Welcome to the ARC Centre of Excellence in Bioinformatics

Winter School in Mathematical and Computational Biology

2010 WINTER SCHOOL IN MATHEMATICAL AND COMPUTATIONAL BIOLOGY
Organised and hosted by the ARC Centre of Excellence in Bioinformatics
Queensland Bioscience Precinct, University of Queensland
5-9 July 2010

For speakers' presentations please go to the Winter School 2010 website.

Day 1  – Monday 5 July
NEXT-GENERATION SEQUENCING AND BIOINFORMATICS
Organised in collaboration with Queensland Facility for Advanced Bioinformatics

What are genomes, why sequence them, and why is genome sequencing a mathematically and computationally interesting problem? (Introduction)
Professor Mark Ragan, ARC Centre of Excellence in Bioinformatics and IMB-UQ

Technologies: classical and next gen approaches
Dr Mark Crowe, Bioplatforms Australia - Australian Genome Research Facility

Applications of next-generation sequencing technologies
Dr Annette McGrath, Queensland Facility for Advanced Bioinformatics

Genome assembly strategies - yesterday, today and tomorrow
Dr Torsten Seemann, Victorian Bioinformatics Consortium, Monash University

Short-read mapping
Dr John Pearson, Queensland Centre for Medical Genomics, IMB-UQ

Analysing genomic aberrations using next-generation sequencing
Dr Nic Waddell, Queensland Centre for Medical Genomics, IMB-UQ

Transcriptome analysis and discovery using RNA-seq: the good, the bad and the challenging
Dr Karin Kassahn, Queensland Centre for Medical Genomics, IMB-UQ

Day 2 – Tuesday 6 July
NEXT-GENERATION SEQUENCING AND BIOINFORMATICS (continued)
Organised in collaboration with Queensland Facility for Advanced Bioinformatics

Defining the MYB transcriptional network using ChIP-seq
Dr Evgeny Glazov, Diamantina Institute, University of Queensland

Analysing RNA-seq: from reads to results
Dr Alicia Oshlack, Walter & Eliza Hall Institute of Medical Research

Differential expression analysis for RNA-seq experiments
Mr Davis McCarthy Walter & Eliza Hall Institute of Medical Research

Coming full-circle: a journey from metagenomics back to single-cell sequencing
Ms Lauren Bragg, Advanced Water Management Centre, University of Queensland, and CSIRO Mathematics, Informatics and Statistics

The future of next-gen sequencing
Dr Brooke Gardiner, Queensland Centre for Medical Genomics, IMB-UQ

Day 3 – Wednesday 7 July
MOLECULAR SYSTEMS BIOLOGY

Introduction to systems biology
Professor John Quackenbush, Dana-Farber Cancer Institute and Harvard School of Public Health

COBRA: metabolic and signalling networks
I- Network reconstruction, topology and feasible solution space
II- Constraint-based reconstruction and analysis of networks
Professor Lars Nielsen, Australian Institute for Bioengineering & Nanotechnology, UQ

Algorithms and computation for large systems I: algorithms and implementations
Professor Michael Langston, University of Tennessee, and Oak Ridge National Laboratory

An introduction to and demonstration of the Cytoscape application
Dr Melissa Davis, Queensland Facility for Advanced Bioinformatics

Day 4 – Thursday 8 July
MOLECULAR SYSTEMS BIOLOGY (continued)

Statistical modeling of dynamic gene networks in cancer
I- Models and algorithms for estimating dynamic gene networks
II- Can dynamic gene networks predict novel therapeutic targets and clinical outcomes?
A/Professor Seiya Imoto, Human Genome Centre, Institute of Medical Science, University of Tokyo

Algorithms and computation for large systems II: applications and analysis
Professor Michael Langston, University of Tennessee, and Oak Ridge National Laboratory

A model-based approach to personalised medicine
A/Professor Gilles Clermont MD, McGowan Institute for Regenerative Medicine, University of Pittsburgh

Day 5 – Friday 9 July
MOLECULAR SYSTEMS BIOLOGY (continued)

Decomposition of gene expression state space trajectories to model cell fate transitions
Dr Jessica Mar, Dana-Farber Cancer Institute, and Harvard School of Public Health

Using expression and expressivity to build canalised gene regulatory networks
Dr Christine Wells, National Centre for Adult Stem Cell Research, and The Eskitis Institute for Cell and Molecular Therapies, Griffith University

Information integration approaches to network modeling
Professor John Quackenbush, Dana-Farber Cancer Institute, and Harvard School of Public Health

Dynamic protein-protein interaction networks in yeast
Professor Marc Wilkins, University of New South Wales