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Bernhard O. Palsson
Bernhard Ø. Palsson
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- affiliation: University of California, San Diego, USA
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2020 – today
- 2024
- [j85]Sizhe Qiu
, Xinlong Wan
Inferred regulons are consistent with regulator binding sequences in E. coli. PLoS Comput. Biol. 20(1) (2024) - [j84]Jiao Zhao, Ke Chen, Bernhard O. Palsson
StressME: Unified computing framework of Escherichia coli metabolism, gene expression, and stress responses. PLoS Comput. Biol. 20(2) (2024) - [j83]Anand V. Sastry
iModulonMiner and PyModulon: Software for unsupervised mining of gene expression compendia. PLoS Comput. Biol. 20(10): 1012546 (2024) - 2023
- [j82]Ina Bang, Sang-Mok Lee
Deep-learning optimized DEOCSU suite provides an iterable pipeline for accurate ChIP-exo peak calling. Briefings Bioinform. 24(2) (2023) - 2022
- [j81]Max van 't Hof
High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917. BMC Bioinform. 23(1): 566 (2022) - [j80]Katherine Decker
proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms. Nucleic Acids Res. 50(D1): 1077-1090 (2022) - [j79]Amir Akbari
Positively charged mineral surfaces promoted the accumulation of organic intermediates at the origin of metabolism. PLoS Comput. Biol. 18(8) (2022) - 2021
- [j78]John Luke McConn, Cameron R. Lamoureux, Saugat Poudel, Bernhard O. Palsson, Anand V. Sastry:
Optimal dimensionality selection for independent component analysis of transcriptomic data. BMC Bioinform. 22(1): 584 (2021) - [j77]Amir Akbari, Bernhard O. Palsson:
Scalable computation of intracellular metabolite concentrations. Comput. Chem. Eng. 145: 107164 (2021) - [j76]Kevin Rychel
iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning. Nucleic Acids Res. 49(Database-Issue): D112-D120 (2021) - [j75]Ke Chen
Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types. PLoS Comput. Biol. 17(1) (2021) - [j74]Zachary B. Haiman
MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics. PLoS Comput. Biol. 17(1) (2021) - [j73]Anand V. Sastry
Independent component analysis recovers consistent regulatory signals from disparate datasets. PLoS Comput. Biol. 17(2) (2021) - [j72]Colton J. Lloyd, Jonathan Monk
Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth. PLoS Comput. Biol. 17(6) (2021) - 2020
- [j71]Nathan Mih, Jonathan M. Monk, Xin Fang, Edward Catoiu, David Heckmann, Laurence Yang, Bernhard O. Palsson
Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes. BMC Bioinform. 21(1): 162 (2020) - [j70]Charles J. Norsigian
BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic Acids Res. 48(Database-Issue): D402-D406 (2020) - [j69]Jason C. Hyun
Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens. PLoS Comput. Biol. 16(3) (2020)
2010 – 2019
- 2019
- [j68]Laurence Yang
DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression. BMC Syst. Biol. 13(1): 2:1-2:15 (2019) - [j67]Patrick V. Phaneuf
ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation. Nucleic Acids Res. 47(Database-Issue): D1164-D1171 (2019) - [j66]Yara Seif, Jonathan M. Monk
A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types. PLoS Comput. Biol. 15(1) (2019) - [j65]Jean-Christophe Lachance
BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data. PLoS Comput. Biol. 15(4) (2019) - [j64]Chuankai Cheng
Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism. PLoS Comput. Biol. 15(6) (2019) - [j63]Bin Du
Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli. PLoS Comput. Biol. 15(12) (2019) - [j62]Jinyuan Yan, Henri Estanbouli, Chen Liao
Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection. PLoS Comput. Biol. 15(12) (2019) - [c2]Laurence Yang, Michael A. Saunders
Estimating Cellular Goals from High-Dimensional Biological Data. KDD 2019: 2202-2211 - 2018
- [j61]Nathan Mih
ssbio: a Python framework for structural systems biology. Bioinform. 34(12): 2155-2157 (2018) - [j60]Erol S. Kavvas, Yara Seif, James T. Yurkovich, Charles J. Norsigian, Saugat Poudel, William W. Greenwald
Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions. BMC Syst. Biol. 12(1): 25:1-25:15 (2018) - [j59]James T. Yurkovich
Systems biology as an emerging paradigm in transfusion medicine. BMC Syst. Biol. 12(1): 31:1-31:9 (2018) - [j58]Xin Fang, Jonathan M. Monk
Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa. BMC Syst. Biol. 12(1): 66:1-66:10 (2018) - [j57]Elliot Rowe, Bernhard O. Palsson, Zachary A. King:
