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May 16 -19, 2016 | Full Agenda

FULL AGENDA


Conference is being held at Victoria, College, University of Toronto.

Go directly to: [Tuesday - May 17] [Wednesday - May 18] [Thursday - May 19]

*As of May 16, 2016. Subject to change without notice.

MONDAY – DAY 1 – May 16, 2016
START TIME END TIME SESSION TYPE
9:00 am 6:00 pm Registration
Location: 1st Floor Foyer
10:30 am 12:30 pm Workshop 1
Microbiome Analysis: 16S & Metagenomics

Morgan Langille, Rob Beiko, & Mike Hall

Location: VC 213
Workshop 2
Jupyter Notebooks for Performing & Sharing Bioinformatics Analyses

Jonathan Dursi

Location: VC 101
Workshop 3
Quick Guide to Best Practices in Software Carpentry


Marcelo Ponce & Erik Spence

Location: VC 215
12:30 pm 1:30 pm Lunch on own
or Career Session in VC 115
1:30 pm 3:30 pm Workshop 1 - continued
Microbiome Analysis: 16S & Metagenomics

Morgan Langille, Rob Beiko, & Mike Hall

Location: VC 213
Workshop 3 - continued
Quick Guide to Best Practices in Software Carpentry


Marcelo Ponce & Erik Spence

Location: VC 215
Workshop 4
Network visualization and analysis with Cytoscape


Ruth Isserlin, Jeff Liu, Veronique Voisin (Bader lab)

Location: VC 101
3:30 pm 4:00 pm Coffee break
Location: 1st Floor Foyer
4:00 pm 5:00 pm Keynote 1

STEVEN JONES
Genomic analysis of cancer genomes to aid in clinical decision making

Location: Frye Auditorium
5:00 pm 6:30 pm Research Session 1

Location:
Frye Auditorium
Research Session 2

Location: VC 213
5:00 pm 5:30 pm TOPIC LEADER:
Brendan Frey
Precision Medicine

Location:
Frye Auditorium
TOPIC LEADER:
Sheelagh Carpendale
Information Visualization and Visual Analysis


Location: VC 213
5:30 pm 5:45 pm Jüri Reimand
Network-driven discovery and interpretation of cancer driver mutations

Location:
Frye Auditorium
 
5:30 pm 5:50 pm   Paper:
Alex Lu and
Alan Moses

An unsupervised kNN Method to systematically detect changes in protein localization in high-throughput microscopy images

Location: VC 213
5:45 pm 6:00 pm Peter Rogan, Yanxin Li, Ruth Wilkins, Farrah Flegal and Joan Knoll
Radiation Dose Estimation by Automated Cytogenetic Biodosimetry

Location:
Frye Auditorium
 
5:50 pm 6:05 pm   Yannan Fan, Paula Ribeiro, Sarah Kimmins and Jianguo Xia
miRNet - dissecting miRNA-target interactions and functional associations through network-based visual analysis

Location: VC 213
6:00 pm 6:15 pm Shraddha Pai, Shirley Hui, Ruth Isserlin, Hussam Kaka and Gary Bader
Patient similarity networks as a framework for genetic case-control prediction in autism spectrum disorders

Location:
Frye Auditorium
 
6:05 pm 6:20 pm   Achal Dhariwal and Jeff Xia
Statistical, Visual and Functional Analysis of 16S rRNA Marker Gene Data

Location: VC 213
6:15 pm 6:30 pm Eric Minwei Liu, Alexander Martinez Fundichely, Priyanka Dhingra, Andrea Sboner and Ekta Khurana
Computational methods to identify cancer-driver single nucleotide variants and large rearrangements in non-coding regions

Location:
Frye Auditorium
 
6:20 pm 6:25 pm   Flash Talk:
Houxiang Zhu, Lauren Misel, Mitchell Graham and Chun Liang

CT-Finder: A Web Service for CRISPR Optimal Target Prediction and Visualization

Location: VC 213
6:30 pm 7:00 pm Free Time / Dinner on Own
7:00 pm 9:00 pm Welcome! Networking Reception
at Duke of York Pub

Location: 39 Prince Arthur Ave.
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TUESDAY – DAY 2 – May 17, 2016
START TIME END TIME SESSION TYPE
8:30 am 6:00 pm Registration
Location: 1st Floor Foyer
9:00 am 10:00 am Keynote 2

