Personnel

Paul Boutros


Principal investigator

Paul [dot] Boutrosatoicr [dot] on [dot] ca

2013-08-23

Michael Fraser

2017-01


Director, Prostate Cancer Program


2013-08-23

Natalia Prather

2013-08


Natalia is the Administrative Coordinator for Paul and the Boutros lab. She provides administrative support and assists with organizational tasks to ensure Paul’s schedule and lab operations run smoothly.

Natalia [dot] Pratheratoicr [dot] on [dot] ca

Experimental Biologists

John Watson

2008-12


An aberration in a laboratory which consists of mostly computational and mathematical specialists, John is a Molecular and Cellular Biologist. When necessary, John uses various molecular and in vitro techniques to validate, further examine or extend findings from bioinformatic analyses.

Stephenie Prokopec

2010-05


As a research technician at OICR, Stephenie works to generate high quality data from biological samples which can then be used to identify molecular differences between sample types. For example, her primary project involves studying liver tumour carcinogenesis by evaluating genetic, transcriptomic and proteomic differences between strains of rats and mice that are either sensitive or resistant to the environmental carcinogen TCDD. Her work involves both wet-lab and dry-lab components - everything from data-generation to bioinformatics data-analysis and paper-writing.

Postdoctoral Fellows

Syed Haider

2010-02


Syed Haider initially started as visiting Ph.D. candidate in February 2010, and has since been co-supervised by Dr. Boutros throughout his transition from graduate student to postdoctoral fellow in January 2012. His research is predominantly focused on identifying pathway-based biomarkers of cancer prognosis using multi-modal molecular profiles. Further, he is also working on assessing the impact of tumour cellularity on biomarker discovery. He holds a Ph.D. in Computer Science from Cambridge University.

Julia Hopkins

2014-08


Julia is studying the associations between somatic mitochondrial DNA variants and prostate cancer. She has previously used organelle proteomics to identify proteins targeted to a plastid of secondary endosymbiotic origin. She holds a Ph.D. in Biology from Johns Hopkins University where she studied RNA folding and RNA-protein interactions.

Alexandre Rouette

2017-01


Alexandre holds a Ph.D. in Systems Biology from IRIC at the University of Montreal where he studied the role of tissue-specific proteasomes in immune and cancer cells. His current research work investigates the relationship between genomic germline-encoded structural variants and prostate cancer outcome.

Katayoon Kasaian

2017-05


Katayoon completed her Ph.D. training at the University of British Columbia and the BC Cancer Agency’s Genome Sciences Center in bioinformatics and cancer genomics. Her studies focused on molecular profiling of thyroid cancers. She is currently investigating the driver aberrations and molecular diagnostic and prognostic markers of prostate cancer.

Graduate Students

Natalie Fox

2012-01


Natalie is a Ph.D. candidate in the Department of Medical Biophysics at the University of Toronto. She completed a bachelor of Computer Science with a specialization in bioinformatics at the University of Waterloo. Her current graduate research is developing prognostic biomarkers for localized prostate cancer by integrating genomic and transcriptomic data.

Javier Alfaro

2012-10


At the intersection of proteomics and genomics, proteogenomics represents one of the last frontiers of integrative -omics. There is an abundance of fresh questions in this field, all relating to how technological improvements in genomics and transcriptomics can improve our understanding of the expressed human proteome. Within this field, Javier's Ph.D. in the Department of Medical Biophysics at the University of Toronto (co-supervised by Dr. Thomas Kislinger) focuses in on the detection of aberrent gene products at the peptide level. Borrowing from lessons learned utilizing proteomic data to refine genome models, he is exhaustively benchmarking existing strategies for the detection of aberrant peptides within tumours. See here for more information.

Constance Li

2013-11


Connie is a Ph.D. candidate in the Department of Medical Biophysics at the University of Toronto. She completed her Bachelor of Mathematics with a specialization in Computational Mathematics at the University of Waterloo. She is currently working on a pan-cancer analysis of sex-associated differences in cancer genomics.

