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Items: 1 to 50 of 82

1.

Improved risk-stratification for posterior fossa ependymoma of childhood considering clinical, histological and genetic features - a retrospective analysis of the HIT ependymoma trial cohort.

Jünger ST, Mynarek M, Wohlers I, Dörner E, Mühlen AZ, Velez-Char N, von Hoff K, Rutkowski S, Warmuth-Metz M, Kortmann RD, Timmermann B, Rahmann S, Klein-Hitpass L, von Bueren AO, Pietsch T.

Acta Neuropathol Commun. 2019 Nov 14;7(1):181. doi: 10.1186/s40478-019-0820-5.

2.

Genome-Wide Analysis of the Nucleosome Landscape in Individuals with Coffin-Siris Syndrome.

Kalmbach A, Schröder C, Klein-Hitpass L, Nordström K, Ulz P, Heitzer E, Speicher MR, Rahmann S, Wieczorek D, Horsthemke B, Bramswig NC.

Cytogenet Genome Res. 2019;159(1):1-11. doi: 10.1159/000503266. Epub 2019 Oct 26.

3.

Interaction-Specific Changes in the Transcriptome of Polynucleobacter asymbioticus Caused by Varying Protistan Communities.

Beisser D, Bock C, Hahn MW, Vos M, Sures B, Rahmann S, Boenigk J.

Front Microbiol. 2019 Jul 9;10:1498. doi: 10.3389/fmicb.2019.01498. eCollection 2019.

4.

The Role of Pre-existing Cross-Reactive Central Memory CD4 T-Cells in Vaccination With Previously Unseen Influenza Strains.

Nienen M, Stervbo U, Mölder F, Kaliszczyk S, Kuchenbecker L, Gayova L, Schweiger B, Jürchott K, Hecht J, Neumann AU, Rahmann S, Westhoff T, Reinke P, Thiel A, Babel N.

Front Immunol. 2019 Apr 4;10:593. doi: 10.3389/fimmu.2019.00593. eCollection 2019.

5.

Machine learning-based predictors for immune checkpoint inhibitor therapy of non-small-cell lung cancer.

Wiesweg M, Mairinger F, Reis H, Goetz M, Walter RFH, Hager T, Metzenmacher M, Eberhardt WEE, McCutcheon A, Köster J, Stuschke M, Aigner C, Darwiche K, Schmid KW, Rahmann S, Schuler M.

Ann Oncol. 2019 Apr 1;30(4):655-657. doi: 10.1093/annonc/mdz049. No abstract available.

PMID:
30753264
6.

Impact of RAS mutation subtype on clinical outcome-a cross-entity comparison of patients with advanced non-small cell lung cancer and colorectal cancer.

Wiesweg M, Kasper S, Worm K, Herold T, Reis H, Sara L, Metzenmacher M, Abendroth A, Darwiche K, Aigner C, Wedemeyer HH, Helfritz FA, Stuschke M, Schumacher B, Markus P, Paul A, Rahmann S, Schmid KW, Schuler M.

Oncogene. 2019 Apr;38(16):2953-2966. doi: 10.1038/s41388-018-0634-0. Epub 2018 Dec 19.

PMID:
30568222
7.

A mechanistic classification of clinical phenotypes in neuroblastoma.

Ackermann S, Cartolano M, Hero B, Welte A, Kahlert Y, Roderwieser A, Bartenhagen C, Walter E, Gecht J, Kerschke L, Volland R, Menon R, Heuckmann JM, Gartlgruber M, Hartlieb S, Henrich KO, Okonechnikov K, Altmüller J, Nürnberg P, Lefever S, de Wilde B, Sand F, Ikram F, Rosswog C, Fischer J, Theissen J, Hertwig F, Singhi AD, Simon T, Vogel W, Perner S, Krug B, Schmidt M, Rahmann S, Achter V, Lang U, Vokuhl C, Ortmann M, Büttner R, Eggert A, Speleman F, O'Sullivan RJ, Thomas RK, Berthold F, Vandesompele J, Schramm A, Westermann F, Schulte JH, Peifer M, Fischer M.

Science. 2018 Dec 7;362(6419):1165-1170. doi: 10.1126/science.aat6768.

PMID:
30523111
8.

Circulating microRNA biomarkers for metastatic disease in neuroblastoma patients.

