Polish Bioinformatics Society

JOB OFFER

Position in the project: 

Post-doc (senior assistant) in the group of researchers

Scientific discipline:

Biological sciences

Laboratory:

Laboratory of Paleogenetics and Conservation Genetics

Keywords

Ancient DNA, genomics, Arvicolinae, Microtus, Pleistocene, filogenetics

Type of contract:

Employment contract

Number of positions:

1

Remuneration/month:

12 750 PLN/month gross grosss

Position starts on:

As soon as the competition is resolved and no later than 1st of April 2024

Maximum period of contract:

6 months with a possible extension up to 18 months

UW unit:

Centre of New Technologies

Project leader:

Dr hab. Mateusz Baca

Project title:

Reconstruction and calibration of genome-based phylogeny of the Microtus genus using the Middle Pleistocene genomes

Project description:

The project aims to clarify the evolutionary history and phylogenetic relationships among Arvicolinae with special reference to Microtus genus using genomes of modern and ancient specimens.

https://cent.uw.edu.pl/en/projects/reconstruction-and-calibration-of-genome-based-phylogeny-of-the-microtus-genus-using-the-middle-pleistocene-genomes/

Key responsibilities include:

The primary task of the employee will be bioinformatic analysis of high throughput sequencing data of modern and ancient mammals (mostly voles), in particular:

· Initial sequencing data processing: quality control, filtering, mapping to a reference genome, duplicate removal (eg. Bwa mem/aln; samtools)

· Variant and consensus sequence calling (eg. Angsd, samtools)

· Phylogenomic analyses including PCA and ADMIXTURE, diversity parameter estimation (heterozygosity, nucleotide diversity, runs of homozygosity; eg. Angsd, ROHan)

· Gene and species tree reconstruction (eg. ASTRAL3), calibration of genome-based phylogenies (eg. mcmctree)

· Detection and estimation of gene flow between populations and species (D statistics eg. Angsd /Dsuite)

· Reconstruction of the effective population size changes through time (PSMC or similar methods)

· Modeling of evolutionary histories using ABC approach (eg. Fastsimcoal2)

· Graphic presentation of the results. Participation in preparation of scientific articles

· Deposition of raw and modified data in appropriate repositories (ENA, GenBank)

The employee may be asked to help students with the analysis of their own data.

Profile of candidate/ requirements:

• The competition is open to persons who meet the conditions specified in:
  - Article 113 of the Act of 20 July 2018 Law on higher education and science (Journal of Laws of 2023, item 742 with later amendments) and the Statutes of the University of Warsaw, and the Regulations on the allocation of resources for the implementation of tasks financed by the National Science Centre for OPUS 20 grant,[1]
• PhD degree in biological sciences (biology, biotechnology or molecular biology or similar). The candidate should hold a PhD degree for no longer than 7 years before the date of signing an employment agreement in the project. PhD degree should be obtained in a country of the EU, EFTA, OECD or nostrified on the date of employment in the project at the latest

· Good knowledge of molecular genetics, basic experience in laboratory work. Experience in ancient DNA oriented laboratory procedures is welcome.

· Experience in working with OS based on unix core and from the command line. Experience in bioinformatic processing of sequencing data and phylogenomic analyses. Experience in processing of ancient DNA genomic data very welcomed.

· Motivation to work

· Knowledge of English at a level allowing to communicate freely, to read specialized literature with understanding and to prepare scientific publications

 Required documents:

· Cover letter (max 1 A4 page)

· Curriculum vitae

· Copy of the PhD diploma or document confirming that the Candidate will obtain the PhD degree prior to the date of employment in the project

· List of scientific publications

· Letter of recommendation from previous employer or PhD supervisor

· Signed information on the processing of personal data

· Signed declaration confirming that the candidate has read and accepted the rules of conducting competitions, covered in the following documents:
Order of the Rector of UW No. 106
Par. 126 of the UW Statutes Resolution No. 443 of 26 June 2019

Enquiries related to the position may be sent to:

m.baca@cent.uw.edu.pl

We offer:

· A friendly and motivating working environment in young and dynamic team

· Participation in an exciting research project using the state-of-the-art research techniques in genomics and ancient DNA

· Access to the fully equipped ancient DNA laboratory and computing resources of CeNT

· Option to work remotely

Please send your application to:

careers@cent.uw.edu.pl with email title  ‘CeNT-33.1-2023’
cc: m.baca@cent.uw.edu.pl

Application deadline:

Call closing date: 15th February 2024

Selected candidates will be invited for an interview at the Centre of New Technologies, University of Warsaw, online, by telephone, or in person. The selection of the candidate will be carried out in accordance with the regulations of the National Science Centre and will be announced no later than 10th March 2023.

Date of announcing the results:

10th March 2023.

Results will be announced by:

e-mail, websites: UW, CeNT UW, Ministry of Education and Science