JENNIFER GARDY
Infectious disease genomics: bioinformatics challenges

Location: Frye Auditorium
10:00 am 10:30 am Coffee break
Location: 1st Floor Foyer
10:30 am 11:20 pm Research Session 3

Location:
Frye Auditorium
Research Session 4

Location: VC 213
10:30 am 11:00 am TOPIC LEADER:
Alexey Nesvizhskii

Informatics of Mass Spectrometry/ Community Computing


Location:
Frye Auditorium
TOPIC LEADER:
Matt Weirauch

Regulatory networks


Location: VC 213
11:00 am 11:20 am Paper:
Beichuan Deng, Hengguang Li, Xiang Zhang and Seongho Kim

Global Peak Alignment for Comprehensive Two-Dimensional Gas Chromatography Mass Spectrometry Using Point Matching Algorithms

Location:
Frye Auditorium
Paper:
Jingting Xu, Hong Hu and Yang Dai

An unlabeled-negative learning framework for human enhancer prediction based on low-methylation regions

Location: VC 213
11:20 am 11:35 am Anne-Christin Hauschild, Jörg Ingo Baumbach and Jan Baumbach
Non-invasive Precision Medicine - Statistical learning of exhaled biomarker profiles

Location:
Frye Auditorium
 
11:20 am 11:40 am   Paper:
Sneha Nishtala, Yaseswini Neelamraju and Sarath Chandra Janga

Dissecting the expression relationships between RNA-binding proteins and their cognate targets in eukaryotic post-transcriptional regulatory networks

Location: VC 213
11:35 am 11:55 am Tech Talk:
Mark Leggott, Scott Henwood

Harnessing the Value of Data and Software to Accelerate Discovery

Location:
Frye Auditorium
 
11:40 am 11:55 am   Kyle Smith, Vinod Yadav and Subhajyoti De
Detecting a novel signature of non-coding, regulatory alterations in cancer genomes

Location: VC 213
11:55 am 12:00 pm    
11:55 am 12:10 pm   Chaitanya Rastogi, Gabriella Martini, H. Tomas Rube and Harmen Bussemaker
A Versatile Framework for Learning Feature-Based Protein-DNA Recognition Models Directly from SELEX Data

Location: VC 213
12:00 pm 12:20 pm Tech Talk:
Greg Newby,
Compute Canada
National Advanced Research Computing Platform and Services Dedicated to Canadian Researchers

Location:
Frye Auditorium
 
12:10 pm 12:15 pm   Flash Talk:
Coby Viner, James Johnson, Nicolas Walker, Hui Shi, Marcela Sjoberg, David J. Adams, Anne C. Ferguson-Smith, Timothy L. Bailey and Michael M. Hoffman

Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet

Location: VC 213
12:20 pm 12:25 pm Flash Talk:
Alexander Ropelewski, Ricardo Gonzalez Mendez, Jimmy Torres, Hugh Nicholas and Pallavi Ishwad

Building and Sustaining Bioinformatics Community Diversity

Location:
Frye Auditorium
 
12:25 pm 2:00 pm Poster Session A with lunch
Location: Alumni Hall
2:00 pm 3:00 pm Keynote 3

ELIZABETH EDWARDS
Metagenomics of Microbial Dechlorinating Consortia

Location: Frye Auditorium
3:00 pm 3:30 pm Coffee break
Location: 1st Floor Foyer
3:30 pm 5:00 pm Research Session 5

Location:
Frye Auditorium
Research Session 6

Location: VC 213
3:30 pm 4:00 pm TOPIC LEADER:
Dannie Durand

Protein domains and evolution


Location: Frye Auditorium
TOPIC LEADER:
James Wasmuth

Infectious disease


Location:
VC 213
4:00 pm 4:15 pm David Curran, John Gilleard and James Wasmuth
Using phylogenetic instability to identify members of large gene families under adaptive evolution

Location:
Frye Auditorium
Javi Zhang, Asis Khan, Andrea Kennard, Michael E. Grigg and John Parkinson
PopNet: Revealing the Impact of Recombination on Population Structure

Location: VC 213
4:15 pm 4:30 pm Charlotte Darby, Maureen Stolzer and Dannie Durand
Xenolog Classification: Steps toward a Xenolog Conjecture

Location:
Frye Auditorium
Gaston Mazandu, Kayleigh Rutherford, Elsa-Gayle Zekeng, Emile Chimusa and Nicola Mulder
Modeling drug repositioning by leveraging drug-target-disease association datasets: A case study of Ebola virus disease

