Publikationen YIG Bioinformatics & Transcriptomics
- 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
Volltext (DOI) - Bray, S., Chilton, J., Bernt, M., Soranzo, N., van den Beek, M., Batut, B., Rasche, H., Čech, M., Cock, P.J.A., Grüning, B., Nekrutenko, A. (2023):
The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond
Genome Res. 33 , 261 - 268
Volltext (DOI) - Fahrner, M., Föll, M.C., Grüning, B.A., Bernt, M., Röst, H., Schilling, O. (2022):
Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the Galaxy framework
GigaScience 11 , giac005
Volltext (DOI) - Ostrovsky, A.E., Mahmoud, A., Lonie, A., Syme, A., Fouilloux, A., Bretaudeau, A., Nekrutenko, A., Kumar, A., Eschenlauer, A.C., DeSanto, A.D., Guerler, A., Serrano-Solano, B., Batut, B., Grüning, B.A., Langhorst, B.W., Carr, B., Blankenberg, D., Goecks, J., Bernt, M., Schatz, M.C., The Galaxy Community (2022):
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update
Nucleic Acids Res. 50 (W1), W345 - W351
Volltext (DOI) - Puiggené, Ò., Cárdenas Espinosa, M.J., Schlosser, D., Thies, S., Jehmlich, N., Kappelmeyer, U., Schreiber, S., Wibberg, D., Kalinowski, J., Harms, H., Heipieper, H.J., Eberlein, C. (2022):
Extracellular degradation of a polyurethane oligomer involving outer membrane vesicles and further insights on the degradation of 2,4-diaminotoluene in Pseudomonas capeferrum TDA1
Sci. Rep. 12 , art. 2666
Volltext (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
Volltext (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
Volltext (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
Volltext (DOI) - Velandia-Huerto, C.A., Yazbeck, A.M., Schor, J., Stadler, P.F. (2022):
Evolution and phylogeny of microRNAs — Protocols, pitfalls, and problems
In: Allmer, J., Yousef, M. (eds.)
miRNomics. MicroRNA biology and computational analysis
Methods in Molecular Biology 2257
Springer Nature, p. 211 - 233
Volltext (DOI) - VijayKrishna, N., Joshi, J., Coraor, N., Hillman-Jackson, J., Bouvier, D., van den Beek, M., Eguinoa, I., Coppens, F., Davis, J., Stolarczyk, M., Sheffield, N.C., Gladman, S., Cuccuru, G., Grüning, B., Soranzo, N., Rasche, H., Langhorst, B.W., Bernt, M., Fornika, D., de Lima Morais, D.A., Barrette, M., van Heusden, P., Petrillo, M., Puertas-Gallardo, A., Patak, A., Hotz, H.-R., Blankenberg, D. (2022):
Expanding the Galaxy’s reference data
Bioinform. Adv. 2 (1), vbac030
Volltext (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
Volltext (DOI) - Cárdenas Espinosa, M.J., Schmidgall, T., Wagner, G., Kappelmeyer, U., Schreiber, S., Heipieper, H.J., Eberlein, C. (2021):
An optimized method for RNA extraction from the polyurethane oligomer degrading strain Pseudomonas capeferrum TDA1 growing on aromatic substrates such as phenol and 2,4-diaminotoluene
PLOS One 16 (11), e0260002
Volltext (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
Volltext (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
Volltext (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
Volltext (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
Volltext (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
Volltext (DOI) - Balogh, G., Bernhart, S.H., Stadler, P.F., Schor, J. (2020):
A probabilistic version of Sankoff’s maximum parsimony algorithm
J. Bioinform. Comput. Biol. 18 (1), art. 2050004
Volltext (DOI) - Canzler, S., Hackermüller, J. (2020):
multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data
BMC Bioinformatics 21 , art. 561
Volltext (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
Volltext (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
Volltext (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
Volltext (DOI) - Olms, C., Schor, J., Yahiaoui-Doktor, M. (2020):
Potential co-factors of an intraoral contact allergy — A cross-sectional study
Dent. J. 8 (3), art. 83
Volltext (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
Volltext (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
