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Selected publicationsSee Google Scholar for all.
Preprints Naderi S, Chen PE, Murall CL, Poujol R, Kraemer SA, Pickering BS, Sagan SM & Shapiro BJ (2022). Zooanthroponotic transmission of SARS-CoV-2 and host-specific viral mutations revealed by genome-wide phylogenetic analysis. bioRxiv Madi N, Chen D, Wolff R, Shapiro BJ & Garud N (2022). Community diversity is associated with intra-species genetic diversity and gene loss in the human gut microbiome. bioRxiv Chen PE & Shapiro BJ (2021). Classic genome-wide association methods are unlikely to identify causal variants in strongly clonal microbial populations. bioRxiv 2022 Leducq J-B et al. Fine-scale adaptations to environmental variation and growth strategies drive phyllosphere Methylobacterium diversity. mBio. bioRxiv Barbosa da Costa N et al. A glyphosate-based herbicide cross-selects for antimicrobial resistance genes in bacterioplankton communities. mSystems. 2021 Murall CL et al. A small number of early introductions seeded widespread transmission of SARS-CoV-2 in Quebec, Canada. Genome Medicine. medRxiv Douglas GM & Shapiro BJ. Genic selection within prokaryotic pangenomes. Genome Biology & Evolution. Levade I et al. . A combination of metagenomic and cultivation approaches reveal hypermutator phenotypes within Vibrio cholerae infected patients. mSystems. bioRxiv 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. bioRxiv 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. bioRxiv 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 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 [bioRxiv] Saber MM, Shapiro BJ. Benchmarking genome-wide association study (GWAS) methods using simulated genomes and phenotypes. Microbial Genomics [bioRxiv] 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 [bioRxiv] 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 [bioRxiv] Fugère V, Hébert M.-P, Costa NB, Xu CCY., Barrett RDH, Beisner BE, Bell G, Fussmann GF, Shapiro BJ, Yargeau V, Gonzalez A. Community rescue in experimental phytoplankton communities facing severe herbicide pollution. Nature Ecology & Evolution [bioRxiv] 2019 Shapiro BJ. Reuniting ecology and evolution. Environmental Microbiology Reports. 11: 13-14. Andersen SB, Shapiro BJ, Vandenbroucke-Grauls C, de Vos MGJ. Microbial evolutionary medicine: from theory to clinical practice. The Lancet Infectious Diseases. [PeerJ] Pérez-Carrascal O, Terrat Y, Giani A, Fortin N, Greer CW, Tromas N, Shapiro BJ. Coherence of Microcystis species revealed through population genomics. The ISME Journal 13: 2887-2900. [biorxiv] 2018 Shapiro BJ. What microbial population genomics has taught us about speciation. In: Population Genomics, eds. Polz MF & Rajora OP. Springer, Cham. [pdf] Tromas N, Taranu ZE, Martin BD, Willis A, Fortin N, Greer CW, Shapiro BJ. Niche separation increases with genetic distance among bloom-forming cyanobacteria. Frontiers in Microbiology. 9, 438. 2017 Levade I, Terrat Y, Leducq JB, Weil AA, Mayo-Smith LM, Chowdhury F, Khan AI, Boncy J, Buteau J, Ivers LC, Ryan ET, Charles RC, Calderwood SB, Qadri F, Harris JB, LaRocque RC, Shapiro BJ. Vibrio cholerae genomic diversity within and between patients. Microbial Genomics 3: doi: 10.1099/mgen.0.000142 Shapiro BJ. The population genetics of pangenomes. Nature Microbiology 2: 1574 Dubois G, Girard C, Lapointe FJ, Shapiro BJ. The Inuit gut microbiome is dynamic over time and shaped by traditional foods. Microbiome 5: 151. Tromas N, Fortin N, Bedrani L, Terrat Y, Cardoso P, Bird D, Greer CW & Shapiro BJ. Characterising and predicting cyanobacterial blooms in an 8-year amplicon sequencing time course. The ISME Journal 11: 1746-1763 [biorxiv] Girard C, Tromas N, Amyot M, Shapiro BJ. Gut microbiome of the Canadian Arctic Inuit. mSphere 2: e00297-16
2016 Shapiro BJ, Levade I, Kovacikova G, Taylor RK, Almagro-Moreno S. Origins of pandemic Vibrio cholerae from environmental gene pools. Nature Microbiology 2: 16240. [biorxiv] Shapiro BJ. How clonal are bacteria over time? Current Opinion in Microbiology 31: 116-123. [biorxiv preprint]
Shapiro BJ, Leducq J-B, Mallet J. What is speciation? PLOS Genetics 12: e1005860
2015 Andersen KG, Shapiro BJ, Matranga CB (co-first authors) et al. Clinical sequencing uncovers origins and evolution of Lassa virus. Cell 162: 738-750 Chen PE & Shapiro BJ. The advent of genome-wide association studies for bacteria. Current Opinion in Microbiology 25: 17-24. 2014 Farhat M, Shapiro BJ, Sheppard SK, Colijn C, Murray M. A phylogeny-based sampling strategy and power calculator informs genome-wide association study design for microbial pathogens. Genome Medicine 6: 101
Seed KS, Yen M, Shapiro BJ, Hilaire IJ, Charles RC, Teng JE, Ivers LC, Boncy J, Harris JB, Camilli A. Evolutionary consequences of intra-patient phage predation on microbial populations. eLife 3: e03497
Shapiro BJ & Polz MF. Ordering microbial diversity into ecologically and genetically cohesive units. Trends in Microbiology 22: 235–247.
Shapiro BJ. Signatures of natural selection and ecological differentiation in microbial genomes. Advances in experimental medicine and biology 781: 339-359. 2013 Farhat M, Shapiro BJ (co-first authors; 23 others), Birren B, Rubin E, Lander E, Sabeti PC, Murray M. Genomic Analysis Identifies Targets of Convergent Positive Selection in Drug-Resistant Mycobacterium tuberculosis. Nature Genetics 45: 1183-1189.
Friedman J, Alm EJ & Shapiro BJ. Sympatric Speciation: When Is It Possible in Bacteria? PLOS ONE 8: e53539. Szabò G, Preheim SP, Kauffman AKM, David LA, Shapiro BJ, Alm EJ, Polz MF. Reproducibility of Vibrionaceae Population Structure in Coastal Bacterioplankton. The ISME Journal 7: 509-519. 2012 Shapiro BJ, Friedman J, Cordero OX, Preheim SP, Timberlake SC, Szabò G, Polz MF, Alm EJ. Population Genomics of Early Events in the Ecological Differentiation of Bacteria. Science 336: 48-51.
earlier Shapiro BJ, David LA, Friedman J, Alm EJ. (2009) Looking for Darwin's Footprints in the Microbial World. Trends in Microbiology 17: 196-204. Shapiro BJ, Alm EJ. (2009) The slow:fast Substitution Ratio Reveals Changing Patterns of Natural Selection in γ-Proteobacterial Genomes. The ISME Journal 4: 1180-1192. Shapiro BJ, Alm EJ. (2008) Comparing Patterns of Natural Selection Across Species Using Selective Signatures. PLOS Genetics 4: e23. |
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