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Author Details

B Jesse Shapiro
McGill University
1964
77
31
Nevan J Krogan (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
37398242Phage predation, disease severity and pathogen genetic diversity in cholera patients.bioRxiv2024
36757364Community diversity is associated with intra-species genetic diversity and gene loss in the human gut microbiome.Elife2023
37599818Selection for immune evasion in SARS-CoV-2 revealed by high-resolution epitope mapping and sequence analysis.iScience2023
37052589Single nucleotide variants in <i>Pseudomonas aeruginosa</i> populations from sputum correlate with baseline lung function and predict disease progression in individuals with cystic fibrosis.Microb Genom2023
37014792Zooanthroponotic transmission of SARS-CoV-2 and host-specific viral mutations revealed by genome-wide phylogenetic analysis.Elife2023
36519836Efficient computation of contributional diversity metrics from microbiome data with FuncDiv.Bioinformatics2023
35265640Population Genomics Approaches for Genetic Characterization of SARS-CoV-2 Lineages.Front Med (Lausanne)2022
36748512Genome-wide association studies reveal distinct genetic correlates and increased heritability of antimicrobial resistance in <i>Vibrio cholerae</i> under anaerobic conditions.Microb Genom2022
35906926Comprehensive Phylogenomics of Methylobacterium Reveals Four Evolutionary Distinct Groups and Underappreciated Phyllosphere Diversity.Genome Biol Evol2022
36355999Impact of Stagnation on the Diversity of Cyanobacteria in Drinking Water Treatment Plant Sludge.Toxins (Basel)2022
36287957Shotgun Metagenomic Sequencing to Assess Cyanobacterial Community Composition following Coagulation of Cyanobacterial Blooms.Toxins (Basel)2022
35073752Fine-Scale Adaptations to Environmental Variation and Growth Strategies Drive Phyllosphere <i>Methylobacterium</i> Diversity.mBio2022
35287928Comparing microscopy and DNA metabarcoding techniques for identifying cyanobacteria assemblages across hundreds of lakes.Harmful Algae2022
35266795A Glyphosate-Based Herbicide Cross-Selects for Antibiotic Resistance Genes in Bacterioplankton Communities.mSystems2022
32610345Predicting Vibrio cholerae Infection and Disease Severity Using Metagenomics in a Prospective Cohort Study.J Infect Dis2021
33794144Elevated rates of horizontal gene transfer in the industrialized human microbiome.Cell2021
34706766A small number of early introductions seeded widespread transmission of SARS-CoV-2 in Québec, Canada.Genome Med2021
34665261Genic Selection Within Prokaryotic Pangenomes.Genome Biol Evol2021
34579777Single-colony sequencing reveals microbe-by-microbiome phylosymbiosis between the cyanobacterium Microcystis and its associated bacteria.Microbiome2021
34427503A Combination of Metagenomic and Cultivation Approaches Reveals Hypermutator Phenotypes within Vibrio cholerae-Infected Patients.mSystems2021
34132784Mobile Gene Sequence Evolution within Individual Human Gut Microbiomes Is Better Explained by Gene-Specific Than Host-Specific Selective Pressures.Genome Biol Evol2021
34324752Resistance, resilience, and functional redundancy of freshwater bacterioplankton communities facing a gradient of agricultural stressors in a mesocosm experiment.Mol Ecol2021
33233813Diversity Assessment of Toxic Cyanobacterial Blooms during Oxidation.Toxins (Basel)2020
31997531The evolution of realized niches within freshwater Synechococcus.Environ Microbiol2020
32100713Benchmarking bacterial genome-wide association study methods using simulated genomes and phenotypes.Microb Genom2020
31363173Coherence of Microcystis species revealed through population genomics.ISME J2019
31185868Trophic structure modulates community rescue following acidification.Proc Biol Sci2019
29096961Cooking and co-ingested polyphenols reduce in vitro methylmercury bioaccessibility from fish and may alter exposure in humans.Sci Total Environ2018
