Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions. - Jeremy S. Edwards; Bernhard O. Palsson (BMC Bioinform., 2000)

Dynamic simulation of the human red blood cell metabolic network. - Neema Jamshidi; Jeremy S. Edwards; Tom Fahland; George M. Church; Bernhard O. Palsson (Bioinform., 2001)

expa: a program for calculating extreme pathways in biochemical reaction networks. - Steven L. Bell; Bernhard O. Palsson (Bioinform., 2005)

Phenotype phase plane analysis using interior point methods. - Steven L. Bell; Bernhard O. Palsson (Comput. Chem. Eng., 2005)

Network-level analysis of metabolic regulation in the human red blood cell using random sampling and singular value decomposition. - Christian L. Barrett; Nathan D. Price 001; Bernhard O. Palsson (BMC Bioinform., 2006)

Metabolite coupling in genome-scale metabolic networks. - Scott A. Becker; Nathan D. Price 001; Bernhard O. Palsson (BMC Bioinform., 2006)

Long-Range Periodic Patterns in Microbial Genomes Indicate Significant Multi-Scale Chromosomal Organization. - Timothy E. Allen; Nathan D. Price 001; Andrew R. Joyce; Bernhard Ø. Palsson (PLoS Comput. Biol., 2006)

Iterative Reconstruction of Transcriptional Regulatory Networks: An Algorithmic Approach. - Christian L. Barrett; Bernhard O. Palsson (PLoS Comput. Biol., 2006)

Matrix Formalism to Describe Functional States of Transcriptional Regulatory Systems. - Erwin P. Gianchandani; Jason A. Papin; Nathan D. Price 001; Andrew R. Joyce; Bernhard Ø. Palsson (PLoS Comput. Biol., 2006)

Identification of Genome-Scale Metabolic Network Models Using Experimentally Measured Flux Profiles. - Markus J. Herrgård; Stephen S. Fong; Bernhard Ø. Palsson (PLoS Comput. Biol., 2006)

Estimation of the number of extreme pathways for metabolic networks. - Matthew Yeung; Ines Thiele; Bernhard O. Palsson (BMC Bioinform., 2007)

Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets. - Neema Jamshidi; Bernhard Ø. Palsson (BMC Syst. Biol., 2007)

Metabolic Reconstruction and Modeling of Nitrogen Fixation in Rhizobium etli. - Osbaldo Resendis-Antonio; Jennifer L. Reed; Sergio Encarnación; Julio Collado-Vides; Bernhard Ø. Palsson (PLoS Comput. Biol., 2007)

Three factors underlying incorrect in silico predictions of essential metabolic genes. - Scott A. Becker; Bernhard O. Palsson (BMC Syst. Biol., 2008)

A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory. - Juan Nogales; Bernhard Ø. Palsson; Ines Thiele (BMC Syst. Biol., 2008)

Context-Specific Metabolic Networks Are Consistent with Experiments. - Scott A. Becker; Bernhard O. Palsson (PLoS Comput. Biol., 2008)

Top-Down Analysis of Temporal Hierarchy in Biochemical Reaction Networks. - Neema Jamshidi; Bernhard Ø. Palsson (PLoS Comput. Biol., 2008)

Decomposing complex reaction networks using random sampling, principal component analysis and basis rotation. - Christian L. Barrett; Markus J. Herrgård; Bernhard Ø. Palsson (BMC Syst. Biol., 2009)

Using in silico models to simulate dual perturbation experiments: procedure development and interpretation of outcomes. - Neema Jamshidi; Bernhard O. Palsson (BMC Syst. Biol., 2009)

Connecting extracellular metabolomic measurements to intracellular flux states in yeast. - Monica L. Mo; Bernhard Ø. Palsson; Markus J. Herrgård (BMC Syst. Biol., 2009)

Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction. - Anu Raghunathan; Jennifer L. Reed; Sook-Il Shin; Bernhard Ø. Palsson; Simon Daefler (BMC Syst. Biol., 2009)

Functional States of the Genome-Scale Escherichia Coli Transcriptional Regulatory System. - Erwin P. Gianchandani; Andrew R. Joyce; Bernhard O. Palsson; Jason A. Papin (PLoS Comput. Biol., 2009)

