Publications by authors named "Manesh Shah"

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Predicting receptor-ligand pairing preferences in plant-microbe interfaces via molecular dynamics and machine learning.
Erica T Prates, Omar Demerdash, Manesh Shah, Tomás A Rush, Udaya C Kalluri

Comput Struct Biotechnol J· June 2025

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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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MENTOR: Multiplex Embedding of Networks for Team-Based Omics Research.
Kyle A Sullivan, J Izaak Miller, Alice Townsend, Mallory Morgan, Matthew Lane, Manesh Shah

bioRxiv· July 2024

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Discovery and Characterization of Fluopipamine, a Putative Cellulose Synthase 1 Antagonist within .
B Kirtley Amos, Victoria Pook, Erica Prates, Jozsef Stork, Manesh Shah

J Agric Food Chem· February 2024

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Exploring the role of plant lysin motif receptor-like kinases in regulating plant-microbe interactions in the bioenergy crop .
Kevin R Cope, Erica T Prates, John I Miller, Omar N A Demerdash, Manesh Shah

Comput Struct Biotechnol J· December 2022

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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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Network Modeling of Complex Data Sets.
Piet Jones, Deborah Weighill, Manesh Shah, Sharlee Climer, Jeremy Schmutz

Methods Mol Biol· March 2021

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Potential Pathogenicity Determinants Identified from Structural Proteomics of SARS-CoV and SARS-CoV-2.
Erica T Prates, Michael R Garvin, Mirko Pavicic, Piet Jones, Manesh Shah

Mol Biol Evol· January 2021

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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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Finding New Cell Wall Regulatory Genes in Using Multiple Lines of Evidence.
Anna Furches, David Kainer, Deborah Weighill, Annabel Large, Piet Jones, Manesh Shah

Front Plant Sci· October 2019

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Multi-Phenotype Association Decomposition: Unraveling Complex Gene-Phenotype Relationships.
Deborah Weighill, Piet Jones, Carissa Bleker, Priya Ranjan, Manesh Shah

Front Genet· May 2019

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Wavelet-Based Genomic Signal Processing for Centromere Identification and Hypothesis Generation.
Deborah Weighill, David Macaya-Sanz, Stephen Paul DiFazio, Wayne Joubert, Manesh Shah

Front Genet· May 2019

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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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Proteomic identification of mammalian cell surface derived glycosylphosphatidylinositol-anchored proteins through selective glycan enrichment.
Leslie K Cortes, Saulius Vainauskas, Nan Dai, Colleen M McClung, Manesh Shah

Proteomics· November 2014

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Colonization state influences the hemocyte proteome in a beneficial squid-Vibrio symbiosis.
Tyler R Schleicher, Nathan C VerBerkmoes, Manesh Shah, Spencer V Nyholm

Mol Cell Proteomics· October 2014

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Environmental proteomics reveals early microbial community responses to biostimulation at a uranium- and nitrate-contaminated site.
Karuna Chourey, Silke Nissen, Tatiana Vishnivetskaya, Manesh Shah, Susan Pfiffner

Proteomics· October 2013

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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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Twelve previously unknown phage genera are ubiquitous in global oceans.
Karin Holmfeldt, Natalie Solonenko, Manesh Shah, Kristen Corrier, Lasse Riemann

Proc Natl Acad Sci U S A· July 2013

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Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease.
Alison R Erickson, Brandi L Cantarel, Regina Lamendella, Youssef Darzi, Emmanuel F Mongodin, Manesh Shah

PLoS One· June 2013

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Metaproteomics reveals abundant transposase expression in mutualistic endosymbionts.
Manuel Kleiner, Jacque C Young, Manesh Shah, Nathan C VerBerkmoes, Nicole Dubilier

mBio· June 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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Coupling a detergent lysis/cleanup methodology with intact protein fractionation for enhanced proteome characterization.
Ritin Sharma, Brian D Dill, Karuna Chourey, Manesh Shah, Nathan C VerBerkmoes

J Proteome Res· December 2012

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