Next Generation Sequencing Competence Network

Next Generation Sequencing Competence Network

e.g. CCGA
(min 2 characters)

Sven Rahmann

Prof.
University of Duisburg-Essen
Genome Informatics
Virchowstraße 183, 45147 Essen, Germany
Essen 45147
+49 201 7234048
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Kleinbongard P, Lieder HR, Skyschally A, Alloosh M, G?decke A, Rahmann S, Sturek M, Heusch G. Non-responsiveness to cardioprotection by ischaemic preconditioning in Ossabaw minipigs with genetic predisposition to, but without the phenotype of the metabolic syndrome. Basic Res Cardiol. 2022 Nov 11; 117(1):58. PMID: 36374343; PMCID: PMC9652280.
      Citations: 3     Fields:    
    2. Hartmann T, Magin S, Schramm A, T?ns AI, Gonz?lez RC, Henssen AG, Rahmann S, K?ster J. Detection and Validation of Circular DNA Fragments Using Nanopore Sequencing. Front Genet. 2022; 13:867018. PMID: 35711922; PMCID: PMC9195511.
      Citations: 2     
    3. Buehring B, Stervbo U, Babel N, Westhoff TH, Pourhassan M, Rahmann S, M?lder F, R?tten S, Trampisch U, Wirth R. Osteosarcopenia, an Asymmetrical Overlap of Two Connected Syndromes: Data from the OsteoSys Study. Nutrients. 2021 Oct 26; 13(11). PMID: 34836043; PMCID: PMC8618221.
      Citations: 6     Fields:    Translation:Humans
    4. Stervbo U, Babel N, M?lder F, Loyal L, Bacher P, Rahmann S. Rapid T-cell receptor interaction grouping with ting. Bioinformatics. 2021 Oct 25; 37(20):3444-3448. PMID: 33983394.
      Citations:    Fields:    
    5. Markowski J, Kempfer R, Kukalev A, Irastorza-Azcarate I, Loof G, Kehr B, Pombo A, Rahmann S, Schwarz RF. GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data. Bioinformatics. 2021 Oct 11; 37(19):3128-3135. PMID: 33830196; PMCID: PMC8504635.
      Citations: 2     Fields:    
    6. Schulz T, Wittler R, Rahmann S, Hach F, Stoye J. Detecting high-scoring local alignments in pangenome graphs. Bioinformatics. 2021 Aug 25; 37(16):2266-2274. PMID: 33532821; PMCID: PMC8388040.
      Citations: 2     Fields:    
    7. Zentgraf J, Rahmann S. Fast lightweight accurate xenograft sorting. Algorithms Mol Biol. 2021 Apr 02; 16(1):2. PMID: 33810805; PMCID: PMC8017614.
      Citations: 4     
    8. Subramaniam N, Bottek J, Thiebes S, Zec K, Kudla M, Soun C, de Dios Panal E, Lill JK, Pfennig A, Herrmann R, Bruderek K, Rahmann S, Brandau S, Johansson P, Reinhardt HC, Seiffert M, Bracht T, Sitek B, Engel DR, D?rig J. Proteomic and bioinformatic profiling of neutrophils in CLL reveals functional defects that predispose to bacterial infections. Blood Adv. 2021 03 09; 5(5):1259-1272. PMID: 33651101; PMCID: PMC7948268.
      Citations: 5     Fields:    Translation:HumansAnimalsCells
    9. Jablonski KP, Letcher B, Hall MB, Tomkins-Tinch CH, Sochat V, Forster J, Lee S, Kanitz A, Wilm A, Rahmann S, M?lder F, Twardziok SO, Holtgrewe M, Nahnsen S, K?ster J. Sustainable data analysis with Snakemake. F1000Res. 2021; 10:33. PMID: 34035898; PMCID: PMC8114187.
      Citations: 343     Fields:    
    10. Stervbo U, Rahmann S, Roch T, Westhoff TH, Babel N. Epitope similarity cannot explain the pre-formed T cell immunity towards structural SARS-CoV-2 proteins. Sci Rep. 2020 11 04; 10(1):18995. PMID: 33149224; PMCID: PMC7642385.
      Citations: 6     Fields:    Translation:HumansCellsPHPublic Health
    11. Mairinger F, Reis H, Goetz M, Hager T, Zaun G, Stuschke M, Schmid KW, Rahmann S, Wiesweg M, Kollmeier J, Misch D, Stephan-Falkenau S, Mairinger T, Walter RFH, Metzenmacher M, Eberhardt WEE, K?ster J, Aigner C, Darwiche K, Schuler M. Machine learning reveals a PD-L1-independent prediction of response to immunotherapy of non-small cell lung cancer by gene expression context. Eur J Cancer. 2020 11; 140:76-85. PMID: 33059196.
