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CSIRO Machine Learning in Genome Biology Symposium

Genome biology is generating data sets of unprecedented size and complexity in health, livestock and agricultural sciences. The effective analysis of this data presents a significant challenge in realising the potential “big-data” offers to science and industry, which has been difficult to achieve with traditional approaches. This meeting will address advances in the application of a broad array of “artificial intelligence” methods to effectively integrate large-scale ‘omic’ data in health, livestock and agriculture, with a particular focus on predicting biological outcomes.

The venue

Kiama is a scenic coastal town in New South Wales, about an hour and a half south of Sydney, boasting beautiful beaches and stunning coastal views, nestled among temperate rainforest of the Illawarra hinterland.

Visit Kiama NSW

Keynote speakers

Christian Maltecca Dr Christian Maltecca, North Carolina State University
Christian is an associate professor of quantitative genetics and breeding in the animal science department as well as part of the genetics, comparative medicine institute, and bioinformatics programs at NCSU. His research is focused on the genomic improvement of economically relevant traits in livestock. My main interests are in the area of genomic prediction and genome-wide association for functional traits. Additional research in my group is focused on the impact of genomic selection on long-term variation and fitness and the optimization of statistical methods and breeding schemes under genomic selection. In my research, I typically make use of a combination of simulated data, large cross-sectional field data, as well as designed experiments.
Denis Bauer Dr Denis Bauer, CSIRO Health and Biosecurity
Dr Denis Bauer is an internationally recognised expert in machine learning, specifically in processing big genomic data to help unlock the secrets in human DNA – secrets that could change the course of human history. Her achievements include developing an open-source, artificial intelligence-based search engine that helps researchers pinpoint the exact genes they need to study or edit to cure disease. As CSIRO’s transformational bioinformatics leader, Denis is involved in Australian and international initiatives to integrate genomics into medical practice. She is frequently invited as a keynote at heavyweight IT conferences including Amazon Web Services Summit ‘17/’18, Alibaba Infinity Singapore ’18 and Open Data Science Conference India ’18. Her revolutionary achievements have been featured in international press such as GenomeWeb, ZDNet, Computer World, CIO Magazine, the AWS Jeff Barr blog, and was in ComputerWeekly’s Top 10 IT stories of 2017. Denis holds a BSc from Germany and PhD in Bioinformatics from the University of Queensland, and has completed postdoctoral research in both biological machine learning and high-throughput genetics.
Jen Spindel Dr Jennifer Spindel, Bayer Crop Science
Dr. Spindel is interested in how genomic data and large phenotype datasets (phenomic and/or historical datasets) can be used to improve crop breeding programs. Her research has focused primarily on developing genomic selection models that incorporate genome-wide association for public rice and sorghum breeding programs and developing new approaches to performing high density phenotype genome-wide association studies (GWAS) in grains. She received her PhD in 2015 from Cornell University (Ithaca, NY) where she worked in the lab of Dr. Susan McCouch, then worked as a post-doc in the lab of Dr. John Vogel at the Joint Genome institute (Berkeley, CA) before taking her current position as a computational geneticist in Global Breeding at Bayer Crop Science.
Mikael Boden Dr Mikael Boden, University of Queensland
Mikael gained a PhD from the University of Exeter, UK, in computer science, AI and machine learning. He was a postdoctoral research fellow in the School of Computer Science and Electrical Engineering at The University of Queensland. I was a senior research fellow in the Institute for Molecular Bioscience before my current appointment as Associate Professor at the School of Chemistry and Molecular Biosciences, both at UQ. I am the Director of Bioinformatics postgraduate programs. My research has been awarded funding from various grant agencies, including the Australian Research Council and National Health and Medical Research Council. With biological data available at phenomenal scales, my group and I use data driven, probabilistic and algorithmic approaches to solve problems in genomics, systems and protein biology. Sequence analysis, regulatory genomics and phylogenetics are major themes in my group. We are also developing tools for exploring the evolution of proteins, with applications in protein engineering. We work closely with collaborators across the disciplines, including genomics, genetics, stem and developmental biology, biochemistry and structural biology. In the last two years our work has been published in journals such as Bioinformatics, Nucleic Acids Research and Nature Catalysis.
Alex Calderwood Dr Alex Calderwood, John Innes Centre
I am working as a part of the Brassica Rapeseed and Vegetable Optimisation (BRAVO) project to identify gene regulatory networks underlying developmental transitions in Canola. To identify networks, we have collected large, gene expression time-course datasets in multiple Brassica lines. As Brassicas are also closely related to the model organism Arabidopsis, we are interested primarily in network inference approaches which integrate information derived from related-but-different data sources. I received my PhD in 2016 from the University of East Anglia for work on the analysis of large-scale metabolic networks. I then worked with Judith Irwin on flowering time, before starting on BRAVO as a post-doc in Richard Morris’ group at the John Innes Centre.

Program

The symposium will run over three days, starting with an evening welcome event and poster session on the first day, and symposium dinner held on day two.

Seven sessions covering four major themes will address the application of machine learning methods to problems in human, animal and plant genome science. This will include a speed talk session and conclude with a “Un-conference” panel discussion. The four symposium themes are:

  • Phenotype-genotype association
  • Gene-gene and gene-environment interactions
  • Modelling biological outcomes
  • Genome characterisation

A detailed program will be released in the new year.

Registration and Abstract submission

Participation in this meeting is by invitation, and numbers have been capped. If you would like to participate, please indicate your interest via email to Sharon.Barber@csiro.au by 15th of December.

$300 registration fee, includes welcome event, lunch, morning and afternoon tea each day, beverages and the symposium dinner.

Transport to and from Kiama

There are several options for travel to and from Kiama.

Car: For those arriving from Sydney and its surrounds, follow the Princes Highway south to Kiama. If you plan on driving from Canberra, the Hume Highway travels northeast to Kiama.

Google map directions

Train: Services run regularly to Kiama from Sydney, offering a relaxing way to sit back and take in some of Australia’s most scenic coastline.

Visit Sydney Trains

Bus: There are a number of coach services which operate to and from Kiama, Sydney and Melbourne.

Visit Greyhound Australia, Premier Motor Service

Diversity and inclusion policy

We will actively promote a culture of diversity and inclusion, to welcome and encourage participation in the symposium regardless of gender, gender expression, sexual orientation, ethnicity, nationality, disability, religion or age.

To ensure gender balance across the symposium we will work to achieve balanced representation (40:60 parity) of male and female invited speakers, conference talks, session chairs and organising committee.

We will provide support structures that facilitate attendance at the symposium by parents with dependents, including discounted rates for family suites and options for child care.

Organising Committee

Shannon Dillon (CSIRO, Agriculture and Food)

Saul Newman (Australian National University)

Ben Trevaskis (CSIRO, Agriculture and Food)

Jana Sperschneider (Australian National University)

Yutao Li (CSIRO, Agriculture and Food)

Jen Taylor (CSIRO, Agriculture and Food)

Sharon Barber (CSIRO, Agriculture and Food)

Denis Bauer et al. (CSIRO, Health and Biosecurity)

Kaito Lai (CSIRO, Health and Biosecurity)

Klara Verbyla (CSIRO, Data61)

Cheng Ong (CSIRO, Data61)

Almamun Hawlader (CSIRO, Data 61)

Eric Stone (Australian National University-CSIRO Centre for Genomics, Metabolomics and Bioinformatics)

Support

This Symposium is supported by funding received from the CSIRO Research Office, Cutting Edge Science Symposium program.

Beach with tide out

Sebel Kiama Buildings