29636727Niche Separation Increases With Genetic Distance Among Bloom-Forming Cyanobacteria.Front Microbiol2018
28070563Gut Microbiome of the Canadian Arctic Inuit.mSphere2017
28444332Mitochondrial Recombination and Introgression during Speciation by Hybridization.Mol Biol Evol2017
29306353Vibrio cholerae genomic diversity within and between patients.Microb Genom2017
29176697The population genetics of pangenomes.Nat Microbiol2017
29145891The Inuit gut microbiome is dynamic over time and shaped by traditional foods.Microbiome2017
28524869Characterising and predicting cyanobacterial blooms in an 8-year amplicon sequencing time course.ISME J2017
27030977What Is Speciation?PLoS Genet2016
27821851Phenotypic differentiation of Streptococcus pyogenes populations is induced by recombination-driven gene-specific sweeps.Sci Rep2016
27688962Environment and host species shape the skin microbiome of captive neotropical bats.PeerJ2016
27991885Origins of pandemic Vibrio cholerae from environmental gene pools.Nat Microbiol2016
27057964How clonal are bacteria over time?Curr Opin Microbiol2016
25835153The advent of genome-wide association studies for bacteria.Curr Opin Microbiol2015
26276630Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus.Cell2015
26354896Microbial Speciation.Cold Spring Harb Perspect Biol2015
26483462Population genomics of Mycobacterium tuberculosis in the Inuit.Proc Natl Acad Sci U S A2015
24277308Signatures of natural selection and ecological differentiation in microbial genomes.Adv Exp Med Biol2014
25484920A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens.Genome Med2014
25161196Evolutionary consequences of intra-patient phage predation on microbial populations.Elife2014
24630527Ordering microbial diversity into ecologically and genetically cohesive units.Trends Microbiol2014
23349716Sympatric speciation: when is it possible in bacteria?PLoS One2013
23995135Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis.Nat Genet2013
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Collaborators

Eric J Alm
Massachusetts Institute of Technology 21 Ames St. Cambridge
Co-authored papers 7
Graham Bell
McGill University
Co-authored papers 3
Howard Bussey
McGill University
Co-authored papers 3
Shamiza Hussein
Co-authored papers 3
Anne-Marie Sdicu
McGill University
Co-authored papers 3
Edward T Ryan
Massachusetts General Hospital
Co-authored papers 3
Guillaume Lesage
Institute of Molecular Biology, University of Zurich
Co-authored papers 3
Patrice Menard
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark
Co-authored papers 3
Charles Boone
University of Toronto
Co-authored papers 2
Peter E Chen
McGill University
Co-authored papers 2
Pardis C Sabeti
Harvard University
Co-authored papers 2
Bruce W Birren
Broad Institute of MIT and Harvard
Co-authored papers 2
Amy Hin Yan Tong
University of Toronto
Co-authored papers 2
Fran??ois-Joseph Lapointe
Universite de Montreal
Co-authored papers 2
Eric S Lander
Vanderbilt-Ingram Cancer Center, Vanderbilt University
Co-authored papers 2
Richelle C Charles
Massachusetts General Hospital
Co-authored papers 2
James A Foster
University of Idaho
Co-authored papers 2
Guillaume Bourque
Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University
Co-authored papers 2
Jennifer Haynes
Joan C. Edwards School of Medicine, Marshall University
Co-authored papers 1
Joshua N Levinson
MedStar Washington Hospital Center
Co-authored papers 1
Chris Sander
Broad Institute of MIT and Harvard
Co-authored papers 1
Hilary K Finucane
Co-authored papers 1
Grace He
Co-authored papers 1
James Bochicchio
Co-authored papers 1
Xin Cheng
New York University School of Medicine
Co-authored papers 1
Nevan J Krogan (CM4AI)
University of California San Francisco
Co-authored papers 1
David Bujold
McGill University
Co-authored papers 1
Joseph B McCormick
Co-authored papers 1
Lan V Zhang
Harvard Medical School
Co-authored papers 1
Christine Humphries
University of Toronto
Co-authored papers 1
Release 1.2