Postdoc for the project on modern approaches for phylogenetic reconstruction

Wyniki konkursu:

W ramach przeprowadzonego postępowania Komisja Konkursowa rekomendowała kandydaturę dr Macieja Jasińskiego, dr Krzysztofa Szczepaniaka oraz dr Antonio Marinho na stanowisko młody doktor.



Title of the position: Postdoc

Scientific discipline: Bioinformatics

Job typeContract

Number of job offers: 1

Stipend amount/month: Gross = 14,000 PLN / month (Expected net = 8,000 pLN / month)

Position starts on: 01.03.2019

Maximum period of contract agreement: 35

Institution: Laboratory of Structural Bioinformatics;

Project leader: Dr. Stanisław Dunin-Horkawicz

Project title: An evolutionary-based approach to design the substrate specificity of the Rossmann fold enzymes

Project description: The goal of the project is to infer a detailed evolutionary history of the Rossmann fold, which is one of the most prominent protein folds and by far the most functionally diverse one, with >300 different functions. To this end, we will perform a comprehensive bioinformatics analysis, with the aim of integrating data from different sources to obtain a reliable phylogenetic tree that encompasses all the major Rossmann enzymes classes. Unraveling the natural history of the Rossmann enzymes will open the possibility (i) to reveal the principles that governed the divergence of cofactor specificity of Rossmann enzymes, (ii) use these principles to rationally re-engineer cofactor specificity in Rossmann enzymes, and (iii) to identify the rudimentary Rossmann fold, and thereby design a functional minimal Rossman. The proposed project involves experimental validations, including structure determination of natural and re-engineered proteins together with the cofactors. The project includes collaboration with two partners: (i) Core Facility for Crystallography and Biophysics, University of Warsaw (Poland) and (ii) Department of Biomolecular Sciences, Weizmann Institute of Science (Israel).

Key responsibilities include:
1. Implementation of an efficient computational pipeline for the identification, classification, and storage of protein sequence and structural data
2. Implementation of a procedure for the incorporation of protein design methods and coevolutionary analysis into the phylogenetic reconstruction
3. Performing phylogenetic reconstructions and preparing data suitable for Machine Learning

Profile of candidates/requirements:
1. PhD degree in bioinformatics, biology, biochemistry, biophysics or related discipline (obtained no more than 5 years ago)
2. Extensive experience in Python programming. Good knowledge of libraries such as sci-kit, numpy, pandas, biopython. Experience with high-performance computing and Linux environment
3. Experience related to some of the following: protein sequence and structure analysis, protein design, molecular dynamics, machine learning, phylogenetic analysis, ancestral sequence reconstruction
4. Strong publication record in peer-reviewed journals
5. Good writing and oral communication skills in English, and competence in scientific writing. Knowledge of Polish is not a requirement.

Required documents:
1. Curriculum vitae, including a list of publications and a cover letter
2. Up to three letters of recommendation
3. A copy of PhD diploma

We offer:
1. An opportunity to participate in a multidisciplinary project conducted in a collaboration with scientists from the University of Warsaw and Weizmann Institute of Science
2. Access to the high-end computing equipment (CPU and GPU clusters)
3. Work in a young research team well-networked with international partners (Germany, Israel)
4. Competitive salary

Please submit the following documents to:

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“I hereby consent to have my personal data processed by the University of Warsaw with its registered office at ul. Krakowskie Przedmieście 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.”

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Termin nadsyłania aplikacji: 18/01/2019

Słowa kluczowe: Bioinformatics, machine learning, phylogeny, protein evolution, protein re-engineering