Philip Awadalla Laboratory
Philip Awadalla - Malaria

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Our Team

ASHG meeting ASHG meeting 2

Principal Investigator


Philip Awadalla

Our research includes work relevant to all types of human diseases: genetic, immunological, infectious, chronic and cancer. Using genomic data from single-nucleotide polymorphisms (SNP), next-generation re-sequencing, and gene expression, along with modern statistical tools, we are able to locate genome regions that are associated with disease pathology and virulence as well as study the mechanisms that cause the mutations.

 


------ Postdocs ------

Marie-Julie Favé

I am broadly interested in uncovering the evolutionary processes and environmental factors underlying gene expression changes and regulation differences within and between populations. I joined the group of Philip Awadalla in November 2013 after a PhD in evolutionary developmental biology at McGill University. I recently became interested in human populations, which offer tremendous power to study the genetic and environmental contributions to phenotypes and diseases. Particularly, the CARTaGENE cohort provides a unique framework to test hypotheses about how demographic events can shape spatial genetic variation, gene expression, endophenotypic variation and disease susceptibility. In addition, this cohort has been well characterized for several environmental factors, and therefore, offers the possibility to discover how these interact with one’s individual genetic background to affect gene expression and disease susceptibility. I am also exploring the dynamic interactions between viruses and the host immune system in the CARTaGENE cohort. In the last few years, it has become clear that our virome and microbiome can affect physiological processes, inflammation status, and more generally, can modulate our susceptibility to complex diseases. I am also involved in other projects exploring the population genetic processes underlying the evolution of genetic variants contributing to various neurological disorders.

Hilary Edgington

Prior to joining the Awadalla lab in July, 2015, I completed my graduate studies in ecology and evolutionary biology at the University of Virginia. My training broadly encompassed elucidating population and trait histories through the use of population genetic and phylogenetic tools, and involved the study of cave-dwelling Plethodontid salamanders. Recently I have become interested in our ability to use the wealth of available human genomic data to study the impacts of population history and demography on traits of interest, such as health outcomes and genomic architecture.

Fabien Lamaze

I am interested in understanding how epigenomic processes control the information encoded in the genomes of an organism, in an evolutionary, developmental and disease context.

I aim, by joining the Awadalla Lab in 2015, to develop a comprehensive understanding of how each cell of complex eukaryotes uses the epigenome to determine the critical roles it plays in development of disease states. This can be achieved through the integration of molecular biology, bioinformatics, population genetic and evolutionary concepts. During my first postdoctoral fellowship, at the Cancer Research Center of Laval University, I investigated the transcriptional mechanisms in cancer expression programmes, and how the chromatin structure affects developmental and cancer diseases, by integrating large amounts of publicly available data.

Isabel Alves

My research interests lie in understanding the role of evolutionary forces such as demography and recombination in shaping genomic patterns of diversity across the human genome. During my PhD, at the University of Bern, Switzerland, I investigated the demographic history of modern human populations by using a model-based approach, which allowed me to provide new insights on the process of colonisation of modern humans across the world and their interactions with archaic populations. By joining the Awadalla lab, I aim at applying my knowledge on human population genetics to better understand the impact of diversity heterogeneity across genomes on individual/population disease susceptibility.

David Soave

Prior to joining the Awadalla lab in November 2016, I graduated from the PhD program in the Department of Biostatistics at the Dalla Lana School of Public Health. I am also an alumni of the CIHR Strategic Training in Advanced Genetic Epidemiology (STAGE) program at the University of Toronto, and was a member of the Strug lab at SickKids in Toronto, working on the discovery and understanding of genetic modifiers of various comorbidities of Cystic Fibrosis. My research interests are currently focused on developing statistical methods for genetics research including variant detection in the presence of genetic interaction, rare variant effects, and improvement and evaluation of disease risk prediction models incorporating genetic factors.



------ Phd. students ------

Armande Ang Houle

Before joining the Awadalla lab at the University of Toronto as a PhD student in 2015 I was awarded a BSc and a MSc in bioinformatics from the University of Montreal. In the context of my MSc, I created methods to analyze the allelic variation of polymorphic repetitive genes from Next-Generation Sequencing data. I am broadly interested in the integration of heterogeneous sources of biological data. The goal of my dissertation is to further understand the expression of meiosis specific genes, especially those involved in recombination processes. I aim to investigate how these genes influence the genomic landscape across different cancer types.

Elyssa Bader

I completed my BSc in forensic science at Trent University in April 2015. During my undergrad I had the opportunity to do research at NRDPFC (Natural Resources DNA Profiling & Forensic Centre) where I helped develop an assay to determine the susceptibility of goats to scrapie. In September 2015 I joined the department of Molecular Genetics at the University of Toronto and I am now working towards completing my MSc in the Awadalla lab. My research interests include identifying disease-linked variants that can be used for the development of personalized medicine and genetic diagnostic testing.


Heather Gibling

My research interests are in next-generation sequencing technologies and pipelines and in better understanding genetic diseases such as cancer. I have a BSc in Cellular, Molecular and Microbial Biology from the University of Calgary and an MBinf (Bioinformatics) from the University of Guelph. After completing a research rotation with the Awadalla lab in the fall of 2015, I joined in January 2016 to begin studying alignment of cancer genomes to the human reference genome. I am co-supervised with OICR’s Dr. Jared Simpson.