Location: VC 213
4:30 pm 4:45 pm Shobhit Jain and Gary Bader
Predicting physiologically relevant SH3 domain mediated protein-protein interactions in human

Location:
Frye Auditorium
Alexandre Drouin, Sébastien Giguère, Maxime Déraspe, Mario Marchand, Jacques Corbeil and Franois Laviolette
Set Covering Machines and Reference-Free Genome Comparisons Uncover Predictive Biomarkers of Antibiotic Resistance

Location: VC 213
4:45 pm 4:50 pm Flash Talk:
James Morton, Stefan Freed, Md Nafiz Hamid, Shaun Lee and Iddo Friedberg

Mining for new antimicrobial agents: predicting bacteriocin gene blocks

Location:
Frye Auditorium
Flash Talk:
Pingchuan Li, Sylvie Cloutier and Frank You

RGAugury: A pipeline for genome-wide prediction of resistance gene analogs (RGAs) in plants

Location: VC 213
4:50 pm 4:55 pm Flash Talk:
Yanbin Yin and Alex Ekstrom

ORFanFinder: automated identification of taxonomically restricted orphan genes

Location:
Frye Auditorium
Flash Talk:
Rajeev Azad, Mehul Jani and Kalai Mathee

Identification of novel genomic islands in Liverpool epidemic strain of Pseudomonas aeruginosa using segmentation and clustering

Location: VC 213
4:55 pm 5:30 pm Free Time / Dinner on Own
5:30 pm 7:00 pm Discussion Forum for Canadian Investigators

Location:  Room 115
5:30 pm 9:30 pm Workshop 5
Hands-on workshop on Machine Learning with Applications to Bioinformatics

Ivan Kryukov & Jeff Wintersinger

Location: VC 215
5:30 pm 7:00 pm Workshop 6
Exploring and Refining Core Competencies for Bioinformatics
(ISCB Curriculum Task Force
)

Lonnie Welch, Michelle Brazas, & Russell Schwart

Location: VC 213
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WEDNESDAY – DAY 3 – May 18, 2016
START TIME END TIME SESSION TYPE
8:30 am 6:00 pm Registration
Location: 1st Floor Foyer
9:00 am 10:00 am Keynote 4

MATHIEU BLANCHETTE
Know thy ancestors to know thyself: Improving our understanding of the human genome using paleogenomics

Location: Frye Auditorium
10:00 am 10:30 am Coffee break
Location: 1st Floor Foyer
10:30 am 12:20 pm Research Session 7

Location:
Frye Auditorium
Research Session 8

Location: VC 213
10:30 am 11:00 am TOPIC LEADER:
Guillaume Bourque
Genome analysis

Location:
Frye Auditorium
TOPIC LEADER:
Amy Caudy

Metabolomics and Chemoinformatics

Location: VC 213
11:00 am 11:20 am Paper:
Zachary Stephens, Matthew Hudson, Liudmila Mainzer, Morgan Taschuk, Matthew Weber and Ravishankar Iyer

Simulating Next-Generation Sequencing Datasets From Empirical Mutation and Sequencing Models

Location:
Frye Auditorium
Paper:
Miroslava Cuperlovic-Culf, Nandhakishore Rajagopalan, Dan Tulpan and Michele Loewen

Metabolomics and Cheminformatics analysis guiding the Discovery of Antifungal Metabolites for Crop Protection

Location: VC 213
11:20 am 11:40 am Paper:
Daniel Sanchez-Taltavull, Parameswaran Ramachandran, Nelson Lau and Theodore Perkins

Bayesian Correlation Analysis for Sequence Count Data

Location:
Frye Auditorium
 
11:20 am 11:35 am   Yin Lu, Yi-Cheng Tu and Feng Cheng
A novel algorithm for analyzing drug-drug interactions from MEDLINE literature

Location: VC 213
11:35 am 11:50 am   Zhaleh Safikhani, Benjamin Haibe-Kains, Kelsie Thu, Petr Smirinov, David Cescon and Mathieu Lupien
Meta-analysis of large pharmacogenomics studies to develop isoform-based biomarkers predictive of response to targeted therapies

Location: VC 213
11:40 am 11:55 am Greg Gloor, Jean Megan Macklaim and Jia Wu
CoDaSeq: compositional data analysis for high throughput sequencing data

Location:
Frye Auditorium
 
11:50 am 12:05 pm   Seyed Ali Madani Tonekaboni, Zhaleh Safikhani and Benjamin Haibe-Kains
In-silico pipeline for tissue-specific drug combination discovery

