Genomics and Bioinformatics

Dr. Jochen Wilhelm

Jochen Wilhelm is senior scientist at the Institute for Lung Health (ILH), Justus Liebig University Giessen (JLU), Germany, where he leads the platform “Genomics and Bioinformatics” together with Marek Bartkuhn. He is also faculty member at the German Center for Lung Research (Deutsches Zentrum für Lungenforschung, DZL) and chief statistician of the European IPF Registry and Biobank (eurIPFreg).

Jochen Wilhelm was born in Giessen and studies Biology and practical informatics at the JLU Giessen. After receiving his Diploma in Biology, he received a scholarship of the graduate college “Molecular biology and pharmacology” and finished his PhD (Dr. rer. nat) in Biochemistry at the department of biochemistry in the faculty of biology. After his PhD he started a lab for microarray analyses in a collaborative research centre in the faculty of medicine and became principle investigator for biostatistics andmicroarray analytics at the Max-Plack-Institute for Heart and Lung Research in Bad Nauheim. Since this time, he is given lectures for biostatistics and bioinformatics in the PhD program Molecular Biology and Medicine of the Lung (MBML) at the University of Giessen and Marburg Lung Center (UGMLC). As UGMLC faculty member and head of the UGMLC microarray core facility he also became principle investigator for systems biology of the lung at the DZL. Dr. Wilhelm is currently project leader of the central resource facility Virus genomics and host transcriptomics of the collaborative research centre 1021 (RNA viruses) and of the core unit Genome signatures  of pathogen-host interaction in the infected and injured lung of the clinical research unit 309 (Virus-induced lung injury). He published 114 research papers (up to 03/2021) in well-renowned scientific journals such as Nature Metabolism, Nature Communications, Circulation, Journal of Clinical Investigation, American Journal of Respiratory and Critical Care Medicine, European Respiratory Journal, Cardiovascular Research, Thorax, Clinical Chemistry, Nucleic Acids Research and others. He contributed chapters in several books about gene expression measurement technologies.


Prof. Dr. Marek Bartkuhn

Marek Bartkuhn is an FCMH professor for Biomedical Informatics and Systems Medicine in the medical faculty of the JLU. Together with Dr. Jochen Wilhelm he runs the Genomics and Bioinformatics core facility within the ILH.

Marek Bartkuhn was born in Hanau, Germany, and studied biology at the JLU Giessen. After he had finished is PhD (Dr. rer. nat.) he performed his postdoc and intensified his studies on epigenetic control of gene transcription and the regulation of higher order chromatin structure by insulator proteins. During this time, he started to focus his scientific endeavors towards different -omics approaches like gene expression microarrays or tiling arrays for the genome-wide identification of binding sites of DNA-binding proteins like transcription factors. Thereafter, he went on and became principle investigator of the bioinformatics service project of the international collaborative research center TRR81, providing bioinformatics support to a large community of scientific groups interested in the complex regulatory circuits underlying gene regulation. He published in many renowned journals like Nature, Nature Cell Biology, Nature Communications, Molecular Cell, Cell Reports, Genome Research, Leukemia, PNAS, EMBO and Nucleic Acid Research.


The genomics and bioinformatics platform will make transcriptomic, genomic, and epigenetic analysis by next-generation sequencing available to all groups in the ILH. This includes the generation, management, analysis and interpretation of the resulting data with state-of-the art analyses including single-cell-, spatial-, pseudo-time- and RNA velocity analyses to get the most complete picture of cellular organization, differentiation and fate. The subsequent figure gives an overview of the various technological approaches. Concretely, the collaboration with the different experimental ILH scientists include:

  • helping collaborators with experimental and statistical design of their studies
  • preparing sequencing libraries and performing the sequencing
  • analyzing genome-wide data sets
  • integrating different sources of data in systems biology approaches
  • presenting analyzed data in form of state of the art evaluation charts and publication.ready figures
  • developing, improving and providing automated pipelines in order to make analysis tools and workflows more easily available to collaborators (via a Galaxy server)


Dr. Jochen Wilhelm
Institute for lung health (ILH)
Member of the German Center for Lung Research (DZL)
Universities of Giessen and Marburg Lung Center (UGMLC)
Justus Liebig University Giessen
Aulweg 132
35392 Giessen

Tel: +49 (0) 641 99 36470 (office)
Tel: +49 (0) 641 99 36463 (lab)



Prof. Dr. Marek Bartkuhn
Biomedical Informatics and Systems Medicine
Science Unit for Basic and Clinical Medicine
Institute for lung health (ILH)
Justus Liebig University Giessen
Aulweg 128
35392 Giessen

Tel: +49 (0) 641 99 36470 (CIGL )
Tel: +49 (0) 641 99 30522 (ForMed )



