files
2010 Winter School Program.pdf
030712Bailey
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, click here.
Venue: Auditorium, Queensland Bioscience Precinct (Building #80), The University of Queensland, St Lucia campus.
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
Abstract Full Presentation
09:45 a.m. - 10:30 a.m. Short-read mapping
Mr John Pearson
Queensland Centre for Medical Genomics
Institute for Molecular Bioscience, The University of Queensland
Abstract Full Presentation
10:30 a.m. - 11:00 a.m. Morning tea
11:00 a.m. - 11:45 a.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
Abstract Full Presentation
11:45 a.m. - 12:30 p.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
Abstract Full Presentation
12:30 p.m. - 1:30 p.m. Lunch
1:30 a.m. - 2:15 p.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
Abstract Full Presentation
2:15 p.m. - 2:45 p.m. Transcriptomics 101
Dr Nicole Cloonan
Queensland Centre for Medical Genomics
Institute for Molecular Bioscience, The University of Queensland
Abstract Full Presentation
2:45 p.m. - 3:15 p.m. Afternoon tea
3:15 p.m. - 4:00 p.m. Differential expression analysis of RNA-seq read counts
Professor Gordon Smyth
Bioinformatics Division
Walter and Eliza Hall Institute of Medical Research
Abstract Full Presentation
4:00 p.m. - 4:45 p.m. RNA-seq analysis pipelines
Dr Alicia Oshlack
Murdoch Childrens Research Institute, Melbourne
Abstract Full Presentation
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. Metagenomics - characterising the composition and function of
natural microbial communities
Dr Lutz Krause
Queensland Institute of Medical Research
The University of Queensland
Abstract Full Presentation
9:45 a.m. - 10:30 a.m. Assembling next-generation data
Dr Torsten Seemann
Victorian Bioinformatics Consortium
Monash University
Abstract Full Presentation
10:30 a.m. - 11:00 a.m. Morning tea
11:00 a.m. - 11:30 a.m. ChIP-seq and epigenetics
Dr Alicia Oshlack
Murdoch Childrens Research Institute, Melbourne
Abstract Full Presentation
11:30 a.m. - 12:00 p.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
Abstract Full Presentation
12:00 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 for regulation and epigenomics
Dr Timothy Bailey
Institute for Molecular Bioscience, The University of Queensland
Abstract Full Presentation MP4 Video
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
Abstract Full Presentation MP4 Video
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 sequencing: how many sites should a transcription
factor bind?
Professor Jacques van Helden
Lab. Technological Advances for Genomics and Clinics
Université d'Aix-Marseille, France
Abstract Full Presentation MP4 Video
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
Abstract Full Presentation MP4 Video
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
Abstract Full Presentation MP4 Video
9:45 a.m. - 10:30 a.m. Probablistic data integration: putting sequence in context
Dr Mikael Bodén
School of Chemistry & Molecular Biosciences, The University of Queensland
Abstract Full Presentation MP4 Video
10:30 a.m. - 11:00 a.m. Morning tea
11:00 a.m. - 11:30 a.m. The future of genome sequencing technology
Mr David Miller
Queensland Centre for Medical Genomics
Institute for Molecular Bioscience, The University of Queensland
Abstract Full Presentation MP4 Video
11:130a.m. - 12:30 p.m. Panel discussion MP4 Video
** 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
Abstract Full Presentation MP4 Video
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
Abstract Full Presentation MP4 Video
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
Abstract Full Presentation MP4 Video
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
Abstract Full Presentation MP4 Video
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
Abstract Full Presentation MP4 Video
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
Abstract Full Presentation MP4 Video
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
Abstract Full Presentation
9:45 a.m. - 10:15 a.m. Modelling the ecological implications of complex dispersal networks
Dr Michael Bode
ARC Centre of Excellence for Environmental Decisions
School of Botany
University of Melbourne
Abstract Full Presentation
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
Abstract Full Presentation
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
Abstract Full Presentation
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
School of Mathematics and Physics
The University of Queensland
Abstract Full Presentation
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
Abstract Full Presentation
2:30 p.m. - 3:00 p.m. How artificial intelligence techniques can help protect Biodiversity:
the use of Markov decision processes
Dr Iadine Chadès
CSIRO Ecosystems Sciences, Queensland
Abstract Full Presentation
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
