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Author Details

Manesh Shah
University of Tennessee Knoxville
1993
72
34
PMIDPaper TitleJournal TitlePublished Year
36789259Exploring the role of plant lysin motif receptor-like kinases in regulating plant-microbe interactions in the bioenergy crop <i>Populus</i>.Comput Struct Biotechnol J2022
35832622Evaluating the performance of random forest and iterative random forest based methods when applied to gene expression data.Comput Struct Biotechnol J2022
35554915Antiviral Strategies Against SARS-CoV-2: A Systems Biology Approach.Methods Mol Biol2022
32941612Potential Pathogenicity Determinants Identified from Structural Proteomics of SARS-CoV and SARS-CoV-2.Mol Biol Evol2021
32720156Network Modeling of Complex Data Sets.Methods Mol Biol2020
33357233Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models.Genome Biol2020
31134130Multi-Phenotype Association Decomposition: Unraveling Complex Gene-Phenotype Relationships.Front Genet2019
31649710Finding New Cell Wall Regulatory Genes in <i>Populus trichocarpa</i> Using Multiple Lines of Evidence.Front Plant Sci2019
31214244Wavelet-Based Genomic Signal Processing for Centromere Identification and Hypothesis Generation.Front Genet2019
28053665Improved growth rate in <i>Clostridium thermocellum</i> hydrogenase mutant via perturbed sulfur metabolism.Biotechnol Biofuels2017
25739499Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes.Nature2015
25038065Colonization state influences the hemocyte proteome in a beneficial squid-Vibrio symbiosis.Mol Cell Proteomics2014
25262930Proteomic identification of mammalian cell surface derived glycosylphosphatidylinositol-anchored proteins through selective glycan enrichment.Proteomics2014
23190730Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community.ISME J2013
23858439Twelve previously unknown phage genera are ubiquitous in global oceans.Proc Natl Acad Sci U S A2013
23894087Environmental proteomics reveals early microbial community responses to biostimulation at a uranium- and nitrate-contaminated site.Proteomics2013
23645202Insights into the structure and metabolic function of microbes that shape pelagic iron-rich aggregates ("iron snow").Appl Environ Microbiol2013
23645189New group in the Leptospirillum clade: cultivation-independent community genomics, proteomics, and transcriptomics of the new species "Leptospirillum group IV UBA BS".Appl Environ Microbiol2013
23781067Metaproteomics reveals abundant transposase expression in mutualistic endosymbionts.mBio2013
21881617Sustainable syntrophic growth of Dehalococcoides ethenogenes strain 195 with Desulfovibrio vulgaris Hildenborough and Methanobacterium congolense: global transcriptomic and proteomic analyses.ISME J2012
23209564Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease.PLoS One2012
23001646Heterotrophic archaea contribute to carbon cycling in low-pH, suboxic biofilm communities.Appl Environ Microbiol2012
23126408Coupling a detergent lysis/cleanup methodology with intact protein fractionation for enhanced proteome characterization.J Proteome Res2012
22705714The temporal analysis of yeast exponential phase using shotgun proteomics as a fermentation monitoring technique.J Proteomics2012
22517752Metaproteomics of a gutless marine worm and its symbiotic microbial community reveal unusual pathways for carbon and energy use.Proc Natl Acad Sci U S A2012
22666452Phage-induced expression of CRISPR-associated proteins is revealed by shotgun proteomics in Streptococcus thermophilus.PLoS One2012
22395897Shotgun proteomic monitoring of Clostridium acetobutylicum during stationary phase of butanol fermentation using xylose and comparison with the exponential phase.J Ind Microbiol Biotechnol2012
22003893Defining the boundaries and characterizing the landscape of functional genome expression in vascular tissues of Populus using shotgun proteomics.J Proteome Res2012
22179257Global transcriptomic and proteomic responses of Dehalococcoides ethenogenes strain 195 to fixed nitrogen limitation.Appl Environ Microbiol2012
21068774Environmental proteomics of microbial plankton in a highly productive coastal upwelling system.ISME J2011
22008648Comparative shotgun proteomic analysis of Clostridium acetobutylicum from butanol fermentation using glucose and xylose.Proteome Sci2011
22132090Strategies for metagenomic-guided whole-community proteomics of complex microbial environments.PLoS One2011