      Citations: 19     Fields:    Translation:Humans
    12. Horsthemke B, Rahmann S, Laurentino S, Cremers JF, T?ttelmann F, Czeloth K, Zitzmann M, Pohl E, Schr?der C, Berres S, Redmann K, Krallmann C, Schlatt S, Kliesch S, Gromoll J. A germ cell-specific ageing pattern in otherwise healthy men. Aging Cell. 2020 10; 19(10):e13242. PMID: 32951333; PMCID: PMC7576283.
      Citations: 17     Fields:    Translation:HumansCells
    13. Hood ME, Brachmann A, Bueker B, Guerreiro MA, Rahmann S, Begerow D. Meiotic recombination in the offspring of Microbotryum hybrids and its impact on pathogenicity. BMC Evol Biol. 2020 09 17; 20(1):123. PMID: 32942986; PMCID: PMC7499883.
      Citations:    Fields:    Translation:Animals
    14. Andreiuolo F, Mynarek M, Wohlers I, Rahmann S, Klein-Hitpass L, Velez-Char N, von Hoff K, Kortmann RD, Timmermann B, von Bueren A, Rutkowski S, Pietsch T, J?nger ST, D?rner E, Zur M?hlen A, Warmuth-Metz M. CDKN2A deletion in supratentorial ependymoma with RELA alteration indicates a dismal prognosis: a retrospective analysis of the HIT ependymoma trial cohort. Acta Neuropathol. 2020 09; 140(3):405-407. PMID: 32514758; PMCID: PMC7423858.
      Citations: 19     Fields:    Translation:Humans
    15. W?ste M, Leit?o E, Laurentino S, Horsthemke B, Rahmann S, Schr?der C. wg-blimp: an end-to-end analysis pipeline for whole genome bisulfite sequencing data. BMC Bioinformatics. 2020 May 01; 21(1):169. PMID: 32357829; PMCID: PMC7195798.
      Citations: 9     Fields:    Translation:HumansCells
    16. Mynarek M, Wohlers I, Velez-Char N, von Hoff K, Rutkowski S, Kortmann RD, Timmermann B, Rahmann S, Klein-Hitpass L, von Bueren AO, Pietsch T, J?nger ST, D?rner E, M?hlen AZ, Warmuth-Metz M. Improved risk-stratification for posterior fossa ependymoma of childhood considering clinical, histological and genetic features - a retrospective analysis of the HIT ependymoma trial cohort. Acta Neuropathol Commun. 2019 11 14; 7(1):181. PMID: 31727173; PMCID: PMC6857225.
      Citations: 14     Fields:    Translation:HumansCTClinical Trials
    17. Kalmbach A, Klein-Hitpass L, Ulz P, Heitzer E, Speicher MR, Rahmann S, Wieczorek D, Horsthemke B, Bramswig NC, Schr?der C, Nordstr?m K. Genome-Wide Analysis of the Nucleosome Landscape in Individuals with Coffin-Siris Syndrome. Cytogenet Genome Res. 2019; 159(1):1-11. PMID: 31658463.
      Citations: 2     Fields:    Translation:HumansCells
    18. Beisser D, Bock C, Hahn MW, Vos M, Sures B, Rahmann S, Boenigk J. Interaction-Specific Changes in the Transcriptome of Polynucleobacter asymbioticus Caused by Varying Protistan Communities. Front Microbiol. 2019; 10:1498. PMID: 31354646; PMCID: PMC6629928.
      Citations: 2     
    19. Stervbo U, Kaliszczyk S, Gayova L, Schweiger B, Hecht J, Rahmann S, Westhoff T, Nienen M, M?lder F, Kuchenbecker L, J?rchott K, Neumann AU, Reinke P, Thiel A, Babel N. The Role of Pre-existing Cross-Reactive Central Memory CD4 T-Cells in Vaccination With Previously Unseen Influenza Strains. Front Immunol. 2019; 10:593. PMID: 31019503; PMCID: PMC6458262.
      Citations: 15     Fields:    Translation:HumansCellsPHPublic Health
    20. Wiesweg M, Mairinger F, Reis H, Goetz M, Walter RFH, Hager T, Metzenmacher M, Eberhardt WEE, McCutcheon A, Stuschke M, Aigner C, Darwiche K, Schmid KW, Rahmann S, Schuler M, K?ster J. Machine learning-based predictors for immune checkpoint inhibitor therapy of non-small-cell lung cancer. Ann Oncol. 2019 04 01; 30(4):655-657. PMID: 30753264.
