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Author Details

Bernhard O Palsson
University of California San Diego
1981
668
122
Trey Ideker (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36702751Deep-learning optimized DEOCSU suite provides an iterable pipeline for accurate ChIP-exo peak calling.Brief Bioinform2023
37662221A data-driven approach for timescale decomposition of biochemical reaction networks.bioRxiv2023
38001096Global pathogenomic analysis identifies known and candidate genetic antimicrobial resistance determinants in twelve species.Nat Commun2023
37999241Modeling Red Blood Cell Metabolism in the Omics Era.Metabolites2023
37999223Differential Expression Analysis Utilizing Condition-Specific Metabolic Pathways.Metabolites2023
37713610A multi-scale expression and regulation knowledge base for Escherichia coli.Nucleic Acids Res2023
37713311Laboratory evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance.Cell Rep2023
37638727Machine learning uncovers the <i>Pseudomonas syringae</i> transcriptome in microbial communities and during infection.mSystems2023
37636038Adaptive evolution of a minimal organism with a synthetic genome.iScience2023
37567624Pangenome analysis reveals the genetic basis for taxonomic classification of the Lactobacillaceae family.Food Microbiol2023
37553643Reconstruction of the last bacterial common ancestor from 183 pangenomes reveals a versatile ancient core genome.Genome Biol2023
37285268Systems biology of competency in Vibrio natriegens is revealed by applying novel data analytics to the transcriptome.Cell Rep2023
37090546The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions.Res Sq2023
37278526Elucidation of independently modulated genes in <i>Streptococcus pyogenes</i> reveals carbon sources that control its expression of hemolytic toxins.mSystems2023
37026477The Escherichia coli Fur pan-regulon has few conserved but many unique regulatory targets.Nucleic Acids Res2023
37147430E. coli allantoinase is activated by the downstream metabolic enzyme, glycerate kinase, and stabilizes the putative allantoin transporter by direct binding.Sci Rep2023
36507678Revealing Causes for False-Positive and False-Negative Calling of Gene Essentiality in Escherichia coli Using Transposon Insertion Sequencing.mSystems2023
36702751Deep-learning optimized DEOCSU suite provides an iterable pipeline for accurate ChIP-exo peak calling.Brief Bioinform2023
37011218Whole-genome sequences from wild-type and laboratory-evolved strains define the alleleome and establish its hallmarks.Proc Natl Acad Sci U S A2023
37126695Metabolic homeostasis and growth in abiotic cells.Proc Natl Acad Sci U S A2023
37002859A model industrial workhorse: Bacillus subtilis strain 168 and its genome after a quarter of a century.Microb Biotechnol2023
37310465Elucidating the CodY regulon in <i>Staphylococcus aureus</i> USA300 substrains TCH1516 and LAC.mSystems2023
36865326Proteome allocation is linked to transcriptional regulation through a modularized transcriptome.bioRxiv2023
36738854Laboratory evolution reveals general and specific tolerance mechanisms for commodity chemicals.Metab Eng2023
36685725Model-driven experimental design workflow expands understanding of regulatory role of Nac in <i>Escherichia coli</i>.NAR Genom Bioinform2023
36685102Comprehensive whole genome sequencing with hybrid assembly of multi-drug resistant <i>Candida albicans</i> isolate causing cerebral abscess.Curr Res Microb Sci2023
37296102Empowering drug off-target discovery with metabolic and structural analysis.Nat Commun2023
37292890Establishing comprehensive quaternary structural proteomes from genome sequence.Res Sq2023
37292663CyuR is a Dual Regulator for L-Cysteine Dependent Antimicrobial Resistance in <i>Escherichia coli</i>.bioRxiv2023
37636038Adaptive evolution of a minimal organism with a synthetic genome.iScience2023
37713610A multi-scale expression and regulation knowledge base for Escherichia coli.Nucleic Acids Res2023
37713311Laboratory evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance.Cell Rep2023
37662221A data-driven approach for timescale decomposition of biochemical reaction networks.bioRxiv2023
