Our Students
2023 Cohorts:
- Mohammed Mahdi Asmae – M.Sc. student with Faraz Hach
- Ali Balpour – M.Sc. student with Faraz Hach
- Joel Campbell – M.Sc. student with Adi Steif
- Thomas Deckers- M.Sc. student with Maria Tokuyama
- Maxwell Douglas – M.Sc. student with Yongjin Park
- Matt Faltyn- Ph.D. student with Carl de Boer
- Ekaterina Manskaia- M.Sc. student with Art Cherkasov
- Mayur Mallya- Ph.D. student with Ali Bahashati
- Maedeh Mirzazadeh- M.Sc. student with Ali Bashashati
- Irvin Ng – M.Sc. student with Keegan Korthauer and Bruce Vallance
- Katherine Rich – Ph.D. student with Ali Bashashati
- Riya Saju – M.Sc. student with Jan Friedman and Steven Jones
- Raam Sivakumar – M.Sc. student with Amrit Singh
- Taghrid Aloraini- Ph.D. student with Jan Friedman and Inanc Birol
- Berke Ucar – M.Sc. student with Inanc Birol
- Chun Hei Yiu – M.Sc. student with Adi Steif
2022 Cohorts:
- Alexander Adrian- Hamazaki- M.Sc. student with Paul Pavlidis
- Helena Alvarenga- M.Sc. student with Khanh Dao Duc
- Madison Chapel – M.Sc. student with Carl de Boer
- Nairuz Elazzabi – Ph.D. student with Paul Pavlidis – 4YF awardee
- Emilia Hurtado – M.Sc. student with Andrew Roth
- Yerin Kim – M.Sc. student with Steven Jones and Ly Vu
- Eric Lee – Ph.D. student with Andrew Roth
- Tony Liu- Ph.D. student with Steven Hallam
- Haley MacDonald – M.Sc. student with Adi Steif
- Ali Mirabadi – Ph.D. student with Ali Bashashati
- Brooks Perkins-Jechow – M.Sc. student with Jorge Gsponer
- Sishir Subedi- Ph.D. student with Yongjin Park
- Cindy Shi – M.Sc. student with Ali Bashashati
- Karanvir Singh – M.Sc. student with Jessica Dennis
- Yolanda Yang -Ph.D. student with Raymond Ng
- Michael Yoon – M.Sc. student with Christopher Carlsten and Gabriela Cohen-Freue
- Jordan Yu – M.Sc. student with Roger Tam and Sophia Frangou
- Yukai Wang – M.Sc. student with Tao Huan
- Johnathan Wong – M.Sc. student with Inanc Birol
- Cindy Zhang – M.Sc. student with Wyeth Wasserman and Catrina Loucks
2021 Cohorts:
- Rituparna Banerjee – Ph.D. student with Matt Pennell and Daniel Coombs
- Charlotte Barclay – M.Sc. student with Steven Plotkin
- Guiliano Cruz- M.Sc. student with Keegan Korthauer
- Dolly Dodina – Ph.D. student with Aline Talhouk
- Hossein Ebrahimikondori – M.Sc. student with Inanc Birol
- Anne-Sophie Fratzscher – Ph.D. with Andrew Roth
- Olivia Garland – M.Sc. with Art Cherkasov
- Hans Ghezzi – Ph.D. student with Carolina Tropini – 4YF awardee
- Parham Kazemi – Ph.D. student with Inanc Birol
- Aditi Nallan- Ph.D. student with Steve Hallam
- Erick Navarro Delgado – M.Sc. student with Keegan Korthauer and Michael Kobor
- Alireza Omidi – Ph.D. student with Joerg Gsponer
- Mohit Pandey – Ph.D. student with Art Cherkasov
- Neera Patadia – Ph.D. student with Paul Pavlidis
- Armaghan Sarvar – M.Sc. student with Inanc Birol
- Denitsa Vasileva – Ph.D. student with Denise Daley
- Lingyu Yang – M.Sc. student with Inanc Birol
- Patricia Ye – M.Sc. student with Yongjin Park
- Jiaying You – Ph.D. student with Art Cherkasov
- Irem Yucel – M.Sc. student with Inanc Birol
2020 Cohorts:
- Alejandro Aguirre- Ph.D. student with Wyeth Wasserman
- Angus Campbell – M.Sc. student with Paul Pavlidis
- Yixuan Chen – M.Sc. student with Ryan Brinkman
- Sarah Dada – Ph.D. student with Steven Jones
- Jeremy Fan – M.Sc. student with Steven Jones – 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
- Theodora Lo – M.Sc. student with Inanc Birol – CREATE Scholarship awardee
- Mariia Radaeva – Ph.D. student with Art Cherkasov
- Cara Reisle – Ph.D. student with Steven Jones
- 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