      Citations: 15     Fields:    Translation:Humans
    21. Wiesweg M, Kasper S, Worm K, Herold T, Reis H, Sara L, Metzenmacher M, Abendroth A, Wedemeyer HH, Helfritz FA, Stuschke M, Schumacher B, Markus P, Paul A, Rahmann S, Schmid KW, Schuler M, Darwiche K, Aigner C. Impact of RAS mutation subtype on clinical outcome-a cross-entity comparison of patients with advanced non-small cell lung cancer and colorectal cancer. Oncogene. 2019 04; 38(16):2953-2966. PMID: 30568222.
      Citations: 24     Fields:    Translation:Humans
    22. Ackermann S, Cartolano M, Hero B, Welte A, Kahlert Y, Roderwieser A, Bartenhagen C, Walter E, Gecht J, Volland R, Menon R, Heuckmann JM, Gartlgruber M, Hartlieb S, Henrich KO, Okonechnikov K, 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, Speleman F, O'Sullivan RJ, Thomas RK, Berthold F, Vandesompele J, Schramm A, Westermann F, Peifer M, Fischer M, Kerschke L, Altm?ller J, N?rnberg P, B?ttner R, Eggert A, Schulte JH. A mechanistic classification of clinical phenotypes in neuroblastoma. Science. 2018 12 07; 362(6419):1165-1170. PMID: 30523111; PMCID: PMC7875194.
      Citations: 137     Fields:    Translation:Humans
    23. Zeka F, Decock A, Van Goethem A, Vanderheyden K, Demuynck F, Lammens T, Helsmoortel HH, Noguera R, Berbegall AP, Schleiermacher G, Schramm A, Schulte JH, Rahmann S, 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, Vermeulen J, Combaret V, Laureys G, Bienertov?-Va?ku J, Maz?nek P. Circulating microRNA biomarkers for metastatic disease in neuroblastoma patients. JCI Insight. 2018 12 06; 3(23). PMID: 30518699; PMCID: PMC6328024.
      Citations: 11     Fields:    Translation:HumansAnimals
    24. Rahmann S, K?ster J. Snakemake-a scalable bioinformatics workflow engine. Bioinformatics. 2018 10 15; 34(20):3600. PMID: 29788404.
      Citations: 115     Fields:    
    25. Rahmann S, Bock C, Zimmermann S, Beisser D, Dinglinger SM, Engelskirchen S, Giesemann P, Klink S, Olefeld JL, Vos M, Boenigk J, Sures B. Silver stress differentially affects growth of phototrophic and heterotrophic chrysomonad flagellate populations. Environ Pollut. 2019 Jan; 244:314-322. PMID: 30343232.
      Citations: 1     Fields:    Translation:AnimalsCells
    26. Zamir E, Rahmann S, St?cker BK, K?ster J. Modeling and simulating networks of interdependent protein interactions. Integr Biol (Camb). 2018 05 21; 10(5):290-305. PMID: 29676773.
      Citations: 2     Fields:    Translation:Humans
    27. Rahmann S, Graupner N, Jensen M, Bock C, Marks S, Beisser D, Boenigk J. Evolution of heterotrophy in chrysophytes as reflected by comparative transcriptomics. FEMS Microbiol Ecol. 2018 04 01; 94(4). PMID: 29518196; PMCID: PMC6019013.
      Citations: 11     Fields:    Translation:AnimalsCells
    28. Rahmann S, Schulte M, K?ster J, Schramm A. Cancer evolution, mutations, and clonal selection in relapse neuroblastoma. Cell Tissue Res. 2018 May; 372(2):263-268. PMID: 29478075.
      Citations: 11     Fields:    Translation:HumansAnimalsCells
    29. Beygo J, Zeschnigk M, Klein-Hitpass L, Bargull M, Rahmann S, Horsthemke B, Leit?o E. Locus-Specific DNA Methylation Analysis by Targeted Deep Bisulfite Sequencing. Methods Mol Biol. 2018; 1767:351-366. PMID: 29524145.
      Citations: 11     Fields:    Translation:HumansAnimalsCells
    30. Timm H, Weigand H, Weiss M, Leese F, Rahmann S. ddrage: A data set generator to evaluate ddRADseq analysis software. Mol Ecol Resour. 2018 May; 18(3):681-690. PMID: 29194981.
      Citations: 1     Fields:    
    31. Timm H, Rahmann S, Beisser D, Graupner N, Grossmann L, Boenigk J. TaxMapper: an analysis tool, reference database and workflow for metatranscriptome analysis of eukaryotic microorganisms. BMC Genomics. 2017 Oct 16; 18(1):787. PMID: 29037173; PMCID: PMC5644092.
      Citations: 2     Fields:    Translation:Animals
    32. Horsch S, Kopczynski D, Kuthe E, Rahmann S, Baumbach JI, Rahnenf?hrer J. A detailed comparison of analysis processes for MCC-IMS data in disease classification-Automated methods can replace manual peak annotations. PLoS One. 2017; 12(9):e0184321. PMID: 28910313; PMCID: PMC5598980.