Location: VC 213
11:55 am 12:10 pm Davide Chicco and Michael M. Hoffman
Distal chromatin loop prediction with deep siamese neural networks

Location:
Frye Auditorium
 
12:05 pm 12:15 pm   Jiun Yen, Glenda Gillaspy and Ryan Senger
A genome-scale algorithmic approach for metabolic engineering of plants
12:10 pm 12:15 pm Flash Talk:
Musaddeque Ahmed, Haiyang Guo and He Housheng

Integrative analysis for identification and functional prediction of long non-coding RNAs in cancer

Location:
Frye Auditorium
 
12:15 pm 12:20 pm Flash Talk:
Armin Rouhi, Janneke Wit and James Wasmuth
Investigating the usefulness of long-read sequencing technologies on the study of large eukaryotic gene families

Location:
Frye Auditorium
 
12:30 pm 2:00 pm Poster Session B with lunch
Location: Alumni Hall
2:00 pm 3:00 pm Keynote 5

CHRISTINA LESLIE
Decoding gene regulatory programs in cellular differentiation

Location: Frye Auditorium
3:00 pm 3:30 pm Coffee break
Location: 1st Floor Foyer
3:30 pm 5:30 pm Workshop 7
Next generation sequencing


Adam Rosebrock

>>Sign up here<<

Location: 115
3:30 pm 5:30 pm Research Session 9

Location:
Frye Auditorium
Research Session 10

Location: VC 213
3:30 pm 4:00 pm TOPIC LEADER:
Sushmita Roy

Biological networks

Location:
Frye Auditorium
TOPIC LEADER:
Rob Beiko

Metagenomics


Location: VC 213
4:00 pm 4:20 pm Paper:
Matthew O'Meara, Sara Ballouz, Brian Shoichet and Jesse Gillis
Ligand similarity complements sequence, physical interaction, and co-expression for gene function prediction

Location:
Frye Auditorium
Paper:
Ruth G. Wong, Jia R. Wu and Gregory B. Gloor
Expanding the UniFrac toolbox

Location: VC 213

4:20 pm 4:35 pm Bundalovic-Torma and John Parkinson
Biological Interaction Networks in Bacteria - Generation and Evolutionary Insights

Location:
Frye Auditorium
 
4:20 pm 4:40 pm   Paper:
Ahmed Metwally, Yang Dai, Patricia Finn and David Perkins
WEVOTE: Weighted Voting Taxonomic Identification Method of Microbial Sequences

Location: VC 213
4:35 pm 4:50 pm Li Zhu, Ying Ding, Cho-Yi Chen, Zhiguang Huo, Sunghwan Kim, Steffi Oesterreich and George Tseng
MetaDCN: meta-analysis framework for differential coexpression network detection with an application in breast cancer

Location:
Frye Auditorium
 
4:40 pm 4:55 pm   Frederic Raymond, Maxime Déraspe, Sébastien Boisvert, Alexander Culley, Paul H. Roy, François Laviolette and Jacques Corbeil
Ray Surveyor: phenetic comparison of genomes and its application in microbial evolution

Location: VC 213
4:50 pm 5:05 pm Lu Cheng and Mu Zhu
Compositional Epistasis Detection Using A Few Prototype Disease Models

Location:
Frye Auditorium
 
4:55 pm 5:10 pm   Jean Megan Macklaim, Amy McMillan, Mark Sumarah, Jonathan Swann, Gregor Reid and Greg Gloor
Insights into the metatranscriptome and metabolome of the vaginal microbiome

Location: VC 213
5:05 pm 5:20 pm Robin Haw
Reactome Revolutions - Pathways and Networks

Location:
Frye Auditorium
 
5:10 pm 5:25 pm   Michael Hall, Jonathan Perrie and Robert Beiko
Time-series clustering enables the exploration of temporal patterns in marker gene data

Location: VC 213
5:20 pm 5:25 pm Flash Talk:
Bahram Samanfar, Andrew Schoenrock, Frank Dehne, Ashkan Golshani, Elroy Cober, Martin Charette and Steve Molnar
PIPE (Protein-protein Interaction Prediction Engine): A computational approach for comprehensive soybean functional genomics

Location:
Frye Auditorium
 
5:30 pm 6:00 pm Free Time
6:00 pm 9:00 pm Banquet with Keynote 6

ALED EDWARDS

Open science: From computational biology to the real world

Location: Burwash Hall
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THURSDAY – DAY 4 – May 19, 2016
START TIME END TIME SESSION TYPE
8:30 am 3:00 pm Registration
Location: 1st Floor Foyer
9:00 am 10:00 am Keynote 7

