Computational modelling MSc Student

Field: Biophysics, bioinformatics


Title of the position: computational modelling MSc student
Scientific discipline: Biophysics, bioinformatics, the role of 3D chromatin structure in storing, processing and evolving biological information; Spatiotemporal 4D genome organization and transcription regulation in human population
Job type: Scholarship
Number of job offers: 1
Remuneration/month: 2500
Position starts on: 2019-11-01
Maximum period of contrac: 11 months
Institution: Laboratory of Functional and Structural Genomics
Project leader: Dariusz Plewczynski, PhD
Project title: Three-dimensional Human Genome structure at the population scale: computational algorithm and experimental validation for lymphoblastoid cell lines of selected families from 1000 Genomes Project
Project Description: 3DGenome TEAM project recently funded by Foundation for Polish Science (FNP) aims at exploring at the whole Human population scale the relation between the three-dimensional structure variability of cell nucleus, and the emergence and the nature of the genomic sequence alterations. The research team will use public and proprietary experimental results of large-scale next-generation sequencing studies, and recently developed theoretical algorithms. The project will establish novel multi-scale computational method that is able to predict the 3D structure of genome for an individual using only its 1D genomic sequence by applying biopolymer theory, statistical learning and the biophysical properties of chromatin. The results will be validated in Centre of New Technologies University of Warsaw by chromatin conformation capture (ChIA-PET, Hi-C, HiChIP) experiments for selected families from 1000 Genomes Project, with the additional aim to better understand both normal and pathological structural changes occurring during evolution of Human genome. Project is carried out within the TEAM programme of the Foundation for Polish Science

Key responsibilities include:
1. Three-dimensional computational modeling using ChIA-PET, Hi-C and HiChIP experimental data
2. Statistical analysis of epigenomic data, ATAC-seq, ChIP-seq, RNAseq experimental data
3. Analyzing the biophysical simulations results

Profile of candidates/requirements:
1. BSc in computer science, biophysics, biochemistry, bioinformatics or related discipline
2. Prefered experience in population genomics, DNA sequencing data, epigenomics, RNAseq, ATAC-seq data analysis
3. Priority will be given to candidates with expertise relevant to the TEAM project and in agreement with the general profile of the laboratory. Preliminary work done by applicant in the context of 3DGenomics will be treated as the strong asset.

Required documents:
1. CV
2. Motivation letter (why I would like to join 3DGenomics field?)
3. BSc certificate
4. Short written document about recent advances in 3D genomics

We offer:
We offer stimulating and friendly work environment. TEAM project provides moreover unique opportunities for interdisciplinary work between biology, physics, and computer sciences, as well as well established and long-lasting international collaborations with recognized academic institutes and universities in US. Close collaboration with industry will be present as well. We provide also the access to modern 1D and 3D genomics equipment and support from other experienced researchers. International partner (Prof. Yijun Ruan) will be co-supervising your work at the laboratory.

Please submit the following documents to: Please send your application to:



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Deadline: 12/10/2019

Attachment: download

Tags: Deep learning, Machine learning, 3D genome structure, Epigenomics, Transcription factors, Biophysical modeling