TorBUG meets on the last Wednesday of every month from September through April. Research presentations by bioinformatics leaders, students and industry representatives are followed by networking over pizza and refreshments.

Meetings are held in the Red Room at the Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street at 4:00 pm and are free and open to all.

Meeting Format:

4:00pm – 4:15pm Trainee Presentation (Red Room, Terrence Donnelly Centre)
4:15pm – 5:00pm Speaker Presentation (Red Room, Terrence Donnelly Centre)
5:00pm – 7:00pm Pizza and Beverage Session with Speaker and Bioinformatics community (Red Room, Terrence Donnelly Centre)

2019-2020 Season

Next Talk:January 29, 2020

4:00-5:00 - Main Event in CCBR Red Room
Trainee Speaker: Lauren Erdman, PhD Candidate, Anna Goldenberg lab, University of Toronto
Title: Predicting surgical intervention for hydronephrosis from ultrasound alone: a proof of concept

Guest Speaker: Anne Martel, Professor, Medical Biophysics, University of Toronto, and Senior Scientist, Sunnybrook Research Institute
Title: Deep learning in digital pathology

Upcoming Speakers 2019-2020

  • September 25, 2019 – Mohammed AlQuraishi, Systems Biology, Harvard Medical School
  • October 30, 2019 – John Quackenbush, Chair Department of Biostatistics, Harvard T.H. Chan School of Public Health
  • November 27, 2019 – Christie Bahlai, Assistant Professor, Department of Biological Sciences, Kent State University
  • January 29, 2020 – Anne Martel, Professor, Medical Biophysics, University of Toronto, and Senior Scientist, Sunnybrook Research Institute
  • February 26, 2020 – Rob Patro, Assistant Professor Computer Science, University of Maryland
  • March 25, 2020 – Shiva Amiri, Director Research Infrastructure, 23andMe
  • April 29, 2020 – Sarah Adamowicz, Associate Professor, Department of Integrative Biology, University of Guelph

Past Speakers

Watch our past presentations on YouTube

Wednesday September 24, 2012

Speaker: Lincoln Stein, Director of Informatics and Bio-computing at the Ontario Institute for Cancer Research.
YouTube Presentation: modENCODE: The Good, the Bad and the "Uggh"

Short Presentation: Marc Fiume, PhD Candidate in Computer Science, Brudno Lab, University of Toronto.
YouTube Presentation: Next-generation genome browsing

Wednesday October 31, 2012

Speaker: Brian O'Connor
YouTube Presentation: Hack a What? Doing bioinformatics the Hack-a-thon Way

Speaker: Robin Haw
YouTube Presentation: Google Summer of Code: Bringing Google to Bioinformatics

Short Presentation: Yue Dong
YouTube Presentation: My Experience in the Google world

Speaker: Jean Lozach, Senior Scientist at Illumina Bioinformatics.
YouTube Presentation: BASE Space: Open Tools in the Cloud

Wednesday November 28, 2012

Speaker: Lars Jorgensen, Director of Genome Informatics, Personalized Genomics & Innovative Medicine at Mount Sinai Hospital.
Title: Bioinformatics in a Clinical Setting

Short Presentation: Omar Wagih, Masters Student in Computer Science, Bader Lab, University of Toronto
Title: SGATools: tools for image analysis, normalization and scoring SGA screens

Wednesday January 30, 2013

Speaker: Michael Brudno, Director, Centre for Computational Medicine, Hospital for Sick Children & Associate Professor, University of Toronto.
Title: Analyzing and Visualizing High Throughput Sequencing Data

Short Presentation: Leopold Parts, Research Associate, Boone & Andrews Labs, University of Toronto
Title: How come I have my father's nose? Quantitative genetics of protein traits.

