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Items: 42

1.

Specific induction of the unique GPR15 expression in heterogeneous blood lymphocytes by tobacco smoking.

Bauer M, Hackermüller J, Schor J, Schreiber S, Fink B, Pierzchalski A, Herberth G.

Biomarkers. 2019 May;24(3):217-224. doi: 10.1080/1354750X.2018.1539769. Epub 2018 Nov 13.

PMID:
30387691
2.

Roquin targets mRNAs in a 3'-UTR-specific manner by different modes of regulation.

Essig K, Kronbeck N, Guimaraes JC, 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.

Nat Commun. 2018 Sep 19;9(1):3810. doi: 10.1038/s41467-018-06184-3.

3.

A translational silencing function of MCPIP1/Regnase-1 specified by the target site context.

Behrens G, Winzen R, Rehage N, Dörrie A, Barsch M, Hoffmann A, Hackermüller J, Tiedje C, Heissmeyer V, Holtmann H.

Nucleic Acids Res. 2018 May 4;46(8):4256-4270. doi: 10.1093/nar/gky106.

4.

Binding of NUFIP2 to Roquin promotes recognition and regulation of ICOS mRNA.

Rehage N, Davydova E, Conrad C, Behrens G, Maiser A, Stehklein JE, 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.

Nat Commun. 2018 Jan 19;9(1):299. doi: 10.1038/s41467-017-02582-1.

5.

A generic Transcriptomics Reporting Framework (TRF) for 'omics data processing and analysis.

Gant TW, Sauer UG, Zhang SD, Chorley BN, Hackermüller J, Perdichizzi S, Tollefsen KE, van Ravenzwaay B, Yauk C, Tong W, Poole A.

Regul Toxicol Pharmacol. 2017 Dec;91 Suppl 1:S36-S45. doi: 10.1016/j.yrtph.2017.11.001. Epub 2017 Nov 4. Review.

6.

Framework for the quality assurance of 'omics technologies considering GLP requirements.

Kauffmann HM, Kamp H, Fuchs R, Chorley BN, Deferme L, Ebbels T, Hackermüller J, Perdichizzi S, Poole A, Sauer UG, Tollefsen KE, Tralau T, Yauk C, van Ravenzwaay B.

Regul Toxicol Pharmacol. 2017 Dec;91 Suppl 1:S27-S35. doi: 10.1016/j.yrtph.2017.10.007. Epub 2017 Oct 5. Review.

7.

Applying 'omics technologies in chemicals risk assessment: Report of an ECETOC workshop.

Buesen R, Chorley BN, da Silva Lima B, Daston G, Deferme L, Ebbels T, Gant TW, Goetz A, Greally J, Gribaldo L, Hackermüller J, Hubesch B, Jennen D, Johnson K, Kanno J, Kauffmann HM, Laffont M, McMullen P, Meehan R, Pemberton M, Perdichizzi S, Piersma AH, Sauer UG, Schmidt K, Seitz H, Sumida K, Tollefsen KE, Tong W, Tralau T, van Ravenzwaay B, Weber RJM, Worth A, Yauk C, Poole A.

Regul Toxicol Pharmacol. 2017 Dec;91 Suppl 1:S3-S13. doi: 10.1016/j.yrtph.2017.09.002. Epub 2017 Sep 25. Review.

8.

The challenge of the application of 'omics technologies in chemicals risk assessment: Background and outlook.

Sauer UG, Deferme L, Gribaldo L, Hackermüller J, Tralau T, van Ravenzwaay B, Yauk C, Poole A, Tong W, Gant TW.

Regul Toxicol Pharmacol. 2017 Dec;91 Suppl 1:S14-S26. doi: 10.1016/j.yrtph.2017.09.020. Epub 2017 Sep 18. Review.

9.

STAT3-induced long noncoding RNAs in multiple myeloma cells display different properties in cancer.

Binder S, Hösler N, Riedel D, Zipfel I, Buschmann T, Kämpf C, Reiche K, Burger R, Gramatzki M, Hackermüller J, Stadler PF, Horn F.

Sci Rep. 2017 Aug 11;7(1):7976. doi: 10.1038/s41598-017-08348-5.

10.

The complete genome of the tetrachloroethene-respiring Epsilonproteobacterium Sulfurospirillum halorespirans.

Goris T, Schenz B, Zimmermann J, Lemos M, Hackermüller J, Schubert T, Diekert G.

