Sam Lukowski Takes Post-doc in Geneva

Sadly for QBI, Dr. Sam Lukowski resigned on March 23rd and has a taken up his first post-doctoral position at the University of Geneva, Switzerland. We wish Sam and his wife Prue the very best in their venture overseas and thank him for his enormous contribution to the Genomics Facility at QBI, from September 2011.

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Farewell: Dr. Denis Bauer

Dr. Denis Bauer is leaving QBI’s sequencing facility as the postdoctoral research fellow in bioinformatics. We wish her all the best at her new position at CSIRO (Sydney, Mathematics, Informatics and Statistics).

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New team member: Zong-Hong Zhang

QBI has successfully recruited a fantastic Bioinformatician for the sequencing facility: Zong-Hong Zhang.

Zong–Hong completed her Bachelor degree in Computer Science (software development) in Deakin University in Melbourne and a Bachelor degree in Medicine from China. She then went on to receive her master degree in science from the school of computing of National University of Singapore by Bioinformatics Research. Since then, she worked in bioinformatics research for about 7 years before joining QBI.
Her previous projects include protein sequence analysis for functional specialization, database establishment and maintenance, and web server development, microarray data analysis by data mining. She has more than 10 publications in bioinformatics research.

With her extensive experience in both bioinformatics research and IT-administration, Zong-Hong will be a key contributor towards answering neuroscience-specific research questions using NGS data.

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Vikki Marshall: new Vice President of AMATA

Vikki Marshall (University of Queensland, Brisbane) was today (1st October 2011) appointed as the new Vice President of AMATA (Australasian Microarray and Associated Technologies Association). She relieves Dr. Daniel Catchpoole from The Children’s Hospital at Westmead, Sydney and is very much looking forward to shaping the direction of AMATA’s future involvement in genomic technologies.

May 2012

AMATA changes its ‘long name’ from “Australasian Microarray and Associated Technologies Association” to Australasian Genomics Technologies Association” to more accurately reflect its role in the rapidly changing genomics arena, switching much of its focus to 2nd Generation DNA Sequencing (2GS) technologies. The acronym “AMATA” however shall remain for branding and legal reasons.


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Dr. Denis Bauer is a finalist for the 2011 WiT Infotech Research Award

Dr. Denis Bauer is one of the three finalists for this year’s Infotech Research Award from Women in Technology (WiT), which is intended to “celebrate, recognise and reward the outstanding contribution to information & communication technology of an established researcher with an excellent track record in their field”.

Though Denis lost the award to Prof. Janet Wiles, having been nominated as a finalist in this high ranking category is already a great honor and she had a fantastic time speaking to the other inspirational and enthusiastic people at the awards dinner.

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New team member: Dr. Sam Lukowski

QBI’s Centre for Brain Genomics managed to attract another outstanding individual to join the team:  Dr. Sam Lukowski.

Sam obtained a PhD in 2011 for his work on the post-transcriptional regulation of the human CFTR gene – the gene responsible for the fatal, inherited disease cystic fibrosis – with Associate Professors Ann Trezise and Joe Rothnagel at The University of Queensland. Previously, he completed a BSc at Griffith University and a Master of Molecular Biology at the University of Queensland. Following the completion of his doctoral studies, he worked as a Research Officer at the Australian Equine Genetics Research Centre. In 2010, he was awarded a UniQuest Pathfinder grant, under which he continued to work on the modulation of CFTR gene expression using exogenous DNA.

Sam brings a wealth of knowledge and experience in both diagnostic and research-based molecular genetics and will enable the application and development of new library-preparation protocols to realize QBI’s vision of boutique sequencing project to answer neuroscience-specific research questions.

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GATK-CASAVA comparison receives international attention

The preliminary comparison between two variant-calling methods that Denis Bauer published in Nature Precedings [1] receives much attention: The informatics section of the largest online news organization focused on advanced research tools in genomics, proteomics, and bioinformatics, genome-web, interviewed Denis and wrote an article about this topic in August 2011 (“Comparison to Broad’s GATK Shows Illumina’s CASAVA 1.8 Good for SNPs, Short on Indels“). The editor of the New York based publishing center said that the article received over 1000 reads in just three days of being published.

1. Bauer, Denis. “Variant calling comparison CASAVA1.8 and GATK“. Available from Nature Precedings <> (2011)

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QBI’s Bioinformatics Seminar Series

QBI has organized a bioinformatics seminar series to give our researchers a better understanding of bioinformatics, specifically with respect to second generation sequencing data production and analysis. It is advised that all groups planning to use the sequencer send a member to these seminars to give them a better understanding of time frames, analysis steps and the research contribution that they can expect from the bioinformatics analysis for their projects.
Along with the seminar series, there will be a “walk-in-clinic” set up where you can ask bioinformatics questions and get some of the smaller tasks solved directly.
The seminar series and subsequent “walk-in-clinic” will be Thursdays 10am starting from the 16th June, further announcements will be made closer to the date.

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