BABS is recruiting - academic positions available in bioinformatics, systems biology, medical genomics and biotechnology

The School of Biotechnology and Biomolecular Sciences (BABS) at the University of New South Wales, Sydney, Australia, is seeking to recruit world class scholars with outstanding and recognised research records in Biotechnology, Bioinformatics, Systems Biology or Medical Genomics.

Our School, located at the Kensington campus in Sydney, is part of the Faculty of Science. We have an international reputation in biotechnology, molecular and cellular biology, and microbiology. Particular areas of research strength within these fields include proteomics and genomics, gene regulation, metabolism,environmental microbiology and infectious diseases.

We currently have combined track (research and teaching) opportunities to join BABS as part of a strategic initiative in Systems level Biology and Genomics in the School. BABS hosts the Ramaciotti Centre for Genomics, which has world class facilities for sequencing and is arguably Australia’s premier facility for research genomics. BABS is also home to the Systems Biology Initiative, which is supported by high performance computing facilities, including national supercomputers. Our researchers also have access to outstanding proteomics and metabolomics facilities at the UNSW Bioanalytical Mass Spectrometry Facility and the Mark Wainwright Analytical Centre which provide state-of-the-art facilities and services for animal studies; in vivo and ex vivo preclinical imaging; flow cytometry; biochemical, biophysical and chemical analyses; and electron microscopy. We have collaborative links with the Garvan Institute, the Lowy Cancer Research Centre and other biomedical research organisations within and outside Sydney.

For more information about the School, please visit: www.babs.unsw.edu.au/

About UNSW Australia

• UNSW Australia is a research-intensive university ranked in the world’s top 50 (QS 2016)
• Strong regional and global engagement improving and transforming lives through excellence in research, outstanding education and a commitment to advancing a just society
• The top university in the state of New South Wales in the 2015 Excellence in Research for Australia

UNSW is at the cutting edge of academia with a strong and growing international reputation. A global leader in discovery, innovation, impact, education and thought leadership, can make an enormous difference to the lives of people in Australia and around the world. The recently launched UNSW 2025 Strategy is an innovative, ambitious and altruistic agenda, reflecting a conviction across our University to achieve great things for society during the next decade.

Further details

Further details can be found here:

• Bioinformatics, Systems Biology or Medical Genomics.
• Biotechnology.

Any enquiries contact: Associate Professor Mark Tanaka

Applications close: Sunday 13 November 2016 (AEST)

Transcriptome analysis of human brain tissue identifies reduced expression of complement complex C1Q Genes in Rett syndrome

Lin P, Nicholls L, Assareh H, Fang Z, Amos TG, Edwards RJ, Assareh AA, Voineagu I (2016): Transcriptome analysis of human brain tissue identifies reduced expression of complement complex C1Q Genes in Rett syndrome. BMC Genomics 17(1):427. doi: 10.1186/s12864-016-2746-7.

Abstract

BACKGROUND: MECP2, the gene mutated in the majority of Rett syndrome cases, is a transcriptional regulator that can activate or repress transcription. Although the transcription regulatory function of MECP2 has been known for over a decade, it remains unclear how transcriptional dysregulation leads to the neurodevelopmental disorder. Notably, little convergence was previously observed between the genes abnormally expressed in the brain of Rett syndrome mouse models and those identified in human studies.

METHODS: Here we carried out a comprehensive transcriptome analysis of human brain tissue from Rett syndrome brain using both RNA-seq and microarrays.

RESULTS: We identified over two hundred differentially expressed genes, and identified the complement C1Q complex genes (C1QA, C1QB and C1QC) as a point of convergence between gene expression changes in human and mouse Rett syndrome brain.

CONCLUSIONS: The results of our study support a role for alterations in the expression level of C1Q complex genes in RTT pathogenesis.

PMID: 27267200

In Conversation With Dr Rich Edwards, CI On 2016 ARC Linkage Grant

The latest UNSW School of Biotechnology and Biolomolecular Sciences new article is a brief interview about our recent ARC Linkage success. You can read it here.

Belated congrats to the Wilkins Lab for their #BABSFEST win!

This got a bit buried in all the conference excitement but congratulations to our lab neighbours and journal club buddies for winning the Research Category at the inaugural #BABSFEST video competition:

New EdwardsLab Homepage

The EdwardsLab has a new homepage:

http://www.slimsuite.unsw.edu.au

This blog will remain as the primary source of news and information but the new page gives a fresh landing page and some additional links to resources:

The old pages should now redirect but please point any out of date pages and/or link rot that you come across.

How to apply for a PhD in the Edwards Lab

Choosing the right lab and project in which to do a PhD is one of the most important decisions in the life of a scientist. It is in the best interests of all concerned to make sure that there is a good fit. To this end, there is now a lab PhD application form for all interested applicants. (Click the link or image to download.)

The purpose of the form is two-fold:

1. To assess the skills, experience, and interests of applicants.
2. To assess key CV points for those intending to apply for UNSW Scholarships.