      Citations: 2     Fields:    Translation:Humans
    33. Rahmann S, Schr?der C. A hybrid parameter estimation algorithm for beta mixtures and applications to methylation state classification. Algorithms Mol Biol. 2017; 12:21. PMID: 28828033; PMCID: PMC5563068.
      Citations: 3     
    34. Wallner S, Schmitz G, Klein-Hitpass L, Sinha A, Heilmann-Heimbach S, Hoffmann P, Steffens M, Rahmann S, Schr?der C, Leit?o E, J?ckel KH, N?then MM, Ebert P, Horsthemke B. Regions of common inter-individual DNA methylation differences in human monocytes: genetic basis and potential function. Epigenetics Chromatin. 2017 07 26; 10(1):37. PMID: 28747224; PMCID: PMC5530492.
      Citations: 8     Fields:    Translation:HumansCells
    35. Beisser D, Graupner N, Bock C, Wodniok S, Grossmann L, Vos M, Sures B, Rahmann S, Boenigk J. Comprehensive transcriptome analysis provides new insights into nutritional strategies and phylogenetic relationships of chrysophytes. PeerJ. 2017; 5:e2832. PMID: 28097055; PMCID: PMC5228505.
      Citations: 15     Fields:    
    36. Beisser D, Rahmann S, Kaschani F, Graupner N, Grossmann L, Jensen M, Ninck S, Schulz F, Boenigk J, Kaiser M. Quantitative Proteomics Reveals Ecophysiological Effects of Light and Silver Stress on the Mixotrophic Protist Poterioochromonas malhamensis. PLoS One. 2017; 12(1):e0168183. PMID: 28056027; PMCID: PMC5215829.
      Citations: 4     Fields:    Translation:AnimalsCells
    37. Grossmann L, Beisser D, Bock C, Chatzinotas A, Jensen M, Psenner R, Rahmann S, Wodniok S, Boenigk J, Preisfeld A. Trade-off between taxon diversity and functional diversity in European lake ecosystems. Mol Ecol. 2016 Dec; 25(23):5876-5888. PMID: 27747959.
      Citations: 7     Fields:    Translation:AnimalsCells
    38. Wallner S, Rahmann S, Richter AS, Manke T, Arrigoni L, Barann M, Rosenstiel P, Brors B, Zipprich G, Klein-Hitpass L, Attenberger C, Schmitz G, Schr?der C, Leit?o E, Berulava T, Haak C, Bei?er D, B?nisch U, Fr?hler S, Klironomos F, Chen W, Rajewsky N, M?ller F, Ebert P, Lengauer T, Gasparoni G, Nordstr?m K, Walter J, Felder B, Horsthemke B. Epigenetic dynamics of monocyte-to-macrophage differentiation. Epigenetics Chromatin. 2016; 9:33. PMID: 27478504; PMCID: PMC4967341.
      Citations: 43     Fields:    
    39. Rahmann S, St?cker BK, K?ster J. SimLoRD: Simulation of Long Read Data. Bioinformatics. 2016 09 01; 32(17):2704-6. PMID: 27166244.
      Citations: 37     Fields:    
    40. Oldenburg M, Chebrolu C, Beisser D, Kolter J, Sigmund AM, Hochrein H, Rahmann S, Wagner H, Henneke P, Hornung V, Buer J, Kirschning CJ, Kr?ger A, Steinmann J, Sch?fer S. Human TLR8 senses UR/URR motifs in bacterial and mitochondrial RNA. EMBO Rep. 2015 Dec; 16(12):1656-63. PMID: 26545385; PMCID: PMC4687425.
      Citations: 50     Fields:    Translation:HumansAnimalsCells
    41. Johansson P, Bergmann A, Rahmann S, Wohlers I, Przekopowitz M, Seifert M, Tschurtschenthaler G, Webersinke G, Siebert R, Klein-Hitpass L, Scholtysik R, J?ger U, D?hrsen U, D?rig J, K?ppers R. Recurrent alterations of TNFAIP3 (A20) in T-cell large granular lymphocytic leukemia. Int J Cancer. 2016 Jan 01; 138(1):121-4. PMID: 26199174.
      Citations: 20     Fields:    Translation:Humans
    42. Schramm A, Assenov Y, Althoff K, Peifer M, Mahlow E, Odersky A, Beisser D, Ernst C, Henssen AG, Stephan H, Heukamp L, Engesser A, Kahlert Y, Theissen J, Hero B, Roels F, 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, K?ster J, Schr?der C, Altm?ller J, N?rnberg P, Astrahantseff K, Eggert A, Schulte JH. Mutational dynamics between primary and relapse neuroblastomas. Nat Genet. 2015 Aug; 47(8):872-7. PMID: 26121086.
