Connecting Australian researchers to Europe and Japan: EMBL Australia in November

EMBL Australia

In this month’s newsletter:

Posted on behalf of Nadia Rosenthal, Scientific Head, EMBL Australia

We have just said ‘sayonara’ for now to a series of distinguished Japanese visitors who came to Australia to make new connections and to learn more about Australian life science. All reports suggest that they were impressed with what they saw and are keen to collaborate.

They visited Melbourne, Canberra, Adelaide and Sydney, toured some of Australia’s top research facilities and institutions, and discussed ideas around internationalising research with academics and industry leaders along the way. I’m pleased that we’re starting to use EMBL Australia to build a triangle of research connections linking Australia to Europe and Japan.

Professor Makoto Asashima, Director of the Japan Society for the Promotion of Science, met with government and academy representatives in Canberra and spoke at Questacon and at Monash.

At a Nature Café event in Melbourne – the first held outside Japan – we heard about the challenges of internationalising research from both Japanese and Australian perspectives. At a reception for a RIKEN delegation in Melbourne, we learned how Japanese systems approaches might even assist the Australian minerals industry. These types of events where we can personally meet with our overseas counterparts are particularly important for initiating collaborations, and we hope that the events of the last month will help catalyse ideas for future research collaborations with Japanese life scientists.

This month we welcome a visitor from Europe, EMBL alumnus, Professor Lars Juhl Jensen from the Novo Nordisk Foundation Center for Protein Research, Disease Systems Biology in Copenhagen. Lars heads a disease systems biology group that has been analysing health records, literature and experimental datasets to understand the principles that govern complex biological systems such as the cell cycle, signaling networks and diseases. He’ll be speaking at symposiums in Melbourne where he’ll share some of his data mining techniques.

Systems biology received a big boost in Sydney two weeks ago when Barbara Fazekas de St Groth and her team from the Centenary Institute and The University of Sydney received a $1 million grant to establish the Ramaciotti Centre for Human Systems Biology in Sydney. It’s an exciting development.

On the national bioinformatics front, Professor Terry Speed, a longstanding supporter of EMBL Australia, met with the Prime Minister last Wednesday and discussed how maths and statistics are changing biomedical research. He received the $300,000 Prime Minister’s Prize for Science for his lifetime of achievements using statistical methods to solve biomedical problems, including pinpointing malaria proteins responsible for initiating infection in human red blood cells, and recent work in identifying areas in the human genome that contribute to cancer. We send Terry our warmest congratulations.

Finally, I’d like to wish this year’s group of Australian PhD students attending the EMBL PhD Symposium all the best as they head to Europe later this month. I look forward to hearing about your experiences when you return.

Best wishes,

Professor Nadia Rosenthal
Scientific Head, EMBL Australia
Please note that all replies to this newsletter go to If you wish to email me directly, my address is

Catalysing collaboration with Japan

EMBL Australia has just wrapped up ‘Japan Month’ – a series of even

Australia's first ever Nature Café panel discussed the challenges and benefits of internationalising Australian research. (Credit: Toni Stevens, Science in Public)

Australia’s first ever Nature Café panel discussed the challenges and benefits of internationalising Australian research. (Credit: Toni Stevens, Science in Public)

ts featuring our Japanese visitors from RIKEN, SBI and JSPS. The events focussed on internationalising Australian research and making connections with Japan.

The highlight of the program was the ‘Nature Café’event – an informal panel discussion with academic and industry leaders hosted in partnership with science journal Nature. The topic on the menu focussed on the benefits and challenges of internationalising research.

So how do institutions successfully internationalise their research, in this age where universities and industries compete globally for scientific discovery and in attracting and retaining the best and brightest?

Read more about the event.

As part of Japan Month we also co-hosted a reception with Club Melbourne at the Melbourne Convention and Exhibition Centre where the RIKEN delegation and Hiroaki Kitano

(SBI) met with academics and industry leaders from around Victoria to share stories of successful scientific collaborations with Japan, and spark new ideas. From mapping the kangaroo’s genome to growing Australia’s seaweed industry, collaborations with Japan have been fruitful. Read more about the event.


Prof Asashima gave a public lecture on research and policy trends in life sciences in Japan at Questacon in Canberra. (Credit: Questacon)

Japan Month also saw visits from Professor Makoto Asashima, head of the Japan Society for the Promotion of Science (JSPS), and Dr Hiroki Ueda, University of Tokyo’s rising star of systems biology, who also visited EMBL Australia’s node in South Australia.

Hiroki Ueda gave interactive talks in Melbourne and Adelaide to show how he is using systems biology to model complex systems such as the mammalian circadian clock. Read more about Hiroki’s symposium.

Professor Asashima met with researchers at Monash University in Melbourne, and with government officials and the Australian Academy of Science in Canberra. Befittingly, he also gave a public lecture at Questacon – The National Science and Technology Centre in Canberra, which was originally established in 1988 as a joint venture between Australia and Japan.

