Jakub Orzechowski Westholm

Jakub Orzechowski Westholm NBIS expert

RNA-seq, non-coding RNA, ChIP-seq, gene regulation


Jakub got his PhD in bioinformatics from Uppsala University in 2009, studying gene regulation, metabolic signaling and epigenomics. He then did a post doc at Memorial Sloan-Kettering Cancer Center, investigating neural development and various aspects of RNA biology (mRNA isoforms, microRNAs, circularRNAs).

Jakub joined NBIS in 2014 as part of the bioinformatics long term support team, and mainly works on projects related to RNA, gene regulation and chromatin.

Technical skills include analysis of RNA-seq and ChIP-seq data, as well as combinatorial optimization, machine learning and statistical modeling.

Selected publications

Ståhl, P. L., Salmén, F., Vickovic, V., Lundmark, A., Fernández Navarro, J., Magnusson, J., Giacomello, S., Asp, M., Westholm, J. O., Huss, M., Mollbrink, A., Linnarsson, S., Codeluppi, S., Borg, Å., Pontén, F., Costea, P. I., Sahlén, P., Mulder, J., Bergmann, O., Lundeberg, J., and Frisén, J. (2016) Science, 353, 78–82.

Westholm, J. O., Miura, P., Olson, S., Shenker, S., Celniker, S. E., Graveley, B. R., and E.C., L. (2014) Genomewide analysis in Drosophila reveals structural properties and age-dependent neural accumulation of circular RNAs. Cell Reports, 9, 1966–1980.

Westholm, J. O., Ladewig, E., Bortolamiol-Becet, D., Robine, N., and Lai, E. C. (2012) Common and distinct patterns of terminal modifications to mirtrons and canonical microRNAs. RNA, 18, 177–192.

Smibert, P., Miura, P., Westholm, J. O., Shenker, S., G., M., Duff, M. O., Zhang, D., Eads, B. D., Carlson, J., Brown, B., Eisman, R. C., Andrews, J., Kaufman, T., Cherbas, P., Celniker, S. E., Graveley, B. R., and Lai, E. C. (2012) Global patterns of tissue-specific alternative polyadenylation in Drosophila. Cell Reports, 1, 277–289.

Westholm, J. O. and Lai, E. C. (2011) Mirtrons: microRNA biogenesis via splicing. Biochimie, 93, 1897–1904.