      Citations: 145     Fields:    Translation:HumansCells
    43. Kopczynski D, Rahmann S. An online peak extraction algorithm for ion mobility spectrometry data. Algorithms Mol Biol. 2015; 10:17. PMID: 26157473; PMCID: PMC4495807.
      Citations: 2     
    44. Berulava T, Rahmann S, Rademacher K, Klein-Hitpass L, Horsthemke B. N6-adenosine methylation in MiRNAs. PLoS One. 2015; 10(2):e0118438. PMID: 25723394; PMCID: PMC4344304.
      Citations: 63     Fields:    Translation:HumansCells
    45. Rahmann S, K?ster J. Massively parallel read mapping on GPUs with the q-group index and PEANUT. PeerJ. 2014; 2:e606. PMID: 25289191; PMCID: PMC4184027.
      Citations: 1     Fields:    
    46. Boenigk J, Beisser D, Zimmermann S, Bock C, Jakobi J, Grabner D, Rahmann S, Barcikowski S, Sures B, Gro?mann L. Effects of silver nitrate and silver nanoparticles on a planktonic community: general trends after short-term exposure. PLoS One. 2014; 9(4):e95340. PMID: 24755991; PMCID: PMC3995725.
      Citations: 15     Fields:    Translation:CellsPHPublic Health
    47. Pietsch T, Wohlers I, Goschzik T, Dreschmann V, Denkhaus D, Rahmann S, Klein-Hitpass L, D?rner E. Supratentorial ependymomas of childhood carry C11orf95-RELA fusions leading to pathological activation of the NF-?B signaling pathway. Acta Neuropathol. 2014 Apr; 127(4):609-11. PMID: 24562983.
      Citations: 55     Fields:    Translation:HumansCells
    48. D'Addario M, Kopczynski D, Rahmann S, Baumbach JI. A modular computational framework for automated peak extraction from ion mobility spectra. BMC Bioinformatics. 2014 Jan 22; 15:25. PMID: 24450533; PMCID: PMC3930762.
      Citations: 6     Fields:    Translation:Humans
    49. Beleggia F, Pohl E, Li Y, Milz E, Martin M, Thiele H, Alanay Y, Klein-Hitpass L, 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, Hayek J, Houge G, Kilic E, Kuechler A, Lyonnet S, Mari F, Marozza A, Mikat B, Morin G, Morice-Picard F, Ozkinay F, Rauch A, Renieri A, Tinschert S, Utine GE, Vilain C, Vivarelli R, Zweier C, Rahmann S, Vermeesch J, Zeschnigk M, Wollnik B, Wieczorek D, B?gershausen N, Steiner-Haldenst?tt S, Altm?ller J, Kayserili H, B?hringer S, Guill?n-Navarro E, Simsek-Kiper P?, L?pez-Gonz?lez V, Mathieu Dramard M, N?rnberg P, L?decke HJ. A comprehensive molecular study on Coffin-Siris and Nicolaides-Baraitser syndromes identifies a broad molecular and clinical spectrum converging on altered chromatin remodeling. Hum Mol Genet. 2013 Dec 20; 22(25):5121-35. PMID: 23906836.
      Citations: 99     Fields:    Translation:Humans
    50. Neveling K, Czeschik JC, Albrecht B, Callewaert B, von Deimling F, Hehr A, Falkenberg Smeland M, 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, Wieczorek D, Voigt C, M?garban? A, K?nig R, L?decke HJ. Oto-facial syndrome and esophageal atresia, intellectual disability and zygomatic anomalies - expanding the phenotypes associated with EFTUD2 mutations. Orphanet J Rare Dis. 2013 Jul 24; 8:110. PMID: 23879989; PMCID: PMC3727992.
      Citations: 21     Fields:    Translation:Humans
    51. Martin M, Temming P, Rahmann S, Metz C, Bornfeld N, van de Nes J, Klein-Hitpass L, Hinnebusch AG, Horsthemke B, Lohmann DR, Zeschnigk M, Ma?h?fer L. Exome sequencing identifies recurrent somatic mutations in EIF1AX and SF3B1 in uveal melanoma with disomy 3. Nat Genet. 2013 Aug; 45(8):933-6. PMID: 23793026; PMCID: PMC4307600.
      Citations: 236     Fields:    Translation:HumansCells
    52. Kopczynski D, D'Addario M, Rahmann S, Hauschild AC, Baumbach JI, Baumbach J. Peak detection method evaluation for ion mobility spectrometry by using machine learning approaches. Metabolites. 2013 Apr 16; 3(2):277-93. PMID: 24957992; PMCID: PMC3901270.
      Citations: 6     
    53. Allhoff M, Martin M, Costa IG, Rahmann S, Marschall T, Sch?nhuth A. Discovering motifs that induce sequencing errors. BMC Bioinformatics. 2013; 14 Suppl 5:S1. PMID: 23735080; PMCID: PMC3622629.