Zeka F, Decock A, Van Goethem A, Vanderheyden K, Demuynck F, Lammens T, Helsmoortel HH, Vermeulen J, Noguera R, Berbegall AP, Combaret V, Schleiermacher G, Laureys G, Schramm A, Schulte JH, Rahmann S, Bienertová-Vašků J, Mazánek P, Jeison M, Ash S, Hogarty MD, Moreno-Smith M, Barbieri E, Shohet J, Berthold F, Van Maerken T, Speleman F, Fischer M, De Preter K, Mestdagh P, Vandesompele J.

JCI Insight. 2018 Dec 6;3(23). pii: 97021. doi: 10.1172/jci.insight.97021.

9.

Silver stress differentially affects growth of phototrophic and heterotrophic chrysomonad flagellate populations.

Bock C, Zimmermann S, Beisser D, Dinglinger SM, Engelskirchen S, Giesemann P, Klink S, Olefeld JL, Rahmann S, Vos M, Boenigk J, Sures B.

Environ Pollut. 2019 Jan;244:314-322. doi: 10.1016/j.envpol.2018.09.146. Epub 2018 Oct 11.

PMID:
30343232
10.

Snakemake-a scalable bioinformatics workflow engine.

Köster J, Rahmann S.

Bioinformatics. 2018 Oct 15;34(20):3600. doi: 10.1093/bioinformatics/bty350. No abstract available.

PMID:
29788404
11.

Modeling and simulating networks of interdependent protein interactions.

Stöcker BK, Köster J, Zamir E, Rahmann S.

Integr Biol (Camb). 2018 May 21;10(5):290-305. doi: 10.1039/c8ib00012c.

PMID:
29676773
12.

Locus-Specific DNA Methylation Analysis by Targeted Deep Bisulfite Sequencing.

Leitão E, Beygo J, Zeschnigk M, Klein-Hitpass L, Bargull M, Rahmann S, Horsthemke B.

Methods Mol Biol. 2018;1767:351-366. doi: 10.1007/978-1-4939-7774-1_19.

PMID:
29524145
13.

Evolution of heterotrophy in chrysophytes as reflected by comparative transcriptomics.

Graupner N, Jensen M, Bock C, Marks S, Rahmann S, Beisser D, Boenigk J.

FEMS Microbiol Ecol. 2018 Apr 1;94(4). doi: 10.1093/femsec/fiy039.

14.

Cancer evolution, mutations, and clonal selection in relapse neuroblastoma.

Schulte M, Köster J, Rahmann S, Schramm A.

Cell Tissue Res. 2018 May;372(2):263-268. doi: 10.1007/s00441-018-2810-5. Epub 2018 Feb 24. Review.

PMID:
29478075
15.

ddrage: A data set generator to evaluate ddRADseq analysis software.

Timm H, Weigand H, Weiss M, Leese F, Rahmann S.

Mol Ecol Resour. 2018 May;18(3):681-690. doi: 10.1111/1755-0998.12743. Epub 2017 Dec 27.

PMID:
29194981
16.

TaxMapper: an analysis tool, reference database and workflow for metatranscriptome analysis of eukaryotic microorganisms.

Beisser D, Graupner N, Grossmann L, Timm H, Boenigk J, Rahmann S.

BMC Genomics. 2017 Oct 16;18(1):787. doi: 10.1186/s12864-017-4168-6.

17.

A detailed comparison of analysis processes for MCC-IMS data in disease classification-Automated methods can replace manual peak annotations.

Horsch S, Kopczynski D, Kuthe E, Baumbach JI, Rahmann S, Rahnenführer J.

PLoS One. 2017 Sep 14;12(9):e0184321. doi: 10.1371/journal.pone.0184321. eCollection 2017.

18.

A hybrid parameter estimation algorithm for beta mixtures and applications to methylation state classification.

Schröder C, Rahmann S.

Algorithms Mol Biol. 2017 Aug 18;12:21. doi: 10.1186/s13015-017-0112-1. eCollection 2017.

19.

Regions of common inter-individual DNA methylation differences in human monocytes: genetic basis and potential function.

Schröder C, Leitão E, Wallner S, Schmitz G, Klein-Hitpass L, Sinha A, Jöckel KH, Heilmann-Heimbach S, Hoffmann P, Nöthen MM, Steffens M, Ebert P, Rahmann S, Horsthemke B.

Epigenetics Chromatin. 2017 Jul 26;10(1):37. doi: 10.1186/s13072-017-0144-2.

20.

Comprehensive transcriptome analysis provides new insights into nutritional strategies and phylogenetic relationships of chrysophytes.

Beisser D, Graupner N, Bock C, Wodniok S, Grossmann L, Vos M, Sures B, Rahmann S, Boenigk J.

PeerJ. 2017 Jan 10;5:e2832. doi: 10.7717/peerj.2832. eCollection 2017.

