Research Fellow- (Quantitative geneticist/ genomicist)

Employer: James Cook University

Applications close: 26th Feb 2018

Position Overview: The Research Fellow will guide and conduct research activities within a collaborative CRC DNA project, Breeding for resistance to juvenile pearl oyster mortality syndrome (JOMS). The incumbent will primarily determine correlative factors associated with the occurrence of JOMS and gather the essential genetic knowledge required to instigate a selective breeding program within a functional pearling farm via commercial partners.

The Research Fellow will conduct research activities within the research team under the primary supervision of the project leader. The incumbent will also complete project specific administration functions, report writing and the co-supervision of postgraduate students.

Principal Accountabilities:

1. Contribute to the design and conduct of experiments, including acquisition and modelling of phenotypic / environmental data to understand tolerance to JOMS in pearl oysters.

2. Undertake quantitative genetic analyses to estimate phenotypic genetic parameters (eg., heritability, breeding values and trait correlations)

3. Undertake quantitative genetic and QTL localisation analyses to identify any genes of major effect and trait architecture.

4. Undertake bio-statistical analyses to estimate correlative relationships between JOMS resistance; and nutritional, physiological, bacterial and environmental factors.

5. Use Genotype by Sequencing (GBS) methodology, incorporating computational and statistical approaches, to determine relatedness and diversity of pearl oysters to inform a selective breeding program.

6. Co-supervise honours and higher degree research students.

7. Communicate quality research in high ranking international scientific journals and provide conceptual support to projects.

8. Utilize appropriate and current techniques/protocols in experimental laboratory management to ensure integrity, security and replicability of experimental procedures.

 Website: https://www.jcu.edu.au/careers-at-jcu/vacancies/research-jobs

Contact Phone: (07) 4781 6532

Contact Name: Kyall Zenger

Contact Email: kyall.zenger@jcu.edu.au

BIOINFORMATICS CANCER GENOMICS ANALYST

Employer: University of Melbourne Centre for Cancer Research

Closing date: 25 March 2018

Brief position description: The Rare Disease Oncogenomics Laboratory (Tothill Laboratory) with the University of Melbourne Centre for Cancer Research (UMCCR) is seeking an early career bioinformatician to contribute to a large cancer genome sequencing study (A5 SDHB Genomics Study) involving analysis and integration of whole genome DNA sequencing with other genomic datasets. You are required to possess in-depth knowledge of the principles and practice of bioinformatics as it relates to genome and transcriptome interrogation, be fluent in Unix/Linux and proficient in one or more scripting languages (eg. Perl, Python, etc). The successful applicant will become integrated into a collaborative working environment of wet lab scientists and bioinformaticians within the UMCCR working on translational and clinical cancer genomics across a number of disease types.

Job website: http://jobs.unimelb.edu.au/caw/en/job/892128/bioinformatics-cancer-genomics-analyst

Contact name: Richard Tothill

Contact email: rtothill@unimelb.edu.au

Research for development (R4D) Implementation Officer

Employer: Agricultural Impact International Pty Ltd (AgImpact) 

Closing Date: 16th Feb 2018

Description: 

AgImpact is a research for development (R4D) organization that specialises in the implementation of CommCare1 for digital data collection in both the agriculture and health sectors. CommCare is an open source mobile data collection platform that is actively used in over 60 countries, and is the most widely adopted, technically advanced, and evidence-based mobile platform for low-resource settings.

Agimpact also provides project management and technical advisory services for R4D projects, and strategically tells our partners’ stories of impact through the written word, photography and short film.

We work with universities and research entities, multilateral agencies, social enterprises, nonprofit agencies and the private sector, to improve their R4D outcomes and impact, primarily in emerging economies.

AgImpact is based in Sydney, Australia, but works globally, with a focus in Southern Asia, Southeast Asia and the Pacific. AgImpact’s diverse team is bound together by a common purpose and values: we care about what we do and the people we work with; we do our best always and love solving problems; we learn from our mistakes and celebrate our successes; we want our work to matter.

