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Author Details

Paramvir S Dehal
Lawrence Berkeley National Laboratory
2001
36
25
PMIDPaper TitleJournal TitlePublished Year
38078749A bacterial sensor taxonomy across earth ecosystems for machine learning applications.mSystems2024
36376589Metagenome-assembled genome extraction and analysis from microbiomes using KBase.Nat Protoc2023
36451056Publisher Correction: Metagenome-assembled genome extraction and analysis from microbiomes using KBase.Nat Protoc2023
33208936Publisher Correction: A genomic catalog of Earth's microbiomes.Nat Biotechnol2021
36765102iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology.ISME Commun2021
29979655KBase: The United States Department of Energy Systems Biology Knowledgebase.Nat Biotechnol2018
28194258Complete genome sequence of <i>Pseudomonas stutzeri</i> strain RCH2 isolated from a Hexavalent Chromium [Cr(VI)] contaminated site.Stand Genomic Sci2017
25767232High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater.Genome Announc2015
23203984MetaMicrobesOnline: phylogenomic analysis of microbial communities.Nucleic Acids Res2013
22700702RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics.Nucleic Acids Res2012
21695235Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis.PLoS Genet2011
21992415Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium.Genome Biol2011
19906701MicrobesOnline: an integrated portal for comparative and functional genomics.Nucleic Acids Res2010
21148394Signatures of adaptation to obligate biotrophy in the Hyaloperonospora arabidopsidis genome.Science2010
20494978A universal TagModule collection for parallel genetic analysis of microorganisms.Nucleic Acids Res2010
20224823FastTree 2--approximately maximum-likelihood trees for large alignments.PLoS One2010
19031428Metabolic flux analysis of Shewanella spp. reveals evolutionary robustness in central carbon metabolism.Biotechnol Bioeng2009
19737303Contribution of mobile genetic elements to Desulfovibrio vulgaris genome plasticity.Environ Microbiol2009
19377059FastTree: computing large minimum evolution trees with profiles instead of a distance matrix.Mol Biol Evol2009
19321007Snapshot of iron response in Shewanella oneidensis by gene network reconstruction.BMC Genomics2009
18179685Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli.Genome Biol2008
18845759Environmental genomics reveals a single-species ecosystem deep within Earth.Science2008
18974889FastBLAST: homology relationships for millions of proteins.PLoS One2008
17334359Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis.Nat Biotechnol2007
17545284Cell-wide responses to low-oxygen exposure in Desulfovibrio vulgaris Hildenborough.J Bacteriol2007
17845071Orthologous transcription factors in bacteria have different functions and regulate different genes.PLoS Comput Biol2007
16381935TreeFam: a curated database of phylogenetic trees of animal gene families.Nucleic Acids Res2006
16946064Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis.Science2006
16608522A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) database.BMC Bioinformatics2006
16128622Two rounds of whole genome duplication in the ancestral vertebrate.PLoS Biol2005
15057824The DNA sequence and biology of human chromosome 19.Nature2004
12805271Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii.Genome Res2003
12481130The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins.Science2002
12142439Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes.Science2002
11386749Homology-driven assembly of a sequence-ready mouse BAC contig map spanning regions related to the 46-Mb gene-rich euchromatic segments of human chromosome 19.Genomics2001
11441184Human chromosome 19 and related regions in mouse: conservative and lineage-specific evolution.Science2001
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Collaborators

Adam P Arkin
Lawrence Berkeley National Laboratory
Co-authored papers 23
Dylan Chivian
Lawrence Berkeley National Laboratory
Co-authored papers 9
Morgan N Price
Lawrence Berkeley National Laboratory
Co-authored papers 8
Miriam Land
Oak Ridge National Laboratory
Co-authored papers 6
Terry C Hazen
University of Tennessee
Co-authored papers 5
Marcin P Joachimiak
E O Lawrence Berkeley National Laboratory, UCSF Medical Center, University of California, Berkeley, University of Chicago
Co-authored papers 5
Inna Dubchak
Lawrence Berkeley National Laboratory
Co-authored papers 5
Asaf Salamov
US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory
Co-authored papers 4
William J Riehl
Lawrence Berkeley National Laboratory
Co-authored papers 4
Christopher S Henry
Argonne National Laboratory
Co-authored papers 4
Elisha M Wood-Charlson
Lawrence Berkeley National Laboratory
Co-authored papers 4
Pavel S Novichkov
Lawrence Berkeley National Laboratory
Co-authored papers 4
Trevor Hawkins
Co-authored papers 4
Benjamin H Allen
Oak Ridge National Laboratory
Co-authored papers 3
Jizhong Zhou
Institute for Environmental Genomics, University of Oklahoma
Co-authored papers 3
Roman A Sutormin
Lawrence Berkeley National Laboratory
Co-authored papers 3
Robert W Cottingham
Oak Ridge National Laboratory
Co-authored papers 3
Michael W Sneddon
Lawrence Berkeley National Laboratory
Co-authored papers 3
Zamin K Yang
Oak Ridge National Laboratory
Co-authored papers 3
Romy Chakraborty
Lawrence Berkeley National Laboratory
Co-authored papers 3
Simon Roux
DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
Co-authored papers 2
Tanja Woyke
Co-authored papers 2
Judy D Wall
University of Missouri
Co-authored papers 2
Nikos C Kyrpides
Co-authored papers 2
Adam M Deutschbauer
Lawrence Berkeley National Laboratory
Co-authored papers 2
Thomas Brettin
University of Chicago
Co-authored papers 2
Eric J Alm
Massachusetts Institute of Technology 21 Ames St. Cambridge
Co-authored papers 2
Keith Keller
Co-authored papers 2
Brett M Tyler
Oregon State University
Co-authored papers 2
Jay D Keasling
University of California berkeley
Co-authored papers 2
Release 1.2