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ID Publikation
17871 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
Volltext (DOI)
15362 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
Volltext (DOI)
21108 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
Volltext (DOI)
13236 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
Volltext (DOI)
19972 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
Volltext (DOI)
19111 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
Volltext (DOI)
12164 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
Volltext (DOI)
19333 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
Volltext (DOI)
22778 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
Volltext (DOI)
22169 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
Volltext (DOI)
18200 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
Volltext (DOI)
20951 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
Volltext (DOI)
23081 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
Volltext (DOI)
19615 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
Volltext (DOI)
14744 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
Volltext (DOI)
18956 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
Volltext (DOI)
14688 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
Volltext (DOI)
14689 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
Volltext (DOI)
11731 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
Volltext (DOI)
18496 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
Volltext (DOI)
21674 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
Volltext (DOI)
18351 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
Volltext (DOI)
22544 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
Volltext (DOI)
19425 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
Volltext (DOI)
16196 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
Volltext (DOI)
23348 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
Volltext (DOI)
22921 Nitsche, A., Arnold, C., Ueberham, U., Reiche, K., Fallmann, J., Hackermüller, J., Horn, F., Stadler, P.F., Arendt, T. (2020):
Alzheimer-related genes show accelerated evolution
Mol. Psychiatr.
Volltext (DOI)
12542 Otto, C., Reiche, K., Hackermüller, J. (2012):
Detection of differentially expressed segments in tiling array data
Bioinformatics 28 (11), 1471 - 1479
Volltext (DOI)
19823 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
Volltext (DOI)
15341 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
Volltext (DOI)
12938 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
Volltext (DOI)
14621 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
Volltext (DOI)
11359 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
Volltext (DOI)
19238 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
Volltext (DOI)
22287 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
Volltext (DOI)
22367 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
Volltext (DOI)
12992 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
Volltext (DOI)
12114 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
Volltext (DOI)
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