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Long fragments achieve lower base quality in Illumina paired-end sequencing.

Tan G, Opitz L, Schlapbach R, Rehrauer H.

Sci Rep. 2019 Feb 27;9(1):2856. doi: 10.1038/s41598-019-39076-7.


An experimental genetically attenuated live vaccine to prevent transmission of Toxoplasma gondii by cats.

Ramakrishnan C, Maier S, Walker RA, Rehrauer H, Joekel DE, Winiger RR, Basso WU, Grigg ME, Hehl AB, Deplazes P, Smith NC.

Sci Rep. 2019 Feb 6;9(1):1474. doi: 10.1038/s41598-018-37671-8.


Mutant MRPS5 affects mitoribosomal accuracy and confers stress-related behavioral alterations.

Akbergenov R, Duscha S, Fritz AK, Juskeviciene R, Oishi N, Schmitt K, Shcherbakov D, Teo Y, Boukari H, Freihofer P, Isnard-Petit P, Oettinghaus B, Frank S, Thiam K, Rehrauer H, Westhof E, Schacht J, Eckert A, Wolfer D, Böttger EC.

EMBO Rep. 2018 Nov;19(11). pii: e46193. doi: 10.15252/embr.201846193. Epub 2018 Sep 20.


Non-Coding Transcript Heterogeneity in Mesothelioma: Insights from Asbestos-Exposed Mice.

Felley-Bosco E, Rehrauer H.

Int J Mol Sci. 2018 Apr 11;19(4). pii: E1163. doi: 10.3390/ijms19041163.


How asbestos drives the tissue towards tumors: YAP activation, macrophage and mesothelial precursor recruitment, RNA editing, and somatic mutations.

Rehrauer H, Wu L, Blum W, Pecze L, Henzi T, Serre-Beinier V, Aquino C, Vrugt B, de Perrot M, Schwaller B, Felley-Bosco E.

Oncogene. 2018 May;37(20):2645-2659. doi: 10.1038/s41388-018-0153-z. Epub 2018 Mar 6.


Transcriptome analysis reveals differences in mechanisms regulating cessation of luteal function in pregnant and non-pregnant dogs.

Zatta S, Rehrauer H, Gram A, Boos A, Kowalewski MP.

BMC Genomics. 2017 Sep 27;18(1):757. doi: 10.1186/s12864-017-4084-9.


RNA-Seq Data Analysis: From Raw Data Quality Control to Differential Expression Analysis.

Qi W, Schlapbach R, Rehrauer H.

Methods Mol Biol. 2017;1669:295-307. doi: 10.1007/978-1-4939-7286-9_23.


A Dual Role of Caspase-8 in Triggering and Sensing Proliferation-Associated DNA Damage, a Key Determinant of Liver Cancer Development.

Boege Y, Malehmir M, Healy ME, Bettermann K, Lorentzen A, Vucur M, Ahuja AK, Böhm F, Mertens JC, Shimizu Y, Frick L, Remouchamps C, Mutreja K, Kähne T, Sundaravinayagam D, Wolf MJ, Rehrauer H, Koppe C, Speicher T, Padrissa-Altés S, Maire R, Schattenberg JM, Jeong JS, Liu L, Zwirner S, Boger R, Hüser N, Davis RJ, Müllhaupt B, Moch H, Schulze-Bergkamen H, Clavien PA, Werner S, Borsig L, Luther SA, Jost PJ, Weinlich R, Unger K, Behrens A, Hillert L, Dillon C, Di Virgilio M, Wallach D, Dejardin E, Zender L, Naumann M, Walczak H, Green DR, Lopes M, Lavrik I, Luedde T, Heikenwalder M, Weber A.

Cancer Cell. 2017 Sep 11;32(3):342-359.e10. doi: 10.1016/j.ccell.2017.08.010.


Epigenetically-driven anatomical diversity of synovial fibroblasts guides joint-specific fibroblast functions.

Frank-Bertoncelj M, Trenkmann M, Klein K, Karouzakis E, Rehrauer H, Bratus A, Kolling C, Armaka M, Filer A, Michel BA, Gay RE, Buckley CD, Kollias G, Gay S, Ospelt C.