2019 Cohorts:
- Abhijit Chinchani – Ph.D. student with Todd Woodward
- Sean Formby – Ph.D. student with Steve Hallam and Guus Bakkeren- CREATE Scholarship awardee
- Nicole Knoetze – Ph.D student with Robert Holt
- Ishika Luthra – Ph.D. student with Carl de Boer – CREATE Scholarship awardee
- Angela McLaughlin – Ph.D. student with Jeff Joy – CREATE Scholarship awardee
- Sebastiano Montante – Ph.D. student with Ryan Brinkman – CREATE Scholarship awardee
- Aishwarya Sridhar – Ph.D student with Will Hsiao – CREATE Scholarship awardee
- Shanwei Tong – M.Sc. student with Will Hsiao
- Shaocheng Wu – Ph.D. student with Andrew Roth – 4YF awardee
2018 Cohorts:
- Amirhossein Afshinfard – Ph.D. student with Inanc Birol – 4YF awardee
- Ryan McLaughlin – Ph.D. student with Steve Hallam – 4YF awardee
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
2016 Cohorts:
- Dalia Alghamdi – Ph.D. student with William Hsiao
- Eric Chu – Ph.D. student with Paul Pavlidis – CREATE Scholarship awardee
- Albina Rahim – Ph.D. student with Ryan Brinkman – CREATE Scholarship awardee
Alumni:
- Ivan Gill: M.Sc. – April 20, 2023 – Interactive visualizations for two large public health datasets (Dr. Will Hsiao)(NSERC-CREATE awardee)
- Pouya Ahmadvand: M.Sc. – April 6, 2023- A deep learning approach for classification of pancreatic adenocarcinoma whole-slide pathology images. (Dr. Ali Bashashati)
- Matthew Nguyen: M.Sc. – April 3, 2023- Genomic characterization and global contextualization of ESBL-producing E. coli from pediatric patients in Qatar (Dr. Will Hsiao)(NSERC-CREATE awardee)
- Ka Ming Nip: Ph.D. – March 30, 2023 – Transcriptome assembly and visualization for RNA-sequencing date (Dr. Inanc Birol) (NSERC-CREATE awardee)
- Talha Goktas: M.Sc. – February 10, 2023- K-Mer-based data structures and pipelines for sequence mapping and analysis. (Dr. Inanc Birol)
- Lisa Wei: M.Sc. – January 30, 2023: Characterizing gene expression patterns associated with heterogeneity and relapse in pediatric acute myeloid leukemia (Dr. Marco Marra)
- Tunc Morova: Ph.D. – December 7, 2022: Deciphering non-coding driver mutations in prostate cancer (Dr.(s): Faraz Hach and Wilfred Jeffries) (NSERC-CREATE awardee)
- Jose Dimayacyac: M.Sc. – December 6, 2022: Evaluating the adequacy of widely used phylogenetic models of gene expression evolution (Dr. Matt Pennell)
- Reza Soltani: M.Sc. – December 6, 2022: A machine learning and algorithmic tool to advance Peyronie’s disease assessment (Dr. Faraz Hach)
- Hazem Mslati: M.Sc.- December 5, 2022: Computational strategies for the discovery of small molecule therapeutics against SARS-CoV2 virus. (Dr. Art Cherkasov)
- Kevin Yang: M.Sc. – December 5, 2022: LiquidBayes: a Bayesian network for monitoring cancer progression using liquid biopsies (Dr (s): Andrew Roth and Yongjin Park)
- Armita Safa: M.Sc.: December 5, 2022: Discovery of mid-range novel sequence insertions using long-read sequencing (Dr. Faraz Hach)
- Ryan Riley: M.Sc. – December 2, 2022: Peptide detectability algorithm and mass tag labeling, fractionation and ion acquisition methods in mass spectrometry-based proteomics. (Dr(s): Gregg Morin and Ryan Morin)
- Tiffany Leung: M.Sc. – October 12, 2022: Identification of regulatory mechanisms in governing gene expression from the inactivated X chromosome (Dr. Wyeth Wasserman)
- Anh-Tien Ton: Ph.D. – September 8, 2022: Development and application of consensus hit-calling protocols for the virtual screening of “undruggable” and difficulty drug targets. (Dr. Artem Cherkasov)