The Role

The R4D Implementation Officer is an important member of AgImpact’s multidisciplinary, geographically dispersed team offering implementation solutions in the R4D space. This will primarily be through the delivery of CommCare implementation, training and support to project partners.

The R4D Implementation Officer will:

• Work with clients to assess their needs for planning the effective adoption of CommCare for digital data collection.

• Advise projects on how best to structure applications, modules and forms in CommCare to maximize efficient data management.

• Transform paper-based surveys into CommCare forms, working closely with projects and/or researchers to fine-tune form-building and applications. 

• Test CommCare apps prior to their release to clients, and work with clients to revise their mobile app following testing as necessary.

• Provide capacity-building to select projects in the ongoing use and management of CommCare, as required.

• Problem solve and provide solutions for clients in the application and use of CommCare as required.

• Travel for short periods throughout SE Asia, Southern Asia, Pacific and Australia, to perform ‘face to face’ training and support to clients in the adoption and use of CommCare.

• Provide ongoing programmatic support and monitoring of project activity, as required.

• Assist in the preparation and periodic review of AgImpact’s training and support materials.

• Design and build dashboards (excel, tableau, shiny) for data and field worker performance monitoring for clients.

  The conditions of employment (location, time commitment and remuneration package) are dependent on the quality of the applicant.

  Personal Requirements

  To effectively perform this position, the R4D Implementation Officer will be:

• Highly competent in computer programming, information technology and database management.

• Highly competent in the use of CommCare, including form-building, data management and application building. Note: AgImpact is prepared to invest in training for the right individual to become CommCare certified.2

• Experienced in data analysis and statistical software such as R, Stata and SPSS is desirable.

• Experienced in designing dashboards for data monitoring in excel, shiny or Tableau is desirable. Note: Training is available for the right individual.

• A background in Agriculture, International Public Health or International R4D projects.

• Genuinely enthusiastic for supporting colleagues/clients.

• Passionate about international research for development (R4D).

• Reliable, self-directed, adaptable and responsive.

• A problem-solver who is always looking for ways to add value to the people they support.

• Experienced in training groups of non-technical users on technical matters. 

• Lines of Reporting

  The R4D Implementation Officer reports to the AgImpact Director.

  The R4D Implementation Officer will be working closely with the R4D Support Lead.

  Application

  Please reply to Stuart Higgins (Director) with an up to date CV (including references) and a cover letter highlighting:

• -  what appeals to you about the role,

• -  examples of past experience and/or qualifications that demonstrate your

  skills/ability/experience against the role requirements, and

• -  examples of past experiences that demonstrate your skills or ability to

  acquire new skills. 

Contact name: Stuart Higgins

All applications should be submitted via email to: stuart@agimpact.org with cc to: chaseley@agimpact.org. 

Bioinformatics PhD scholarship available in Auckland, New Zealand

Employer: Massey University Auckland

Closing date: We are reviewing applications as they are received, as such candidates are encouraged to submit their application as soon as possible.

Brief position description: We have a PhD position, including scholarship covering fees and living expenses, available in our group in Auckland, New Zealand. The prospective candidate will analyse transcriptomics and genomics data sets from high-throughput experiments in mammalian systems with a focus on gene regulation, non-coding RNAs, and epigenetics. Please have a look at our recent publications to get an idea what topics we work on. However, if you have specific interests within the wider scope of gene regulation and/or non-coding RNAs, we are happy to discuss those as well.

You have experience in the analysis of next-generation sequencing datasets, e.g. RNA-seq, WGS, ChIP-seq, etc.? You have a MSc or BSc(Hons) degree (or equivalent) in a related discipline? You have a curious mind and enjoy doing research? You feel comfortable on the Linux command-line and have good English language skills? You might just be the right person to fill this position! Both local and international students are encouraged to apply.

The studentship covers all university fees and includes an annual tax-exempt stipend of up to NZ$27,500 for three years.

To apply for this position, please email your complete application to Dr. Schmeier. The application should include a cover letter explaining why you are a great fit for our group, a current curriculum vitae including the names of two referees, your academic transcripts, as well as proof of English language skills if your past degrees are not from an English speaking institution (might be handed in at a later stage). If you think of applying for this position, please also have a look at the general guide for applicants (http://sschmeier.com/team/application/).



