2010 Winter School Program.pdf
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ARC Centre of Excellence in Bioinformatics
Institute for Molecular Bioscience
Queensland Cuber Infrastructure Foundation
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EMBL Australia
BPA
EMBL_Aust
Program
Download program (available soon)
Monday 2 July 2012
NEXT GENERATION SEQUENCING & BIOINFORMATICS
8:15 a.m. - 9:00 a.m. Registration
9:00 a.m. - 9:05 a.m. Welcome & introduction
Dr Nicholas Hamilton
Institute for Molecular Bioscience
The University of Queensland
9:05 a.m. - 9:45 a.m. Next-generation sequencing: an overview of technologies and applications
Mr Matthew Tinning
Next-Generation Sequencing Manager
Australian Genome Research Facility Ltd
9:45 a.m. - 10:30 a.m. Assembling next generation data
Dr Torsten Seemann
Victorian Bioinformatics Consortium
Monash University
10:30 a.m. - 11:00 a.m. Morning tea
11:00 a.m. - 11:45 a.m. Short-read mapping
Mr John Pearson
Queensland Centre for Medical Genomics
Institute for Molecular Bioscience, The Unviersity of Queensland
11:45 a.m. - 12:30 p.m. Mutation detection in massively parallel sequencing data
Dr Ann-Marie Patch
Queensland Centre for Medical Genomics
Institute for Molecular Bioscience, The University of Queensland
12:30 p.m. - 1:30 p.m. Lunch
1:30 p.m. - 2:00 p.m. Transcriptomics 101
Dr Nicole Cloonan
Queensland Centre for Medical Genomics
Institute for Molecular Bioscience, The University of Queensland
2:00 p.m. - 2:45 p.m. RNA-seq analysis pipelines
Dr Alicia Oshlack
Murdoch Childrens Research Institute, Melbourne
2:45 p.m. - 3:15 p.m. Afternoon tea
3:15 p.m. - 4:00 p.m. Differential expresion analysis of RNA-seq read counts
Professor Gordon Smyth
Bioinformatics Division
Walter and Eliza Hall Institute of Medical Research
4:00 p.m. - 4:45 p.m. Metagenomics - characterising the composition and function of natural microbial communities
Dr Lutz Krause
Queensland Institute of Medical Research
The University of Queensland
5:00 p.m. till late Welcoming barbeque
Sponored by SGI
Tuesday 3 July 2012
NEXT GENERATION SEQUENCING & BIOINFORMATICS
9:00 a.m. - 9:45 a.m. ChiP-seq and epigenetics
Dr Alicia Oshlack
Murdoch Childrens Research Institute, Melbourne
9:45 a.m. - 10:15 a.m. Infrastructure for genomics: workflows and visualisation
A/Professor Andrew Lonie
Life Sciences Computation Centre, VLSCI
The University of Melbourne
and
Dr Michael Pheasant
Genome Research Computing
The University of Queensland
10:15 a.m. - 10:45 a.m. Morning tea
10:45 a.m. 11:15 a.m. The future of genome sequencing technology
Mr David Miller
Queensland Centre for Medical Genomics
Institute for Molecular Bioscience, The University of Queensland
11:15 a.m. - 12:15 p.m. Panel discussion
12:15 p.m. - 1:30 p.m. Lunch
12:30 p.m. - 1:30 p.m. Workshop - Introduction to the genomics virtual laboratory
A/Professor Andrew Lonie & Dr Michael Pheasant
3.141 Multi-media room, QBP
NEXT GENERATION SEQUENCE ANALYSIS
1:30 p.m. - 2:00 p.m. NGS sequence analysis 101
Dr Timothy Bailey
Institute for Molecular Bioscience, The University of Queensland
2:00 p.m. - 2:45 p.m. Word-based approaches to discover transcription factor binding motifs in
full-size ChIP-seq datasets
Professor Jacques van-Helden
Lab. Technological Advances for Genomics and Clinics
Université d'Aix-Marseille, France
2:45 p.m. - 3:15 p.m. Afternoon tea
3:15 p.m. - 4:00 p.m. Understanding genetic regulation in the era of massively parallel
sequening: how many sites should a transcription factor bind?
