PROGRAM

2013 Winter School Program

Venue:
Auditorium, Queensland Bioscience Precinct (Building #80)
The University of Queensland, St Lucia Campus

Monday 1 July 2013
NEXT GENERATION SEQUENCING & BIOINFORMATICS
09:00 Welcome and introduction
Dr Nicholas Hamilton
Institute for Molecular Bioscience, The University of Queensland

09:05 Next-generation sequencing: an overview of technologies and applications
Mr Matthew Tinning
Australian Genome Research Facility Ltd
Biography     Abstract     Full presentation

09:45 Short read mapping
Mr John Pearson
Queensland Centre for Medical Genomics
Institute for Molecular Bioscience, The University of Queensland
Biography     Abstract

10:30 Morning tea

11:00 Error/bias profiles and quality control in next-generation sequencing
Dr David Humphreys
Victor Chang Cardiac Research Institute
St Vincents Hospital
Biography     Abstract     Full presentation

11:45 De novo genome assembly
Dr Torsten Seemann
Victorian Bioinformatics Consortium
Monash University
Biography     Abstract     Full presentation

12:30 Lunch

13:30 Introduction to RNA-seq
Mr David Wood
Queensland Centre for Medical Genomics
Institute for Molecular Bioscience, The University of Queensland
Biography     Abstract     Full presentation

14:00 Differential expression analysis of RNA-seq read counts
Prof. Gordon Smyth
Walter and Eliza Hall Institute of Medical Research
Biography     Abstract     Full presentation

14:30 De novo transcriptome assembly
Dr Nicole Cloonan
Genomic Biology Laboratory
Queensland Institute of Medical Research
Biography     Abstract     Full presentation

15:00 Afternoon tea

15:30 Mutation detection in massively parallel sequencing data
Dr Ann-Marie Patch
Queensland Centre for Medical Genomics
Institute for Molecular Bioscience, The University of Queensland
Biography     Abstract

16:00 Metagenomics 101
Dr Michael Immelfort
Advanced Water Management Centre, The University of Queensland
Biography     Abstract     Full presentation

16:30 Improving genome assemblies, assessing structural variation and trait association
using chromosome genomics and Illumina skim genotyping by sequencing

Prof. David Edwards
School of Agriculture and Food Sciences, The University of Queensland
Biography     Abstract     Full presentation

17:30 Welcoming BBQ

Tuesday 2 July 2013
NEXT GENERATION SEQUENCING & BIOINFORMATICS (Morning)

09:00 NGS experimental design and statistical power
Dr Stephen Rudd
QFAB Bioinformatics
Biography     Abstract

09:30 Genomics infrastructure for NGS
Dr Mark Crowe
QFAB Bioinformatics
Biography     Abstract     Full presentation

10:00 Integrating multiple omics data sets
A/Prof. Christine Wells
Australian Institute for Bioengineering & Nanotechnology
The University of Queensland
Biography     Abstract

10:30 Morning tea

NGS, MUTATIONS, DISEASE AND ALGORITHMS
11:00  Moving genomics from bench to bedside: application of high throughput
sequencing to paediatric patients with unresolved diagnoses

Dr Ryan Taft
Institute for Molecular Bioscience, The University of Queensland
Biography     Abstract

11:45 Characterising genome regions from public data: a case study of Numts
Dr Paul Horton
AIST Computational Biology Research Center, Tokyo
Biography     Abstract     Full presentation

12:30 Lunch

13:30 Recent advances in understanding of protein sub-cellular localisation signals
Dr Paul Horton
AIST Computational Biology Research Center, Tokyo
Biography     Abstract     Full presentation

14:15 Visualising genome sequence data
Dr Scott Beatson
School of Chemistry & Molecular Biosciences, The University of Queensland
Biography     Abstract     Full presentation

15:00 Afternoon tea

15:30 Population genetics and genomics using next-generation sequencing data
Dr Lachlan Coin
Institute for Molecular Bioscience, The University of Queensland
Biography     Abstract

16:15 NGS sequence analysis for regulation and epigenomics
A/Prof. Timothy Bailey
Institute for Molecular Bioscience, The University of Queensland
Biography     Abstract     Full presentation

Wednesday 3 July 2013
NGS, MUTATIONS, DISEASE AND ALGORITHMS
(Morning)

09:00 Omics in translational biomarker research
Dr Michelle Hill
The University of Queensland Diamantina Institute
Biography     Abstract     Full presentation

09:30 Using genetic and transcriptomics data to understand disease aetiology
Dr Joseph Powell
The University of Queensland Diamantina Institute
Biography     Abstract     Full presentation