Enquiries and applications to Dr. Sebastian Schmeier (s.schmeier@massey.ac.nz)

More information can be found at the Schmeier Group website: https://sschmeier.com/

Link to official job ad: http://sschmeier.com/posts/20180126-phd-scholarship/

Job website: http://sschmeier.com/posts/20180126-phd-scholarship/

Contact name: Sebastian Schmeier

Contact email: s.schmeier@massey.ac.nz

Junior - Senior Bioinformatic Scientists (Epigenetics Research Laboratory)

Employer: Garvan Institute of Medical Research

Closing date: We are reviewing applications as they are received, as such candidates are encouraged to submit their application as soon as possible.

Brief position description: At Garvan our research is focused upon understanding the role of genes and molecular and cellular processes in health and disease as the basis for developing future preventions, treatments and cures. Our scientists are researchers who work towards making significant breakthroughs in scientific discovery to positively impact human health.

About Us

The Epigenetics Research Laboratory bioinformatics team focuses on the development and implementation of cutting-edge software for the analyses of multi-omic sequencing data to elucidate how epigenetic and resulting transcriptional processes are disrupted in cancer and to translate this knowledge to improve health outcomes through development of cancer biomarkers and potential therapeutic targets.

The Opportunity

We are now seeking to expand our bioinformatics team in the Clark Lab with talented and highly skilled Junior to Senior Bioinformatic Scientists for the development and implementation of statistical and bioinformatic tools and analyses of large genomic, epigenomic and chromatin conformation sequencing data. In addition, projects in DNA methylation breast and prostate cancer biomarker discovery and validation are available. The incumbents will have close interaction with post-doctoral scientists, PhD students and Research Assistants in the Epigenetics laboratory, which is a leading epigenetic research group in Australia, as well as within the wider Genomics and Epigenetics Division, and The Kinghorn Cancer Centre, making it a world-leading genomic research environment.

Key Responsibilities

• Lead the computational and statistical analysis of whole genome bisulphite sequencing and genomic sequencing data sets and integration with RNA, chromatin immunoprecipitation sequencing data to define new paradigms of cancer epigenome regulation.
• Lead the computational and statistical analysis of chromatin conformation sequencing and capture sequencing data to determine three dimensional epigenome regulation.
• Lead DNA methylation biomarker discovery and validation projects, using large scale DNA methylation array based studies and multiplex PCR bisulphite sequencing.
• The experimental design, statistical analysis and bioinformatics needs of research projects in the Epigenetics Laboratory in the Genomics and Epigenetics Division. 
• Development and implementation of existing and new bioinformatics tools and systems available for large scale genome and epigenome analysis. 
• Manage data storage, and maintain and update computational pipelines to ensure best practice.

About You

To be successful in this position, you will be a highly talented individual with experience in computational and statistical analysis of genomic and epigenomic sequencing data and who is results driven and motivated by being part of a dynamic environment. You will be a team player and collaborator who thrives in a culture of innovation and delivery. You will also possess the following key skills and attributes: 

• A PhD degree in statistics, computer science, software engineering, information technology or a related field
• Experience with machine learning methods and multivariate statistics operating at a senior level
• Experience with Stata, R and BioConductor
• Proficient programming skills in Java (preferably experience with Java 8) with the ability to work comfortably in a Linux environment is desirable
• Familiarity with the Unix command line
• Familiarity with web-based bioinformatics resources such as NCBI, UCSC and NetAffx
• Knowledge of the fundamentals of molecular biology: DNA transcription and translation
• Skills in analysis of whole-genome bisulphite sequencing data, RNA-seq, ChIP-seq, HiC-seq data
• Strong commitment to data organisation and implementation of quality controls
• Excellent communication skills for written reports and oral presentations
• Capacity to work co-operatively with other team members
• Be well organised and a good time manager

Qualifications

A PhD in a quantitative discipline (statistics, bioinformatics, mathematics, physics, engineering and computer science) who is looking to develop an independent research career.