Travel to Europe with an EMBL Aus Travel Grant – Apply Now


Simone Li, PhD Candidate, EMBL Heidelberg Germany.

Simone Li is an Australian PhD candidate studying at EMBL in Germany. She never really planned to study overseas, but her travel experiences have been life-changing.
“It has been an eye-opening experience – making friends not only from Europe but all over the world, seeing renowned scientists in the corridor everyday…and living it up in Europe of course!”
If you’re an Australian University PhD candidate, you too can kick start your overseas research experience and begin to build international networks with an EMBL Australia Travel Grant.
Use the grant to take a short course, attend a conference, or work alongside some of the young researchers like Simone at one of EMBL’s five facilities: Heidelberg and Hamburg in Germany; Grenoble in France; Hinxton in England; or Monterotondo in Italy.
There is still time to apply for Round 1 travel between 1 January and 30 June 2014. Round 1 will close on Friday 8 November.
Find out more and submit your application now.

In other news

A Human System Biology Centre for Sydney

Prof Nicholas King (University of Sydney) with Dr Adrian Smith and Prof Barbara Fazekas de St Groth (Centenary Institute). (Credit: Kat Finch, Centenary Institute)

Prof Nicholas King (University of Sydney) with Dr Adrian Smith and Prof Barbara Fazekas de St Groth (Centenary Institute). (Credit: Kat Finch, Centenary Institute)

With SBI Australia continuing to grow, and now with the planned establishment of the Ramaciotti Centre for Human Systems Biology at the Centenary Institute in Sydney, we are excited to see systems biology really taking off in Australia.

The new centre will be funded by the Ramaciotti Biomedical Research Award prize of $1 million, which has been won by the Centenary Institute’s Prof Barbara Fazekas de St Groth and her colleagues Prof Nicholas King (The University of Sydney) and Dr Adrian Smith, (Centenary Institute). EMBL Australia sends congratulations to all.
The centre will also purchase Australia’s first CyTOF (cytometry by time of flight) mass spectrometer, which will allow researchers to track up to 100 different cellular processes simultaneously in a thousand cells each second.
“We’ll be able to ask individual immune cells where they’ve been and who they’ve been talking to…” Professor Fazekas, says. Read the full story.

A closer look at coral draws genomic data to Australian shores

Most tourists flock to Australia’s coral reefs for the colourful seascapes and bustling marine life. But what Dr Guy Cochrane, a Group Leader of EMBL’s European Bioinformatics Institute (EBI) and head of its European Nucleotide Archive (ENA), finds most exciting about Australia’s coral is its genome.

“Coral is interesting because it’s not just one creature, it’s a whole community or ecosystem in one organism. Sequencing this is a challenging project.”
Brought out by EMBL Australia, Guy travelled the country in October discussing corals at the Australian Institute of Marine Science (AIMS) in Townsville, and visiting the Bioinformatics Research Australia EMBL (BRAEMBL) to talk about the EBI and ENA and their current interests.

The ENA is a set of databases of sequencing information – one of three major facilities, in Europe, the US and Japan. “We hold information on about 800,000 different organisms,” says Guy – but not on research involving human subjects. One major area of research and development, he says, is data compression – how to store data more efficiently and cost-effectively.

During his visit he was gathering information to work out how the ENA and EBI can serve Australian researchers better, both directly and by catering to more local needs through the Bioinformatics Research Australia EMBL (BRAEMBL) data mirror site based at the University of Queensland. Read the full story.

Terry Speed wins top science prize for a lifetime with numbers

Terry Speed's top science award is helping to place bioinformatics in the national spotlight. (Credit: Prime Minister's Prizes for Science/Bearcage)

Terry Speed’s top science award is helping to place bioinformatics in the national spotlight. (Credit: Prime Minister’s Prizes for Science/Bearcage)

Australian statistician, Terry Speed – a friend and valued supporter of EMBL Australia, and pioneer of bioinformatics, has won the 2013 Prime Minister’s Prize for Science.
Terry received the prize at Parliament House earlier this week for his life’s work using mathematics and statistics to solve real world issues. For the past few years he has been the world’s most cited mathematician and Australia’s most celebrated researcher in his field.

Terry is regarded internationally as the world expert on the analysis of microarray data. The ingenuity of his approaches, together with his commitment to working closely with biomedical scientists, has enabled him to grasp the opportunities and challenges of new methodologies as they are applied to biomedical problems. Terry’s work has greatly enhanced our understanding of infectious disease, the immune system, heritable human diseases and cancer. Read more about Terry’s work and the award.

phdAustralian PhD students enter Race for Survival in Germany
Twenty PhD Students from around Australia will head off in mid-November to the annual EMBL PhD Symposium at EMBL headquarters in Heidelberg.
This year’s successful applicants came from Victoria, NSW and Queensland, from institutes including University of NSW, University of Sydney, ANZAC Research Institute, the Institute of Molecular Bioscience, the University of Queensland, Queensland Institute of Medical Research, Deakin University, University of Ballarat, University of Melbourne and Monash University.
A report on the symposium will be included in the December newsletter.
The theme of this year’s symposium is Competition in Biology.