Professor Jacques van-Helden
Lab. Technological Advances for Genomics and Clinics
Université d'Aix-Marseille, France
4:00 p.m. - 4:45 p.m. Understanding transcription with NGS - a biologist's perspective
Dr Michael Tallack
Mater Medical Research Institute, South Brisbane
Wednesday 4 July 2012
NEXT GENERATION SEQUENCE ANALYSIS
9:00 a.m. - 9:45 a.m. Machine learning in anger
Dr Stefan Maetschke
Institute for Molecular Bioscience, The University of Queensland
9:45 a.m. - 10:15 a.m. To trim or not to trim? A closer look at next-gen sequencing data and errors
Dr Michael Imelfort
Advanced Water Management Centre, The University of Queensland
10:15 a.m. - 11:00 a.m. Morning tea
11:00 a.m. - 11:45 a.m. ARS-seq: high-resolution mapping and mutational scanning of autonomously
replicating sequences
Dr Uri Keich
School of Mathematics and Statistics
The University of Sydney
11:45 a.m. - 12:30 p.m. Probablistic data integration: putting sequence in context
Dr Mikael Bodén
School of Chemistry & Molecular Biosciences, The University of Queensland
** FREE WEDNESDAY AFTERNOON **
Thursday 5 July 2012
SYSTEMS BIOLOGY
9:00 a.m. - 10:00 a.m. Introduction to systems biology
Professor Eberhard Voit
David D. Flanagan Chair
Georgia Research Alliance Eminent Scholar in Systems Biology
Georgia Institute of Technology, Georgia, USA
10:00 a.m. - 10:30 a.m. Morning Tea
10:30 a.m. - 11:00 a.m. Essential graph theory for biologists
Dr Nicholas Hamilton
Institute for Molecular Bioscience, The University of Queensland
11:00 a.m. - 12:00 p.m. Overview of network methods in systems biology
Dr Daniel Hurley
Research Fellow, Faculty of Medical and Health Sciences
The University of Auckland, NZ
12:00 p.m. - 1:00 p.m. Lunch
1:00 p.m. - 2:00 p.m. Pathway analysis
Professor Eberhard Voit
David D. Flanagan Chair
Georgia Research Alliance Eminent Scholar in Systems Biology
Georgia Institute of Technology, Georgia, USA
2:00 p.m. - 3:00 p.m. Constraint-based reconstruction and analysis of metabolic and regulatory networks
Professor Lars Nielsen
Australian Institute for Bioengineering and Nanotechnology
The University of Queensland
3:00 p.m. - 3:30 p.m. Afternoon tea
3:30 p.m. - 4:15 p.m. An introduction to the use of ontology in computational and molecular biology
Dr Melissa Davis
Institute for Molecular Bioscience, The University of Queensland
4:15 p.m. - 5:00 p.m. Panel discussion
Friday 6 Juy 2012
ECOLOGY AND POPULATIONS
9:00 a.m. - 9:15 a.m. Introduction
9:15 a.m. - 9:45 a.m. Biophysical modeling and network analysis for exploring spatial patterns in marine
population connectivity
Dr Eric Treml
Department of Zoology
University of Melbourne
9:45 a.m. - 10:15 a.m. Modelling the ecological implications of complex dispersal networks
Dr Michael Bode
School of Botany
University of Melbourne
10:15 a.m. - 10:45 a.m. Managing food webs using Bayesian networks
Dr Eve McDonald-Madden
ARC Centre of Excellence for Environmental Decisions
The University of Queensland
10:45 a.m. - 11:15 a.m. Morning tea
11:15 a.m. - 11:45 a.m. Modelling the extinction risk of genetically structured turtle populations
Dr Peter Baxter
Centre for Applications in Natural Resource Mathematics
School of Mathematics and Physics
The University of Queensland
12:00 p.m. - 1:00 p.m. How can mathematics help save the planet?
Professor Hugh Possingham
ARC Centre of Excellence for Environmental Decisions
The University of Queensland
1:00 p.m. - 2:00 p.m. Lunch
2:00 p.m. - 2:30 p.m. Searching for needles in haystacks
A/Professor Michael McCarthy
ARC Centre of Excellence for Environmental Decisions
The University of Melbourne
2:30 p.m. - 3:00 p.m. How artificial intelligence techniques can help protect diversity: the
use of Markov decision processes
Dr Iadine Chadès
CSIRO Ecosystems Sciences, Queensland
3:00 p.m. - 3:30 p.m. Afternoon tea
3:30 p.m. - 4:15 p.m Panel discussion
4:15 p.m. - 4:30 p.m. Recognition of student travel awardees & close of 2012 Winter School