21.

Quantitative Proteomics Reveals Ecophysiological Effects of Light and Silver Stress on the Mixotrophic Protist Poterioochromonas malhamensis.

Beisser D, Kaschani F, Graupner N, Grossmann L, Jensen M, Ninck S, Schulz F, Rahmann S, Boenigk J, Kaiser M.

PLoS One. 2017 Jan 5;12(1):e0168183. doi: 10.1371/journal.pone.0168183. eCollection 2017.

22.

Trade-off between taxon diversity and functional diversity in European lake ecosystems.

Grossmann L, Beisser D, Bock C, Chatzinotas A, Jensen M, Preisfeld A, Psenner R, Rahmann S, Wodniok S, Boenigk J.

Mol Ecol. 2016 Dec;25(23):5876-5888. doi: 10.1111/mec.13878. Epub 2016 Nov 14.

PMID:
27747959
23.

Epigenetic dynamics of monocyte-to-macrophage differentiation.

Wallner S, Schröder C, Leitão E, Berulava T, Haak C, Beißer D, Rahmann S, Richter AS, Manke T, Bönisch U, Arrigoni L, Fröhler S, Klironomos F, Chen W, Rajewsky N, Müller F, Ebert P, Lengauer T, Barann M, Rosenstiel P, Gasparoni G, Nordström K, Walter J, Brors B, Zipprich G, Felder B, Klein-Hitpass L, Attenberger C, Schmitz G, Horsthemke B.

Epigenetics Chromatin. 2016 Jul 29;9:33. doi: 10.1186/s13072-016-0079-z. eCollection 2016.

24.

SimLoRD: Simulation of Long Read Data.

Stöcker BK, Köster J, Rahmann S.

Bioinformatics. 2016 Sep 1;32(17):2704-6. doi: 10.1093/bioinformatics/btw286. Epub 2016 May 10.

PMID:
27166244
25.

Human TLR8 senses UR/URR motifs in bacterial and mitochondrial RNA.

Krüger A, Oldenburg M, Chebrolu C, Beisser D, Kolter J, Sigmund AM, Steinmann J, Schäfer S, Hochrein H, Rahmann S, Wagner H, Henneke P, Hornung V, Buer J, Kirschning CJ.

EMBO Rep. 2015 Dec;16(12):1656-63. doi: 10.15252/embr.201540861. Epub 2015 Nov 6.

26.

Recurrent alterations of TNFAIP3 (A20) in T-cell large granular lymphocytic leukemia.

Johansson P, Bergmann A, Rahmann S, Wohlers I, Scholtysik R, Przekopowitz M, Seifert M, Tschurtschenthaler G, Webersinke G, Jäger U, Siebert R, Klein-Hitpass L, Dührsen U, Dürig J, Küppers R.

Int J Cancer. 2016 Jan 1;138(1):121-4. doi: 10.1002/ijc.29697. Epub 2015 Jul 30.

27.

An online peak extraction algorithm for ion mobility spectrometry data.

Kopczynski D, Rahmann S.

Algorithms Mol Biol. 2015 May 13;10:17. doi: 10.1186/s13015-015-0045-5. eCollection 2015.

28.

Mutational dynamics between primary and relapse neuroblastomas.

Schramm A, Köster J, Assenov Y, Althoff K, Peifer M, Mahlow E, Odersky A, Beisser D, Ernst C, Henssen AG, Stephan H, Schröder C, Heukamp L, Engesser A, Kahlert Y, Theissen J, Hero B, Roels F, Altmüller J, Nürnberg P, Astrahantseff K, Gloeckner C, De Preter K, Plass C, Lee S, Lode HN, Henrich KO, Gartlgruber M, Speleman F, Schmezer P, Westermann F, Rahmann S, Fischer M, Eggert A, Schulte JH.

Nat Genet. 2015 Aug;47(8):872-7. doi: 10.1038/ng.3349. Epub 2015 Jun 29.

PMID:
26121086
29.

N6-adenosine methylation in MiRNAs.

Berulava T, Rahmann S, Rademacher K, Klein-Hitpass L, Horsthemke B.

PLoS One. 2015 Feb 27;10(2):e0118438. doi: 10.1371/journal.pone.0118438. eCollection 2015.

30.

Massively parallel read mapping on GPUs with the q-group index and PEANUT.

Köster J, Rahmann S.

PeerJ. 2014 Sep 30;2:e606. doi: 10.7717/peerj.606. eCollection 2014.

31.

Effects of silver nitrate and silver nanoparticles on a planktonic community: general trends after short-term exposure.

