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Imb 2014 Winterinin Schoolin Mathematicalmathematicalmathematical&& Computationalcomputationalin & Computational Biologybiology Biology 20142014 WINTERWINTER2014 WINTERSCHOOLSCHOOL SCHOOL IMB 2014 WINTERININ SCHOOLIN MATHEMATICALMATHEMATICALMATHEMATICAL&& COMPUTATIONALCOMPUTATIONALIN & COMPUTATIONAL BIOLOGYBIOLOGY BIOLOGY MATHEMATICAL & COMPUTATIONAL BIOLOGY in in of Centre ARC Bioinformatics Excellence 7-117-11 JulyJuly 201420147-11 July 2014 7-11 July 2014 Hosted by: Hosted Auditorium AuditoriumAuditoriumAuditorium Queensland Bioscience Precinct QueenslandQueenslandQueensland Bioscience BioscienceBioscience Precinct PrecinctPrecinct TheTheThe UniversityUniversity UniversityThe University ofof QueenslandQueensland of Queensland Brisbane,Brisbane,Brisbane, AustraliaAustraliaBrisbane, Australia PROGRAM PROGRAMPROGRAMPROGRAMPROGRAM Brisbane, Australia Brisbane, The University of Queensland of University The Queensland Bioscience Precinct Bioscience Hosted by: Queensland Auditorium HostedHosted by:by: Hosted by: 7-11 July 2014 July 7-11 ARCARC CentreCentre ofof ExcellenceExcellenceARC Centreinin BioinformaticsBioinformatics of Excellence in Bioinformatics & COMPUTATIONAL BIOLOGY COMPUTATIONAL & MATHEMATICAL IN IN IMIMBIMBB IMB 2014 WINTER SCHOOL WINTER 2014 2014 Winter School in Mathematical and Computational Biology 7-11 July 2014 http://bioinformatics.org.au/ws14 Queensland Bioscience Precinct (Building #80) The University of Queensland Brisbane, Australia Monday 7 July 2014 NEXT GENERATION SEQUENCING & BIOINFORMATICS 8:15 a.m. REGISTRATION OPENS 9:00 a.m. Welcome and introduction Dr Nicholas Hamilton Institute for Molecular Bioscience The University of Queensland 09:05 a.m. Next-generation sequencing: an overview of technologies and applications Dr Ken McGrath Australian Genome Research Facility Ltd (AGRF) Brisbane Node (The University of Queensland) 09:45 a.m. NGS mapping, errors and quality control Dr Felicity Newell The University of Queensland Diamantina Institute 10:30 a.m. Morning Tea 11:00 a.m. 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 11:45 a.m. Structural variants detection using whole genome sequencing Dr Ann-Marie Patch Queensland Centre for Medical Genomics Institute for Molecular Bioscience The University of Queensland 12:30 p.m. Lunch 13:30 p.m. De novo genome assembly Dr Torsten Seemann Victorian Bioinformatics Consortium Monash University 14:00 p.m. Introduction to RNA-seq Dr Nadia Davidson Murdoch Childrens Research Institute Royal Children’s Hospital 14:30 p.m. RNA-seq differential expression Dr Annette McGrath CSIRO Canberra 15:00 p.m. Afternoon Tea i 15:30 p.m. MicroRNAs – sequencing, analysis … and then what? Dr Nicole Cloonan Genomic Biology Laboratory QIMR Berghofer Medical Research Institute 16:00 p.m. NGS experimental design and statistical power Dr Stephen Rudd QFAB Bioinformatics 16:30 p.m. Genomic infrastructure for NGS A/Professor Mik Black School of Medical Sciences University of Otago 17:00 p.m. What the Australian Bioinformatics Network can do for you Dr David Lovell CSIRO 17:30 p.m. Welcoming BBQ ii Tuesday 8 July 2014 NEXT GENERATION SEQUENCING & BIOINFORMATICS 09:00 a.m. Great expectations or why sequencing platforms are not magic wands Dr Lauren Bragg CSIRO Dr Michael Imelfort School of Chemistry & Molecular Biosciences, The University of Queensland 10:00 a.m. Phlogeny-based methods for analysing and comparing uncultured microbial communities A/Professor Aaron Darling University of Technology, Sydney 10:30 a.m. Morning Tea MODELLING FROM HIGH-THROUGHPUT BIO-DATA 11:00 a.m. Exploring the structure of whole-genome conservation profiles using Bayesian segmentation Dr Jonathan Keith School of Mathematical Sciences Monash University 11:45 a.m. Machine learning in action Ms Tatyana Goldberg Technische Universitat München, Germany 12:30 p.m. Lunch 13:30 p.m. Detection of recombination events in bacterial genomes Dr Nouri Ben Zakour School of Chemistry and Molecular Sciences The University of Queensland 14:15 p.m. Epigenomics: The many garments of the genome sequence Dr Fabian Buske Garvan Institute of Medical Research 15:00 p.m. Afternoon Tea 15:30 p.m. Mixed linear model analyses of human complex traits using SNP data Dr Jian Yang Queensland Brain Institute The University of Queensland 16:15 p.m. Detection and replication of epistasis influencing transcription in humans Dr Joseph Powell Queensland Brain Institute The University of Queensland 17:00 p.m. An introduction to BRAEMBL services Dr Webber Liao BRAEMBL iii WedneSday 9 July 2014 MODELLING FROM HIGH-THROUGHPUT BIO-DATA 09:00 a.m. The future of DNA sequencing technology Professor Graham Taylor University of Melbourne 09:45 a.m. Population-scale high-throughput sequencing data analysis Dr Denis Bauer Computational Informatics (CCI) CSIRO