Photo credit: Owen Egan
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Graduate students / Étudiants gradués
Naíla Barbosa da Costa
Microbial communities can rapidly adapt to different environmental constraints but the evolutionary mechanisms of their differentiation are still not clear. During my PhD I intend to contribute to a better understanding of the ecological and evolutionary processes underlying the genetic differentiation in aquatic bacterial communities subjected to different chemical stressors, and also in cyanobacterial communities naturally exposed to phage that act as predators.
Previous research: I received my B.S. in Biology and my M.S. in Ecology from the Federal University of Minas Gerais, Brazil. As an undergrad I studied the cyanobacterial community diversity in saline alkaline lakes from the Pantanal wetland, and during my Masters I focused on molecular methods for detecting bloom-forming cyanobacteria in an urban reservoir.
Microbial communities can rapidly adapt to different environmental constraints but the evolutionary mechanisms of their differentiation are still not clear. During my PhD I intend to contribute to a better understanding of the ecological and evolutionary processes underlying the genetic differentiation in aquatic bacterial communities subjected to different chemical stressors, and also in cyanobacterial communities naturally exposed to phage that act as predators.
Previous research: I received my B.S. in Biology and my M.S. in Ecology from the Federal University of Minas Gerais, Brazil. As an undergrad I studied the cyanobacterial community diversity in saline alkaline lakes from the Pantanal wetland, and during my Masters I focused on molecular methods for detecting bloom-forming cyanobacteria in an urban reservoir.
Arnaud N'Guessan
Research interests: The human body provides multiple niches for microbial communities (the microbiota). Microbes in the gut have a complex dynamic and exchange genetic material frequently via
horizontal gene transfer (HGT), contributing to the variation of their gene content (pangenome evolution). As part of my Master’s project, I am interested in determining which evolutionary forces and selective pressures are the most important for pangenomes evolution on short timescales within the gut.
Background: I graduated with a BSc in Bioinformatics from Université Laval in Québec City. During my undergrad years, I had the opportunity to do an internship with Dr. Steve Charette, during which time I nurtured my passion for microbial evolution. I also did an internship at the CERVO research centre with Dr. Simon Hardy, during which time I developed mathematical modeling skills. I joined the Shapiro lab in fall 2018.
Research interests: The human body provides multiple niches for microbial communities (the microbiota). Microbes in the gut have a complex dynamic and exchange genetic material frequently via
horizontal gene transfer (HGT), contributing to the variation of their gene content (pangenome evolution). As part of my Master’s project, I am interested in determining which evolutionary forces and selective pressures are the most important for pangenomes evolution on short timescales within the gut.
Background: I graduated with a BSc in Bioinformatics from Université Laval in Québec City. During my undergrad years, I had the opportunity to do an internship with Dr. Steve Charette, during which time I nurtured my passion for microbial evolution. I also did an internship at the CERVO research centre with Dr. Simon Hardy, during which time I developed mathematical modeling skills. I joined the Shapiro lab in fall 2018.
Postdocs
Nicolas Tromas
Research interests: I am interested in the evolutionary biology of microbes. More concretely, I am especially interested in mechanisms that generate and maintain genetic variability, in dynamics of infection and more generally in host-pathogen interactions.
Previous research: I did my PhD with Santiago F. Elena at the IBMCP (Instituto de Biologia Molecular y Celular de Plantas) of the Polytechnic University of Valencia, Spain. I used the plant virus TEV (Tobacco etch virus) as a model to address evolutionary questions. I estimated in vivo mutation and recombination rates, multiplicity and dynamics of infection during TEV infection in Nicotiana tabacum.
Research interests: I am interested in the evolutionary biology of microbes. More concretely, I am especially interested in mechanisms that generate and maintain genetic variability, in dynamics of infection and more generally in host-pathogen interactions.
Previous research: I did my PhD with Santiago F. Elena at the IBMCP (Instituto de Biologia Molecular y Celular de Plantas) of the Polytechnic University of Valencia, Spain. I used the plant virus TEV (Tobacco etch virus) as a model to address evolutionary questions. I estimated in vivo mutation and recombination rates, multiplicity and dynamics of infection during TEV infection in Nicotiana tabacum.
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Gavin Douglas
Website: www.gavindouglas.ca Research interests: broad range of questions related to microbial evolutionary genetics. Currently I am focused on applying standard population genetics approaches to prokaryotic strains found in natural communities. I would like to leverage this approach to assess the strength of selection acting on accessory genes across different strains. This work is currently focused on strains found in the honey bee gut microbiome, which has low taxonomic richness and so somewhat simplifies the task of profiling strain-level variation. I am also interested more generally in the importance of gene-level vs. individual-level selection in shaping prokaryotic pangenomes. Previous research: I did my PhD at Dalhousie University with Morgan Langille, where my work focused on integrating functional and taxonomic data types for microbiome data analysis. Prior to that, I worked as a bioinformatician for a year at the Integrated Microbiome Resource at Dalhousie University. I completed my BSc and MSc degrees both at the University of Toronto. I worked with Alan Moses during my MSc project, which involved investigating the evolutionary forces acting upon primate transcription factor binding sites. |
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> Join the lab !
Applicants should have a strong background in microbiology, genomics, computational biology or evolutionary biology (or all of the above).
The lab has very limited funding for salaries, so applicants are expected to apply for external scholarships or fellowships, such as NSERC, FQRNT and CIHR. Prospective students can apply to either the Microbiology or Quantitative Life Sciences graduate programs.
Email Jesse to apply. Please include:
- a description of your background and research interests
- what you would like to work on in the lab
- contact information for 2 references
The lab has very limited funding for salaries, so applicants are expected to apply for external scholarships or fellowships, such as NSERC, FQRNT and CIHR. Prospective students can apply to either the Microbiology or Quantitative Life Sciences graduate programs.
Email Jesse to apply. Please include:
- a description of your background and research interests
- what you would like to work on in the lab
- contact information for 2 references
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Dr. Morteza M. Saber (postdoc 2018-2021): Now a bioinformatician/data scientist at MIMS Dr. Olga Pérez Carrascal (postdoc 2017-2021): Now a postdoc with Michael Shapira at UC Berkeley Dr. Yves Terrat (postdoc 2015-2021): Now a data scientist at UdeM/IVADO Dr. Inès Levade (PhD, 2020): Now a scientist at the Quebec Institute for Public Health (INSPQ) Kiri Stern (MSc, 2020). Now starting a PhD in Quantitative Life Sciences at McGill. Dr. Jean-Baptiste Leducq (postdoc 2016-2019): Now a research scientist with Chris Marx at U Idaho Dr. Catherine Girard (PhD, 2017): Now a faculty member at UQAC Dr. Larbi Bedrani (bioinformatics intern, summer-fall 2015): Now a postdoc at the University of Toronto, Mount Sinai Hospital, Department of Gastroenterology Dr. Coralie Deladrière (field & lab assistant, summer 2015): Now an analytical chemist at PCAS Canada. Romane Marcoz (undergrad, summer 2015): Now doing a Masters in Public Health at UdeM Yoann Santin (undergrad, winter 2015): Now doing a PhD in Microbiology at the Faculté des Sciences de Luminy (Marseille) Aix-Marseille Université Simone Périnet (lab tech, winter-summer 2014): Now doing a Masters in Public Health at UdeM |