Wednesday February 27, 2013

Speaker: Fritz Roth, Senior Scientist, Samuel Lunenfeld Research Institute and Canada Research Chair in Integrative Biology.
Title: 1) Pointing to causal genes on a prix fixe GWAS menu, and 2) protein network mapping via wild sex and sequencing

Short Presentation: Juri Reimand, Postdoctoral Fellow in Bader Lab, University of Toronto
Title: Chasing cancer drivers in cell signalling networks

Wednesday March 27, 2013

Speaker: Sara Diamond, President and Vice-Chancellor, OCAD University.
Title: Information and Scientific Visualization: Experiments in Aesthetics, Meaning and Process

Short Presentation: Jamie Waese, PhD Candidate, Department of Cell & Systems Biology, University of Toronto
Title: Building Data Visualization Tools for Large Biological Data Sets

Wednesday April 24, 2013, 4:00pm

Speaker: Dr. Wyeth Wasserman, Professor of Medical Genetics, Senior Scientist and Co-Director at CMMT at the University of British Columbia.
Title: Discovery of Regulatory Variations in Whole Genome Sequences

Short Presentation: Dr. Nuno Barbosa-Morais, Senior Postdoctoral Fellow, University of Toronto
Title: Studying the evolution of tissue-specific alternative splicing using RNA-Seq data

Wednesday September 25, 2013

Speaker: Brian Shoichet, Professor at Leslie Dan Faculty of Pharmacy, University of Toronto.
Title: The Metabolic Code

Short Presentation: Maria Safi, PhD Candidate, University of Toronto
Title: Efficient a priori modeling of drug resistance: structural models

Wednesday October 30, 2013

Speaker: Paul Boutros, Principal Investigator, Informatics and Bio-computing, OICR.
YouTube Presentation: World War B: Making Benchmarking Exciting

Short Presentation: Carl de Boer, PhD Candidate, University of Toronto
YouTube Presentation: Poly-dA:dT tracts form a directional nucleosomal turnstile in vivo

November 27, 2013

Speaker: Michael Hoffman, Princess Margaret Cancer Centre
YouTube Presentation: Semi-automated annotation of the human genome using chromatin and RNA-seq data

Short Presentation: Sarah Gagliano, Joanne Knight lab at CAMH
YouTube Presentation: A method to incorporate hundreds of functional characteristics with association evidence to improve SNP prioritization

January 29, 2014

Guest Speaker: Jared Simpson, Ontario Institute for Cancer Research
YouTube Presentation: Designing scalable algorithms for sequence analysis

Short Presentation: Lee Zamparo, Zhang Lab at University of Toronto
YouTube Presentation: Dimensionality reduction for high-content screening data

February 26, 2014

Guest Speaker: Guillaume Bourque, McGill University and Genome Quebec Innovation Center
Title: Mapping the functional elements in the human genome

Short Presentation: Oren Kraus, Frey Lab at University of Toronto
YouTube Presentation: Outlier Detection for High-Content Cell Screening

March 26, 2014

Guest Speaker: Michael Lawrence, Genentech
Title:Scalable and Integrative Genomics with R/Bioconductor

Short Presentation: David Shih, Taylor Lab at Sick Kids
YouTube Presentation: Investigating the molecular subgroups of medulloblastoma: means, motive and opportunity

April 30, 2014

Guest Speaker: Titus Brown, Michigan State University
YouTube Presentation: Building khmer, a platform for research in scalable sequence analysis

Short Presentation: Julio Diaz Caballero, David Guttman's lab at University of Toronto
YouTube Presentation: Periodic Selection Drives Pseudomonas aeruginosa Diversity in the Cystic Fibrosis Lung

September 24, 2014

Guest Speaker: Sandrine Dudoit, University of California Berkeley
YouTube Presentation: Normalization and Differential Expression in RNA-Seq

Short Presentation: Joseph O'Neill, University of Guelph
YouTube Presentation: Multi-locus GWAS analysis/genomic selection as a "clique" problem solved through evolutionary computation

October 29, 2014

Guest Speaker: Dr. Heng Li, Broad Institute
Title: Experimenting FM-index for multiple human samples

Short Presentation: Ladislav Rampasek, University of Toronto
Title: Probabilistic Method for Detecting Copy Number Variation in a Fetal Genome Using Maternal Plasma Sequencing

November 26, 2014

Guest Speaker: Dr. Mads Kaern, University of Ottawa
Title: Evidence for non-genetic causes of eukaryotic drug resistance

Short Presentation: David Kim, Cowen Lab, University of Toronto
Title: Investigating the Fungal Microbiome of Cystic Fibrosis Patient Lungs

January 28, 2015

Guest Speaker: Dr. Anna Goldenberg, University of Toronto
Title: Patient network-based framework for data integration in complex human diseases

