Recent papers

For a complete list, please see Google Scholar.

Preprints

Douglas GM, Doolittle WF, Shapiro BJ (2023). Pseudogenes as a neutral reference for detecting selection in prokaryotic pangenomes. bioRxiv.

N’Guessan A et al. (2022) Detection of prevalent SARS-CoV-2 variant lineages in wastewater and clinical sequences from cities in Québec, Canada. medRxiv.

N’Guessan A et al. (2022) Selection for immune evasion in SARS-CoV-2 revealed by high-resolution epitope mapping combined with genome sequence analysis. bioRxiv.

Chen PE & Shapiro BJ (2021). Classic genome-wide association methods are unlikely to identify causal variants in strongly clonal microbial populations. bioRxiv.

2023
Madi N, Chen D, Wolff R, Shapiro BJ & Garud N. Community diversity is associated with intra-species genetic diversity and gene loss in the human gut microbiome. eLife.

Naderi S, Chen PE, Murall CL, Poujol R, Kraemer SA, Pickering BS, Sagan SM & Shapiro BJ. Zooanthroponotic transmission of SARS-CoV-2 and host-specific viral mutations revealed by genome-wide phylogenetic analysis. eLife

Saber MM, Donner M et al. Single nucleotide variants in Pseudomonas aeruginosa populations from sputum correlate with baseline lung function and predict disease progression in individuals with cystic fibrosis. Microbial Genomics

Douglas GM, Kim S, Langille MGI & Shapiro BJ. Efficient computation of contributional diversity metrics from microbiome data with FuncDiv. Bioinformatics.

2022
Leducq J-B et al. Fine-scale adaptations to environmental variation and growth strategies drive phyllosphere Methylobacterium diversity. mBio

Barbosa da Costa N et al. A glyphosate-based herbicide cross-selects for antimicrobial resistance genes in bacterioplankton communities. mSystems

Creasy-Marrazzo A, Saber MM et al. Genome-wide association studies reveal distinct genetic correlates and increased heritability of antimicrobial resistance in Vibrio cholerae under anaerobic conditions. Microbial Genomics

2021
Murall CL et al. A small number of early introductions seeded widespread transmission of SARS-CoV-2 in Quebec, Canada. Genome Medicine

Douglas GM & Shapiro BJ. Genic selection within prokaryotic pangenomes. Genome Biology & Evolution

Levade I, Saber MM, Midani F, Chowdhury F, Khan AI, Begum YA, Ryan ET, David LA, Calderwood SB, Harris JB, LaRocque RC, Qadri F, Shapiro BJ, Weil AA. Predicting Vibrio cholerae infection and disease severity using metagenomics in a prospective cohort study. The Journal of Infectious Diseases

Levade I et al. A combination of metagenomic and cultivation approaches reveal hypermutator phenotypes within Vibrio cholerae infected patients. mSystems

Barbosa da Costa N, V Fugère, M Hébert, CC Xu, RD Barrett, B Beisner, G Bell, V Yargeau, GF Fussmann, A Gonzalez, BJ Shapiro. Resistance, resilience, and functional redundancy of freshwater microbial communities facing multiple agricultural stressors in a mesocosm experiment. Molecular Ecology

Olga M. Pérez-Carrascal, N Tromas, Y Terrat, E Moreno, A Giani, Laisa CB Marques, N Fortin, BJ Shapiro. Single-colony sequencing reveals microbe-by-microbiome phylosymbiosis between the cyanobacterium Microcystis and its associated bacteria. Microbiome

N’Guessan A, Brito IL, Serohijos AWR, Shapiro BJ. Mobile gene sequence evolution within individual human gut microbiomes is better explained by gene-specific than host-specific selective pressures. Genome Biology & Evolution

2020
Madi N, Vos M, Murall CL, Legendre P, Shapiro BJ. Does diversity beget diversity in microbiomes? eLife

Saber MM, Shapiro BJ. Benchmarking genome-wide association study (GWAS) methods using simulated genomes and phenotypes. Microbial Genomics

Tromas N, Castelli M, Taranu ZE, Pimentel J, Pereira D, Marcoz R, Giani A, Shapiro BJ. The evolution of realized niches in freshwater Synechococcus. Environmental Microbiology

Terrat Y, Farnaes L, Bradley J, Tromas N, Shapiro BJ. Two cases of type-a Haemophilus influenzae meningitis within the same week in the same hospital are phylogenetically unrelated but recently exchanged capsule genes. Microbial Genomics