21685158Identification of biofilm matrix-associated proteins from an acid mine drainage microbial community.Appl Environ Microbiol2011
21368207Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics.Proc Natl Acad Sci U S A2011
21367939Discovery and annotation of small proteins using genomics, proteomics, and computational approaches.Genome Res2011
21498747Use of label-free quantitative proteomics to distinguish the secreted cellulolytic systems of Caldicellulosiruptor bescii and Caldicellulosiruptor obsidiansis.Appl Environ Microbiol2011
20218729Computational prediction and experimental validation of signal peptide cleavages in the extracellular proteome of a natural microbial community.J Proteome Res2010
20954746Direct cellular lysis/protein extraction protocol for soil metaproteomics.J Proteome Res2010
20485387Posttranslational modification and sequence variation of redox-active proteins correlate with biofilm life cycle in natural microbial communities.ISME J2010
20482812Proteomics reveals a core molecular response of Pseudomonas putida F1 to acute chromate challenge.BMC Genomics2010
20531404Ecological distribution and population physiology defined by proteomics in a natural microbial community.Mol Syst Biol2010
18971961Shotgun metaproteomics of the human distal gut microbiota.ISME J2009
19717633Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation.Appl Environ Microbiol2009
19714879Impact of phenolic substrate and growth temperature on the Arthrobacter chlorophenolicus proteome.J Proteome Res2009
19429552Community genomic and proteomic analyses of chemoautotrophic iron-oxidizing "Leptospirillum rubarum" (Group II) and "Leptospirillum ferrodiazotrophum" (Group III) bacteria in acid mine drainage biofilms.Appl Environ Microbiol2009
19118451Comparative temporal proteomics of a response regulator (SO2426)-deficient strain and wild-type Shewanella oneidensis MR-1 during chromate transformation.J Proteome Res2009
18826438Proteomics-inferred genome typing (PIGT) demonstrates inter-population recombination as a strategy for environmental adaptation.Environ Microbiol2009
18449217Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal.ISME J2008
18463612Cytochrome 572 is a conspicuous membrane protein with iron oxidation activity purified directly from a natural acidophilic microbial community.ISME J2008
18590317A general system for studying protein-protein interactions in Gram-negative bacteria.J Proteome Res2008
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Collaborators

Miriam Land
Oak Ridge National Laboratory
Co-authored papers 5
Steven W Singer
Co-authored papers 4
Ying Xu
Oak Ridge National Laboratory
Co-authored papers 4
Dong Xu
University of Missouri
Co-authored papers 3
Priya Ranjan
Pondicherry University
Co-authored papers 3
Dongsup Kim
Korea Advanced Institute of Science and Technology
Co-authored papers 2
Jizhong Zhou
Institute for Environmental Genomics, University of Oklahoma
Co-authored papers 2
David L Tabb
Co-authored papers 2
Brandi L Cantarel
University of Texas Southwestern Medical Center
Co-authored papers 2
Claire M Fraser
Institute for Genome Sciences, University of Maryland School of Medicine
Co-authored papers 2
Philip F LoCascio
University of Oxford
Co-authored papers 2
Jonas Halfvarson
Co-authored papers 2
Paul Wilmes
University of Luxembourg
Co-authored papers 2
Omar Demerdash
Co-authored papers 2
Christopher S Miller
University of Colorado Denver.
Co-authored papers 2
Ian T Paulsen
Macquarie University
Co-authored papers 1
Jeroen Raes
KU Leuven - University of Leuven
Co-authored papers 1
Eric E Allen
Co-authored papers 1
Li Wang
Co-authored papers 1
Ying Xu
The China-Japan Union Hospital, Jilin University
Co-authored papers 1
David T Jones
University College London
Co-authored papers 1
Dawn M Klingeman
Oak Ridge National Laboratory
Co-authored papers 1
Patrik D'haeseleer
Lawrence Livermore National Laboratory
Co-authored papers 1
Deanna L Auberry
Pacific Northwest National Laboratory
Co-authored papers 1
Rodolphe Barrangou
Innovative Genomics Institute, University of California berkeley
Co-authored papers 1
Konstantinos Mavromatis
Celgene Corporation
Co-authored papers 1
Patrick S G Chain
Los Alamos National Laboratory
Co-authored papers 1
Kyle Ellrott
Oregon Health & Science University
Co-authored papers 1
Sergei Passovets
Co-authored papers 1
S A Matis
Co-authored papers 1
Release 1.2