Short Presentation: Amit Deshwar, Morris Lab, University of Toronto
Title: Reconstructing the evolutionary history of tumours

February 25, 2015

Guest Speaker: Dr. Benjamin Haibe-Kains, Princess Margaret Bioinformatics and Computational Genomics Laboratory
Title: Biomarker Discovery Using In Vitro Drug Sensitivity: The Good, the Bad and the Ugly

Short Presentation: Sunny Yu Liu, Wrana Lab, University of Toronto
Title: Translational bioinformatics: the key to precision medicine

March 25, 2015

Guest Speaker: Dr. Nicholas Provart, University of Toronto
Title: Raising the BAR for Integrative Biological Data Visualization Tools for Hypothesis Generation in Research and Education

Short Presentation: Dr. Mohammed Uddin, Scherer Lab, TCAG
Title: Integrated Genomic Approach to Identify Genes Associated with Developmental Delay

April 29, 2015

Guest Speaker: Dr. Paul Flicek, EMBL-EBI
Title: Evolutionary re-wiring: understanding transcriptional regulation using comparative regulatory genomics

Short Presentation: Dr. Ivan Borozan, Ferretti Lab, OICR
Title: Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification

September 30, 2015

Guest Speaker: Dr. Jo Knight, Associate Professor, CAMH
Title: Fool's Gold? Identifying Genetic Variants that Play A Role in Complex Traits.

Short Presentation: Dr. Richard Jovelin (Awadalla Lab)
Title: Worming evolutionary changes out of nematode genomes

October 28, 2015

Guest Speaker: Dr. Alan Moses, Associate Professor, Cell & Systems Biology, University of Toronto
Title: Short linear motifs: a long, strange trip from bioinformatics to systems biology

Short Presentation: Shobhit Jain, Ph.D. student, Computer Science, University of Toronto
Title: Predicting high confidence PRM mediated PPIs in yeast

November 25, 2015

Short Presentation: Ontario Genomics
Title: Upcoming bioinformatics competitions

Guest Speaker: Dr. Alfonso Valencia, Director, Spanish National Bioinformatics Institute
Title: Initial Reconstruction of the Mouse Embryonic Stem Cell Epigenetic Network

January 27, 2016

Short Presentation: Coby Viner from Michael Hoffman's Lab
Title: Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet

Guest Speaker: Dr. Melissa Haendel, Associate Professor, Oregon Health and Science University
Title: The Monarch Initiative: An integrated genotype-phenotype platform for disease discovery

February, 2016

Short Presentation: Fan Yang, Graduate student, Roth Lab, University of Toronto
Title:Protein Domain-Level Landscape of Cancer-Type-Specific Somatic Mutations

Guest Speaker: Alex Bateman, Head of Protein Sequence Resources, EMBL-EBI
Title:Rfam and RNAcentral: Tools for understanding the RNA universe

March, 2016

Short Presentation: Deena Gendoo, Post-doctoral Fellow, Haibe-Kains Lab, PMCC
Title:Investigating Pharmacological Drug Classification Using Integrative Approaches

Guest Speaker: Joel Dudley, Director of Biomedical Informatics at Mount Sinai School of Medicine, Mt. Sinai, NY
Title:Raising the BAR for Integrative Biological Data Visualization Tools for Hypothesis Generation in Research and Education

April 27, 2016

Short Presentation: Julian Mazzitelli, 3rd yr undergraduate
Title: BioRender: An Interactive Cell for the Web

Guest Speaker: Dr. Gary Bader, Associate Professor, CCBR, University of Toronto
Title: Computational Approaches to Identify Functional Genetic Variants in Cancer

September 28, 2016

Short Presentation: Dr. Cristina Baciu, Post-doctoral Fellow, OICR
Title: PGMLab for Biomarker Discovery in Cancer

Guest Speaker: Dr. Joseph Ecker, Director, Genomic Analysis Laboratory, The Salk Institute
Title: Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain

October 26, 2016

Short Presentation: Albi Celaj, Graduate Student, Roth Lab, University of Toronto
Title: Using Engineered Populations to Study Complex Genetic Bases of ABC Transporter Mediated Drug Resistance in Yeast