Escher-FBA: a web application for interactive flux balance analysis. BMC Syst. Biol. 12(1): 84:1-84:7 (2018) - [j56]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
Reframing gene essentiality in terms of adaptive flexibility. BMC Syst. Biol. 12(1): 143:1-143:20 (2018) - [j55]Alyaa M. Abdel-Haleem
Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting. PLoS Comput. Biol. 14(1) (2018) - [j54]Colton J. Lloyd
COBRAme: A computational framework for genome-scale models of metabolism and gene expression. PLoS Comput. Biol. 14(7) (2018) - [j53]James T. Yurkovich
Network-level allosteric effects are elucidated by detailing how ligand-binding events modulate utilization of catalytic potentials. PLoS Comput. Biol. 14(8) (2018) - [i1]Laurence Yang, José Bento, Jean-Christophe Lachance, Bernhard O. Palsson:
Genome-scale estimation of cellular objectives. CoRR abs/1807.04245 (2018) - 2017
- [j52]Anand Sastry
Machine learning in computational biology to accelerate high-throughput protein expression. Bioinform. 33(16): 2487-2495 (2017) - [j51]James T. Yurkovich, Laurence Yang, Bernhard O. Palsson:
Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells. PLoS Comput. Biol. 13(3) (2017) - [c1]James T. Yurkovich, Laurence Yang, Bernhard O. Palsson:
Utilizing biomarkers to forecast quantitative metabolite concentration profiles in human red blood cells. CCTA 2017: 961-966 - 2016
- [j50]Laurence Yang, Ding Ma
solveME: fast and reliable solution of nonlinear ME models. BMC Bioinform. 17: 391 (2016) - [j49]Elizabeth Brunk, Nathan Mih
Systems biology of the structural proteome. BMC Syst. Biol. 10: 26 (2016) - [j48]Bin Du, Daniel C. Zielinski
Evaluation of rate law approximations in bottom-up kinetic models of metabolism. BMC Syst. Biol. 10: 40 (2016) - [j47]Zachary A. King, Justin Lu, Andreas Dräger
BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. Nucleic Acids Res. 44(Database-Issue): 515-522 (2016) - [j46]James T. Yurkovich, Bernhard O. Palsson:
Solving Puzzles With Missing Pieces: The Power of Systems Biology [Point of View]. Proc. IEEE 104(1): 2-7 (2016) - [j45]Edward J. O'Brien, Jose Utrilla
Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments. PLoS Comput. Biol. 12(6) (2016) - [j44]Nathan Mih
A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism. PLoS Comput. Biol. 12(7) (2016) - 2015
- [j43]Nicolas Rodriguez
JSBML 1.0: providing a smorgasbord of options to encode systems biology models. Bioinform. 31(20): 3383-3386 (2015) - [j42]Andreas Dräger
SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks. BMC Syst. Biol. 9: 68 (2015) - [j41]Zachary A. King, Andreas Dräger
Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways. PLoS Comput. Biol. 11(8) (2015) - 2014
- [j40]Joanne K. Liu, Edward J. O'Brien, Joshua A. Lerman, Karsten Zengler
Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale. BMC Syst. Biol. 8: 110 (2014) - [j39]Hojung Nam
A Systems Approach to Predict Oncometabolites via Context-Specific Genome-Scale Metabolic Networks. PLoS Comput. Biol. 10(9) (2014) - 2013
- [j38]Brian J. Schmidt
GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data. Bioinform. 29(22): 2900-2908 (2013) - [j37]Ali Ebrahim
COBRApy: COnstraints-Based Reconstruction and Analysis for Python. BMC Syst. Biol. 7: 74 (2013) - [j36]Sirus Palsson, Timothy P. Hickling
The development of a fully-integrated immune response model (FIRM) simulator of the immune response through integration of multiple subset models. BMC Syst. Biol. 7: 95 (2013) - [j35]Roger L. Chang
Antibacterial mechanisms identified through structural systems pharmacology. BMC Syst. Biol. 7: 102 (2013) - 2012
- [j34]Jan Schellenberger, Daniel C. Zielinski
Predicting outcomes of steady-state 13C isotope tracing experiments using Monte Carlo sampling. BMC Syst. Biol. 6: 9 (2012) - [j33]Jeffrey D. Orth, Bernhard Ø. Palsson:
Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions. BMC Syst. Biol. 6: 30 (2012) - 2011
- [j32]Ines Thiele
A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. BMC Syst. Biol. 5: 8 (2011) - [j31]Aarash Bordbar
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. 5: 110 (2011) - [j30]Ottar Rolfsson
The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions. BMC Syst. Biol. 5: 155 (2011) - [j29]Pep Charusanti
An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92. BMC Syst. Biol. 5: 163 (2011) - [j28]Aarash Bordbar
A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology. BMC Syst. Biol. 5: 180 (2011) - 2010
