Jesse Shapiro

Assistant Professor,
Université de Montréal

Département de sciences biologiques
Pavillon Marie-Victorin 90 avenue Vincent-d’Indy, Montréal, QC H2V 2S9
Tel: (514) 343-6033
E-mail: jesse.shapiro@umontreal.ca
Institution page
Personal page



Education
Postdoc, 2012, Harvard (Organismic & Evolutionary Biology and The Center for Communicable Disease Dynamics) PhD, 2010, MIT (Computational & Systems Biology) MSc, 2004, Oxford (Integrative Bioscience) BSc, 2003, McGill (Biology)


Research
Most of the genetic and metabolic diversity that exists on earth – and has existed for billions of years – is microbial. Arguably more impressive than the sheer quantity of microbial diversity is its dynamic nature: microbes are constantly evolving and adapting. Our ongoing research tracks evolving microbial populations in real time, using whole-genome and whole-community DNA sequencing to understand their evolution and predict how they adapt to changing environments. For example: (1) freshwaters subject to seasonal cyanobacterial blooms, (2) the human gut, focusing on cholera infections, (3) viral hemorrhagic fevers (Lassa and Ebola), (4) evolution of antibiotic resistance in Mycobacterium tuberculosis.

QCBS students
Nicolas TROMAS, Chercheur(e) invité(e) / Invited researcher
(Start: 2014)

Other (co-)supervisor: Angus Buckling, Exeter University
Thesis title: ECOLOGICAL AND EVOLUTIONARY RESPONSES OF NATURAL FRESHWATER MICROBIAL POPULATIONS IN REAL TIME
Naíla Barbosa da Costa, Ph.D.
(Start: 2016)

Other (co-)supervisor: Jesse Shapiro
Other QCBS (co-)supervisor: Gregor Fussmann
Thesis title: Phage-cyanobacteria antagonistic interactions and their prospective use in bloom control
Personal page
Inès Levade, Ph.D.
(Start: 2014)
Thesis title: Genomic analysis of cholera micro-evolution and transmission
Previous students (since 2009)
Naima Madi, Ph.D.
(Start: 2017)
Courses
BIO 3260 - Génomique microbienne (Fall / Automne)
BIO 6260 - Génomique microbienne (Winter / Hiver)

Publications
33- The population genetics of pangenomes
Shapiro B.J.
2017 Nature Microbiology (Date Added: 2017-12-06)

31- Mitochondrial recombination and introgression during speciation by hybridization
Leducq J., Henault M., Charron G., Nielly-Thibault L., Terrat Y., Fiumera H.L., Shapiro B.J., Landry C.R.
2017 Molecular Biology and Evolution (Date Added: 2017-09-09)

30- Gut Microbiome of the Canadian Arctic Inuit
Girard, C., Tromas, N., Amyot, M., Shapiro, B.J.
2017 MSphere (Date Added: 2017-08-16)

29- Characterising and predicting cyanobacterial blooms in an 8-year amplicon sequencing time course
Tromas N., Fortin N., Bedrani L., Terrat Y., Cardoso P., Bird D., Greer C.W., Shapiro B.J.
2017 ISME Journal (Date Added: 2017-08-03)

28- AD-LIBS: Inferring ancestry across hybrid genomes using low-coverage sequence data
Schaefer N.K., Shapiro B., Green R.E.
2017 BMC Bioinformatics (Date Added: 2017-04-20)

27- The evolutionary and phylogeographic history of woolly mammoths: A comprehensive mitogenomic analysis
Chang D., Knapp M., Enk J., Lippold S., Kircher M., Lister A., MacPhee R.D.E., Widga C., Czechowski P., Sommer R., Hodges E., Stümpel N., Barnes I., Dalén L., Derevianko A., Germonpré M., Hillebrand-Voiculescu A., Constantin S., Kuznetsova T., Mol D., Rathgeber T., Rosendahl W., Tikhonov A.N., Willerslev E., Hannon G., Lalueza-Fox C., Joger U., Poinar H., Hofreiter M., Shapiro B.
2017 Scientific Reports (Date Added: 2017-04-05)

