Bioinformatician - Pathogen Genomics, NSW

Position title: Bioinformatician - Pathogen Genomics

Employer: NSW Health Pathology

Closing date: 16/12/2018

Brief position description: This position is based at the Public Health Pathogen Genomics Laboratory, Centre for Infectious Disease and Microbiology Laboratory Services, NSWHP-ICPMR at Westmead and plays a key role in the delivery of NSW state-wide pathogen genomics services. The Pathogen genomics bioinformatician is responsible for: 
Lead and manage genome sequencing projects as directed by relevant supervising pathologists and laboratory management from initiation to implementation including the review and evaluation of systems and processes to ensure effectiveness of service delivery. Support reliable and secure collection, storage and archival of genomic data and relevant metadata in accordance with national and international regulations and guidelines. Develop, implement and maintain genomic data QC and analysis pipelines. Organise, coordinate and deliver training in microbial bioinformatics for relevant laboratory staff and other peers.

Refer to the URL for more details.

Job website: http://iworkfor.nsw.gov.au/job/bioinformatician-pathogen-genomics-136518

Contact name: Prof. Vitali Sintchenko

Contact email: Vitali.Sintchenko@health.nsw.gov.au

Two Bioinformatics/Genome analyst positions in South Australia

Employer: Centre of Cancer Biology, an Alliance between the University of South Australia and SA Pathology

Closing date: 9am Thursday November 29

Brief position description: The Centre for Cancer Biology in Adelaide is advertising two bioinformatics/genome analyst positions within the Molecular Pathology/Lymphatic Development/Bioinformatics groups. The positions will involve analysis and interpretation of RNASeq, ChIPSeq, ATACSeq, HiC, WES and WGS data. Further information is available from Hamish Scott (hamish.scott@sa.gov.au), Natasha Harvey (natasha.harvey@unisa.edu.au)
or Andreas Schreiber (andreas.schreiber@sa.gov.au).

Job website: https://workingatunisa.nga.net.au/cp/index.cfm?event=jobs.checkJobDetailsNewApplication&returnToEvent=jobs.listJobs&jobid=0B2C3592-40A4-BA78-C358-A4A55C37DA9A&CurATC=External&CurBID=62AFB35D-9273-4A11-8DCC-9DB401354197&JobListID=22fc4f47-e994-46a3-b8c9-9bc901269f43&jobsListKey=382f5055-dc54-4de6-ab3d-0677eb4185c5&persistVariables=CurATC,CurBID,JobListID,jobsListKey,JobID&lid=57152020078

Contact name: Andreas Schreiber

Contact email: andreas.schreiber@sa.gov.au



Associate Research Fellow in Bioinformatics at Deakin University

Position title: Associate Research Fellow in Bioinformatics

Employer: Deakin University

Closing date: 18/11/2018

Brief position description: SALARY RANGE: $67,562 to $90,827 pa (plus 17% super)
EMPLOYMENT TYPE: Full-time and fixed term for 2 years
LOCATION: Geelong Waurn Ponds Campus
FURTHER INFORMATION: Previous applicants need not apply

ABOUT THE ROLE

The Associate Research Fellow will initiate and conduct research in the area of Bioinformatics. The position will be part of the Bioinformatics Core Unit at Deakin University. In this role you will be involved in computer programming, systems administration, web page management and bioinformatics analysis.

This will include:

Initiating and conducting research under limited supervision either as a member of a team, or independently, to achieve the objectives of the Deakin University Core Bioinformatics unit.
Contributing to building an active national research record, preparing findings for oral and written communication including publications and the generation of external research income.
Effectively producing data, maintaining data protocols and entering data into the appropriate internal and public databases. Conduct preliminary data cleaning, screening and analysis.
Constructively contributing to a vibrant research team, including participating with colleagues in developing and maintaining links and partnerships with industry and the wider community.

ABOUT YOU 

Honours or higher level degree (PhD) in bioinformatics or computer science with a substantial research component.
Demonstrated skills in the coordination of data collection, data entry and analysis for high throughput sequencing technologies.
Experience in working with computer based data acquisition and analysis systems.
Proficiency with Java programming and/or web page development.
For a full list of the selection criteria please see the position description

CONTACT FOR FURTHER INFORMATION: Associate Professor Tamsyn Crowley, Email: tamsyn.crowley@deakin.edu.au

CLOSING DATE: Sunday 18 November 2018

Job website: http://jobs.deakin.edu.au/psc/HCMP/EMPLOYEE/HRMS/c/HRS_HRAM_FL.HRS_CG_SEARCH_FL.GBL?FOCUS=Applicant&SiteId=1&_ga=2.199518574.1704097410.1540162040-1093997198.1532864010&