10:00 Systems biology for personalised medicine?
Prof. Marc Wilkins
School of Biotechnology and Biomolecular Sciences
University of New South Wales
Biography     Abstract     Full presentation

11:00 Morning tea

11:30 The next-generation of sequencing: what’s next?
Dr Jason Steen
Australian Centre for Ecogenomics, The University of Queensland
Biography     Abstract

12:00 Panel discussion

*** FREE WEDNESDAY AFTERNOON ***

~~~~~~~~~~
You may want to attend the 2013 Skerman Lecture.

Professor Norman Pace from the University of Colorado will present a special seminar on Thursday (4 July 2013) afternoon of the Winter School. He will also present a 2013 Skerman Lecture “Into the natural microbial world: metagenomics and the tree of life” on Wednesday 3 July 2013 at 4:00 p.m., followed by drinks, in Room 360, Physiology Building (63). Winter School registrants are invited and will be receiving an email invitation to attend, RSVP before Monday 1 July 2013.

The Skerman Lecture recognises Dr Vic Skerman, Foundation Professor of Microbiology at The University of Queensland and a major contributor to the development of Microbiology at The University of Queensland and within Australia. The Skerman Lecture, delivered by an outstanding microbiologist, is a major event on the calendar of Microbiology events at The University of Queensland.

For more details, please visit the website or call (07) 3365 4043. To request a meeting with Professor Pace, please contact Caroline Moniz (email: c.moniz@uq.edu.au).
~~~~~~~~~~

Thursday 4 July 2013
ECOLOGIES & POPULATIONS

09:00 Optimisation tools for biodiversity conservation
Prof. Hugh Possingham
ARC Centre of Excellence for Environmental Decisions (CEED)
The University of Queensland
Biography     Abstract     MP4 Video

09:45 The ecological and economic implications of larval dispersal in reef fish communities
Dr Michael Bode
School of Botany
University of Melbourne
Biography     Abstract     Full presentation     MP4 Video

10:30 Morning tea

11:00 Disease transmission in spatially structured animal populations and
the implications for disease control

Dr Hawthorne Beyer
Environmental Decisions Group
The University of Queensland
Biography     Abstract     MP4 Video

11:45 Management of invasive species, pests and diseases: making
decisions in an uncertain and complex world

A/Prof. Yvonne Buckley
School of Biological Sciences
The University of Queensland
Biography     Abstract     Full presentation     MP4 Video

12:30 Lunch

13:30 Building and using detection models for ecological surveys
Dr Cindy Hauser
Quantitative & Applied Ecology Group
University of Melbourne
Biography     Abstract     Full presentation     MP4 Video

14:15 Using Markov decision processes to find optimal ways to manage ecological systems
Dr Tracy Rout
School of Botany
University of Melbourne
Biography     Abstract     MP4 Video

15:00 Species distribution modelling
Dr Jane Elith
School of Botany
University of Melbourne
Biography     Abstract     Full presentation

15:45 Afternoon tea

Special Seminar
16:15 Interpreting the molecular tree of life – What happened in early evolution?
Dr Norman Pace
Distinguished Professor of Molecular, Cellular and Developmental Biology
University of Colorado-Boulder, USA
Biography     Abstract     Full presentation     MP4 Video

Friday 5 July 2013
SYSTEMS & SYNTHETIC BIOLOGY

09:00 Introduction to integrative systems approaches to modelling biological processes
Prof. John Quackenbush
Computational Biology and Bioinformatics
Dana-Farber Cancer Institute & Harvard School of Public Health, USA
Biography     Abstract     MP4 Video

09:50 Essential graph theory for biologists
Dr Nicholas Hamilton
Institute for Molecular Bioscience, The University of Queensland
Biography     Abstract     Full presentation     MP4 Video

10:15 Morning tea

10:45 Overview of network methods in systems biology
Dr Daniel Hurley
Faculty of Medical and Health Sciences, University of Auckland
Biography     Abstract     MP4 Video

IMB Friday Seminar
12:00 The road to genomic medicine is paved with data and information
Prof. John Quackenbush
Computational Biology and Bioinformatics
Dana-Farber Cancer Institute & Harvard School of Public Health, USA
Biography     Abstract     MP4 Video

13:00 Lunch

14:00 Introduction to pathway analysis
Dr Melissa Davis
Institute for Molecular Bioscience, The University of Queensland
Biography     Abstract     MP4 Video

14:30 Rational design of genetic circuits for use in synthetic biology
Dr Keith Shearwin
School of Molecular and Biomedical Science, The University of Adelaide
Biography     Abstract     Full presentation     MP4 Video

15:30 Open forum/questions
Introduced & moderated by Prof. Mark Ragan
Institute for Molecular Bioscience, The University of Queensland

16:30 Student travel award presentation & close Winter School