Vinayak Bhandari

2015/05 - 2015/10; 2016/01


Vinayak has a B.Sc in Chemical Biology from McMaster University. His current work focuses on analyzing breast cancer data using multiple statistical models.

Adriana Salcedo

2015-09


Katie Houlahan

2013/05 - 2013/08; 2014/01 - 2015/06; 2017/01


Katie is a Ph.D. candidate in the Department of Medical Biophysics at the University of Toronto. She holds a B.Sc from McMaster University in Chemical Biology. Currently, Katie is looking at the association between germline and somatic variants in prostate cancer.

Undergraduate Students and Interns

Dorota Sendorek

2015-05


Dorota holds a B.Sc. in Life Sciences from the University of Toronto and a Bioinformatics graduate certificate. Her current work involves implementing and running structural variant callers on next generation sequencing data.

Lesia Szyca

2016-06


Lesia is an undergraduate student majoring in Honours Biology with a minor in Visual Arts, in the concurrent Education program at York University. She will be helping create graphics for the lab.

June Lee

2017-05


June is an undergraduate student at the University of Toronto specializing in cell and molecular biology and minoring in physiology and immunology. She is currently working with Dr. Jenster on DrDisco.

Eric Huang

2017-06


Eric is a medical student at the University of Toronto and holds a B.Sc. from Duke University and a M.Sc. from University of Toronto. He is studying the integration of germline variants with somatic variants in predicting prostate cancer biochemical recurrence.

Harry Brastianos

2017-07


Harry is currently a medical resident at Queen's University . He has completed his PhD at the University of British Columbia and medical school at Queen's University. He is currently studying prognostic factors in both high and intermediate risk prostate cancer.

Vincent Stimper

2017-07


Vincent is studying Physics with focus on Biophysics, Statistics and Machine Learning at the Technical University of Munich . Currently, he compares the performance of standard machine learning methods with SIMMS, developed by Syed Haider and coworkers.

Teyden Nguyen

2017-08


Arnon Adler

2017-09


Software Engineers

Christopher Lalansingh

2013-08


Chris' work at the OICR involves the maintenance and expansion of software systems used by members of the Boutros lab related to the development environment for Perl and R, as well as the optimization of bioinformatics software prior to public distribution. He also works with lab members to help write better, more maintainable code, and provides guidance in using lab resources such as the computing cluster and version control.

John Macdonald

2014-03


John works at the lab as a software engineer, specializing mostly in Perl. He is the developer of the HPCI module, used for computing on high performance computer clusters without being limited to only working on a single specific type of cluster. He has a M. Math in Computer Science from the University of Waterloo.

Jeff Green

2014/01 – 2014/04, 2017-07


Data Scientists

Cindy Yao

2010-05


Cindy graduated with an M.Sc. from the Department of Medical Biophysics at the University of Toronto. She is co-supervised by Dr. John Bartlett. Her current research work focuses on developing novel prognostic markers in early breast cancer patients, as well as validating existing ones in large patient trials.

Veronica Sabelnykova

2013-07


Veronica holds a M.A. in Applied Statistics from York University and a M.Sc. in Biostatistics from the University of Victoria. At OICR she applies statistics to large scale genomic projects and is currently responsible for statistical analysis of over 100 prostate genomes. Her main project is developing a statistical model in a Bayesian framework to relate somatic genomic alterations to prostate tumorigenesis. Her side projects include analysing young breast cancer exomes and various array analyses with SGC.

Fouad Yousif

2014-05


After completing his Bachelor's degree in Biochemistry from McMaster University, Fouad obtained a Bioinformatics graduate certificate and a Masters degree in Biostatistics from the University of Toronto. Fouad's current role involves algorithm development and biomarker discovery analysis for different types of cancers including Prostate and Breast. Prior to joining the team, Fouad was a member of the sequencing production team at OICR that is responsible for the optimization and parallelization of algorithms for the analysis of genome-sequencing data.

