Current Students

Our Students

2021 Cohorts:

  • Rituparna Banerjee – Ph.D. student with Matt Pennell
  • Charlotte Barclay – M.Sc. student with Steven Plotkin
  • Guiliano Cruz- M.Sc. student wit Keegan Korthauer
  • Jose Rafael Dimayacyac- M.Sc. student with Matt Pennell
  • Dolly Dodina – M.Sc. student with Aline Talhouk
  • Hossein Ebrahimikondori – M.Sc. student with Inanc Birol
  • Hans Ghezzi – M.Sc. student with Carolina Tropini
  • Talha Goktas – M.Sc. student with Inanc Birol
  • Parham Kazemi – Ph.D. student with Inanc Birol
  • Hazem Mslati – M.Sc. student with Art Cherkasov
  • Aditi  Nallan- M.Sc. student with Steve Hallam
  • Erick Navarro Delgado – M.Sc. student with Keegan Korthauer and Michael Kobor
  • Mohit Pandey – Ph.D. student with Art Cherkasov
  • Rebecca Ridings – M.Sc. student with Steve Jones and Pamela Hoodless
  • Armita Safa – M.Sc. student with Faraz Hach
  • Armaghan Sarvar – M.Sc. student with Inanc Birol
  • Ashleigh Thomas – Ph.D. student with Paul Pavlidis
  • Denitsa Vasileva – Ph.D. student with Denise Daley
  • Kevin Yang – M.Sc. student with Andrew Roth
  • Lingyu Yang – M.Sc. student with Inanc Birol
  • Patricia Ye – M.Sc. student with Yongjin Park
  • Jiaying You – Ph.D. student with Aft Cherkasov
  • Irem Yucel – M.Sc. student with Denise Dennis

2020 Cohorts:

  • Alejandro Aguirre- M.Sc. student with Wyeth Wasserman
  • Rhiannon Cameron- M.Sc. student with Will Hsiao- CREATE Scholarship awardee
  • Angus Campbell – M.Sc. student with Sophia Frangou and Paul Pavlidis
  • Yixuan Chen – M.Sc. student with Ryan Brinkman
  • Sarah Dada – Ph.D. student with Steven Jones
  • Ghazal Ebrahimi – M.Sc. student with Faraz Hach – CREATE Scholarship awardee
  • Jeremy Fan – M.Sc. student with Steven Jones – CREATE Scholarship awardee
  • Ivan Gill – M.Sc. student with Will Hsiao- CREATE Scholarship awardee
  • Jorge Holguin – M.Sc. student with Joerg Gsponer – CREATE Scholarship awardee
  • Sebastian Hunter – M.Sc. student with Brett Finlay and Sara Mostafavi
  • Madeline Iseminger – M.Sc. student with Will Hsiao – CREATE Scholarship awardee
  • Faeze Keshavarz- Rahaghi – Ph.D. student with Steven Jones – 4YF awardee
  • Eric Lee – M.Sc. student with Andrew Roth
  • Tiffany Leung – M.Sc. student with Wyeth Wasserman
  • Janet Li – M.Sc. student with Inanc Birol
  • Theodora Lo – M.Sc. student with Inanc Birol – CREATE Scholarship awardee
  • Matthew Nguyen – M.Sc. student with Will Hsiao- CREATE Scholarship awardee
  • Mariia Radaeva – Ph.D. student with Art Cherkasov
  • Cara Reisle – Ph.D. student with Steven Jones
  • Ryan Riley – M.Sc. with Gregg Morin and Ryan Morin
  • Reza Soltani – M.Sc. student with Faraz Hach
  • Ye Sue – Ph.D. student with Philipp Lange
  • Derek Tam – M.Sc. student with Aly Karsan and Andrew Roth
  • Marco Tello  – M.Sc. student with Keegan Korthauer- CREATE Scholarship awardee
  • Jenkin Tsui – Ph.D. student with Andrew Roth – 4YF awardee
  • Christine Yang- M.Sc. student with Robert Hancock
  • Pouya Ahmadvand – M.Sc. student with Ali Bashashati

