The quantitative metabolome is shaped by abiotic constraints

by Amir Akbari, James T. Yurkovich, Daniel C. Zielinski, Bernhard O. Palsson
Published 2021-05-01

Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens.

by Jason C Hyun, Erol S Kavvas, Jonathan M Monk, Bernhard O Palsson
Published 2020-03-01

Network-level allosteric effects are elucidated by detailing how ligand-binding events modulate utilization of catalytic potentials.

by James T Yurkovich, Miguel A Alcantar, Zachary B Haiman, Bernhard O Palsson
Published 2018-08-01

Reconstruction and Validation of a Genome-Scale Metabolic Model of Streptococcus oralis (iCJ415), a Human Commensal and Opportunistic Pathogen

by Christian S. Jensen, Charles J. Norsigian, Xin Fang, Xiaohui C. Nielsen, Jens Jørgen Christensen, Jens Jørgen Christensen, Bernhard O. Palsson, Bernhard O. Palsson, Jonathan M. Monk
Published 2020-03-01

Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth.

by Colton J Lloyd, Jonathan Monk, Laurence Yang, Ali Ebrahim, Bernhard O Palsson
Published 2021-06-01

Systems Biology and Pangenome of Salmonella O-Antigens

by Yara Seif, Jonathan M. Monk, Henrique Machado, Erol Kavvas, Bernhard O. Palsson
Published 2019-08-01

Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli.

by Bin Du, Laurence Yang, Colton J Lloyd, Xin Fang, Bernhard O Palsson
Published 2019-12-01

Functional states of the genome-scale Escherichia coli transcriptional regulatory system.

by Erwin P Gianchandani, Andrew R Joyce, Bernhard Ø Palsson, Jason A Papin
Published 2009-06-01

Cumulative number of cell divisions as a meaningful timescale for adaptive laboratory evolution of Escherichia coli.

by Dae-Hee Lee, Adam M Feist, Christian L Barrett, Bernhard Ø Palsson
Published 2011-01-01

Identification of growth-coupled production strains considering protein costs and kinetic variability

by Hoang V. Dinh, Zachary A. King, Bernhard O. Palsson, Adam M. Feist
Published 2018-12-01

Long-range periodic patterns in microbial genomes indicate significant multi-scale chromosomal organization.

by Timothy E Allen, Nathan D Price, Andrew R Joyce, Bernhard Ø Palsson
Published 2006-01-01

A biochemically-interpretable machine learning classifier for microbial GWAS

by Erol S. Kavvas, Laurence Yang, Jonathan M. Monk, David Heckmann, Bernhard O. Palsson
Published 2020-05-01

Drug off-target effects predicted using structural analysis in the context of a metabolic network model.

by Roger L Chang, Li Xie, Lei Xie, Philip E Bourne, Bernhard Ø Palsson
Published 2010-09-01

iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of Acinetobacter baumannii AYE

by Charles J. Norsigian, Erol Kavvas, Yara Seif, Bernhard O. Palsson, Jonathan M. Monk
Published 2018-04-01

MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics.

by Zachary B Haiman, Daniel C Zielinski, Yuko Koike, James T Yurkovich, Bernhard O Palsson
Published 2021-01-01

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

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
Published 2021-02-01

Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage.

by Ines Thiele, Ronan M T Fleming, Richard Que, Aarash Bordbar, Dinh Diep, Bernhard O Palsson
Published 2012-01-01

Metabolic reconstruction and modeling of nitrogen fixation in Rhizobium etli.

by Osbaldo Resendis-Antonio, Jennifer L Reed, Sergio Encarnación, Julio Collado-Vides, Bernhard Ø Palsson
Published 2007-10-01