Invited Speakers

Single cell - Melbourne Hub

Bio: Vento-Tormo’s research interest is to understand the influence of cellular microenvironments on individual cellular identities and responses, in the context of immunity and development. Her team (https://ventolab.org/) employs single-cell and spatial transcriptomics methods to deconstruct the cell signals in human organs and tissues, and utilise this information to inform the reconstruction of novel in vitro models. Essential for this work, is the novel computational tools her team develops to build cell–cell interactions networks from transcriptomics data. Her training in genomics and bioinformatics puts her in a unique position to lead multidisciplinary projects. In her predoctoral research, she studied the interplay between cell signalling and epigenetic machinery key to regulating cellular fate decisions in myeloid cells. She pursued her postdoctoral studies in the Teichmann laboratory as an EMBO / HFSP fellow, where she developed CellPhoneDB.org, a computational tool to study cell-cell communication from single-cell transcriptomics data, and use it to disentangle the complex communication between maternal and fetal cells in the uterine-placental interface during early human pregnancy. Vento-Tormo work has been funded by many recognised international agencies (H2020, MRC, CZI, Wellcome-LEAP), and she has recently obtained the Early Career Research Award from the Biochemistry Society (2021).

Presentation title: Gene regulatory dynamics of plant embryos from bulk tissue to single-cell resolution

Bio: I am a hands-on lab biologist turned data-crunching genome scientist. My lab studies how plants perceive the world around them and interact with their environments by regulation of their genomes. We apply this work with commercial partners who grow a range of agricultural crops including cannabis, opium poppies, barley, oats and peas. I completed my PhD in Molecular Virology at the University of Cambridge with Prof John Carr. I next conducted postdoctoral research at the Salk Institute (La Jolla, USA) with Prof Joe Ecker and at the Centro Nacional de Biotecnología (Madrid, Spain) with Prof Roberto Solano. My projects at that time focused on applying functional genomics to understand plant hormone biology and small RNA signalling between organs. This work was performed in both labs as part of my Marie Curie Fellowship. I joined La Trobe University in April 2016 to further my interests in genomics, systems biology and plant science. In 2017 I became Director of the La Trobe Genomics Platform, and in 2019 Co-Deputy Director of the ARC Research Hub for Medicinal Agriculture.

Presentation title: Single-cell and spatial transcriptomics to dissect modulators of radionuclide therapy response in prostate cancer

Bio: Dr. Anna Trigos is a postdoctoral researcher at the Peter MacCallum Cancer Centre in the team of A/Prof. Shahneen Sandhu in Prof. Rick Pearson’s lab. She was recently awarded two NHMRC Ideas grants and a CASS Foundation grant to investigate prostate cancer evolution and heterogeneity and develop novel spatial analysis methods to study the tumour immune microenvironment. In 2019 she was awarded the Joseph Sambrook Prize for Research Excellence and the Peter Mac Postgraduate Research Medal, and in 2020 she received the Lea Medal Award recognising emerging female researchers.

Phylogenetics - Hobart Hub

Bio: Professor Arndt von Haeseler is the scientific director of the Max F. Perutz Laboratories at the Vienna Biocenter and a professor of bioinformatics at the University of Vienna and the Medical University of Vienna. Arndt obtained his doctorate in mathematics from the University of Bielefeld in 1988. He habilitated in 1994 at the Department of Zoology of the University of Munich, where he remained as a lecturer until 1998. From 1998 until 2001, von Haeseler was a group leader at the Max Planck Institute for Evolutionary Anthropology in Leipzig. Subsequently, he was professor of bioinformatics at the University of Düsseldorf and, in 2005, he joined the Max F. Perutz Laboratories (MFPL), where he leads the Center for Integrative Bioinformatics Vienna (CIBIV). At the University of Vienna, he is the dean of the Center for Molecular Biology and at the Medical University of Vienna, he is the head of the Department for Medical Biochemistry.Arndt's research focuses on developing computational methods for the reconstruction of phylogenetic trees. He co-authored the phylogenetics software packages TREEFINDER, TREE-PUZZLE, and its successor, IQ-TREE. He sits on the editorial boards of Molecular Biology and Evolution and BMC Evolutionary Biology. In 2015, von Haeseler was elected as a corresponding member of the mathematics and science class of the Austrian Academy of Sciences. Since 1999, he holds an honorary professorship in theoretical biology at the University of Leipzig.

