PhD position in bioinformatics

Employer: University of Technology Sydney

Closing date: Open until filled

Brief position description: Project description:
We are looking for a talented PhD student to develop methods for real-time analysis of bacterial and viral outbreaks. The project will be part of a larger effort with international collaborators in the UK and USA that aims to develop methods that efficiently and accurately analyse data streams being generated by laboratories around the world. The project will provide the student experience in statistical modeling, programming, bioinformatics, and evolutionary biology.

Requirements:
Undergraduate or postgraduate degree in bioinformatics, computer science, statistics, engineering or a related quantitative field.

Knowledge and skills to be developed:
- Bayesian statistics
- Phylogenetics and evolutionary biology
- Software development in R, Python, Java, C or C++
- Production software engineering
- Linux command-line, HPC and cloud computing
- Excellent written and oral communication skills

Project supervisors:
Associate Professor Aaron Darling and Dr. Mathieu Fourment

Research environment:
This role is within the ithree institute in the Faculty of Science, one of the largest faculties at UTS, which is Australia's top ranked young university, with a particular focus on research translation. The ithree institute brings together a team of scientists with diverse skill sets who collectively address key challenges in the understanding and control of infectious diseases in humans and animals.

Commencement date:
Applicants would be expected to commence studies in the Spring 2018 or Autumn 2019 terms (August 2018 or March 2019).

Contact:
Informal enquiries can be sent to aaron.darling@uts.edu.au or mathieu.fourment@uts.edu.au

Job website: http://darlinglab.org

Contact name: Mathieu Fourment

Contact email: mathieu.fourment@uts.edu.au

Bioinformatician - Software Developer (Part Time)

Employer: James Cook University

Closing date: 6 May 2018

Brief position description: The department of molecular and cell biology at James Cook University is seeking to appoint a bioinformatician to work on a human cancer genetics project in collaboration with a clinical genetics group in Brisbane. The appointee will take responsibility for development and implementation of a best practice computational software infrastructure for the analysis of patient sequence information. The initial goal will be to mirror the infrastructure already in operation in Brisbane but it is expected that
the appointee will interact with research teams and clinicians to identify opportunities for expansion and improvement. The goal of the system developed will be to perform variant identification in human sequence data with the output utilized for personalized medicine within the Townsville hospital. The position is funded for 18 months at half time.

To view selection criteria for this position and submit an application please visit https://www.jcu.edu.au/careers-at-jcu/vacancies and look for vacancy number 16347 . Applications are due at Midnight 6 May 2018

Job website: http://www.jcu.edu.au/careers-at-jcu/vacancies

Contact name: Ira Cooke

Contact email: ira.cooke@jcu.edu.au

Bioinformatics and Computational Biology Lead

Employer: Pharmalytics

Closing date: 16th May 2018

Brief position description: Are you intrigued by the advances in big data in healthcare? Are you excited by the opportunity to develop a company’s technological backbone from the ground up? If so, we can’t wait to hear from you. Our start-up company needs a Computational /Bioinformatics specialist CTO who can provide technical leadership to develop a novel algorithm which will the first of its kind here in Australia!
If this sounds of interest to you, we would love to hear from you

Job website:

Contact name: Doron Nadler

Contact email: nadlerdoron@gmail.com

Employer: Pharmalytics

Closing date: 16th May 2018

Brief position description: Are you intrigued by the advances in big data in healthcare? Are you excited by the opportunity to develop a company’s technological backbone from the ground up? If so, we can’t wait to hear from you. Our start-up company needs a Computational /Bioinformatics specialist CTO who can provide technical leadership to develop a novel algorithm which will the first of its kind here in Australia!
If this sounds of interest to you, we would love to hear from you

Contact name: Doron Nadler

Contact email: nadlerdoron@gmail.com

 

Computational Biology Group Leader

Employer: Children's Cancer Institute

Closing date: 01/09/2018 

Brief position description: • Innovative, collaborative and positive team-orientated environment
• Modern, world-class facilities
• Convenient Randwick location, close to transport

Children’s Cancer Institute is the only medical research institute in Australia wholly dedicated to curing childhood cancer and one of the leading medical childhood cancer research institutes worldwide. Our vision is to save the lives of all children with cancer and improve their long-term health, we don’t just hope to do it, we will do it; and we’re looking for the brightest minds to help us get there. Children’s Cancer Institute provides the best possible environment for our staff thrive with state-of-the-art facilities at the Lowy Cancer Research Centre, UNSW Australia – one of the leading cancer research centres in the world. 


We are leading the national Zero Childhood Cancer personalised medicine program for children with the most aggressive cancers, in partnership with the Sydney Children’s Hospitals Network. Zero Childhood Cancer is the most exciting childhood cancer research initiative ever undertaken in Australia and is a world-leading initiative www.zerochildhoodcancer.org.au. 