Contact name: Tamsyn Crowley

Contact email: tamsyn.crowley@deakin.edu.au


Postdoctoral Research Fellow (Single Cell Transcriptomics). Singapore

Position title: Postdoctoral Research Fellow (Single Cell Transcriptomics)

Employer: Singapore Immunology Network (ASTAR, Singapore)

Closing date: 10/12/2018

Brief position description: Note: 3 positions available

A Bioinformatician research fellow (postdoctoral) position is available in Dr Jinmiao Chen’s Single-Cell Computational Immunology (SCCI) lab. The position will perform single-cell RNA-seq data analysis and derive knowledge from the data by applying state-of-the-art tools or developing novel computational methods. The analytical scope may include data pre-processing, quality control to remove low quality cells, normalization/batch effect correction, dimensionality reduction, clustering analysis, automatic cell type identification, cell lineage and pseuedotime inference, cell-to-cell interactions, integration of heterogeneous datasets and data types, building human single-cell atlas, and etc. The work will involve a wide range of exciting and cutting-edge research projects including human cancer immunology (ex Leukemia, Gasstric Cancer, Lung Cancer, etc), infectious diseases (ex TB, Dengue, HIV, HBV, etc), autoimmune diseases (ex SLE, psoriasis, atopic dermatitis, etc), and fundamental research to understand immune system (ex. heterogeneity, origins and functions of dendritic cells, macrophages, T cells, B cells and etc). Where existing computational methods are not adequate to handle the data, the candidate will have the opportunity to develop novel methods under the PI’s supervision and with help from other lab members. The lab is currently focusing on developing Single-Cell Big Data & Artificial Intelligence framework and several AI analytical tools under development are to be released in near future. The candidate will have the opportunity to work in a collaborative environment, interact with excellent scientists from multiple disciplines, and grow rapidly in both biological and computational knowledge and skills. The position will have the opportunity to publish first-authored and co-authored papers in high-impact journals and international conferences, as well as patent publication and potential commercialization of the tools to be developed. In addition, the candidate will have the opportunity to work with MNC pharmaceutical companies via industrial collaborations

Job website:

Contact name: Jinmiao Chen

Contact email: chen_jinmiao@immunol.a-star.edu.sg

Bioinformatician position in Sydney

Position title: Bioinformatician

Employer: The Sydney Head and Neck Cancer Institute (SHNCI) at the Chris O’Brien Lifehouse

Closing date: 31st October 2018

Brief position description: The Sydney Head and Neck Cancer Institute (SHNCI) at the Chris O’Brien Lifehouse aims to integrate both basic and clinical research to develop preventive strategies, improve cure rate, and enhance the quality of life of patients with head and neck cancer. A major aspect of our research programme is focused on understanding the role of genes and molecular and cellular processes in the development and progression of head and neck cancers.
The opportunity:
We are now seeking Bioinformatics Research Officer for a position based between the core SHNCI research team and our collaborators at the Charles Perkins Center, University of Sydney. This can be negotiated as a part time (minimum 0.6FTE) or a full time position. The position will be based at the Charles Perkins Center, University of Sydney. The successful candidate will have the opportunity to work with both DNA and RNA sequencing data. There are multiple opportunities to work with whole genome, transcriptome and targeted panel sequencing outputs of a variety of head and neck malignancies including skin, mucosal and salivary gland tumours. The candidate will be supervised jointly by Prof Jean Yang and Dr. Kitty Lo and will be reporting directly to Professor Jonathan Clark, Associate Professor Ruta Gupta and Dr Bruce Ashford.
Essential duties:
• Working/developing research grade head and neck cancer genomic analysis pipelines
• Work within a team environment to undertake translational research in head and neck cancer with an emphasis on developing biological insights that are relevant to patient outcome.
• Staying abreast on advances in genomics and/or next generation sequencing technology in general, maintaining knowledge on precision medicine
• Develop and maintain software packages of developed methods as well as maintenance of related webpages.
• Day-to-day support and training of PhD students as required.
• Input into manuscript design, development and editing of studies based on sequencing data analysis.
This position is a key role within our highly collaborative multidisciplinary research team. The successful candidate will be responsible for curating and analysing large volumes of genomic data from our ongoing research effort, and thereby contribute to advancing our translational research programme.
Selection Criteria:
1. A minimum of a Bachelor’s degree in bioinformatics or a related area of science
2. Highly developed skills in bioinformatics and genomics. In particular, experience with low level processing or performing initial data analysis on recent platforms of omics data such as next generation sequencing (essential).
3. Superior computer programming or software development skills, a preference in R but not essential.
4. Demonstrated understanding of the incorporation into University life of the principles of Equal Employment Opportunity and Affirmative Action; and ability to work positively with staff and students from a diverse range of backgrounds
5. Experience working with clinical research or medicine is desirable, but not essential
6. Good communication skills (both written and oral).
7. Ability and willingness to assist others within the team.
Apply by sending your cover letter and resume to careers@lh.org.au
To find out more, please contact Dr Aniko Huizer-Pajkos on 0285140365 or aniko.huizer-pajkos@lh.org.au
Applications close: 19th October 2018

