Current Students | Graduate Program in Bioinformatics

Our Students

2017 Cohorts:

Vibudh Agrawal – M.Sc. student with Steve Plotkin- CREATE Scholarship awardee
William Cassazza – Ph.D. student with Sara Mostafavi – CREATE Scholarship awardee
Luka Culibrk – M.Sc. student with Steven Jones
Enes Ergin – M.Sc. student with Philipp Lange
Margot Gunning – M.Sc. student with Paul Pavlidis- CREATE Scholarship awardee
Saber HafezQorani – Ph.D. student with Inanc Birol
Sina Jafarzadeh – Ph.D. student with Sara Mostafavi – 4YF awardee
Bradley Jones – Ph.D. student with Jeff Joy
Fariha Khan – M.Sc. student with Ryan Morin and Christian Steidl
Chenkai Li – Ph.D. student with Inanc Birol – 4YF awardee
Yee Fay Lim – M.Sc. student with Inanc Birol – CREATE Scholarship awardee
Alexandra Maslova – M.Sc. student with Sara Mostafavi – CREATE Scholarship awardee
Carl-Adam Mattsson – M.Sc. student with William Hsiao and Intan Schrader
Ali Mizra – Ph.D. student with Helen Tremlett and William Hsiao
Alex Morin – M.Sc. student with Paul Pavlidis – – CREATE Scholarship awardee
Ka Ming Nip – Ph.D. student with Inanc Birol – CREATE Scholarship awardee
German Novakovskiy – Ph.D. student with Wyeth Wassserman – IDF awardee
Theodore Smith – M.Sc. student with Philipp Lange – CREATE Scholarship awardee
My-Lihn Thibodeau – M.Sc. student with Steven Jones
Sherrie Wang – M.Sc. student with Ryan Brinkman
Andrew Yeager – Ph.D. student with Joerg Gsponer – CREATE Scholarship awardee

2016 Cohorts:

Dalia Alghamdi – Ph.D. student with William Hsiao
Zac Alperstein – M.Sc.. student with Artem Cherkasov
Rebecca Asiimwe – M.Sc. student with Sohrab Shah
Arjun Baghela – M.Sc. student with Robert Hancock
Anna Cavalla – M.Sc. student with Marco Marra
Jack Chen- Ph.D. student with Colin Collins
Eric Chu – M.Sc. student with Paul Pavlidis – CREATE Scholarship awardee
Kristina Gagalova – Ph.D. student with Inanc Birol – 4YF awardee
Emma Graham – M.Sc. student with Sara Mostafavi – CREATE Scholarship awardee
Albina Rahim – Ph.D. student with Ryan Brinkman – CREATE Scholarship awardee
Allison Tai – M.Sc. student with Anne Condon – CREATE Scholarship awardee
Nivretta Thatra – M.Sc. student with Joerg Gsponer and Paul Pavlidis – CREATE Scholarship awardee
Lisa Wei – M.Sc. student with Marco Marra

2015 Cohorts:

Farnush Kiadeh – M.Sc.. student with Sara Mostafavi – CREATE Scholarship awardee
Jasleen Grewal – Ph.D. student with Steven Jones- 4YF awardee
Phillip Richmond – Ph.D. student with Wyeth Wasserman – CREATE Scholarship awardee
Sam Hinshaw – Ph.D. student with Robert Hancock-4YF awardee
Shams Bhuiyan – Ph.D. student with Paul Pavlidis – CREATE Scholarship awardee
Sohrab Salehi – Ph.D. student with Sohrab Shah and Alex Bouchard

2014 Cohorts:

Alice Kaye – Ph.D. student with Wyeth Wasserman
Allan Zhang – MD/PhD student with Wyeth Wasserman
Chen Yang – Ph.D. student with Inanc Birol- 4YF awardee
Connor Morgan-Lang – M.Sc. student with Steven Hallam – CREATE Scholarship awardee
Rashedul Islam – M.Sc. student with Martin Hirst
Tyler Funnell – Ph.D. student with Sohrab Shah

2013 Cohorts:

Abdur Rahman Basher – Ph.D. student with Steven Hallam –4YF awardee
Eric Zhao – MD/PhD student with Steven Jones –Vanier scholar
Justin Chu – Ph.D. student with Inanc Birol
Ogan Mancarci – Ph.D. student with Paul Pavlidis
Varune Ramnarine – Ph.D. student with Colin Collins

