Current Students

Our Students

2024 Cohorts:

  • Moritz Aubermann – M.Sc. student with Paul Pavlidis
  • Runtong Cai – M. Sc. student with Jiarui Ding
  • Hastisadat Jalalichimeh – M.Sc. student with Faraz Hach
  • Tina Hsu – Ph.D. student with Yongjin Park- 4YF awardee
  • Maple Lei – M.Sc. student with Steven Jones
  • Samuel Leung – M.Sc. student with Amrit Singh and Ying Wang
  • Junyu Li – M.Sc. student with Steven Jones
  • Tony Liang – M.Sc. student with Amrit Singh
  • Behnam Maneshgar – Ph.D. student with Ali Bashashati- 4YF awardee
  • Anika Nag – M.Sc. student with Steven Hallam
  • Elahe Ranjbari – M.Sc. student with Ali Bashashati
  • Ivana Sanchez – M.Sc. student with Inanc Birol
  • Rachel Schwartz – M.Sc. student with Paul Pavlidis
  • Ivan Semenov – Ph.D. student with Art Cherkasov- 4YF awardee
  • Selina Sun – M. Sc. student with Adi Steif and Pamela Hoodless
  • Jeffrey Tang – M.Sc. student with Amrit Singh
  • Yiyang Wang – M.Sc. student with Ali Bashashati
  • Cindy Zhang – Ph.D. student with Wyeth Wasserman
  • Erica Zeng – M.Sc. student with Todd Woodward
  • Emily Zhang – M.Sc. student with Inanc Birol
  • Kevin  Zhang- M.Sc. student with Paul Pavlidis

 

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
  • 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:

  • Madison Chapel – M.Sc. student with Carl de Boer
  • Nairuz Elazzabi – Ph.D. student with Paul Pavlidis – 4YF awardee
  • Emilia Hurtado – Ph.D.. student with Andrew Roth
  •  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- 4YF awardee
  • Brooks Perkins-Jechow – M.Sc. student with Jorge Gsponer
  • Sishir Subedi- Ph.D. student with Yongjin Park- 4YF awardee
  • Cindy Shi – M.Sc. student with Ali Bashashati
  • Yolanda Yang -Ph.D. student with Raymond Ng
  • Michael Yoon – Ph.D. student with Christopher Carlsten and Amrit Singh
  • Yuetong Yu – Ph.D. student with Roger Tam and Sophia Frangou
  • Johnathan Wong – Ph.D. student with Inanc Birol

2021 Cohorts:

  • Rituparna Banerjee – Ph.D. student with Matt Pennell and Daniel Coombs
  • Dolly Dodina – Ph.D. student with Aline Talhouk
  • Anne-Sophie Fratzscher – Ph.D. with Andrew Roth
  • Hans Ghezzi – Ph.D. student with Carolina Tropini – 4YF awardee
  • Parham Kazemi – Ph.D. student with Inanc Birol
  • Erick Navarro Delgado – Ph.D. student with Keegan Korthauer and Michael Kobor- 4YF awardee
  • Alireza Omidi – Ph.D. student with Joerg Gsponer
  • Mohit Pandey – Ph.D. student with Art Cherkasov
  • Neera Patadia – Ph.D. student with Paul Pavlidis
  • Denitsa Vasileva – Ph.D. student with Denise Daley-4YF awardee
  • Jiaying You – Ph.D. student with Art Cherkasov

2020 Cohorts:

  • Alejandro Aguirre- Ph.D. student with Wyeth Wasserman
  • Sarah Dada – Ph.D. student with Steven Jones
  • Madeline Iseminger – M.Sc. student with Will Hsiao – CREATE Scholarship awardee
  • Faeze Keshavarz- Rahaghi – Ph.D. student with Steven Jones – 4YF awardee
  • Cara Reisle – Ph.D. student with Steven Jones
  • Jenkin Tsui – Ph.D. student with Andrew Roth – 4YF awardee

2019 Cohorts:

  • 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
  • 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:

  • Enes Ergin – Ph.D. student with Philipp Lange – 4YF awardee

2016 Cohorts:

  • Dalia Alghamdi – Ph.D. student with William Hsiao
  • Albina Rahim – Ph.D. student with Ryan Brinkman – CREATE Scholarship awardee

Alumni:

  • Derek Tam: M.Sc. – October 17, 2024: Tracking clonal structure from leukemia diagnosis to relapse using mitochondrial variants (Drs. Aly Karsan and Andrew Roth)
  • Yukai Wang:  M.Sc. – October 9, 2024: Development of computational solutions to process and interpret mass spectrometry-based metabolomics data (Dr.  Tao Huan)
  • Alexander Adrian-Hamazaki: M.Sc. – September 25, 2024: Investigations into the contributions of co-expression to computational gene function prediction (Dr. Paul Pavlidis)
  • Abhijit Chinchani: Ph.D. – August 28, 2024: Supervised Dimensionality Reduction Applications in Identifying Cognitive Correlates of Psychiatric Symptoms and Extracting Low-Dimensional EEG Signals to Study the Effects of tACS (Dr. Todd Woodward)
  • Mariia Radaeva:  Ph.D. – August 23, 2024: Development of Small Molecule Inhibitors of Protein Nucleic Acid Interactions with the Use of Computer-Aided Drug Discovery Tools (Dr. Artem Cherkasov) (NSERC-CREATE awardee)
  • Alexander Morin: Ph.D. – August 13, 2024: Meta-analysis strategies for inference of transcriptional regulatory targets. (Dr. Paul Pavlidis) (NSERC-CREATE awardee)
  • Angela McLaughlin: Ph.D. – August 12, 2024: Phylogenetic Inference of Transmission and Migration Dynamics of Severe Acute Respiratory Syndrome Coronavirus 2 and
    Human Immunodeficiency Virus 1 in Canada (Dr. Jeffrey Joy) (NSERC-CREATE awardee)
  • Eric Chu: Ph.D. – July 31, 2024: Preservation and Detection of Dynamic Transcriptional Regulatory Signals in Gene Co-Expression Analysis (Dr. Paul Pavlidis) (NSERC-CREATE awardee)
  • Saber Hafezqorani: Ph.D.- June 27, 2024: Machine learning in transcriptome analysis using long RNA sequencing data (Dr. Inanc Birol)
  • Karanvir Singh: M.Sc. – June 25, 2024: Genetics of anorexia nervosa and associations with childhood psychopathology. (Dr. Jessica Dennis)
  • Andrew Galbraith: M.Sc. – June 12, 2024: Characterization of Allele-Specific 5-Methylcytosine and Quantification of 8-Oxoguanine using Nanopore Sequencing (Dr. Steven Jones)
  • Sebastiano Montante: Ph.D. – April 9, 2024: Machine learning algorithms in flow cytometry data analysis (Dr. Ryan Brinkman) (NSERC-CREATE awardee)
  • Yerin Kim: M.Sc. – April 5, 2024: Long-read based native RNA sequencing of human transcriptomes reveals complexity of mRNA modification and crosstalk between RNA regulatory features (Drs. Steven Jones and Ly Vu)
  • Patricia Ye: M.Sc. – April 4, 2024: Learning cellular hierarchies trhough structured topic modelling (Drs. Yongjin Park and Ramon Klein Geltink)
  • Hossein Ebrahimikondori: M.Sc. – April 4, 2024: Structure-aware deep learning model for peptide toxicity prediction (Dr. Inanc Birol)
  • Luka Culibrk: Ph.D. – March 28, 2024: Methods and analysis of somatic copy number variation in advanced human cancers (Dr. Steven Jones)
  • Chenkai Li: Ph.D. – January 31, 2024: Machine learning for antimicrobial peptide discovery and design (Dr. Inanc Birol)
  • Jeremy Fan: M.Sc. -January 22, 2024: Structural variant calling and resolution from long reads sequencing data (Dr. Steven Jones)(NSERC-CREATE awardee)
  • Marco Tello Palencia: M.Sc. – December 21, 2023: Application of supervised learning models to compare epigenetic predictors of gene expression across healthy breast cell types (Dr. Keegan Korthauaer) (NSERC-CREATE awardee)
  • Olivia Garland: M.Sc. – December 15, 2023: Development and application of machine-learning based tools for the discovery of small molecule inhibitors of SARS-CoV-2 Papain-like Protease (PLpro). (Dr. Artem Cherkaov)
  • Helena de Castro Alvarenga: M.Sc. – December 13, 2023: Simulation-based inference of micelle geometry from 2D cryo-EM images of membrane proteins. (Dr. Khanh Dao Duc)
  • Irem Yucel: M.Sc. – December 8, 2023:Improving white spruce genome annotation and generation of chromosome-scale epigenetic map (Dr. Inanc Birol)
  • Theodora Lo: M.Sc. – November 23, 2023: The Genome of Black Spruce: Annotation & Analyses (Dr. Inanc Birol) (NSERC-CREATE awardee)
  • Armaghan Sarvar: M.Sc. – November 17, 2023: Genome mis-assembly detection using Stash: a data structure based on stochastic tile hashing (Dr. Inanc Birol)
  • Lingyu Yang: M.Sc. – October 31, 2023: Streamlined high throughput assembly and standardization of reference-grade animal mitochondrial genomes (Dr. Inanc Birol)
  • Ali Mirza: Ph.D. – October 26, 2023: The gut microbiome in pediatric onset multiple sclerosis (Drs. Helen Tremlett and William Hsiao)
  • Sebastian Hunter Moreno: M.Sc. – October 19, 2023: Microbiome associations with the gut-brain axis: gut-microbiota changes in major depressive disorder and infant neurodevelopment (Drs. Brett Finlay and Sara Mostafavi)
  • Xiao Yu Zhang: M.Sc.: October 6, 2023: Identification of pharmacogenetic variants influencing the likelihood of developing treatment-induced mucositis in pediatric oncology patients using pathway analysis. (Drs. Wyeth Wasserman and Catrina Loucks)
  • Giuliano Netto Flores Cruz: M.Sc. – August 25, 2023: Evaluating omics-based tests with Bayesian decision curve analysis (Dr. Keegan Korthauer)
  • Bradley Jones: Ph.D. – August 21, 2023: Phylogenetic methods for estimating human immunodeficiency virus 1 proviral integration dates (Dr. Jeff Joy)
  • William Casazza: Ph.D. – August 3, 2023: Finding the Functional Consequences of Genetic Risk Loci on Gene Expression and DNA Methylation by Integrating Contextual Information (Drs. Jessica Dennis and Sara Mostafavi) (NSERC-CREATE awardee)
  • Angus Campbell: M.Sc. – August 3, 2023: Investigations into Transcriptomic Engram Neurons (Dr. Paul Pavlidis)
  • Jorge Holguin Cruz: M.Sc.- August 1, 2023: Widespread alteration of protein autoinhibition in human cancers (Dr. Joerg Gsponer)(NSERC-CREATE awardee)
  • Charlotte Barclay: M.Sc. – July 18, 2023- 3D genomic insights of an early branching metazoan: a chromosome-scale assembly of mnemiopsis leidyi and differential expression in early development (Dr. Steven Plotkin).
  • Shanwei Tong: M.Sc. – May 11. 2023- Whole genome sequencing of Camplobacter in chicken abattoir to characterize the population dynamics (Dr. William Hsiao)
  • 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)