Selected publications



2017
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. [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
  • One of the top 50 most downloaded PLOS Genetics articles of 2016

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
  • Highly Accessed

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.
  • Faculty of 1000 recommended article

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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