How to Apply

All applications must be submitted via Garvan’s Careers website: 
http://garvan.applynow.net.au/jobs/GC201845 

Please prepare and submit your application as per the directions below: 
• A cover letter addressing the selection criteria above
• Your resume including three (3) referees
• Copies of relevant qualifications and academic transcripts

Closing Date

We are reviewing applications as they are received, as such candidates are encouraged to submit their application as soon as possible.

Job website: http://garvan.applynow.net.au/jobs/GC201845

Contact name: Human Resources

Contact email: hr@garvan.org.au

Scientific Officer – Centre for Biological Data Visualisation

Employer: Garvan Institute of Medical Research

Closing date: 2 February 2018

Brief position description: At Garvan our research is focused upon understanding the role of molecular and cellular processes in health and disease, as the basis for developing future preventions, treatments, and cures. Our scientists work towards making significant breakthroughs in scientific discovery to positively impact human health.

The Opportunity:
We are seeking an exceptional individual to take up a key role as a Scientific Officer in Garvan’s Centre for Biological Data Visualisation. Reporting directly to the Centre Head, the appointee will be responsible for management, coordination, and administration of complex, multi-institutional projects. 

The successful candidate will be an excellent negotiator who can work very well in a collaborative environment of innovation and empowerment. You will also possess the following key skills and attributes:

• Bachelor’s degree and/or an advanced degree in relevant area of science
• At least two years of prior experience in a similar environment
• Excellent written and oral communication skills
• Strong problem solving and analytical skills
• Strong negotiation and strategic skills
• Be highly organised
• Be strongly detail-oriented
• Have a flexible, proactive, can-do attitude

The Centre for Biological Data Visualisation:
The Centre for Biological Data Visualisation develops novel solutions to cutting-edge data challenges, with the goal of accelerating discovery in biomedical research. We collaborate with strategic initiatives and institutions in biomedical research, both in Australia and internationally, with a particular focus on diseases of relevance to Australian society. 

How to Apply: 

Please submit your application by visiting our careers website: http://garvan.applynow.net.au/jobs/GC201841. 
To be considered for this position, applications should be submitted by 2 February 2018.
In addition to your CV and cover letter, please also attach relevant qualifications.
Garvan is an equal opportunity employer and encourages all qualified applications to apply for this position.

Job website: http://garvan.applynow.net.au/jobs/GC201841

Contact name: Human Resources

Contact email: hr@garvan.org.au

Computational System Biology position for SynBio projects

Employer: CSIRO

Closing date: 11th February 2018

Brief position description:

The Synthetic Biology FSP (SynBioFSP) is developing a research portfolio which will be spread across CSIRO and a wide variety of partner organisations (universities, industry, NGOs, other research organisations, etc.), both national and international. The research portfolio is dynamic and will evolve over time on the basis of strategy and performance. Research projects will sit within one or more priority Application Domains (Environment & Biocontrol, Chemicals & Fibres, Organelles & Endosymbionts) and one or more Science Domains (Integrative Biological Modelling, Engineering Novel Biological Components, Assembling Novel Biosystems, Maximising Impact). The SynBio FSP will embed a social and behavioural science agenda to address issues around social licence to operate.

In this position, you will provide systems biology and data modelling support across two research projects, one on the in-vitro resynthesis of the lichen symbiosis and the other on the design of biorthogonal redox metabolic pathways in yeast and E. coli.

Job website: https://jobs.csiro.au/job/Canberra%2C-ACT-Research-Scientist-in-Computational-&-Systems-Biology/451287000/

Contact name: Dr Cécile Gueidan

Contact email: cecile.Gueidan@csiro.au

Postdoctoral Research Fellow in Computational Biology and Modelling

Employer: EMBL Australia, The University of New South Wales

Closing date: 28th February 2018

Brief position description: Applications are invited for a research fellow to join an Australian Research Council-funded project on the in silico optimisation of search strategies employed by cancer-targeting immune cells. This interdisciplinary project spans cell and computational biology, mathematics and statistics, agent-based modelling, live-cell microscopy, image analysis-based tracking of individual cell behaviours, and swarm robotics. The team comprises researchers based in Australia, the UK and North America.

