Bernhard O. Palsson
Orcid: 0000-0003-2357-6785Affiliations:
- University of California, San Diego, USA
According to our database1,
Bernhard O. Palsson
authored at least 88 papers
between 2000 and 2024.
Collaborative distances:
Collaborative distances:
Timeline
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Bibliography
2024
StressME: Unified computing framework of Escherichia coli metabolism, gene expression, and stress responses.
PLoS Comput. Biol., February, 2024
PLoS Comput. Biol., January, 2024
2023
Deep-learning optimized DEOCSU suite provides an iterable pipeline for accurate ChIP-exo peak calling.
Briefings Bioinform., March, 2023
2022
High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917.
BMC Bioinform., December, 2022
Positively charged mineral surfaces promoted the accumulation of organic intermediates at the origin of metabolism.
PLoS Comput. Biol., 2022
Nucleic Acids Res., 2022
2021
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
Comput. Chem. Eng., 2021
Optimal dimensionality selection for independent component analysis of transcriptomic data.
BMC Bioinform., 2021
2020
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
2019
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
Proceedings of the 25th ACM SIGKDD International Conference on Knowledge Discovery & Data Mining, 2019
2018
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
BMC Syst. Biol., 2018
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
Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa.
BMC Syst. Biol., 2018
2017
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
2016
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
Proc. IEEE, 2016
BiGG Models: A platform for integrating, standardizing and sharing genome-scale models.
Nucleic Acids Res., 2016
BMC Syst. Biol., 2016
2015
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
Bioinform., 2015
2014
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
2013
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
BMC Syst. Biol., 2013
BMC Syst. Biol., 2013
GIM<sup>3</sup>E: condition-specific models of cellular metabolism developed from metabolomics and expression data.
Bioinform., 2013
2012
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
2011
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
2010
Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model.
PLoS Comput. Biol., 2010
BMC Syst. Biol., 2010
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions.
BMC Bioinform., 2010
2009
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
2008
PLoS Comput. Biol., 2008
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
2007
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
BMC Bioinform., 2007
2006
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
Network-level analysis of metabolic regulation in the human red blood cell using random sampling and singular value decomposition.
BMC Bioinform., 2006
2005
Comput. Chem. Eng., 2005
Bioinform., 2005
2001
2000
Metabolic flux balance analysis and the <i>in silico</i> analysis of <i>Escherichia coli</i> K-12 gene deletions.
BMC Bioinform., 2000