2012 Cohorts:

Elizabeth Chun – Ph.D. student with Marco Marra
Jake Lever – Ph.D. student with Steven Jones- Vanier scholar
Marjan Farahbod – Ph.D. student with Paul Pavlidis
Shaun Jackman – Ph.D. student with Inanc Birol

2011 Cohorts:

Raunak Shrestha – Ph.D. student with Colin Collins
Shing Zhan – Ph.D. student with Sarah Otto

Alumni:

Rebecca Johnston – March 15, 2018: The biology and clinical significance of the micro-environment of pediatric Hodgkin lymphoma (Dr. Christian Steidl)
Rodrigo Goya – November 22, 2017: Bioinformatics approaches for identifying single nucleotide variants and profiling alternative expression in cancer transcriptomes (Dr. Marco Marra)
Rachelle Farkas – October 5, 2017: Bioinformatics design of cis-regulatory elements controlling human gene expression. (Dr. Wyeth Wasserman)
Ka Ming Nip – August 4, 2017: RNA-Bloom: de novo RNA-seq assembly with Bloom filters (Dr. Inanc Birol)
James Topham – July 18, 2017: Comprehensive and integrative analysis of the KMT2D regulome (Dr. Marco Marra)
William Evan Durno – June 2, 2017: Precise correlation and metagenomic biomining uncovers fine microbial community structure (Dr. Steven Hallam)
Wenqiang Shi – May 23, 2017: Revealing the impact of sequence variants on transcripton factor binding and gene expression (Dr. Wyeth Wasserman)
Hamid Mohamidi – May 23, 2017: Parallel algorithms and software tools for high-throughput sequencing data (Dr. Inanc Birol)
Kyle Lesack – May 9, 2017: Nomenclature errors in public 16S rRNA gene databases: stategies to improve the accuracy of sequence annotations (Dr. Inanc Birol)
Alborz Mazaloomian – April 27, 2017: Analysis of alternative splicing using transcriptome data (Drs. Irmtraud Meyer and Sohrab Shah)
Erdi Kucuk – M.Sc. – April 10, 2017: Kollector: transcript-informed targeted de novo assembly of gene loci (Dr. Inanc Birol)
Beryl Zhuang – M.Sc. – March 24, 2017: Meta-analysis of gene expression in mouse models of neurogenerative disorders (Dr. Paul Pavlidis)
Fong Chun Chan – Ph.D. – March 10, 2017: Analysis of cancer genomes and transcriptomes (Drs. Christian Steidl and Sohrab Shah)
Celia Siu – M.Sc. – February 28, 2017: Characterization of the human thyroid epigenome (Dr. Steven Jones)
Santina Lin – M.Sc. – February 22, 2017: Latent semantic analysis for retrieving related biomedical articles (Dr. Steven Jones)
Dmitry Tebaykin – M.Sc. – December 12, 2016: Exploring sources of variability in electrophysiology data of mammalian neurons (Dr. Paul Pavlidis)
Michael Gottlieb – M.Sc. – December 8, 2016: Text-based methods of variant prioritization for TIDE BC (Dr. Aly Karsan)
Hamza Khan – M.Sc. – December 7, 2016: De Novo annotation of non-model organisms using whole genome an transcriptome shotgun sequencing (Dr. Inanc Birol)
Naman Paul – M.Sc. – November 8, 2016: The use of cheminformatics methods to predict adverse drug responses by human androgen receptor (Dr. Art Cherkasov)
Julie Chen – Ph.D. – September 8, 2016: Computational analysis of transcriptional regulation from local sequence features to three dimensional chromatin domains (Dr. Wyeth Wasserman)
Maia Smith – M.Sc. – August 29, 2016: E-scape: interactive visualization of single cell phylogenetics and spatio-temperal evolution in cancer (Dr. Sohrab Shah)
Rosemary McCloskey – M.Sc. – July 26, 2016: Phylogenetic estimation of contact network parameters with approximate Bayesian computation (Dr. Art Poon)
Thuy Nguyen – M.Sc. – June 10, 2016: Overcoming missing data in phylogenetic analysis of shotgun sequencing to detect HIV adaptation to immune response (Dr. Art Poon)
Dean Attali – M.Sc. – April 21, 2016: Automatic analysis of dual-channel droplet digital PCR experiments to detect BRAF-V600 mutations (Dr. Jenny Bryan)
Casper Shyr – Ph.D. – April 21, 2016: Development and evaluation of software interface for applied clinical genomics (Dr. Wyeth Wasserman)