JANE CARLTON
Harnessing genomics to study the global public health burden of malaria

Location: Frye Auditorium
10:00 am 10:30 am Coffee break
Location: 1st Floor Foyer
10:30 pm 12:00 pm Workshop 8
Computational approaches to synthetic biology


Cathy Su, Esther Jang, Alexander Sullivan (iGEM Toronto)

>>Sign up here<<

Location: VC 115
10:30 am 12:00 pm Research Session 11

Location:
Frye Auditorium
Research Session 12

Location: VC 213
10:30 am 11:00 am TOPIC LEADER:
Carlos Camacho

Structural biology

Location:
Frye Auditorium
TOPIC LEADER:
Igor Jurisica

Integrative data analysis

Location: VC 213
11:00 am 11:20 am Flash Talk:
Eric Stahlberg, Carl McCabe and George Zaki

High-Performance and Exascale Computing Frontiers in Cancer Applications

Location:
Frye Auditorium
Cancelled
Paper:

Sumaiya Iqbal and Md Tamjidul Hoque
Estimation of Free Energy Contribution of Protein Residues as Feature for Structure Prediction from Sequence

Location:
Frye Auditorium
11:00 am 11:15 am   Fazle Faisal, Yuriy Hulovatyy, Huili Chen and Tijana Milenkovic
Dynamic and integrative biological network research of aging

Location: VC 213
11:15 am 11:30 am   Hamed Najafabadi, Pouria Jandaghi, Shraddha Solanki, Andreas Papadakis, Maryam Safisamghabadi, Cristina Storoz, Mark Lathrop, Sidong Huang, Simon Tanguay, Fadi Brimo and Yasser Riazalhosseini
A regulatory model for discovering aberrant post-transcriptional programs in cancer

Location: VC 213
11:20 am 11:35 am Devashish Das, Pravin Kumar, Naveen Kulkarni and Anurag Kumar
A novel atomistic motional correlation method combined with thermodynamics to delineate the intricate mechanism of substrate specific catalysis: enzyme engineering perspective

Location:
Frye Auditorium
 
11:30 am 11:45 am

Heather Wheeler, Kaanan Shah, Jonathon Brenner and Hae Kyung Im
Survey of the Heritability and Sparsity of Gene Expression Traits Across Human Tissues

Location: VC 213
11:35 am 11:50 am Frazier Baker and Alexey Porollo
Prediction of Metal Binding Sites in Proteins Using Coevolution Data

Location:
Frye Auditorium
 
11:45 am 12:00 pm   Christian Wiwie, Jan Baumbach and Richard Röttger
On the clustering of biomedical datasets - a data-driven perspective

Location: VC 213
11:50 am 11:55 am Flash Talk:
Nehme El-Hachem, Deena Gendoo, Benjamin Haibe-Kains
Decoding compound mechanism of action using integrative pharmacogenomics

Location:
Frye Auditorium
 
12:00 pm 1:00 pm Lunch on own
1:00 pm 2:00 pm Research Session 13

Location:
Frye Auditorium
Research Session 14

Location: VC 213
1:00 pm 1:30 pm TOPIC LEADER:
Mads Kaern
Dynamic systems modeling


Location:
Frye Auditorium
TOPIC LEADER:
Belinda Chang
Phylogenetics


Location: VC 213
1:30 pm 1:50 pm Paper:
Joachim von Wulffen, Oliver Sawodny and Ronny Feuer
Balancing mRNA and Protein Levels in a Demand-Directed Dynamic Flux Balance Analysis Describes Effects of the Transition of an Anaerobic Escherichia coli Culture to Aerobic Conditions

Location:
Frye Auditorium
 
1:30 pm 1:45 pm   Ivan Kryukov, Bianca de Sanctis and A.P. Jason de Koning
Efficient techniques for direct analysis of discrete-time population genetic models

Location: VC 213
1:45 pm 2:00 pm   Maureen Stolzer and Dannie Durand
How plastic are multidomain proteins? Quantifying domain co-evolution in primate genomes

Location: VC 213
2:00 pm 3:00 pm Keynote 8

TIMOTHY HUGHES

Decoding Gene Regulation

Location: Frye Auditorium
3:00 pm 3:15 pm Closing Ceremonies
Location: Frye Auditorium
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