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I am a computational evolutionary biologist interested in identifying ecologically and clinically important signatures of positive natural selection in microbial genomes. My basic approach can be described as 'reverse ecology,' where patterns of variation in microbial genomes are analyzed to learn about the underlying ecology of wild populations.
Note: I am now much older and wiser than shown in the photo. But I can (probably) still juggle pumpkins. |
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.
Yves Terrat
Research interests: I am currently working on structural variants and possible horizontal gene transfer events in Vibrio cholerae & enterotoxic strains of Escherichia coli.
Previous research: My interest in genome plasticity began during my PhD, which was focused on mobile DNA in deep sea crustacean species (always keeping Barbara McClintock in mind!). Then I moved to the fascinating world of toxins in snakes and cone snails, before developing and applying metagenomic tools to study one of the most diverse and unknown habitats on earth (i.e soil).
Research interests: I am currently working on structural variants and possible horizontal gene transfer events in Vibrio cholerae & enterotoxic strains of Escherichia coli.
Previous research: My interest in genome plasticity began during my PhD, which was focused on mobile DNA in deep sea crustacean species (always keeping Barbara McClintock in mind!). Then I moved to the fascinating world of toxins in snakes and cone snails, before developing and applying metagenomic tools to study one of the most diverse and unknown habitats on earth (i.e soil).
Olga Pérez Carrascal
Research interests: I am interested in bacterial evolutionary genomics; how bacterial populations are organized in ecological and evolutionary units, and the extent of horizontal gene transfer and recombination within and among populations.
Previous research: I received my M.S. in Biotechnology from the National University of Colombia and obtained my PhD in Biochemistry in the Center for Genomic Sciences at the National Autonomous University of Mexico (UNAM). During my PhD I worked on comparative and population genomic analysis of sympatric nitrogen-fixing rhizobia.
Research interests: I am interested in bacterial evolutionary genomics; how bacterial populations are organized in ecological and evolutionary units, and the extent of horizontal gene transfer and recombination within and among populations.
Previous research: I received my M.S. in Biotechnology from the National University of Colombia and obtained my PhD in Biochemistry in the Center for Genomic Sciences at the National Autonomous University of Mexico (UNAM). During my PhD I worked on comparative and population genomic analysis of sympatric nitrogen-fixing rhizobia.
Masih M. Saber
Current research: Antibiotic resistance is one of the biggest threats to global health and antibiotic resistant pathogens, so-called ‘superbugs’, are rendering current treatments of pneumonia, tuberculosis, gonorrhea, and salmonellosis ineffective. My research focuses on benchmarking machine learning and regression-based methods of genome wide association analysis using gene-phenotype simulations. The ultimate goal of my work is to optimize the methods for unravelling the genomic basis of antibiotic resistance in bacterial pathogens.
Previous research: I received my B.S. and M.S., respectively in microbiology and molecular genetics. During my PhD at the University of Tokyo and RIKEN research institute in Japan, I worked on identification and characterization of novel coding and noncoding genomic elements using comparative and evolutionary genomics methods.
Current research: Antibiotic resistance is one of the biggest threats to global health and antibiotic resistant pathogens, so-called ‘superbugs’, are rendering current treatments of pneumonia, tuberculosis, gonorrhea, and salmonellosis ineffective. My research focuses on benchmarking machine learning and regression-based methods of genome wide association analysis using gene-phenotype simulations. The ultimate goal of my work is to optimize the methods for unravelling the genomic basis of antibiotic resistance in bacterial pathogens.
Previous research: I received my B.S. and M.S., respectively in microbiology and molecular genetics. During my PhD at the University of Tokyo and RIKEN research institute in Japan, I worked on identification and characterization of novel coding and noncoding genomic elements using comparative and evolutionary genomics methods.
> 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. Inès Levade (PhD, 2020): Now a postdoc with Dao Nguyen at McGill University 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. Kiri Stern (summer student, 2015): Now doing an MSc in Quantitative Biology at UdeM 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 |
