Selected publications


See Google Scholar for all.​

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]

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

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

Madi N, Vos M, Legendre P, Shapiro BJ. Diversity begets diversity in microbiomes. 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
  • 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.
See Google Scholar for more.