- German Novakovskiy: Ph.D. – August 22, 2022: Advancing our understanding of genome regulation via optimization of stem cell differentiatic and interpretable deep learning (Dr. Wyeth Wasserman) (International Doctoral Fellowship awardee)
- Ghazal Ebrahimi: M.Sc. – August 19, 2022: Integrative analysis of short and long read single cell RNA-seq to understand transcriptomic landscape changes in non-obstructive Azoospermia. (Dr. Faraz Hach) (NSERC-CREATE awardee)
- Ogan Mancarci: M.Sc. – June 27, 2022: Identification cell type marker genes of the brain and their use in estimation of cell type proportions. (Dr. Paul Pavlidis)
- Almas Khan: M.Sc. – June 10, 2022: Investigating and correcting for the technical, clinical and biological contributors to variation in placental methylation (Dr.s Elodie Portales-Casamar and Wendy Robinson) (NSERC-CREATE awardee)
- Janet Li: M.Sc. – May 31, 2022: Genomic and transcriptomic signatures of virulence and UV resistance in Beauveria bassiana (Dr. Inanc Birol)
- Saelin Bjornson: M.Sc. – May 27, 2022: Elastic net regression for the selection of orthogroups predictive of trophic mechanisms in diverse eukaryotes (Dr. Patrick Keeling)(NSERC-CREATE awardee)
- Rachel Miller: M.Sc.- April 22, 2022: Phylodynamic quantification of pathogen transmission dynamics (Dr. Jeff Joy) (NSERC-CREATE awardee)
- Arjun Baghela: Ph.D.- April 6, 2022: Identifying predictive gene expression signatures of sepsis severity (Dr. Robert Hancock and Dr. Gabriela Cohen Freue)
- Connor Morgan-Lang: Ph.D. March 31 2022: Linking function and phlogeny in microbiomes using TreeSAPP (Dr. Steven Hallam)(NSERC-CREATE awardee)
- Kristina Gagalova: Ph.D. – March 9, 2022: Annotation of complex genomes for comparative genomics. (Dr. Inanc Birol)
- Christine Yang: M.Sc. – February 28, 2022: Genome-wide association study of Pseudomonas aeruginosa in swarming and biofilm formation. (Dr. Robert Hancock)
- Rashedul Islam: Ph.D. – December 6, 2021: Epigenetic dysregulation in lymphoid leukemias (Dr. Martin Hirst)
- Eric Lee: M.Sc. – December 1, 2021: SpatialSort: Characterizing cellular heterogeneity in the tumour microenvironment with spatially aware clustering (Dr. Andrew Roth
- Diana Lin: M.Sc. – September 29, 2021: High throughput in silico discovery of anti-microbial peptides in amphibian and insect transcriptomes. (Dr. Inanc Birol)
- Will (Yue) Huang: M.Sc. – September 27, 2021: Single-cell analytics for phospho flow cytometry reveals dynamic interactions between molecular pathways (Drs. Paul Pavlidis and Kurt Haas)
- Qinkai Wu: M.Sc. – September 23, 2021: Cellular composition variation drives coexpression-based gene function prediction (Dr. Paul Pavlidis)(NSERC-CREATE awardee)
- Nicole Zhang: M.Sc. – August 6, 2021: Cell-conditional generative adversarial network. (Drs. Wyeth Wasserman and Sara Mostafavi)(NSERC-CREATE awardee)
- Kristina Wright: M.Sc. – August 5, 2021: Seasonal and sex-dependent gene expression in Emu (Dromaius novaehollandiae) fat tissue. (Dr. Ianc Birol)
- Jordan Sicherman: M.Sc. – August 5, 2021: Large-scale mining of differential expression data for insight into gene function. (Dr. Paul Pavlidis)(NSERC-CREATE awardee)
- Denitsa Vasileva: M.Sc.- August 3, 2021: Assessing accuracy and utility of epigenetic age prediction algorithm in a large-scale targeted methylation sequencing study. (Dr. Denise Daley)
- Alice Kaye: Ph.D. – July 27, 2021: Approaches to genome analysis through the application of graph theory. (Dr. Wyeth Wasserman)
- 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)
- 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)
- (NSERC-CREATE awardee)
- 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)