A new look for a new era in genomic technologies

National Representation

Dr. Mark Waltham

President

St. Vincent’s Institute of Medical Research and Department of Surgery

University of Melbourne
Melbourne, Australia

Email: mwaltham@unimelb.edu.au

Dr. Ruby C Y Lin

Convenor AGTA 2016

President (2013 -2015)

Conjoint Associate Professor
University of New South Wales
Sydney, Australia

Email: rubycylin@gmail.com

rubyl@unsw.edu.au

Ruby is conjoint Associate Professor at the University of NSW. Previously she was a senior research fellow at the Ramaciotti Centre for Genomics, University of New South Wales from 2003. Her research interests for the last 15 years have expanded from cardiovascular disease and transcriptomics to systems biology and non-coding RNA species. During this time, she was awarded a NHMRC project grant ...

Ruby is conjoint Associate Professor at the University of NSW. Previously she was a senior research fellow at the Ramaciotti Centre for Genomics, University of New South Wales from 2003. Her research interests for the last 15 years have expanded from cardiovascular disease and transcriptomics to systems biology and non-coding RNA species. During this time, she was awarded a NHMRC project grant with A/Prof Julie McMullen to look at transcriptomics of myocardial infarction in a PI3K mouse model. Interestingly, she also had two of her own functional genomics experiments that resulted in 8 months of maternity leave with her first child and 1 year of maternity leave with her second. Despite the lengthy break, she managed to secure another NHMRC project grant with A/Prof Julie McMullen for 2013-5 and had 9 publications during this time. She is now focussing on using systems biology to address underlying pathogenesis of cardiovascular disease and overlapping disease conditions with mesothelioma. And to make it more interesting, she is analysing 73 samples of miRNA-seq data and 36 samples of RNA-seq datasets.
Ruby collaborates with A/Prof Julie R McMullen (Baker IDI), Prof Margaret J Morris (UNSW), Prof Sakari Kauppinen (Aalborg University, Denmark), Prof Robert H Yang (UNSW) and many other which can be viewed in her LinkedIn: au.linedin.com/pub/ruby-lin/12/80/334/. Ruby remains an active member of AGTA, HBPRCA and ASMR, as well as being part of the UNSW women in research network as a mentor.

Dr. Carsten Kulheim

Vice President

Student Education Working Group
Convenor for AMATA 2011

Research Fellow
Research School of Biology,
Australian National University (ANU),
Canberra, Australia

Email: carsten.kulheim@anu.edu.au

Carsten Kulheim graduated from Umea University in Sweden with a major in Plant Molecular Biology in 2000. He completed his PhD in 2005 at Umea University, having worked with short term adaptation mechanisms in photosynthesis to changes in light environment. Carsten then moved on for a two-year Post Doc at The University of British Columbia in Vancouver, Canada, where he worked on plant-herbivor...

Carsten Kulheim graduated from Umea University in Sweden with a major in Plant Molecular Biology in 2000. He completed his PhD in 2005 at Umea University, having worked with short term adaptation mechanisms in photosynthesis to changes in light environment. Carsten then moved on for a two-year Post Doc at The University of British Columbia in Vancouver, Canada, where he worked on plant-herbivore interactions using poplar as a model system. In 2008 he joined the Australian National University continuing in the field of plant-herbivore interactions with the focus on Australian Myrtaceae. His current work focuses on the genetic basis of quantitative and qualitative variation of plant secondary metabolites in eucalypts and tea tree. These variations are implicated in the interactions of the plants with their environment, including herbivores, pathogens and abiotic stress mitigation. Carsten’s research is applicable to conservation biology, nurseries and reforestation industries as well as essential oil producing industries.

Mr. Mark van der Hoek

Treasurer

Co-convenor for AMATA/Combio 2012

Manager, David R Gunn Genomics Suite
South Australian Health and Medical Research Institute (SAHMRI)
Adelaide, Australia

Email: Mark.VanderHoek@sahmri.com

Mark is currently the manager of the David R Gunn Genomics Suite at SAHMRI in Adelaide.  After graduating from the University of Adelaide in 1993 in Chemistry, he was initially employed in the private sector doing mass spectrometry before moving in 1996 to the Hanson Centre for Cancer Research to assist establish a peptide synthesis and mass spectrometry service.  Following this he...

Mark is currently the manager of the David R Gunn Genomics Suite at SAHMRI in Adelaide.  After graduating from the University of Adelaide in 1993 in Chemistry, he was initially employed in the private sector doing mass spectrometry before moving in 1996 to the Hanson Centre for Cancer Research to assist establish a peptide synthesis and mass spectrometry service.  Following this he worked for local biotechnology companies Geneworks and Bresagen before moving back to SA Pathology in 2001 to establish a microarray facility in a joint partnership with the University of Adelaide.  He became manager of the microarray facility in 2006, rebranding it as Adelaide Microarray Centre and establishing an Affymetrix based array service.  During this time he became involved in genomic data analysis for local research projects and became AGTA Treasurer in 2010.  In 2011 the microarray centre became part of the newly forming ACRF Cancer Genomics Facility where he played significant roles in the design, setup and operation of the new facility.

