Prof. Dr. Jörg Hackermüller
Head of Department Computational Biology
Helmholtz Centre for Environmental Research - UFZ
Permoserstr. 15
04318 Leipzig, Germany
Phone: +49 341 235 1561
Social network
Research interests
- Bioinformatic method development for omics data analysis and integration
- Non-coding RNAs in disease and toxicity, drug discovery, and as biomarkers
- Using omics data in chemical risk assessment and for understanding mechanisms of toxicity
- Environmental epigenetics, gene – environment interactions
- Developing artificial intelligence approaches for toxicological problems
- Investigating the potential of single-cell omics in toxicology and environmental health
- RNA-based mechanisms
CV
Professional experience
| Since 2021 |
Head of Department, Department Computational Biology, Helmholtz Centre for Environmental Research – UFZ Professor of Computational Biology at the Faculty of Mathematics and Computer Science at Leipzig University |
| 2011 - 2021 |
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
- Amorim, M.J.B., Peijnenburg, W., Greco, D., Saarimäki, L.A., Dumit, V.I., Bahl, A., Haase, A., Tran, L., Hackermüller, J., Canzler, S., Scott-Fordsmand, J.J. (2023):
Systems toxicology to advance human and environmental hazard assessment: A roadmap for advanced materials
Nano Today 48 , art. 101735
full text (doi) - Scholz, S., Brack, W., Escher, B.I., Hackermüller, J., Liess, M., von Bergen, M., Wick, L.Y., Zenclussen, A.C., Altenburger, R. (2022):
The EU chemicals strategy for sustainability: an opportunity to develop new approaches for hazard and risk assessment
Arch. Toxicol. 96 (8), 2381 - 2386
full text (doi) - Scholz, S., Nichols, J.W., Escher, B.I., Ankley, G.T., Altenburger, R., Blackwell, B., Brack, W., Burkhard, L., Collette, T.W., Doering, J.A., Ekman, D., Fay, K., Fischer, F., Hackermüller, J., Hoffman, J.C., Lai, C., Leuthold, D., Martinovic-Weigelt, D., Reemtsma, T., Pollesch, N., Schroeder, A., Schüürmann, G., von Bergen, M. (2022):
The eco‐exposome concept: Supporting an integrated assessment of mixtures of environmental chemicals
Environ. Toxicol. Chem. 41 (1), 30 - 45
full text (doi) - Schor, J., Scheibe, P., Bernt, M., Busch, W., Lai, C., Hackermüller, J. (2022):
AI for predicting chemical-effect associations at the chemical universe level — deepFPlearn
Brief. Bioinform. 23 (5), bbac257
full text (doi) - Völkner, M., Wagner, F., Steinheuer, L.M., Carido, M., Kurth, T., Yazbeck, A., Schor, J., Wieneke, S., Ebner, L.J.A., Del Toro Runzer, C., Taborsky, D., Zoschke, K., Vogt, M., Canzler, S., Hermann, A., Khattak, S., Hackermüller, J., Karl, M.O. (2022):
HBEGF-TNF induce a complex outer retinal pathology with photoreceptor cell extrusion in human organoids
Nat. Commun. 13 , art. 6183
full text (doi) - Huhn, S., Escher, B.I., Krauss, M., Scholz, S., Hackermüller, J., Altenburger, R. (2021):
Unravelling the chemical exposome in cohort studies: routes explored and steps to become comprehensive
Environ. Sci. Eur. 33 , art. 17
full text (doi) - Nitsche, A., Arnold, C., Ueberham, U., Reiche, K., Fallmann, J., Hackermüller, J., Horn, F., Stadler, P.F., Arendt, T. (2021):
Alzheimer-related genes show accelerated evolution
Mol. Psychiatr. 26 (10), 5790 - 5796
full text (doi) - Schubert, K., Karkossa, I., Schor, J., Engelmann, B., Steinheuer, L.M., Bruns, T., Rolle-Kampczyk, U., Hackermüller, J., von Bergen, M. (2021):
A multi-omics analysis of mucosal-associated-invariant T cells reveals key drivers of distinct modes of activation
Front. Immunol. 12 , art. 616967
full text (doi) - Völkner, M., Kurth, T., Schor, J., Ebner, L.J.A., Bardtke, L., Kavak, C., Hackermüller, J., Karl, M.O. (2021):
Mouse retinal organoid growth and maintenance in longer-term culture
Front. Cell. Dev. Biol. 9 , art. 645704
full text (doi) - Wang, Z., Karkossa, I., Großkopf, H., Canzler, S., Rolle-Kampczyk, U., Hackermüller, J., von Bergen, M., Schubert, K. (2021):
Quantitative proteomics reveal mechanistic insights into direct and indirect drug-induced thyroid toxicity in rats
Toxicol. Lett. 350 (Suppl.), S129
full text (doi) - Canzler, S., Hackermüller, J. (2020):
multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data
BMC Bioinformatics 21 , art. 561
full text (doi) - Canzler, S., Schor, J., Busch, W., Schubert, K., Rolle-Kampczyk, U.E., Seitz, H., Kamp, H., von Bergen, M., Buesen, R., Hackermüller, J. (2020):
Prospects and challenges of multi‑omics data integration in toxicology
Arch. Toxicol. 94 (2), 371 - 388
full text (doi) - Friedrich, M., Wiedemann, K., Reiche, K., Puppel, S.-H., Pfeifer, G., Zipfel, I., Binder, S., Köhl, U., Müller, G.A., Engeland, K., Aigner, A., Füssel, S., Fröhner, M., Peitzsch, C., Dubrovska, A., Rade, M., Christ, S., Schreiber, S., Hackermüller, J., Lehmann, J., Toma, M.I., Muders, M.H., Sommer, U., Baretton, G.B., Wirth, M., Horn, F. (2020):
The role of lncRNAs TAPIR-1 and -2 as diagnostic markers and potential therapeutic targets in prostate cancer