Presentation title: Model selection on empirical data using deep learning

Bio: Barbara completed a PhD in Mathematical Biology at Massey University in New Zealand followed by postdoctoral studies at the Ruhr Universität Bochum (Germany) and in the Allan Wilson Centre for Molecular Ecology and Evolution (New Zealand). Prior to joining the University of Tasmania she worked as a Mathematics lecturer and researcher at Massey University. Since beginning her PhD she has enjoyed the challenge of working with biologists in trying to translate the problems they face into the language of mathematics. Biology is awash with data since the advent of DNA sequencing technology and this has opened up a range of very interesting research questions that require a combination of skills from mathematics, biology and computer science.

Metagenomics/Long reads - Sydney Hub

Presentation title: Long (and short) read metagenome analysis of complex microbial communities: progress, problems and prospects

Bio: Rohan Williams is an Australian computational biologist based at the Singapore Centre for Environmental Life Sciences Engineering (SCELSE), a Research Centre of Excellence co-hosted by the National University of Singapore and Nanyang Technological University. At SCELSE he is Head of the Integrative Analysis Unit, which combines research, service and training activity in bioinformatics and computational biology. His research interests lie in metagenomics and multi-omics of microbiomes and complex microbial communities, mostly in the context of wastewater bioprocess systems. Previously he was a research group leader at the Australian National University (2077-2011) and an NHMRC Peter Doherty Fellow at UNSW (2003-2007). He holds a PhD (UNSW) in Medicine and a BAppSc (UTS) in Physics. Williams is cofounder of the ASEAN Industrial Wastewater Genomics Consortium, a new initiative targeting microbial communities underpinning the agri-industrial systems in South East Asia and a scientific confounder of BluMaiden Biosciences Pte Ltd, a Singapore headquartered biotechnology platform company that is developing new small molecule therapeutics derived from human microbiomes.

https://www.linkedin.com/in/rohan-williams-24424613/

https://twitter.com/rbhwilliams1

Biomedical - Adelaide Hub

Bio: Dr Katherine Pillman is a bioinformatician and RAH Florey Fellow at the Centre for Cancer Biology in South Australia. She uses a variety of transcriptomic methods and next-gen sequencing data types to dissect gene regulation through analysis of microRNA biology and targeting, circular RNAs, alternative splicing, epigenetic modifications, gene regulatory networks and expression.

She obtained her PhD in Molecular Biology from the University of Adelaide in 2009 working on transcriptional regulation in barley plants. Her postdoctoral research at Oregon State University involved RNA-seq analysis of stress-responsive gene regulatory networks in potato plants, which fuelled her interest and transition into the field of Bioinformatics. In 2012, she returned to Australia to take up her current role as Lead Bioinformatician in the Gene Regulatory Section at the Centre for Cancer Biology, working in collaboration with Prof. Greg Goodall. Career highlights include a seminal paper in Cell which identified the first protein known to control the formation of circular RNAs, and the subsequent discovery that this protein, Quaking, is a key emerging player in circular splicing and linear alternative splicing in cancer (published in EMBO J). Other work has identified genome-wide microRNA regulatory networks controlling cell invasion (also in EMBO J) and uncovered the cooperative role of microRNAs in cancer (published in Nucleic Acids Research and Cell Systems). In addition to her fellowship, she is a Co-Investigator on NHMRC Ideas and MRFF grants which fund her current work.

Presentation title: The ENCODE Registry of candidate Cis-Regulatory Elements: a summary of curation and applications

Bio: Dr. Moore’s research focuses on the large scale integration of multi-omic datasets to better understand gene regulation, particularly in the context of human disease. She received her Bachelors of Science in Mathematics with minors in Biology and Chemistry as a member of the Commonwealth Honors College from the University of Massachusetts Amherst. She received her PhD in 2017 from the University of Massachusetts Medical School under Prof. Zhiping Weng where she was an active member of the Encyclopedia of DNA Elements (ENCODE) project. Since completing her graduate training, Dr. Moore has continued working with the ENCODE consortium as the Project Manager for the Data Analysis Center. In this role, she is very interested in improving ways to make multi-omic data and computational analyses accessible to the wider biological community.