Anna Lee

2014-10


Anna’s current work involves the analysis of different computational approaches for identifying somatic mutations in cancer genomes. (See the ICGC-TCGA DREAM Mutation Calling Challenge for more details.)

Clare (Jouhyun) Jeon

2015-02


Clare's current research is identifying novel diagnostic and prognositic biomarkers for prostate cancer by integrating clinical and genome-wide high-throughput data sets. She holds a Ph.D. in Systems Biology from Pohang University of Science and Technology where she studied protein structures and protein-protein interactions.

Robert Lesurf

2016-10


Robert hold a B.Sc. in Biomedical Computing from Queen's University , a M.Sc. in Computer Science from McGill University, and a Ph.D. in Biochemistry from McGill University. Prior to joining the team, he completed a postdoc with Elaine Mardis and Obi Griffith at the McDonnell Genome Institute of Washington University in St Louis. His current work is focused on investigating clonal heterogeneity in cancer.

Computational Biologists

Takafumi Yamaguchi

2013-09


Taka studied genetics and molecular biology at the Univeristy of Manitoba, before beginning a Master of Science at the Univeristy of Toronto, where he learned systems biology, programming and next generation sequencing (NGS) data analysis under the supervision of Dr. Fritz Roth. Upon graduation in 2013, Taka started working with Dr. Paul Boutros at OICR. His current research focus is on NGS data analysis and the development of NGS analysis pipelines, including DNA read quality control, alignment and mutation calling. His projects include the Canadian Prostate Cancer Genome Network (CPC-GENE) Project, International Cancer Genome Consortium (ICGC) Cancer Genome Project, and The Cancer Genome Atlas(TCGA) DREAM Challenge.

Julie Livingstone

2014-01


Julie is currently part of two large projects: The Canadian Prostate Cancer Genome Network (CPC-GENE) and The Tamoxifen Exemestane Adjuvant Multinational (TEAM) clinical trial, where her role is to analyze Affymetrix OncoScan copy number arrays to discover recurrent amplifications and deletions in prostate and breast cancer respectively. She has her M.Sc. in Bioinformatics from McGill University and B.Sc in Biology from Queen's University.

Vincent Huang

2014-06


As a part of the team working on the Canadian Prostate Cancer Genome Network (CPC-GENE) project, Vince is responsible for the analyses of genomic rearrangements. This involves calling the variants from next generation sequencing (NGS) data using a variety of tools, to downstream statistical analyses. He has an M.Sc in Environmental Biology from Guelph University, and a B.Sc in Botany from the University of Toronto.

Sylvia (Yu-Jia) Shiah

2015-03


Sylvia graduated with an M.Sc. from the Department of Medical Biophysics at the University of Toronto. She is part of The Canadian Prostate Cancer Genome Network (CPC-GENE) project. Her work currently focuses on developing microarray analysis pipeline, which include Affymetrix mRNA arrays and Illumina 450K Methylation arrays.

Shadrielle Espiritu

2015-05


Shadrielle continues to help organize the DREAM SMC Meta-pipeline challenge, a sequel to the ICGC-TCGA DREAM SMC-DNA challenge aimed at identifying cancer-associated mutations and rearrangements in whole-genome sequencing data. He is currently working to improve the quality of synthetic tumour simulation using the BAMsurgeon tool. He performs sub-clonality assessments on the entire CPC-GENE patient cohort and will perform machine-learning analyses on these data. He continues to update core alignments and pipelines to improve accuracy and reusability.

Adrien Foucal

2016-09


Adrien holds a M.Sc. of Bioinformatics from the Université Paris Diderot - Paris 7. He studied the french colonisation of Québec and the effect of range expansion under the supervision of Pr. Laurent Excoffier at the University of Bern. Adrien's current work in the Boutros lab will focus on colon cancer data and the POP-CURE project.

