Fraunhofer-Institut für Zelltherapie und Immunologie IZI
Fraunhofer-Institut für Zelltherapie und Immunologie IZI

Bioinformatik

Publikationen

  • Beyer K, Straten V, Remmers S, MacLennan S, MacLennan S, Gandaglia G, Willemse P-P M, Herrera R, Omar M I, Russel B, Huber J, Kreuz M, Asiimwe A, Abbott T, Briganti A, Hemelrijck M van, Roobol M J, Prias Consortium, Erspc Rotterdam Study Group, Pioneer Consortium. Secondary treatment for men with localized prostate cancer: a pooled analysis of PRIAS and ERSPC-Rotterdam data within the PIONEER data platform. J Pers Med. 2022 May 5;12(5):751. doi: 10.3390/jpm12050751 
  • Donnadieu E , Luu M, Alb M, Anliker B, Arcangeli S, Bonini C, De Angelis B, Choudhary R, Espie D, Galy A, Holland C, Ivics Z, Kantari-Mimoun C, Kersten M J, Koehl U, Kuhn C, Laugel B, Locatelli F, Marchiq I, Markman J, Moresco M A, Morris E, Negre H, Quintarelli C, Rade M, Reiche K, Renner M, Ruggiero E, Sanges C, Stauss H, Themeli M, Van den Brulle J, Hudecek M, Casucci M. Time to evolve: predicting engineered T cell-associated toxicity with next-generation models. J Immunother Cancer. 2022 May;10(5):e003486. doi: 10.1136/jitc-2021-003486
  • Guedan S, Luu M, Ammar D, Barbao P, Bonini C, Bousso P, Buchholz C J, Casucci M, De Angelis B, Donnadieu E, Espie D, Greco B, Groen R, Huppa J B, Kantari-Mimoun C, Laugel B, Mantock M, Markman J, Morris E, Quintarelli C, Rade M, Reiche K, Rodriguez-Garcia A, Rodriguez-Madoz J R, Ruggiero E, Themeli M, Hudecek M, Marchig I. Time 2EVOLVE: predicting efficacy of engineered T-cells - how far is the bench from the bedside? J Immunother Cancer. 2022 May;10(5):e003487. doi: 10.1136/jitc-2021-003487 
  • Haehnel S, Rade M, Kaiser N, Reiche K, Horn A, Loeffler D, Blumert C, Rapp F, Horn F, Meixensberger J, Renner C, Mueller W, Gaunitz F, Bechmann I, Winter K. RNA sequencing of glioblastoma tissue slice cultures reveals the effects of treatment at the transcriptional level. FEBS Open Bio. 2022 Feb;12(2):480-493. doi: 10.1002/2211-5463.13353. Epub 2021 Dec 29 
  • Loeffler-Wirth H, Kreuz M, Schmidt M, Ott G, Siebert R, Binder H. Classifying germinal center derived lymphomas - navigate a complex transcriptional landscape. Cancers (Basel). 2022 Jul 14;14(14):3434. doi: 10.3390/cancers14143434 
  • Loeffler-Wirth H, Rade M, Arakelyan A, Kreuz M, Loeffler M, Koehl U, Reiche K, Binder H. Transcriptional states of CAR-T infusion relate to neurotoxicity - lessons from high-resolution single-cell SOM expression portraying. Front Immunol. 2022 Sep 28;13:994885. doi: 10.3389/fimmu.2022.994885. eCollection 2022
  • Binder S, Zipfel I, Müller C, Wiedemann K, Schimmelpfennig C, Pfeifer G, Reiche K, Hauschildt S, Lehmann J, Köhl U, Horn F, Friedrich M. The noncoding RNA LINC00152 conveys contradicting effects in different glioblastoma cells. Sci Rep. (2021), 11, 18499. doi: 10.1038/s41598-021-97533-8
  • Meyer S, Handke D, Mueller A, Biehl K, Kreuz M, Bukur J, Koehl U, Lazaridou MF, Berneburg M, Steven A, Massa C, Seliger B. Distinct molecular mechanisms of altered HLA class II expression in malignant melanoma. Cancers (Basel). 2021 Aug 3;13(15):3907. doi: 10.3390/cancers13153907
  • Reschke R, Gussek P, Boldt A, Sack U, Köhl U, Lordick F, Gora T, Kreuz M, Reiche K, Simon JC, Ziemer M, Kunz M. Distinct immune signatures indicative of treatment response and immune-related adverse events in melanoma patients under immune checkpoint inhibitor therapy. Int J Mol Sci. 22 (2021), 15, 8017. doi: 10.3390/ijms22158017
  • Walcher L, Kistenmacher AK, Sommer C, Böhlen S, Ziemann C, Dehmel S, Braun A, Tretbar US, Klöß S, Schambach A, Morgan M, Löffler D, Kämpf C, Blumert C, Reiche K, Beckmann J, König U, Standfest B, Thoma M, Makert GR, Ulbert S, Kossatz-Böhlert U, Köhl U, Dünkel A, Fricke S. Low energy electron irradiationiIs a potent alternative to gamma irradiation for the inactivation of (CAR-)NK-92 cells in ATMP manufacturing. Front Immunol. (2021), 12, 684052. doi: 10.3389/fimmu.2021.684052