Cancers 12 (5), art. 1122
full text (doi) - Kreuz, M., Otto, D.J., Fuessel, S., Blumert, C., Bertram, C., Bartsch, S., Loeffler, D., Puppel, S.-H., Rade, M., Buschmann, T., Christ, S., Erdmann, K., Friedrich, M., Froehner, M., Muders, M.H., Schreiber, S., Specht, M., Toma, M.I., Benigni, F., Freschi, M., Gandaglia, G., Briganti, A., Baretton, G.B., Loeffler, M., Hackermüller, J., Reiche, K., Wirth, M., Horn, F. (2020):
ProstaTrend—A multivariable prognostic RNA expression score for aggressive prostate cancer
Eur. Urol. 78 (3), 452 - 459
full text (doi) - Shatilina, Z., Drozdova, P., Bedulina, D., Rivarola-Duarte, L., Schreiber, S., Otto, C., Jühling, F., Aulhorn, S., Busch, W., Lubyaga, Y., Kondrateva, E., Pobezhimova, T., Jakob, L., Lucassen, M., Sartoris, F.J., Hackermüller, J., Pörtner, H.-O., Stadler, P.F., Luckenbach, T., Timofeyev, M. (2020):
Transcriptome-level effects of the model organic pollutant phenanthrene and its solvent acetone in three amphipod species
Comp. Biochem. Physiol. D-Genomics Proteomics 33 , art. 100630
full text (doi) - Wang, Z., Karkossa, I., Großkopf, H., Rolle-Kampczyk, U., Hackermüller, J., von Bergen, M., Schubert, K. (2020):
Comparison of quantitation methods in proteomics to define relevant toxicological information on AhR activation of HepG2 cells by BaP
Toxicology 448 , art. 152652
full text (doi) - 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 (doi) - Drozdova, P., Rivarola-Duarte, L., Bedulina, D., Axenov-Gribanov, D., Schreiber, S., Gurkov, A., Shatilina, Z., Vereshchagina, K., Lubyaga, Y., Madyarova, E., Otto, C., Jühling, F., Busch, W., Jakob, L., Lucassen, M., Sartoris, F.J., Hackermüller, J., Hoffmann, S., Pörtner, H.-O., Luckenbach, T., Timofeyev, M., Stadler, P.F. (2019):
Comparison between transcriptomic responses to short-term stress exposures of a common Holarctic and endemic Lake Baikal amphipods
BMC Genomics 20 , art. 712
full text (doi) - 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. 47 , art. 100667
full text (doi) - Kämpf, C., Specht, M., Scholz, A., Puppel, S.-H., Doose, G., Reiche, K., Schor, J., Hackermüller, J. (2019):
uap: reproducible and robust HTS data analysis
BMC Bioinformatics 20 , art. 664
full text (doi) - Schubert, K., Schor, J., Kratochvil, I., Hackermüller, J., von Bergen, M. (2019):
Multi-omics profiling of MAIT cells reveals specific patterns of antigen-dependent and -independent activation
Eur. J. Immunol. 49 (Suppl. 1), 141
full text (doi) - 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 (doi) - 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 (doi) - 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 (doi) - 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 (doi) - 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 (doi) - 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 (doi) - 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 (doi) - 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 (doi) - 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 (doi) - 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 (doi) - 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 (doi) - 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 (doi) - 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 (doi) - 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 (doi) - 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 (doi) - 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 (doi) - 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 (doi) - 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 (doi) - 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 (doi) - 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 (doi) - 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 (doi) - 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 (doi) - Otto, C., Reiche, K., Hackermüller, J. (2012):
Detection of differentially expressed segments in tiling array data
Bioinformatics 28 (11), 1471 - 1479
full text (doi) - 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 (doi) - 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 (doi) - 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 (doi) - 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
Springer Nature, p. 299 - 330
full text (doi) - 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 (doi)
Recent preprints
Lisa Maria Steinheuer, Sebastian Canzler, Jörg Hackermüller. Benchmarking scRNA-seq imputation tools with respect to network inference highlights deficits in performance at high levels of sparsity.
bioRxiv 2021.04.02.438193; doi: https://doi.org/10.1101/2021.04.02.438193
Sebastian Canzler, Jörg Hackermüller. multiGSEA: A GSEA-based pathway enrichment analysis for multi-omics data. bioRxiv 2020.07.17.208215; doi: https://doi.org/10.1101/2020.07.17.208215
Sebastian Canzler, Jörg Hackermüller, Jana Schor. MOD-Finder: Identify multi-omics data sets related to defined chemical exposure. 2019. arXiv:1907.06346