J Biotechnol. 2017 Aug 10;255:33-36. doi: 10.1016/j.jbiotec.2017.06.1197. Epub 2017 Jun 22.

PMID:
28648395
11.

Maternal phthalate exposure promotes allergic airway inflammation over 2 generations through epigenetic modifications.

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 JC, von Bergen M, Hackermüller J, Eils R, Lehmann I, Polte T.

J Allergy Clin Immunol. 2018 Feb;141(2):741-753. doi: 10.1016/j.jaci.2017.03.017. Epub 2017 Apr 6.

12.

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.

Kallies R, Kiesel B, Schmidt M, Kacza J, Ghanem N, Narr A, Zopfi J, Wick LY, Hackermüller J, Harms H, Chatzinotas A.

Stand Genomic Sci. 2017 Feb 2;12:20. doi: 10.1186/s40793-017-0235-5. eCollection 2017.

13.

From the exposome to mechanistic understanding of chemical-induced adverse effects.

Escher BI, Hackermüller J, Polte T, Scholz S, Aigner A, Altenburger R, Böhme A, Bopp SK, Brack W, Busch W, Chadeau-Hyam M, Covaci A, Eisenträger A, Galligan JJ, Garcia-Reyero N, Hartung T, Hein M, Herberth G, Jahnke A, Kleinjans J, Klüver N, Krauss M, Lamoree M, Lehmann I, Luckenbach T, Miller GW, Müller A, Phillips DH, Reemtsma T, Rolle-Kampczyk U, Schüürmann G, Schwikowski B, Tan YM, Trump S, Walter-Rohde S, Wambaugh JF.

Environ Int. 2017 Feb;99:97-106. doi: 10.1016/j.envint.2016.11.029. Epub 2016 Dec 8. Review.

14.

Advancing the use of noncoding RNA in regulatory toxicology: Report of an ECETOC workshop.

Aigner A, Buesen R, Gant T, Gooderham N, Greim H, Hackermüller J, Hubesch B, Laffont M, Marczylo E, Meister G, Petrick JS, Rasoulpour RJ, Sauer UG, Schmidt K, Seitz H, Slack F, Sukata T, van der Vies SM, Verhaert J, Witwer KW, Poole A.

Regul Toxicol Pharmacol. 2016 Dec;82:127-139. doi: 10.1016/j.yrtph.2016.09.018. Epub 2016 Sep 20.

15.

Dissecting the genetics of the human transcriptome identifies novel trait-related trans-eQTLs and corroborates the regulatory relevance of non-protein coding loci†.

Kirsten H, Al-Hasani H, Holdt L, Gross A, Beutner F, Krohn K, Horn K, Ahnert P, Burkhardt R, Reiche K, Hackermüller J, Löffler M, Teupser D, Thiery J, Scholz M.

Hum Mol Genet. 2015 Aug 15;24(16):4746-63. doi: 10.1093/hmg/ddv194. Epub 2015 May 27.

16.

Long non-coding RNAs differentially expressed between normal versus primary breast tumor tissues disclose converse changes to breast cancer-related protein-coding genes.

Reiche K, Kasack K, Schreiber S, Lüders T, Due EU, Naume B, Riis M, Kristensen VN, Horn F, Børresen-Dale AL, Hackermüller J, Baumbusch LO.

PLoS One. 2014 Sep 29;9(9):e106076. doi: 10.1371/journal.pone.0106076. eCollection 2014.

17.

CEM-designer: design of custom expression microarrays in the post-ENCODE Era.

Arnold C, Externbrink F, Hackermüller J, Reiche K.

J Biotechnol. 2014 Nov 10;189:154-6. doi: 10.1016/j.jbiotec.2014.09.012. Epub 2014 Sep 28.

PMID:
25262644
18.

Generation of IL-8 and IL-9 producing CD4⁺ T cells is affected by Th17 polarizing conditions and AHR ligands.

Gasch M, Goroll T, Bauer M, Hinz D, Schütze N, Polte T, Kesper D, Simon JC, Hackermüller J, Lehmann I, Herberth G.

Mediators Inflamm. 2014;2014:182549. doi: 10.1155/2014/182549. Epub 2014 Feb 20.

19.

A first glimpse at the genome of the Baikalian amphipod Eulimnogammarus verrucosus.

Rivarola-Duarte L, Otto C, Jühling F, Schreiber S, Bedulina D, Jakob L, Gurkov A, Axenov-Gribanov D, Sahyoun AH, Lucassen M, Hackermüller J, Hoffmann S, Sartoris F, Pörtner HO, Timofeyev M, Luckenbach T, Stadler PF.

