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Publikationen

Hier finden Sie eine Liste der Publikationen, bei denen Mitglieder des BIUM-MZ einen Beitrag leisteten:


  1. Gaonkar KS, Marini F, Rathi KS, Jain P, Zhu Y, Chimicles NA, Brown MA, Naqvi AS, Zhang B, Storm PB, Maris JM, Raman P, Resnick AC, Strauch K, Taroni JN, Rokita JL. annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions. BMC Bioinformatics. 2020;21(1). doi:10.1186/s12859-020-03922-7.
  2. Bogucka K, Marini F, Rosigkeit S, Schloeder J, Jonuleit H, David K, Schlackow M, Rajalingam K. ERK3/MAPK6 is required for KRAS-mediated NSCLC tumorigenesis. Cancer Gene Therapy. 2020. doi:10.1038/s41417-020-00245-w.
  3. Marini F, Linke J, Binder H. ideal: an R/Bioconductor package for interactive differential expression analysis. BMC Bioinformatics. 2020;21(1). doi:10.1186/s12859-020-03819-5.
  4. Marini F, Scherzinger D, Danckwardt S. TREND-DB—a transcriptome-wide atlas of the dynamic landscape of alternative polyadenylation. Nucleic Acids Research. 2020;49(D1):D243–D253. doi:10.1093/nar/gkaa722.
  5. Brackmann LK, Poplawski A, Grandt CL, Schwarz H, Hankeln T, Rapp S, Zahnreich S, Galetzka D, Schmitt I, Grad C, Eckhard L, Mirsch J, Blettner M, Scholz-Kreisel P, Hess M, Binder H, Schmidberger H, Marron M. Comparison of time and dose dependent gene expression and affected pathways in primary human fibroblasts after exposure to ionizing radiation. Molecular Medicine. 2020;26(1). doi:10.1186/s10020-020-00203-0.
  6. Roewe J, Stavrides G, Strueve M, Sharma A, Marini F, Mann A, Smith SA, Kaya Z, Strobl B, Mueller M, Reinhardt C, Morrissey JH, Bosmann M. Bacterial polyphosphates interfere with the innate host defense to infection. Nature Communications. 2020;11(1). doi:10.1038/s41467-020-17639-x.
  7. Soneson C, Marini F, Geier F, Love MI, Stadler MB. ExploreModelMatrix: Interactive exploration for improved understanding of design matrices and linear models in R. F1000Research. 2020;9:512. doi:10.12688/f1000research.24187.1.
  8. Hauptmann J, Johann L, Marini F, Kitic M, Colombo E, Mufazalov IA, Krueger M, Karram K, Moos S, Wanke F, Kurschus FC, Klein M, Cardoso S, Strauß J, Bolisetty S, Lühder F, Schwaninger M, Binder H, Bechman I, Bopp T, Agarwal A, Soares MP, Regen T, Waisman A. Interleukin-1 promotes autoimmune neuroinflammation by suppressing endothelial heme oxygenase-1 at the blood–brain barrier. Acta Neuropathologica. 2020;140(4):549–567. doi:10.1007/s00401-020-02187-x.
  9. Bogucka K, Pompaiah M, Marini F, Binder H, Harms G, Kaulich M, Klein M, Michel C, Radsak MP, Rosigkeit S, Grimminger P, Schild H, Rajalingam K. ERK3/MAPK6 controls IL-8 production and chemotaxis. eLife. 2020;9. doi:10.7554/elife.52511.
  10. Mohebiany AN, Ramphal NS, Karram K, Di Liberto G, Novkovic T, Klein M, Marini F, Kreutzfeldt M, Härtner F, Lacher SM, Bopp T, Mittmann T, Merkler D, Waisman A. Microglial A20 Protects the Brain from CD8 T-Cell-Mediated Immunopathology. Cell Reports. 2020;30(5):1585–1597.e6. doi:10.1016/j.celrep.2019.12.097.