Lauren Chong – M.Sc. – March 23, 2016: Detection of genomic rearrangements in archival lymphoma tissues using targeted capture sequence (Drs. Christian Steidl & Ryan Morin)
Daniel Lai – Ph.D. – March 7, 2016: Computational Analysis of Ribonucleic Acid Basepairs in RNA Structure and RNA-RNA Interactions (Dr. Irmtraud Meyer)
Emilia Lim – Ph.D. – March 4, 2016: miRNA Sequence Analysis Reveals Cancer Subtypes That Correlate With Tumour Characteristics and Patient Outcomes (Dr. Marco Marra)
Sohrab Salehi – M.Sc. – December 14, 2015: dd-PyClone: Improving clonal sub-population inference from single cells and bulk sequencing data (Drs. Sohrab Shah and Alex Bouchard)
Andrew Roth – Ph.D. – November 26, 2015: Probabilistic models for the identification and interpretation of somatic single nucleotide variants in cancer genomes (Dr. Sohrab Shah)
Katayoon Kasaian – Ph.D. – September 2, 2015: Genomic analysis of head and neck endocrine glands (Dr. Steven Jones)
Alice Zhu – M.Sc. – August 28, 2015: Beyond the one-sequence one-structure dogma: predicting and analyzing transient and alternative RNA secondary structures that are evolutionarily conserved (Dr. Irmtraud Meyer)
Emily Hindalong – M.Sc. – August 10, 2015: A study of methods for learning phylogenies of cancer cell populations from binary SNV profiles (Dr. Sohrab Shah)
Andrew McPherson – Ph.D. – July 24, 2015: Characterization of genome rearrangements from tumour sequencing data (Drs. Sohrab Shah and Cenk Sahinalp)
Huifang Li – Ph.D. – July 16, 2015: Discovery of novel androgen receptor inhibitors as prospective therapeutics for advanced prostate cancer (Dr. Art Cherkasov)
Sarah Perez – M.Sc. – May 22, 2015: Exploring microbial community structure and resilience through visualization and analysis of microbial co-occurrence networks (Dr. Steven Hallam)
Calvin Lefebvre – M.Sc. – May 12, 2015: Cis-regulatory somatic mutations and gene expression alteration in B cell lymphomas (Dr. Sohrab Shah)
Niels Hanson – Ph.D. – April 1, 2015: MetaPathways: A module pipeline for the analysis of environmental sequence information (Dr. Steven Hallam)
Alvin (Xi) Tian – M.Sc. – March 20, 2015: The use of high-throughput amplicon deep sequencing to explore aquatic virus communities (Dr. Curtis Suttle)
Tyler Funnell – M.Sc. – December 2, 2014: Transcriptomic consequences of RNA processing disruption via a novel CDC-like kinase inhibitor (Dr. Sohrab Shah)
Christine Rebecca Hunt – Ph.D. – November 24, 2014: Improving the detection of transcription factor binding regions (Dr. Wyeth Wasserman)
Adriana Estela Sedeño Cortés – M.Sc. – October 9, 2014: Identification and exploration of gene product annotation instability and its impact on current uses (Dr. Paul Pavlidis)
Kieran O’Neill – Ph.D. – October 8, 2014: Bioinformatics of flow cytometry and other high through-put single cell methods (Dr. Ryan Brinkman)
Gavin Ha – Ph.D. – June 27, 2014: Probabilistic Approaches for profiling copy number aberrations and loss of heterozygosity landscapes in cancer genomes (Drs. Sohrab Shah and Sam Aparicio)
Melanie Courtot – Ph.D. – May 12, 2014: Semantic models in Biomedicine: Building interoperating ontologies for biomedical data representation and processing in Pharmacovigilance (Dr. Ryan Brinkman)
Carolyn Ch’ng – M.Sc. – August 16, 2013: Meta-analysis of gene expression in individuals with autism spectrum disorder (Dr. Paul Pavlidis)
Soroush Samadian – Ph.D. – June 14, 2013: Constructing and applying semantic models of clinical phenotypes to support web-embedded clinical research (Dr. Mark Wilkinson)
Young Song – M.Sc. – April 17, 2013: Exploring microbial controls on methane cycling using MLTreeMap (Dr. Steven Hallam)
Patrick Tan – M.Sc. – November 22, 2012: Gene expression analysis of human and rodent brains (Dr. Paul Pavlidis)
