Rafał Gumienny

Bioinformatician, scientific programmer, brewing enthusiast...

Rafał Gumienny - Profile picture

I'm a scientific software developer and bioinformatician currently working at Novartis Institutes for BioMedical Research (NIBR). At work, I enjoy to combine my biological background with programming skills to support biologists with state of the art tools.
In my spare time I brew beer, make sausages and play bass guitar.

I obtained my PhD in Bioinformatics from Basel University (Switzerland), and my MSc in Biotechnology from Jagiellonian University (Poland). I also hold MSc degree in Molecular Biology from Université d'Orléans (France).

papers

  1. Gumienny R, Jedlinski D, Martin G, Vina-Villaseca A, et al. High-throughput identification of C/D box snoRNA targets with CLIP and RiboMeth-seq. Nucleic Acids Res. 2016,
  2. Gumienny R, Zavolan M. Accurate transcriptome-wide prediction of microRNA targets and small interfering RNA off-targets with MIRZA-G. Nucleic Acids Res. 2015,
  3. Haas J, Barbato A, Behringer D, Studer G, Roth S, Bertoni M, Mostaguir K, Gumienny R, Schwede T. Continuous Automated Model EvaluatiOn (CAMEO) complementing the critical assessment of structure prediction in CASP12. Proteins. 2018
  4. Jorjani H, Kehr S, Jedlinski DJ, Gumienny R, et al. An updated human snoRNAome. Nucleic Acids Res. 2016
  5. Breda J, Rzepiela AJ, Gumienny R, van Nimwegen E, Zavolan M. Quantifying the strength of miRNA-target interactions. Methods. 2015
  6. Gruber AR, Martin G, Mueller P, Schmidt A, Gruber AJ, Gumienny R, et al. Global 3' UTR shortening has a limited effect on protein abundance in proliferating T cells. Nat Commun. 2014

projects

Science

MIRZA-G
A tool and a model used for miRNA target prediction
snoRNA Hybrid Search
A pipeline to discover snoRNA-target chimeric reads in CLIP/HTS experiments
GEOparse
Python library to access Gene Expression Omnibus Database (GEO)
uShuffle
A Cython wrapper around uShuffle - a useful tool for shuffling biological sequences while preserving the k-let counts

Web

SPHN DCC
The Swiss Personalized Health Network (SPHN) Data Cooridination Centre website
QMEAN
Front-end for QMEAN - homology model quality estimation tool

see more projects and other miscellaneous stuff (scripts, config files...) on github...