  11. Lückel C, Picard F, Raifer H, Campos Carrascosa L, Guralnik A, Zhang Y, Klein M, Bittner S, Steffen F, Moos S, Marini F, Gloury R, Kurschus FC, Chao Y-Y, Bertrams W, Sexl V, Schmeck B, Bonetti L, Grusdat M, Lohoff M, Zielinski CE, Zipp F, Kallies A, Brenner D, Berger M, Bopp T, Tackenberg B, Huber M. IL-17+ CD8+ T cell suppression by dimethyl fumarate associates with clinical response in multiple sclerosis. Nature Communications. 2019;10(1). doi:10.1038/s41467-019-13731-z.
  12. Amezquita RA, Lun ATL, Becht E, Carey VJ, Carpp LN, Geistlinger L, Marini F, Rue-Albrecht K, Risso D, Soneson C, Waldron L, Pagès H, Smith ML, Huber W, Morgan M, Gottardo R, Hicks SC. Orchestrating single-cell analysis with Bioconductor. Nature Methods. 2019;17(2):137–145. doi:10.1038/s41592-019-0654-x.
  13. Graf C, Wilgenbus P, Pagel S, Pott J, Marini F, Reyda S, Kitano M, Macher-Göppinger S, Weiler H, Ruf W. Myeloid cell–synthesized coagulation factor X dampens antitumor immunity. Science Immunology. 2019;4(39):eaaw8405. doi:10.1126/sciimmunol.aaw8405.
  14. Akhtar J, More P, Albrecht S, Marini F, Kaiser W, Kulkarni A, Wojnowski L, Fontaine J-F, Andrade-Navarro MA, Silies M, Berger C. TAF-ChIP: an ultra-low input approach for genome-wide chromatin immunoprecipitation assay. Life Science Alliance. 2019;2(4):e201900318. doi:10.26508/lsa.201900318.
  15. Marini F, Binder H. pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components. BMC Bioinformatics. 2019;20(1). doi:10.1186/s12859-019-2879-1.
  16. Akhtar J, Kreim N, Marini F, Mohana G, Brüne D, Binder H, Roignant J-Y. Promoter-proximal pausing mediated by the exon junction complex regulates splicing. Nature Communications. 2019;10(1). doi:10.1038/s41467-019-08381-0.
  17. Ogorodnikov A, Levin M, Tattikota S, Tokalov S, Hoque M, Scherzinger D, Marini F, Poetsch A, Binder H, Macher-Göppinger S, Probst HC, Tian B, Schaefer M, Lackner KJ, Westermann F, Danckwardt S. Transcriptome 3′end organization by PCF11 links alternative polyadenylation to formation and neuronal differentiation of neuroblastoma. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-07580-5.
  18. Nührenberg TG, Cederqvist M, Marini F, Stratz C, Grüning BA, Trenk D, Binder H, Gilsbach R, Neumann F-J, Hein L. Uncontrolled Diabetes Mellitus Has No Major Influence on the Platelet Transcriptome. BioMed Research International. 2018;2018:1–9. doi:10.1155/2018/8989252.
  19. Rue-Albrecht K, Marini F, Soneson C, Lun ATL. iSEE: Interactive SummarizedExperiment Explorer. F1000Research. 2018;7:741. doi:10.12688/f1000research.14966.1.
  20. Goesswein D, Habtemichael N, Gerhold-Ay A, Mazur J, Wünsch D, Knauer SK, Künzel J, Matthias C, Strieth S, Stauber RH. Expressional analysis of disease-relevant signalling-pathways in primary tumours and metastasis of head and neck cancers. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-25512-7.
  21. Foerster F, Hess M, Gerhold-Ay A, Marquardt JU, Becker D, Galle PR, Schuppan D, Binder H, Bockamp E. The immune contexture of hepatocellular carcinoma predicts clinical outcome. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-21937-2.
  22. Shen L, Tenzer S, Hess M, Distler U, Tubbe I, Montermann E, Schimmer S, Dittmer U, Grabbe S, Bros M. Friend virus limits adaptive cellular immune responses by imprinting a maturation-resistant and T helper type 2-biased immunophenotype in dendritic cells. Santiago ML, ed. PLOS ONE. 2018;13(2):e0192541. doi:10.1371/journal.pone.0192541.