Nat Commun. 2017 Mar 23;8:14852. doi: 10.1038/ncomms14852.


Characterization of miRNA-regulated networks, hubs of signaling, and biomarkers in obstruction-induced bladder dysfunction.

Gheinani AH, Kiss B, Moltzahn F, Keller I, Bruggmann R, Rehrauer H, Fournier CA, Burkhard FC, Monastyrskaya K.

JCI Insight. 2017 Jan 26;2(2):e89560. doi: 10.1172/jci.insight.89560.


Prognostic value of cross-omics screening for kidney clear cell renal cancer survival.

Dimitrieva S, Schlapbach R, Rehrauer H.

Biol Direct. 2016 Dec 20;11(1):68.


Diurnal changes in the histone H3 signature H3K9ac|H3K27ac|H3S28p are associated with diurnal gene expression in Arabidopsis.

Baerenfaller K, Shu H, Hirsch-Hoffmann M, Fütterer J, Opitz L, Rehrauer H, Hennig L, Gruissem W.

Plant Cell Environ. 2016 Nov;39(11):2557-2569. doi: 10.1111/pce.12811. Epub 2016 Sep 30.


SUSHI: an exquisite recipe for fully documented, reproducible and reusable NGS data analysis.

Hatakeyama M, Opitz L, Russo G, Qi W, Schlapbach R, Rehrauer H.

BMC Bioinformatics. 2016 Jun 2;17(1):228. doi: 10.1186/s12859-016-1104-8.


Field Trial and Molecular Characterization of RNAi-Transgenic Tomato Plants That Exhibit Resistance to Tomato Yellow Leaf Curl Geminivirus.

Fuentes A, Carlos N, Ruiz Y, Callard D, Sánchez Y, Ochagavía ME, Seguin J, Malpica-López N, Hohn T, Lecca MR, Pérez R, Doreste V, Rehrauer H, Farinelli L, Pujol M, Pooggin MM.

Mol Plant Microbe Interact. 2016 Mar;29(3):197-209. doi: 10.1094/MPMI-08-15-0181-R. Epub 2016 Feb 11.


H. pylori-Induced DNA Strand Breaks Are Introduced by Nucleotide Excision Repair Endonucleases and Promote NF-κB Target Gene Expression.

Hartung ML, Gruber DC, Koch KN, Grüter L, Rehrauer H, Tegtmeyer N, Backert S, Müller A.

Cell Rep. 2015 Oct 6;13(1):70-79. doi: 10.1016/j.celrep.2015.08.074. Epub 2015 Sep 24.


Hypoxia attenuates the proinflammatory response in colon cancer cells by regulating IκB.

Müller-Edenborn K, Léger K, Glaus Garzon JF, Oertli C, Mirsaidi A, Richards PJ, Rehrauer H, Spielmann P, Hoogewijs D, Borsig L, Hottiger MO, Wenger RH.

Oncotarget. 2015 Aug 21;6(24):20288-301.


Insight into the beneficial immunomodulatory mechanism of the sevoflurane metabolite hexafluoro-2-propanol in a rat model of endotoxaemia.

Urner M, Schläpfer M, Herrmann IK, Hasler M, Schimmer RR, Booy C, Roth Z'graggen B, Rehrauer H, Aigner F, Minshall RD, Stark WJ, Beck-Schimmer B.

Clin Exp Immunol. 2015 Sep;181(3):468-79. doi: 10.1111/cei.12648. Epub 2015 Jul 7.


The Phosphoinositide 3-Kinase p110α Isoform Regulates Leukemia Inhibitory Factor Receptor Expression via c-Myc and miR-125b to Promote Cell Proliferation in Medulloblastoma.

Salm F, Dimitrova V, von Bueren AO, Ćwiek P, Rehrauer H, Djonov V, Anderle P, Arcaro A.

PLoS One. 2015 Apr 27;10(4):e0123958. doi: 10.1371/journal.pone.0123958. eCollection 2015.