Guest Speaker: Dr. Laura Hug, Assistant Professor of Biology, University of Waterloo
Title: Uncovering microbial diversity and function in the environment

November 30, 2017

Short Presentation: Jochen Weile, Graduate Student, Roth Lab, University of Toronto
Title: An Atlas of Functional Missense Variation in Human Disease Genes

Guest Speaker: Arfon Smith, Scientist at GitHub (moving to Space Telescope Science Institute)
Title: Academia's biggest blind spot

January 25, 2017

Short Presentation: Davide Chicco, Post-doctoral Fellow, Princess Margaret Cancer Centre
Title: Siamese neural network for prediction of long-range interactions in chromatin

Guest Speaker: Katie Pollard, Director and Senior Investigator, Gladstone Institutes
Title: Most transcription factors recognize DNA shape

February 22, 2017

Short Presentation: Brett Trost, Research Fellow, Scherer Lab
Title: Development and validation of a comprehensive workflow for identifying copy number variants using whole-genome sequencing data

Guest Speaker: Lisa Strug, Senior Scientist and Associate Director of the Centre for Applied Genomics at the Research Institute of the Hospital for Sick Children
Title: Integrating whole genome sequence across studies for analysis of genetic association

March 29, 2017

Short Presentation: Hassan Jaferi
Title: Bitnobi – Secure Sharing of Big Data

Guest Speaker: Anne-Claude Gingras, Principal Investigator, Lunenfeld-Tanenbaum Research Institute
Title: A proximity map of a human cell

April 26, 2017

Short Presentation: Wail Ba-alawi
Title: Exploiting Bimodality of Gene Expression for the Enhancement of Drug Sensitivity Prediction

Guest Speaker: Andrew McArthur, Associate Professor & Cisco Research Chair in Bioinformatics, McMaster University
Title: Bioinformatics of antimicrobial resistance in the age of molecular epidemiology

September 27, 2017

Trainee Speaker: Roozbeh Manshaei
Title: Exploring Structural Features of Biological Networks using Multi-Surface and Tangible Interactions

Guest Speaker: Ali Mazalek, Canada Research Chair Digital Media and Innovation, Ryerson University
Title: Grasping the Numerical World: Bringing Bioinformatics Out of the Box

October 25, 2017

Trainee Speaker: Brendan Innes, PhD Candidate, Bader Lab, University of Toronto
Title: Cell types in single-cell RNAseq

Guest Speaker: Jeff Wintersinger, PhD Candidate, Morris Lab, University of Toronto
Title: Correcting discordance between copy-calling methods in 2778 cancer genomes

Guest Speaker: Yulia Rubanova, PhD Candidate, Morris Lab, University of Toronto
Title: Tracking tumour evolution over time

November 29, 2017

Trainee Speaker: Mehran Karimzadeh, Graduate Student, Hoffman Lab, University of Toronto
Title: Virtual ChIP-seq: predicting transcription factor binding by learning from the transcriptome

Guest Speaker: Jason Williams, Assistant Director, CSHL DNA Learning Center
Title: The Bioinformatics Training Landscape

January 31, 2018

Trainee Speaker: Nil Sahin, Graduate Student, Brenda Andrews and Quaid Morris Labs, University of Toronto
Title: Machine learning and computer vision approaches for phenotypic profiling in yeast

Guest Speaker: Daniel Ashlock, Professor, Mathematics and Statistics, University of Guelph
Title: The Stability of Clustering Algorithms and Visualizing High-Dimensional Data

February 28, 2018

Trainee Speaker: Ali Madani Tonekaboni, Graduate student, Haibe-Kains and Lupien Labs, University of Toronto
Title: Clusters of cis-regulatory elements as epigenomic features predictive of drug response

Guest Speaker: Benjamin Haibe-Kains, Scientist, Princess Margaret Cancer Centre
Title: Integrative drug classification based on big pharmacogenomic data

March 28, 2018

Trainee Speaker: Renan Nascimento De Almeida, Graduate Student, Guttman Lab
Title: Identification of Pseudomonas syringae type III secreted effector sequences associated with adaptation to coffee plants

Guest Speaker: Morgan Langille, Canada Research Chair in Human Microbiomics, Dalhousie University
Title: Disease signatures of the human microbiome

