Biomedical Genomics

Biomedical Genomics Overview

Heidelberg

The Biomedical Genomics group at the Health Data Science Unit, Medical Faculty Heidelberg and BioQuant is focusing on deciphering the molecular mechanisms of gene regulation and its alterations in a disease context, in particular in cancer. We develop computational methods to combine various omics datasets to characterize patient data at a molecular level, by performing primary data analysis as well as applying statistical methods to combine molecular and clinical data sources. These methods are increasingly used to include single cell datasets and provide computational methods to combine single cell and bulk datasets. We initiated the OpenLab Epigenomics, which provides ready-to-use pipelines for processing of various NGS datasets as well as expertise and assistance.

Topics

We are involved in a large consortium focusing on the study of comorbidities in schizophrenia patients and the molecular stratification of patient with mental disorders. This is done by applying a transfer learning strategy to jointly learn signatures from multiple, distributed cohorts with non-overlapping data types. At the same time, these signatures are compared to those derived from cohorts of patients with T2D or cardiovascular diseases to highlight commonalities and specific mechanisms.

We are applying computational methods in datasets related to HIV or HCV infection to describe the response of the host cell to infection both at transcriptional and regulatory level by combining scRNA-seq and scATAC-seq. We are using these two data types to reconstruct the regulatory networks and identify master regulators driving these processes.

Publications

Kumar S.*, Warrel J.*, Shantao L., McGillivray P., Meyerson W., Salichos L., Harmanci, A., Martinez-FGundichely, A., Chan, C. W. Y., Nielsen, M. M., Locjovsky, L., Zhang, Y., Li, X., Pedersen, J. S., Herrmann C., Getz G., Khurana E. & Gerstein M. B.^§ (2018). Passenger mutations in 2500 cancer genomes: Overall molecular functional impact and consequences, Cell, in Press, bioRxiv, doi: 10.1101/280446

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, J.L., 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. Nature Communications, 10(1), 470. doi: 10.1038/s41467-018-08205-7

Chan, C.W.Y., Gu, Z., Bieg, M., Eils, R. & Herrmann, C.^§ (2019). Impact of cancer mutational signatures on transcription factor motifs in the human genome. BMC Medical Genomics, 12(1), 64. doi: 10.1186/s12920-019-0525-4

Bauer, T.*, Trump, S.*, Ishaque, N.*, Thurmann, L.*, Gu, L.*, Bauer, M.*, Bieg, M., Gu, Z.G., Weichenhan, D., Mallm, J.P., Roder, S., Herberth, G., Takada, E., Mucke, O., Winter, M., Junge, K.M., Grutzmann, K., Rolle-Kampczyk, U., Wang, Q., Lawerenz, C., Borte, M., Polte, T., Schlesner, M., Schanne, M., Wiemann, S., Georg, C., Stunnenberg, H.G., 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. Molecular Systems Biology, 12(3). doi: 10.15252/msb.20156520

Peifer, M.*^§, Hertwig, F.*, Roels, F.*, Dreidax, D.*, Gartlgruber, M.*, Menon, R., Krämer, A., Roncaioli, J.L., Sand, F., Heukmann J. M., Ikram, F., Ackermann, S., Engesser, A., Kahlert, Y., Altmüller, J., Nürnberg, P., Thierry-Mieg, J., Thierry-Mieg, D., Mariappan, A., Heynck, S., Mariotti, E., Henrich, K.-O., Gloeckner, C., Bosco, G., Leuscher, I., Schweiger, M. R., Savelyeya, L., Watkins, S. C., Shao, C., Bell, E., Höfer, T., Achter, V., Lang, U., Theissen, J., Volland, R., Saadati, M., Eggert, A., de Wilde, B., Peng, Z., Zhao, C., Shi, L., Ortmann, M., Büttner, R., Perner, S., Hero, B., Schramm, A., Schulte, J. H., Herrmann C., O’Sullivan R., Westermann F.^§, Thomas R. K.^§ & Fischer M.^§ (2015). Telomerase activation by genomic rearrangements in high-risk neuroblastoma. Nature, 526(7575), 700–704. doi: 10.1038/nature14980

*these authors contributed equally

^§corresponding author