Differential gene expression patterns in developing sexually dimorphic rat brain regions exposed to antiandrogenic, estrogenic, or complex endocrine disruptor mixtures: glutamatergic synapses as target.

Lichtensteiger W, Bassetti-Gaille C, Faass O, Axelstad M, Boberg J, Christiansen S, Rehrauer H, Georgijevic JK, Hass U, Kortenkamp A, Schlumpf M.

Endocrinology. 2015 Apr;156(4):1477-93. doi: 10.1210/en.2014-1504. Epub 2015 Jan 21.


MicroRNA MiR-199a-5p regulates smooth muscle cell proliferation and morphology by targeting WNT2 signaling pathway.

Hashemi Gheinani A, Burkhard FC, Rehrauer H, Aquino Fournier C, Monastyrskaya K.

J Biol Chem. 2015 Mar 13;290(11):7067-86. doi: 10.1074/jbc.M114.618694. Epub 2015 Jan 16.


Optimization of Critical Hairpin Features Allows miRNA-based Gene Knockdown Upon Single-copy Transduction.

Myburgh R, Cherpin O, Schlaepfer E, Rehrauer H, Speck RF, Krause KH, Salmon P.

Mol Ther Nucleic Acids. 2014 Oct 28;3:e207. doi: 10.1038/mtna.2014.58.


Induction of the nuclear receptor PPAR-γ by the cytokine GM-CSF is critical for the differentiation of fetal monocytes into alveolar macrophages.

Schneider C, Nobs SP, Kurrer M, Rehrauer H, Thiele C, Kopf M.

Nat Immunol. 2014 Nov;15(11):1026-37. doi: 10.1038/ni.3005. Epub 2014 Sep 28.


Circadian behavior is light-reprogrammed by plastic DNA methylation.

Azzi A, Dallmann R, Casserly A, Rehrauer H, Patrignani A, Maier B, Kramer A, Brown SA.

Nat Neurosci. 2014 Mar;17(3):377-82. doi: 10.1038/nn.3651. Epub 2014 Feb 16.


Blind spots of quantitative RNA-seq: the limits for assessing abundance, differential expression, and isoform switching.

Rehrauer H, Opitz L, Tan G, Sieverling L, Schlapbach R.

BMC Bioinformatics. 2013 Dec 24;14:370. doi: 10.1186/1471-2105-14-370.


Genome-wide analysis of H4K5 acetylation associated with fear memory in mice.

Park CS, Rehrauer H, Mansuy IM.

BMC Genomics. 2013 Aug 8;14:539. doi: 10.1186/1471-2164-14-539.


An ER-directed transcriptional response to unfolded protein stress in the absence of conserved sensor-transducer proteins in Giardia lamblia.

Spycher C, Herman EK, Morf L, Qi W, Rehrauer H, Aquino Fournier C, Dacks JB, Hehl AB.

Mol Microbiol. 2013 May;88(4):754-71. doi: 10.1111/mmi.12218. Epub 2013 Apr 26.


PKC signaling prevents irradiation-induced apoptosis of primary human fibroblasts.

Bluwstein A, Kumar N, Léger K, Traenkle J, Oostrum Jv, Rehrauer H, Baudis M, Hottiger MO.

Cell Death Dis. 2013 Feb 14;4:e498. doi: 10.1038/cddis.2013.15.


Targeting the phosphoinositide 3-kinase p110-α isoform impairs cell proliferation, survival, and tumor growth in small cell lung cancer.

Wojtalla A, Fischer B, Kotelevets N, Mauri FA, Sobek J, Rehrauer H, Wotzkow C, Tschan MP, Seckl MJ, Zangemeister-Wittke U, Arcaro A.

Clin Cancer Res. 2013 Jan 1;19(1):96-105. doi: 10.1158/1078-0432.CCR-12-1138. Epub 2012 Nov 21.


Role of hedgehog signaling in malignant pleural mesothelioma.

Shi Y, Moura U, Opitz I, Soltermann A, Rehrauer H, Thies S, Weder W, Stahel RA, Felley-Bosco E.

