Bernhard O. Palsson

  • University of California, San Diego, USA

According to our database1, Bernhard O. Palsson authored at least 82 papers between 2000 and 2021.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.



In proceedings 
PhD thesis 


Online presence:



Independent component analysis recovers consistent regulatory signals from disparate datasets.
PLoS Comput. Biol., 2021

Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth.
PLoS Comput. Biol., 2021

MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics.
PLoS Comput. Biol., 2021

Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types.
PLoS Comput. Biol., 2021

iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning.
Nucleic Acids Res., 2021

Scalable computation of intracellular metabolite concentrations.
Comput. Chem. Eng., 2021

Optimal dimensionality selection for independent component analysis of transcriptomic data.
BMC Bioinform., 2021

Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens.
PLoS Comput. Biol., 2020

BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree.
Nucleic Acids Res., 2020

Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes.
BMC Bioinform., 2020

Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection.
PLoS Comput. Biol., 2019

A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types.
PLoS Comput. Biol., 2019

BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data.
PLoS Comput. Biol., 2019

Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli.
PLoS Comput. Biol., 2019

Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism.
PLoS Comput. Biol., 2019

ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation.
Nucleic Acids Res., 2019

DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression.
BMC Syst. Biol., 2019

Estimating Cellular Goals from High-Dimensional Biological Data.
Proceedings of the 25th ACM SIGKDD International Conference on Knowledge Discovery & Data Mining, 2019

Network-level allosteric effects are elucidated by detailing how ligand-binding events modulate utilization of catalytic potentials.
PLoS Comput. Biol., 2018

COBRAme: A computational framework for genome-scale models of metabolism and gene expression.
PLoS Comput. Biol., 2018

Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting.
PLoS Comput. Biol., 2018

Genome-scale estimation of cellular objectives.
CoRR, 2018

Systems biology as an emerging paradigm in transfusion medicine.
BMC Syst. Biol., 2018

Escher-FBA: a web application for interactive flux balance analysis.
BMC Syst. Biol., 2018

Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions.
BMC Syst. Biol., 2018

Reframing gene essentiality in terms of adaptive flexibility.
BMC Syst. Biol., 2018

Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa.
BMC Syst. Biol., 2018

ssbio: a Python framework for structural systems biology.
Bioinform., 2018

Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells.
PLoS Comput. Biol., 2017

Machine learning in computational biology to accelerate high-throughput protein expression.
Bioinform., 2017

Utilizing biomarkers to forecast quantitative metabolite concentration profiles in human red blood cells.
Proceedings of the IEEE Conference on Control Technology and Applications, 2017

Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments.
PLoS Comput. Biol., 2016

A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism.
PLoS Comput. Biol., 2016

Solving Puzzles With Missing Pieces: The Power of Systems Biology [Point of View].
Proc. IEEE, 2016

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models.
Nucleic Acids Res., 2016

Evaluation of rate law approximations in bottom-up kinetic models of metabolism.
BMC Syst. Biol., 2016

Systems biology of the structural proteome.
BMC Syst. Biol., 2016

solveME: fast and reliable solution of nonlinear ME models.
BMC Bioinform., 2016

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways.
PLoS Comput. Biol., 2015

SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks.
BMC Syst. Biol., 2015

JSBML 1.0: providing a smorgasbord of options to encode systems biology models.
Bioinform., 2015

A Systems Approach to Predict Oncometabolites via Context-Specific Genome-Scale Metabolic Networks.
PLoS Comput. Biol., 2014

Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale.
BMC Syst. Biol., 2014

The development of a fully-integrated immune response model (FIRM) simulator of the immune response through integration of multiple subset models.
BMC Syst. Biol., 2013

COBRApy: COnstraints-Based Reconstruction and Analysis for Python.
BMC Syst. Biol., 2013

Antibacterial mechanisms identified through structural systems pharmacology.
BMC Syst. Biol., 2013

GIM<sup>3</sup>E: condition-specific models of cellular metabolism developed from metabolomics and expression data.
Bioinform., 2013

Predicting outcomes of steady-state <sup>13</sup>C isotope tracing experiments using Monte Carlo sampling.
BMC Syst. Biol., 2012

Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions.
BMC Syst. Biol., 2012

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2.
BMC Syst. Biol., 2011

The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions.
BMC Syst. Biol., 2011

An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92.
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.
BMC Syst. Biol., 2011

A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology.
BMC Syst. Biol., 2011

Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model.
PLoS Comput. Biol., 2010

A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1.
BMC Syst. Biol., 2010

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions.
BMC Bioinform., 2010

Metabolic Systems Biology.
Proceedings of the Encyclopedia of Complexity and Systems Science, 2009

Genome-Scale Reconstruction of <i>Escherichia coli</i>'s Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization.
PLoS Comput. Biol., 2009

Identification of Potential Pathway Mediation Targets in Toll-like Receptor Signaling.
PLoS Comput. Biol., 2009

Functional States of the Genome-Scale <i>Escherichia Coli</i> Transcriptional Regulatory System.
PLoS Comput. Biol., 2009

Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction.
BMC Syst. Biol., 2009

Connecting extracellular metabolomic measurements to intracellular flux states in yeast.
BMC Syst. Biol., 2009

Using in silico models to simulate dual perturbation experiments: procedure development and interpretation of outcomes.
BMC Syst. Biol., 2009

Decomposing complex reaction networks using random sampling, principal component analysis and basis rotation.
BMC Syst. Biol., 2009

Top-Down Analysis of Temporal Hierarchy in Biochemical Reaction Networks.
PLoS Comput. Biol., 2008

Context-Specific Metabolic Networks Are Consistent with Experiments.
PLoS Comput. Biol., 2008

A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory.
BMC Syst. Biol., 2008

Three factors underlying incorrect in silico predictions of essential metabolic genes.
BMC Syst. Biol., 2008

Metabolic Reconstruction and Modeling of Nitrogen Fixation in <i>Rhizobium etli</i>.
PLoS Comput. Biol., 2007

Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets.
BMC Syst. Biol., 2007

Estimation of the number of extreme pathways for metabolic networks.
BMC Bioinform., 2007

Identification of Genome-Scale Metabolic Network Models Using Experimentally Measured Flux Profiles.
PLoS Comput. Biol., 2006

Matrix Formalism to Describe Functional States of Transcriptional Regulatory Systems.
PLoS Comput. Biol., 2006

Iterative Reconstruction of Transcriptional Regulatory Networks: An Algorithmic Approach.
PLoS Comput. Biol., 2006

Long-Range Periodic Patterns in Microbial Genomes Indicate Significant Multi-Scale Chromosomal Organization.
PLoS Comput. Biol., 2006

Metabolite coupling in genome-scale metabolic networks.
BMC Bioinform., 2006

Network-level analysis of metabolic regulation in the human red blood cell using random sampling and singular value decomposition.
BMC Bioinform., 2006

Phenotype phase plane analysis using interior point methods.
Comput. Chem. Eng., 2005

expa: a program for calculating extreme pathways in biochemical reaction networks.
Bioinform., 2005

Dynamic simulation of the human red blood cell metabolic network.
Bioinform., 2001

Metabolic flux balance analysis and the <i>in silico</i> analysis of <i>Escherichia coli</i> K-12 gene deletions.
BMC Bioinform., 2000