J Exp Zool B Mol Dev Evol. 2014 May;322(3):177-89. doi: 10.1002/jez.b.22560. Epub 2014 Feb 12.

PMID:
24677529
20.

Cell cycle, oncogenic and tumor suppressor pathways regulate numerous long and macro non-protein-coding RNAs.

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 PF, Horn F.

Genome Biol. 2014 Mar 4;15(3):R48. doi: 10.1186/gb-2014-15-3-r48.

21.

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection.

Hoffmann S, Otto C, Doose G, Tanzer A, Langenberger D, Christ S, Kunz M, Holdt LM, Teupser D, Hackermüller J, Stadler PF.

Genome Biol. 2014 Feb 10;15(2):R34. doi: 10.1186/gb-2014-15-2-r34.

22.

Detection of differentially expressed segments in tiling array data.

Otto C, Reiche K, Hackermüller J.

Bioinformatics. 2012 Jun 1;28(11):1471-9. doi: 10.1093/bioinformatics/bts142. Epub 2012 Apr 6.

PMID:
22492638
23.

MiR-130a, miR-203 and miR-205 jointly repress key oncogenic pathways and are downregulated in prostate carcinoma.

Boll K, Reiche K, Kasack K, Mörbt N, Kretzschmar AK, Tomm JM, Verhaegh G, Schalken J, von Bergen M, Horn F, Hackermüller J.

Oncogene. 2013 Jan 17;32(3):277-85. doi: 10.1038/onc.2012.55. Epub 2012 Mar 5.

PMID:
22391564
24.

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.

Wuttig D, Zastrow S, Füssel S, Toma MI, Meinhardt M, Kalman K, Junker K, Sanjmyatav J, Boll K, Hackermüller J, Rolle A, Grimm MO, Wirth MP.

Int J Cancer. 2012 Sep 1;131(5):E693-704. doi: 10.1002/ijc.27419. Epub 2012 Feb 28.

25.

Computational discovery of human coding and non-coding transcripts with conserved splice sites.

Rose D, Hiller M, Schutt K, Hackermüller J, Backofen R, Stadler PF.

Bioinformatics. 2011 Jul 15;27(14):1894-900. doi: 10.1093/bioinformatics/btr314. Epub 2011 May 26.

PMID:
21622663
26.

Bioinformatics for RNomics.

Reiche K, Schutt K, Boll K, Horn F, Hackermüller J.

Methods Mol Biol. 2011;719:299-330. doi: 10.1007/978-1-61779-027-0_14.

PMID:
21370090
27.

The primary transcriptome of the major human pathogen Helicobacter pylori.

Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, Sittka A, Chabas S, Reiche K, Hackermüller J, Reinhardt R, Stadler PF, Vogel J.

Nature. 2010 Mar 11;464(7286):250-5. doi: 10.1038/nature08756. Epub 2010 Feb 17.

PMID:
20164839
28.

Fast mapping of short sequences with mismatches, insertions and deletions using index structures.

Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermüller J.

PLoS Comput Biol. 2009 Sep;5(9):e1000502. doi: 10.1371/journal.pcbi.1000502. Epub 2009 Sep 11.

29.

Evolution of vault RNAs.

Stadler PF, Chen JJ, Hackermüller J, Hoffmann S, Horn F, Khaitovich P, Kretzschmar AK, Mosig A, Prohaska SJ, Qi X, Schutt K, Ullmann K.

Mol Biol Evol. 2009 Sep;26(9):1975-91. doi: 10.1093/molbev/msp112. Epub 2009 Jun 2.

PMID:
19491402
30.

Duplicated RNA genes in teleost fish genomes.

Rose D, Jöris J, Hackermüller J, Reiche K, Li Q, Stadler PF.

J Bioinform Comput Biol. 2008 Dec;6(6):1157-75.

PMID:
19090022
31.

Detection of small RNAs in Pseudomonas aeruginosa by RNomics and structure-based bioinformatic tools.

Sonnleitner E, Sorger-Domenigg T, Madej MJ, Findeiss S, Hackermüller J, Hüttenhofer A, Stadler PF, Bläsi U, Moll I.

Microbiology. 2008 Oct;154(Pt 10):3175-87. doi: 10.1099/mic.0.2008/019703-0.

PMID:
18832323
32.