Clin Cancer Res. 2012 Sep 1;18(17):4646-56. doi: 10.1158/1078-0432.CCR-12-0599. Epub 2012 Jun 25.


Evaluation of alternative RNA labeling protocols for transcript profiling with Arabidopsis AGRONOMICS1 tiling arrays.

Müller M, Patrignani A, Rehrauer H, Gruissem W, Hennig L.

Plant Methods. 2012 Jun 13;8(1):18. doi: 10.1186/1746-4811-8-18.


RIP-chip-SRM--a new combinatorial large-scale approach identifies a set of translationally regulated bantam/miR-58 targets in C. elegans.

Jovanovic M, Reiter L, Clark A, Weiss M, Picotti P, Rehrauer H, Frei A, Neukomm LJ, Kaufman E, Wollscheid B, Simard MJ, Miska EA, Aebersold R, Gerber AP, Hengartner MO.

Genome Res. 2012 Jul;22(7):1360-71. doi: 10.1101/gr.133330.111. Epub 2012 Mar 27.


Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields.

Huwiler SG, Beyer C, Fröhlich J, Hennecke H, Egli T, Schürmann D, Rehrauer H, Fischer HM.

Bioelectromagnetics. 2012 Sep;33(6):488-96. doi: 10.1002/bem.21709. Epub 2012 Feb 13.


Synthetic transactivation screening reveals ETV4 as broad coactivator of hypoxia-inducible factor signaling.

Wollenick K, Hu J, Kristiansen G, Schraml P, Rehrauer H, Berchner-Pfannschmidt U, Fandrey J, Wenger RH, Stiehl DP.

Nucleic Acids Res. 2012 Mar;40(5):1928-43. doi: 10.1093/nar/gkr978. Epub 2011 Nov 10.


LIN-39 and the EGFR/RAS/MAPK pathway regulate C. elegans vulval morphogenesis via the VAB-23 zinc finger protein.

Pellegrino MW, Farooqui S, Fröhli E, Rehrauer H, Kaeser-Pebernard S, Müller F, Gasser RB, Hajnal A.

Development. 2011 Nov;138(21):4649-60. doi: 10.1242/dev.071951.


Interaction of HIF and USF signaling pathways in human genes flanked by hypoxia-response elements and E-box palindromes.

Hu J, Stiehl DP, Setzer C, Wichmann D, Shinde DA, Rehrauer H, Hradecky P, Gassmann M, Gorr TA.

Mol Cancer Res. 2011 Nov;9(11):1520-36. doi: 10.1158/1541-7786.MCR-11-0090. Epub 2011 Oct 7.


Pleural mesothelioma side populations have a precursor phenotype.

Frei C, Opitz I, Soltermann A, Fischer B, Moura U, Rehrauer H, Weder W, Stahel R, Felley-Bosco E.

Carcinogenesis. 2011 Sep;32(9):1324-32. doi: 10.1093/carcin/bgr127. Epub 2011 Jul 5.


CD133 positive embryonal rhabdomyosarcoma stem-like cell population is enriched in rhabdospheres.

Walter D, Satheesha S, Albrecht P, Bornhauser BC, D'Alessandro V, Oesch SM, Rehrauer H, Leuschner I, Koscielniak E, Gengler C, Moch H, Bernasconi M, Niggli FK, Schäfer BW; CWS Study Group.

PLoS One. 2011;6(5):e19506. doi: 10.1371/journal.pone.0019506. Epub 2011 May 13.


Myc-mediated repression of microRNA-34a promotes high-grade transformation of B-cell lymphoma by dysregulation of FoxP1.

Craig VJ, Cogliatti SB, Imig J, Renner C, Neuenschwander S, Rehrauer H, Schlapbach R, Dirnhofer S, Tzankov A, Müller A.

Blood. 2011 Jun 9;117(23):6227-36. doi: 10.1182/blood-2010-10-312231. Epub 2011 Apr 1.


Epigenetic silencing of microRNA-203 dysregulates ABL1 expression and drives Helicobacter-associated gastric lymphomagenesis.