Visual Scientists

Alumni

Ashley Mao

2017/06 - 2017/09


Ashley is an undergraduate student at the University of Toronto specializing in pharmacology. She is currently working with pipeline maintainers to run SNVcallers on 18 samples.

Jay Jayalath

2017/06 - 2017/08


Jay is studying the interplay between germline structural variants and somatic RNA expression in prostate cancer. He is a medical student at the University of Toronto and holds a M.Sc. from the University of Guelph .

Imaad Umar

2016/07 - 2017/08


Imaad's work at the Boutros Lab involves optimizing software for high performance computing, creating pipelines, maintenance of lab systems as well as assisting researchers with software development. He has a B.ASc in Systems Design Engineering from University of Waterloo.

Ren Sun

2013/09 - 2017/06


Ren is a graduate student with the Department of Pharmacology at the University of Toronto. Previously, she completed her Bachelor of Science at the University of Toronto, with a double-major in Biomedical Toxicology and Nutritional Sciences. She has worked on several toxicology-related projects but her current main project focuses on the genomics of drug response in HPV+ head and neck cancer.

Sandy Lee

2016/08 - 2017/05


Sandy is a fourth year thesis student double majoring in Health and Disease and Cell and Molecular Biology at the University of Toronto. She is currently working on liver tumour carcinogens through the effect of an environmental carcinogen, TCDD.

David Park

2016/09 - 2017/04


David is finishing his graduate studies with the Department of Physics at the University of Guelph . He holds a B.Sc. in Biophysics from McMaster University. His current work involves studying the spatial heterogeneity of tumours in prostate cancer.

Minjeong Ko

2014/09 - 2017/01


Minjeong has a M.Sc. in Computer Science from the Unversity of Toronto, where did she studied machine learning analysis under the supervision of Dr. Fritz Roth. Her current research focuses on developing a simulator from sequencing data to generate sub-clonal structures and feed those alterations into BAMSurgeon.

Nathaniel Schmitz

2016/08 - 2016/12


Nathaniel is an undergraduate student majoring in Mechatronics Engineering at the University of Waterloo. His current work involves pan-cancer analysis of sex-associated differences in cancer genomics.

Erle Holgersen

2016/05 - 2016/12


Erle is a statistics graduate student at the University of Waterloo . She will be helping the lab with statistical analyses.

Joseph Somody

2016/04 - 2016/10


After graduating with an Hon. B.Sc. in Bioinformatics and Computational Biology from the University of Toronto , Joseph obtained an M.Sc. in Computational Biology & Bioinformatics from ETH Zürich. Joseph's current work here consists predominantly of the analysis of microarray or short-read sequencing data from collaborative experiments in induced carcinogenesis.

Holly Babaran

2015/07 - 2016/10


Holly currently works on improving the performance and efficiency of Boutros Lab's software and systems. At the moment she is focused on SeqKat and reorganizing the way the lab uses SVN. She recently graduated with a B. Software Engineering at the University of Waterloo .

Yiyang (Lydia) Liu

2015/05 - 2016/09


Lydia is an undergraduate student studying Life Science and Computer Science at the University of Toronto. Her current work focuses on incorporating cancer trinucleotide signatures into BAMsurgeon: a tool for generating in silico cancer genomes by spiking somatic mutations into sequencing data.

Kim Nguyen

2016/05 - 2016/09


Kim is a student at the University of Waterloo majoring in Honours Biology Joint Mathematics. She is with the Boutros Lab for the Summer and will be working on the auto-parameterization of BPG package.

Rodrigo Sousa

2015/06 - 2016/09


Rodrigo is a Ph.D. candidate from the University of Sao Paulo, Brazil, where he also completed his Bachelor of Science in Biomedical Informatics and Masters of Science in Genetics. He is currently working with RNAseq to study the formation of new blood vessels (angiogenesis). He is supported during his research internship at OICR by the Sao Paulo Research Foundation (FAPESP) .

