Yara Seif, Kumari Sonal Choudhary, Christopher Dalldorf, Saugat Poudel, Jonathan M. Monk, Bernhard O. Palsson
Publicado 2021

Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655

por Sang Woo Seo, Ye Gao, Donghyuk Kim, Richard Szubin, Jina Yang, Byung-Kwan Cho, Bernhard O. Palsson
Publicado 2017

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

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

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

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

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

por Douglas McCloskey, Sibei Xu, Troy E. Sandberg, Elizabeth Brunk, Ying Hefner, Richard Szubin, Adam M. Feist, Bernhard O. Palsson
Publicado 2018

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

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

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

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

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

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

The Escherichia coli transcriptome mostly consists of independently regulated modules

por Anand V. Sastry, Ye Gao, Richard Szubin, Ying Hefner, Sibei Xu, Donghyuk Kim, Kumari Sonal Choudhary, Laurence Yang, Zachary A. King, Bernhard O. Palsson
Publicado 2019

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

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

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

por 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
Publicado 2018

Genetic Determinants Enabling Medium-Dependent Adaptation to Nafcillin in Methicillin-Resistant <named-content content-type="genus-species">Staphylococcus aureus</named-content>

por 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
Publicado 2020