Children’s Cancer Institute is seeking an ambitious, driven rising star to establish and lead a world class and innovative program in child cancer computational biology on a Full-time fixed-term contract for approximately 5 years with great prospects for extension. You will harness the power of our Zero Childhood Cancer national child cancer personalised medicine program to develop an expanding program involving computational biology approaches to understanding child cancer biology with the goal of translating this knowledge into improved treatment for children with cancer and other rare diseases. 


The data that will be generated by the Zero Childhood Cancer program will be a globally unique resource, providing opportunities to explore paediatric cancers in greater depth than ever before. The ability to analyse and mine these data is a core component of the Institute’s ultimate goal, which is to improve the clinical outcomes for children with cancer and their families. With an expected 400 patients to be enrolled on the program, the Institute must be in a position to engage with, explore, and link data, to invent solutions for the future, to generate new knowledge and new connections, driving further basic and translational research in the context of an expanding child cancer precision medicine program and associated research projects and programs across the institute. In addition, working with our clinical and research partners in child health research and clinical care across Sydney, there will be opportunities to access additional data sets in other rare diseases of childhood. 


You are a senior computational biologist who is motivated to build a strong research team undertaking world class research and will embed computational biology expertise throughout all research programs at the institute. In order to be able to analyse and interpret the vast amounts of data that will be yielded by this and other world class Programs housed at Children’s Cancer Institute, it will be essential that you have the skills and expertise to lead the computational analysis and methods development that will leverage and maximise the outputs of the high dimensional multi-‘omics, biological, and clinical data sets. These include Whole Genome Sequencing (WGS), whole transcriptome (RNASeq), single cell and spatial transcriptomics, ctDNA and CTC, proteomics, in vitro high content imaging high throughput drug screening, drug efficacy testing in patient derived xenografts, and drug response prediction. 

There will be strong emphasis on the translation of research in to potential clinical application which will facilitate:
• Prospective research
• Enabling point of care applications
• Focus on clinically / medically relevant problem solving
• Developing efficient, scalable, cloud-based algorithms for clinically robust data analysis, and archiving and housing of data knowledgebase
• Developing the building blocks for ‘omics literate workforce of the future, creating a nimble, diverse centre for education, training, and mentorship, to co-create knowledge, and improve knowledge transfer and mobilisation

Supported by a team including a Head of Research Computing, software engineer, postdoctoral researchers, and graduate students, you will be expected to take leadership of exciting research questions we are actively pursuing in the domains of exploring relationships between omics and biological profiles and individual responses or resistance to existing and novel therapeutics, better understanding the impact of inherited cancer risk, single cell analysis to study tumour heterogeneity and microenvironment, and the impact it has on treatment response, and liquid biopsy solid tumour minimal residual disease. You will be experienced in attracting ongoing independent research funding in to the future to ensure sustainability of your group long term, and demonstrate excellent open, transparent communication and relationship management skills to nurture existing collaborations and pursue new ones globally to leverage and contribute to child cancer data sets internationally.

Children’s Cancer Institute is strongly committed to the growth of their employees, so all team members can fulfil their aspirations. You'll be rewarded with a friendly and professional flexible work environment, comprehensive on-campus facilities, competitive salary, salary packaging options, on-site parking options, access to a leading EAP program and regular social activities. Join a group of dedicated people in a performance-driven environment to achieve success and discover what it's like to look forward to coming to work every day and make a real difference. We're looking for people who share our values of accountability, integrity and camaraderie, teamwork, sharing and excellence, success and satisfaction. 


This is an exciting opportunity for a highly motivated rising star to form the backbone of Australia’s first computational paediatric oncology group, which will give Australia an international leadership position in this exciting new field. A detailed job description and additional information about Children's Cancer Institute can be found on our website at: www.childrenscancerinstitute.org.au. We embrace diversity and encourage applications from people from diverse backgrounds and cultures. 

To apply, please apply though our website: https://ccia.org.au/home/join-us/job-vacancies/ and forward both your resume AND cover letter clearly addressing the qualifications, experience and skills required. Note: Applications will be reviewed prior to the closing date; which is dependent on the status of the recruitment process. For any advertisement related queries, please contact Vanessa Tyrrell, Personalised Medicine Program Leader at VTyrrell@ccia.org.au or on +61 (02) 9385 1302. Otherwise contact Recruitment at Recruitment@ccia.org.au or on +61 (02) 9385 1660. 