Ms. Vikki Marshall

Secretary

Website and Communications Working Group
AMATA 2010 Convenor

Operations Manager
Melbourne Neuroscience Institute, University of Melbourne
Melbourne, Australia

Email: vikki.marshall@unimelb.edu.au

Vikki has recently commenced as Operations Manager of the Melbourne Neuroscience Institute (May 2015). Previously she was Genomics Technical Manager at the Murdoch Children’s Research Institute (MCRI) Parkville, where she was involved in both clinical and research-based  sequencing and the Ian Potter Foundation for Personalized Medicine, a joint collaborative effort between the WEHI and the ...

Vikki has recently commenced as Operations Manager of the Melbourne Neuroscience Institute (May 2015). Previously she was Genomics Technical Manager at the Murdoch Children’s Research Institute (MCRI) Parkville, where she was involved in both clinical and research-based  sequencing and the Ian Potter Foundation for Personalized Medicine, a joint collaborative effort between the WEHI and the MCRI. She has been involved with AMATA/AGTA since 2008, being convenor of the highly successful AMATA 2010 conference in Hobart and Vice President and Vice-Treasurer of AMATA from 2011-2013.

Vikki has vast experience in high-throughput genomic technologies and specialist expertise in Second Generation DNA Sequencing (2GS) technologies. Her main interests lay in scientifically accurate and optimally efficient use of genomic technologies, methods development, experimental design, laboratory design and management as well as protocol optimisation.

Vikki holds a Bachelor of Applied Science (MLS) from RMIT University and a Masters of Science by thesis (Dept. Medical Biology) from the University of Melbourne. She completed her tertiary education part-time whilst being employed by the WEHI for some 25 years, where she held positions as Research Officer and Laboratory Manager. At the WEHI, among other projects, Vikki was involved for 14 years in studies of the genetics of host resistance to malaria using mouse models, the subject of her Masters thesis. From lab-based research at the WEHI, Vikki moved to microarray and genomics facility management both at the Peter MacCallum Cancer Centre and at the Queensland Brain Institute, University of Qld.

Dr. Alicia Oshlack

Student Education Working Group

Head of Bioinformatics
Murdoch Children’s Research Institute
Melbourne, Australia

Email: alicia.oshlack@mcri.edu.au

Twitter: @AliciaOshlack

Alicia Oshlack is the head of bioinformatics at the Murdoch Children’s Research Institute in Melbourne. She focuses on the analysis of high-throughput genomics data in the areas of transcriptomics, epigenetics and clinical sequencing. She has been a member of AGTA (AMATA) since 2004.

Dr. Richard Tothill

Post Doctoral Scientist

Research Division
Cancer Therapeutics Program
Peter MacCallum Cancer Centre
Melbourne, Australia

Email: richard.tothill@petermac.org

Richard Tothill is a senior post-doctoral scientist within the Cancer Therapeutics Program at the Peter MacCallum Cancer Centre (Peter Mac). His research interests encompass the use of genomic technologies to understand the genetic basis of cancer, which extends to cancer cell biology, transcription and epigenetics. His past highly cited work has involved the use gene-expression profiling for t...

Richard Tothill is a senior post-doctoral scientist within the Cancer Therapeutics Program at the Peter MacCallum Cancer Centre (Peter Mac). His research interests encompass the use of genomic technologies to understand the genetic basis of cancer, which extends to cancer cell biology, transcription and epigenetics. His past highly cited work has involved the use gene-expression profiling for the molecular classification of solid tumours such as ovarian cancer and cancers of unknown primary. In recent times his focus has shifted to neuroendocrine cancers encompassing rare cancer types such as phaeochromocytoma and Merkel cell carcinoma as well as haematological malignancies with an emphasis on understanding tumour heterogeneity and cancer evolution. He is also involved with the clinical translation of genomic technologies at the Peter Mac with an active role in the co-development of clinical sequencing methods for the deployment of personalised genomic medicine. Richard has been on the AGTA executive committee since 2010 and previously occupied the dual role of Public Officer and Meeting Secretary until 2013.

Prof. Erik (Rik) Thompson

Founding AMATA President

Small Grants Scheme Working Group

Professor and Chair in Breast Cancer Research, School of Biomedical Sciences
Team Leader, Chronic Disease and Aging, Institute of Health and Biomedical Innovation (IHBI)
Queensland Institute of Technology
Brisbane, Australia

Email: e2.thompson@qut.edu.au

Prof Erik (Rik) Thompson was the founding president (2004-2007) of the Australasian Microarray and Associated Technologies Association (AMATA), and is currently President of The International EMT Association (TEMTIA). He has also been President of the Matrix Biology Society of Australia & NZ (2001-2003) and the (International) Metastasis Research Society (MRS). He recently created OzMRS, an...