2019 Cohorts:

  • Saelin Bjornson – M.Sc. student with Patrick Keeling- CREATE Scholarship awardee
  • Abhijit Chinchani – Ph.D. student with Todd Woodward
  • Sean Formby – Ph.D. student with Steve Hallam and Guus Bakkeren- CREATE Scholarship awardee
  • Yue Huang – M.Sc. student with Paul Pavlidis and Kurt Haas
  • Almas Khan – M.Sc. student with Elodie Portales-Casamar and Wendy Robinson- CREATE Scholarship awardee
  • Nicole Knoetze – Ph.D student with Robert Holt
  • Diana Lin – M.Sc. student with Inanc Birol
  • Ishika Luthra – Ph.D. student with Sara Mostafavi – CREATE Scholarship awardee
  • Angela McLaughlin – Ph.D. student with Jeff Joy – CREATE Scholarship awardee
  • Rachel Miller – M.Sc. student with Jeff Joy- CREATE Scholarship awardee
  • Sebastiano Montante – Ph.D. student with Ryan Brinkman – CREATE Scholarship awardee
  • Tunc Morova – Ph.D. student with Faraz Hach – CREATE Scholarship awardee
  • Jordan Sicherman – M.Sc. student with Paul Pavlidis- CREATE Scholarship awardee
  • Aishwarya Sridhar – Ph.D student with Will Hsiao – CREATE Scholarship awardee
  • Shanwei Tong – M.Sc. student with Will Hsiao and Xiaonan Lu
  • Kristina Wright – M.Sc. student with Inanc Birol
  • Qinkai Wu – M.Sc. student with Paul Pavlidis- CREATE Scholarship awardee
  • Shaocheng Wu – Ph.D. student with Andrew Roth – 4YF awardee
  • Nicole Zhang – M.Sc. student with Wyeth Wasserman- CREATE Scholarship awardee

2018 Cohorts:

  • Amirhossein Afshinfard – Ph.D. student with Inanc Birol – 4YF awardee
  • Ryan McLaughlin – Ph.D. student with Steve Hallam – 4YF awardee
  • Simran Rai – M.Sc. student (on LOA)
  • Anh-Tien Ton – Ph.D.. student with Art Cherkasov

2017 Cohorts:

  • William Cassazza – Ph.D. student with Sara Mostafavi and Jessica Dennis- CREATE Scholarship awardee
  • Luka Culibrk – Ph.D. student with Steven Jones
  • Enes Ergin – Ph.D. student with Philipp Lange – 4YF awardee
  • Saber HafezQorani – Ph.D. student with Inanc Birol
  • Bradley Jones – Ph.D. student with Jeff Joy
  • Chenkai Li – Ph.D. student with Inanc Birol – 4YF awardee
  • Ali Mizra – Ph.D. student with Helen Tremlett and William Hsiao
  • Alex Morin – Ph.D. 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
  • Andrew Yeager – Ph.D. student with Joerg Gsponer – CREATE Scholarship awardee

2016 Cohorts:

  • Dalia Alghamdi – Ph.D. student with William Hsiao
  • Arjun Baghela – Ph.D. student with Robert Hancock
  • Eric Chu – Ph.D. student with Paul Pavlidis – CREATE Scholarship awardee
  • Kristina Gagalova – Ph.D. student with Inanc Birol – 4YF awardee
  • Albina Rahim – Ph.D. student with Ryan Brinkman – CREATE Scholarship awardee
  • Lisa Wei – Ph.D. student with Marco Marra

2014 Cohorts:

  • Alice Kaye – Ph.D. student with Wyeth Wasserman
  • Connor Morgan-Lang – Ph.D. student with Steven Hallam – CREATE Scholarship awardee
  • Rashedul Islam – Ph.D. student with Martin Hirst

2013 Cohorts:

  • Ogan Mancarci – Ph.D. student with Paul Pavlidis

Alumni:

  • Chen Yang: Ph.D. – June 7, 2021: Computational modelling, simulation, and prediction of biological sequences. (Dr. Inanc Birol)
  • Vladimir Nikolic: M.Sc. – April 19, 2021: Scalable methods for improving genome assemblies. (Dr. Inanc Birol)(NSERC-CREATE awardee)
  • Yee Fay Lim: M.Sc. – February 26, 2021: Copy number estimation for high-throughput short read shotgun sequencing de novo whole genome assembly contigs. (Dr. Inanc Birol)(NSERC-CREATE awardee)
  • Teyden Nguyen: M.Sc.- February 25, 2021: Evaluating feature selection techniques for finding microbial signatures in 16S microbiome sequencing data (Drs. Raymond Ng and Sara Mostafavi)
  • Michael Disyak: M.Sc. – February 3, 2021: A multi-task machine learning pipeline for the classification and analysis of cancers from gene expression data (Dr. Steven Jones)
  • Javier Castillo Arnemann: M.Sc. – January 25, 2021: Network-based Integration and Visualization of High-throughput Datasets in Pseudomonas aeruginosa (Dr. Robert Hancock)
  • Sohrab Salehi: Ph.D.- January 25, 2021: Quantitative fitness modelling in cancer using single-cell time series population dynamics (Drs. Sohrab Shah and Alexandre Bouchard-Cote)
  • Elizabeth Chun: Ph.D. – December 9, 2020: Molecular characterization of rhabdoid tumours from multiple anatomical sites. (Dr. Marco Marra)
  • Sina Jafarzadeh: M.Sc. – December 4, 2020: Interpretable clustering of epigenetic marks by incorporating their relationships to genes and their functions. (Dr. Sara Mostafavi)
  • Shamsuddin Bhuiyan: Ph.D. – November 24, 2020: Prioritizing genes with functionally distinct splice isoforms. (Dr. Paul Pavlidis) (NSERC-CREATE awardee)
  • Phillip Richmond: Ph.D. – October 8, 2020:Expanding the utility of whole genome sequencing in the diagnosis of rare genetic disorders (Dr. Wyeth Wasserman)(NSERC-CREATE awardee)
  • Elijiah Willie: M.Sc. – October 5, 2020: Robust methods for inferring cluster structure in scRNA-seq data (Dr. Sara Mostafavi)(NSERC-CREATE awardee)
  • Abdur Rahman Modh Abul Basher: Ph.D. – September 18, 2020: Machine Learning Methods for Metabolic Pathway Inference from Genomic Sequence Information (Dr. Steven Hallam)
  • Jenny Yang: M.Sc. – September 2, 2020: Using Convolutional Neural Networks to Predict NRG1-Fusions from PDAC Biopsy Images. (Dr. Steven Jones)
  • Divya Bafna: M.Sc. – August 26, 2020: Rational design of Notch2 and ER-AF2 inhibitors for bladder cancer and breast cancer therapy. (Dr. Art Cherkasov)
  • Figali Taho: M.Sc. – August 20, 2020: Antimicrobial peptide host toxicity prediction with transfer learning for proteins (Dr. Inanc Birol)(NSERC-CREATE awardee)
  • Jasleen Grewal: Ph.D.- August 13, 2020: Utility of machine learning approaches for cancer diagnosis and analysis from RNA sequencing (Dr. Steven Jones)
  • Shing Zhan: Ph.D. August 8, 2020: Phylogenetic analysis of chromosome numbers and genetic markers (Dr. Sarah Otto)
  • Mariia Radaeva: M.Sc. August 6, 2020:The use of computer-aided drug design methodology to target DNA-protein, RNA-protein and protein-protein interactions implicated in cancer. (Dr. Art Cherkasov)(NSERC-CREATE awardee)
  • Emre Erhan: M.Sc. – July 23, 2020:Support vector machines predict advanced cancer patient response to therapies from bulk RNA sequencing data (Dr. Steven Jones)(NSERC-CREATE awardee)
  • Michelle Kang: M.Sc. – June 12, 2020:Linking CIS-regulatory regions using transcription factor binding signatures, (Dr. Wyeth Wasserman)
  • Evan Gatev: Ph.D. – April 20, 2020: DNA methylation microarray data reduction for co-methylation analysis (Drs. Micheal Kobor and Sara Mostafavi)
  • Alexandra Maslova: M.Sc. – April 15, 2020: Understanding gene regulatory mechanisms of mouse immune cells using a convolutional neural network (Dr. Sara Mostafavi)
  • Sherrie Wang: M. Sc.- April 8, 2020: Flow cytometry data analysis pipeline – data quality control tool development and biomarker discovery (Dr. Ryan Brinkman)(NSERC-CREATE awardee)
  • Carl-Adam Mattsson: M.Sc. – April 6, 2020: A bioinformatics workflow to analyse single cell template strand sequencing data (Drs. Peter Lansdorp and Martin Hirst)
  • Marjan Farahbod: Ph.D. – December 11, 2019: The interpretation of gene coexpression in systems biology. (Dr. Paul Pavlidis)
  • Margot Gunning: M.Sc. – December 6, 2019: An investigation into the utility of GBA machine learning algorithms for the prioritization of ASD candidate risk genes (Dr. Paul Pavlidis)