Job website: https://ccia.org.au/home/join-us/job-vacancies/

Contact name: Lindsay Kilgour

Contact email: Recruitment@ccia.org.au

Senior Data Manager

Employer: CSL Limited

Closing date: 20th of April, 2018

Brief position description: The Opportunity


In this critical role you will overview and coordinate data storage and data handling strategy within CSL Research department and provide advice and support towards high data integrity. You will help scientists to enable data sharing and data mining within CSL Research as well as with other parts of CSL and with external collaborators such as medical authorities. In this role you will support CSL Research towards the implementation and ongoing maintenance of the IDBS Electronic Lab Notebook (ELN). You will also be involved in the implementation of data standards and guide the Business Technology team to the implementation of data warehouses enriched with biomedical ontologies to support inferences on CSL Research data.


Key responsibilities include:

Develop and promote data quality strategy across the group including development of best practice guidelines.
Develop a strategy for data standardisation and governance across the Research group.
Design and lead the implementation of database systems that empowers scientists with data mining and reporting capabilities.
Educate and support scientists towards the implementation of a sound data system, and develop training materials to achieve this.
Manage and maintain the newly implemented ELN system across R&D in order to ensure the maximum benefit from using such a system.
Support ELN users in their day-to-day activities and help resolve their issues, e.g., with respect to permissions, templates, folder structure, inventory manager, dictionaries etc.
Help Research groups to develop standard data formats and templates using for example Excel, Prism, JMP, ELN or via interface applications like Shiny or Jupyter.
Identify and integrate publicly available data sources to enhance CSL knowledge of its targets/indications of interest.
Guide scientists to adhere to CSL Information Management policies and standards.
Develop strategies to manage data generated by third parties on CSL’s behalf.
Where needed, help groups with more advanced data formats like CDISC.

More info: https://csl.wd1.myworkdayjobs.com/CSL_External/job/APAC-AU-Victoria-Parkville-CSL-Limited-Australia/Senior-Data-Manager_R-064165

Job website: http://csl.wd1.myworkdayjobs.com/CSL_External/job/APAC-AU-Victoria-Parkville-CSL-Limited-Australia/Senior-Data-Manager_R-064165

Contact name: Monther Alhamdoosh

Contact email: monther.alhamdoosh@csl.com.au

Post Doctoral Fellow

Employer: University of Otago (New Zealand)

Closing date: 16 th April

Brief position description: We are seeking a highly motivated Postdoctoral Fellow (bioinformatician) to join a Genomics Aotearoa team working on human population epigenetics.



This position is funded by Genomics Aotearoa and will be co-located with Professor Greg Jones as part of the University of Otago’s Epigenetics Users Group. Genomics Aotearoa is a national network funded to improve capability in, and outcomes from, New Zealand Genomics.



The Role



This project provides an exciting opportunity, working with an outstanding network of biomedical scientists and clinicians, to generate epigenetic data and analysis tools to investigate a wide range of human health conditions.



Skills and Experience



• Applicants must have a PhD in bioinformatics or genomics.

• Prior experience in epigenetic analysis is preferable.

• Experience in large-scale/integrated bioinformatic analysis of large data sets.

• Programming languages (such as Python or C) and a high capability with R.

• Experience working with both sequence and beadchip array derived epigenome data is desirable.

• The ability to be an effective member of a technical training team is desirable.



Further details



This is a full-time, fixed term appointment for three years. The successful applicant will be expected to take up the position before June 2018.



Enquiries should be directed to Professor Greg Jones or Dr Aniruddha Chatterjee via the email addresses below.



How to apply



To submit your application please click the apply button below. Applications quoting reference number 1800511 will close on Monday, 16 April 2018.

Apply: https://otago.taleo.net/careersection/2/jobdetail.ftl?job=1800511

Job website: http://otago.taleo.net/careersection/2/jobdetail.ftl?job=1800511

Contact name: Aniruddha Chatterjee

Contact email: aniruddha.chatterjee@otago.ac.nz

Computational Mathematician / Bioinformatician (C++)

Employer: Children's Medical Research Institute

Closing date: 4th April 2018

Brief position description: Children's Medical Research Institute (CMRI) is seeking an experienced computational mathematician to help us deploy a data processing and analytics pipeline for clinical cancer proteomics. The successful candidate will be passionate about bringing to bear their experience on challenging problems that have tangible benefit to patient wellbeing. 

One of CMRI’s flagship projects, ProCan, is an exciting international initiative that is building a proteomics database for all types of cancer – in children and adults – to increase the accuracy of cancer treatment decisions for each individual patient. Equipped with six SCIEX mass spectrometers and local high-performance computing (700TB / 480 cores), ProCan processes tumour samples through a proteomic method, SWATH-MS, that allows fast mass spectrometric conversion of small amounts of tissue (biopsy level) into a single, permanent digital file representing the quantitative proteome of the sample. ProCan will analyze approximately 70,000 individual cancer samples over the next 5-7 years, and a major outcome of the initiative will be the creation of a high-availability database and data visualization system which can be used for discovery research, and by clinicians to inform their treatment decisions.

