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