Philip Awadalla Laboratory
Philip Awadalla - Malaria

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Our Team

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Philip Awadalla

Principal Investigator

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.

 

Marie-Julie Favé

Post - Doc

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

Post - Doc

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.

Richard Jovelin

Post - Doc

I joined the Awadalla Lab in 2015, after doing a postdoc at the University of Toronto in the Department of Ecology and Evolutionary Biology. I am broadly interested in molecular evolution. In the past, I investigated the evolution of gene families and I examined the distribution of selective constraints within genetic pathways and networks. I am particularly interested in understanding how changes in gene regulation contribute to phenotypic diversification and to the origin of disease. Recently, my work has taken new directions with analyses of genome-wide nucleotide variation and analyses of sequence evolution of the intriguing small RNAs.

Fabien Lamaze

Post - Doc

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

Post - Doc

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

Post - Doc

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.

Armande Ang Houle

Phd. Student

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

MSc Student

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

MSc Student

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.

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.

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.

Mawussé Agbessi

Research Assistant - Bioinformatics

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.

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.





>>>> Alumni >>>>

Jean-Christophe Grenier

Research Assistant - Bioinformatics

I joined Awadalla lab in march 2011 as a research assistant and currently work for both Philip Awadalla's and Luis Barreiro's laboratories. I have a M.sc in bioinformatics that I got at the University of Montreal and worked on phylogenomics of the Archaea. In this lab, I'm an all around bioinformatician providing support for assembling and analyzing the genomic data that came from next-generation sequencers. I'm also providing support in writing programs to analyze the data and the results coming from the sequencers and public available databases.

Aurélien Chateigner

Post - Doc

After a PhD at the Université François Rabelais de Tours, where I studied the influence of the environment on the evolution of baculovirus genomes in the EVIL team of the IRBI, I joined the Awadalla lab in September 2015. During my PhD, I worked on unravelling the evolution of very low frequency mutations and showed that even a natural population of virus can contain a huge catalogue of evolutionary possibilities. I will now try to adapt my knowledge and skills to cancer research and study labs data with the population geneticist point of view.

Valérie Hay

DESS Student

I joined the bioinformatic group of Dr Awadalla`s Lab in Montréal as a summer interne in bioinformatic. Before undertaking a one year specialized diploma in bioinformatic in UQAM to redirect my career, I have worked as a Senior scientists for Novartis in PEI developing vaccine for the aquaculture industry. I was fortunate to be part of the team working on the development of the first DNA vaccine for the European Union market. Previously, as a research assistant at McGill University for different professors in the fields of immunology and virology, I have acquired practical knowledge in molecular biology, immunology and virology as well as lab and project management.

Héloise Gauvin

Phd. Student

Before starting in 2010 my PhD in Public Health, I was awarded a BSc in mathematics and a MSc in biostatistics. I am broadly interested in theoretical models and statistical tool development in genetics. Up until now my main interest has been to study identity-by-descent detection methods and to use the infered information to observe what it could tell us about relatedness between individuals. I used the population of Quebec since it is a structured population with cryptic relatedness in addition to have extended genealogical records. Since we can now state that patterns of identity-by-descent sharing are giving us insight on types of distant relationships shared, the next step of my project will be to see how it can help us with CARTaGENE analyses.

Alan Hodgkinson

Post - Doc

I did my PhD with Adam Eyre-Walker at the University of Sussex, UK, and joined the Awadalla Lab in October 2011. In the past I have looked at the patterns and processes associated with mutation rate variation in mammalian genomes, in particular looking at how mutation rates vary across the genome in a cryptic fashion, as well as variation in the mutation rate in cancer genomes. More recently I have become interested in the fitness effects of such mutations, particularly in a disease setting.

Thibault de Malliard

Research Assistant - Bioinformatics

I began working in the Awadalla Lab in 2010. Before, I worked 1.5 years for the french National Institute for Agricultural Research (INRA) with the MIG laboratory (Mathematics, Informatics et Genomics). There I participated to the european project Nanomubiop. I was in charge to develop a software to produce probes for a HPV chip.