  • Warnat-Herresthal S, Schultze H, Shastry K L, Blumert C, Horn F, Reiche K. Swarm learning for decentralized and confidential clinical machine learning. Nature (2021), 594, 7862, Seite 265-270. doi: 10.1038/s41586-021-03583-3
  • Binder S, Zipfel I, Friedrich M, Riedel D, Ende S, Kämpf C, Wiedemann K, Buschmann T, Puppel SH, Reiche K, Stadler PF, Horn F. Master and servant: LINC00152 - a STAT3-induced long noncoding RNA regulates STAT3 in a positive feedback in human multiple myeloma. BMC medical genomics 13 (Februar 2020) Artikelnr.: 22, 13 Seiten. dx.doi.org/10.1186/s12920-020-0692-3
  • Friedrich M, Wiedemann K, Reiche K, Puppel SH, Pfeifer G, Zipfel I, Binder S, Koehl U, Mueller GA, Engeland K, Aigner A, Füssel, S, Fröhner M, Peitzsch C, Dubrovska A, Rade M, Christ S, Schreiber S, Hackermüller J, Lehmann J, Toma MI, Muders MH, Sommer U, Baretton GB, Wirth MP, Horn F. The role of lncRNAs TAPIR-1 and-2 as diagnostic markers and potential therapeutic targets in prostate cancer. Cancers 12 (Mai 2020) 5, 1122, 27 Seiten. dx.doi.org/10.3390/cancers12051122
  • Kreuz M, Otto DJ, Fuessel S, Blumert C, Bertram C, Bartsch S, Loeffler D, Puppel SH, Rade M, Buschmann T, Christ S, Erdmann K, Friedrich M, Froehner M, Muders MH, Schreiber S, Specht M, Toma MI, Benigni F, Freschi M, Gandaglia G, Briganti A, Baretton GB, Loeffler M, Hackermüller J, Reiche K, Wirth M, Horn F. ProstaTrend-A Multivariable Prognostic RNA Expression Score for Aggressive Prostate Cancer. European Urology 78 (2020), 3, Seite 452-459. dx.doi.org/10.1016/j.eururo.2020.06.001
  • Nitsche A, Arnold C, Ueberham U, Reiche K, Fallmann J, Hackermüller J, Stadler PF, Arendt T. Alzheimer-related genes show accelerated evolution. Molecular psychiatry (2020) 7 Seiten. dx.doi.org/10.1038/s41380-020-0680-1
  • Omar MI, Roobol MJ, Ribal MJ, Abbott T, Agapow PM, Araujo S, Asiimwe A, Auffray C, Balaur I, Beyer K, Bernini C, Bjartell A, Briganti A, Butler-Ransohoff JE, Campi R, Cavelaars M, De Meulder B, Devecseri Z, Voss MD, Dimitropoulos K, Evans-Axelsson S, Franks B, Fullwood L, Horgan D, Smith EJ, Kiran A, Kivinummi K, Lambrecht M, Lancet D, Lindgren P, MacLennan S, MacLennan S, Nogueira MM, Moen F, Moinat M, Papineni K, Reich C, Reiche K, Rogiers S, Sartini C, van Bochove K, van Diggelen F, Van Hemelrijck M, Van Poppel H, Zong J, N'Dow J; PIONEER Consortium. Introducing PIONEER: a project to harness big data in prostate cancer research. Nature Reviews Urology 17 (2020), 6, Seite 351-362. dx.doi.org/10.1038/s41585-020-0324-x
  • Kämpf C, Specht M, Scholz A, Puppel SH, Doose G, Reiche K, Schor J, Hackermüller J. uap: reproducible and robust HTS data analysis. BMC Bionformatics, 20 (2019), 664, 9 Seiten. dx.doi.org/10.1186/s12859-019-3219-1
  • Schüttler A, Altenburger R, Ammar M, Bader-Blukott M, Jakobs G, Knapp J, Krüger J, Reiche K, Wu GM, Busch W. Map and model-moving from observation to prediction in toxicogenomics. GigaScience 8 (2019), 6, 22 Seiten, dx.doi.org/10.1093/gigascience/giz057
  • 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. Roquin targets mRNAs in a 3'-UTR-specific manner by different modes of regulation. Nat Commun. 2018 Sep 19;9(1):3810. dx.doi.org/10.1038/s41467-018-06184-3
  • 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. Binding of NUFIP2 to Roquin promotes recognition and regulation of ICOS mRNA. Nat Commun. 2018 Jan 19;9(1):299. dx.doi.org/10.1038/s41467-017-02582-1
  • Binder S, Hösler N, Riedel D, Zipfel I, Buschmann T, Kämpf C, Reiche K, Burger R, Gramatzki M, Hackermüller J, Stadler PF, Horn F. STAT3-induced long noncoding RNAs in multiple myeloma cells display different properties in cancer. Sci Rep. 2017 Aug 11;7(1):7976
  • Schüttler A, Reiche K, Altenburger R, Busch W. The Transcriptome of the Zebrafish Embryo After Chemical Exposure: A Meta-Analysis. Toxicol Sci. 2017 Jun 1;157(2):291-304.
