Postdoctoral Researcher in Plankton Genomics/Genomics and Regulatory Systems Unit

The Okinawa Institute of Science and Technology Graduate University (OIST; see www.oist.jp) is a dynamic new graduate university of science and technology in Okinawa Prefecture, Japan. The university is located on 85 hectares of protected forestland overlooking beautiful shoreline and coral reefs. The campus is striking architecturally, and the facilities are outstanding (OIST campus video tour). There are no academic departments, which facilitates multidisciplinary research. Outstanding resources and equipment are provided and managed to encourage easy access and collaboration. English is the official language of the University, and the university research community is fully international, with more than 50 countries represented. OIST is rapidly gaining recognition in the worldwide academic community as a model for excellence in education and research.

Position summary:

We seek a talented, motivated computational biology postdoc to join Nick Luscombe’s Genomics and Regulatory Systems Unit (www.luscombelab.org). The postdoc will apply state-of-the-art computational biology and bioinformatics techniques to analyse chromosomal organisation, evolution and population structure using whole genomes of individual zooplanktons sampled from local and distant oceans (video). The lab is happy, international and interactive; the ~8 students, technicians and senior scientists are recruited worldwide and come from a range of academic backgrounds. Postdocs from our lab have an excellent track record of moving onto PI positions.

Oikopleura dioica is a globally distributed, tunicate plankton that is commonly used for developmental studies due to its short life cycle (5 days), high fecundity and small genome (50 times smaller than ours). As a close relative of vertebrates, it occupies a key phylogenetic position within the chordate phylum and so is of great evolutionary interest. The genome of a North Atlantic strain revealed that O. dioica is the fastest-evolving metazoan reported so far. Its 70-megabase genome has undergone extreme compaction possibly resulting from the loss of multiple DNA repair pathways. This process has been coincided with the extensive gene rearrangements, including the Hox genes. However, despite such changes, O. dioica still has around 18,000 genes, maintains a typical chordate body plan and shares similar early developmental trajectories. Using nanopore sequencing, we have produced de-novo chromosomal assemblies for single individuals of the Okinawan O. dioica strain, which displays extraordinary divergence from the Atlantic one, despite their identical morphologies. Our dataset is unique in its kind, leveraging methodologies that will be at the core of genomic studies in the future, while at the same time being computationally accessible thanks to the much smaller size of O. dioica’s genome.

Location 

1919‐1 Tancha, Onna‐son, Okinawa, Japan 904-0495

Responsibilities 

1. To analyse data obtained from genome sequencing and other functional high-throughput sequencing experiments alongside publicly available genomic and other databases. Computational analysis will include genome assembly and annotation, comparative and population genomic analysis between zooplanktonic species, identification and characterization of genetic regulatory regions, and integration of marine environmental data.

2. When appropriate, to design new tools for analyzing genomic/molecular data in novel ways.

3. To contribute to design of experiments in consultation; this includes recording analyzing and writing up results, maintaining a permanent record of methods so that results can be reproduced by others.

4. To read the relevant literature in depth, keeping up with new developments that could contribute usefully to the project and to use this knowledge as appropriate to benefit the project.

5. To prepare and present scientific findings to colleagues and at scientific meetings, and for review purposes.

6. To contribute to the writing, submission and revision of papers to be submitted to appropriate peer reviewed journals, collaborating with others as appropriate.

7. To contribute to the overall activities of the research unit, acting as an effective collaborator and team member.

8. To contribute to the induction and direction of other research staff and students if so requested by the unit head.

9. To supervise the day-to-day work of junior staff, students and interns if so requested by the unit head.

10. To carry our routine administrative tasks associated with the research project to ensure it is completed on time and within budget as needed.

11. To plan own day-to-day activity within framework of the agreed research programme to allow timely submission and acceptance of manuscripts for peer-review publication.

12. To liaise with colleagues and students to build contacts, exchange information and form relationships for future collaboration.

Qualifications 

(Required)

  1.   PhD degree in Biology (molecular biology, genetics, genomics), Computational Biology (bioinformatics, molecular evolution), Biostatistics.
  2. Computing experience, fluency in Linux/Unix, excellent knowledge in a programming language (Python, R, C/C++ etc). 
  3. Language requirements. English (fluent), Japanese (beneficial)

(Preferred)

  1. Experience in the field of genomics (analysis of genome sequence and high-throughput sequencing data).
  2. Proven knowledge of basic principles of biology, especially molecular biology, molecular evolution and population genomics including relevant research techniques and methodologies.
  3. Strong demonstrable skills and ability in computational biology including comparative genomic analysis, identification and characterization of genetic regulatory regions, analysis of high-throughput sequencing data.
  4. Strong demonstrable skills in using a wide range of software and online resources for genomic analysis.
  5. Proven ability to analyse and write up data.
  6. Excellent communication skills.
  7. Proven ability to work in a team with diverse technical expertise towards a common goal and also independently.
  8. Peer-review publications in international scientific journals.
  9. Ability to conduct research with integrity and accountability such that the results obtained can be reproduced easily by others.

Commitment to equal opportunity and the ability to work harmoniously with colleagues of all cultures and backgrounds.

Report to 

Professor Nicholas Luscombe

Starting Date 

1 August 2019 onwards

Term & Working Hours 

Term: Full-time, fixed term appointment for 2 years. This contract may be renewed up to total of 3 years

Working hours: 9:00-17:30 (Discretionary)

Compensation & Benefits 

In accordance with the OIST Employee Compensation Regulations

Benefits:
Relocation, housing and commuting allowances
Annual paid leave and summer holidays
Health insurance (Private School Mutual Aid http://www.shigakukyosai.jp/ )
Welfare pension insurance (kousei-nenkin)
Worker’s accident compensation insurance (roudousha-saigai-hoshou-hoken)

How To Apply 

Apply by emailing your Submission Documents to:
nicholas.luscombe[at]oist.jp and charles.plessy[at]oist.jp

(Please replace [at] with @ before using this email address)

or send by post to the following address:

Genomics and Regulatory Systems Unit

Okinawa Institute of Science and Technology Graduate University

1919-1, Onna, Onna-son, Okinawa 904-0495, Japan

Submission Documents 

  • Cover letter in English
  • Curriculum vitae in English
  • Names and contact information of 3 referees, one of which should be a previous employer

* Please be sure to indicate where you first saw the job advertisement.

Application Due Date 

July 31, 2019 (Applications will be screened upon arrival)

Declaration 

  • OIST Graduate University is an equal opportunity, affirmative action educator and employer and is committed to increasing the diversity of its faculty, students and staff. The University strongly encourages women and minority candidates to apply.
  • Information provided by applicants or references will be kept confidential, documents will not be returned. All applicants will be notified regarding the status of their applications.
  • Please view OIST policy for rules on external professional activities
  • Further details about the University can be viewed on the OIST website www.oist.jp.