Identification of Potential Pathway Mediation Targets in Toll-like Receptor Signaling. - Fan Li 002; Ines Thiele; Neema Jamshidi; Bernhard O. Palsson (PLoS Comput. Biol., 2009)

Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization. - Ines Thiele; Neema Jamshidi; Ronan M. T. Fleming; Bernhard O. Palsson (PLoS Comput. Biol., 2009)

Metabolic Systems Biology. - Nathan E. Lewis; Neema Jamshidi; Ines Thiele; Bernhard O. Palsson (Encyclopedia of Complexity and Systems Science, 2009)

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. - Jan Schellenberger; Junyoung O. Park; Tom M. Conrad; Bernhard O. Palsson (BMC Bioinform., 2010)

A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1. - Martin I. Sigurdsson; Neema Jamshidi; Eiríkur Steingrímsson; Ines Thiele; Bernhard Ø. Palsson (BMC Syst. Biol., 2010)

Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model. - Roger L. Chang; Li Xie 002; Lei Xie 006; Philip E. Bourne; Bernhard Ø. Palsson (PLoS Comput. Biol., 2010)

A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology. - Aarash Bordbar; Adam M. Feist; Renata Usaite-Black; Joseph Woodcock; Bernhard O. Palsson; Iman Famili (BMC Syst. Biol., 2011)

iAB-RBC-283: A proteomically derived knowledge-base of erythrocyte metabolism that can be used to simulate its physiological and patho-physiological states. - Aarash Bordbar; Neema Jamshidi; Bernhard O. Palsson (BMC Syst. Biol., 2011)

An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92. - Pep Charusanti; Sadhana Chauhan; Kathleen McAteer; Joshua A. Lerman; Daniel R. Hyduke; Vladimir L. Motin; Charles Ansong; Joshua N. Adkins; Bernhard O. Palsson (BMC Syst. Biol., 2011)

The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions. - Ottar Rolfsson; Bernhard Ø. Palsson; Ines Thiele (BMC Syst. Biol., 2011)

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. - Ines Thiele; Daniel R. Hyduke; Benjamin Steeb; Guy Fankam; Douglas K. Allen; Susanna Bazzani; Pep Charusanti; Feng-Chi Chen; Ronan M. T. Fleming; Chao A. Hsiung; Sigrid C. J. De Keersmaecker; Yu-Chieh Liao; et al. (BMC Syst. Biol., 2011)

Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions. - Jeffrey D. Orth; Bernhard Ø. Palsson (BMC Syst. Biol., 2012)

Predicting outcomes of steady-state 13C isotope tracing experiments using Monte Carlo sampling. - Jan Schellenberger; Daniel C. Zielinski; Wing Choi; Sunthosh Madireddi; Vasiliy Portnoy; David A. Scott; Jennifer L. Reed; Andrei Osterman; Bernhard Ø. Palsson (BMC Syst. Biol., 2012)

GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data. - Brian J. Schmidt; Ali Ebrahim; Thomas O. Metz; Joshua N. Adkins; Bernhard Ø. Palsson; Daniel R. Hyduke (Bioinform., 2013)

Antibacterial mechanisms identified through structural systems pharmacology. - Roger L. Chang; Lei Xie 006; Philip E. Bourne; Bernhard O. Palsson (BMC Syst. Biol., 2013)

COBRApy: COnstraints-Based Reconstruction and Analysis for Python. - Ali Ebrahim; Joshua A. Lerman; Bernhard Ø. Palsson; Daniel R. Hyduke (BMC Syst. Biol., 2013)

The development of a fully-integrated immune response model (FIRM) simulator of the immune response through integration of multiple subset models. - Sirus Palsson; Timothy P. Hickling; Erica L. Bradshaw-Pierce; Michael Zager; Karin Jooss; Peter O'Brien; Mary E. Spilker; Bernhard Ø. Palsson; Paolo Vicini (BMC Syst. Biol., 2013)

Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale. - Joanne K. Liu; Edward J. O'Brien; Joshua A. Lerman; Karsten Zengler; Bernhard O. Palsson; Adam M. Feist (BMC Syst. Biol., 2014)