      Citations: 32     Fields:    Translation:HumansCells
    54. 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, Martin M, Rahmann S, Schweiger B, Splitt M, Wollnik B, Zeschnigk M, Wieczorek D, Czeschik JC, L?pez-Gonz?lez V, L?decke HJ. Clinical and mutation data in 12 patients with the clinical diagnosis of Nager syndrome. Hum Genet. 2013 Aug; 132(8):885-98. PMID: 23568615.
      Citations: 30     Fields:    Translation:HumansCells
    55. Marschall T, Herms I, Kaltenbach HM, Rahmann S. Probabilistic arithmetic automata and their applications. IEEE/ACM Trans Comput Biol Bioinform. 2012 Nov-Dec; 9(6):1737-50. PMID: 22868683.
      Citations: 4     Fields:    
    56. Rahmann S, Martin M, Schulte JH, Marschall T, Schramm A, K?ster J. Identifying transcriptional miRNA biomarkers by integrating high-throughput sequencing and real-time PCR data. Methods. 2013 Jan; 59(1):154-63. PMID: 23098880.
      Citations: 3     Fields:    Translation:Humans
    57. Schramm A, Schowe B, Fielitz K, Heilmann M, Martin M, Marschall T, Vandesompele J, Vermeulen J, de Preter K, Koster J, Versteeg R, Noguera R, Speleman F, Rahmann S, Eggert A, Morik K, Schulte JH, K?ster J. Exon-level expression analyses identify MYCN and NTRK1 as major determinants of alternative exon usage and robustly predict primary neuroblastoma outcome. Br J Cancer. 2012 Oct 09; 107(8):1409-17. PMID: 23047593; PMCID: PMC3494449.
      Citations: 16     Fields:    Translation:HumansCells
    58. Schramm A, Marschall T, Martin M, Schwermer M, Fielitz K, Barann M, Esser D, Rosenstiel P, Rahmann S, Eggert A, Schulte JH, K?ster J, B?chel G. 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. Int J Cancer. 2013 Feb 01; 132(3):E106-15. PMID: 22907398.
      Citations: 14     Fields:    Translation:HumansAnimalsCells
    59. Rahmann S, K?ster J. Snakemake--a scalable bioinformatics workflow engine. Bioinformatics. 2012 Oct 01; 28(19):2520-2. PMID: 22908215.
      Citations: 950     Fields:    
    60. Zamir E, Rahmann S, K?ster J. Efficiently mining protein interaction dependencies from large text corpora. Integr Biol (Camb). 2012 Jul; 4(7):805-12. PMID: 22706334.
      Citations: 3     Fields:    Translation:HumansCells
    61. Herms I, Rahmann S, Hartmann AK, Wolfsheimer S. Accurate statistics for local sequence alignment with position-dependent scoring by rare-event sampling. BMC Bioinformatics. 2011 Feb 03; 12:47. PMID: 21291566; PMCID: PMC3042914.
      Citations:    Fields:    
    62. Rahmann S, Weigel W, Rabsch W, Fruth A, Ron E, Gunzer F, Dandekar T, Dobrindt U, Friedrich T, Hacker J, M?ller T. High-throughput microarray technology in diagnostics of enterobacteria based on genome-wide probe selection and regression analysis. BMC Genomics. 2010 Oct 21; 11:591. PMID: 20964857; PMCID: PMC3017858.
      Citations: 4     Fields:    Translation:Cells
    63. Wittkop T, Emig D, Lange S, Rahmann S, Albrecht M, Morris JH, Stoye J, Baumbach J, B?cker S. Partitioning biological data with transitivity clustering. Nat Methods. 2010 Jun; 7(6):419-20. PMID: 20508635.
      Citations: 39     Fields:    Translation:HumansAnimals
    64. Schulte JH, Marschall T, Martin M, Rosenstiel P, Mestdagh P, Schlierf S, Thor T, Vandesompele J, Eggert A, Schreiber S, Rahmann S, Schramm A. Deep sequencing reveals differential expression of microRNAs in favorable versus unfavorable neuroblastoma. Nucleic Acids Res. 2010 Sep; 38(17):5919-28. PMID: 20466808; PMCID: PMC2943620.
      Citations: 88     Fields:    Translation:HumansCells
    65. Wittkop T, Rahmann S, Baumbach J. Efficient online transcription factor binding site adjustment by integrating transitive graph projection with MoRAine 2.0. J Integr Bioinform. 2010 Mar 25; 7(3). PMID: 20375458.