37553643Reconstruction of the last bacterial common ancestor from 183 pangenomes reveals a versatile ancient core genome.Genome Biol2023
38001096Global pathogenomic analysis identifies known and candidate genetic antimicrobial resistance determinants in twelve species.Nat Commun2023
37999241Modeling Red Blood Cell Metabolism in the Omics Era.Metabolites2023
37999223Differential Expression Analysis Utilizing Condition-Specific Metabolic Pathways.Metabolites2023
37567624Pangenome analysis reveals the genetic basis for taxonomic classification of the Lactobacillaceae family.Food Microbiol2023
37638727Machine learning uncovers the <i>Pseudomonas syringae</i> transcriptome in microbial communities and during infection.mSystems2023
37292663CyuR is a Dual Regulator for L-Cysteine Dependent Antimicrobial Resistance in <i>Escherichia coli</i>.bioRxiv2023
37090546The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions.Res Sq2023
37285268Systems biology of competency in Vibrio natriegens is revealed by applying novel data analytics to the transcriptome.Cell Rep2023
37147430E. coli allantoinase is activated by the downstream metabolic enzyme, glycerate kinase, and stabilizes the putative allantoin transporter by direct binding.Sci Rep2023
37310465Elucidating the CodY regulon in <i>Staphylococcus aureus</i> USA300 substrains TCH1516 and LAC.mSystems2023
37278526Elucidation of independently modulated genes in <i>Streptococcus pyogenes</i> reveals carbon sources that control its expression of hemolytic toxins.mSystems2023
37011218Whole-genome sequences from wild-type and laboratory-evolved strains define the alleleome and establish its hallmarks.Proc Natl Acad Sci U S A2023
37002859A model industrial workhorse: Bacillus subtilis strain 168 and its genome after a quarter of a century.Microb Biotechnol2023
37296102Empowering drug off-target discovery with metabolic and structural analysis.Nat Commun2023
37292890Establishing comprehensive quaternary structural proteomes from genome sequence.Res Sq2023
37126695Metabolic homeostasis and growth in abiotic cells.Proc Natl Acad Sci U S A2023
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Collaborators

Nathan E Lewis
University of California San Diego
Co-authored papers 31
Nathan D Price
Institute for Systems Biology
Co-authored papers 24
Jason A Papin
University of Virginia
Co-authored papers 21
Jeremy S Edwards
Co-authored papers 19
Victor Nizet
university of california san diego School of Medicine
Co-authored papers 14
Jens Nielsen
Chalmers University of Technology
Co-authored papers 13
Jay D Keasling
University of California berkeley
Co-authored papers 10
Joshua N Adkins
Co-authored papers 9
Pieter C Dorrestein
Co-authored papers 6
Angelo D'Alessandro
University of Colorado Anschutz Medical Campus
Co-authored papers 6
Thomas O Metz
Pacific Northwest National Laboratory
Co-authored papers 6
Rob Knight
University of California
Co-authored papers 6
Irina A Rodionova
University of California at San Diego
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Richard D Smith
Pacific Northwest National Laboratory
Co-authored papers 5
Andrei L Osterman
Sanford Burnham Prebys Medical Discovery Institute
Co-authored papers 5
Alex Thomas
University of Alabama
Co-authored papers 5
Bj??rn G Voldborg
Technical University of Denmark
Co-authored papers 5
Dmitry A Rodionov
Sanford Burnham Prebys Medical Discovery Institute
Co-authored papers 4
Adam Godzik
University of California Riverside
Co-authored papers 4
Travis Nemkov
University of Colorado Anschutz Medical Campus
Co-authored papers 4
Nicolas Le Nov??re
Babraham Institute
Co-authored papers 4
Maciek R Antoniewicz
Massachusetts Institute of Technology
Co-authored papers 4
Neil Swainston
Institute of Systems, University of Liverpool
Co-authored papers 4
Samuel O Purvine
Pacific Northwest National Laboratory
Co-authored papers 4
Sanjay K Nigam
university of california san diego
Co-authored papers 3
Ernesto S Nakayasu
Co-authored papers 3
Larry Smarr
Co-authored papers 3
Milton H Saier
University of California at San Diego
Co-authored papers 3
Jason E McDermott
Pacific Northwest National Laboratory
Co-authored papers 3
George M Church
Harvard Medical School
Co-authored papers 3
Release 1.2