Statistics & Method Development - Brisbane Hub

Presentation Title: Scalable community profiling of shotgun metagenomes

Bio: Starting from a computational background at the University of Queensland, Ben’s broad interest in biological systems was sparked by an undergraduate project in protein structure with Dr. Nicholas Hamilton, then an honours project in Prof. Bernie Degnan’s marine biology laboratory studying the genome structure of the most basal animals, sponges. Then he moved south to the University of Melbourne for his PhD, under the guidance of A/Prof. Stuart Ralph and Prof. Terry Speed, concentrating on the development of bioinformatic tools to understand the malaria parasite’s complex cell biology.

During his post-doctoral studies with Prof. Gene Tyson at the Australian Centre for Ecogenomics, UQ, and continuing until the present time as microbial informatics team leader within the Centre for Microbiome Research at QUT, he has studied the microbial world using informatic techniques. Direct sequencing of DNA and RNA derived from natural microbial systems has great scientific and applied potential, and the wealth of sequencing data bring many bioinformatic opportunities and challenges, including the recovery and annotation of genomes with strain-level specificity, exploring large public datasets and linking microbial communities with their function.

A primary study site he has been involved with is Stordalen Mire, in northern Sweden, a permafrost thaw gradient home to complex microbial ecosystems. This system serves as a model for understanding how climate change is affecting microbial communities in thawing permafrost, which are in turn generating the potent greenhouse gas methane, exacerbating global warming. Primary contributions at this site involved the recovery of >1000 high quality genomes from the site, discovery of novel methanogenic lineages and linking specific community members to the isotopic composition of released methane, with implications for global climate modeling.

Bio: Smita Krishnaswamy is an Associate professor in Genetics and Computer Science. She is affiliated with the applied math program, computational biology program, Yale Center for Biomedical Data Science and Yale Cancer Center. Her lab works on the development of machine learning techniques to analyze high dimensional high throughput biomedical data. Her focus is on unsupervised machine learning methods, specifically manifold learning and deep learning techniques for detecting structure and patterns in data. She has developed algorithms for non-linear dimensionality reduction and visualization, learning data geometry, denoising, imputation, inference of multi-granular structure, and inference of feature networks from big data. Her group has applied these techniques to many data types such as single cell RNA-sequencing, mass cytometry, electronic health record, and connectomic data from a variety of systems. Specific application areas include immunology, immunotherapy, cancer, neuroscience, developmental biology and health outcomes. Smita has a Ph.D. in Computer Science and Engineering from the University of Michigan.

Plants & Non-model Organisms - Perth Hub

Bio: Isobel Parkin has been a Research Scientist with Agriculture and Agri-Food Canada (AAFC) since 1999 and an adjunct Professor at the University of Saskatchewan since 2004. Her research interests include Brassica genomics, comparative genome organisation, global gene expression analysis, and abiotic stress responses. Together with Prof. Andrew Sharpe, she co-led the Canadian Canola Genome Sequencing (CanSeq) industry consortium project that developed a high quality genome sequence as part of the multinational Brassica Genome Sequencing initiative. Isobel’s current research funding sources include the Global Institute for Food Security (GIFS), Saskatchewan Agriculture Development Fund, AAFC Crop Genomics Initiative, and canola producer groups.

Presentation Title: Breaking Barriers: From conventional to next generation genetics

Bio: Assoc. Prof. Parwinder Kaur leads an innovative Translational Genomics research program that aims to translate fundamental science into ready-to-use solutions across the agricultural and medical sectors. Her DNA Lab team enables research to span the spectrum of scientific activities beyond the traditional ‘Lab-to-Landscape’ model, using new age technologies such as CRISPR, single-cell and 3D genomics. With DNA Zoo Australia she is on a mission to provide genomic empowerment to unique Australian biodiversity facilitating conservation efforts for the threatened and endangered species.

She has made substantial contributions to the field of biotechnology and appointed as UWA “Be Inspired” for Agricultural & Environmental Biotechnology in 2019. Her studies tracking genomic variation to breed low methanogenic forages in Australia provided a new paradigm for reducing the environmental footprint of ruminants. She has been honored by the prestigious “Science and Innovation Award” for Young People in Agriculture, Fisheries and Forestry by the Australian Academy of Sciences in 2013. For DNA Zoo innovative work developments won the Microsoft's AI for Earth award for 2019-20. She is an active mentor for gender equity and GirlsXTech international ambassador working to close the gender gap in technology.