Computational and Digital Genomics
We develop computational tools to identify genetic risk factors associated with chronic diseases, using large biobank-scale datasets.
Lead
Professor of Computational Genomics
+43 512 9003 70579
sebastian.schoenherr@i-med.ac.at
About
We develop computational methods to identify genetic risk factors underlying chronic diseases, using large-scale biobank datasets, including wet-lab validation. Our current research focuses on complex genomic regions, such as variable number tandem repeats (VNTRs), to elucidate their contribution to missing heritability, with a particular emphasis on the LPA VNTR.
We have previously developed widely used resources including the Michigan Imputation Server, a core infrastructure for the global GWAS community, and the mitochondrial DNA classification tool Haplogrep. In addition, we contribute to numerous large-scale data analysis projects, delivering reproducible and scalable solutions for cohorts.
News
- October 2025: Silvia received a TnF project (Tiroler Nachwuchsforscher*innenförderung) to push her research on VNTR. Congrats!
- October 2025: We are back at American Society of Human Genetics (ASHG) Conference with an invited workshop on imputation servers. See you in Boston!
- October 2025: Silvia wins both the scientific prize of the Austrian Society of Human Genetics (ÖGH) and the Helmut-Sinzinger Prize for her recent work on medically relevent VNTRs. Congrats!
- October 2024: Sebastian will give a talk on the Michigan Imputation Server at the Nextflow Summit in Barcelona.
- July 2024: Big news: our latest work on VNTR has been published in Genome Biology and covered on the MUI website.
- May 2024: Silvia joins the Computational Group. Welcome!
- November 2023: We extended our UK Biobank project for another 3 years. Thanks to the financial support from the Medical University of Innsbruck!
Team
The students are partially co-supervised by Johanna-Schachtl-Rieß and Silvia Di Maio.
We are always seeking highly motivated students. If you’re interested in joining our team and contributing to innovative research, please reach out!
Genepi Investigators
We work closely with many researchers at Genepi.
AISCM Faculty
Please take a look at our Faculty of AI and Scientific Computing at MUI. We are proud to have been involved in founding this initiative, which aims to bring together researchers and medical doctors across disciplines.
Ongoing Projects
The Computational Genomics group maintains a close collaboration with the Genome Informatics team. These projects are listed in both groups.
- Contamination detection in mtDNA
- GWAS Nextflow pipeline
- Michigan Imputation Server
- Resolving intra-repeat variation in medically relevant VNTRs
- Variant calling in mtDNA
Cooperations
- Eurac Research Bozen/Bolzano (Christian Fuchsberger)
- University of Michigan (Gonçalo Abecasis, Albert Smith, Michael Boehnke)
- Johns Hopkins University (Enis Afgan)
Consortia activities
- gnomAD, TOPMed, HRC, GenomeAsia, GCKD, ncRNAPain, nonHFE
Key Publications
Di Maio S, Zöscher P, Weissensteiner H, Forer L, Schachtl-Riess JF, Amstler S, Streiter G, Pfurtscheller C, Paulweber B, Kronenberg F, Coassin S, Schönherr S: Resolving intra-repeat variation in medically relevant VNTRs from short-read sequencing data using the cardiovascular risk gene LPA as a model. Genome Biol. 25:167, 2024. PMID: 38926899 Journal Article
Weissensteiner H, Forer L, Kronenberg F, Schönherr S: mtDNA-Server 2: advancing mitochondrial DNA analysis through highly parallelized data processing and interactive analytics. Nucleic Acids Res. 52:W102-W107, 2024. PMID: 38709886 Journal Article
Das S, Forer L, Schönherr S*, Sidore C, Locke AE, Kwong A, Vrieze SI, Chew EY, Levy S, McGue M, Schlessinger D, Stambolian D, Loh PR, Iacono WG, Swaroop A, Scott LJ, Cucca F, Kronenberg F, Boehnke M, Abecasis GR, Fuchsberger C: Next-generation genotype imputation service and methods. Nat. Genet. 48:1284-1287, 2016. PMID: 27571263 Journal Article
McCarthy S, Das S, Kretzschmar W, Delaneau O, Wood AR, Teumer A, Kang HM, Fuchsberger C, Danecek P, Sharp K, Luo Y, Sidore C, Kwong A, Timpson N, Koskinen S, Vrieze S, Scott LJ, Zhang H, Mahajan A, Veldink J, Peters U, Pato C, van Duijn CM, Gillies CE, Gandin I, Mezzavilla M, Gilly A, Cocca M, Traglia M, Angius A, Barrett JC, Boomsma D, Branham K, Breen G, Brummett CM, Busonero F, Campbell H, Chan A, Chen S, Chew E, Collins FS, Corbin LJ, Smith GD, Dedoussis G, Dorr M, Farmaki AE, Ferrucci L, Forer L, Fraser RM, Gabriel S, Levy S, Groop L, Harrison T, Hattersley A, Holmen OL, Hveem K, Kretzler M, Lee JC, McGue M, Meitinger T, Melzer D, Min JL, Mohlke KL, Vincent JB, Nauck M, Nickerson D, Palotie A, Pato M, Pirastu N, McInnis M, Richards JB, Sala C, Salomaa V, Schlessinger D, Schoenherr S, Slagboom PE, Small K, Spector T, Stambolian D, Tuke M, Tuomilehto J, Van den Berg LH, Van Rheenen W, Volker U, Wijmenga C, Toniolo D, Zeggini E, Gasparini P, Sampson MG, Wilson JF, Frayling T, de Bakker PI, Swertz MA, McCarroll S, Kooperberg C, Dekker A, Altshuler D, Willer C, Iacono W, Ripatti S, Soranzo N, Walter K, Swaroop A, Cucca F, Anderson CA, Myers RM, Boehnke M, McCarthy MI, Durbin R, Haplotype Reference Consortium: A reference panel of 64,976 haplotypes for genotype imputation. Nat. Genet. 48:1279-1283, 2016. PMID: 27548312 Journal Article
Loh PR, Danecek P, Palamara PF, Fuchsberger C, A Reshef Y, K Finucane H, Schoenherr S, Forer L, McCarthy S, Abecasis GR, Durbin R, L Price A: Reference-based phasing using the Haplotype Reference Consortium panel. Nat. Genet. 48:1443-1448, 2016. PMID: 27694958 Journal Article
GenomeAsia100K Consortium: The GenomeAsia 100K Project enables genetic discoveries across Asia. Nature 576:106-111, 2019. PMID: 31802016 Journal Article
Weissensteiner H, Forer L, Fendt L, Kheirkhah A, Salas A, Kronenberg F, Schoenherr S: Contamination detection in sequencing studies using the mitochondrial phylogeny. Genome Res. 31:309-316, 2021. PMID: 33452015 Journal Article