Publikationen YIG Bioinformatics & Transcriptomics

  • 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 (URL)
  • 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 (URL)
  • 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 (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.
    Volltext (URL)
  • 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 (URL)
  • Schüttler, A., Altenburger, R., Ammar, M.P., 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 (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
    Volltext (URL)
  • Canzler, S., Stadler, P.F., Schor, J., (2018):
    The fungal snoRNAome
    RNA 24 (3), 342 - 360
    Volltext (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
    Volltext (URL)
  • Hartmann, T., Bernt, M., Middendorf, M., (2018):
    EqualTDRL: illustrating equivalent tandem duplication random loss rearrangements
    BMC Bioinformatics 19 , art. 192
    Volltext (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
    Volltext (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
    Volltext (URL)
  • 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 (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
    Volltext (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
    Volltext (URL)
  • 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 (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
    Volltext (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
    Volltext (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
    Volltext (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
    Volltext (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
    Volltext (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
    Volltext (URL)
  • 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 (URL)
  • 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 (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
    Volltext (URL)
  • 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 (URL)
  • 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 (URL)
  • 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 (URL)
  • 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 (URL)
  • 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 (URL)
  • 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 (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
    Volltext (URL)
  • 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 (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
    Volltext (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
    Volltext (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
    Volltext (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
    Volltext (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
    Volltext (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
    Volltext (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
    Volltext (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
    Volltext (URL)
  • 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 (URL)
  • Otto, C., Reiche, K., Hackermüller, J., (2012):
    Detection of differentially expressed segments in tiling array data
    Bioinformatics 28 (11), 1471 - 1479
    Volltext (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
    Volltext (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
    Volltext (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
    Volltext (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
    Volltext (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
    Volltext (URL)
  • 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 (URL)