Next Generation Sequencing Competence Network

Next Generation Sequencing Competence Network

e.g. CCGA
(min 2 characters)

Johannes Köster

Dr.
University of Duisburg-Essen
Genome Informatics
Virchowstraße 183, 45147 Essen, Germany
Essen 45147
+49 201 7231908
Download vCard

    Collapse Bibliographic 
    Collapse selected publications
    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.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    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. Bergkamp ND, van Senten JR, Brink HJ, Bebelman MP, van den Bor J, ?obanoglu TS, Dinkla K, K?ster J, Klau G, Siderius M, Smit MJ. A virally encoded GPCR drives glioblastoma through feed-forward activation of the SK1-S1P1 signaling axis. Sci Signal. 2023 08 15; 16(798):eade6737. PMID: 37582160.
      Citations:    Fields:    Translation:HumansCells
    2. Hartmann T, Schr?der C, Kuthe E, L?hnemann D, K?ster J. Insane in the vembrane: filtering and transforming VCF/BCF files. Bioinformatics. 2023 01 01; 39(1). PMID: 36519840; PMCID: PMC9825764.
      Citations:    Fields:    Translation:Humans
    3. Falkenhorst J, Grunewald S, Krzeciesa D, Herold T, Ketzer J, Christoff M, Hamacher R, Kostbade K, Treckmann J, K?ster J, Farzaliyev F, Fletcher BS, Dieckmann N, Kaths M, M?hlenberg T, Schildhaus HU, Bauer S. Plasma Sequencing for Patients with GIST-Limitations and Opportunities in an Academic Setting. Cancers (Basel). 2022 Nov 09; 14(22). PMID: 36428589.
      Citations:    
    4. 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     
    5. McHardy AC, L?hnemann D, K?ster J, Fischer U, Borkhardt A, Sch?nhuth A. Accurate and scalable variant calling from single cell DNA sequencing data with ProSolo. Nat Commun. 2021 11 18; 12(1):6744. PMID: 34795237; PMCID: PMC8602313.
      Citations: 6     Fields:    Translation:Humans
    6. Cui Y, Wang Z, Liao X, Peng S, Tang T, Huang C, Yang C, K?ster J. VISPR-online: a web-based interactive tool to visualize CRISPR screening experiments. BMC Bioinformatics. 2021 Jun 24; 22(1):344. PMID: 34167459; PMCID: PMC8223366.
      Citations:    Fields:    Translation:Cells
    7. Cormier MJ, Belyeu JR, Pedersen BS, Brown J, Quinlan AR, K?ster J. Go Get Data (GGD) is a framework that facilitates reproducible access to genomic data. Nat Commun. 2021 04 12; 12(1):2151. PMID: 33846313; PMCID: PMC8041854.
      Citations: 8     Fields:    
    8. 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:    
    9. 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
    10. Such L, Zhao F, Liu D, Thier B, Le-Trilling VTK, Sucker A, Coch C, Pieper N, Howe S, Bhat H, Kalkavan H, Ritter C, Brinkhaus R, Ugurel S, Seifert U, Dittmer U, Schuler M, Lang KS, Kufer TA, Hartmann G, Horn S, Ferrone S, Liu D, Van Allen EM, Schadendorf D, Griewank K, Trilling M, Paschen A, K?ster J, Becker JC. Targeting the innate immunoreceptor RIG-I overcomes melanoma-intrinsic resistance to T cell immunotherapy. J Clin Invest. 2020 08 03; 130(8):4266-4281. PMID: 32427578; PMCID: PMC7410049.
      Citations: 27     Fields:    Translation:HumansAnimalsCells
    11. Dijkstra LJ, K?ster J, Marschall T, Sch?nhuth A. Varlociraptor: enhancing sensitivity and controlling false discovery rate in somatic indel discovery. Genome Biol. 2020 04 28; 21(1):98. PMID: 32345333; PMCID: PMC7187499.
      Citations: 9     Fields:    Translation:Humans