Boenigk J, Beisser D, Zimmermann S, Bock C, Jakobi J, Grabner D, Groβmann L, Rahmann S, Barcikowski S, Sures B.

PLoS One. 2014 Apr 22;9(4):e95340. doi: 10.1371/journal.pone.0095340. eCollection 2014. Erratum in: PLoS One. 2014;9(8):e107092.

32.

Supratentorial ependymomas of childhood carry C11orf95-RELA fusions leading to pathological activation of the NF-κB signaling pathway.

Pietsch T, Wohlers I, Goschzik T, Dreschmann V, Denkhaus D, Dörner E, Rahmann S, Klein-Hitpass L.

Acta Neuropathol. 2014 Apr;127(4):609-11. doi: 10.1007/s00401-014-1264-4. Epub 2014 Feb 22. No abstract available.

PMID:
24562983
33.

A modular computational framework for automated peak extraction from ion mobility spectra.

D'Addario M, Kopczynski D, Baumbach JI, Rahmann S.

BMC Bioinformatics. 2014 Jan 22;15:25. doi: 10.1186/1471-2105-15-25.

34.

A comprehensive molecular study on Coffin-Siris and Nicolaides-Baraitser syndromes identifies a broad molecular and clinical spectrum converging on altered chromatin remodeling.

Wieczorek D, Bögershausen N, Beleggia F, Steiner-Haldenstätt S, Pohl E, Li Y, Milz E, Martin M, Thiele H, Altmüller J, Alanay Y, Kayserili H, Klein-Hitpass L, Böhringer S, Wollstein A, Albrecht B, Boduroglu K, Caliebe A, Chrzanowska K, Cogulu O, Cristofoli F, Czeschik JC, Devriendt K, Dotti MT, Elcioglu N, Gener B, Goecke TO, Krajewska-Walasek M, Guillén-Navarro E, Hayek J, Houge G, Kilic E, Simsek-Kiper PÖ, López-González V, Kuechler A, Lyonnet S, Mari F, Marozza A, Mathieu Dramard M, Mikat B, Morin G, Morice-Picard F, Ozkinay F, Rauch A, Renieri A, Tinschert S, Utine GE, Vilain C, Vivarelli R, Zweier C, Nürnberg P, Rahmann S, Vermeesch J, Lüdecke HJ, Zeschnigk M, Wollnik B.

Hum Mol Genet. 2013 Dec 20;22(25):5121-35. doi: 10.1093/hmg/ddt366. Epub 2013 Aug 1.

35.

Oto-facial syndrome and esophageal atresia, intellectual disability and zygomatic anomalies - expanding the phenotypes associated with EFTUD2 mutations.

Voigt C, Mégarbané A, Neveling K, Czeschik JC, Albrecht B, Callewaert B, von Deimling F, Hehr A, Falkenberg Smeland M, König R, Kuechler A, Marcelis C, Puiu M, Reardon W, Riise Stensland HM, Schweiger B, Steehouwer M, Teller C, Martin M, Rahmann S, Hehr U, Brunner HG, Lüdecke HJ, Wieczorek D.

Orphanet J Rare Dis. 2013 Jul 24;8:110. doi: 10.1186/1750-1172-8-110.

36.

Exome sequencing identifies recurrent somatic mutations in EIF1AX and SF3B1 in uveal melanoma with disomy 3.

Martin M, Maßhöfer L, Temming P, Rahmann S, Metz C, Bornfeld N, van de Nes J, Klein-Hitpass L, Hinnebusch AG, Horsthemke B, Lohmann DR, Zeschnigk M.

Nat Genet. 2013 Aug;45(8):933-6. doi: 10.1038/ng.2674. Epub 2013 Jun 23.

37.

Discovering motifs that induce sequencing errors.

Allhoff M, Schönhuth A, Martin M, Costa IG, Rahmann S, Marschall T.

BMC Bioinformatics. 2013;14 Suppl 5:S1. doi: 10.1186/1471-2105-14-S5-S1. Epub 2013 Apr 10.

38.

Clinical and mutation data in 12 patients with the clinical diagnosis of Nager syndrome.

Czeschik JC, Voigt C, Alanay Y, Albrecht B, Avci S, Fitzpatrick D, Goudie DR, Hehr U, Hoogeboom AJ, Kayserili H, Simsek-Kiper PO, Klein-Hitpass L, Kuechler A, López-González V, Martin M, Rahmann S, Schweiger B, Splitt M, Wollnik B, Lüdecke HJ, Zeschnigk M, Wieczorek D.