A Systems Approach to Predict Oncometabolites via Context-Specific Genome-Scale Metabolic Networks. - Hojung Nam; Miguel Campodonico; Aarash Bordbar; Daniel R. Hyduke; Sangwoo Kim; Daniel C. Zielinski; Bernhard O. Palsson (PLoS Comput. Biol., 2014)

JSBML 1.0: providing a smorgasbord of options to encode systems biology models. - Nicolas Rodriguez 001; Alex Thomas; Leandro H. Watanabe; Ibrahim Y. Vazirabad; Victor Kofia; Harold F. Gómez; Florian Mittag; Jakob Matthes; Jan Rudolph; Finja Wrzodek; Eugen Netz; Alexander Diamantikos; et al. (Bioinform., 2015)

SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks. - Andreas Dräger; Daniel C. Zielinski; Roland Keller; Matthias Rall; Johannes Eichner; Bernhard O. Palsson; Andreas Zell (BMC Syst. Biol., 2015)

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways. - Zachary A. King; Andreas Dräger; Ali Ebrahim; Nikolaus Sonnenschein; Nathan E. Lewis; Bernhard O. Palsson (PLoS Comput. Biol., 2015)

solveME: fast and reliable solution of nonlinear ME models. - Laurence Yang 001; Ding Ma 003; Ali Ebrahim; Colton J. Lloyd; Michael A. Saunders; Bernhard O. Palsson (BMC Bioinform., 2016)

Systems biology of the structural proteome. - Elizabeth Brunk; Nathan Mih; Jonathan Monk; Zhen Zhang; Edward J. O'Brien; Spencer E. Bliven; Ke Chen; Roger L. Chang; Philip E. Bourne; Bernhard O. Palsson (BMC Syst. Biol., 2016)

Evaluation of rate law approximations in bottom-up kinetic models of metabolism. - Bin Du; Daniel C. Zielinski; Erol S. Kavvas; Andreas Dräger; Justin Tan; Zhen Zhang; Kayla E. Ruggiero; Garri A. Arzumanyan; Bernhard O. Palsson (BMC Syst. Biol., 2016)

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. - Zachary A. King; Justin Lu; Andreas Dräger; Philip Miller; Stephen Federowicz; Joshua A. Lerman; Ali Ebrahim; Bernhard O. Palsson; Nathan E. Lewis (Nucleic Acids Res., 2016)

Solving Puzzles With Missing Pieces: The Power of Systems Biology [Point of View]. - James T. Yurkovich; Bernhard O. Palsson (Proc. IEEE, 2016)

A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism. - Nathan Mih; Elizabeth Brunk; Aarash Bordbar; Bernhard O. Palsson (PLoS Comput. Biol., 2016)

Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments. - Edward J. O'Brien; Jose Utrilla; Bernhard O. Palsson (PLoS Comput. Biol., 2016)

Utilizing biomarkers to forecast quantitative metabolite concentration profiles in human red blood cells. - James T. Yurkovich; Laurence Yang 001; Bernhard O. Palsson (CCTA, 2017)

Machine learning in computational biology to accelerate high-throughput protein expression. - Anand Sastry 002; Jonathan Monk; Hanna Tegel; Mathias Uhlen; Bernhard O. Palsson; Johan Rockberg; Elizabeth Brunk (Bioinform., 2017)

Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells. - James T. Yurkovich; Laurence Yang 001; Bernhard O. Palsson (PLoS Comput. Biol., 2017)

ssbio: a Python framework for structural systems biology. - Nathan Mih; Elizabeth Brunk; Ke Chen; Edward Catoiu; Anand Sastry 002; Erol S. Kavvas; Jonathan M. Monk; Zhen Zhang; Bernhard O. Palsson (Bioinform., 2018)

Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa. - Xin Fang; Jonathan M. Monk; Nathan Mih; Bin Du; Anand Sastry 002; Erol S. Kavvas; Yara Seif; Larry Smarr; Bernhard O. Palsson (BMC Syst. Biol., 2018)