Volltext (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
Volltext (DOI) - Donath, A., Jühling, F., Al-Arab, M., Bernhart, S.H., Reinhardt, F., Stadler, P.F., Middendorf, M., Bernt, M. (2019):
Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes
Nucleic Acids Res. 47 (20), 10543 - 10552
Volltext (DOI) - Drozdova, P., Bedulina, D., Madyarova, E., Rivarola-Duarte, L., Schreiber, S., Stadler, P.F., Luckenbach, T., Timofeyev, M. (2019):
Description of strongly heat-inducible heat shock protein 70 transcripts from Baikal endemic amphipods
Sci. Rep. 9 , art. 8907
Volltext (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
Volltext (DOI) - Hartmann, T., Bernt, M., Middendorf, M. (2019):
An exact algorithm for sorting by weighted preserving genome rearrangements
IEEE-ACM Trans. Comput. Biol. Bioinform. 16 (1), 52 - 62
Volltext (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
Volltext (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
Volltext (DOI) - Li, Y., Kocot, K.M., Tassia, M.G., Cannon, J.T., Bernt, M., Halanych, K.M. (2019):
Mitogenomics reveals a novel genetic code in Hemichordata
Genome Biol. Evol. 11 (1), 29 - 40
Volltext (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
Volltext (DOI) - Schüttler, A., Altenburger, R., Ammar, M., Bader-Blukott, M., Jakobs, G., Knapp, J., Krüger, J., Reiche, K., Wu, G.-M., Busch, W. (2019):
Map and model—moving from observation to prediction in toxicogenomics
GigaScience 8 (6), giz057
Volltext (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
Volltext (DOI) - Canzler, S., Stadler, P.F., Schor, J. (2018):
The fungal snoRNAome
RNA 24 (3), 342 - 360
Volltext (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
Volltext (DOI) - Hartmann, T., Bernt, M., Middendorf, M. (2018):
EqualTDRL: illustrating equivalent tandem duplication random loss rearrangements
BMC Bioinformatics 19 , art. 192
Volltext (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
Volltext (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
Volltext (DOI) - Al Arab, M., Bernt, M., Höner zu Siederdissen, C., Tout, K., Stadler, P.F. (2017):
Partially local three-way alignments and the sequence signatures of mitochondrial genome rearrangements
Algorithms Mol. Biol. 12 , art. 22
Volltext (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
Volltext (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
Volltext (DOI) - Canzler, S., Stadler, P.F., Hertel, J. (2017):
Evolution of fungal U3 snoRNAs: Structural variation and introns
Non-Coding RNA 3 (1), art. 3
Volltext (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
Volltext (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
Volltext (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
Volltext (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
Volltext (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
Volltext (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
Volltext (DOI) - Schüttler, A., Reiche, K., Altenburger, R., Busch, W. (2017):
The transcriptome of the zebrafish embryo after chemical exposure: a meta-analysis
Toxicol. Sci. 157 (2), 291 - 304
Volltext (DOI) - Yazbeck, A.M., Tout, K.R., Stadler, P.F., Hertel, J. (2017):
Towards a consistent, quantitative evaluation of microRNA evolution
J. Integr. Bioinform. 14 (1)
Volltext (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
Volltext (DOI) - Bhattacharya, D.P., Canzler, S., Kehr, S., Hertel, J., Grosse, I., Stadler, P.F. (2016):
Phylogenetic distribution of plant snoRNA families
BMC Genomics 17 , art. 969
Volltext (DOI) - Braasch, I., Gehrke, A.R., Smith, J.J., Kawasaki, K., Manousaki, T., Pasquier, J., Amores, A., Desvignes, T., Batzel, P., Catchen, J., Berlin, A.M., Campbell, M.S., Barrell, D., Martin, K.J., Mulley, J.F., Ravi, V., Lee, A.P., Nakamura, T., Chalopin, D., Fan, S., Wcisel, D., Cañestro, C., Sydes, J., Beaudry, F.E.G., Sun, Y., Hertel, J., Beam, M.J., Fasold, M., Ishiyama, M., Johnson, J., Kehr, S., Lara, M., Letaw, J.H., Litman, G.W., Litman, R.T., Mikami, M., Ota, T., Saha, N.R., Williams, L., Stadler, P.F., Wang, H., Taylor, J.S., Fontenot, Q., Ferrara, A., Searle, S.M.J., Aken, B., Yandell, M., Schneider, I., Yoder, J.A., Volff, J.-N., Meyer, A., Amemiya, C.T., Venkatesh, B., Holland, P.W.H., Guiguen, Y., Bobe, J., Shubin, N.H., Di Palma, F., Alföldi, J., Lindblad-Toh, K., Postlethwait, J.H. (2016):