Coming up this month

Mining the medical data for valuable gems of information

Professor Lars Juhl Jensen

Professor Lars Juhl Jensen

The medical world is now more data-rich than ever, and this wealth of

data is growing all the time. In the lab we are collecting molecular data, and in our hospitals, detailed health records. So how do we bridge the gap between the two types of data to predict health outcomes and offer the right treatments for patients?

Lars Juhl Jensen, head of the disease systems biology group at the Novo Nordisk Foundation Center for Protein Research in Copenhagen, has been using data and text mining methods to find correlations between datasets from health records, literature, and experimental studies to help medical professionals give patients the most appropriate treatments, and predict adverse outcomes.
To learn more, join him in Melbourne this month at:
University of Melbourne Computing and Information Systems Seminar

When: 12 noon, Tuesday 12 November

Where: NICTA, Denis Driscoll Theatrette (Room 3.09), Doug McDonell Building, The University of Melbourne, Victoria

RSVP: as places are limited
Topic: ‘Data and Text Mining’ – At the symposium, Lars will talk about data text mining methods using the STRING Database, and introduce some web-based resources that enable a systems biology approach to examining disease. Read more online.

Monash Systems Biology Seminar

When: 2pm, Wednesday 13 November

Where: Level 2 Seminar Room, Monash Institute of Medical Research, 27-31 Wright St, Clayton, Victoria

Topic: ‘Medical Data Mining’ – Lars will talk about the centralised Danish health registry, and how to perform text mining to reveal correlations and clinical narratives that can help predict a patient’s adverse reactions to a drug. Read more online.

BioinfosummerBioInfoSummer 2013 University of Adelaide 2 to 6 December
BioInfoSummer – an annual summer school in bioinformatics held by the Australian Mathematical Sciences Institute (AMSI) – introduces students, researchers and others working in related areas to bioinformatics.

This year, EMBL Australia is continuing to support both BioInfoSummer and the Winter School through the Australian Bioinformatics Network initiative. Through the ABN, EMBL Australia has committed funding to support these programs for the next three years.

Find more about this year’s BioInfoSummer program, including registrations and application for travel funding.

AMSI is seeking companies, students and mentors interested in bioinformatics industry applications

Are you a company or research organisation with a research interest in bioinformatics? Or a student with a desire to use your bioinformatics skills in real world applications? Then a BioInfoSummer Internship could be your opportunity.

The EMBL Australia and BioPlatforms Australia BioInfoSummer internships scheme offers bioinformatics business and research organisations access to subsidised AMSI Internship placements. Under the guidance of a supervisor, students will complete a 4-5 month research project identified by the partner and present their project at BioInfoSummer 2014.
For more information visit the AMSI Intern website.

Upcoming events and deadlines

Upcoming events and deadlines
If you have events to add to the EMBL Australia events calendar, drop us a note on with the details and a link for more information.

12 November – Uni of Melbourne Computing and Information Systems Seminar – Lars Juhl Jensen

13 November – Monash Systems Biology Seminar – Lars Juhl Jensen

20 November – Next Generation Sequencing Bioinformatics, Sydney

20 November – Victorian Systems Biology Collaborative on Microbiome, Monash University.
21 November – EMBL PhD Symposium, Heidelberg, Germany

25 November – Next Generation Sequencing Bioinformatics, Brisbane

Other upcoming

2 December – BioInfoSummer, Adelaide

13 January – 15th International Conference on Systems Biology

Australia’s membership of EMBL

EMBL – the European Molecular Biology Laboratory – is Europe’s flagship for the life sciences. The Australian government joined EMBL as an Associate Member in 2008.
EMBL Australia was created to maximise the benefits of Australia’s associate membership of EMBL. It creates opportunities for:

  • internationalising Australian research
  • empowering and training our best early career researchers/research leaders
  • embedding powerful new enabling tools such as bioinformatics and systems biology in Australian life science.

EMBL Australia comprises:

  • Victorian node at Monash University, with two research groups and SBI Australia (Systems Biology Institute)
  • South Australian node at SAHMRI, opening in 2013 with three research groups
  • Queensland node at the University of Queensland with the Bioinformatics Resource Australia and plans for future research groups
  • NSW node at the University of Sydney with one research group (currently based in Europe) and plans for future research groups
  • Australian Bioinformatics Network, based at CSIRO
  • A node will be developed at the University of Western Australia as funds and opportunities arise.

EMBL Australia is an unincorporated joint venture between members of the Group of Eight universities and the CSIRO, supported by the Australian government.

Read more about EMBL Australia at:

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