2016 Winter School Program

Venue: Auditorium, Queensland Bioscience Precinct (Bldg #80), Institute for Molecular Bioscience, The University of Queensland, St Lucia campus


08:00 Registration desk open

Next generation sequencing & bioinformatics

09:00 – 09:05 Welcome and introduction

Dr Nicholas Hamilton
Research Computing Centre and Institute for Molecular Bioscience
The University of Queensland

09:05 – 09:45 Next-generation sequencing overview (Game of Thrones Edition)

Dr Ken McGrath
Australian Genome Research Facility Ltd, Brisbane

09:45 – 10:30 NGS mapping, errors and quality control

Dr Felicity Newell
Queensland University of Technology

10:30 – 11:00 Morning Tea
11:00 – 11:45 Mutation detection in whole genome sequencing

Dr Ann-Marie Patch
QIMR Berghofer Medical Research Institute

11:45 – 12:30 De novo genome assembly

A/Professor Torsten Seemann
Victorian Life Sciences Computation Initiative, The University of Melbourne

12:30 – 13:30 Lunch
13:30 – 14:30 Long read sequencing: an overview of technologies and applications

Dr Mathieu Bourgey
Montréal Node McGill University and Genome Quebec Innovation Centre, Canada

14:30 – 15:15 Genomics resources – feeding your inner bioinformatician

A/Professor Mik Black
University of Otago, New Zealand

15:15 – 15:45 Afternoon Tea
15:45 – 16:30 Defensive NGS informatics – what can go wrong and how do you know when to throw in the towel?

Mr John Pearson
QIMR Berghofer Medical Research Institute

16:30 – 17:15 The next challenges and opportunities in bioinformatics

Dr Annette McGrath
DATA61 | CSIRO, Canberra

17:15 – 17:30 Resource talk: What the Australian Bioinformatics and Computational Biology Society can do for you

Professor David Lovell
Queensland University of Technology

17:45 Social BBQ

Venue: Auditorium foyer

Next generation sequencing & bioinformatics

09:00 – 09:45 Analysing RNA-seq data: differential expression and beyond

Dr Alicia Oshlack
Murdoch Childrens Research Institute, Melbourne

09:45 – 10:30 MicroRNAs – sequencing, analysis … and then what?

Dr Pamela Mukhopadhyay
QIMR Berghofer Medical Research Institute

10:30 – 11:00 Morning Tea


Bioinformatics methods, models and applications to disease

11:00 – 11:45 Evolution teaches protein prediction

Professor Burkhard Rost
Technische Universität München (TUM), Munich, Germany

11:45 – 12:45 Lunch
12:45 – 13:30 Personalised health: the harnessing power of diversity

Professor Burkhard Rost
Technische Universität München (TUM), Munich, Germany

13:30 –  14:15 The predictive power of machine learning techniques in data-driven biomedical knowledge discovery

Dr Jiangning Song
Monash University

14:15 – 15:00 Personalised medicine: Discriminating disease-causing from neutral genetic variations

Professor Yaoqi Zhou
Griffith University

15:00 – 15:30 Afternoon Tea
15:3-0 – 16:15 Processing, integrating and analysing chromatin immunoprecipitation followed by sequencing (ChIP-seq) data

Ms Alexandra Essebier
The University of Queensland

16:15 – 17:00 VariantSpark: applying Spark-based machine learning methods to genomic information

Dr Denis Bauer
CSIRO Health Program, Sydney

17:00 – 17:15 Resource talk: How QCIF enables research

Ms Belinda Weaver
QCIF e-Research Analyst Team Manager

Bioinformatics methods, models and applications to disease

09:00 – 09:45 The role of common genetic variations in complex diseases and pharmacogenomics studies

Dr Siew-Kee Amanda Low
The University of Sydney

09:45 – 10:30 I’ve got my list of differentially expressed genes, now what?

Dr Mirana Ramialison
Australian Regenerative Medicine Institute, Monash University

10:30 – 11:00 Morning Tea
11:00 – 12:00 Bioinformatics software testing and quality assurance

Dr Joshua W.K. Ho
Victor Chang Cardiac Research Institute

12:00 – 12:30 Panel discussion

Chair: Professor Mark Ragan
Institute for Molecular Bioscience, The University of Queensland





12:30 – 13:00 IMB tour (1) – Limited to 50 attendees only

Meeting point: Auditorium foyer

13:00 – 13:30 IMB tour (2) – If more requests are received and is also limited to 50 attendees only

Meeting point: Auditorium foyer

14:00 – 17:00 Special Wednesday Afternoon Workshop

An introduction to Galaxy with the NeCTAR Genomics Virtual Laboratory

Dr Igor Makunin
Research Computing Centre, The University of Queensland

Venue: Multi Media Room (Room 3.141, access through the auditorium foyer)

(This workshop is limited to 36 attendees only and is intended for bench scientists, and no previous informatics experience is needed.)

What is required before attending the workshop?

Download Galaxy Workshop Information Sheet


Advanced bio-data visualisation

09:00 – 10:30 Data visualisation in bioinformatics: Exploring the ‘dark’ proteome

Dr Seán O’Donoghue
CSIRO, Sydney

10:30 – 11:00 Morning Tea
11:00 – 12:00 Experimentation at the interface of art and science: narrative, cognitive embodiment and alternative visual language

Dr Kate Patterson
Garvan Institute of Medical Research

12:00 – 13:00 Lunch
13:00 – 14:00 Network and data visualisation and analysis in Cytoscape

Dr Melissa Davis
Walter and Eliza Hall Institute for Medical Research

14:00 – 15:00 Big data visual analytics

Prof. Seok-Hee Hong
University of Sydney

15:00 – 15:30 Afternoon Tea
15:30 – 17:00 Creating data visualisations that won’t be forgotten using the R programming language

Dr Chris Brown
Australian Rivers Institute, Griffith University

17:00 – 17:15 Resource talk: What COMBINE does for students and ECRs in Bioinformatics and Computational Biology
Ms Leah Roberts
Vice President
**COMBINE would like to invite interested students and ECRs to join them after Leah’s talk for a social meet up at the Pizza Cafe.**


09:00 – 09:05 Welcome & introduction

Professor Gene Tyson
Australian Centre for Ecogenomics
The University of Queensland

09:0509:45 The extraordinary evolution of the great ape microbiome

Professor Howard Ochman
The University of Texas at Austin, USA

09:45 – 10:30 Tools and methods for microbial ecological genomics

Dr David Wood
The University of Queensland

10:30 – 11:00 Morning Tea
11:00 – 11:45 Illuminating microbial dark matter via single-cell genomics

Dr Christian Rinke
The University of Queensland

12:00 – 13:00 IMB Friday Noon Seminar in conjunction with Winter School

Towards 4 dimensional (eco) systems biology in the sea

Professor Edward F. DeLong
University of Hawaii, USA

13:00 – 13:45 Lunch
13:45 – 14:30 Genomes from metagenomes: recovery and analysis of population genomes

Dr Kate Ormerod
The University of Queensland

14:30 – 15:15 Community diversity in metagenomes: one, many and thousands

Dr Ben Woodcroft
The University of Queensland

15:15 – 16:00 Comparing the variome and pan-genome of bacterial isolates

A/Professor Torsten Seemann
Victorian Life Sciences Computation Initiative
The University of Melbourne

16:00 Winter School wrap-up and refreshment with IMB/ECR’s