Pei Lin Li

2016/05 - 2016/08


Pei Lin is an undergraduate student studying Software Engineering at the University of Waterloo . He is currently working with Christopher Lalansingh to improve BPG- a generalized R plotting library. In addition, Pei Lin will be developing a test suite for BPG to ensure the functionality and compatibility of future modifications.

Anqi (Joyce) Yang

2016/05 - 2016/08


Joyce is an undergraduate student studying Computer Science at the University of Waterloo . Her current work focuses on writing a SLURM driver for the lab's HPCI module, so that computing jobs can be run on cluster managed by SLURM in the future.

William Zou

2016/05 - 2016/08


William is enrolled in the Software Engineering program at the Universtiy of Waterloo . His current work involves optimizing the script that will score the SMC-Het challenge, which is part of an effort to improve standard methods for subclonal reconstruction.

Jennifer Aguiar

2016-01 - 2016/08


Jennifer is a third year Honours Biochemistry coop student with a Bioinformatics Specialization at the University of Waterloo. She has joined the Boutros lab as a Computational Cancer Biologist for 8 months where she will be working with Dr. Julia Hopkins on the identification of mitochondrial DNA mutations in prostate cancer and their relation to other prostate cancer variables.

Jennifer Lin

2016/01 - 2016/08


Jennifer is currently in her third year at the University of Waterloo in the Honours Biology Co-op program. She is working in the lab on an 8 month placement working with Anna Lee on identifying dysregulated genes and pathways associated with radioresistance in prostate cancer cells.

Drew Neish

2016/01 - 2016/08


Drew holds an M.Sc. in Statistics from the University of Guelph, as well as a B.Math in Statistics from the University of Waterloo . He joins the lab for an 8 month placement working with Anna Lee, and his work is split between development of a computational pipeline for the PRONTO project, and analysis of radioresistance in prostate cancer cells.

Emilie Lalonde

2011/08 - 2016/06


Emilie is a Ph.D. candidate in the Department of Medical Biophysics at the University of Toronto, and is co-supervised by Dr. Robert Bristow. Previously, she completed her M.Sc. in Human Genetics from McGill University. She applies bioinformatics and machine learning to clinical and genome-wide omic profiles to develop prognostic biomarkers for localized prostate cancer. Two major problems remain in managing localized prostate cancer: one third of patients are failing primary treatment and simultaneously men with indolent disease are burdened with unnecessary treatment. Emilie's research addresses this issue by identifying genomic markers of poor prognosis which can be used to identify candidates for treatment intensification or de-intensification trials. Using copy-number profiles, Emilie has examined genomic variables associated the heterogeneous outcome of prostate cancer patients using single-gene biomarkers (see here and here for more information) and multi-gene approaches including measures of genomic instability, genomic subtypes, and a 100-loci gene signature (see here for more information). Importantly, she found a synergistic relationship between genomic instability and tumour hypoxia on patient outcome, identifying a major role integrative indices in better stratifying patients with different clinical outcome. Emilie is also involved in examining the clinical impact of genomic alterations in the CPC-GENE study.

Kevin Thai

2016/01 - 2016/04


Kevin is currently in his fourth year of Bioinformatics at the University of Waterloo. His primary work will be to assist in the analysis of sex-associated differences in cancer genomics.

Pragash Sivasundaram

2016/01 - 2016/04


Pragash is an undergraduate student studying Computer Engineering at the University of Waterloo . He is currently working on adding features and improving the source code in software tools such as BoutrosLab.plotting.general and BAMQL. He also contributes to the maintenance of the R nightly build system.

Eva Ho

2015/04 - 2015/09; 2016/01 - 2016/04


Eva is in her third year of biology co-op at the University of Waterloo. Her main area of focus is developing an online cancer biology course for the Boutros lab. This course will aim to provide those without a strong biology knowledge with a resource for learning this material. This course will cover basic cell biology, cancer biology and related research.

Bryan Lo

2013/08 – 2013/12; 2015/12 - 2016/04


Bryan is studying Systems Design Engineering at the University of Waterloo . He spends most of his time developing and optimizing analysis pipelines for the lab.