  23. Hess M, Lenz S, Blätte TJ, Bullinger L, Binder H. Partitioned learning of deep Boltzmann machines for SNP data. Hancock J, ed. Bioinformatics. 2017;33(20):3173–3180. doi:10.1093/bioinformatics/btx408.
  24. Hahn M, Bürckert J-P, Luttenberger CA, Klebow S, Hess M, Al-Maarri M, Vogt M, Reißig S, Hallek M, Wienecke-Baldacchino A, Buch T, Muller CP, Pallasch CP, Wunderlich FT, Waisman A, Hövelmeyer N. Aberrant splicing of the tumor suppressor CYLD promotes the development of chronic lymphocytic leukemia via sustained NF-κB signaling. Leukemia. 2017;32(1):72–82. doi:10.1038/leu.2017.168.
  25. Campos Carrascosa L, Klein M, Kitagawa Y, Lückel C, Marini F, König A, Guralnik A, Raifer H, Hagner-Benes S, Rädler D, Böck A, Kang C, Lohoff M, Garn H, Schaub B, Berberich-Siebelt F, Sakaguchi S, Bopp T, Huber M. Reciprocal regulation of the Il9 locus by counteracting activities of transcription factors IRF1 and IRF4. Nature Communications. 2017;8(1). doi:10.1038/ncomms15366.
  26. Iglesias AI, der Lee SJ, Bonnemaijer PWM, Höhn R, Nag A, Gharahkhani P, Khawaja AP, Broer L, Foster PJ, Hammond CJ, Hysi PG, Leeuwen EM, MacGregor S, Mackey DA, Mazur J, Nickels S, Uitterlinden AG, Klaver CCW, Amin N, Duijn CM. Haplotype reference consortium panel: Practical implications of imputations with large reference panels. Human Mutation. 2017;38(8):1025–1032. doi:10.1002/humu.23247.
  27. Yurugi H, Marini F, Weber C, David K, Zhao Q, Binder H, Désaubry L, Rajalingam K. Targeting prohibitins with chemical ligands inhibits KRAS-mediated lung tumours. Oncogene. 2017;36(33):4778–4789. doi:10.1038/onc.2017.93.
  28. De Vries PS, Sabater-Lleal M, Chasman DI, Trompet S, Ahluwalia TS, Teumer A, Kleber ME, Chen M-H, Wang JJ, Attia JR, Marioni RE, Steri M, Weng L-C, Pool R, Grossmann V, Brody JA, Venturini C, Tanaka T, Rose LM, Oldmeadow C, Mazur J, Basu S, Frånberg M, Yang Q, Ligthart S, Hottenga JJ, Rumley A, Mulas A, de Craen AJM, Grotevendt A, Taylor KD, Delgado GE, Kifley A, Lopez LM, Berentzen TL, Mangino M, Bandinelli S, Morrison AC, Hamsten A, Tofler G, de Maat MPM, Draisma HHM, Lowe GD, Zoledziewska M, Sattar N, Lackner KJ, Völker U, McKnight B, Huang J, Holliday EG, McEvoy MA, Starr JM, Hysi PG, Hernandez DG, Guan W, Rivadeneira F, McArdle WL, Slagboom PE, Zeller T, Psaty BM, Uitterlinden AG, de Geus EJC, Stott DJ, Binder H, Hofman A, Franco OH, Rotter JI, Ferrucci L, Spector TD, Deary IJ, März W, Greinacher A, Wild PS, Cucca F, Boomsma DI, Watkins H, Tang W, Ridker PM, Jukema JW, Scott RJ, Mitchell P, Hansen T, O’Donnell CJ, Smith NL, Strachan DP, Dehghan A. Comparison of HapMap and 1000 Genomes Reference Panels in a Large-Scale Genome-Wide Association Study. Yao Y-G, ed. PLOS ONE. 2017;12(1):e0167742. doi:10.1371/journal.pone.0167742.
  29. Poplawski A, Binder H. Feasibility of sample size calculation for RNA-seq studies. Briefings in Bioinformatics. 2017:bbw144. doi:10.1093/bib/bbw144.