Craig VJ, Cogliatti SB, Rehrauer H, Wündisch T, Müller A.

Cancer Res. 2011 May 15;71(10):3616-24. doi: 10.1158/0008-5472.CAN-10-3907. Epub 2011 Mar 31.


CDCOCA: a statistical method to define complexity dependence of co-occuring chromosomal aberrations.

Kumar N, Rehrauer H, Cai H, Baudis M.

BMC Med Genomics. 2011 Mar 3;4:21. doi: 10.1186/1755-8794-4-21.


Application of a nifH microarray to assess the impact of environmental factors on free-living diazotrophs in a glacier forefield.

Duc L, Neuenschwander S, Rehrauer H, Zeyer J.

Can J Microbiol. 2011 Feb;57(2):105-14. doi: 10.1139/w10-100.


Chronic exposure to cigarette smoke condensate in vitro induces epithelial to mesenchymal transition-like changes in human bronchial epithelial cells, BEAS-2B.

Veljkovic E, Jiricny J, Menigatti M, Rehrauer H, Han W.

Toxicol In Vitro. 2011 Mar;25(2):446-53. doi: 10.1016/j.tiv.2010.11.011. Epub 2010 Nov 21.


Induction of senescence markers after neo-adjuvant chemotherapy of malignant pleural mesothelioma and association with clinical outcome: an exploratory analysis.

Sidi R, Pasello G, Opitz I, Soltermann A, Tutic M, Rehrauer H, Weder W, Stahel RA, Felley-Bosco E.

Eur J Cancer. 2011 Jan;47(2):326-32. doi: 10.1016/j.ejca.2010.09.044. Epub 2010 Oct 29.


Late-gestational systemic hypoxia leads to a similar early gene response in mouse placenta and developing brain.

Trollmann R, Rehrauer H, Schneider C, Krischke G, Huemmler N, Keller S, Rascher W, Gassmann M.

Am J Physiol Regul Integr Comp Physiol. 2010 Dec;299(6):R1489-99. doi: 10.1152/ajpregu.00697.2009. Epub 2010 Oct 6.


Ablation of Dicer from murine Schwann cells increases their proliferation while blocking myelination.

Bremer J, O'Connor T, Tiberi C, Rehrauer H, Weis J, Aguzzi A.

PLoS One. 2010 Aug 27;5(8):e12450. doi: 10.1371/journal.pone.0012450.


The transcriptional response to encystation stimuli in Giardia lamblia is restricted to a small set of genes.

Morf L, Spycher C, Rehrauer H, Fournier CA, Morrison HG, Hehl AB.

Eukaryot Cell. 2010 Oct;9(10):1566-76. doi: 10.1128/EC.00100-10. Epub 2010 Aug 6.


Absence of poly(ADP-ribose) polymerase 1 delays the onset of Salmonella enterica serovar Typhimurium-induced gut inflammation.

Altmeyer M, Barthel M, Eberhard M, Rehrauer H, Hardt WD, Hottiger MO.

Infect Immun. 2010 Aug;78(8):3420-31. doi: 10.1128/IAI.00211-10. Epub 2010 Jun 1.


Rhizobial adaptation to hosts, a new facet in the legume root-nodule symbiosis.

Koch M, Delmotte N, Rehrauer H, Vorholt JA, Pessi G, Hennecke H.

Mol Plant Microbe Interact. 2010 Jun;23(6):784-90. doi: 10.1094/MPMI-23-6-0784.


A global network of coexisting microbes from environmental and whole-genome sequence data.

Chaffron S, Rehrauer H, Pernthaler J, von Mering C.

Genome Res. 2010 Jul;20(7):947-59. doi: 10.1101/gr.104521.109. Epub 2010 May 10.


The Streptococcus mutans serine/threonine kinase, PknB, regulates competence development, bacteriocin production, and cell wall metabolism.

Banu LD, Conrads G, Rehrauer H, Hussain H, Allan E, van der Ploeg JR.

Infect Immun. 2010 May;78(5):2209-20. doi: 10.1128/IAI.01167-09. Epub 2010 Mar 15.

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