Winter School 2018 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 – 09:35 Next-generation sequencing – technology overview

Dr Christopher Noune
Australian Genome Research Facility Ltd (AGRF)

09:40 – 10:10 NGS mapping, errors and quality control

Dr Felicity Newell
Queensland University of Technology

10:15 – 10:45 Mutation detection in whole genome sequencing

Dr Ann-Marie Patch
QIMR Berghofer Medical Research Institute

10:45 – 11:15 Morning Tea
11:15 – 11:55 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

12:00 – 12:40 De novo genome assembly

A/Prof. Torsten Seemann
The University of Melbourne

12:45 – 13:30 Lunch
13:30 – 14:10 Exploring epigenome using ChiPseq and ATACseq technology

Dr Sonika Tyagi
Monash University

14:15 – 14:55 Genomic signatures predict response to cancer immunotherapy

A/Prof. Lutz Krause
The University of Queensland

15:00 – 15:40 Proteogenomics for accurate assembly and annotation of genomes

Dr Harsha Gowda
The University of Queensland

15:45 – 16:15 Afternoon Tea
16:15 – 16:45 Artificial intelligence for genomics

Mr Nicholas Therkelsen
Max Kelsen Brisbane

16:50 – 17:20 A holistic view of Public Cloud

Mr Steve Nicoll
Amazon Web Services

17:45 Social BBQ

Venue: Auditorium foyer

Next generation sequencing & bioinformatics

09:00 – 09:45 An Introduction to RNA-seq

A/Prof. Nicole Cloonan
University of Auckland, New Zealand

09:45 – 10:30  Bioinformatics analysis of single-cell RNA-seq data

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

10:30 – 11:00 Morning Tea


Data science and machine learning for bioinformatics

11:00 – 11:30 What’s hot in AI and machine learning in 2018

A/Prof. Marcus Gallagher
The University of Queensland

11:30 – 12:00 A need for caution in clustering and classifying high-dimensional data

Prof. Geoff McLachlan
The University of Queensland

12:00 – 12:30 Computational and infrastructure support for the biosciences

Prof. David Abramson
The University of Queensland

12:30 – 13:30 Lunch
13:30 – 14:15 Classification and prediction ‘omics style

Dr Nicola Armstrong
Murdoch University, Western Australia

14:15 –  15:00 How novel compute technology and artificial intelligence transforms life science research

Dr Denis Bauer

15:00 – 15:30 Afternoon Tea
15:30 – 16:00 Exploring regulation through integration of high throughput sequencing data

Ms Alexandra Essebier
The University of Queensland

16:00 – 16:30  The benefits of collaboration for bioinformatic tool development

Mr Gabriel Foley
The University of Queensland

16:30 – 17:00 A newbie’s guide to building a bioinformatics pipeline

Ms Kate Wathen Dunn
Sugar Research Australia, Brisbane

17:00 – 17:15 Resource Talk – Galaxy-Australia, the nationwide free bioinformatics toolshed and compute platform

Dr Gareth Price
Queensland Facility for Advanced Bioinformatics (QFAB)

Data science and machine learning for bioinformatics

09:00 – 09:45 Statistics and machine learning for metagenomics: current solutions and open challenges

A/Prof. Aaron Darling
University of Technology Sydney

09:45 – 10:30 Algorithms to reconstruct phylogenetic networks

Dr Simone Linz
University of Auckland, New Zealand

10:30 – 11:00 Morning Tea
11:00 – 12:00 Planning digital research infrastructure for life science: the Australian biomolecular data capability

A/Prof. Andrew Lonie, The University of Melbourne

12:00 – 12:45 Panel discussion

A/Prof. Andrew Lonie, The University of Melbourne



12:45 – 13:15 IMB tour  – 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


Bio-data analysis and visualisation

09:00 – 10:30 Using networks to link genotype to phenotype

Prof. John Quackenbush
Dana-Farber Cancer Institute and
Harvard T.H. Chan School of Public Health, USA

10:30 – 11:00 Morning Tea
11:00 – 12:00 Visualisation of biomedical data

Prof. Seán O’Donoghue
CSIRO, Garvan Institute of Medical Research

12:00 – 12:30 How to make a really bad visualisation

A/Prof. Jim Hogan
Queensland University of Technology (QUT)

12:30 – 13:30 Lunch
13:30 – 14:15 Single sample analysis and the visualisation of molecular phenotypes

Dr Melissa Davis
Walter and Eliza Hall Institute for Medical Research

14:15 – 15:00 Faithful visual analytics of big complex data

Prof. Seokhee Hong
University of Sydney

15:00 – 15:30 Afternoon Tea
15:30 – 17:00 Creating memorable data visualisations using the R programming language

Dr Christopher Brown
Australian Rivers Institute, Griffith University

17:00 – 17:15 Resource talk: What COMBINE does for students and ECRs in bioinformatics and computational biology

Mr Gabriel Foley
Queensland Representative, COMBINE
**COMBINE would like to invite interested students and ECRs to join them after Gabriel’s talk for a social meet up at the Pizza Cafe.**

Advanced microscopy analysis and modelling

09:00 – 09:35 Systems microscopy: linking form and function in complex cellular processes

Dr John Lock
University of New South Wales

09:35– 10:10 Understanding kidney development through multi-scale imaging and modelling

Dr Alexander Combes
The University of Melbourne

10:10 – 10:40 Morning Tea
10:40 – 11:15 Optical micromanipulation and neurosciences

Prof. Halina Rubinsztein-Dunlop
The University of Queensland

11:15 – 11:50 Designing effective vaccines

Dr Justine Mintern
The University of Melbourne

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

A view into human kidney morphogenesis using stem cells

Prof. Melissa Little
Murdoch Children’s Research Institute

13:00 – 14:00 Lunch
14:00 – 15:00 Quantitative analysis of single molecule tracking in live cells: from Brownian motion to function

Prof.  Frederic Meunier
The University of Queensland

15:00 – 16:00 Whole-brain imaging of sensory processing in larval zebrafish

A/Prof. Ethan Scott
School of Biomedical Sciences, The University of Queensland

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