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Author Details

John-Marc Chandonia
Lawrence Berkeley National Laboratory
1995
48
21
PMIDPaper TitleJournal TitlePublished Year
37065130Large-scale genetic characterization of the model sulfate-reducing bacterium, <i>Desulfovibrio vulgaris</i> Hildenborough.Front Microbiol2023
34850923SCOPe: improvements to the structural classification of proteins - extended database to facilitate variant interpretation and machine learning.Nucleic Acids Res2022
35475637Complete Genome Sequence of Bacillus cereus Strain CPT56D-587-MTF, Isolated from a Nitrate- and Metal-Contaminated Subsurface Environment.Microbiol Resour Announc2022
36251274CORAL: A framework for rigorous self-validated data modeling and integrative, reproducible data analysis.Gigascience2022
36053980Ecophysiological and genomic analyses of a representative isolate of highly abundant Bacillus cereus strains in contaminated subsurface sediments.Environ Microbiol2022
33947809Correction for Vangay et al., "Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities".mSystems2021
33622857Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities.mSystems2021
34184913Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental Tolerance.mSystems2021
33122416Draft Genome Sequence of <i>Bacillus</i> sp. Strain EB106-08-02-XG196, Isolated from High-Nitrate-Contaminated Sediment.Microbiol Resour Announc2020
33193240Characterization of a Metal-Resistant <i>Bacillus</i> Strain With a High Molybdate Affinity ModA From Contaminated Sediments at the Oak Ridge Reservation.Front Microbiol2020
30500919SCOPe: classification of large macromolecular structures in the structural classification of proteins-extended database.Nucleic Acids Res2019
30808697Large Circular Plasmids from Groundwater Plasmidomes Span Multiple Incompatibility Groups and Are Enriched in Multimetal Resistance Genes.mBio2019
29979655KBase: The United States Department of Energy Systems Biology Knowledgebase.Nat Biotechnol2018
27914894SCOPe: Manual Curation and Artifact Removal in the Structural Classification of Proteins - extended Database.J Mol Biol2017
28112946Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation.Environ Sci Technol2017
28397312Lessons from the CAGI-4 Hopkins clinical panel challenge.Hum Mutat2017
27099342Quantitative Tagless Copurification: A Method to Validate and Identify Protein-Protein Interactions.Mol Cell Proteomics2016
26873250Bacterial Interactomes: Interacting Protein Partners Share Similar Function and Are Validated in Independent Assays More Frequently Than Previously Reported.Mol Cell Proteomics2016
26313554The value of protein structure classification information-Surveying the scientific literature.Proteins2015
24304899SCOPe: Structural Classification of Proteins--extended, integrating SCOP and ASTRAL data and classification of new structures.Nucleic Acids Res2014
23098413High-throughput isolation and characterization of untagged membrane protein complexes: outer membrane complexes of Desulfovibrio vulgaris.J Proteome Res2012
21258060WIST: toolkit for rapid, customized LIMS development.Bioinformatics2011
21908633Generalized schemes for high-throughput manipulation of the Desulfovibrio vulgaris genome.Appl Environ Microbiol2011
21738675Towards a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough.PLoS One2011
19805340Survey of large protein complexes in D. vulgaris reveals great structural diversity.Proc Natl Acad Sci U S A2009
18000004Data growth and its impact on the SCOP database: new developments.Nucleic Acids Res2008
18542885Structural genomics of minimal organisms: pipeline and results.Methods Mol Biol2008
17355171The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families.PLoS Biol2007
17537750StrBioLib: a Java library for development of custom computational structural biology applications.Bioinformatics2007
17764033Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center.J Struct Funct Genomics2007
17680349NMR structure of the N-terminal domain of the replication initiator protein DnaA.J Struct Funct Genomics2007
16276528Target selection and deselection at the Berkeley Structural Genomics Center.Proteins2006
16397008ANDY: a general, fault-tolerant tool for database searching on computer clusters.Bioinformatics2006
16424331The impact of structural genomics: expectations and outcomes.Science2006
16566839Structural proteomics of minimal organisms: conservation of protein fold usage and evolutionary implications.BMC Struct Biol2006
15790427Comparative mapping of sequence-based and structure-based protein domains.BMC Bioinformatics2005
17282292Update on the pfam5000 strategy for selection of structural genomics targets.Conf Proc IEEE Eng Med Biol Soc2005
16211501Structural genomics of minimal organisms and protein fold space.J Struct Funct Genomics2005
15521074Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches.Proteins2005
14681391The ASTRAL Compendium in 2004.Nucleic Acids Res2004
15173120WebLogo: a sequence logo generator.Genome Res2004
15345043Structural genomics and structural biology: compare and contrast.Genome Biol2004
12972255New local potential useful for genome annotation and 3D modeling.J Mol Biol2003
11752310ASTRAL compendium enhancements.Nucleic Acids Res2002
10328264New methods for accurate prediction of protein secondary structure.Proteins1999
10222205High-resolution autoreactive epitope mapping and structural modeling of the 65 kDa form of human glutamic acid decarboxylase.J Mol Biol1999
8845767The importance of larger data sets for protein secondary structure prediction with neural networks.Protein Sci1996
7757016Neural networks for secondary structure and structural class predictions.Protein Sci1995
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Collaborators

University of California berkeley
Co-authored papers 22
University of Tennessee
Co-authored papers 12
Lawrence Berkeley National Laboratory
Co-authored papers 12
Lawrence Berkeley National Laboratory
Co-authored papers 6
University of Georgia
Co-authored papers 5
E O Lawrence Berkeley National Laboratory, UCSF Medical Center, University of California, Berkeley, University of Chicago
Co-authored papers 5
University of California berkeley
Co-authored papers 5
University of Georgia
Co-authored papers 5
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Co-authored papers 4
Lawrence Berkeley National Laboratory
Co-authored papers 4
Lawrence Berkeley National Laboratory
Co-authored papers 4
Lawrence Berkeley National Laboratory
Co-authored papers 4
Lawrence Berkeley National Laboratory
Co-authored papers 4
University of Georgia
Co-authored papers 4
Lawrence Berkeley National Laboratory
Co-authored papers 4
University of Missouri
Co-authored papers 4
University of California San Francisco
Co-authored papers 3
Lawrence Berkeley National Laboratory
Co-authored papers 3
Lawrence Berkeley National Laboratory
Co-authored papers 3
Co-authored papers 3
Lawrence Berkeley National Laboratory
Co-authored papers 3
Hospital El Carmen de Maipu
Co-authored papers 3
Harvard University
Co-authored papers 3
Co-authored papers 3
Oak Ridge National Laboratory
Co-authored papers 3
University of Missouri
Co-authored papers 3
DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
Co-authored papers 3
University of Maryland School of Medicine, Institute for Genome Sciences
Co-authored papers 2
Stanford University
Co-authored papers 2
Oak Ridge National Laboratory
Co-authored papers 2