The position will be based in the Biro group, EMBL Australia, the University of New South Wales, Sydney, Australia (www.emblaustralia.org/research-leadership/nsw-node-biro-group), co-supervised by Dr. Mark Read at the University of Sydney (www.sydney.edu.au/science/people/mark.read).


Selection criteria

Required:
- PhD or equivalent industry experience in computational biology, maths/stats, computer science, robotics, bioinformatics, physics or related discipline
- Demonstrated proficiency in programming and mathematical/statistical methods
- Proven capacity for working collaboratively within an interdisciplinary team
- Strong track record in communicating research outcomes (eg. via conference and/or journal publications)

Experience in any of the following highly desirable:
- Biological and/or agent-based modelling and simulations
- Artificial immune systems
- Swarm intelligence or robotics, or
- Image analysis algorithm development


The successful candidate will develop novel theoretical and computational platforms to determine the optimal strategy for a population of agents seeking targets in a given environment. Initially deployed for assessing and optimising immune cells searching for tumour targets, the project will translate these findings into swarm robotics, where collectives of robots perform environmental monitoring and search & rescue operations.

Highly competitive salary package (starting at A$113,000-136,000 per annum incl. superannuation and leave loading); assistance with visas; full-time contract, 12 months initially, renewable up to 3 years. Access to high-performance computing infrastructure, EMBL and ARC Centre of Excellence in Advanced Molecular Imaging facilities.


Application and enquiries

Applications including cover letter addressing selection criteria, CV, and contact details of referees should be emailed to Dr. Maté Biro (m.biro@unsw.edu.au) by February 28th, 2018. For enquiries, contact m.biro@unsw.edu.au or mark.read@sydney.edu.au.

Job website: http://markread.info/docs/EMBLA_CompBio_postdoc_ad_Jan2018.pdf

Contact name: Maté Biro

Contact email: m.biro@unsw.edu.au

Postdoctoral Fellow in Computational Systems Biology/Bioinformatic

Employer: SAHMRI

Closing date: 9 February 2018

Brief position description: An exciting opportunity now exists for a Postdoctoral Researcher in Computational Systems Biology/Bioinformatics in the Lynn EMBL Australia Group, at The South Australian Health and Medical Research Institute (SAHMRI), in Adelaide, Australia (https://www.sahmriresearch.org/). The successful candidate will have a PhD in bioinformatics/computational biology (or in a related discipline) and a clear track record in the field as evidenced by publications in international peer-reviewed journals. The ideal candidate will have demonstrated experience in at least some of the following areas: network/systems biology; Using statistical approaches to relate high-throughput genomics data to clinical phenotypes; next generation sequencing data analysis; metagenomics. The successful candidate will work as part of a team that includes both computational biologists and wet-lab scientists investigating the immune system and cancer from a systems biology perspective - knowledge of immunology/cancer biology would therefore be an advantage. Prior postdoctoral experience would also be an asset, but exceptional recent PhD graduates will also be considered. The ability to work as part of a team and to manage multiple different projects simultaneously is essential. An initial 2-year full-time contract is available, potentially renewable subject to performance and availability of funding.

Job website: http://www.sahmriresearch.org/human-resources/careers/157

Contact name: David Lynn

Contact email: david.lynn@sahmri.com

Bioinformatics analyst

Employer: University of Technology Sydney

Closing date: 07/02/2018

Brief position description: The successful applicant will become part of a team developing and deploying novel long read sequencing technologies. You would interact directly with a team of molecular biologists developing novel approaches to sequence and assemble genomes with long read platforms. 

Day to day tasks include:

* Analyse and assemble long read genome data.
* Quantify accuracy of genome assemblies.
* Develop documentation and usage guides for long read data analysis. 

UTS position reference: IRC101988

Job website: https://recruitment.uts.edu.au/OA_HTML/OA.jsp?OAFunc=IRC_VIS_VAC_DISPLAY&p_svid=101988&p_spid=3070661

Contact name: Aaron Darling

Contact email: aaron.darling@uts.edu.au