Reframing gene essentiality in terms of adaptive flexibility. - Gabriela I. Guzmán; Connor A. Olson; Ying Hefner; Patrick V. Phaneuf; Edward Catoiu; Lais B. Crepaldi; Lucas Goldschmidt Micas; Bernhard O. Palsson; Adam M. Feist (BMC Syst. Biol., 2018)

Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions. - Erol S. Kavvas; Yara Seif; James T. Yurkovich; Charles J. Norsigian; Saugat Poudel; William W. Greenwald; Sankha Ghatak; Bernhard O. Palsson; Jonathan M. Monk (BMC Syst. Biol., 2018)

Escher-FBA: a web application for interactive flux balance analysis. - Elliot Rowe; Bernhard O. Palsson; Zachary A. King (BMC Syst. Biol., 2018)

Systems biology as an emerging paradigm in transfusion medicine. - James T. Yurkovich; Aarash Bordbar; Ólafur E. Sigurjónsson; Bernhard O. Palsson (BMC Syst. Biol., 2018)

Genome-scale estimation of cellular objectives. - Laurence Yang 001; José Bento 001; Jean-Christophe Lachance; Bernhard O. Palsson (CoRR, 2018)

Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting. - Alyaa M. Abdel-Haleem; Hooman Hefzi; Katsuhiko Mineta; Xin Gao 001; Takashi Gojobori; Bernhard O. Palsson; Nathan E. Lewis; Neema Jamshidi (PLoS Comput. Biol., 2018)

COBRAme: A computational framework for genome-scale models of metabolism and gene expression. - Colton J. Lloyd; Ali Ebrahim; Laurence Yang 001; Zachary A. King; Edward Catoiu; Edward J. O'Brien; Joanne K. Liu; Bernhard O. Palsson (PLoS Comput. Biol., 2018)

Network-level allosteric effects are elucidated by detailing how ligand-binding events modulate utilization of catalytic potentials. - James T. Yurkovich; Miguel A. Alcantar; Zachary B. Haiman; Bernhard O. Palsson (PLoS Comput. Biol., 2018)

Estimating Cellular Goals from High-Dimensional Biological Data. - Laurence Yang 001; Michael A. Saunders; Jean-Christophe Lachance; Bernhard O. Palsson; José Bento 001 (KDD, 2019)

DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression. - Laurence Yang 001; Ali Ebrahim; Colton J. Lloyd; Michael A. Saunders; Bernhard O. Palsson (BMC Syst. Biol., 2019)

ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation. - Patrick V. Phaneuf; Dennis Gosting; Bernhard O. Palsson; Adam M. Feist (Nucleic Acids Res., 2019)

Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism. - Chuankai Cheng; Edward J. O'Brien; Douglas McCloskey; Jose Utrilla; Connor A. Olson; Ryan A. LaCroix; Troy E. Sandberg; Adam M. Feist; Bernhard O. Palsson; Zachary A. King (PLoS Comput. Biol., 2019)

Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli. - Bin Du; Laurence Yang 001; Colton J. Lloyd; Xin Fang; Bernhard O. Palsson (PLoS Comput. Biol., 2019)

BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data. - Jean-Christophe Lachance; Colton J. Lloyd; Jonathan M. Monk; Laurence Yang 001; Anand Sastry 002; Yara Seif; Bernhard O. Palsson; Sébastien Rodrigue; Adam M. Feist; Zachary A. King; Pierre-Étienne Jacques (PLoS Comput. Biol., 2019)

A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types. - Yara Seif; Jonathan M. Monk; Nathan Mih; Hannah Tsunemoto; Saugat Poudel; Cristal Zuñiga; Jared Broddrick; Karsten Zengler; Bernhard O. Palsson (PLoS Comput. Biol., 2019)

Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection. - Jinyuan Yan; Henri Estanbouli; Chen Liao; Wook Kim; Jonathan M. Monk; Rayees Rahman; Mini Kamboj; Bernhard O. Palsson; Weigang Qiu; João B. Xavier (PLoS Comput. Biol., 2019)

Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes. - Nathan Mih; Jonathan M. Monk; Xin Fang; Edward Catoiu; David Heckmann; Laurence Yang 001; Bernhard O. Palsson (BMC Bioinform., 2020)

BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. - Charles J. Norsigian; Neha Pusarla; John Luke McConn; James T. Yurkovich; Andreas Dräger; Bernhard O. Palsson; Zachary A. King (Nucleic Acids Res., 2020)

Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens. - Jason C. Hyun; Erol S. Kavvas; Jonathan M. Monk; Bernhard O. Palsson (PLoS Comput. Biol., 2020)

Optimal dimensionality selection for independent component analysis of transcriptomic data. - John Luke McConn; Cameron R. Lamoureux; Saugat Poudel; Bernhard O. Palsson; Anand V. Sastry (BMC Bioinform., 2021)

Scalable computation of intracellular metabolite concentrations. - Amir Akbari; Bernhard O. Palsson (Comput. Chem. Eng., 2021)

iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning. - Kevin Rychel; Katherine Decker; Anand V. Sastry; Patrick V. Phaneuf; Saugat Poudel; Bernhard O. Palsson (Nucleic Acids Res., 2021)

Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types. - Ke Chen; Amitesh Anand; Connor A. Olson; Troy E. Sandberg; Ye Gao; Nathan Mih; Bernhard O. Palsson (PLoS Comput. Biol., 2021)

MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics. - Zachary B. Haiman; Daniel C. Zielinski; Yuko Koike; James T. Yurkovich; Bernhard O. Palsson (PLoS Comput. Biol., 2021)

Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth. - Colton J. Lloyd; Jonathan Monk; Laurence Yang 001; Ali Ebrahim; Bernhard O. Palsson (PLoS Comput. Biol., 2021)

Independent component analysis recovers consistent regulatory signals from disparate datasets. - Anand V. Sastry; Alyssa Hu; David Heckmann; Saugat Poudel; Erol S. Kavvas; Bernhard O. Palsson (PLoS Comput. Biol., 2021)

proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms. - Katherine Decker; Ye Gao; Kevin Rychel; Tahani Al Bulushi; Siddharth M. Chauhan; Donghyuk Kim; Byung-Kwan Cho; Bernhard O. Palsson (Nucleic Acids Res., 2022)

Positively charged mineral surfaces promoted the accumulation of organic intermediates at the origin of metabolism. - Amir Akbari; Bernhard O. Palsson (PLoS Comput. Biol., 2022)

High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917. - Max van 't Hof; Omkar S. Mohite; Jonathan M. Monk; Tilmann Weber; Bernhard O. Palsson; Morten O. A. Sommer (BMC Bioinform., 2022)

Deep-learning optimized DEOCSU suite provides an iterable pipeline for accurate ChIP-exo peak calling. - Ina Bang; Sang-Mok Lee; Seojoung Park; Joon Young Park; Linh Khanh Nong; Ye Gao; Bernhard O. Palsson; Donghyuk Kim (Briefings Bioinform., 2023)

iModulonMiner and PyModulon: Software for unsupervised mining of gene expression compendia. - Anand V. Sastry; Yuan Yuan; Saugat Poudel; Kevin Rychel; Reo Yoo; Cameron R. Lamoureux; Gaoyuan Li; Joshua T. Burrows; Siddharth Chauhan; Zachary B. Haiman; Tahani Al Bulushi; Yara Seif; et al. (PLoS Comput. Biol., 2024)

Inferred regulons are consistent with regulator binding sequences in E. coli. - Sizhe Qiu; Xinlong Wan; Yueshan Liang; Cameron R. Lamoureux; Amir Akbari; Bernhard O. Palsson; Daniel C. Zielinski (PLoS Comput. Biol., 2024)

StressME: Unified computing framework of Escherichia coli metabolism, gene expression, and stress responses. - Jiao Zhao; Ke Chen; Bernhard O. Palsson; Laurence Yang 001 (PLoS Comput. Biol., 2024)

RBC-GEM: A genome-scale metabolic model for systems biology of the human red blood cell. - Zachary B. Haiman; Alicia Key; Angelo D'alessandro; Bernhard O. Palsson (PLoS Comput. Biol., 2025)