Dr. Jörg Hackermüller

Head of Young Investigators Group Bioinformatics & Transcriptomics


Helmholtz Centre for Environmental Research - UFZ
Permoserstr. 15
04318 Leipzig, Germany

Phone: +49 341 235 1561
Fax: +49 341 235 1786


Social network


Research interests

  • Functional, non-coding RNAs
  • Non-coding RNAs in disease and toxicity, drug discovery, and biomarkers
  • Environmental epigenetics
  • Gene – environment interactions
  • Data integration in systems biology
  • Bioinformatic method development for omics data analysis
  • Regulatory networks involving non-coding RNAs
  • RNA structural bioinformatics
  • Immune cell differentiation
  • RNA-protein interactions
  • RNA stability regulation

CV

Professional experience

Since 2011 Head of Group, Helmholtz-University Young Investigators Group Bioinformatics & Transcriptomics
Helmholtz Centre for Environmental Research – UFZ and University of Leipzig, Faculty for Mathematics and Informatics
2010 Junior Faculty, University of Leipzig, Faculty for Mathematics and Informatics
2007 - 2014 Head of Group, RNomics Group
Fraunhofer Institute for Cell Therapy and Immunology IZI
(Since 2010 as secondary employment)
2005 - 2007 Post Doctoral Scientist, RNomics Group
Fraunhofer Institute for Cell Therapy and Immunology IZI 
2005 Post Doctoral Scientist, Innovative Screening Technologies Unit
Novartis Institutes for Biomedical Research
2002 - 2005 PhD Student, In Silico Sciences Unit
Novartis Institutes for Biomedical Research
Education  
2005 PhD (Dr. rer. nat.) in Chemistry
University Vienna
2001 Diploma in Chemistry (Biochemistry, Theoretical Chemistry)
University Vienna