Job website: http://www.seek.com.au/job/37413569?_ga=2.78607517.803453506.1538962444-1878375570.1517369122

Contact name: Aniko Huizer-Pajkos

Contact email: aniko.huizer-pajkos@lh.org.au

PhD scholarships (Bioinformatics) at the University of Hong Kong

Employer: The University of Hong Kong

Closing date: 15 November 2018

Brief position description: The Ho Laboratory at the School of Biomedical Sciences of the University of Hong Kong (https://holab-hku.github.io/) focuses on the use of bioinformatics and systems biology approaches to tackle longstanding problems in basic and transnational medicine. Most projects in this laboratory involve integrative analysis next-generation sequencing (NGS) data such as single-cell RNA-seq, ChIP-seq, and whole genome sequencing data. Some research areas include:

- Scalable algorithm for single cell RNA-seq analysis
- 3D virtual reality visualisation of biological data
- Wearable devices, physical activity and heart rate dynamics
- Causal disease mutation identification in whole genome sequencing data
- A cloud-based approach for incorporating scalability into genome informatics
- Integrative metagenomics analysis

We are seeking outstanding PhD students to join our laboratory. Very strong candidates are eligible to apply for a prestigious Hong Kong PhD Fellowship, which will provide a tax-free scholarship of HKD$301,200 (AUD$54,460) per year. The fellowship also provides a travel allowance of HKD$12,600 (AUD$2,280) per year for the duration of the candidature. 

Qualifications:
- Bachelor degree in a quantitative discipline (bioinformatics computer science, statistics, mathematics, physics, engineering, etc), with first class honours or equivalent. 
- Proficient in at least one programming / scripting language (R, python, perl, C, C++, Java, etc)
- Familiarity with the Unix operating system
- Prior experience in bioinformatics is desirable

Eligible candidates may also be considered for employment as a research assistant or postdoctoral fellow (for PhD holders).

Job website: http://www.sbms.hku.hk/staff/joshua-wing-kei-ho

Contact name: Joshua Ho

Contact email: jwkho@hku.hk

Senior Research Fellow / Associate Professor (Bioinformatics), UNSW

Employer: UNSW

Closing date: 11pm on Sunday 21st October 2018.

Brief position description: We are seeking an exceptional Senior Lecturer or Associate Professor to deliver outstanding research in bioinformatics and integrative genomics with a focus in cancer research. The successful candidate will be based within the Adult Cancer Program of the Prince of Wales Clinical School at the Lowy Cancer Research Centre, UNSW Sydney.

Job website: http://external-careers.jobs.unsw.edu.au/cw/en/job/494839/senior-research-fellow-associate-professor-bioinformatics

Contact name: Ian Jones

Contact email: i.jones@unsw.edu.au

2019 PhD Scholarship in Bioinformatics, James Cook University

Employer: James Cook University

Closing date: 30 September

Brief position description: Considering Bioinformatics/Computational Biology? Interested in Tropical diseases/health?

JCU Scholarships for Higher Degree by Research Candidates are awarded annually on a competitive basis to the top ranking applicants.

JCU Research Scholarship applications to start in 2019 are now open!

Applications close on 30 September 2018.

James Cook University (JCU) offers a range of competitive scholarships for domestic and international applicants. When you apply for a scholarship, you will be considered for all the scholarships for which you are eligible, starting from the scholarship with the highest value.

For more information on how your scholarship applications are ranked, or if you will be eligible.

Job website: http://www.jcu.edu.au/graduate-research-school/candidates/postgraduate-research-scholarships

Contact name: Ashley Waardenberg

Contact email: ashley.waardenberg@jcu.edu.au



Junior to Senior Research Officers - Computational Genomics, Garvan

Employer: Garvan Institute of Medical Research

Closing date: This position will remain open until filled.

Brief position description: About Us
The Computational Genomics Laboratory focuses on demonstrating the genomic mechanisms by which loci contribute to complex human diseases, and working towards early stage diagnosis methods and targeted therapeutics. To do so, we apply existing computational approaches, and develop our own statistical genetics methods for analysis of large-scale next generation sequencing data. Following in silico experiments, we perform functional validation of statistical observations using molecular techniques such as high-throughput genome editing and cell phenotyping. We have a very significant focus on the use of single cell sequence data and technology, due to the phenomenal resolution it offers in being able to identify differences in the genomics processes between individual cells. The laboratory drives projects in a number of areas of medical genomics research, but we also believe strongly in the value of collaboration between groups with differing expertise. We are committed to reproducible research practices, and open data policies. 

