Bernhard O. Palsson

According to our database1, Bernhard O. Palsson authored at least 66 papers between 2000 and 2019.

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

Timeline

Legend:

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PhD thesis 
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Bibliography

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

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

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

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

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

Genome-scale estimation of cellular objectives.
CoRR, 2018

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

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

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

Reframing gene essentiality in terms of adaptive flexibility.
BMC Systems Biology, 2018

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

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

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

Machine learning in computational biology to accelerate high-throughput protein expression.
Bioinformatics, 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 Computational Biology, 2016

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

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

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

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

Systems biology of the structural proteome.
BMC Systems Biology, 2016

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

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

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

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

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

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

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

COBRApy: COnstraints-Based Reconstruction and Analysis for Python.
BMC Systems Biology, 2013

Antibacterial mechanisms identified through structural systems pharmacology.
BMC Systems Biology, 2013

GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data.
Bioinformatics, 2013

2012
Predicting outcomes of steady-state 13C isotope tracing experiments using Monte Carlo sampling.
BMC Systems Biology, 2012

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

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

The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions.
BMC Systems Biology, 2011

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

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

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

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

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

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

Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization.
PLoS Computational Biology, 2009

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

Functional States of the Genome-Scale Escherichia Coli Transcriptional Regulatory System.
PLoS Computational Biology, 2009

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

Connecting extracellular metabolomic measurements to intracellular flux states in yeast.
BMC Systems Biology, 2009

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

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

2008
Top-Down Analysis of Temporal Hierarchy in Biochemical Reaction Networks.
PLoS Computational Biology, 2008

Context-Specific Metabolic Networks Are Consistent with Experiments.
PLoS Computational Biology, 2008

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

Three factors underlying incorrect in silico predictions of essential metabolic genes.
BMC Systems Biology, 2008

2007
Metabolic Reconstruction and Modeling of Nitrogen Fixation in Rhizobium etli.
PLoS Computational Biology, 2007

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

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

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

Matrix Formalism to Describe Functional States of Transcriptional Regulatory Systems.
PLoS Computational Biology, 2006

Iterative Reconstruction of Transcriptional Regulatory Networks: An Algorithmic Approach.
PLoS Computational Biology, 2006

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

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

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

2005
Phenotype phase plane analysis using interior point methods.
Computers & Chemical Engineering, 2005

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

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

2000
Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions.
BMC Bioinformatics, 2000


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