Genome Informatics

We develop and use innovative informatics approaches like machine learning technologies to advance our understanding of genomics.

Lead

Co-Lead

---

Team

Former Members

Genepi Investigators

• Sebastian Schönherr

• Hansi Weissensteiner

• Stefan Coassin

Research Objectives

Cloud Computing for Genomics: Harnessing the power of cloud computing to enhance storage, accessibility, and processing of large-scale genomic datasets. Improving scalability and collaboration through cloud-based platforms.(see Cloudgene).

Precision Medicine: Customizing medical approaches by leveraging genomic information to predict the risk of diseases for individuals (see pgs-calc).

Data Integration and Visualization: Developing user-friendly tools to effectively combine and display complex genomic data, supporting researchers in making informed decisions (see rsq-browser).

Reproducible Science: Promoting reproducibility in genomics research by establishing transparent methodologies, documenting data analysis pipelines, and advocating for open science practices (see nf-test).

Projects

We maintain a close collaboration with the Computational and Digital Genomics group. These projects are listed in both groups.

• Automate Michigan Imputation Server
• GWAS Nextflow pipeline
• Michigan Imputation Server

Cooperations

• Eurac Research Bozen/Bolzano (Christian Fuchsberger)
• Institute of Human Genetics, Medical University of Innsbruck (Simon Schnaiter und Gunda Schwaninger)
• University of Michigan (Gonçalo Abecasis, Albert Smith, Michael Boehnke)
• University of Innsbruck (Günther Specht)

Consortia activities

• TOPMed
• HRC
• GenomeAsia
• GCKD
• ncRNAPain
• nonHFE
• ApoA-IV-GWAS
• HEVACC

Key Publications

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

Forer L, Taliun D, LeFaive J, Smith AV, Boughton AP, Coassin S, Lamina C, Kronenberg F, Fuchsberger C, Schönherr S: Imputation Server PGS: an automated approach to calculate polygenic risk scores on imputation servers. Nucleic Acids Res. 52:W70-W77, 2024. PMID: 38709879   Journal Article

Schönherr S, Schachtl-Riess JF, Di Maio S*, Filosi M, Mark M, Lamina C, Fuchsberger C, Kronenberg F, Forer L: Performing highly parallelized and reproducible GWAS analysis on biobank-scale data. NAR Genom Bioinform 6:lqae015, 2024. PMID: 38327871   Journal Article

Schönherr S, Weissensteiner H, Kronenberg F, Forer L: Haplogrep 3 - an interactive haplogroup classification and analysis platform. Nucleic Acids Res. 51:W263-W268, 2023. PMID: 37070190   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

Weissensteiner H, Forer L, Fuchsberger C, Schöpf B, Kloss-Brandstätter A, Specht G, Kronenberg F, Schönherr S: mtDNA-Server: next-generation sequencing data analysis of human mitochondrial DNA in the cloud. Nucleic Acids Res. 44:W64-9, 2016. PMID: 27084948   Journal Article

---