- [j27]Jan Schellenberger, Junyoung O. Park
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. BMC Bioinform. 11: 213 (2010) - [j26]Martin I. Sigurdsson
A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1. BMC Syst. Biol. 4: 140 (2010) - [j25]Roger L. Chang
Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model. PLoS Comput. Biol. 6(9) (2010)
2000 – 2009
- 2009
- [j24]Christian L. Barrett, Markus J. Herrgård, Bernhard Ø. Palsson:
Decomposing complex reaction networks using random sampling, principal component analysis and basis rotation. BMC Syst. Biol. 3: 30 (2009) - [j23]Monica L. Mo, Bernhard Ø. Palsson, Markus J. Herrgård:
Connecting extracellular metabolomic measurements to intracellular flux states in yeast. BMC Syst. Biol. 3: 37 (2009) - [j22]Anu Raghunathan, Jennifer L. Reed, Sook-Il Shin, Bernhard Ø. Palsson, Simon Daefler:
Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction. BMC Syst. Biol. 3: 38 (2009) - [j21]Neema Jamshidi
Using in silico models to simulate dual perturbation experiments: procedure development and interpretation of outcomes. BMC Syst. Biol. 3: 44 (2009) - [j20]Fan Li
Identification of Potential Pathway Mediation Targets in Toll-like Receptor Signaling. PLoS Comput. Biol. 5(2) (2009) - [j19]Ines Thiele
Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization. PLoS Comput. Biol. 5(3) (2009) - [j18]Erwin P. Gianchandani, Andrew R. Joyce, Bernhard O. Palsson, Jason A. Papin
Functional States of the Genome-Scale Escherichia Coli Transcriptional Regulatory System. PLoS Comput. Biol. 5(6) (2009) - [r1]Nathan E. Lewis, Neema Jamshidi, Ines Thiele, Bernhard O. Palsson:
Metabolic Systems Biology. Encyclopedia of Complexity and Systems Science 2009: 5535-5552 - 2008
- [j17]Scott A. Becker, Bernhard O. Palsson:
Three factors underlying incorrect in silico predictions of essential metabolic genes. BMC Syst. Biol. 2: 14 (2008) - [j16]Juan Nogales
A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory. BMC Syst. Biol. 2: 79 (2008) - [j15]Scott A. Becker, Bernhard O. Palsson:
Context-Specific Metabolic Networks Are Consistent with Experiments. PLoS Comput. Biol. 4(5) (2008) - [j14]Neema Jamshidi
Top-Down Analysis of Temporal Hierarchy in Biochemical Reaction Networks. PLoS Comput. Biol. 4(9) (2008) - 2007
- [j13]Matthew Yeung, Ines Thiele
Estimation of the number of extreme pathways for metabolic networks. BMC Bioinform. 8 (2007) - [j12]Neema Jamshidi
Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets. BMC Syst. Biol. 1: 26 (2007) - [j11]Osbaldo Resendis-Antonio
Metabolic Reconstruction and Modeling of Nitrogen Fixation in Rhizobium etli. PLoS Comput. Biol. 3(10) (2007) - 2006
- [j10]Scott A. Becker, Nathan D. Price
Metabolite coupling in genome-scale metabolic networks. BMC Bioinform. 7: 111 (2006) - [j9]Christian L. Barrett, Nathan D. Price
Network-level analysis of metabolic regulation in the human red blood cell using random sampling and singular value decomposition. BMC Bioinform. 7: 132 (2006) - [j8]Timothy E. Allen, Nathan D. Price
Long-Range Periodic Patterns in Microbial Genomes Indicate Significant Multi-Scale Chromosomal Organization. PLoS Comput. Biol. 2(1) (2006) - [j7]Christian L. Barrett, Bernhard O. Palsson:
Iterative Reconstruction of Transcriptional Regulatory Networks: An Algorithmic Approach. PLoS Comput. Biol. 2(5) (2006) - [j6]Markus J. Herrgård, Stephen S. Fong, Bernhard Ø. Palsson:
Identification of Genome-Scale Metabolic Network Models Using Experimentally Measured Flux Profiles. PLoS Comput. Biol. 2(7) (2006) - [j5]Erwin P. Gianchandani, Jason A. Papin
Matrix Formalism to Describe Functional States of Transcriptional Regulatory Systems. PLoS Comput. Biol. 2(8) (2006) - 2005
- [j4]Steven L. Bell, Bernhard O. Palsson:
expa: a program for calculating extreme pathways in biochemical reaction networks. Bioinform. 21(8): 1739-1740 (2005) - [j3]Steven L. Bell, Bernhard O. Palsson:
Phenotype phase plane analysis using interior point methods. Comput. Chem. Eng. 29(3): 481-486 (2005) - 2001
- [j2]Neema Jamshidi
Dynamic simulation of the human red blood cell metabolic network. Bioinform. 17(3): 286-287 (2001) - 2000
- [j1]Jeremy S. Edwards, Bernhard O. Palsson:
Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions. BMC Bioinform. 1: 1 (2000)
Coauthor Index
Jonathan Monk
aka: Jonathan M. Monk
aka: Jonathan M. Monk
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last updated on 2024-12-02 21:25 CET by the dblp team
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