      Citations:    Fields:    Translation:Cells
    66. Schwarz R, Seibel PN, Rahmann S, Schoen C, Huenerberg M, Dandekar T, Karchin R, M?ller-Reible C, Schultz J, M?ller T. Detecting species-site dependencies in large multiple sequence alignments. Nucleic Acids Res. 2009 Oct; 37(18):5959-68. PMID: 19661281; PMCID: PMC2764451.
      Citations: 9     Fields:    
    67. Marschall T, Rahmann S. Efficient exact motif discovery. Bioinformatics. 2009 Jun 15; 25(12):i356-64. PMID: 19478010; PMCID: PMC2687942.
      Citations: 15     Fields:    Translation:Cells
    68. Martin M, Betzl G, Kalbe A, Sirsch C, Buiting K, Gross S, Fritzilas E, Frey B, Rahmann S, Horsthemke B, Zeschnigk M. Massive parallel bisulfite sequencing of CG-rich DNA fragments reveals that methylation of many X-chromosomal CpG islands in female blood DNA is incomplete. Hum Mol Genet. 2009 Apr 15; 18(8):1439-48. PMID: 19223391.
      Citations: 19     Fields:    Translation:HumansCells
    69. Baumbach J, Rahmann S, Tauch A. Reliable transfer of transcriptional gene regulatory networks between taxonomically related organisms. BMC Syst Biol. 2009 Jan 15; 3:8. PMID: 19146695; PMCID: PMC2653031.
      Citations: 14     Fields:    Translation:Cells
    70. Baumbach J, Tauch A, Rahmann S. Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks. Brief Bioinform. 2009 Jan; 10(1):75-83. PMID: 19074493; PMCID: PMC2638629.
      Citations: 7     Fields:    Translation:Cells
    71. Rahmann S, Wolf M, Fritzilas E, Kneitz S, Dandekar T, Engelmann JC, Schultz J, M?ller T. Modelling cross-hybridization on phylogenetic DNA microarrays increases the detection power of closely related species. Mol Ecol Resour. 2009 Jan; 9(1):83-93. PMID: 21564570.
      Citations: 11     Fields:    
    72. Baumbach J, Wittkop T, Weile J, Kohl T, Rahmann S. MoRAine--a web server for fast computational transcription factor binding motif re-annotation. J Integr Bioinform. 2008 Aug 25; 5(2). PMID: 20134062.
      Citations: 5     Fields:    Translation:Cells
    73. Pape UJ, Rahmann S, Sun F, Vingron M. Compound poisson approximation of the number of occurrences of a position frequency matrix (PFM) on both strands. J Comput Biol. 2008 Jul-Aug; 15(6):547-64. PMID: 18631020; PMCID: PMC2607244.
      Citations: 6     Fields:    Translation:Cells
    74. Rahmann S, de Carvalho SA. Better genechip microarray layouts by combining probe placement and embedding. J Bioinform Comput Biol. 2008 Jun; 6(3):623-41. PMID: 18574866.
      Citations:    Fields:    
    75. Pape UJ, Rahmann S, Vingron M. Natural similarity measures between position frequency matrices with an application to clustering. Bioinformatics. 2008 Feb 01; 24(3):350-7. PMID: 18174183.
      Citations: 30     Fields:    Translation:Cells
    76. Neuweger H, Baumbach J, Albaum S, Bekel T, Dondrup M, Oehm S, Rahmann S, Weile J, Goesmann A, H?ser AT, Kalinowski J, P?hler A. CoryneCenter - an online resource for the integrated analysis of corynebacterial genome and transcriptome data. BMC Syst Biol. 2007 Nov 22; 1:55. PMID: 18034885; PMCID: PMC2212648.
      Citations: 7     Fields:    Translation:Cells
    77. Wittkop T, Baumbach J, Lobo FP, Rahmann S. Large scale clustering of protein sequences with FORCE -A layout based heuristic for weighted cluster editing. BMC Bioinformatics. 2007 Oct 17; 8:396. PMID: 17941985; PMCID: PMC2147039.
      Citations: 25     Fields:    Translation:Cells
    78. Wittkop T, Baumbach J, Martin M, Truss A, Rahmann S, B?cker S. Exact and heuristic algorithms for weighted cluster editing. Comput Syst Bioinformatics Conf. 2007; 6:391-401. PMID: 17951842.
      Citations: 12     Fields:    
    79. Rahmann S, de Carvalho SA. Improving the design of genechip arrays by combining placement and embedding. Comput Syst Bioinformatics Conf. 2007; 6:417-27. PMID: 17951844.
      Citations:    Fields:    Translation:Cells
    80. Wolf M, Dandekar T, Pokorny A, Rahmann S, Gerlach D, M?ller T. Deep metazoan phylogeny. In Silico Biol. 2007; 7(2):151-4. PMID: 17688440.