------ MSc. students ------



------ Staff ------

Vanessa Bruat

Bioinformatics and Laboratory Manager

Prior to joining the Awadalla Lab in august 2010, I worked over 8 years at Genizon Biosciences Inc, a biotechnology company. During this time, as bioinformatician and manager I was responsible for providing support in key areas of the gene discovery process such as genetic marker selection, genotyping primer design, gene data mining, genomic sequence annotation, sequence analysis and patent preparation.

At the Awadalla Lab I oversee all bioinformatics projects and participate in the development of tools to analyze and manage the next-generation sequencing data. Through a close working relationship with post-doc and students from the Lab, the bioinformatics team is in charge of selecting, integrating, developping, and applying appropriate bioinformatics tools to support all the laboratory researches.

Elias Gbeha

Research Assistant - Molecular biology

I was Initially trained as a molecular biologist and population geneticist studying the patterns of genetic diversity of West-African populations as well as that of pathogens such as Plasmodium falciparum and Papillomavirus that impinge upon the health of these populations. I joined the Awadalla lab after completion of an MSc in Molecular Biology at the University of Montreal where I conducted a research project involving extensive field work in West Africa to document genetic diversity within the region. Since joining the Awadalla group, I have been involved in designing and executing genetic and genomic experiments for various research projects in the lab and currently I am in charge of several human genetics experiments using second-generation sequencing approaches.

Kimberly Skead

Research Technical Assistant

Prior to joining the Awadalla laboratory in May 2016, I completed my Hon. B.Sc. in Global Health and Genome Biology at Trinity College, University of Toronto. My previous research activities include working as part of the International Centre for Disability and Rehabilitation Cameroon team, and looking at the reach of vital registration systems in South Africa. Recently I have become interested in looking at the various factors impacting health behaviour and practices in different contexts and how health outcomes can be improved through early diagnosis. Through working at the Awadalla laboratory, I hope to study disease markers at a molecular level in order to identify patterns of association, which could stand to increase the accuracy of early diagnostic testing and have a large scale public health impact.

Marcus Tutert

Research Assistant







Mawussé Agbessi

Bioinformatician

After my M. Sc in Bioinformatics obtained in 2013 at the University of Montpellier (FRANCE), I worked for a year within the Palm tree's development biology Lab in CIRAD (French Agricultural Research Centre for International Development). The aim of the project I worked on was to design a molecular detection kit allowing the early detection of mantled somaclonal variation in Oil palm tree ( Elaesis guineensis) through the exploration of genes families affected by the mantled abnormality. Hence, I was in charge to analyse the E. guineensis inflorescence and cellular suspension transcriptomes data, in order to identify potential genes controlling changes in the somatic embryogenesis in these cultivar.

I joined the Awadalla Lab in November 2014 as a Bioinformatics Research Assistant. My position allows me to work as a bioinformatics support but also provide me the opportunity to reach new objectives in data analysis.

Pamela Mehanna

Bioinformatician

After obtaining a bachelor's degree in bioinformatics from the University of Montreal, I completed my education with a master's degree in the same field at the CHU Sainte-Justine in Montreal. During these studies, using next-generation sequencing data, I conducted a project aiming to characterize new small circular extra-chromosomal DNA fragments called microDNAs and their modulation by anti-cancer treatments. I also participated in the development of SNooPer, a machine learning-based method for somatic variant identification from low-pass next-generation sequencing. My research interests include population genetics, cancer genomics and pharmacogenomics. I joined Dr. Awadalla's team in July 2017 as a bioinformatician. My main tasks are bioinformatics support to grad students as well as participating in the analysis of sequencing and genotyping data.




>>>> ALUMNI >>>>



------ Postdocs ------

                                               Current affiliation

Richard Jovelin

.....................

Aurélien Chateigner

Postdoc
Equipe Prédiction et Gestion de la Diversité
des Génomes et des Populations
INRA
France

Alan Hodgkinson

Research Fellow
Department of Medical and Molecular Genetics
Bioinformatics and Population Genomics Group
King's College
London
United Kingdom

Mélanie Capredon

.....................

Youssef Idaghdour

Assistant Professor of Biology
Biology Department
New York University Abu Dhabi
Abu Dhabi, UAE

Martine Zilversmit

Gerstner Scholar in Bioinformatics and Computational Biology
The Sackler Institute of Comparative Genomics
American Museum of Natural History
Harvard University
New York, NY

Franck Prugnolle

Researcher

HEALTH: Ecology and Evolution
CNRS/IRD/Universités de Montpellier
Montpellier, France


------ Phd. Students ------

Julie Hussin

Principal Investigator
Montreal Heart Institute
University of Montreal
Montreal, CANADA

Jacklyn Quinlan

Epidemiologist
Migration Health
Immigration, Refugees and Citizenship Canada
Government of Canada

Héloise Gauvin

Methodologist
Statistics Canada
Ottawa, CANADA

Jonathan Keebler

Solutions Architect
Cloudera
North Carolina State University
United States

Kate McGee

..................












------ MSc. / DESS Students ------

Valérie Hay

DESS Student












------ Staff ------

Jean-Christophe Grenier

Bioinformatician

Thibault de Malliard

Bioinformatician

Jean-Philippe Goulet

Research Assistant

Élodie Hip-Ki

Laboratory Technician

Diego Czul

Research Assistant - Programmer









Natalia Tichshenko

Research Assitant - Programmer