Our three major research projects are: 

1. Population genetics meets single cell sequencing
We have generated single cell RNA-sequence data from blood samples, along with SNP genotypes for a large cohort of healthy and unrelated individuals. This project will develop single cell eQTL mapping methods to firstly produce an atlas of cell-type specific and ubiquitous genetic effects on gene expression. Subsequently, by integrating population level GWAS and bulk RNA-sequence data, with medical records and vaccination history available to this cohort, work to identify the genetic and cell type specific mechanisms contributing to disease risk and immune response to pathogens. 

2. Resolving the genetic mechanisms of complex human disease using stem cells
Using induced pluripotent stem cells, and differentiating them through intermediate to mature cell states allows us to study the genetic mechanisms that contribute to common diseases. This project will build on recent work from the Computational Genomics group to address two fundamental questions. Firstly, do the genetic (allelic) effects that contribute to disease vary as cells transit across their developmental lineage? Secondly, does genetic variation influence cell fate and cell developmental phenotypes? 

3. Clinical translation of single cell sequencing for diagnosis and precision medicine
This project will focus on the further development of statistical methods for the prediction of cell states or types from clinical samples and their use in clinical decision making for precision treatment. The research will predominately focus on the development of new statistical and analytical methods, but with initial applications using single cell sequence data generated from liquid biopsies from lung diseases, cancers, and immune profiling. 

The Opportunity
We are seeking Junior to Senior Research Officers to join Associate Professor Joseph Powell’s newly formed Computational Genomics Laboratory at Garvan.

The key responsibilities include:
• Performing experiments and analysis of data generated either by the Computational Genomics Laboratory, collaborators, or publicly available
• Recording and assisting with design and interpretation of experimental procedures and results
• Develop work priorities and review research progress with Research Divisions such as Cancer and Genomics & Epigenetics
• Conducting leading-edge informatic analysis of genetic and genomic datasets
• Publish research outcomes under joint authorship in leading scientific journals 
• Provide data for research proposal submissions to external funding bodies
• Discussing and reviewing current and future techniques within Garvan’s Bioinformatics (BUG) meetings
• Gain peer recognition by presentations at national scientific meetings in relevant field
• Provide general research guidance to more junior research staff 

The position will be full-time for 3 years in the first instance.

About You
A strong background in human genetics, cancer genetics and genomics, genetic epidemiology, and/or computational biology, bioinformatics preferred. Highly motivated individuals with a recent PhD and a strong track record of research as evidenced by publications; excellent written and verbal communication; expertise in bioinformatics DNA analysis software; strong attention to detail, good multi-tasking skills; and a willingness to learn new technologies are encouraged to apply. The applicant should have published in top tier journals and demonstrated an ability to successfully complete projects independently. The Research Officer is expected to establish independent research projects and to generate high impact publications, providing outstanding opportunity for further career development in academia.

How to Apply 

All applications must be submitted via Garvan’s Careers site via the link below. Applications from other sites/channels will unfortunately not be considered.
http://garvan.applynow.net.au/jobs/GC201897 

Please include the following in your application:
• A cover letter
• Your resume including at least 2 referees
• Copies of relevant qualifications / academic transcripts

Closing Date

This position will remain open until 7 October 2018. 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/GC201897

Contact name: Human Resources

Contact email: hr@garvan.org.au

Data Scientist / Biostatistician / Bioinformatician

Employer: Children's Medical Research Institute

Closing date: 15th October 2018

Brief position description: We are seeking a suitably qualified Data Scientist/Bioinformatician to join the Bioinformatics and Data Science Research Facility. This role will involve collaborating with medical researchers from the CMRI and collaborating institutions to develop and tailor computation tools, statistical and mathematical solutions around specific research questions. It will involve engaging in experimental design, building novel algorithms or using ‘best practices’ tools to transform experimental and clinical data into relevant knowledge that may lead to actionable novel research findings or improvements to clinical decision-making. The successful applicant will have opportunities to explore and interrogate a diverse range of data, some of which include: genomics, epi-genomics, transcriptomics, proteomics, structural biology, cell imaging and clinically relevant data. Additionally, the successful applicant will reside closely with highly experienced medical research data scientists/bioinformaticians.

Job website: http://www.cmri.org.au/getattachment/About-Us/Job-Vacancies-and-Careers/PV1825-Job-ad_Medical-Research-Data-Scientist-Bioinformatician.pdf.aspx?lang=en-AU

Contact name: Paulina Baranowski

Contact email: recruitment@cmri.org.au