Rached Alkallas

2015/05 - 2016/04


Rached's main project entails adding a variety of modules to a recurrent genomic copy number aberration analysis pipeline. In addition, he generates figures for a proteogenomics study and experiments with different feature ranking and selection metrics to use with machine learning algorithms for prognostic signature discovery.

Denis Osipov

2016/02 - 2016/04


Denis received his Hons BSc and MSc from the University of Toronto, specializing in Neuroscience. Working on the neurobiology of learning, he would routinely produce, interpret, and visualize heavy amounts of electrophysiological data. Denis joined Boutros Lab in order to apply his expertise towards the analysis of large genomic datasets in the R and Perl environments.

Alina Ma

2015/08 - 2016/03


Geoffrey Hunter

2014/05 - 2016/02


Geoffrey A. M. Hunter started as a postdoctoral fellow in May 2014. He is looking for associations between germline and somatic variants to identify novel cancer subtypes that more accurately prognose patients with intermediate risk prostate cancer. His other activities in the lab involve participating in the Machine Learning group and DREAM9 challenges as well as developing a program to identify kataegis regions. He holds a B.Math (Applied Math) from the University of Waterloo and a M.S. (Mathematical Biology) and Ph.D. (Systems Biology) from the University of Utah.

Maud Starmans

2010/01 - 2016/02


Maud is co-supervised by Dr. Philippe Lambin.

Christine P'ng

2015/04 - 2016/01


Christine works on a range of graphics-related work, from illustrating experimental designs to designing data visualizations to selecting appropriate colour palettes. She also spends time developing and improving a suite of plotting functions in R for the generation of publication-quality graphs.

Matei David

2013/09 - 2016/01


Matei is developing new algorithms and software for the analysis of second- and third-generation sequencing data. He is interested in read mapping, de novo assembly, and combining data produced by different sequencing technologies to improve variation detection. Matei is co-supervised by Dr. Jared Simpson.

Fan Fan

2015/05 - 2015/12


Fan is a graduate student with the Department of Statistics and Actuarial Science at the University of Waterloo. She is currently working on survival simulations and analysis through machine learning.

Xihui (Eric) Lin

2013/04 - 2015/12


Xihui's current work involves biomarker discovery using statistical models and machine learning algorithms, DREAM challenges, machine-learning package with auto hyper-parameters, and model and feature selection.

Delia Yao

2015/01 – 2015/05; 2015/09 - 2015/12


Delia is an undergraduate student studying software engineering at the University of Waterloo. Her current work involves an analysis of genome instability using pan-cancer data. She has also contributed to software tools developed and used in the lab.

Jennifer Chan

2015/09 - 2015/12


Jennifer is an undergraduate student studying computer science at the University of Waterloo. She is working on the scoring metrics for the SMC-RNA challenge.

Nathan Wilson

2015/09 - 2015/12


Nathan is an undergraduate student at the University of Waterloo studying Mathematical Optimization. He is helping to run the SMC-Het challenge with collaborations from other labs. In particular he is developing the scoring metrics used for this challenge.

Tonny Huang

2015/11 - 2015/12


Barbara Huang

2014/10 - 2015/12


Barbara is researching the effects of parametrization on random forests. She holds an undergraduate in Zoology and a Master's in Bioinformatics from the University of Guelph.

Leslie Oldfield

2015/10 - 2015/11


Leslie is a graduate student with the Department of Medical Biophysics at the University of Toronto. Her current work involves using random forests to predict patient sex in the absence of sex chromosomes.

Catalina Anghel

2013/11 - 2015/11


Catalina Anghel works on computational deconvolution of tumour gene expression profiles. She has translated the ISOpure algorithm to R so that it can be used in existing computational pipelines and is currently working on incorporating micro-environment data. She holds a Ph.D. in mathematics from the University of Toronto.

