Post-doctoral fellow in Bioinformatics with plants

Subject description

This position is a bioinformatics/genomics focused postdoc who will be part of a team of researchers, post docs, and PhD students working on the genomics of sex-determination in the Hawaiian radiation of flowering plants within the genus Wikstroemia. The position involves the application of a wide variety of bioinformatics skills applied to whole-genome sequence data for non-model species, and focused on identification, annotation, and analysis of sex-linked genome regions in young sex chromosomes. 

Work duties

The main duties involved in a post-doctoral posistion is to conduct research. Teaching may also be included, but up to no more than 20% of working hours. The position shall include the opportunity for three weeks of training in higher education teaching and learning.

Detailed description of the work duties:

• Management & curation of WGS and RNAseq data for around 11 species.
• De novo genome assembly and quality assessments
• Genome annotation & development of interactive genome exploration tools.
• Application and development of new and existing analyses focused on identifying sex-linked and sex-determining genes.
• Training of PhD student(s) in the above as needed.
• Up to a maximum of 20% teaching in the first, second and third cycles of studies.
• Supervision of degree projects and doctoral students.
• Actively seeking external research funding.
• Administration related to the work duties listed above.

Qualification requirements 

Appointment to a post-doctoral position requires that the applicant has a PhD, or an international degree deemed equivalent to a PhD, within the subject of the position, completed no more than 2 years before the date of employment decision. Under special circumstances, the doctoral degree can have been completed earlier. 

Additional requirements

• Experience with management, curation, and analysis of WGS and gene expression data.
• Experience in data processing, statistical computing, and scripting in R, Python, bash, UNIX, and other relevant computer programming language.
• Experience in working with workflow languages (e.g., Snakemake, Nextflow) and version control (e.g., git).
• Experience working with high performance compute clusters and job scheduling in cluster environments (e.g., tmux, vim, SLURM).
• Experience in working with (i) genome assembly and annotation of protein coding genes (e.g., with hifiasm, blobtools, BUSCO, AUGUSTUS), (ii) read mapping and variant calling (e.g., with samtools, FreeBayes), and (iii) synteny analyses (e.g. MCScanX, SynVisio), is considered a strong merit.
• Experience with bioinformatic analyses of polyploid plants is considered a strong merit.
• Excellent oral and written proficiency in English.
• Demonstrated ability for proactive and independent work.

Assessment criteria and other qualifications

This is a career development position primarily focused on research. The position is intended as an initial step in a career, and the assessment of the applicants will primarily be based on their research qualifications and potential as researchers.

Particular emphasis will be placed on research skills within the subject.

For appointments to a post-doctoral position, the following shall form the assessment criteria:

• A good ability to develop and conduct high quality research.
• Teaching skills.
• Knowledge of bioinformatic skills and analyses relevant to the research project.

Additional assessment criteria:

• Experience with management, curation, and analysis of WGS and gene expression data
• Experience in data processing, statistical computing, and scripting in R, Python, bash, UNIX, and other relevant computer programming language
• Experience in working with workflow languages (e.g., Snakemake, Nextflow) and version control (e.g., git).
• Experience in high performance compute clusters and job scheduling in cluster environments (e.g., tmux, vim, SLURM).
• Experience in working with (i) genome assembly and annotation of protein coding genes (e.g. with hifiasm, blobtools, BUSCO, AUGUSTUS), (ii) read mapping and variant calling (e.g., with samtools, FreeBayes), and (iii) synteny analyses (e.g. MCScanX, SynVisio).
• Experience with bioinformatic analyses of polyploid plants

Consideration will also be given to good collaborative skills, drive and independence, and how the applicant’s experience and skills complement and strengthen ongoing research within the department, and how they stand to contribute to its future development.

Terms of employment

This is a full-time, fixed-term employment of 2 years. The period of employment is determined in accordance with the agreement “Avtal om tidsbegränsad anställning som postdoktor” (“Agreement on fixed-term employment as a post-doctoral fellow”) between Lund University, SACO-S and OFR/S, dated 1st February 2022.

Instructions on how to apply

Applications shall be written in English and be compiled into a PDF-file containing:

• Résumé/CV, including a list of publications
• A general description of past research and future research interests (no more than 2 pages)
• Contact information for at least two references
• Copy of the doctoral degree certificate, and other certificates/qualifications that you wish to be considered.