  30. Sennblad B, Basu S, Mazur J, Suchon P, Martinez-Perez A, van Hylckama Vlieg A, Truong V, Li Y, Gådin JR, Tang W, Grossman V, de Haan HG, Handin N, Silveira A, Souto JC, Franco-Cereceda A, Morange P-E, Gagnon F, Soria JM, Eriksson P, Hamsten A, Maegdefessel L, Rosendaal FR, Wild P, Folsom AR, Trégouët D-A, Sabater-Lleal M. Genome-wide association study with additional genetic and post-transcriptional analyses reveals novel regulators of plasma factor XI levels. Human Molecular Genetics. 2017:ddw401. doi:10.1093/hmg/ddw401.
  31. Paret C, Theruvath J, Russo A, Kron B, Malki KE, Lehmann N, Wingerter A, Neu MA, Gerhold-Ay A, Wagner W, Sommer C, Pietsch T, Seidmann L, Faber J. Activation of the basal cell carcinoma pathway in a patient with CNS HGNET-BCOR diagnosis: consequences for personalized targeted therapy. Oncotarget. 2016;7(50):83378–83391. doi:10.18632/oncotarget.13092.
  32. Hafner C, Wu J, Tiboldi A, Hess M, Mitulovic G, Kaun C, Krychtiuk KA, Wojta J, Ullrich R, Tretter EV, Markstaller K, Klein KU. Hyperoxia Induces Inflammation and Cytotoxicity in Human Adult Cardiac Myocytes. Shock. 2017;47(4):436–444. doi:10.1097/shk.0000000000000740.
  33. Tideman JWL, Fan Q, Polling JR, Guo X, Yazar S, Khawaja A, Höhn R, Lu Y, Jaddoe VWV, Yamashiro K, Yoshikawa M, Gerhold-Ay A, Nickels S, Zeller T, He M, Boutin T, Bencic G, Vitart V, Mackey DA, Foster PJ, MacGregor S, Williams C, Saw SM, Guggenheim JA, Klaver CCW. When do myopia genes have their effect? Comparison of genetic risks between children and adults. Genetic Epidemiology. 2016;40(8):756–766. doi:10.1002/gepi.21999.
  34. Wasser B, Pramanik G, Hess M, Klein M, Luessi F, Dornmair K, Bopp T, Zipp F, Witsch E. Increase of Alternatively Activated Antigen Presenting Cells in Active Experimental Autoimmune Encephalomyelitis. Journal of Neuroimmune Pharmacology. 2016;11(4):721–732. doi:10.1007/s11481-016-9696-3.
  35. Gehrke N, Wörns MA, Huber Y, Hess M, Straub BK, Hövelmeyer N, Waisman A, Kim YO, Schuppan D, Galle PR, Schattenberg JM. Hepatic B cell leukemia-3 promotes hepatic steatosis and inflammation through insulin-sensitive metabolic transcription factors. Journal of Hepatology. 2016;65(6):1188–1197. doi:10.1016/j.jhep.2016.06.026.
  36. Fan Q, Verhoeven VJM, Wojciechowski R, Barathi VA, Hysi PG, Guggenheim JA, Höhn R, Vitart V, Khawaja AP, Yamashiro K, Hosseini SM, Lehtimäki T, Lu Y, Haller T, Xie J, Delcourt C, Pirastu M, Wedenoja J, Gharahkhani P, Venturini C, Miyake M, Hewitt AW, Guo X, Mazur J, Huffman JE, Williams KM, Polasek O, Campbell H, Rudan I, Vatavuk Z, Wilson JF, Joshi PK, McMahon G, St Pourcain B, Evans DM, Simpson CL, Schwantes-An T-H, Igo RP, Mirshahi A, Cougnard-Gregoire A, Bellenguez C, Blettner M, Raitakari O, Kähönen M, Seppälä I, Zeller T, Meitinger T, Ried JS, Gieger C, Portas L, van Leeuwen EM, Amin N, Uitterlinden AG, Rivadeneira F, Hofman A, Vingerling JR, Wang YX, Wang X, Tai-Hui Boh E, Ikram MK, Sabanayagam C, Gupta P, Tan V, Zhou L, Ho CEH, Lim W, Beuerman RW, Siantar R, Tai E-S, Vithana E, Mihailov E, Khor C-C, Hayward C, Luben RN, Foster PJ, Klein BEK, Klein R, Wong H-S, Mitchell P, Metspalu A, Aung T, Young TL, He M, Pärssinen O, van Duijn CM, Jin Wang J, Williams C, Jonas JB, Teo Y-Y, Mackey DA, Oexle K, Yoshimura N, Paterson AD, Pfeiffer N, Wong T-Y, Baird PN, Stambolian D, et al. Meta-analysis of gene–environment-wide association scans accounting for education level identifies additional loci for refractive error. Nature Communications. 2016;7(1). doi:10.1038/ncomms11008.