  • 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. 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. 2015 May 27.
  • Nitsche A, Rose D, Fasold M, Reiche K, Stadler PF. Comparison of splice sites reveals that long noncoding RNAs are evolutionarily well conserved. RNA. 2015 May;21(5):801-12.
  • Arnold C, Externbrink F, Hackermüller J, Reiche K. CEMDesigner: Design of custom expression microarrays in the post-ENCODE Era. Journal of Biotechnology. 2014 Nov 10;189:154-6. DOI http://dx.doi.org/10.1016/j.jbiotec.2014.09.012
  • 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. Cell cycle, oncogenic and tumor suppressor pathways regulate numerous long and macro non-protein-coding RNAs. Genome Biol. 2014 Mar 4;15(3):R48.
  • 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. 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. 2014 Sep 29;9(9):e106076.
  • Boll K, Reiche K, Kasack K, Mörbt N, Kretzschmar AK, Tomm JM, Verhaegh G, Schalken J, von Bergen M, Horn F, Hackermüller J. MiR-130a, miR-203 and miR-205 jointly repress key oncogenic pathways and are downregulated in prostatecarcinoma. Oncogene. 2013 Jan 17;32(3):277-85.
  • Otto C, Reiche K, Hackermüller J. Detection of differentially expressed segments in tiling array data. Bioinformatics. 2012 Jun 1;28(11):1471-9.
  • Tramontano A, Donath A, Bernhart SH, Reiche K, Böhmdorfer G, Stadler PF, Bachmair A. 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. 2011 Mar 30;412(1):75-82.
  • Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, Sittka A, Chabas S, Reiche K, Hackermüller J, Reinhardt R, Stadler PF, Vogel J. The primary transcriptome of the major human pathogen Helicobacter pylori. Nature. 2010 Mar 11;464(7286):250-5.
  • Kaczkowski B, Torarinsson E, Reiche K, Havgaard JH, Stadler PF, Gorodkin J. Structural profiles of human miRNA families from pairwise clustering. Bioinformatics. 2009 Feb 1;25(3):291-4.
  • Rose D, Hertel J, Reiche K, Stadler PF, Hackermüller J. NcDNAlign: plausible multiple alignments of non-protein-coding genomic sequences. Genomics. 2008 Jul;92(1):65-74.
  • Rose D, Jöris J, Hackermüller J, Reiche K, Li Q, Stadler PF. Duplicated RNA genes in teleost fish genomes. J Bioinform Comput Biol. 2008 Dec;6(6):1157-75.
  • 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. RNAs everywhere: genome-wide annotation of structured RNAs. J Exp Zool B Mol Dev Evol. 2007 Jan 15;308(1):1-25.
  • ENCODE Project Consortium. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007 Jun 14;447(7146):799-816.
  • Reiche K, Stadler PF. RNAstrand: reading direction of structured RNAs in multiple sequence alignments. Algorithms Mol Biol. 2007 May 31;2:6.
  • Rose D, Hackermüller J, Washietl S, Reiche K, Hertel J, Findeiss S, Stadler PF, Prohaska SJ. Computational RNomics of drosophilids. BMC Genomics. 2007 Nov 8;8:406.
  • Snyder M, Gerstein MB, Reymond A, Hofacker IL, Stadler PF. Structured RNAs in the ENCODE selected regions of the human genome. Genome Res. 2007 Jun;17(6):852-64.
  • 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, Will S, Reiche K, Hofacker IL, Stadler PF, Backofen R. Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering. PLoS Comput Biol. 2007 Apr 13;3(4):e65.
  • Hertel J, Lindemeyer M, Missal K, Fried C, Tanzer A, Flamm C, Hofacker IL, Stadler PF; Students of Bioinformatics Computer Labs 2004 and 2005. The expansion of the metazoan microRNA repertoire. BMC Genomics. 2006 Feb 15;7:25.
  • Missal K, Cross MA, Drasdo D. Gene network inference from incomplete expression data: transcriptional control of hematopoietic commitment. Bioinformatics. 2006 Mar 15;22(6):731-8.
  • Missal K, Zhu X, Rose D, Deng W, Skogerbø G, Chen R, Stadler PF. Prediction of structured non-coding RNAs in the genomes of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae. J Exp Zool B Mol Dev Evol. 2006 Jul 15;306(4):379-92.
  • Missal K, Rose D, Stadler PF. Non-coding RNAs in Ciona intestinalis. Bioinformatics. 2005 Sep 1;21.
  • Bompfünewerer AF, Flamm C, Fried C, Fritzsch G, Hofacker IL, Lehmann J, Missal K, Mosig A, Müller B, Prohaska SJ, Stadler BM, Stadler PF, Tanzer A, Washietl S, Witwer C. Evolutionary patterns of non-coding RNAs. Theory Biosci. 2005 Apr;123(4):301-69.