April 25, 2018

Trainee Speaker: Petr Smirnov, Graduate Student, Haibe-Kains Lab
Title: Tools for Mining High Throughput PharmacoGenomic Datasets

Guest Speaker: Jeffrey Leek, Professor, Biostatistics and Oncology, John Hopkins Bloomberg School of Public Health
Title: Predicting and using metadata - the last mile of data integration

September 26, 2018

Trainee Speaker: Ibrahim El-Hamamy, Graduate Student, Stein Lab
Title: Tracing the cellular origins of brain tumors using single-cell RNA-seq

Guest Speaker: Juri Reimand, Principal Investigator, Ontario Institute for Cancer Research
Title: Discovery of cancer driver mutations in the non-coding genome

October 31, 2018

Trainee Speaker: Paul Krzyzanowski, OICR
Title: UMIs: Unique Molecular Identifiers and how they are applied to genomics today

Guest Speaker: Chia-Lin Wei, Director of Genome Technologies, Jackson Laboratory
Title: Exploring Genome Structures and Chromatin Organization by Long-read sequencing

November 28, 2018

Trainee Speaker: Alex Lu, PhD Student, Moses Lab, University of Toronto
Title: Learning unsupervised feature representations for single cell microscopy images with paired cell inpainting

Guest Speaker: Andrew Doxey, Assistant Professor and Director of Molecular Biology Core Facility, University of Waterloo
Title: AnnoTree: visualization and exploration of a functionally annotated microbial tree of life

January 30, 2019

Trainee Speaker: James St. Pierre, Master's student, Parkinson Lab, University of Toronto
Title: From relative abundances to absolute abundances: improving normalization in quantitative microbiome sequencing

Guest Speaker: Jennifer Gardy, Associate Professor, UBC School of Population and Public Health
Title: Ten Years and Two Thousand TB Genomes Later: Lessons Learned from Public Health Genomics & Bioinformatics

February 27, 2019

Trainee Speaker: Helen Zhu, Graduate student, Reimand Lab, University of Toronto
Title: Driver Discovery in Primary Localized Prostate Cancer

Guest Speaker: Jennifer Brooks, Assistant Professor in Epidemiology, Dalla Lana School of Public Health
Title: Linkage of whole genome sequencing with administrative health data for the study of autism spectrum disorder: Feasibility, opportunities and challenges

March 27, 2019

Trainee Speaker: Taraneh Zarin, PhD Candidate, Moses Lab, University of Toronto
Title: Proteome-wide signatures of function in highly diverged disordered regions

Guest Speaker: Julie Hussin, Assistant Professor, Department of Medicine, Université de Montréal
Title: Multi-omics data analysis in cardiovascular research

April 24, 2019

Trainee Speaker: Vinayak Bhandari, Graduate student, University of Toronto
Title: Up in the air: what does oxygen have to do with cancer?

Guest Speaker: Shannon McWeeney, Associate Director, Computational Biomedicine, OHSU Knight Cancer Institute
Title: A Path Forward: Moving from Data to Knowledge to Actionability to Support Precision Oncology

September 25, 2019

Trainee Speaker: Mandeep Mann, PhD Candidate, Schapira Lab, Structural Genomics Consortium
Title: Discovery of protein interaction inhibitors by virtual screening and reporting data at

Guest Speaker: Mohammed AlQuraishi, Systems Biology, Harvard Medical School
Title: Machine-learned molecular models for protein structure, networks, and design

October 30, 2019

Trainee Speaker: Hassan Mahmoud, Post-doctoral Fellow, Benjamin Haibe-Kains lab, UHN, University of Toronto
Title: Biomarker discovery using proteomics and transcription factors

Guest Speaker: John Quackenbush, Chair Department of Biostatistics, Harvard T.H. Chan School of Public Health
Title: Using networks to link genotype to phenotype

November 27, 2019

Trainee Speaker: Mickael Mendez, PhD Candidate, Michael Hoffman lab, Princess Margaret Cancer Centre
Title: Automated identification of cell-type-specific genes

Guest Speaker: Leon French, Independent Scientist, Krembil Centre for Neuroinformatics, CAMH
Title: Transcriptomic analysis of brain hypometabolism links hypotheses of Alzheimer’s disease causation