Publications by authors named "Manesh B Shah"

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Morpho-physiological and transcriptomic responses of field pennycress to waterlogging.
Rachel Combs-Giroir, Manesh B Shah, Hari B Chhetri, Mallory Morgan, Erica Teixeira Prates

Front Plant Sci· December 2024

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Evaluating the performance of random forest and iterative random forest based methods when applied to gene expression data.
Angelica M Walker, Ashley Cliff, Jonathon Romero, Manesh B Shah, Piet Jones

Comput Struct Biotechnol J· June 2022

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Antiviral Strategies Against SARS-CoV-2: A Systems Biology Approach.
Erica T Prates, Michael R Garvin, Piet Jones, J Izaak Miller, Kyle A Sullivan, Manesh B Shah

Methods Mol Biol· May 2022

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Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models.
Michael R Garvin, Erica T Prates, Mirko Pavicic, Piet Jones, B Kirtley Amos, Manesh B Shah

Genome Biol· December 2020

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Improved growth rate in hydrogenase mutant via perturbed sulfur metabolism.
Ranjita Biswas, Charlotte M Wilson, Richard J Giannone, Dawn M Klingeman, Thomas Rydzak, Manesh B Shah

Biotechnol Biofuels· January 2017

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Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes.
Jenni Hultman, Mark P Waldrop, Rachel Mackelprang, Maude M David, Jack McFarland, Manesh B Shah

Nature· May 2015

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New group in the Leptospirillum clade: cultivation-independent community genomics, proteomics, and transcriptomics of the new species "Leptospirillum group IV UBA BS".
Daniela S Aliaga Goltsman, Mauna Dasari, Brian C Thomas, Manesh B Shah, Nathan C VerBerkmoes

Appl Environ Microbiol· September 2013

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Insights into the structure and metabolic function of microbes that shape pelagic iron-rich aggregates ("iron snow").
Shipeng Lu, Karuna Chourey, Marco Reiche, Sandor Nietzsche, Manesh B Shah

Appl Environ Microbiol· July 2013

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Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community.
Kim M Handley, Nathan C VerBerkmoes, Carl I Steefel, Kenneth H Williams, Itai Sharon, Manesh B Shah

ISME J· April 2013

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The temporal analysis of yeast exponential phase using shotgun proteomics as a fermentation monitoring technique.
Eric L Huang, Valérie Orsat, Manesh B Shah, Robert L Hettich, Nathan C VerBerkmoes

J Proteomics· September 2012

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Sustainable syntrophic growth of Dehalococcoides ethenogenes strain 195 with Desulfovibrio vulgaris Hildenborough and Methanobacterium congolense: global transcriptomic and proteomic analyses.
Yujie Men, Helene Feil, Nathan C Verberkmoes, Manesh B Shah, David R Johnson

ISME J· February 2012

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Use of label-free quantitative proteomics to distinguish the secreted cellulolytic systems of Caldicellulosiruptor bescii and Caldicellulosiruptor obsidiansis.
Adriane Lochner, Richard J Giannone, Miguel Rodriguez, Manesh B Shah, Jonathan R Mielenz

Appl Environ Microbiol· June 2011

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Discovery and annotation of small proteins using genomics, proteomics, and computational approaches.
Xiaohan Yang, Timothy J Tschaplinski, Gregory B Hurst, Sara Jawdy, Paul E Abraham, Manesh B Shah

Genome Res· April 2011

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Posttranslational modification and sequence variation of redox-active proteins correlate with biofilm life cycle in natural microbial communities.
Steven W Singer, Brian K Erickson, Nathan C VerBerkmoes, Mona Hwang, Manesh B Shah

ISME J· November 2010

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Ecological distribution and population physiology defined by proteomics in a natural microbial community.
Ryan S Mueller, Vincent J Denef, Linda H Kalnejais, K Blake Suttle, Brian C Thomas, Manesh B Shah

Mol Syst Biol· June 2010

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Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation.
Michael J Wilkins, Nathan C Verberkmoes, Kenneth H Williams, Stephen J Callister, Paula J Mouser, Manesh B Shah

Appl Environ Microbiol· October 2009

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Community genomic and proteomic analyses of chemoautotrophic iron-oxidizing "Leptospirillum rubarum" (Group II) and "Leptospirillum ferrodiazotrophum" (Group III) bacteria in acid mine drainage biofilms.
Daniela S Aliaga Goltsman, Vincent J Denef, Steven W Singer, Nathan C VerBerkmoes, Mark Lefsrud, Manesh B Shah

Appl Environ Microbiol· July 2009

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Proteomics-inferred genome typing (PIGT) demonstrates inter-population recombination as a strategy for environmental adaptation.
Vincent J Denef, Nathan C VerBerkmoes, Manesh B Shah, Paul Abraham, Mark Lefsrud

Environ Microbiol· February 2009

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Cross-species global proteomics reveals conserved and unique processes in Phytophthora sojae and Phytophthora ramorum.
Alon Savidor, Ryan S Donahoo, Oscar Hurtado-Gonzales, Miriam L Land, Manesh B Shah

Mol Cell Proteomics· August 2008

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A general system for studying protein-protein interactions in Gram-negative bacteria.
Dale A Pelletier, Gregory B Hurst, Linda J Foote, Patricia K Lankford, Catherine K McKeown, Manesh B Shah

J Proteome Res· August 2008

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Implications of strain- and species-level sequence divergence for community and isolate shotgun proteomic analysis.
Vincent J Denef, Manesh B Shah, Nathan C Verberkmoes, Robert L Hettich, Jillian F Banfield

J Proteome Res· August 2007

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Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria.
Ian Lo, Vincent J Denef, Nathan C Verberkmoes, Manesh B Shah, Daniela Goltsman

Nature· March 2007

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Expressed peptide tags: an additional layer of data for genome annotation.
Alon Savidor, Ryan S Donahoo, Oscar Hurtado-Gonzales, Nathan C Verberkmoes, Manesh B Shah

J Proteome Res· November 2006

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Determination of peptide and protein ion charge states by Fourier transformation of isotope-resolved mass spectra.
David L Tabb, Manesh B Shah, Michael Brad Strader, Heather M Connelly, Robert L Hettich

J Am Soc Mass Spectrom· July 2006

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Determination and comparison of the baseline proteomes of the versatile microbe Rhodopseudomonas palustris under its major metabolic states.
Nathan C VerBerkmoes, Manesh B Shah, Patricia K Lankford, Dale A Pelletier, Michael B Strader

J Proteome Res· February 2006

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