I am currently in charge to provide bioinformatics support to the lab crew, and develop bioinformatics solutions about the next-generation sequencing.

Jean-Philippe Goulet

Analyste - Épidémiologie Génétique

As a scientific member from CARTaGENE's collaborative service, I am constantly looking for new genetic analysis methods to improve the achievement of our aims. I assist researchers and collaborators in their experimental designs, their biostatistical and bioinformatic analyses as well as in the interpretation of the results thus obtained.

CARTaGENE's research platform offers scientists a plethora of information about Quebec population on an unprecedented integrative scale: phenomics, genomics, environmental, geographical, medical records, etc. Integrating these factors together has the potential to facilitate the emergence of new practices for health care, improving prevention, diagnosis and treatment, thus paving the way for personalized medicine.

Élodie Hip-Ki

Laboratory Technician

I had my BSc in Biochemistry at the University of Montreal in 2010. During my BSc, I did an internship in Molecular Biology with Dr André Tremblay, at Ste-Justine Research Center. I joined the Awadalla lab in January 2012. My work focuses on genomic techniques including DNA and RNA extraction, sample quality control, sample preparation for genotyping and RNASeq/Exom library construction for next-generation sequencing with the Illumina platform. My work in the laboratory contributes to several projects including CARTaGENE and the sickle cell disease.

Julie Hussin

Phd. Student

I joined the Awadalla lab in January 2009 as a Ph. D. student in Bioinformatics, at University of Montreal. My broad interests are in developing bioinformatics and statistical genetic tools to understand evolutionary forces that shaped the human genome and their impact in medical genetics. In particular, I am interested in the rate of de novo genetic events occurring during meiosis, namely mutations and recombination breakpoints, and how they contribute to human diseases and genomic instabilities. I am currently examining genomic data from families having offsprings with pediatric cancer and cardiovascular conditions.

Jacklyn Quinlan

Phd. Student

I have a BSc in biochemistry and a MSc in human genetics. I am in the process of obtaining my PhD in Public Health with Epidemiology as my option. My main interest is in genetic epidemiology of tropical diseases and international health. My project aims at identifying genetic and environmental determinants that differentially affect gene expression in malaria and sickle cell disease, which in the latter case, results in a wide range of disease severity. Using a longitudinal study design in two African cohorts, I will be able to address this issue by obtaining clinical data, which includes whole- genome sequences and genetic expression information. Results from my project will increase scientific knowledge of population genetics for these two diseases.

Mélanie Capredon

Post - Doc

I did my PhD with Pr. Bernard Champion, at the CRLHOI laboratory (Centre de Recherche Littéraire et Historique de l’Océan Indien) at the University of La Reunion, and with Dr. Jean-Michel Dugoujon at the AMIS laboratory (Laboratoire d’Anthropologie Moléculaire et d’Imagerie de Synthèse) in Toulouse. During my PhD I was interested in the human biological history of Madagascar, most especially in the ethnic group of the Antemoro, by analyzing genetic markers on the NRY and the mtDNA. I joined the Awadalla Laboratory in January 2012. Now I have become interested in understanding the evolution of the host response to malaria and sickle cell anemia by developing population genetics data.

Youssef Idaghdour

Post - Doc

I am broadly interested in understanding the genetic basis of functional variation in humans and the role gene-by-environment interactions play in shaping variation in immune system response. My aim is to better understand the genetic and environmental contributions to variation in susceptibility to diseases, particularly sickle cell disease and Malaria. Study populations in Montreal and Western Africa will be sampled and genotypic and endophenotypic data generated using a systems genetics approach and a combination of genomic and field-based techniques. The main objectives are to identify the key genetic regulatory factors that modulate sickle cell severity and response to malaria infection and test hypotheses regarding the immunological consequences of genotypic and endophenotypic patterns of variation.

Diego Czul

Research Assistant - Programmer









Jonathan Keebler

Phd. Student









Kate McGee

Phd. Student










Franck Prugnolle

CV





Natalia Tichshenko

Research Assitant - Programmer










Martine Zilversmit

Post - Doc