Development of SNPstar 2.0 and computational prediction of putative proteoform candidates with high functional proteoform variation
Project D02 focuses on genomic research, aiming to develop a web-based tool, SNPstar 2.0, for the prediction of proteoforms with high functional variation utilizing pangenome data. SNPstar 2.0 will incorporate three-dimensional structural models and highlight amino acid residues affected by nsSNPs. It will also extend to a variety of plant species. The project will create a quantitative score to predict SNPs’ functional impact on proteoform structure and function. This initiative supports the CRC by providing computational predictions of SNP effects on proteoform structure and function, integrating both primary sequences as well as structural information from project D01. Additionally, D02 will serve as a data platform for the consortium, generating scientific resources for future CRC development.
Specifically, this includes developing SNPstar 2.0 and predicting proteoform candidates; developing a Plant Pangenome Browser for constructing, visualizing, and analyzing pangenomes of various plants, and creating bioinformatics and machine learning approaches for analyzing orthology relationships, integrating sequence and 3D-structure data to predict functionally modified proteoforms, and elucidating the effects of non-coding SNPs using diverse omics data.
Free positions in D02
Postdoc position, TV-L E13, 100% – Computer Science Expertise
TASKS // Construction of a Plant Pangenome Browser; Machine Learning; integration of various omics (DAP-seq, GHT-SELEX, ChIP-seq, RNA-seq) data and 3D protein structure structure data for elucidating SNP effects of proteoforms; analysis of orthology relationships
WORK PLACE // Martin Luther University Halle-Wittenberg, Institute of Computer Sciences
PI // Marcel Quint and Ivo Große
Job advertisement // Reg.-Nr. 5-5524/24-D
PhD position, TV-L E13, 100% – Computer Science Expertise
TASKS // Analysis of SNP properties using different measures and bioinformatics methods; Analysis and comparison of proteoforms based on SNP properties and additional measures and methods for pairwise sequence comparison; Design and implementation of ranking and prioritization methods on the level of individual SNPs and on the level of proteoforms
WORK PLACE // Martin Luther University Halle-Wittenberg, Institute of Computer Science
PI // Ivo Große
Job advertisement // Reg.-Nr. 5-5517/24-D
SNP2Prot currently provides additional free positions that you might be interested in.
See an overview of all open positions here:
https://snp2prot.uni-halle.de/positions/