Researcher in hybrid epigenetics and gene expression

Subject description
We are recruiting an early career researcher for a career development position within the ERC-funded project “Hybridization derived novel patterns of gene expression”.
This project broadly addresses the role of gene expression in how novel, potentially adaptive, variation can arise from hybridization. The main question of the project is the extent to which alterations to chromatin distribution and methylation arise, and how they contribute to altered patterns of gene expression. We have assembled a unique data set of three independent lineages of Italian sparrow Passer italiae and their parental species, with data on gene expression and tissue samples from ca 10 individuals of each sex common garden populations of these. The researcher is expected to take a lead on wet lab extraction strategies for cut-and-run.
The researcher will work in a collaborative lab performing analyses of gene expression, EM-seq, ATACseq and cut-and-run data, and will analyze and synthesize and write up the work for publication and work closely with the HybridExpress team consisting of a lab manager, a PhD-student and a post doc.
The project is led by Senior Lecturer Anna Runemark, and set within the SPeciation, Adaptation and Co-Evolution lab in the biodiversity and evolution division.
Work duties
The main duties involved in a researcher posistion is to conduct research.
Detailed description of the work duties:
Bioinformatical analysis of gene expression data
Analysis of methylation and histone modifications as well as cut-and-run data, with focus on their effects on gene expression
Interpretation of bioinformatical results, figure preparation
Synthesizing the data for publication
The candidate can potentially contribute to the teaching on the bioinformatics program.
Qualification requirements
Appointment to this career development position requires that the applicant has a PhD, or an international degree deemed equivalent to a PhD, within the subject of biology or evolutionary biology using bioinformatical approaches and addressing evolutionary questions. While there are no formal career age requirements, the position is aimed for career development for a research career and merits will be considered in the light of the career age.
Further requirements are:
Strong skills in bioinformatics and epigenetics, including analysis of methylation and histone modifications, gene expression data and/or analysis of hybrid genomes.
Documentend experience in analysis of EMseq data
Documentend ability to develop Nextflow bioinformatics pipelines
Experience of using nf-core/rnaseq nf-core/methylseq nf-core/differentialabundance nf-core/sarek
Assessment criteria and other qualifications
This is a position intended for career development for a future academic career focused on research. The position is intended as an early step in a career, and the assessment of the applicants will primarily be based on their research qualifications i.e. career stage strength of publication record, and their potential as researchers. Particular emphasis will be placed on research skills within the subject i.e. regulation of gene expression and how epigenetic modification affects this.
A good ability to develop and conduct high quality research, assessed by a publication record with strong independent contributions and high-quality publications; and a proven track-record of presenting research findings at international conferences.
Meriting bioinformatics experience is:
gene annotation with BRAKER and functional annotation with InterProScan and EnTAP
mapping RNA seq data to a pangenome graph using vg
experience with hybrid species and transgressive gene expression
Consideration will also be given to good collaborative skills, drive and independence. Specific consideration will be given to how the canddiate fits into the group and how their experience and skills complement and strengthen ongoing research within the group and department, and how they stand to contribute to its future development.
Terms of employment
This is a full-time permanent employment, starting 2027-01-01, a 6-month probationary period may be applied.
Contact person: Anna Runemark anna.runemark@biol.lu.se
Instructions on how to apply
Applications shall be written in English and be compiled into a PDF-file containing:
Résumé/CV (no more than one page Times New Roman 12pt)
List of publications
A cover letter detailing how your past research experience fits the position (no more than one page Times New Roman 12pt)
Contact information for at least two academic references
Copy of the doctoral degree certificate