Hum Genet. 2013 Aug;132(8):885-98. doi: 10.1007/s00439-013-1295-2. Epub 2013 Apr 9.

PMID:
23568615
39.

Peak detection method evaluation for ion mobility spectrometry by using machine learning approaches.

Hauschild AC, Kopczynski D, D'Addario M, Baumbach JI, Rahmann S, Baumbach J.

Metabolites. 2013 Apr 16;3(2):277-93. doi: 10.3390/metabo3020277.

40.

Identifying transcriptional miRNA biomarkers by integrating high-throughput sequencing and real-time PCR data.

Rahmann S, Martin M, Schulte JH, Köster J, Marschall T, Schramm A.

Methods. 2013 Jan;59(1):154-63. doi: 10.1016/j.ymeth.2012.10.005. Epub 2012 Oct 23.

PMID:
23098880
41.

Exon-level expression analyses identify MYCN and NTRK1 as major determinants of alternative exon usage and robustly predict primary neuroblastoma outcome.

Schramm A, Schowe B, Fielitz K, Heilmann M, Martin M, Marschall T, Köster J, Vandesompele J, Vermeulen J, de Preter K, Koster J, Versteeg R, Noguera R, Speleman F, Rahmann S, Eggert A, Morik K, Schulte JH.

Br J Cancer. 2012 Oct 9;107(8):1409-17. doi: 10.1038/bjc.2012.391.

42.

Snakemake--a scalable bioinformatics workflow engine.

Köster J, Rahmann S.

Bioinformatics. 2012 Oct 1;28(19):2520-2. Epub 2012 Aug 20. Erratum in: Bioinformatics. 2018 Oct 15;34(20):3600.

PMID:
22908215
43.

Next-generation RNA sequencing reveals differential expression of MYCN target genes and suggests the mTOR pathway as a promising therapy target in MYCN-amplified neuroblastoma.

Schramm A, Köster J, Marschall T, Martin M, Schwermer M, Fielitz K, Büchel G, Barann M, Esser D, Rosenstiel P, Rahmann S, Eggert A, Schulte JH.

Int J Cancer. 2013 Feb 1;132(3):E106-15. doi: 10.1002/ijc.27787. Epub 2012 Sep 26.

44.

Probabilistic arithmetic automata and their applications.

Marschall T, Herms I, Kaltenbach HM, Rahmann S.

IEEE/ACM Trans Comput Biol Bioinform. 2012 Nov-Dec;9(6):1737-50.

PMID:
22868683
45.

Efficiently mining protein interaction dependencies from large text corpora.

Köster J, Zamir E, Rahmann S.

Integr Biol (Camb). 2012 Jul;4(7):805-12. doi: 10.1039/c2ib00126h. Epub 2012 Jun 15.

PMID:
22706334
46.

Accurate statistics for local sequence alignment with position-dependent scoring by rare-event sampling.

Wolfsheimer S, Herms I, Rahmann S, Hartmann AK.

BMC Bioinformatics. 2011 Feb 3;12:47. doi: 10.1186/1471-2105-12-47.

47.

High-throughput microarray technology in diagnostics of enterobacteria based on genome-wide probe selection and regression analysis.

Friedrich T, Rahmann S, Weigel W, Rabsch W, Fruth A, Ron E, Gunzer F, Dandekar T, Hacker J, Müller T, Dobrindt U.

BMC Genomics. 2010 Oct 21;11:591. doi: 10.1186/1471-2164-11-591.

48.

Partitioning biological data with transitivity clustering.

Wittkop T, Emig D, Lange S, Rahmann S, Albrecht M, Morris JH, Böcker S, Stoye J, Baumbach J.

Nat Methods. 2010 Jun;7(6):419-20. doi: 10.1038/nmeth0610-419. No abstract available.

PMID:
20508635
49.

Deep sequencing reveals differential expression of microRNAs in favorable versus unfavorable neuroblastoma.

Schulte JH, Marschall T, Martin M, Rosenstiel P, Mestdagh P, Schlierf S, Thor T, Vandesompele J, Eggert A, Schreiber S, Rahmann S, Schramm A.

Nucleic Acids Res. 2010 Sep;38(17):5919-28. doi: 10.1093/nar/gkq342. Epub 2010 May 13.

50.

Efficient online transcription factor binding site adjustment by integrating transitive graph projection with MoRAine 2.0.

Wittkop T, Rahmann S, Baumbach J.

J Integr Bioinform. 2010 Mar 25;7(3). doi: 10.2390/biecoll-jib-2010-117.

PMID:
20375458

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