HLA-DRB1*0401 and HLA-DRB1*0408 are strongly associated with the development of antibodies against interferon-beta therapy in multiple sclerosis.

Hoffmann S, Cepok S, Grummel V, Lehmann-Horn K, Hackermüller J, Stadler PF, Hartung HP, Berthele A, Deisenhammer F, Wassmuth R, Hemmer B.

Am J Hum Genet. 2008 Aug;83(2):219-27. doi: 10.1016/j.ajhg.2008.07.006. Epub 2008 Jul 24. Erratum in: Am J Hum Genet. 2008 Oct;83(4):541.. Hackermueller, Jorg [corrected to Hackermüller, Jörg]; Wasmuth, Ralf [corrected to Wassmuth, Ralf].

33.

NcDNAlign: plausible multiple alignments of non-protein-coding genomic sequences.

Rose D, Hertel J, Reiche K, Stadler PF, Hackermüller J.

Genomics. 2008 Jul;92(1):65-74. doi: 10.1016/j.ygeno.2008.04.003. Epub 2008 Jun 3.

34.

Computational RNomics of drosophilids.

Rose D, Hackermüller J, Washietl S, Reiche K, Hertel J, Findeiss S, Stadler PF, Prohaska SJ.

BMC Genomics. 2007 Nov 8;8:406.

35.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA; NISC Comparative Sequencing Program; Baylor College of Medicine Human Genome Sequencing Center; Washington University Genome Sequencing Center; Broad Institute; Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ.

Nature. 2007 Jun 14;447(7146):799-816.

36.

Structured RNAs in the ENCODE selected regions of the human genome.

Washietl S, Pedersen JS, Korbel JO, Stocsits C, Gruber AR, Hackermüller J, Hertel J, Lindemeyer M, Reiche K, Tanzer A, Ucla C, Wyss C, Antonarakis SE, Denoeud F, Lagarde J, Drenkow J, Kapranov P, Gingeras TR, Guigó R, Snyder M, Gerstein MB, Reymond A, Hofacker IL, Stadler PF.

Genome Res. 2007 Jun;17(6):852-64.

37.

RNA maps reveal new RNA classes and a possible function for pervasive transcription.

Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermüller J, Hofacker IL, Bell I, Cheung E, Drenkow J, Dumais E, Patel S, Helt G, Ganesh M, Ghosh S, Piccolboni A, Sementchenko V, Tammana H, Gingeras TR.

Science. 2007 Jun 8;316(5830):1484-8. Epub 2007 May 17.

38.

Interleukin-6 dependent survival of multiple myeloma cells involves the Stat3-mediated induction of microRNA-21 through a highly conserved enhancer.

Löffler D, Brocke-Heidrich K, Pfeifer G, Stocsits C, Hackermüller J, Kretzschmar AK, Burger R, Gramatzki M, Blumert C, Bauer K, Cvijic H, Ullmann AK, Stadler PF, Horn F.

Blood. 2007 Aug 15;110(4):1330-3. Epub 2007 May 11.

39.

RNAs everywhere: genome-wide annotation of structured RNAs.

Athanasius F Bompfünewerer Consortium, Backofen R, Bernhart SH, Flamm C, Fried C, Fritzsch G, Hackermüller J, Hertel J, Hofacker IL, Missal K, Mosig A, Prohaska SJ, Rose D, Stadler PF, Tanzer A, Washietl S, Will S.

J Exp Zool B Mol Dev Evol. 2007 Jan 15;308(1):1-25. Review.

PMID:
17171697
40.

Thermodynamics of RNA-RNA binding.

Mückstein U, Tafer H, Hackermüller J, Bernhart SH, Stadler PF, Hofacker IL.

Bioinformatics. 2006 May 15;22(10):1177-82. Epub 2006 Jan 29.

PMID:
16446276
41.

The effect of RNA secondary structures on RNA-ligand binding and the modifier RNA mechanism: a quantitative model.

Hackermüller J, Meisner NC, Auer M, Jaritz M, Stadler PF.

Gene. 2005 Jan 17;345(1):3-12. Epub 2005 Jan 7.

PMID:
15716109
42.

mRNA openers and closers: modulating AU-rich element-controlled mRNA stability by a molecular switch in mRNA secondary structure.

Meisner NC, Hackermüller J, Uhl V, Aszódi A, Jaritz M, Auer M.

Chembiochem. 2004 Oct 4;5(10):1432-47.

PMID:
15457527

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