The lab does not currently have any funding for students but I am happy to receive applications from funded students and students wishing to apply for UNSW scholarships or other schemes. Please check the UNSW key dates page for application deadlines etc. - students may want to delay their application and strengthen their experience/CV in the meantime.

Informal enquiries are welcome but generic “Dear Sir/Professor” emails will be ignored. Please read this blog post, “How (not) to apply for a PhD”, before applying.

Note: Applicants with insufficient bioinformatics experience will not be considered (see below). It is simply too much of a risk (for both student and supervisor) to take such a student on, as not everyone takes to purely computational work. You must also demonstrate good communication in English, which includes all email communication.

Available projects

There are no specific projects on offer and PhD research topics will ultimately be a collaborative decision based on the skills and interests of the student as well as the current status of various research in the lab. Available projects range from algorithm and bioinformatics resource development to primarily data analysis projects. Examples include, but are not limited to:

• Yeast genomics using long-read PacBio sequencing. We are particularly keen to get a student to work on aspects of our ARC Linkage grant, investigating the evolution of a novel biochemical pathway in yeast.
• De novo whole genome sequencing and assembly of the cane toad.
• The role of gene duplication in the evolution of snakes.
• The development of diploid genome assembly analysis tools.
• Development of network approaches to understanding SLiM-mediated protein-protein interactions. (Strong maths required.)
• Predictions of molecular mimicry from host-pathogen interaction data.
• Exploring the role of SLiM mutations in cancer and other human diseases.
• Development of a database of SLiM predictions.
• Benchmarking, optimising and extending SLiM discovery tools.

There is no single perfect applicant profile: please provide a frank and honest appraisal of your interests, skills and future goals in your application.

Submitting your application

Completed applications forms should be emailed with a CV and degree transcript to richard.edwards@unsw.edu.au. Please name each file with your family name, initials and document type, e.g.

EdwardsRJ.Application.docx
EdwardsRJ.CV.pdf
EdwardsRJ.Transcript.pdf

PDFs are preferred but MS Word *.docx files are also OK. Remember: attention to detail is very important in bioinformatics. Boxes in the application form may be resized but please keep answers succinct; you will be judged on the quality of your writing.

Note: Applicants will also need to submit a formal application through the UNSW Graduate Research School. This is not recommended until an agreement has been made to sponsor your application. Please also note that any agreement to sponsor your application is not agreement to take you on as a student. The final decision regarding supervision will not be made until after all of the applications have been received and processed by UNSW.

Masters and undergraduate project applicants

Applicants for undergraduate projects (Honours/SVRS) or Masters programs should use the same form but indicate the program that they are applying for.

Bioinformatics Experience Requirements

All projects are 100% computational. To be considered as an international PhD applicant, you must have completed at least one 100% computational project as part of your undergrad or masters, or have equivalent computational experience (e.g. work placement as a programmer or data analyst). Taught courses are not sufficient at this level unless you can also provide some evidence of skill at scripting/programming, such as an extensive body of work at Rosalind. Unfortunately, the risks are simply too high otherwise.

Vicky Schneider BABS seminar this friday - My journey through biology and bioinformatics: my family and other animals

Following InCoB2014, we are lucky enough to be hosting Dr Vicky Schneider to discuss bioinformatics training. As part of her visit, Vicky will be giving a special BABS Seminar this Friday (8 Aug) at 3pm.

The seminar will be followed by “Happy Hour” at 4pm in the Wilton Room 113, Samuels building, UNSW. All welcome!

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My journey through biology and bioinformatics: my family and other animals

Friday 8 August @3pm
Rountree Room 356, Level 3,
Biological Sciences Building D26, UNSW.

Speaker: Dr Vicky Schneider

Affiliation: The Genome Analysis Centre (TGAC), Norwich, UK

Abstract: From my roots and growing passion for nature an biology, I will share with you my career pathway and the progression that brought me from an evolutionary field biologists to bioinformatics and a passion for building communities, working and engaging with others to achieve goals, share experiences and best practice in bioinformatics. More than ever, in the era of Next Generation Sequencing and OMICs we need to proactively create the opportunities and activities towards bridging the gap between biologists and computational researchers. Similarly, best practice in programming, storing, annotating and sharing data are crucial towards reproducibility and open science. I will also give you an overview of The Genome Analysis Centre (TGAC), in Norwich, UK where I am currently a member of its Senior Management team and lead the 361° Division on Scientific Training, Education and Learning.

Biography: Before her current post at TGAC, Vicky was the European Bioinformatics Institute (EMBL-EBI) User Training Coordinator. Prior to joining EMBL-EBI in 2007 she held an Assistant Professor position at the University of Bern and the Institute for Aquatic Sciences (EAWAG) and postdocs at the University of Zurich and University of Rome (Torvergata). She studied biology at the University of Rome and obtained her PhD on the evolution of sex at the University of Leiden (NL) and Lyon (France). Vicky played a key role in the creation and establishment of the Bioinformatics Training Network (BTN) which has now evolved into the Global Organisation for Bioinformatics Learning, Education & Training (GOBLET). For more information, see: http://www.tgac.ac.uk/training-outreach/vicky-schneider/.