  37. Tuettenberg A, Hahn SA, Mazur J, Gerhold-Ay A, Scholma J, Marg I, Ulges A, Satoh K, Bopp T, Joore J, Jonuleit H. Kinome Profiling of Regulatory T Cells: A Closer Look into a Complex Intracellular Network. Unutmaz D, ed. PLOS ONE. 2016;11(2):e0149193. doi:10.1371/journal.pone.0149193.
  38. Feldmeyer B, Mazur J, Beros S, Lerp H, Binder H, Foitzik S. Gene expression patterns underlying parasite-induced alterations in host behaviour and life history. Molecular Ecology. 2016;25(2):648–660. doi:10.1111/mec.13498.
  39. De Vries PS, Chasman DI, Sabater-Lleal M, Chen M-H, Huffman JE, Steri M, Tang W, Teumer A, Marioni RE, Grossmann V, Hottenga JJ, Trompet S, Müller-Nurasyid M, Zhao JH, Brody JA, Kleber ME, Guo X, Wang JJ, Auer PL, Attia JR, Yanek LR, Ahluwalia TS, Lahti J, Venturini C, Tanaka T, Bielak LF, Joshi PK, Rocanin-Arjo A, Kolcic I, Navarro P, Rose LM, Oldmeadow C, Riess H, Mazur J, Basu S, Goel A, Yang Q, Ghanbari M, Willemsen G, Rumley A, Fiorillo E, de Craen AJM, Grotevendt A, Scott R, Taylor KD, Delgado GE, Yao J, Kifley A, Kooperberg C, Qayyum R, Lopez LM, Berentzen TL, Räikkönen K, Mangino M, Bandinelli S, Peyser PA, Wild S, Trégouët D-A, Wright AF, Marten J, Zemunik T, Morrison AC, Sennblad B, Tofler G, de Maat MPM, de Geus EJC, Lowe GD, Zoledziewska M, Sattar N, Binder H, Völker U, Waldenberger M, Khaw K-T, Mcknight B, Huang J, Jenny NS, Holliday EG, Qi L, Mcevoy MG, Becker DM, Starr JM, Sarin A-P, Hysi PG, Hernandez DG, Jhun MA, Campbell H, Hamsten A, Rivadeneira F, Mcardle WL, Slagboom PE, Zeller T, Koenig W, Psaty BM, Haritunians T, Liu J, Palotie A, Uitterlinden AG, Stott DJ, et al. A meta-analysis of 120 246 individuals identifies 18 new loci for fibrinogen concentration. Human Molecular Genetics. 2015;25(2):358–370. doi:10.1093/hmg/ddv454.
  40. Bruttger J, Karram K, Wörtge S, Regen T, Marini F, Hoppmann N, Klein M, Blank T, Yona S, Wolf Y, Mack M, Pinteaux E, Müller W, Zipp F, Binder H, Bopp T, Prinz M, Jung S, Waisman A. Genetic Cell Ablation Reveals Clusters of Local Self-Renewing Microglia in the Mammalian Central Nervous System. Immunity. 2015;43(1):92–106. doi:10.1016/j.immuni.2015.06.012.
  41. Poplawski A, Marini F, Hess M, Zeller T, Mazur J, Binder H. Systematically evaluating interfaces for RNA-seq analysis from a life scientist perspective. Briefings in Bioinformatics. 2015;17(2):213–223. doi:10.1093/bib/bbv036.