Publications

  • Bauer, M., Hackermüller, J., Schor, J., Schreiber, S., Fink, B., Pierzchalski, A., Herberth, G., (2019):
    Specific induction of the unique GPR15 expression in heterogeneous blood lymphocytes by tobacco smoking
    Biomarkers 24 (3), 217 - 224
    full text (url)
  • Kallies, R., Kiesel, B., Schmidt, M., Ghanem, N., Zopfi, J., Hackermüller, J., Harms, H., Wick, L.Y., Chatzinotas, A., (2019):
    Complete genome sequence of Pseudoalteromonas virus vB_PspP-H6/1 that infects Pseudoalteromonas sp. strain H6
    Mar. Genom.
    full text (url)
  • Behrens, G., Winzen, R., Rehage, N., Dörrie, A., Barsch, M., Hoffmann, A., Hackermüller, J., Tiedje, C., Heissmeyer, V., Holtmann, H., (2018):
    A translational silencing function of MCPIP1/Regnase-1 specified by the target site context
    Nucleic Acids Res. 46 (8), 4256 - 4270
    full text (url)
  • Essig, K., Kronbeck, N., Guimaraes, J.C., Lohs, C., Schlundt, A., Hoffmann, A., Behrens, G., Brenner, S., Kowalska, J., Lopez-Rodriguez, C., Jemielity, J., Holtmann, H., Reiche, K., Hackermüller, J., Sattler, M., Zavolan, M., Heissmeyer, V., (2018):
    Roquin targets mRNAs in a 3′-UTR-specific manner by different modes of regulation
    Nat. Commun. 9 , art. 3810
    full text (url)
  • Jahreis, S., Trump, S., Bauer, M., Bauer, T., Thürmann, L., Feltens, R., Wang, Q., Gu, L., Grützmann, K., Röder, S., Averbeck, M., Weichenhan, D., Plass, C., Sack, U., Borte, M., Dubourg, V., Schüürmann, G., Simon, J.C., von Bergen, M., Hackermüller, J., Eils, R., Lehmann, I., Polte, T., (2018):
    Maternal phthalate exposure promotes allergic airway inflammation over 2 generations through epigenetic modifications
    J. Allergy Clin. Immunol. 141 (2), 741 - 753
    full text (url)
  • Rehage, N., Davydova, E., Conrad, C., Behrens, G., Maiser, A., Stehklein, J.E., Brenner, S., Klein, J., Jeridi, A., Hoffmann, A., Lee, E., Dianzani, U., Willemsen, R., Feederle, R., Reiche, K., Hackermüller, J., Leonhardt, H., Sharma, S., Niessing, D., Heissmeyer, V., (2018):
    Binding of NUFIP2 to Roquin promotes recognition and regulation of ICOS mRNA
    Nat. Commun. 9 , art. 299
    full text (url)
  • Binder, S., Hösler, N., Riedel, D., Zipfel, I., Buschmann, T., Kämpf, C., Reiche, K., Burger, R., Gramatzki, M., Hackermüller, J., Stadler, P.F., Horn, F., (2017):
    STAT3-induced long noncoding RNAs in multiple myeloma cells display different properties in cancer
    Sci. Rep. 7 , art. 7976
    full text (url)
  • Buesen, R., Chorley, B.N., da Silva Lima, B., Daston, G., Deferme, L., Ebbels, T., Gant, T.W., Goetz, A., Greally, J., Gribaldo, L., Hackermüller, J., Hubesch, B., Jennen, D., Johnson, K., Kanno, J., Kauffmann, H.-M., Laffont, M., McMullen, P., Meehan, R., Pemberton, M., Perdichizzi, S., Piersma, A.H., Sauer, U.G., Schmidt, K., Seitz, H., Sumida, K., Tollefsen, K.E., Tong, W., Tralau, T., van Ravenzwaay, B., Weber, R.J.M., Worth, A., Yauk, C., Poole, A., (2017):
    Applying 'omics technologies in chemicals risk assessment: Report of an ECETOC workshop
    Regul. Toxicol. Pharmacol. 91 (Suppl. 1), S3 - S13
    full text (url)
  • Escher, B.I., Hackermüller, J., Polte, T., Scholz, S., Aigner, A., Altenburger, R., Böhme, A., Bopp, S.K., Brack, W., Busch, W., Chadeau-Hyam, M., Covaci, A., Eisenträger, A., Galligan, J.J., Garcia-Reyero, N., Hartung, T., Hein, M., Herberth, G., Jahnke, A., Kleinjans, J., Klüver, N., Krauss, M., Lamoree, M., Lehmann, I., Luckenbach, T., Miller, G.W., Müller, A., Phillips, D.H., Reemtsma, T., Rolle-Kampczyk, U., Schüürmann, G., Schwikowski, B., Tan, Y.-M., Trump, S., Walter-Rohde, S., Wambaugh, J.F., (2017):
    From the exposome to mechanistic understanding of chemical-induced adverse effects
    Environ. Int. 99 , 97 - 106
    full text (url)
  • Gant, T.W., Sauer, U.G., Zhang, S.-D., Chorley, B.N., Hackermüller, J., Perdichizzi, S., Tollefsen, K.E., van Ravenzwaay, B., Yauk, C., Tong, W., Poole, A., (2017):
    A generic Transcriptomics Reporting Framework (TRF) for 'omics data processing and analysis
    Regul. Toxicol. Pharmacol. 91 (Suppl. 1), S36 - S45
    full text (url)
  • Goris, T., Schenz, B., Zimmermann, J., Lemos, M., Hackermüller, J., Schubert, T., Diekert, G., (2017):
    The complete genome of the tetrachloroethene-respiring Epsilonproteobacterium Sulfurospirillum halorespirans
    J. Biotechnol. 255 , 33 - 36
    full text (url)
  • Kallies, R., Kiesel, B., Schmidt, M., Kacza, J., Ghanem, N., Narr, A., Zopfi, J., Wick, L.Y., Hackermüller, J., Harms, H., Chatzinotas, A., (2017):
    Complete genome sequence of Pseudoalteromonas phage vB_PspS-H40/1 (formerly H40/1) that infects Pseudoalteromonas sp. strain H40 and is used as biological tracer in hydrological transport studies
    Stand. Genomic Sci. 12 , art. 20
    full text (url)
  • Kauffmann, H.-M., Kamp, H., Fuchs, R., Chorley, B.N., Deferme, L., Ebbels, T., Hackermüller, J., Perdichizzi, S., Poole, A., Sauer, U.G., Tollefsen, K.E., Tralau, T., Yauk, C., van Ravenzwaay, B., (2017):
    Framework for the quality assurance of ’omics technologies considering GLP requirements
    Regul. Toxicol. Pharmacol. 91 (Suppl. 1), S27 - S35
    full text (url)
  • Sauer, U.G., Deferme, L., Gribaldo, L., Hackermüller, J., Tralau, T., van Ravenzwaay, B., Yauk, C., Poole, C., Tong, W., Gant, T.W., (2017):