Nima Aghaeepour – Ph.D. – November 19, 2012: Computational exploratory analysis of high-dimensional flow cytometry data for diagnosis and biomarker (Dr. Ryan Brinkman)
Jeff Proctor – M.Sc. – September 24, 2012: CoFold : an RNA structure prediction method that takes co-transcriptional folding into account (Dr. Irmtraud Meyer)
Evan Morien – M.Sc. – August 29, 2012: Characterization of wild salmon transcriptome (Dr. Paul Pavlidis)
Warren Cheung – Ph.D. – July 27, 2012: Inferring novel relationships through over-representation analysis of medical subjects in biomedical bibliographies (Dr. Wyeth Wasserman)
Meeta Mistry – Ph.D. – July 6, 2012: Meta-anaylses of expression profiling data in the postmortem human brain (Dr. Paul Pavlidis)
Ryan Giuliany – Ph.D. – July 5, 2012: Probablistic modeling of RNA-editing in human cancers. (Drs. Sohrab Shah and David Huntsman)
Olena Morozova – Ph.D. – May 1, 2012: Genomic studies of the normal and malignant neural crest. (Dr. Marco Marra)
Anthony Fejes – Ph.D. – March 30, 2012: Algorithms and Applications of Next-Generation of DNA Sequencing (Dr. Steven Jones)
Kendric Wang – M.Sc. – March 13, 2012: A Systems Biology Approach for Identifying Predictive Markers of Chemotherapy Response (Dr. Colin Collins)
Leon French – Ph.D. – January 27, 2012: Bioinformatics for Neuroanatomical Connectivity (Dr. Paul Pavlidis)
Fong Chun Chan – M.Sc. – December 16, 2011: Detection of differentially expressed alternative transcripts using conventional microarrays (Dr. Randy Gascoyne)
Ryan Morin – Ph.D. – December 15, 2011: Mutation discovery and characterization in lymphoid neoplasms using massively parallel RNA and DNA sequencing. (Dr. Marco Marra)
Yvonne Li – Ph.D. – November 21, 2011: Bioinfomatics Approaches to drug Repositioning (Dr. Steven Jones)
Raymond Lim – M.Sc. – August 19, 2011: Wide-scale comparison of transcriptome data and the role of microRNA in major depression and suicide. (Dr. Paul Pavlidis)
Hisanaga Mark Okada – M.Sc. – February 28, 2011: Classification of coding and non-coding RNA in RNA-Seq data. (Dr. Martin Ester)
Denil Wickrama – M.Sc. – February 23, 2011: Mapping putative regulatory regions using histone H3 lysine 4 monomethylation marks in breast cancer cell lines. (Dr. Steven Jones)
Ben Vandervalk – M.Sc. – February 3, 2011: The SHARE System: A Semantic Web Based Approach for Evaluating Queries Across Distributed Bioinformatics Databases and Software (Dr. Mark Wilkinson)
Bora Uyar – M.Sc. – December 3, 2010: Homology and evidence-based genome annotation of Caenorhabditis species (Dr. Jack Chen)
Adam Hall – M.Sc. – November 3, 2010: Short-read DNA sequence alignment with custom designed FPGA-based hardware (Dr. Steven Jones)
Varun Ramraj – M.Sc. – September 17, 2010: Computational analysis of clinical practice guidelines (Dr. Kendall Ho)
Anamaria Crisan – M.Sc. – September 14, 2010: Mutation discovery in regions of segmental cancer genome amplifications from next generation sequencing of tumours (Drs. Sam Aparicio and Sohrab Shah)
Nicholas Wiebe – M.Sc. – August 30, 2010: Transat: a method for detecting evolutionarily conserved helices in alignment of RNA sequences and its application inidentifying transient or alternative structures. (Dr. Irmtraud Meyer)
Elizabeth (Hye-Jung) Chun – M.Sc. – August 17, 2010: Bioinformatics approach to investigate genetic differences underlying breast tumours with specific outcomes of adoptive T-Cell therapy using a mouse model (Dr. Steven Jones)
Carri-Lyn Mead – Ph.D. – April 1, 2010: Investigation of Novel Schizophrenia Candidate Genes through Biochemical and Computational Methods (Dr. Robert Holt)
Kelvin (Xi) Zhang – Ph.D. – March 30, 2010: Knowledge Discovery from Large-scale Biological Networks and their Relationships (Dr. Francis Ouellette)
Adrian Cortes – M.Sc. – February 11, 2010: Automated Analysis of High-Throughput Flow Cytometry Data from Hemoatopoietic Stem Cell Experiments (Dr. Ryan Brinkman)
