Publications by authors named "Paramvir Dehal"

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RWRtoolkit: multi-omic network analysis using random walks on multiplex networks in any species.
David Kainer, Matthew Lane, Kyle A Sullivan, J Izaak Miller, Mikaela Cashman, Paramvir Dehal

Gigascience· January 2025

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A bacterial sensor taxonomy across earth ecosystems for machine learning applications.
Helen Park, Marcin P Joachimiak, Sean P Jungbluth, Ziming Yang, William J Riehl, Paramvir S Dehal

mSystems· January 2024

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Publisher Correction: Metagenome-assembled genome extraction and analysis from microbiomes using KBase.
Dylan Chivian, Sean P Jungbluth, Paramvir S Dehal, Elisha M Wood-Charlson, Richard S Canon

Nat Protoc· February 2023

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Metagenome-assembled genome extraction and analysis from microbiomes using KBase.
Dylan Chivian, Sean P Jungbluth, Paramvir S Dehal, Elisha M Wood-Charlson, Richard S Canon

Nat Protoc· January 2023

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iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology.
Benjamin Bolduc, Olivier Zablocki, Jiarong Guo, Ahmed A Zayed, Dean Vik, Paramvir Dehal

ISME Commun· December 2021

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A genomic catalog of Earth's microbiomes.
Stephen Nayfach, Simon Roux, Rekha Seshadri, Daniel Udwary, Neha Varghese, Paramvir Dehal

Nat Biotechnol· April 2021

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Publisher Correction: A genomic catalog of Earth's microbiomes.
Stephen Nayfach, Simon Roux, Rekha Seshadri, Daniel Udwary, Neha Varghese, Paramvir Dehal

Nat Biotechnol· April 2021

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Author Correction: A genomic catalog of Earth's microbiomes.
Stephen Nayfach, Simon Roux, Rekha Seshadri, Daniel Udwary, Neha Varghese, Paramvir Dehal

Nat Biotechnol· April 2021

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KBase: The United States Department of Energy Systems Biology Knowledgebase.
Adam P Arkin, Robert W Cottingham, Christopher S Henry, Nomi L Harris, Rick L Stevens, Paramvir Dehal

Nat Biotechnol· July 2018

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Complete genome sequence of strain RCH2 isolated from a Hexavalent Chromium [Cr(VI)] contaminated site.
Romy Chakraborty, Hannah Woo, Paramvir Dehal, Robert Walker, Marcin Zemla

Stand Genomic Sci· February 2017

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High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater.
Bradley D Ramsay, Chiachi Hwang, Hannah L Woo, Sue L Carroll, Susan Lucas, Paramvir Dehal

Genome Announc· March 2015

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MetaMicrobesOnline: phylogenomic analysis of microbial communities.
Dylan Chivian, Paramvir S Dehal, Keith Keller, Adam P Arkin

Nucleic Acids Res· January 2013

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RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics.
Pavel S Novichkov, Thomas S Brettin, Elena S Novichkova, Paramvir S Dehal, Adam P Arkin

Nucleic Acids Res· July 2012

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Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium.
Lara Rajeev, Eric G Luning, Paramvir S Dehal, Morgan N Price, Adam P Arkin

Genome Biol· October 2011

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Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis.
Stephen B Goodwin, Sarrah Ben M'barek, Braham Dhillon, Alexander H J Wittenberg, Charles F Crane, Paramvir Dehal

PLoS Genet· June 2011

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Signatures of adaptation to obligate biotrophy in the Hyaloperonospora arabidopsidis genome.
Laura Baxter, Sucheta Tripathy, Naveed Ishaque, Nico Boot, Adriana Cabral, Paramvir Dehal

Science· December 2010

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A universal TagModule collection for parallel genetic analysis of microorganisms.
Julia Oh, Eula Fung, Morgan N Price, Paramvir S Dehal, Ronald W Davis

Nucleic Acids Res· August 2010

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FastTree 2--approximately maximum-likelihood trees for large alignments.
Morgan N Price, Paramvir S Dehal, Adam P Arkin

PLoS One· March 2010

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MicrobesOnline: an integrated portal for comparative and functional genomics.
Paramvir S Dehal, Marcin P Joachimiak, Morgan N Price, John T Bates, Jason K Baumohl

Nucleic Acids Res· January 2010

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Contribution of mobile genetic elements to Desulfovibrio vulgaris genome plasticity.
Christopher B Walker, Sergey Stolyar, Dylan Chivian, Nicolas Pinel, Jeffrey A Gabster, Paramvir S Dehal

Environ Microbiol· September 2009

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FastTree: computing large minimum evolution trees with profiles instead of a distance matrix.
Morgan N Price, Paramvir S Dehal, Adam P Arkin

Mol Biol Evol· July 2009

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Metabolic flux analysis of Shewanella spp. reveals evolutionary robustness in central carbon metabolism.
Yinjie J Tang, Hector Garcia Martin, Paramvir S Dehal, Adam Deutschbauer, Xavier Llora

Biotechnol Bioeng· March 2009

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Snapshot of iron response in Shewanella oneidensis by gene network reconstruction.
Yunfeng Yang, Daniel P Harris, Feng Luo, Wenlu Xiong, Marcin Joachimiak, Paramvir Dehal

BMC Genomics· March 2009

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FastBLAST: homology relationships for millions of proteins.
Morgan N Price, Paramvir S Dehal, Adam P Arkin

PLoS One· February 2009

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Environmental genomics reveals a single-species ecosystem deep within Earth.
Dylan Chivian, Eoin L Brodie, Eric J Alm, David E Culley, Paramvir S Dehal

Science· October 2008

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