Program

Program in pdf available here.

Day 1  – Monday 5 July
NEXT-GENERATION SEQUENCING AND BIOINFORMATICS
Organised in collaboration with QFAB

08:50-09:00  WELCOME

9:00-9:15         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
                           Abstract     

9:15-10:15       Technologies: classical and next gen approaches
                           Dr Mark Crowe, Bioplatforms Australia - Australian Genome Research Facility
                           Abstract     Full presentation

10:15-10:45     Morning tea

10:45-11:45     Applications of next-generation sequencing technologies
                           Dr Annette McGrath, Queensland Facility for Advanced Bioinformatics
                           Abstract     Full presentation

11:45-12:45     Genome assembly strategies - yesterday, today and tomorrow
                           Dr Torsten Seemann, Victorian Bioinformatics Consortium, Monash University
                           Abstract     Full presentation

12:45-2:00        Lunch

2:00-3:00         Short-read mapping  
                            Dr John Pearson, Queensland Centre for Medical Genomics, IMB-UQ
                            Abstract     Full presentation

3:00-3:30          Afternoon tea

3:30-4:30          Analysing genomic aberrations using next-generation sequencing 
                           Dr Nic Waddell, Queensland Centre for Medical Genomics, IMB-UQ
                           Abstract     Full presentation

4:30-5:30          Transcriptome analysis and discovery using RNA-seq: the good, the bad and the challenging 
                            Dr Karin Kassahn, Queensland Centre for Medical Genomics, IMB-UQ
                           Abstract     Full presentation

5:30-7:30          Welcome BBQ

Day 2 – Tuesday 6 July
NEXT-GENERATION SEQUENCING AND BIOINFORMATICS (continued)
Organised in collaboration with QFAB

9:00-10:00        Defining the MYB transcriptional network using ChIP-seq
                            Dr Evgeny Glazov, Diamantina Institute, University of Queensland
                            Abstract     Full presentation

10:00-10:30      Morning tea

10:30-11:30      Analysing RNA-seq: from reads to results
                            Dr Alicia Oshlack, Walter & Eliza Hall Institute of Medical Research
                           Abstract     Full presentation

11:30-12:30     Differential expression analysis for RNA-seq experiments
                           Mr Davis McCarthy, Walter & Eliza Hall Institute of Medical Research
                           Abstract     Full presentation

12:30-2:00        Lunch

2:00-3:00          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
                            Abstract     Full presentation

3:00-3:30           Afternoon tea

3:30-4:30          The future of next-gen sequencing
                            Dr Brooke Gardiner, Queensland Centre for Medical Genomics, IMB-UQ
                            Abstract     Full presentation

Day 3 – Wednesday 7 July
MOLECULAR SYSTEMS BIOLOGY

9:00-10:15        Introduction to systems biology
                            Professor John Quackenbush, Dana-Farber Cancer Institute and Harvard School of Public Health
                            Abstract     Full presentation     Video

10:15-10:45      Morning tea

10:45-12:45     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
                           Abstract     Full presentation

12:45-2:00        Lunch

2:00-3:00          Algorithms and computation for large systems I: algorithms and implementations
                            Professor Michael Langston, University of Tennessee, and Oak Ridge National Laboratory
                            Abstract     Full presentation    Video

3:00-3:30          Afternoon tea

3:30-4:30          An introduction to and demonstration of the Cytoscape application
                            Dr Melissa Davis, Queensland Facility for Advanced Bioinformatics
                            Abstract     Full presentation

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

9:00-10:15        Statistical modeling of dynamic gene networks in cancer
                            I- Models and algorithms for estimating dynamic gene networks
                            A/Professor Seiya Imoto, Human Genome Centre, Institute of Medical Science, University of Tokyo
                            Abstract     Full presentation    Video

10:15-10:45      Morning tea

10:45-11:30     Statistical modeling of dynamic gene networks in cancer
                            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
                            Video

11:30-12:30     Algorithms and computation for large systems II: applications and analysis
                            Professor Michael Langston, University of Tennessee, and Oak Ridge National Laboratory
                            Abstract     Full presentation    Video

12:30-1:45        Lunch

1:45-3:00         A model-based approach to personalised medicine 
                           A/Professor Gilles Clermont MD, McGowan Institute for Regenerative Medicine, University of Pittsburgh
                           Abstract     Full presentation    Video

3:00-3:30          Afternoon tea

3:30-4:30           A model-based approach to personalised medicine (continued)
                            A/Professor Gilles Clermont MD, McGowan Institute for Regenerative Medicine, University of Pittsburgh

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

9:00-10:15        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
                            Abstract     Full presentation    Video

10:15-10:45     Morning tea

10:45-11:45     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
                            Abstract     Full presentation    Video

12:00-1:00        Information integration approaches to network modeling
                            Professor John Quackenbush, Dana-Farber Cancer Institute, and Harvard School of Public Health
                            Abstract     Full presentation    Video

1:00-2:00           Lunch

2:00-3:30          Dynamic proten-protein interaction networks in yeast
                           Professor Marc Wilkins, University of New South Wales
                           Abstract     Full presentation    Video

3:30-3:40          CONCLUSION