Current Students

Our Students

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
  • 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
  • Golnaz Jahesh – Ph.D. student
  • Jasleen Grewal – Ph.D. student with Steven Jones
  • Phillip Richmond – Ph.D. student with Wyeth Wasserman – CREATE Scholarship awardee
  • Rachelle Farkas – M.Sc. student with Wyeth Wasserman
  • Sam Hinshaw – Ph.D. student with Robert Hancock
  • 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
  • Connor Morgan-Lang – M.Sc. student with Steven Hallam
  • James Topham – M.Sc. student with Marco Marra
  • Ka Ming Nip – M.Sc. student with Inanc Birol
  • 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
  • Eric Zhao – MD/PhD student with Steven Jones
  • Evan Durno – M.Sc. student with Steven Hallam
  • Justin Chu – Ph.D. student with Inanc Birol
  • Ogan Mancarci – Ph.D. student with Paul Pavlidis
  • Rebecca Johnston – M.Sc. student with Christian Steidl
  • Varune Ramnarine – Ph.D. student with Colin Collins

2012 Cohorts:

  • Elizabeth Chun – Ph.D. student with Marco Marra
  • Hamid Mohamadi – Ph.D. student with Inanc Birol
  • Jake Lever – Ph.D. student with Steven Jones
  • 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

2008 Cohorts:

  • Rodrigo Goya – Ph.D. student with Marco Marra and Irmtraud Meyer

Alumni:

  • 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)

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