Schedule

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

Meetings for 2020-2021 are held virtually via Zoom at 4:00 pm and are FREE and OPEN to all.

VIRTUAL Meeting Format: https://oicr-ca.zoom.us/j/98801025345?pwd=UHJSNjFvVVpnTWtLRDFlYzByT1RKQT09

4:00pm – 4:15pm Trainee Presentation
4:15pm – 5:00pm Speaker Presentation
5:00pm – 6:00pm TorBUG Virtual Social

2020-2021 (Virtual) Season

Next Talk:September 30, 2020

** Zoom Webinar for September 30 due to COVID-19 situation **

You are invited to a Zoom webinar for TorBUG. Please click the link below to join the webinar: https://oicr-ca.zoom.us/j/98801025345?pwd=UHJSNjFvVVpnTWtLRDFlYzByT1RKQT09

4:00-5:00 - Main Event on Zoom
Trainee Speaker: Gurnit Atwal, PhD Candidate, Morris & Bader labs, University of Toronto
Title: Automatic tumour typing based on patterns of somatic passenger mutations

Guest Speaker: Casey Greene, Associate Professor, Systems Pharmacology and Translational Therapeutics, University of Pennsylvania
Title: The bounty of the commons: machine learning from everybody else's data


Upcoming Speakers 2020-2021

  • September 30, 2020 – Casey Greene, Associate Professor, Systems Pharmacology and Translational Therapeutics, University of Pennsylvania
  • October 28, 2020 – Melissa Wilson, Assistant Professor, Center for Evolution and Medicine, Arizona State University
  • November 25, 2020 – Obi Griffith, Assistant Director, McDonnell Genome Institute, Washington University School of Medicine
  • January 27, 2021 – Olivier Gevaerts, Assistant Professor, Biomedical Data Science, Stanford University
  • February 24, 2021 – Touati Benoukraf, Canada Research Chair, Bioinformatics for Personalized Medicine, Memorial University
  • March 31, 2021 – Jeffrey Leek, Professor, Bloomberg School of Public Health, John Hopkins University
  • April 28, 2021 – Cheryl Waldner, Professor, Western College of Veterinary Medicine, University of Saskatchewan

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 openlabnotebooks.org

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


January 29, 2020

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


February 26, 2020

Trainee Speaker: Joanna Pineda, MSc Candidate, Jared Simpson lab, Computer Science, University of Toronto
Title: Exploring a haplotype-based approach to calling somatic mutations in linked-read sequencing data

Guest Speaker: Rob Patro, Professor, Assistant Professor Computer Science, University of Maryland
Title: Addressing uncertainty in bulk and single-cell RNA-seq quantification


March 25, 2020

Trainee Speaker: Elyssa Bader, PhD Candidate, Philip Awadalla lab, Dept. Molecular Genetics, University of Toronto
Title: A population cohort approach to characterize healthy aging of blood

Guest Speaker: Shiva Amiri, Professor, Director Research Infrastructure, 23andMe
Title: The power of large-scale genomics+ data in healthcare and drug discovery


April 29, 2020

Trainee Speaker: Cameron Nugent, Postdoctoral Fellow, Adamowicz Lab, Department of Integrative Biology, University of Guelph
Title: Improving the accuracy of biodiversity analyses from high-throughput sequence data with the R package debar

Trainee Speaker: Alexander Sullivan, MSc Candidate, Provart Lab, Department of Cells & Systems Biology, University of Toronto
Title: GAIA: An “eEcosystem” of aggregated information for plant biology