Ting Ting (Nina) Wang

2015/09 - 2015/10


Nina is a graduate student with the Department of Medical Biophysics at the University of Toronto. She completed her Bachelor of Science at the University of Toronto with a double-major in Human Biology and Cell & Systems Biology . Her current work focuses on tumour heterogeneity and identification of prognostic biomarkers in breast cancer and localized prostate cancer.

Inna Gong

2015/04 - 2015/09


Inna is working on machine learning methods to optimize tumour biomarker prognostic capabilities. The goal is to develop methodologies to better classify survival outcomes using various types of biomarkers, with potential application to a wide spectrum of cancer types. Inna obtained a PhD in Clinical Pharmacology at the University of Western Ontario and is currently attending medical school at the University of Toronto.

Lina Wadi

2014/08 - 2015/09


Lina is currently working on developing a tool for predicting blood types using next generation sequencing data. The programming languages she is using include Perl and R. She will also be looking for associations between blood type and clinical characteristics or somatic mutation profiles of prostate cancer.

David Wang

2015/04 - 2015/09


David is an undergraduate student at the University of Waterloo, studying software engineering. He is working on the BL-ML R package which builds on the already popular mlr machine learning package. This package will include default hyper parameter ranges for tuning, fused feature selection/extraction and model tuning, and integration with the Boutros lab's plotting package.

Felix Lam

2015/04 - 2015/09


Felix is an undergraduate student in a 5-year software engineering program at the University of Waterloo. He is working on developing a web interface for the lab's software and maintaining it's existing code.

René Böttcher

2015/08 - 2015/09


René is a visiting scientist from Erasmus MC (Rotterdam, The Netherlands) where he is a Ph.D. candidate in bioinformatics working on novel biomarkers for prostate cancer. His collaborative project at OICR focuses on copy number alterations and genomic instability in subtypes of prostate cancer.

Andre Masella

2014/04 - 2015/07


Andre works as both a software engineer and bioinformatician. He is currently involved in development and maintenance of in-house software and working on the CPC-GENE prostate cancer project. He has a M.Sc. in Integrative Biology from Wilfrid Laurier University and a B.A.Sc. in Computer Engineering from the University of Waterloo.

Srinivasan Sivanandan

2015/05 - 2015/07


Srinivasan is a final year undergraduate student of Biotechnology and Biochemical Engineering at the Indian Institute of Technology, Kharagpur. He works on the development of a streamlined pipeline for BAMsurgeon: a tool for simulation of tumour/normal genome pairs by spiking in mutations to normal sequencing data. His work also includes benchmarking of SNV callers on simulated tumour data.

Ana Altamirano

2014/09 - 2015/03


Ana is a graduate student participating in the International Visiting Graduate Student Research program with the department of Cell Biology at CINVESTAV in Mexico. Her main project is analysing the differential expression of alternative splicing during the exposure of TCDD using exon microarrays.

Cheryl Lau

2014/09 – 2014/12


David Garcia

2014/08 – 2014/12


Shadrielle Espiritu

2014/08 – 2014/12


Shadrielle has worked on improving and modifying the BWA pipeline, which now gives the option of using two different BWA aligners: bwa aln or bwa mem. He has refactored the code and directory structure, as well as made the pipeline applicable to older and newer versions of BWA. He is currently benchmarking the two BWA aligners regarding detecting somatic mutations using 4 SNV callers. His future goals include looking into an error-correction tool called Trowel and make similar comparisons above.

Nancy Yu

2014/07 – 2015/05


Nancy is currently working on the discovery of novel miRNA biomarkers in a large breast cancer cohort with the ultimate goal of improving patient outcome. She recently graduated from University of Waterloo (2014) with a major in Biomedical Sciences.

Michael Xie

2014/05 – 2015/05


Michael is the maintainer for the RecSNV software pipeline and a member of the 124PG project.