The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons
Nature Genet. 48 (4), 427 - 437
Volltext (DOI) - Canzler, S., Stadler, P.F., Hertel, J. (2016):
U6 snRNA intron insertion occurred multiple times during fungi evolution
RNA Biol. 13 (2), 119 - 127
Volltext (DOI) - de Araujo Oliveira, J.V., Costa, F., Backofen, R., Stadler, P.F., Walter, M.E.M.T., Hertel, J. (2016):
SnoReport 2.0: new features and a refined Support Vector Machine to improve snoRNA identification
BMC Bioinformatics 17 (Suppl 18), art. 464
Volltext (DOI) - Fontenot, Q., Ferrara, A., Searle, S.M.J., Aken, B., Yandell, M., Schneider, I., Yoder, J.A., Volff, J.-N., Meyer, A., Amemiya, C.T., Venkatesh, B., Holland, P.W.H., Guiguen, Y., Bobe, J., Shubin, N.H., Di Palma, F., Alföldi, J., Lindblad-Toh, K., Postlethwait, J.H., Martin, K.J., Mulley, J.F., Ravi, V., Lee, A.P., Nakamura, T., Chalopin, D., Fan, S., Wcisel, D., Cañestro, C., Sydes, J., Beaudry, F.E.G., Sun, Y., Hertel, J., Beam, M.J., Fasold, M., Ishiyama, M., Johnson, J., Kehr, S., Lara, M., Letaw, J.H., Litman, G.W., Litman, R.T., Mikami, M., Ota, T., Saha, N.R., Williams, L., Stadler, P.F., Wang, H., Taylor, J.S., Braasch, I., Gehrke, A.R., Smith, J.J., Kawasaki, K., Manousaki, T., Pasquier, J., Amores, A., Desvignes, T., Batzel, P., Catchen, J., Berlin, A.M., Campbell, M.S., Barrell, D. (2016):
Corrigendum: The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons (vol 48, pg 427, 2016). Corrected after print 25 April 2016
Nature Genet. 48 (6), 700 - 700
Volltext (DOI) - Vorreiter, F., Richter, S., Peter, M., Baumann, S., von Bergen, M., Tomm, J.M. (2016):
Comparison and optimization of methods for the simultaneous extraction of DNA, RNA, proteins, and metabolites
Anal. Biochem. 508 , 25 - 33
Volltext (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
Volltext (DOI) - Nitsche, A., Rose, D., Fasold, M., Reiche, K., Stadler, P.F. (2015):
Comparison of splice sites reveals that long noncoding RNAs are evolutionarily well conserved
RNA 21 (5), 801 - 812
Volltext (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
Volltext (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
Volltext (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
Volltext (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
Volltext (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
Volltext (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
Volltext (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
Volltext (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
Volltext (DOI) - Will, S., Siebauer, M.F., Heyne, S., Engelhardt, J., Stadler, P.F., Reiche, K., Backofen, R. (2013):
LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search
Algorithms Mol. Biol. 8 , art. 14
Volltext (DOI) - Otto, C., Reiche, K., Hackermüller, J. (2012):
Detection of differentially expressed segments in tiling array data
Bioinformatics 28 (11), 1471 - 1479
Volltext (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
Volltext (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
Volltext (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
Volltext (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
Volltext (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
Volltext (DOI) - Tramontano, A., Donath, A., Bernhart, S.H., Reiche, K., Böhmdorfer, C., Stadler, P.F., Bachmair, A. (2011):
Deletion analysis of the 3' long terminal repeat sequence of plant retrotransposon Tto1 identifies 125 base pairs redundancy as sufficient for first strand transfer
Virology 412 (1), 75 - 82
Volltext (DOI)