  • (NSERC-CREATE awardee)
  • Justin Chu: Ph.D. – November 22, 2019: Improving sequence analysis wit probabilistic data structures and algorithms (Dr. Inanc Birol)
  • Allison Tai: M.Sc. – October 9. 2019: Error-free stable computation with polymer-supplemented chemical reaction networks (Dr. Anne Condon) (NSERC-CREATE awardee)
  • My-Linh Thibodeau: M.Sc. – October 4, 2019: Using genome sequence technology to provide insight into cancer biology and other mechanisms (Drs. Steven Jones and Intan Schrader)
  • Vibudh Agrawal – M.Sc. – September 30, 2019: The discovery of small molecule inhibitors for TOX1 and ERG oncotargets with the development and use of progressive docking PD2.0 approach (Dr. Artem Cherkasov) (NSERC-CREATE awardee)
  • Theodore Smith – M.Sc. – August 23, 2019: Detection of enriched patterns in protein sequence data (Dr. Philipp Lange) (NSERC-CREATE awardee)
  • Allen Zhang – M.D./Ph.D. – May 30, 2019: Evolutionary dynamics of ovarian cancer microenvironments and tumour cells. (Dr. Sohrab Shah)
  • Shaun Jackman – Ph.D. – April 16, 2019: Efficient assembly of large genomes. (Dr. Inanc Birol)
  • Nivretta Thatra – M.Sc – April 5, 2019:  Comparative genome analysis in rodent models of Parkinson’s disease and spinocerebellar ataxia type 3. (Dr. Joerg Gsponer) (NSERC-CREATE awardee)
  • Varune Rohan Ramnarine – Ph.D. – March 11, 2019: The long Non-coding RNA landscape of neuroendocrine prostate cancer and its clinical implications, biological dysregulation,and functional impact. (Dr. Colin Collins)
  • Rebecca Asiimwe – M.Sc. – March 4, 2019: Database-driven whole genome profiling for stratifying triple negative breast cancers (TNBC). (Dr. Sohrab Shah)
  • Emma Graham – M.Sc. – October 30, 2018: Integration of genomic and metabolomic data for the prioritization of rare disease variants. (Dr. Sara Mostafavi) (NSERC-CREATE awardee)
  • Zaccary Alperstein – M.Sc. – October 19, 2018: Computer-aided drug discovery tools and piplines for small molecule targeted inhibition of topoisomerases I and II in cancer (Dr. Art Cherkasov)
  • Sam Hinshaw – M.Sc. – October 4, 2018: Network-based integrative analysis of multi-omic data (Dr. Robert Hancock)
  • Jake Lever – Ph.D. – September 21. 2018:Building and inferring knowledge bases using biomedical text mining. (Dr. Steven Jones)
  • Raunak Shrestha – Ph.D. – July 27, 2018: Computational prioritization of cancer driver genes for precision onocology (Dr. Colin Collins)
  • Farnush Kiadeh – M.Sc.- May 31, 2018: Molecular interpretation of genome-wide association studies using multi-omics analysis (Dr. Sara Mostafavi) (NSERC-CREATE awardee)
  • Eric Zhao – M.D./Ph.D.- May 7, 2018: The clinical actionability and evolution of mutational processes in metastatic cancer (Dr. Steven Jones)
  • Rebecca Johnston – M.Sc.- March 15, 2018: The biology and clinical significance of the micro-environment of pediatric Hodgkin lymphoma (Dr. Christian Steidl)
  • Rodrigo Goya – Ph.D.- November 22, 2017: Bioinformatics approaches for identifying single nucleotide variants and profiling alternative expression in cancer transcriptomes (Dr. Marco Marra)
  • Rachelle Farkas – M.Sc.- October 5, 2017: Bioinformatics design of cis-regulatory elements controlling human gene expression. (Dr. Wyeth Wasserman)
  • Ka Ming Nip – M.Sc.- August 4, 2017: RNA-Bloom: de novo RNA-seq assembly with Bloom filters (Dr. Inanc Birol)
  • James Topham –  M.Sc.- July 18, 2017: Comprehensive and integrative analysis of the KMT2D regulome (Dr. Marco Marra)
  • William Evan Durno – M.Sc.- June 2, 2017: Precise correlation and metagenomic biomining uncovers fine microbial community structure (Dr. Steven Hallam)
  • Wenqiang Shi – Ph.D.- May 23, 2017: Revealing the impact of sequence variants on transcripton factor binding and gene expression (Dr. Wyeth Wasserman)
  • Hamid Mohamidi – Ph.D.- May 23, 2017: Parallel algorithms and software tools for high-throughput sequencing data (Dr. Inanc Birol)
  • Kyle Lesack – M.Sc.- May 9, 2017: Nomenclature errors in public 16S rRNA gene databases: stategies to improve the accuracy of sequence annotations (Dr. Inanc Birol)
  • Alborz Mazaloomian – Ph.D. – 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. – February 27, 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)