Sydney 10:30 a.m. Morning Tea 11:00 a.m. Translating exome and whole genome sequencing to the clinic A/Professor Marcel Dinger Garvan Institute of Medical Research 12:00 noon Panel discussion Moderated by Dr Nicole Cloonan QIMR Berghofer Medical Research Institute *** FREE WEDNESDAY AFTERNOON *** iv ThurSday 10 July 2014 BIG DATA, STATISTICS AND APPLICATIONS 08:45 a.m. Taming the Big Data Dragon Professor John Quackenbush Dana-Farber Cancer Institute & Harvard School of Public Health, USA 10:00 a.m. From Big Data to smart knowledge – integrating multimodal biological data and modelling metabolism Professor Falk Schreiber Monash University University Halle-Wittenberg, Germany 10:40 a.m. Morning Tea 11:10 a.m. Visual analytics of Big Data Professor Seok-Hee Hong University of Sydney 11:50 a.m. The life-sciences as a pathfinder in data-intensive research practice Dr Andrew Treloar Australian National Data Service (ANDS) 12:30 p.m. Lunch 13:30 p.m. Statistical experiment design principles for biological studies Dr Alec Zwart CSIRO 14:15 p.m. Genome-wide association studies Professor David Evans The University of Queensland Diamantina Institute 15:00 p.m. Afternoon Tea 15:30 p.m. Mixture models for analysing transcriptome and ChIP-chip data Dr Marie-Laure Martin Magniette Mathématiques et Informatique Appliquées Institut National de la Recherche Agronomique, France 16:15 p.m. Multivariate models for dimension reduction and biomarker selection in omics data Dr Kim-Anh Lê Cao The University of Queensland Diamantina Institute v Friday 11 July 2014 MOLECULAR PHYLOGENETICS 09:00 a.m. An introduction to phylogenetic inference Dr Robert Lanfear Macquarie University 10:15 a.m. Morning Tea 10:45 a.m. Loss of information at deeper divergences, and what we can do about it Distinguished Professor David Penny Institute of Fundamental Sciences Massey University, NZ *** IMB FRIDAY SEMINAR *** 12:00 noon From mutation to macroevolution Professor Lindell Bromham Research School of Biology Australian National University 13:00 p.m. Lunch 14:00 p.m. The application of high throughput DNA barcoding for landscape ecology and management Professor Mike Wilkinson School of Agriculture Food & Wine The University of Adelaide 15:00 p.m. Open forum/questions Moderated by Professor Mark Ragan Institute for Molecular Bioscience The University of Queensland 16:00 p.m. Student travel award preSentation & cloSe of Winter School ~*~*~*~*~ vi BIOGRAPHY AND ABSTRACT Dr Ken McGrath Australian Genome Research Facility Ltd (AGRF) Brisbane Node (The University of Queensland) Biography: Ken McGrath is the manager of the Brisbane Lab of the Australian Genome Research Facility. He completed his undergraduate degree with honours in 2001 at QUT working with the plant biotechnology group on developing transgenic bioreactors, and transitioned to UQ for his PhD work investigating the genetic regulation of plant defence responses to disease, in collaboration with CSIRO and the CRC for Tropical Plant Protection. Following this, his post- doctoral research with the Schmidt and Schenk labs at UQ involved examining the transcriptomes of mixed microbial communities in industrial and agricultural settings. In 2009, Ken joined the AGRF as sequencing supervisor, and currently helps manage submissions and workflows on a range of next-generation sequencing platforms. Date: Monday 7 July 2014 Presentation title: Next-generation sequencing: an overview of technologies and applications Abstract: The “Next-Generation Sequencing” landscape is one of constant change, with new and emerging technologies constantly competing with established platforms. This abundance of competition is resulting in faster and cheaper methods to perform sequencing of DNA and RNA samples, but it also brings with it a confusing array of options, each with its own strengths and weaknesses. Ken will give an overview of the available sequencing technologies and run through some examples projects that can be run on them, as well as describe the typical bioinformatics approaches for these projects, and also take a look at what’s “next” in Next-Gen. 1 BIOGRAPHY AND ABSTRACT Dr Felicity Newell The University of Queensland Diamantina Institute Biography: Felicity originally trained in the fields of molecular and cell biology. In her PhD and first post-doctoral position at the University of Queensland, she investigated the role of growth factors in the differentiation of human preadipocytes. After this, she developed an interest in software development and bioinformatics, obtaining a Master of Information Technology from the Queensland University of Technology. She worked for two years as a software developer developing bioinformatics web applications at QFAB Bioinformatics, before moving to the Queensland Centre for Medical Genomics
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