Scientific Vita
Publi­cations
Con­tact

Prof. Dr.

Carl Herrmann

Since 2023
Professor Dept. Bioinformatics, Institute of Pharmacy and Molecular Biotechnology, University Heidelberg
2018 - 2023
Assistant-professor (Akademischer Oberrat) medical Faculty University Heidelberg
2013 - 2018
Group leader in the Division of theoretical bioinformatics, DKFZ Heidelberg, and assistant-professor (Akademischer Rat) at the Institute of Pharmacy and Molecular Biotechnologie (IPMB), University Heidelberg
2003 - 2013
Assistant-professor, University of Marseille and IBDML, CNRS (France)
2001 - 2003
Postdoc at the department of theoretical physics, University of Turin (Italy)
1999 - 2001
Postdoc at the department of theoretical physics, University Halle-Wittenberg
1. Doncevic D, Herrmann C. (2023) Biologically informed variational autoencoders allow predictive modeling of genetic and drug induced perturbations. Bioinformatics (2023 Jun 1;39(6):btad387. doi: 10.1093/bioinformatics/btad387.

2. Rheinberger M, Costa A, Kampmann M, Glavas D, Shytaj I, Sreeram S, , Penzo C, Tibroni,N, Garcia-Mesa Y, Leskov K, Fackler O, Vlahovicek K, Kar, J, Lucic B, Herrmann C*, Lusic M*. (2023) Genomic profiling of HIV-1 integration in microglia cells links viral integration to the topologically associated domains. Cell Rep. 42,112110. doi.org/10.1016/j.celrep.2023.112110.
3. Cao H, Zhang Y, Baumbach J, Burton P, Dwyer D, Koutsouleris N, Matschinske J, Marcon Y, Rajan S, Rieg T, Ryser-Welch P, Späth J, Consortium, The COMMITMENT, Herrmann C*, Schwarz E* (2022) dsMTL: a computational framework for privacy-preserving, distributed multi-task machine learning. Bioinformatics btac616. doi.org/10.1093/bioinformatics/btac616.
4. Ramirez Alvarez C, Kee C, Sharma A, Thomas L, Schmidt F, Stanifer M, Boulant S*, Herrmann C*. (2021) The endogenous cellular protease inhibitor SPINT2 controls SARS-CoV-2 viral infection and is associated to disease severity. PLOS Pathogens. 17(6), e1009687. doi.org/10.1371/journal.ppat.1009687.
5. Jansky S, Sharma AK, Körber V, Quintero A, Toprak UH, Wecht EM, Gartlgruber M, Greco A, Chomsky E, Grünewald TGP, Henrich K-O, Tanay A, Herrmann C, Höfer T, Westermann F. (2021) Single-cell transcriptomic analyses provide insights into the developmental origins of neuroblastoma. Nat Genet. 53,683–693. doi.org/10.1038/s41588-021-00806-1.
6. Gartlgruber M, Sharma AK, Quintero A, Dreidax D, Jansky S, Park Y, Kreth S, Meder J, Doncevic D, Saary P, Toprak UH, Ishaque N, Afanasyeva E, Wecht E, Koster J, Versteeg R, Grünewald TGP, Jones DTW, Pfister SM, Henrich K, van Nes J, Herrmann C*, Westermann F*. (2021) Super enhancers define regulatory subtypes and cell identity in neuroblastoma. Nat Cancer. 2(1),114–128. doi.org/10.1038/s43018-020-00145-w.
7. Wu Y, Fletcher M, Gu Z, Wang Q, Costa B, Bertoni A, Man K, Schlotter M, Felsberg J, Mangei J, Barbus M, Gaupel A, Wang W, Weiss T, Eils R, Weller M, Liu H, Reifenberger G, Korshunov A, Angel P, Lichter P, Herrmann C*, Radlwimmer B*. (2020) Glioblastoma epigenome profiling identifies SOX10 as a master regulator of molecular tumour subtype. Nat Commun. 11(1), 6434. doi: 10.1038/s41467-020-20225-w.
8. Kumar S, Warrell J, Li S, McGillivray PD, Meyerson W, Salichos L, Harmanci A, Martinez-Fundichely A, Chan CWY, Nielsen MM, Lochovsky L, Zhang Y, Li X, Lou S, Pedersen JS, Herrmann C, Getz G, Khurana E, Gerstein M. (2020) Passenger mutations in more than 2,500 cancer genomes: overall molecular functional impact and consequences. Cell. 180(5), 915-927.e16. doi.org/10.1016/j.cell.2020.01.032.
9. Liu L, Liu C, Quintero A, Wu L, Yuan Y, Wang M, Cheng M, Leng L, Xu L, Dong G, Li R, Liu Y, Wei X, Xu J, Chen X, Lu H, Chen D, Wang Q, Zhou Q, Lin X, Li G, , Liu S, Wang Q, Wang H, Fink JL, Gao Z, Liu X, Hou Y, Zhu S, Yang H, Ye Y, Lin G, Chen F, Herrmann C, Eils,R, Shang Z, Xu X. (2019) Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity. Nat Commun. 10(1),470. doi.org/10.1038/s41467-018-08205-7.
10. Bauer T, Trump S, Ishaque N, Thurmann L, Gu L, Bauer M, Bieg M, Gu Z, Weichenhan D, Mallm J-P, Roder S, Herberth G, Takada E, Mucke O, Winter M, Junge KM, Grutzmann K, Rolle-Kampczyk U, Wang Q, Lawerenz C, Borte M, Polte T, Schlesner M, Schanne M, Wiemann S, Georg C, Stunnenberg HG, Plass C, Rippe K, Mizuguchi J, Herrmann C*, Eils R*, Lehmann I*. (2016) Environment-induced epigenetic reprogramming in genomic regulatory elements in smoking mothers and their children. Mol Syst Biol. 12(3),861–861. doi.org/10.15252/msb.20156520.
Address
Institute of Pharmacy and Molecular Biotechnology & BioQuant
Faculty of Engineering Sciences
Ruprecht-Karls-University
Heidelberg
Phone
06221 54-51249
eMail
carl.herrmann@bioquant.uni-heidelberg.de