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Author Details

Christopher S Henry
Argonne National Laboratory
2005
80
32
Gloria M Sheynkman (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36376589Metagenome-assembled genome extraction and analysis from microbiomes using KBase.Nat Protoc2023
37589572TranSyT, an innovative framework for identifying transport systems.Bioinformatics2023
36857575kb_DRAM: annotation and metabolic profiling of genomes with DRAM in KBase.Bioinformatics2023
36658342Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine.Nat Biotechnol2023
36451056Publisher Correction: Metagenome-assembled genome extraction and analysis from microbiomes using KBase.Nat Protoc2023
36271857Respiratory energy demands and scope for demand expansion and destruction.Plant Physiol2023
34719000Application of the Metabolic Modeling Pipeline in KBase to Categorize Reactions, Predict Essential Genes, and Predict Pathways in an Isolate Genome.Methods Mol Biol2022
35862786Metabolite Damage and Damage Control in a Minimal Genome.mBio2022
35714443Genome-scale modeling of the primary-specialized metabolism interface.Curr Opin Plant Biol2022
36561390Functional characterization of prokaryotic dark matter: the road so far and what lies ahead.Curr Res Microb Sci2022
35961013A roadmap for the functional annotation of protein families: a community perspective.Database (Oxford)2022
36154140Interaction Networks Are Driven by Community-Responsive Phenotypes in a Chitin-Degrading Consortium of Soil Microbes.mSystems2022
34726691ORT: a workflow linking genome-scale metabolic models with reactive transport codes.Bioinformatics2022
32986834The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes.Nucleic Acids Res2021
33869975Quantum Mechanical Methods Predict Accurate Thermodynamics of Biochemical Reactions.ACS Omega2021
33753504The number of catalytic cycles in an enzyme's lifetime and why it matters to metabolic engineering.Proc Natl Acad Sci U S A2021
34729986The Moderately (D)efficient Enzyme: Catalysis-Related Damage <i>In Vivo</i> and Its Repair.Biochemistry2021
33208936Publisher Correction: A genomic catalog of Earth's microbiomes.Nat Biotechnol2021
33179751The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes.Nucleic Acids Res2021
32265554Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing.Nat Biotechnol2020
32943555Draft Genome Sequence of <i>Pseudarthrobacter</i> sp. Strain ATCC 49442 (Formerly Micrococcus luteus), a Pyridine-Degrading Bacterium.Microbiol Resour Announc2020
32879425Chemical composition of material extractives influences microbial growth and dynamics on wetted wood materials.Sci Rep2020
32816982Draft Genome Sequence of 2-Methylpyridine-, 2-Ethylpyridine-, and 2-Hydroxypyridine-Degrading <i>Arthrobacter</i> sp. Strain ATCC 49987.Microbiol Resour Announc2020
32123384MEMOTE for standardized genome-scale metabolic model testing.Nat Biotechnol2020
31048380Draft Genome Sequence of <i>Enterobacter</i> sp. Strain A8, a Carbazole-Degrading Bacterium.Microbiol Resour Announc2019
31221646Draft Genome Sequence of <i>Rhodococcus</i> sp. Strain ATCC 49988, a Quinoline-Degrading Bacterium.Microbiol Resour Announc2019
30864320Implementing and evaluating a Gaussian mixture framework for identifying gene function from TnSeq data.Pac Symp Biocomput2019
29222751Reconstruction and Analysis of Central Metabolism in Microbes.Methods Mol Biol2018
29907310A pathway for every product? Tools to discover and design plant metabolism.Plant Sci2018
30065105Methods for automated genome-scale metabolic model reconstruction.Biochem Soc Trans2018
29979655KBase: The United States Department of Energy Systems Biology Knowledgebase.Nat Biotechnol2018
29924895PlantSEED enables automated annotation and reconstruction of plant primary metabolism with improved compartmentalization and comparative consistency.Plant J2018
29382740A plastidial pantoate transporter with a potential role in pantothenate synthesis.Biochem J2018
27899627Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center.Nucleic Acids Res2017
28168783A novel signal transduction protein: Combination of solute binding and tandem PAS-like sensor domains in one polypeptide chain.Protein Sci2017
28362260Evolution of substrate specificity in a retained enzyme driven by gene loss.Elife2017
28375518Generation and Validation of the iKp1289 Metabolic Model for Klebsiella pneumoniae KPPR1.J Infect Dis2017
29030275Metabolite damage and repair in metabolic engineering design.Metab Eng2017
28827682Metabolic Reconstruction and Modeling Microbial Electrosynthesis.Sci Rep2017
27047450Reconstruction of the Regulatory Network for Bacillus subtilis and Reconciliation with Gene Expression Data.Front Microbiol2016
26667673Metabolite Damage and Metabolite Damage Control in Plants.Annu Rev Plant Biol2016
27933038Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation.Front Microbiol2016
27502787Modeling central metabolism and energy biosynthesis across microbial life.BMC Genomics2016
27231362Draft Genome Sequence of a Multidrug-Resistant Klebsiella quasipneumoniae subsp. similipneumoniae Isolate from a Clinical Source.Genome Announc2016
27379044From DNA to FBA: How to Build Your Own Genome-Scale Metabolic Model.Front Microbiol2016
27186840Microbial Community Metabolic Modeling: A Community Data-Driven Network Reconstruction.J Cell Physiol2016
27284066'Nothing of chemistry disappears in biology': the Top 30 damage-prone endogenous metabolites.Biochem Soc Trans2016
27342196Systematic identification and analysis of frequent gene fusion events in metabolic pathways.BMC Genomics2016
27065985Experimental and Metabolic Modeling Evidence for a Folate-Cleaving Side-Activity of Ketopantoate Hydroxymethyltransferase (PanB).Front Microbiol2016
26929404Co-occurrence of analogous enzymes determines evolution of a novel (βα)8-isomerase sub-family after non-conserved mutations in flexible loop.Biochem J2016
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Collaborators

Computation Institute, University of Chicago
Co-authored papers 23
Argonne National Laboratory
Co-authored papers 20
Argonne National Laboratory
Co-authored papers 11
Argonne National Laboratory
Co-authored papers 11
University of Florida
Co-authored papers 10
University of Chicago
Co-authored papers 9
Hope College
Co-authored papers 8
Hope College
Co-authored papers 8
Scripps Institution of Oceanography, University of California San Diego
Co-authored papers 7
Lawrence Berkeley National Laboratory
Co-authored papers 7
University of Chicago
Co-authored papers 7
Lawrence Berkeley National Laboratory
Co-authored papers 6
University of Chicago
Co-authored papers 6
Oak Ridge National Laboratory
Co-authored papers 5
Oak Ridge National Laboratory
Co-authored papers 5
University of Chicago
Co-authored papers 4
Lawrence Berkeley National Laboratory
Co-authored papers 4
University of Chicago
Co-authored papers 4
University of California davis
Co-authored papers 4
Argonne National Laboratory
Co-authored papers 4
Lawrence Berkeley National Laboratory
Co-authored papers 4
National Cancer Institute
Co-authored papers 4
Argonne National Laboratory
Co-authored papers 3
Lawrence Berkeley National Laboratory
Co-authored papers 3
University of Chicago
Co-authored papers 3
Center for Structural Biology of Infectious Diseases, University of Chicago
Co-authored papers 3
University of California San Diego
Co-authored papers 3
Institute for Artificial Intelligence, University of Duisburg-Essen
Co-authored papers 3
Institute for Systems Biology
Co-authored papers 3
The Fatty Acid Research Institute
Co-authored papers 3