  42. Hermanns MI, Grossmann V, Spronk HMH, Schulz A, Jünger C, Laubert-Reh D, Mazur J, Gori T, Zeller T, Pfeiffer N, Beutel M, Blankenberg S, Münzel T, Lackner KJ, ten Cate-Hoek AJ, ten Cate H, Wild PS. Distribution, genetic and cardiovascular determinants of FVIII:c — Data from the population-based Gutenberg Health Study. International Journal of Cardiology. 2015;187:166–174. doi:10.1016/j.ijcard.2015.03.330.
  43. Binder H, Gefeller O, Schmid M, Mayr A. The Evolution of Boosting Algorithms. Methods of Information in Medicine. 2014;53(06):419–427. doi:10.3414/me13-01-0122.
  44. Schwarz A, Tenzer S, Hackenberg M, Erhart J, Gerhold-Ay A, Mazur J, Kuharev J, Ribeiro JMC, Kotsyfakis M. A Systems Level Analysis Reveals Transcriptomic and Proteomic Complexity in Ixodes Ricinus Midgut and Salivary Glands During Early Attachment and Feeding. Molecular & Cellular Proteomics. 2014;13(10):2725–2735. doi:10.1074/mcp.m114.039289.
  45. Becker D, Sfakianakis I, Krupp M, Staib F, Gerhold-Ay A, Victor A, Binder H, Blettner M, Maass T, Thorgeirsson S, Galle PR, Teufel A. Genetic signatures shared in embryonic liver development and liver cancer define prognostically relevant subgroups in HCC. Molecular Cancer. 2012;11(1):55. doi:10.1186/1476-4598-11-55.
  46. Marini F, Scherzinger D, Danckwardt S. TREND-DB – A Transcriptome-wide Atlas of the Dynamic Landscape of Alternative Polyadenylation. 2020. doi:10.1101/2020.08.04.235804.
  47. Marini F, Linke J, Binder H. ideal: an R/Bioconductor package for Interactive Differential Expression Analysis. 2020. doi:10.1101/2020.01.10.901652.
  48. Amezquita RA, Carey VJ, Carpp LN, Geistlinger L, Lun ATL, Marini F, Rue-Albrecht K, Risso D, Soneson C, Waldron L, Pagès H, Smith M, Huber W, Morgan M, Gottardo R, Hicks SC. Orchestrating Single-Cell Analysis with Bioconductor. 2019. doi:10.1101/590562.
  49. Paret C, Russo A, Lehmann N, Backes N, Roth L, Malki KE, Wingerter A, Neu MA, Seidmann L, Gerhold-Ay A, Wagner W, Faber J. TRTH-08. HIGH GRADE NEUROEPITHELIAL TUMOR OF THE CENTRAL NERVOUS SYSTEM WITH BCOR ALTERATION IS SENSITIVE TO IGF1R INHIBITION. Neuro-Oncology. 2017;19(suppl_4):iv53–iv53. doi:10.1093/neuonc/nox083.220.
  50. Paret C, Theruvath J, Russo A, Kron B, ElMalki K, Lehmann N, Neu M, Gerhold-Ay A, Wagner W, Sommer C, Seidmann L, Faber J. PNR-35CNS HGNET-BCOR - MOLECULAR CHARACTERIZATION AND IDENTIFICATION OF POSSIBLE THERAPEUTIC TARGETS OF A NEW BRAIN TUMOR ENTITY. Neuro-Oncology. 2016;18(suppl 3):iii14.1–iii14. doi:10.1093/neuonc/now067.30.
  51. Marini F, Binder H. Development of Applications for Interactive and Reproducible Research: a Case Study. Genomics and Computational Biology. 2016;3(1):39. doi:10.18547/gcb.2017.vol3.iss1.e39.

Um eine vollständige Liste der Veröffentlichungen einzusehen, besuchen Sie bitte Pubmed und geben Sie die entsprechenden Initialen ein (e.g. "Marini F", "Foerster F", "Poplawski A", "Ludt A", ...).
Einige Manuskripte sind auch zu finden auf https://www.biorxiv.org