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The Australian Bioinformatics Network was initiated by

  AustralianBioinformatics.net

ABACBS (pron.ˈabəkəs) runs the Australian Bioinformatics Network

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Profiles

...information about (or links to) members' professional interests and experience

Thursday
Jan092014

Anushi Shah, Software engineer from Vanderbilt University,USA.

Hi, I have obtained Master’s degree in Computer Science at Vanderbilt University, USA. I worked as a software engineer at the Department of Biomedical Informatics, Vanderbilt University with Dr. Joshua Denny and Dr. Hua Xu.

My work at Vanderbilt involved data mining, software tools and web interface development.
I have been involved in data extraction/information retrieval from structured/unstructured sources(clinical notes) and national tumor registry,development of open source clinical NLP framework, developing algorithms for phenotype identification, development of web interface that provides drug exposure information of patients to researchers.
Have been part of national projects Pharmacogenomics Research Network (PGRN)and the Pharmacogenomics of very large populations (PGPop) network at Vanderbilt site.

My skills set include Python, Java, C++, Perl, Oracle, MySql, Netezza, SQLite, Unix/Linux and have familiarity with R package.

I recently moved to Sydney with family and looking forward to work here in varied areas of bioinformatics. I can be reached at patel.anushi@gmail.com for any questions that you may have.

Thanks.

Friday
Nov152013

Eva Chan, Human Comparative and Prostate Cancer Genomics Lab, Garvan Institute of Medical Research 

On the bioinformatics scale (if there is one), I sit at the statistical genetics/genomics end.  

I've recently returned to Sydney from sunny California where I led the statistical genetics team at the Vegetable Seeds Division at Monsanto. My Post-Doc trainings were at the Kliebenstein lab at UC Davis & in Toni Reverter's Biostatistics group at CSIRO (Brisbane, Australia). I'm currently establishing a Bioinformatics and Biostatistics team within the Human Comparative and Prostate Cancer Genomics lab at the Garvan Institute of Medical Research

My research, in terms of the biology and organism, has been quite varied over the years. However, there is always two underlying themes:  "genetic variation" and "big data analysis".  In essence, I enjoy developing and applying statistical and bioinformatics approaches to -omics data with the aim to better elucidate the link between genetics/genomics and phenotype. 

Find me (or my R scripts) @ evachan.org.

 

Saturday
Aug312013

Joshua Ho, Bioinformatics and Systems Medicine Laboratory, Victor Chang Cardiac Research Institute & UNSW, Sydney

The Ho laboratory focuses on the use of bioinformatics and systems biology approaches to tackle longstanding problems in basic and translational medicine. All projects in this laboratory involve integrative analysis of diverse genome-wide datasets, especially next-generation sequencing (NGS) data such as RNA-seq, ChIP-seq, DNase-seq, and whole genome sequencing data. Multiple projects are available under each theme: (i) reconstruction and analysis of inter-cellular gene regulatory network during mammalian organogenesis; (ii) integrative analysis of epigenomic determinants for cell-type-specific signaling response; (iv) chromatin landscape of fungal epigenomcs; and (iv) causal disease mutation identification using whole genome sequencing data. All projects in this laboratory involve analysis of NGS data. Individual projects can be tailored to fit each team member’s professional interests and skill set. VCCRI has an in-house next-generation sequencer and ample computational resources. The laboratory is also actively involved in a host of exciting collaborations with local and international experimental/clinical collaborators.

Dr. Ho completed a BSc (Hon 1, Medal) in Biochemistry and Computer Science in 2006 and a PhD in Bioinformatics in 2010, both at the University of Sydney. He then completed an interdisciplinary postdoctoral fellowship at the Harvard Medical School (HMS), undertaken jointly in the Computational Genomics Laboratory of A/Professor Peter Park, and the Developmental Genetics Laboratory of Professor Richard Maas. In mid 2012, he became an Instructor in Medicine at HMS. In July 2013, he returned to Australia to set up the Bioinformatics and Systems Medicine Laboratory at the Victor Chang Institute. He is also a conjoint senior lecturer at UNSW.

Sunday
Aug252013

Mark Cowley - Garvan Institute & Kinghorn Cancer for Clinical Genomics

I am the head of Translational Genomics in the Kinghorn Centre for Clinical Genomics (KCCG), within the Garvan Institute. I am also a Cancer Institute NSW early career fellow, a senior bioinformatics research officer, and a conjoint senior lecturer at the St Vincent's Clinical School, UNSW.

My primary area of research is translational genomics, that is the application of genome and transcriptome sequencing technologies in the clinic. This involves the use of exome and genome sequencing to uncover the genetic basis of rare, Mendelian disease; the use of targeted gene-panel sequencing to characterise patient tumours for clinically actionable variants and potential off-label therapeutics; the characterisation of pharmacogenomic variants from otherwise healthy individuals; the use of NGS to study liquid tumour biopsies, that is, to detect circulating tumour DNA fragments to be used as both a diagnostic, and as a tool to better understand tumour evolution.

In my role at the Kinghorn Centre for Clinical Genomics I am playing a large part in establishing one of the world's first Illumina HiSeqX Ten sequencing systems. This exciting technology has the capacity to economically sequence upto 18,000 whole human genomes (30x) per year. As such there is a considerable challenge to setup a genome factory to meet the demands of such throughput, with the rigorous quality demanded by the clinical environment.

Brief bio: I completed a BSc (Bioinformatics, Hons 1) at USYD in 2003, and a PhD in bioinformatics, quantitative genetics and genomics at UNSW in 2008. I have been at the Garvan Insititute since 2007, initially as a bioinformatics officer, then as a senior research officer in the Pancreatic Cancer Group and Australian Pancreatic Cancer Genome Initiative. In 2013 I joined the recently created KCCG as a senior bioinformatics officer, and in early 2014 was awarded an early career fellowship with Cancer Institute NSW. In mid-2014, I became the head of Translational Genomics within KCCG.

 

Monday
Jul152013

Yaoqi Zhou, Bioinformatics & Computational Biology, Institute for Glycomics

My research is centered on proteins: protein structure prediction and modeling; protein folding and design; and protein function prediction and design. This includes discrimination of neural from disease-causing genetic variations. Our group has developed many useful bioinformatics tools for protein structure prediction (SPARKS); secondary structure prediction (SPINE X); intrinsic disorder/semi-disorder prediction (SPINE-D); template-based function prediction (SPOT-DNA/RNA); structural alignment (SPalign); knowledge-based energy function (DFIRE) and etc. All these tools are freely available to academic users at http://sparks-lab.org.

Brief Biography: Dr. Zhou was graduated with a BS in Chemical Physics from University of Science and Technology of China in 1984 and a PhD in Chemical Physics from State University of New York at Stony Brook in 1990. He switched his research field to computational biology when he was a postdoctoral research fellow  at Harvard University with Professor Martin Karplus. He became an Assistant Professor in 2000 and Associate Professor in 2004 at Department of Physiology and Biophysics at State University of New York at Buffalo and a full Professor in 2006 when joining Indiana University Schools of Informatics and Medicine at Indianapolis. Starting this year, he joined Institute of Glycomics and School of Information and Communication Technology of Griffith University, Queensland, Australia, as a Professor of Computational Biology.