Description:
Title of the position: PhD student in Laboratory of Functional and Structural Genomics
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/Stipend amount/month: up to 4500 PLN/month
Position starts on: 2019-02-01
Maximum period of contract/stipend agreement: 8 months (with extension option)
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 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.br /> 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 simulations results, formulating biophysical hyphothesis
4. Publications preparation
Profile of candidates/requirements:
1. MSc in computer science, biophysics, biochemistry, bioinformatics or related discipline
2. Documented experience with genomics data
3. Prefered experience in population genomics, DNA sequencing data, epigenomics, RNAseq, ATAC-seq data analysis
4. 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.
5. Essential requirements cover the ability to work in collaboration with others, within a large research team, performing several parallel scientific tasks, independent thinking and finally the ability to deliver publishable results.
6. Needed the highly motivated individuals willing to work in an interdisciplinary environment under stress and with strict deadlines.
Required documents:
1. CV
2. Motivation letter (why I would like to join 3DGenomics field?)
3. Letter of support
4. MSc certificate
5. PhD studies enrollment certificate
6. Short written document about recent advances in 3D genomics
Please also include a signed statement on the processing of personal data (template below).
We offer:
TEAM project provides 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: dariuszplewczynski@gmail.com
To allow us to process your data, please include the following statement in your application:
“I hereby consent to have my personal data processed by the University of Warsaw with its registered office at ul. KrakowskiePrzedmieście 26/28, 00-927 Warszawa for the purpose of carrying out a recruitment process and selecting an employee and concluding a contract for employment at the University of Warsaw. I have been informed of my rights and duties. I understand that provision of my personal data is voluntary.”
In accordance with Article 13 of REGULATION (EU) 2016/679 OF THE EUROPEAN PARLIAMENT AND OF THE COUNCIL of 27 April 2016 on the protection of natural persons with regard to the processing of personal data and on the free movement of such data – general regulation on data protection (Official Journal of the EU L 119/1 of 4 May 2016) the University of Warsaw informs that:
1. The Controller of your personal data is the University of Warsaw with its registered office at KrakowskiePrzedmieście 26/28, 00-927 Warszawa;
2. The Controller has designated the Data Protection Officer who supervises the processing of personal data, and who can be contacted via the following e-mail address: iod@adm.uw.edu.pl;
3. Your personal data will be processed for the purpose of carrying out a recruitment process and selecting an employee and concluding a contract for employment at the University of Warsaw;
4. The provided data will be processed pursuant to Article 221 § 1 of the Act of 26 June 1974 Labour Code (uniformed text: Dz.U. of 2018, item 917) and your consent for processing of personal data;
5. Provision of data in the scope stipulated in the Labour Code is mandatory, and the remaining data are processed according to your consent for processing of personal data;
6. The data will not be shared with any external entities;
7. The data will be stored until you withdraw your consent for processing of personal data;
8. You have the right to access your personal data, to rectify, erase them, restrict their processing, object to processing, and to withdraw the consent at any time;
9. You have the right to lodge a complaint to the President of the Office for the Protection of Personal Data.”
Deadline: 19/01/2020
Tags: Deep learning, Machine learning, 3D genome structure, Epigenomics, Transcription factors, Biophysical modeling