Michael Hsing – Ph.D. – January 13, 2010: Developing Bioinformatics Tools and Analyses on Protein Indels and Protein-Protein Interactions – Novel Applications for Drug Discovery in Staphyloccocus aureus (Dr. Artem Cherkasov)
Vaneet Lotay – M.Sc. – December 17, 2009: Evaluating co-expression analysis for gene function prediction (Dr. Paul Pavlidis)
Debra Fulton – Ph.D. – December 14, 2009: Computational Prediction of Regulatory Element Combinations and Transcription Factor Cooperativity (Dr. Wyeth Wasserman)
Kaida Ning – M.Sc. – September 21, 2009: Biological Insights of Transcription Factor through Analyzing ChIP-Seq Data (Dr. Raphael Gottardo)
Daniel Horspool – M.Sc. – August 6, 2009: Gene Synthesis by Assembly of Short Oligonucleotides (Dr. Rob Holt)
Morgan Langille – Ph.D. – April 16, 2009: Computational prediction and characterization of genomic islands: insights into bacterial pathogenicity (Dr. Fiona Brinkman)
Benjamin Good – Ph.D. – April 3, 2009: Strategies for amassing, characterizing, and applying third-party metadata in bioinformatics (Dr. Mark Wilkinson)
Tang Lee – M.Sc. – March 23, 2009: Outcome prediction and genome-transcriptome correlation analysis in classical Hodgkin’s lymphoma (Dr. Randy Gascoyne)
James Wagner – M.Sc. – August 28, 2008: Gibbs Sampling for Gapped Motif Discovery in Proteins (Dr. Martin Ester)
Xiaohui Chen – M.Sc. – August 12, 2008: Comparisons of Statistical Modeling for Constructing Gene Regulatory Networks (Dr. Raphael Gottardo & Kevin Murphy)
Recep Colak – M.Sc. – June 23, 2008: Towards finding the complete modulome: density constrained biclustering (Dr. Martin Ester)
Chi Kin Ho – M.Sc. – June 12, 2008: Computationally identifying novel essential genes, including non-coding RNAs, in intergenic sequences in bacterial genomes (Dr. Fiona Brinkman)
Nels Thorsteinson – M.Sc. – May 26, 2008: Computational Ligand Discovery for the Human and Zebrafish Sex Hormone Binding Globulin (Dr. Artem Cherkasov)
Shannan Ho Sui – Ph.D. – March 7, 2008: In silico approaches to investigating mechanisms of gene regulation (Dr. Wyeth Wasserman)
Simon Chan – M.Sc. – November 27, 2007: A Bioinformatics Meta-Analysis of Differentially Expressed Genes in Colorectal Cancer (Dr. Steven Jones)
Ryan Morin – M.Sc. – October 4, 2007: Application of Massively Parellel Sequencing to MicroRNA Profiling and Discovery in Human Embryonic Stem Cells (Dr. Marco Marra)
Siddhartha Srivastava – M.Sc. – September 28, 2007: D-Grip: DNA Genetic Risk Information Profile (Dr. Wyeth Wasserman)
Gozde Cozen – M.Sc. – August 7, 2007: Efficient computational methods for sequence analysis of small RNAS (Dr. Cenk Sahinalp)
Chris Thachuk – M.Sc. – August 3, 2007: Novel algorithms for in vitor gene synthesis (Dr. Arvind Gupta)
Jessica (Shang-Jung) Lee – M.Sc. – April 24, 2007: Prediction of Graft-versus-Host Disease based on Supervised Temporal Analysis on High-Throughput Flow Cytometry (Dr. Ryan Brinkman)
Keith Boroevich – M.Sc. – October 14, 2005: Indentification of cis-acting regulatory elements using orthology biased gibbs sampling (Dr. David Baillie)
Byron Kuo – M.Sc. – September 1, 2005: SAGE2Splice: unmapped sage tags reveal novel splice junctions (Dr. Elizabeth M. Simpson)
Alison Meynert – M.Sc. – August 3, 2005: Common evidence network: an integrated approach to investigating gene relationships (Dr. Arvind Gupta)
Michael Hsing – M.Sc. – February 23, 2005: Modeling of cell signaling pathways in macrophages by semantic networks (Dr. Artem Cherkasov)
Fred Yefang Peng – M.Sc. – September 23, 2004: Computational detection of transciptional regulators of protein complexes in apoptosis (Dr. Frederic Pio)
Perseus Missirlis – M.Sc. – August 13, 2004: Cis-features mediating CAG/CTG repeat instability, the satellog database, and candidate repeat prioritization in schizophrenia (Dr. Robert Holt)