Job website: https://www.seek.com.au/job/35812933?_ga=2.150345014.163219073.1521515679-1002042689.1494473350

Contact name: Paulina Baranowski

Contact email: recruitment@cmri.org.au

Biostatistician Proteogenomics

Employer: Children's Medical Research Institute

Closing date: 19th April 2018

Brief position description: A Biostatistician position is available in the ProCan Cancer Data Science Group, led by Dr. Qing Zhong. ProCan (the ACRF International Centre for the Proteome of Human Cancer) is a world-first initiative developed and launched in September 2016 by Professors Phil Robinson and Roger Reddel, and established with a $10 million grant from the Australian Cancer Research Foundation (ACRF). Equipped with six SCIEX mass spectrometers and a super computer (800TB / 480 cores), ProCan processes tumour samples through a proteomic method, SWATH-MS, which allows fast mass spectrometric conversion of small amounts of tissue (biopsy level) into a single, permanent digital file representing the quantitative proteome of the sample. One of the goals of ProCan is to measure thousands of proteins in about 70,000 cancers of all types with known treatment outcome and correlate tumour proteotypes with clinical phenotypes. The Cancer Data Science Group aims to develop novel computational tools and sophisticated machine learning algorithms to achieve this goal. Other major focuses of the group are 1) big proteogenomic data mining and management, 2) the genome-proteome association analysis and multi-omic data integration for studying cancer, 3) development of advanced statistical tools to account for batch effects caused by large-scale, high throughput proteomics, and 4) implementation of big data-driven, evidence-based computational tools to achieve predictive, preventive, personalized medicine.

Job website: https://www.seek.com.au/job/35811799?_ga=2.184408102.163219073.1521515679-1002042689.1494473350

Contact name: Paulina Baranowski

Contact email: recruitment@cmri.org.au

GENOMICS DATA ANALYST

Employer: University of Melbourne

Closing date: 15/04/2018

Brief position description: The Research Fellow in Genomics Data Analysis will integrate different sources of biological data available from the Stemformatics platform and from our wide range of collaborators. The aim of this project sits at the forefront of systems biology in stem cells and is to establish the first computational principles towards the understanding of stem cell programming and reprogramming stages and will involve data mining to identify molecular signatures and network modelling. The position will sit between Dr Lê Cao’s lab (Melbourne Integrative Genomics & School of Mathematics and Statistics, University of Melbourne) and A/Prof Jess Mar’s lab (Australian Institute for Bioengineering and Nanotechnology, University of Queensland).

Job website: https://careers.pageuppeople.com/422/ci/en/job/894250/genomics-data-analyst

Contact name: Dr Kim-Anh Lê Cao

Contact email: kimanh.lecao@unimelb.edu.au

Bioinformatician (Data Analyst)

Employer: Peter Mac Cancer Institute

Closing date: 27/03/2018

Brief position description: 

The Victorian Centre for Functional Genomics (VCFG) is a core technology platform embedded within the Peter Mac Cancer Research Division and supports researchers Australia-wide to perform cutting edge discovery-based research using CRISPR, RNAi, compound and proteomic screening strategies. We are highly experienced with quantitative cell imaging and are looking for someone who is interested in developing the analytical tools to take this to the next level.

 

An excellent opportunity exists for an enthusiastic, highly motivated and skilled Bioinformatician (Data Analyst) to join the VCFG team.  This position is very diverse as we engage with researchers with varied biological questions who perform their screens in the lab under our guidance. The successful person will work with highly experienced Research Officers to deliver a nationally recognised service of excellence focused on cutting edge technological screening applications coupled with high content imaging.

 

Candidates who wish to apply for this position MUST:

  • Have a PhD or Masters degree in a relevant field OR a bachelors degree and at least three years experience in a quantitative discipline such as mathematics, statistics, physics or computer science, a biological background is a distinct advantage.
  • Have experience in the application of bioinformatics to large data sets.
  • Have excellent skills in R programming.
  • Possess excellent organization, communication, reporting and time management skills.

The position is initially for a fixed period of 12 months with the opportunity for further extension. Remuneration will be commensurate with qualifications and experience.

 

For further information about this opportunity, please review the position description or contact us for a confidential discussion.

 

Peter Mac offers its employees the following benefits:

  • Salary Packaging
  • Employee Assistance Program
  • Central City Location
  • Training and Development Program

Job website: https://petermac.mercury.com.au/ViewPosition.aspx?id=K1MnK0Q4kJc=&jbc=ere

Contact name: - Associate Professor Kaylene Simpson

Contact email: Kaylene.Simpson@petermac.org

 

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