      Citations: 3     Fields:    Translation:Animals
    81. Wittkop T, Rademacher K, Rahmann S, Brinkrolf K, Tauch A, Baumbach J. CoryneRegNet 3.0--an interactive systems biology platform for the analysis of gene regulatory networks in corynebacteria and Escherichia coli. J Biotechnol. 2007 Apr 30; 129(2):279-89. PMID: 17229482.
      Citations: 16     Fields:    Translation:Cells
    82. Schliep A, Rahmann S. Decoding non-unique oligonucleotide hybridization experiments of targets related by a phylogenetic tree. Bioinformatics. 2006 Jul 15; 22(14):e424-30. PMID: 16873503.
      Citations: 3     Fields:    Translation:Cells
    83. Brinkrolf K, Czaja LF, Rahmann S, Tauch A, Baumbach J. CoryneRegNet: an ontology-based data warehouse of corynebacterial transcription factors and regulatory networks. BMC Genomics. 2006 Feb 14; 7:24. PMID: 16478536; PMCID: PMC1382212.
      Citations: 23     Fields:    Translation:Cells
    84. Roepcke S, Grossmann S, Rahmann S, Vingron M. T-Reg Comparator: an analysis tool for the comparison of position weight matrices. Nucleic Acids Res. 2005 Jul 01; 33(Web Server issue):W438-41. PMID: 15980506; PMCID: PMC1160266.
      Citations: 20     Fields:    Translation:Cells
    85. Dieterich C, Rahmann S, Vingron M. Functional inference from non-random distributions of conserved predicted transcription factor binding sites. Bioinformatics. 2004 Aug 04; 20 Suppl 1:i109-15. PMID: 15262788.
      Citations: 5     Fields:    Translation:HumansAnimalsCells
    86. Klau GW, Rahmann S, Schliep A, Vingron M, Reinert K. Optimal robust non-unique probe selection using Integer Linear Programming. Bioinformatics. 2004 Aug 04; 20 Suppl 1:i186-93. PMID: 15262798.
      Citations: 6     Fields:    Translation:Cells
    87. Rahmann S, Dandekar T, Wolf M, M?ller T. Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta). BMC Evol Biol. 2004 Jun 28; 4:20. PMID: 15222898; PMCID: PMC449703.
      Citations: 15     Fields:    Translation:Animals
    88. Rahmann S, Gr?fe C. Mean and variance of the Gibbs free energy of oligonucleotides in the nearest neighbor model under varying conditions. Bioinformatics. 2004 Nov 22; 20(17):2928-33. PMID: 15201179.
      Citations: 1     Fields:    Translation:Cells
    89. Rahmann S, Schuster-B?ckler B, Schultz J. HMM Logos for visualization of protein families. BMC Bioinformatics. 2004 Jan 21; 5:7. PMID: 14736340; PMCID: PMC341448.
      Citations: 109     Fields:    Translation:Cells
    90. Niller HH, Salamon D, Rahmann S, Ilg K, Koroknai A, Schwarzmann F, Wolf H, B?n?ti F, Min?rovits J. A 30 kb region of the Epstein-Barr virus genome is colinear with the rearranged human immunoglobulin gene loci: implications for a "ping-pong evolution" model for persisting viruses and their hosts. A review. Acta Microbiol Immunol Hung. 2004; 51(4):469-84. PMID: 15704335.
      Citations: 4     Fields:    Translation:HumansCells
    91. Vingron M, Rahmann S, M?ller T. On the power of profiles for transcription factor binding site detection. Stat Appl Genet Mol Biol. 2003; 2:Article7. PMID: 16646785.
      Citations: 49     Fields:    
    92. Rahmann S. The shortest common supersequence problem in a microarray production setting. Bioinformatics. 2003 Oct; 19 Suppl 2:ii156-61. PMID: 14534185.
      Citations: 4     Fields:    Translation:Cells
    93. Rahmann S. Fast large scale oligonucleotide selection using the longest common factor approach. J Bioinform Comput Biol. 2003 Jul; 1(2):343-61. PMID: 15290776.
      Citations: 11     Fields:    Translation:Cells
    94. Rahmann S. Fast and sensitive probe selection for DNA chips using jumps in matching statistics. Proc IEEE Comput Soc Bioinform Conf. 2003; 2:57-64. PMID: 16452779.
      Citations: 4     Fields:    Translation:Cells
    95. Schliep A, Torney DC, Rahmann S. Group testing with DNA chips: generating designs and decoding experiments. Proc IEEE Comput Soc Bioinform Conf. 2003; 2:84-91. PMID: 16452782.
      Citations: 5     Fields:    Translation:Cells
    96. Rahmann S. Rapid large-scale oligonucleotide selection for microarrays. Proc IEEE Comput Soc Bioinform Conf. 2002; 1:54-63. PMID: 15838123.
      Citations: 7     Fields:    Translation:Cells

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