    The challenge of the application of 'omics technologies in chemicals risk assessment: Background and outlook
    Regul. Toxicol. Pharmacol. 91 (Suppl. 1), S14 - S26
    full text (url)
  • Aigner, A., Buesen, R., Gant, C., Gooderham, N., Greim, H., Hackermüller, J., Hubesch, B., Laffont, M., Marczylo, E., Meister, G., Petrick, J.S., Rasoulpour, R.J., Sauer, U.G., Schmidt, K., Seitz, H., Slack, F., Sukata, T., van der Vies, S.M., Verhaert, J., Witwer, K.W., Poole, A., (2016):
    Advancing the use of noncoding RNA in regulatory toxicology: Report of an ECETOC workshop
    Regul. Toxicol. Pharmacol. 82 , 127 - 139
    full text (url)
  • Kirsten, H., Al-Hasani, H., Holdt, L., Gross, A., Beutner, F., Krohn, K., Ahnert, P., Burkhardt, R., Reiche, K., Hackermüller, J., Löffler, M., Teupser, D., Thiery, J., Scholz, M., (2015):
    Dissecting the genetics of the human transcriptome identifies novel trait-related trans-eQTLs and corroborates the regulatory relevance of non-protein coding loci
    Hum. Mol. Genet. 24 (16), 4746 - 4763
    full text (url)
  • Arnold, C., Externbrink, F., Hackermüller, J., Reiche, K., (2014):
    CEM-Designer: design of custom expression microarrays in the post-ENCODE era
    J. Biotechnol. 189 , 154 - 156
    full text (url)
  • Gasch, M., Goroll, T., Bauer, M., Hinz, D., Schütze, N., Polte, T., Kesper, D., Simon, J.-C., Hackermüller, J., Lehmann, I., Herberth, G., (2014):
    Generation of IL-8 and IL-9 producing CD4+ T cells is affected by Th17 polarizing conditions and AHR ligands
    Mediat. Inflamm. , 182549
    full text (url)
  • Hackermüller, J., Reiche, K., Otto, C., Hösler, N., Blumert, C., Brocke-Heidrich, K., Böhlig, L., Nitsche, A., Kasack, K., Ahnert, P., Krupp, W., Engeland, K., Stadler, P.F., Horn, F., (2014):
    Cell cycle, oncogenic and tumor suppressor pathways regulate numerous long and macro non-protein coding RNAs
    Genome Biol. 15 (3), R48
    full text (url)
  • Hoffmann, S., Otto, C., Doose, G., Tanzer, A., Langenberger, D., Christ, S., Kunz, M., Holdt, L.M., Teupser, D., Hackermüller, J., Stadler, P.F., (2014):
    A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection
    Genome Biol. 15 (2), R34
    full text (url)
  • Reiche, K., Kasack, K., Schreiber, S., Lüders, T., Due, E.U., Naume, B., Riis, M., Kristensen, VN, Horn, F., Børresen-Dale, A.L., Hackermüller, J., Baumbusch, L.O., (2014):
    Long non-coding RNAs differentially expressed between normal versus primary breast tumor tissues disclose converse changes to breast cancer-related protein-coding genes
    PLOS One 9 (9), e106076
    full text (url)
  • Rivarola-Duarte, L., Otto, C., Jühling, F., Schreiber, S., Bedulina, D.S., Jakob, L., Gurkov, A., Axenov-Gribanov, D., Sahyoun, A.H., Lucassen, M., Hackermüller, J., Hoffmann, S., Sartoris, F., Pörtner, H.-O., Timofeyev, M., Luckenbach, T., Stadler, P.F., (2014):
    A first glimpse at the genome of the Baikalian amphipod Eulimnogammarus verrucosus
    J. Exp. Zool. Part B 322 (3), 177 - 189
    full text (url)
  • Baumann, S., Kalkhof, S., Hackermüller, J., Otto, W., Tomm, J.M., Wissenbach, D.K., Rolle-Kampczyk, U., von Bergen, M., (2013):
    Requirements and perspectives for integrating metabolomics with other omics data
    Current Metabolomics 1 (1), 15 - 27
    full text (url)
  • Boll, K., Reiche, K., Kasack, K., Mörbt, N., Kretzschmar, A.K., Tomm, J.M., Verhaegh, G., Schalken, J., von Bergen, M., Horn, F., Hackermüller, J., (2013):
    MiR-130a, miR-203 and miR-205 jointly repress key oncogenic pathways and are downregulated in prostate carcinoma
    Oncogene 32 , 277 - 285
    full text (url)
  • Otto, C., Reiche, K., Hackermüller, J., (2012):
    Detection of differentially expressed segments in tiling array data
    Bioinformatics 28 (11), 1471 - 1479
    full text (url)
  • von Bergen, M., Reiche, K., Hösler, N., Rockstroh, M., Horn, F., Hackermüller, J., Tomm, J., (2012):
    A time resolved analysis of nc/mRNA and protein expression throughout Th cell activation
    Immunology 137 (Suppl. S1), 364 - 364
    full text (url)
  • Wuttig, D., Zastrow, S., Füssel, S., Toma, M.I., Meinhardt, M., Kalman, K., Junker, K., Sanjmyatav, J., Boll, K., Hackermüller, J., Rolle, A., Grimm, M.O., Wirth, M.P., (2012):
    CD31, EDNRB and TSPAN7 are promising prognostic markers in clear-cell renal cell carcinoma revealed by genome-wide expression analyses of primary tumors and metastases
    Int. J. Cancer 131 (5), E693 - E704
    full text (url)
  • Hösler, N., Hackermüller, J., Reiche, K., Horn, F., (2011):
    Identification of ncRNAs regulating differencoation and function of CD4+ T cells. PS2-061
    Cytokine 56 (1), 81 - 81
    full text (url)
  • Reiche, K., Schutt, K., Boll, K., Horn, F., Hackermüller, J., (2011):
    Bioinformatics for RNomics
    In: Mayer, B., (ed.)
    Bioinformatics for Omics data
    Methods in Molecular Biology 719
    Humana Press, p. 299 - 330
    full text (url)
  • Rose, D., Hiller, M., Schutt, K., Hackermüller, J., Backofen, R., Stadler, P.F., (2011):
    Computational discovery of human coding and non-coding transcripts with conserved splice sites
    Bioinformatics 27 (14), 1894 - 1900
    full text (url)