Most important publications

Eul, B., Cekay, M., Pullamsetti, S.S., Tello, K., Wilhelm, J., Gattenlöhner, S., Sibelius, U., Grimminger, F., Seeger, W., Savai, R., 2021. Noninvasive Surrogate Markers of Pulmonary Hypertension Are Associated with Poor Survival in Patients with Lung Cancer. Am J Respir Crit Care Med 203, 1316–1319, 2021 (IF: 21.4)

Soochit, W., Sleutels, F., Stik, G., Bartkuhn, M., Basu, S., Hernandez, S.C., Merzouk, S., Vidal, E., Boers, R., Boers, J., van der Reijden, M., Geverts, B., van Cappellen, W.A., van den Hout, M., Ozgur, Z., van IJcken, W.F.J., Gribnau, J., Renkawitz, R., Graf, T., Houtsmuller, A., Grosveld, F., Stadhouders, R., Galjart, N., 2021. CTCF chromatin residence time controls three-dimensional genome organization, gene expression and DNA methylation in pluripotent cells. Nat Cell Biol.  (IF 20)

Procida, T., Friedrich, T., Jack, A.P.M., Peritore, M., Bönisch, C., Eberl, H.C., Daus, N., Kletenkov, K., Nist, A., Stiewe, T., Borggrefe, T., Mann, M., Bartkuhn*, M., Hake*, S.B., 2021. JAZF1, A Novel p400/TIP60/NuA4 Complex Member, Regulates H2A.Z Acetylation at Regulatory Regions. Int J Mol Sci 22. * shared corresponding author (IF: 5.9)

Ahmadvand, N., Khosravi, F., Lingampally, A., Wasnick, R., Vazquez-Armendariz, I., Carraro, G., Heiner, M., Rivetti, S., Lv, Y., Wilhelm, J., Gunther, A., Herold, S., Al Alam, D., Chen, C., Minoo, P., Zhang, J.-S., Bellusci, S., 2021. Identification of a novel subset of alveolar type 2 cells enriched in PD-L1 and expanded following pneumonectomy. Eur Respir J 2004168. (IF: 16.67)

Pichl, A., Sommer, N., Bednorz, M., Seimetz, M., Hadzic, S., Kuhnert, S., Kraut, S., Roxlau, E.T., Kojonazarov, B., Wilhelm, J., Gredic, M., Gall, H., Tello, K., Richter, M.J., Pak, O., Petrovic, A., Hecker, M., Schermuly, R.T., Grimminger, F., Seeger, W., Ghofrani, H.A., Weissmann, N., 2019. Riociguat for treatment of pulmonary hypertension in COPD: a translational study. Eur Respir J 53, 1802445. (IF: 16.67)

Kwapiszewska, G., Gungl, A., Wilhelm, J., Marsh, L.M., Thekkekara Puthenparampil, H., Sinn, K., Didiasova, M., Klepetko, W., Kosanovic, D., Schermuly, R.T., Wujak, L., Weiss, B., Schaefer, L., Schneider, M., Kreuter, M., Olschewski, A., Seeger, W., Olschewski, H., Wygrecka, M., 2018. Transcriptome profiling reveals the complexity of pirfenidone effects in idiopathic pulmonary fibrosis. Eur Respir J 52, 1800564. (IF: 16.67)

Link, S., Spitzer, R.M.M., Sana, M., Torrado, M., Völker-Albert, M.C., Keilhauer, E.C., Burgold, T., Pünzeler, S., Low, J.K.K., Lindström, I., Nist, A., Regnard, C., Stiewe, T., Hendrich, B., Imhof, A., Mann, M., Mackay, J.P., Bartkuhn*, M., Hake*, S.B., 2018. PWWP2A binds distinct chromatin moieties and interacts with an MTA1-specific core NuRD complex. Nat Commun 9, 4300. * shared corresponding author (IF 12.1)

Maksimenko*, O., Bartkuhn*, M., Stakhov*, V., Herold, M., Zolotarev, N., Jox, T., Buxa, M.K., Kirsch, R., Bonchuk, A., Fedotova, A., Kyrchanova, O., Renkawitz, R., Georgiev, P., 2015. Two new insulator proteins, Pita and ZIPIC, target CP190 to chromatin. Genome Res 25, 89–99.  * equally contributing first author (IF: 11)

Walz, S., Lorenzin, F., Morton, J., Wiese, K.E., von Eyss, B., Herold, S., Rycak, L., Dumay-Odelot, H., Karim, S., Bartkuhn, M., Roels, F., Wüstefeld, T., Fischer, M., Teichmann, M., Zender, L., Wei, C.-L., Sansom, O., Wolf, E., Eilers, M., 2014. Activation and repression by oncogenic MYC shape tumour-specific gene expression profiles. Nature 511, 483–487.  (IF: 42.8)

Here you can find all ILH-publications