Prof Erik (Rik) Thompson was the founding president (2004-2007) of the Australasian Microarray and Associated Technologies Association (AMATA), and is currently President of The International EMT Association (TEMTIA). He has also been President of the Matrix Biology Society of Australia & NZ (2001-2003) and the (International) Metastasis Research Society (MRS). He recently created OzMRS, an interest group for metastasis researchers in Australia.

Dr. Jac Charlesworth

Senior Research Fellow

Computational Genomics
Menzies Institute for Medical Research
University of Tasmania
Hobart, Australia

Email: Jac.Charlesworth@utas.edu.au

Dr Charlesworth runs a computational genomics research group at The Menzies Institute for Medical Research in Tasmania. She has a particular interest in complex disease gene discovery using next-gen sequencing in large families, and of using ‘normal’ population variation to inform disease research. She has a background in wet lab genetics but eventially saw the light, and in 2006 she did fo...

Dr Charlesworth runs a computational genomics research group at The Menzies Institute for Medical Research in Tasmania. She has a particular interest in complex disease gene discovery using next-gen sequencing in large families, and of using ‘normal’ population variation to inform disease research. She has a background in wet lab genetics but eventially saw the light, and in 2006 she did four years of postdoctoral training in statistical genetics in the USA.  She is currently ‘gene hunting’ for neurological disorders including multiple sclerosis, eye diseases including glaucoma, and other complex traits including cancers, diabetes and normal brain structural variation.

Prof. Ryan Lister

Laboratory Head

Epigenomics
The University of WA
Perth, Western Australia

Email: ryan.lister@uwa.edu.au

Mr. Liam Williams

Convenor AGTA 2016

Centre for Genomics, Proteomics & Metabolomics

Auckland University
Auckland, New Zealand

Email: lc.williams@auckland.ac.nz

Assoc. Prof. Marcel Dinger

Convenor AGTA 2015

Head of Clinical Genomics & Genome Informatics
Centre for Clinical Genomics
Garvan Institute of Medical Research
Sydney, Australia

Email: m.dinger@garvan.org.au

Marcel Dinger is the Head of Clinical Genomics at the Garvan Institute of Medical Research and conjoint Associate Professor with the St Vincents Clinical School in the Faculty of Medicine at UNSW. He is a recipient of several competitive awards and fellowships, including an NHMRC Career Development Award and a Queensland Government Smart Futures Fellowship.

Dr. Kate Howell

Research Fellow

ARC Centre of Excellence in Plant Energy Biology

The University of Western Australia

 

Email: kate.howell@uwa.edu.au

Twitter: @DrKateHowell

Kate Howell is a plant molecular biologist at the UWA node of the ARC Centre of Excellence in Plant Energy Biology where her research focuses on using sequencing technologies to interrogate plant organellar genomes, the transcripts they encode and the RNA-binding proteins that regulate their expression. She is a former recipient of an Alexander von Humboldt Foundation Research Fellowship (2008-...

Kate Howell is a plant molecular biologist at the UWA node of the ARC Centre of Excellence in Plant Energy Biology where her research focuses on using sequencing technologies to interrogate plant organellar genomes, the transcripts they encode and the RNA-binding proteins that regulate their expression. She is a former recipient of an Alexander von Humboldt Foundation Research Fellowship (2008-2009) and an inaugural ARC Discovery Early Career Researcher Award (2012-2015).

Dr. Kirby Siemering

Coopt

Director of Science and Technology
Australian Genome Research Facility (AGRF)
Melbourne, Australia

Email: kirby.siemering@agrf.org.au

Kirby currently manages the science and technology portfolio at the Australian Genome Research Facility and is responsible for the development and management of major genomics projects. Kirby has over 20 years’ experience in the field of genomics, having held senior positions in both academia and ASX-listed and privately held biotechnology companies, along with experience in biotechnology ind...

Kirby currently manages the science and technology portfolio at the Australian Genome Research Facility and is responsible for the development and management of major genomics projects. Kirby has over 20 years’ experience in the field of genomics, having held senior positions in both academia and ASX-listed and privately held biotechnology companies, along with experience in biotechnology industry analysis, strategy, and policy development at State Government level

Dr. Andreas Schreiber

Membership Secretary/ Vice-treasurer

Bioinformatics Group Leader
ACRF Cancer Genomics Facility
Centre for Cancer Biology
Adelaide, Australia

Phone: +61 8 8222 3965

Email: andreas.schreiber@adelaide.edu.au

 

Andreas heads the bioinformatics group at the Centre for Cancer Biology’s ACRF Cancer Genomics Facility. This group focuses on applied bioinformatics of high throughput experiments, ranging from analysis of transcriptomic microarray or RNASeq data, gene regulation studies using ChIP and CLIPSeq, to the search for disease-associated point and structural mutations of the human genome.

