IPG PAS in Poznan, Poland is looking for a PhD student at the Biometry and Bioinformatics Department.Supervisor: dr Grzegorz Koczyk, Functional Evolution of Biological Systems Team. Topic: “Comparative analysis of regulatory and coding regions using alignment-dependent and alignment-free algorithms”. PhD thesis will center on predicting function and structural grouping of function-determining elements within genes and regulatory sequences. A novel functional annotation method based on text compression and unsupervised clustering will be developed and tested; deployment of publicly available web server for protein sequence annotation is planned as well. The novel toolset will be applied to newly sequenced plant (Lupinus sp.) and fungal genomes (mainly phytopathogenic Sordariomycetes and Dothideomycetes), as well as data from high-throughput sequencing of environmental samples. 4 years stipend, 300 Euro per month
Description
Minimal requirements: - MSc thesis in: bioinformatics (preferred), biology (specialty: molecular biology) or computing science, - working knowledge of Python and C/C++ programming languages, - background in biochemistry and genetics, - fluent English in speech and writing Additional: Candidates with additional experience in one or more of the areas listed below will be preferred: - database administration (PostgreSQL/MySQL), - system administration of GNU/Linux systems, - AJAX web programming (HTML+JavaScript), - working experience with Django framework for web pages and services, - algorithms of compression and pattern detection in text, - algorithms of supervised and unsupervised clustering, - information theory, - application of Hidden Markov Models in biological data, Team research areas (possibilities of training and lateral research projects): - functional annotation of sequences (structure-based descriptors of protein function, cluster analysis and statistical analysis of overrepresentation of conserved motifs), - protein structure evolution (evolution of domain architecture, domain decomposition algorithms, coevolution of function-determining residues in spatially conserved motifs), - phylogenomics and phylogenetics (in particular: tree reconciliation algorithms, quick approximate maximum likelihood methods), - evolution of secondary metabolite biosynthesis (focus on regulatory molecules and toxins, analysis of synteny and coregulation themes in evolution of secondary metabolism), - evolution of fungal resistance to toxic compounds (expression analysis, phylogenomics of ABC and MFS transporters). E-mail: gkoc@igr.poznan.pl
Additional Job Details
Team webpage: http://www.cropnet.pl/team_en
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