    12. Szczurek E, McCarthy DJ, Hicks SC, Vallejos CA, Campbell KR, Beerenwinkel N, Mahfouz A, Pinello L, Skums P, Stamatakis A, Attolini CS, Aparicio S, Baaijens J, Balvert M, Barbanson B, Cappuccio A, Corleone G, Dutilh BE, Florescu M, Guryev V, Holmer R, Jahn K, Lobo TJ, Keizer EM, Khatri I, Kielbasa SM, Korbel JO, Kozlov AM, Kuo TH, Lelieveldt BPF, Mandoiu II, Marioni JC, Niknejad A, Raczkowski L, Reinders M, Ridder J, Somarakis A, Stegle O, Yang H, Zelikovsky A, McHardy AC, Raphael BJ, Shah SP, L?hnemann D, K?ster J, Robinson MD, Marschall T, M?lder F, Saliba AE, Theis FJ, Sch?nhuth A, Raczkowska A. Eleven grand challenges in single-cell data science. Genome Biol. 2020 02 07; 21(1):31. PMID: 32033589; PMCID: PMC7007675.
      Citations: 367     Fields:    Translation:HumansAnimals
    13. Baaijens JA, Van der Roest B, Stougie L, K?ster J, Sch?nhuth A. Full-length de novo viral quasispecies assembly through variation graph construction. Bioinformatics. 2019 12 15; 35(24):5086-5094. PMID: 31147688.
      Citations: 12     Fields:    
    14. Brown M, Liu XS, K?ster J. A Bayesian model for single cell transcript expression analysis on MERFISH data. Bioinformatics. 2019 Jul 01; 35(13):2347. PMID: 30358813; PMCID: PMC6596888.
      Citations:    Fields:    
    15. Brown M, Liu XS, K?ster J. A Bayesian model for single cell transcript expression analysis on MERFISH data. Bioinformatics. 2019 03 15; 35(6):995-1001. PMID: 30875429; PMCID: PMC6419903.
      Citations: 3     Fields:    Translation:Cells
    16. Rahmann S, K?ster J. Snakemake-a scalable bioinformatics workflow engine. Bioinformatics. 2018 10 15; 34(20):3600. PMID: 29788404.
      Citations: 115     Fields:    
    17. Dale R, Chapman BA, Rowe J, Tomkins-Tinch CH, Bioconda Team, Gr?ning B, Sj?din A, Valieris R, K?ster J. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 07; 15(7):475-476. PMID: 29967506.
      Citations: 365     Fields:    
    18. Chilton J, Dale R, Soranzo N, van den Beek M, Goecks J, Backofen R, Nekrutenko A, Taylor J, Gr?ning B, K?ster J. Practical Computational Reproducibility in the Life Sciences. Cell Syst. 2018 06 27; 6(6):631-635. PMID: 29953862; PMCID: PMC6263957.
      Citations: 43     Fields:    Translation:Humans
    19. 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
    20. Cornwell M, Vangala M, Taing L, Herbert Z, Li B, Sun H, Li T, Zhang J, Qiu X, Pun M, Jeselsohn R, Brown M, Liu XS, Long HW, K?ster J. VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis. BMC Bioinformatics. 2018 04 12; 19(1):135. PMID: 29649993; PMCID: PMC5897949.
      Citations: 94     Fields:    Translation:Cells
    21. 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
    22. Townsend EC, Murakami MA, Christodoulou A, Christie AL, DeSouza TA, Morgan EA, Kallgren SP, Liu H, Wu SC, Plana O, Montero J, Stevenson KE, Rao P, Vadhi R, Andreeff M, Armand P, Ballen KK, Barzaghi-Rinaudo P, Cahill S, Clark RA, Cooke VG, Davids MS, DeAngelo DJ, Dorfman DM, Eaton H, Ebert BL, Etchin J, Firestone B, Fisher DC, Freedman AS, Galinsky IA, Gao H, Garcia JS, Garnache-Ottou F, Graubert TA, Gutierrez A, Halilovic E, Harris MH, Herbert ZT, Horwitz SM, Inghirami G, Intlekofer AM, Ito M, Izraeli S, Jacobsen ED, Jacobson CA, Jeremias I, Kelliher MA, Koch R, Konopleva M, Kopp N, Kornblau SM, Kung AL, Kupper TS, LeBoeuf NR, LaCasce AS, Lees E, Li LS, Look AT, Murakami M, Muschen M, Neuberg D, Ng SY, Odejide OO, Orkin SH, Paquette RR, Place AE, Roderick JE, Ryan JA, Sallan SE, Shoji B, Silverman LB, Soiffer RJ, Steensma DP, Stegmaier K, Stone RM, Tamburini J, Thorner AR, van Hummelen P, Wadleigh M, Wiesmann M, Weng AP, Wuerthner JU, Williams DA, Wollison BM, Lane AA, Letai A, Bertagnolli MM, Ritz J, Brown M, Long H, Aster JC, Shipp MA, Griffin JD, Weinstock DM, K?ster J, Jeay S. The Public Repository of Xenografts Enables Discovery and Randomized Phase II-like Trials in Mice. Cancer Cell. 2016 07 11; 30(1):183. PMID: 27479034.
      Citations: 37     Fields:    