26- Origins of pandemic Vibrio cholerae from environmental gene pools
Shapiro, B.J., Levade, I., Kovacikova, G., Taylor, R.K., Almagro-Moreno, S.
2016 Nature Microbiology (Date Added: 2017-02-14)

25- Phenotypic differentiation of Streptococcus pyogenes populations is induced by recombination-driven gene-specific sweeps
Bao, Y.-J., Shapiro, B.J., Lee, S.W., Ploplis, V.A., Castellino, F.J.
2016 Scientific Reports (Date Added: 2017-02-14)

24- How clonal are bacteria over time?
Shapiro, B.J.
2016 Current Opinion in Microbiology (Date Added: 2017-02-14)

23- What Is Speciation?
Shapiro, B.J., Leducq, J.-B., Mallet, J.
2016 PLoS Genetics (Date Added: 2017-02-14)

22- Environment and host species shape the skin microbiome of captive neotropical bats
Lemieux-Labonte, V., Tromas, N., Shapiro, B.J., Lapointe, F.-J.
2016 PeerJ (Date Added: 2016-11-28)

21- The advent of genome-wide association studies for bacteria
Chen, P.E., Shapiro, B.J.
2015 Current Opinion in Microbiology (Date Added: 2017-02-15)

20- Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus
Andersen, K.G., Shapiro, B.J., Matranga, C.B., Sealfon, R., Lin, A.E., Moses, L.M., Folarin, O.A., Goba, A., Odia, I., Ehiane, P.E., Momoh, M., England, E.M., Winnicki, S., Branco, L.M., Gire, S.K., Phelan, E., Tariyal, R., Tewhey, R., Omoniwa, O., Fullah, M., Fonnie, R., Fonnie, M., Kanneh, L., Jalloh, S., Gbakie, M., Saffa, S., Karbo, K., Gladden, A.D., Qu, J., Stremlau, M., Nekoui, M., Finucane, H.K., Tabrizi, S., Vitti, J.J., Birren, B., Fitzgerald, M., McCowan, C., Ireland, A., Berlin, A.M., Bochicchio, J., Tazon-Vega, B., Lennon, N.J., Ryan, E.M., Bjornson, Z., Milner, D.A., Jr., Lukens, A.K., Broodie, N., Rowland, M., Heinrich, M., Akdag, M., Schieffelin, J.S., Levy, D., Akpan, H., Bausch, D.G., Rubins, K., McCormick, J.B., Lander, E.S., Günther, S., Hensley, L., Okogbenin, S., Schaffner, S.F., Okokhere, P.O., Khan, S.H., Grant, D.S., Akpede, G.O., Asogun, D.A., Gnirke, A., Levin, J.Z., Happi, C.T., Garry, R.F., Sabeti, P.C.
2015 Cell (Date Added: 2017-02-15)

19- Microbial speciation
Shapiro, B.J., Polz, M.F.
2015 Cold Spring Harbor Perspectives in Biology (Date Added: 2017-02-15)

17- A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens
Farhat, M.R., Shapiro, B.J., Sheppard, S.K., Colijn, C., Murray, M.
2014 Genome Medicine (Date Added: 2017-02-15)

16- Ordering microbial diversity into ecologically and genetically cohesive units
Shapiro, B.J., Polz, M.F.
2014 Trends in Microbiology (Date Added: 2017-02-15)

15- Evolutionary consequences of intra-patient phage predation on microbial populations
Seed, K.D., Yen, M., Shapiro, B.J., Hilaire, I.J., Charles, R.C., Teng, J.E., Ivers, L.C., Boncy, J., Harris, J.B., Camilli, A.
2014 eLife (Date Added: 2017-02-15)

14- Reproducibility of Vibrionaceae population structure in coastal bacterioplankton
Szabo, G., Preheim, S.P., Kauffman, K.M., David, L.A., Shapiro, J., Alm, E.J., Polz, M.F.
2013 The ISME Journal (Date Added: 2017-07-31)

13- Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis
Farhat, M.R., Shapiro, B.J., Kieser, K.J., Sultana, R., Jacobson, K.R., Victor, T.C., Warren, R.M., Streicher, E.M., Calver, A., Sloutsky, A., Kaur, D., Posey, J.E., Plikaytis, B., Oggioni, M.R., Gardy, J.L., Johnston, J.C., Rodrigues, M., Tang, P.K.C., Kato-Maeda, M., Borowsky, M.L., Muddukrishna, B., Kreiswirth, B.N., Kurepina, N., Galagan, J., Gagneux, S., Birren, B., Rubin, E.J., Lander, E.S., Sabeti, P.C., Murray, M.
2013 Nature Genetics (Date Added: 2017-02-15)

12- Sympatric Speciation: When Is It Possible in Bacteria?
Friedman, J., Alm, E.J., Shapiro, B.J.
2013 PLoS ONE (Date Added: 2017-02-15)

11- Population genomics of early events in the ecological differentiation of bacteria
Shapiro, B.J., Friedman, J., Cordero, O.X., Preheim, S.P., Timberlake, S.C., Szabó, G., Polz, M.F., Alm, E.J.
2012 Science (Date Added: 2017-02-15)

9- Looking for Darwin's footprints in the microbial world
Shapiro, B.J., David, L.A., Friedman, J., Alm, E.J.
2009 Trends in Microbiology (Date Added: 2017-02-15)

8- Comparing patterns of natural selection across species using selective signatures
Shapiro, B.J., Alm, E.J.
2008 PLoS Genetics (Date Added: 2017-02-15)

7- Multiple independent origins of a protease inhibitor resistance mutation in salvage therapy patients
Kapoor, A., Shapiro, B., Shafer, R.W., Shulman, N., Rhee, S.-Y., Delwart, E.L.
2008 Retrovirology (Date Added: 2017-02-15)

6- Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: Subtype G is a circulating recombinant form
Abecasis, A.B., Lemey, P., Vidal, N., De Oliveira, T., Peeters, M., Camacho, R., Shapiro, B., Rambaut, A., Vandamme, A.-M.
2007 Journal of Virology (Date Added: 2017-02-15)

5- An experimental test of the causes of small-scale phenotypic differentiation in a population of great tits
Shapiro, B.J., Garant, D., Wilkin, T.A., Sheldon, B.C.
2006 Journal of Evolutionary Biology (Date Added: 2017-02-16)

4- An interactional network of genes involved in chitin synthesis in Saccharomyces cerevisiae
Lesage, G., Shapiro, J., Specht, C.A., Sdicu, A.-M., Menard, P., Hussein, S., Tong, A.H.Y., Boone, C., Bussey, H.
2005 BMC Genetics (Date Added: 2017-02-16)

3- VSG switching in Trypanosoma brucei: antigenic variation analysed using RNAi in the absence of immune selection
Aitcheson, N., Talbot, S., Shapiro, J., Hughes, K., Adkin, C., Butt, T., Sheader, K., Rudenko, G.
2005 Molecular Microbiology (Date Added: 2017-02-16)

1- Global mapping of the yeast genetic interaction network
Tong, A.H.Y., Lesage, G., Bader, G.D., Ding, H., Xu, H., Xin, X., Young, J., Berriz, G.F., Brost, R.L., Chang, M., Chen, Y.Q., Cheng, X., Chua, G., Friesen, H., Goldberg, D.S., Haynes, J., Humphries, C., He, G., Hussein, S., Ke, L., Krogan, N., Li, Z., Levinson, J.N., Lu, H., Menard, P., Munyana, C., Parsons, A.B., Ryan, O., Tonikian, R., Roberts, T., Sdicu, A.-M., Shapiro, J., Sheikh, B., Suter, B., Wong, S.L., Zhang, L.V., Zhu, H., Burd, C.G., Munro, S., Sander, C., Rine, J., Greenblatt, J., Peter, M., Bretscher, A., Bell, G., Roth, F.P., Brown, G.W., Andrews, B., Bussey, H., Boone, C.
2004 Science (New York, N.Y.) (Date Added: 2017-02-16)