NEXT GENERATION SEQUENCING & BIOINFORMATICS

Program

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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