    23. Ma J, Qin Q, Hu S, Li W, Chen C, Cao Q, Wang J, Mei S, Liu Q, Xu H, Liu XS, K?ster J. CRISPR-DO for genome-wide CRISPR design and optimization. Bioinformatics. 2016 11 01; 32(21):3336-3338. PMID: 27402906; PMCID: PMC6095119.
      Citations: 26     Fields:    Translation:HumansAnimalsCells
    24. 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:    
    25. Townsend EC, Murakami MA, Christodoulou A, Christie AL, DeSouza TA, Morgan EA, Kallgren SP, Liu H, Wu SC, Plana O, Montero J, Stevenson KE, Rao P, Vadhi R, Andreeff M, Armand P, Ballen KK, Barzaghi-Rinaudo P, Cahill S, Clark RA, Cooke VG, Davids MS, DeAngelo DJ, Dorfman DM, Eaton H, Ebert BL, Etchin J, Firestone B, Fisher DC, Freedman AS, Galinsky IA, Gao H, Garcia JS, Graubert TA, Gutierrez A, Halilovic E, Harris MH, Herbert ZT, Horwitz SM, Inghirami G, Intlekofer AM, Ito M, Izraeli S, Jacobsen ED, Jacobson CA, Kelliher MA, Koch R, Konopleva M, Kopp N, Kornblau SM, Kung AL, Kupper TS, LeBoeuf NR, LaCasce AS, Lees E, Li LS, Look AT, Murakami M, Muschen M, Neuberg D, Ng SY, Odejide OO, Orkin SH, Paquette RR, Place AE, Roderick JE, Ryan JA, Sallan SE, Shoji B, Silverman LB, Soiffer RJ, Steensma DP, Stegmaier K, Stone RM, Thorner AR, van Hummelen P, Wadleigh M, Wiesmann M, Weng AP, Wuerthner JU, Williams DA, Wollison BM, Lane AA, Letai A, Bertagnolli MM, Ritz J, Brown M, Long H, Aster JC, Shipp MA, Griffin JD, Weinstock DM, K?ster J, Garnache-Ottou F, Jeay S, Jeremias I, Tamburini J. The Public Repository of Xenografts Enables Discovery and Randomized Phase II-like Trials in Mice. Cancer Cell. 2016 04 11; 29(4):574-586. PMID: 27070704; PMCID: PMC5177991.
      Citations: 134     Fields:    Translation:HumansAnimalsCells
    26. Li W, Xu H, Chen CH, Xiao T, Liu JS, Brown M, Liu XS, K?ster J. Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR. Genome Biol. 2015 Dec 16; 16:281. PMID: 26673418; PMCID: PMC4699372.
      Citations: 193     Fields:    
    27. K?ster J. Rust-Bio: a fast and safe bioinformatics library. Bioinformatics. 2016 Feb 01; 32(3):444-6. PMID: 26446134.
      Citations: 15     Fields:    Translation:Humans
    28. 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
    29. Schwermer M, Lee S, van Maerken T, Stephan H, Eggert A, Morik K, Schulte JH, Schramm A, K?ster J. Sensitivity to cdk1-inhibition is modulated by p53 status in preclinical models of embryonal tumors. Oncotarget. 2015 Jun 20; 6(17):15425-35. PMID: 26029996; PMCID: PMC4558161.
      Citations: 23     Fields:    Translation:HumansCells
    30. 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:    
    31. Althoff K, Beckers A, Odersky A, Mestdagh P, Bray IM, Bryan K, Vandesompele J, Speleman F, Stallings RL, Schramm A, Eggert A, Schulte JH, K?ster J, Spr?ssel A. MiR-137 functions as a tumor suppressor in neuroblastoma by downregulating KDM1A. Int J Cancer. 2013 Sep 01; 133(5):1064-73. PMID: 23400681.
      Citations: 51     Fields:    Translation:HumansCells
    32. 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
    33. 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
    34. Rahmann S, K?ster J. Snakemake--a scalable bioinformatics workflow engine. Bioinformatics. 2012 Oct 01; 28(19):2520-2. PMID: 22908215.
      Citations: 950     Fields:    
    35. 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
    36. Schulz A, Becker T, Kopf A, K?ster J, Kr?mker H. [Life threatening neuroleptic malignant syndrome due to olanzapine]. Psychiatr Prax. 2003 Jul; 30(5):279-82. PMID: 12872187.
      Citations: 1     Fields:    Translation:Humans

    Related

    Topics (180)

    Explore

    Co-Authors (3)

    Explore

    Same Department

    Explore
    © 2022 Next Generation Sequencing Competence Network (NGS-CN) | Imprint | Privacy