Tuesday, 20 June 2017

UNSW Genome Annotation Workshop cancelled

Regrettably, due to unforeseen circumstances, EMBL-ABR’s Monica Munoz-Torres Australian tour has been cancelled. As a result, the planned UNSW Genome Annotation Workshop will no longer be going ahead. We hope to organise something similar in future, so will leave the registration page up for a bit longer to get a list of interested parties.

Wednesday, 10 May 2017

UNSW Genome Annotation Workshop

NOTE: Regrettably, this event has now been cancelled. We hope to organise something similar in future and will be in touch with registered individuals to gauge interest.

We are pleased to announce that we are hosting Monica Munoz-Torres from the Berkeley Bioinformatics Open-Source Projects group (BBOP) at Lawrence Berkeley National Laboratory as part of her EMBL-ABR Australian tour, sponsored by the School of Biotechnology and Biomolecular Sciences (BABS) and NSW Systems Biology Initiative (SBI).

In addition to a BABS seminar (details to follow), Monica will be giving a one-day Primer on Genome Annotation workshop at UNSW, with a particular emphasis on collaborative genome annotation using WebApollo.

  • When: 0900-1700, July 7th, 2017
  • Where: Red Centre, UNSW, Sydney, Australia
  • Contact: richard.edwards@unsw.edu.au

You can pre-register for the workshop here or fill in the form below. Places are limited to 30 participants. We will be in touch to let you know if you have a place. Formal registration will require a $20 registration fee.

Friday, 3 February 2017

EMBL-ABR network: an interview with Richard Edwards

From the EMBL-ABR February newsletter:

On 3 February we released an interview with Richard Edwards, the developer of SLiMSuite, an open source bioinformatics tool for the prediction of short linear motifs (SLiMs) and related sequence analysis. In this interview Richard reflects on bioinformatics in Australia as well as the realities of building a sustainable model for the development and maintenance of useful bioinformatics tools such as his.

You can read the full interview: here.

Wednesday, 26 October 2016

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:

Any enquiries contact: Associate Professor Mark Tanaka

Applications close: Sunday 13 November 2016 (AEST)

Friday, 23 September 2016

Predicting Motif Mimicry in Viruses

Sobia will be presenting the initial work from her PhD project today at the EMBO Workshop, The modularity of signalling proteins and networks at Seefeld in Tirol, Austria. Her talk is on:

Predicting Motif Mimicry in Viruses

Viruses mimic host motifs to hijack the host cellular machinery. Their interaction with host protein domains is through Short Linear Motifs (SLiMs). SLiMs are short stretches of amino acids (~3-10) which are involved in post translational modifications (PTMs), protein-protein Interactions (PPIs), cell regulation and cell compartment targeting. To date, several studies have been conducted to identify PPIs, but no specific study to see how well different PPI capturing methods capture SLiMs-mediated interactions. The main objectives of this study are 1) to predict Domain Motif Interactions (DMIs) among viral and host proteins 2) to find whether virhostome (virus-human interaction) data is enriched for DMIs and, 3) to see which PPI method is better for studying DMIs. Results have shown that virhostome data is enriched for DMIs and can be a good source to study motif mimicry in viruses. The permutation test showed more enrichment for TAP data as compared to the Y2H data. Moreover, novel candidate DMIs have been discovered which need further validations. The outcome of this study will be helpful in uncovering unique strategies of viruses to interact with human proteins which will eventually be significant for pathogen research.

Poster to follow.

Thursday, 25 August 2016

Honours and undergrad research opportunities


BABS are currently recruiting the next cohort of Honours students for Semester 1 2017. As usual, the EdwardsLab is looking to recruit enthusiastic students in two main areas:

1. Functional genomics using long-read PacBio sequencing. We are particularly keen to get a student to work on either (a) aspects of our ARC Linkage grant, investigating the evolution of a novel biochemical pathway in yeast, or (b) de novo whole genome sequencing of the cane toad. We also have a number of projects with bacteria for those with a keen interest in microbiology. In each case, the lab is collaborating with experts in the relevant organisms.

2. Applying biological sequence analysis and molecular evolution to study the molecular basis of protein-protein interactions. The main lab software, SLiMSuite has a number of improvements and developments that would benefit from some dedicated attention from a research student. We are also looking for someone who might want to help develop the lab servers.

More details of honours can be found on the BABS website, or please get in touch if you have questions about specific projects. Applications from non-UNSW students are also encouraged.

* BABS are also running an Honours information and networking night on 16th September.*

Summer Vacation Research Scholarships

BABS is once again running its highly successful Summer Vacation Research Scholarship (SVRS) scheme and the EdwardsLab are looking to take on one or two students in the same areas as indicated above.

How to apply

We do not yet have a specific undergraduate application form but it is helpful if you can follow the PhD application process and just make it clear that you are interested in Honours or SVRS. As well as helping select between applicants, this form is also useful for me to make sure that students are assigned an appropriate project.

Friday, 19 August 2016

Plant adaptation or acclimation to rising CO2? Insight from first multigenerational RNA-Seq transcriptome

Watson-Lazowski A, Lin Y, Miglietta F, Edwards RJ, Chapman MA & Taylor G (2016): Plant adaptation or acclimation to rising CO2? Insight from first multigenerational RNA-Seq transcriptome. Glob Chang Biol. Adv. access. doi: 10.1111/gcb.13322


Atmospheric carbon dioxide (CO2 ) directly determines the rate of plant photosynthesis and indirectly effects plant productivity and fitness and may therefore act as a selective pressure driving evolution, but evidence to support this contention is sparse. Using Plantago lanceolata L. seed collected from a naturally high CO2 spring and adjacent ambient CO2 control site, we investigated multigenerational response to future, elevated atmospheric CO2 . Plants were grown in either ambient or elevated CO2 (700 μmol mol-1 ), enabling for the first time, characterization of the functional and population genomics of plant acclimation and adaptation to elevated CO2 . This revealed that spring and control plants differed significantly in phenotypic plasticity for traits underpinning fitness including above-ground biomass, leaf size, epidermal cell size and number and stomatal density and index. Gene expression responses to elevated CO2 (acclimation) were modest [33-131 genes differentially expressed (DE)], whilst those between control and spring plants (adaptation) were considerably larger (689-853 DE genes). In contrast, population genomic analysis showed that genetic differentiation between spring and control plants was close to zero, with no fixed differences, suggesting that plants are adapted to their native CO2 environment at the level of gene expression. An unusual phenotype of increased stomatal index in spring but not control plants in elevated CO2 correlated with altered expression of stomatal patterning genes between spring and control plants for three loci (YODA, CDKB1;1 and SCRM2) and between ambient and elevated CO2 for four loci (ER, YODA, MYB88 and BCA1). We propose that the two positive regulators of stomatal number (SCRM2) and CDKB1;1 when upregulated act as key controllers of stomatal adaptation to elevated CO2 . Combined with significant transcriptome reprogramming of photosynthetic and dark respiration and enhanced growth in spring plants, we have identified the potential basis of plant adaptation to high CO2 likely to occur over coming decades.

PMID: 27539677