Honglei Xie

2014/05 – 2014/12


Honglei is responsible for analysing genomic data, and trying to discover prognostic biomarkers for prostate cancer by developing and implementing machine learning algorithms. She also provides general statistical consulting to other members of the lab.

Vivian Ku

2014/05 – 2014/08


Alister D'Costa

2014/01 – 2014/04; 2014/08 – 2014/12


Heidi Kong

2014/01 – 2014/08


Nicole Simone

2014/01 – 2014/04


Cristian Caloian

2013/12 – 2015/02


Natalie Galant

2013/10 – 2013/11


Jamie Lee

2013/09 – 2014/10


Marco Albuquerque

2013/08 – 2013/12; 2014/04 – 2014/08


Christopher Cooper

2013/06 – 2015/04


As a software engineer at OICR, Chris' work involves teaching and assisting reserachers with software deveolpment, attending to lab systems, and writing libraries to support scientific computing. The lab systems written and maintained by Chris and the other engineers support better computing cluster use and software distribution, sampling, analysis, data storage, continuous integration, code quality, and other aspects related to software.

Amanda Murdoch

2013/05 – 2013/07


Gregory Chen

2013/04 – 2013/08; 2014/05 – 2014/08


Esther Jung

2013/04 – 2013/08


Clement Fung

2013/04 – 2013/08


Saman Vasipour

2013/03


Jaeseung Kim

2012/09 – 2012/10


Julia Buthmann

2012/07 – 2013/04


Melissa Moore

2012/05 – 2012/08


Andrea Critch

2012/05 – 2012/08


Nathalie Moon

2012/05 – 2013/07


Aileen Lu

2012/04 – 2013/08


Richard De Borja

2012/04 – 2014/01


Shaylan Govind

2012/01 – 2012/04; 2013/05 – 2013/08


Lauren Chong

2012/01 – 2013/08


Michal Grzadkowski

2011/11 – 2013/08


Daihai He

2011/11 – 2012/03


Nicholas Harding

2011/10 – 2014/06


Rui Yan

2011/10 – 2013/07


Michael Yan

2011/09 – 2011/12


Trent Simmons

2011/09 – 2013/07


Xinyi Zhang

2011/09 – 2011/12


Hilary Snider

2011/08 – 2012/05


Pablo Hennings-Yeomans

2011/07 – 2013/11


Ekaterina Kouzmina

2011/07 – 2013/04


Peter Raboud

2011/06 – 2011/08


Jianxin Wang

2011/05 – 2015/03


Yonathan Brhane

2011/05 – 2011/12


Ying Wu

2011/05 – 2011/12


Andrew Wald

2011/05 – 2013/08


Jennifer Liu

2011/05 – 2011/08


Kar Yoganathan

2011/05 – 2011/08


Blair Gannon

2011/05 – 2011/08


Amin Zia

2011/05 – 2013/04


Christine P'ng

2011/05 – 2011/08; 2013/05 – 2014/12


Christine works on a range of graphics-related work, from illustrating experimental designs to designing data visualizations to selecting appropriate colour palettes. She also spends time developing and improving a suite of plotting functions in R for the generation of publication-quality graphs.

Renee Pang

2011/04 – 2011/09


Michelle Chan-Seng-Yue

2011/04 – 2014/08


Bianca Liang

2011/01 – 2011/04


Kenneth Chu

2010/10 – 2014/06


Sylvia (Yu-Jia) Shiah

2010/09


Guillermo Elizondo-Azuela

2010/09 – 2011/07


Daryl Waggott

2010/09 – 2014/04


Dorota Sendorek

2010/08 – 2012/08


Francis Nguyen

2010/07 – 2013/04


Ashley Smith

2010/05 – 2010/08


Janice Pong

2010/04 – 2011/08


Alexander Ross

2009


Peili Dai


Nicholas Buchner


Mehrdad Shamsi


James Hawley


Shaoming Yin


Yifan Zhang


Sheshadrie Saha


Ryan Kearns


Monika Torio


Hassaan Amir


Hanbert Chen


Denise Mak