Pär Engström

Pär Engström Joint Head of Long-term Bioinformatics Support

transcriptomics, functional and comparative genomics, genetic variation

emailpar.engstrom@scilifelab.se
phone +46 (0)8 16 22 44
https://orcid.org/0000-0001-5265-2121

Pär worked as a software developer in the telecommunications and internet industry in the early 90s, and then moved on to study biomedicine at Uppsala University, obtained a PhD in genomics and bioinformatics from Karolinska Institutet (2007), followed by postdoctoral studies at the European Bioinformatics Institute. His past research includes studies of gene structure and organization in mammalian genomes using diverse types of RNA sequencing data, with a particular focus on discovery and functional characterization of non-protein coding RNAs; comparisons of animal genomes to identify regulatory elements and examine their evolutionary relationship to chromosomal rearrangements; and studies of transcriptional and genetic alterations in cancer using microarray and sequencing-based approaches.

Pär joined the NBIS Long-term Support (WABI) team in 2013 and has since worked extensively on characterization of genetic variants underlying human disease, as well as genome annotation based on RNA-seq and proteomics. From mid-2016, he leads the Long-term Support team together with Björn Nystedt.

Selected publications

Zhu, Y., Engström, P. G., Tellgren-Roth, C., Baudo, C. D., Kennell, J. C., Sun, S., Billmyre, R. B., Schröder, M. S., Andersson, A., Holm, T., Sigurgeirsson, B., Wu, G., Sankaranarayanan, S. R., Siddharthan, R., Sanyal, K., Lundeberg, J., Nystedt, B., Boekhout, T., Dawson, T. L., Heitman, J., Scheynius, A., and Lehtiö, J. (2017) Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis. Nucleic acids research, 45, 2629–2643.

Dalin, M. G., Engström, P. G., Ivarsson, E. G., Unneberg, P., Light, S., Schaufelberger, M., Gilljam, T., Andersson, B., and Bergo, M. O. (2017) Massive parallel sequencing questions the pathogenic role of missense variants in dilated cardiomyopathy. International journal of cardiology, 228, 742–748.

Tuominen, R., Engström, P. G., Helgadottir, H., Eriksson, H., Unneberg, P., Kjellqvist, S., Yang, M., Lindén, D., Edsgärd, D., Hansson, J., and Höiom, V. (2016) The role of germline alterations in the DNA damage response genes BRIP1 and BRCA2 in melanoma susceptibility. Genes, chromosomes & cancer, 55, 601–611.

Engström, P. G. et al. (2013) Systematic evaluation of spliced alignment programs for RNA-seq data. Nature methods, 10, 1185–1191.

Castelo-Branco, G., Amaral, P. P., Engström, P. G., Robson, S. C., Marques, S. C., Bertone, P., and Kouzarides, T. (2013) The non-coding snRNA 7SK controls transcriptional termination, poising, and bidirectionality in embryonic stem cells. Genome biology, 14, R98.

Engström, P. G., Tommei, D., Stricker, S. H., Ender, C., Pollard, S. M., and Bertone, P. (2012) Digital transcriptome profiling of normal and glioblastoma-derived neural stem cells identifies genes associated with patient survival. Genome medicine, 4, 76.

Engström, P. G., Ho Sui, S. J., Drivenes, Ø., Becker, T. S., and Lenhard, B. (2007) Genomic regulatory blocks underlie extensive microsynteny conservation in insects. Genome research, 17, 1898–1908.