An...

Andreas heads the bioinformatics group at the Centre for Cancer Biology’s ACRF Cancer Genomics Facility. This group focuses on applied bioinformatics of high throughput experiments, ranging from analysis of transcriptomic microarray or RNASeq data, gene regulation studies using ChIP and CLIPSeq, to the search for disease-associated point and structural mutations of the human genome.

Andreas obtained a BSc and MSc from the University of Melbourne, followed by a PhD in theoretical nuclear/particle physics from the University of Adelaide in 1990. He completed postdocs in the Netherlands, Switzerland and Canada before returning to Australia on an ARC Research Fellowship.  In 2002 he switched fields to Bioinformatics by joining the Australian Centre for Plant Functional Genomics at the Waite Campus of the University of Adelaide. He has been with the CCB since 2011.

Dr. Nicole Cloonan

Membership Secretary

ARC Future Fellow
QIMR Berghofer Medical Research Institute
Queensland, Australia

Phone: +61 7 3845 3955

Email: nicole.cloonan@qimrberghofer.edu.au

Nicole Cloonan is an ARC Future Fellow who has recently established the “Genomic Biology Laboratory” at the QIMR Berghofer Medical Research Institute. Her work is multi‐disciplinary in nature, involving bioinformatics, biochemistry, cell biology, and genomics – all of which she uses to understand the complexity, function, and systems biology of RNA. Her previous work has includ...

Nicole Cloonan is an ARC Future Fellow who has recently established the “Genomic Biology Laboratory” at the QIMR Berghofer Medical Research Institute. Her work is multi‐disciplinary in nature, involving bioinformatics, biochemistry, cell biology, and genomics – all of which she uses to understand the complexity, function, and systems biology of RNA. Her previous work has included the development of protocols and analysis techniques for RNAseq, sequencing the genomes of pancreatic cancer patients and their tumours, but most recently has been heavily involved in the miRNA field.

Dr Helen Speirs

Manager, Ramaciotti Centre for Genomics

University of New South Wales (UNSW)

Sydney, Australia

 

Email: h.speirs@unsw.edu.au

Twitter: @RAMAC_Genomics

Helen is the Centre Manager of the Ramaciotti Centre for Gemomics, UNSW. After graduating from the University of Glasgow she went on to complete her PhD at the University of Edinburgh and post-doctoral positions studying the genetics of hypertension. Helen has worked in the field of genomics for 20 years and has been at the Ramaciotti Centre for the past 10 years. Her interests lie in developin...

Helen is the Centre Manager of the Ramaciotti Centre for Gemomics, UNSW. After graduating from the University of Glasgow she went on to complete her PhD at the University of Edinburgh and post-doctoral positions studying the genetics of hypertension. Helen has worked in the field of genomics for 20 years and has been at the Ramaciotti Centre for the past 10 years. Her interests lie in developing genomics technologies and enabling research by making them accessible to the research community.

Dr. Robert Day

Convenor AGTA 2016

Research Fellow
Cancer Genetics
CTCR University of Otago
New Zealand

Email: robert.day@otago.ac.nz

Rob began his research career in 1994 at the University of Bath (UK) studying the defence responses of Cassava plants to bacterial pathogens. He later switched to developmental biology, looking to manipulate the development of seed. In 2004, Rob moved to the University of Otago (NZ) and used Laser Capture Microdissection to interrogate specific seed tissues for mono-allelic expression. This pr...

Rob began his research career in 1994 at the University of Bath (UK) studying the defence responses of Cassava plants to bacterial pathogens. He later switched to developmental biology, looking to manipulate the development of seed. In 2004, Rob moved to the University of Otago (NZ) and used Laser Capture Microdissection to interrogate specific seed tissues for mono-allelic expression. This project involved the comparison of different RNA amplification techniques for use with microarray and RNA sequencing on the Roche 454 FLX and Illumina HiSeq platforms. In 2012 he accepted an appointment at the Otago Genomics Facility to help develop standard operating procedures for sample processing and project management. During this time Rob served on the Project Advisory Committee for New Zealand Genomics Ltd. He currently runs the Illumina MiSeq for the Centre for Translational Cancer Research and is developing new methods for sequence-based diagnostics from single cells and is involved in projects looking at tissue regeneration and fungal endophyte infection. Rob was a member of the AMATA08 conference organising committee and was convenor of the Otago Genomics Facility Meeting 2013-2014.

Previous AGTA Executive Committee Members

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