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OTP: An automatized system for managing and processing NGS data.
Reisinger E, Genthner L, Kerssemakers J, Kensche P, Borufka S, Jugold A, Kling A, Prinz M, Scholz I, Zipprich G, Eils R, Lawerenz C, Eils J. Reisinger E, et al. Among authors: kerssemakers j. J Biotechnol. 2017 Nov 10;261:53-62. doi: 10.1016/j.jbiotec.2017.08.006. Epub 2017 Aug 10. J Biotechnol. 2017. PMID: 28803971 Free article. Review.
Whole genome sequencing puts forward hypotheses on metastasis evolution and therapy in colorectal cancer.
Ishaque N, Abba ML, Hauser C, Patil N, Paramasivam N, Huebschmann D, Leupold JH, Balasubramanian GP, Kleinheinz K, Toprak UH, Hutter B, Benner A, Shavinskaya A, Zhou C, Gu Z, Kerssemakers J, Marx A, Moniuszko M, Kozlowski M, Reszec J, Niklinski J, Eils J, Schlesner M, Eils R, Brors B, Allgayer H. Ishaque N, et al. Among authors: kerssemakers j. Nat Commun. 2018 Nov 14;9(1):4782. doi: 10.1038/s41467-018-07041-z. Nat Commun. 2018. PMID: 30429477 Free PMC article.
Genomic footprints of activated telomere maintenance mechanisms in cancer.
Sieverling L, Hong C, Koser SD, Ginsbach P, Kleinheinz K, Hutter B, Braun DM, Cortés-Ciriano I, Xi R, Kabbe R, Park PJ, Eils R, Schlesner M; PCAWG-Structural Variation Working Group; Brors B, Rippe K, Jones DTW, Feuerbach L; PCAWG Consortium. Sieverling L, et al. Nat Commun. 2020 Feb 5;11(1):733. doi: 10.1038/s41467-019-13824-9. Nat Commun. 2020. PMID: 32024817 Free PMC article.
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.
Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, Shuai S, Lanzós A, Herrmann C, Maruvka YE, Shen C, Amin SB, Bandopadhayay P, Bertl J, Boroevich KA, Busanovich J, Carlevaro-Fita J, Chakravarty D, Chan CWY, Craft D, Dhingra P, Diamanti K, Fonseca NA, Gonzalez-Perez A, Guo Q, Hamilton MP, Haradhvala NJ, Hong C, Isaev K, Johnson TA, Juul M, Kahles A, Kahraman A, Kim Y, Komorowski J, Kumar K, Kumar S, Lee D, Lehmann KV, Li Y, Liu EM, Lochovsky L, Park K, Pich O, Roberts ND, Saksena G, Schumacher SE, Sidiropoulos N, Sieverling L, Sinnott-Armstrong N, Stewart C, Tamborero D, Tubio JMC, Umer HM, Uusküla-Reimand L, Wadelius C, Wadi L, Yao X, Zhang CZ, Zhang J, Haber JE, Hobolth A, Imielinski M, Kellis M, Lawrence MS, von Mering C, Nakagawa H, Raphael BJ, Rubin MA, Sander C, Stein LD, Stuart JM, Tsunoda T, Wheeler DA, Johnson R, Reimand J, Gerstein M, Khurana E, Campbell PJ, López-Bigas N; PCAWG Drivers and Functional Interpretation Working Group; PCAWG Structural Variation Working Group; Weischenfeldt J, Beroukhim R, Martincorena I, Pedersen JS, Getz G; PCAWG Consortium. Rheinbay E, et al. Nature. 2020 Feb;578(7793):102-111. doi: 10.1038/s41586-020-1965-x. Epub 2020 Feb 5. Nature. 2020. PMID: 32025015 Free PMC article.
Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas.
Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L; ICGC MMML-Seq consortium; ICGC DE-Mining consortium; BLUEPRINT consortium; Küppers R, Schlesner M, Siebert R. Hübschmann D, et al. Among authors: kerssemakers jna. Leukemia. 2021 Jul;35(7):2002-2016. doi: 10.1038/s41375-021-01251-z. Epub 2021 May 5. Leukemia. 2021. PMID: 33953289 Free PMC article.
The genomic and transcriptional landscape of primary central nervous system lymphoma.
Radke J, Ishaque N, Koll R, Gu Z, Schumann E, Sieverling L, Uhrig S, Hübschmann D, Toprak UH, López C, Hostench XP, Borgoni S, Juraeva D, Pritsch F, Paramasivam N, Balasubramanian GP, Schlesner M, Sahay S, Weniger M, Pehl D, Radbruch H, Osterloh A, Korfel A, Misch M, Onken J, Faust K, Vajkoczy P, Moskopp D, Wang Y, Jödicke A, Trümper L, Anagnostopoulos I, Lenze D, Küppers R, Hummel M, Schmitt CA, Wiestler OD, Wolf S, Unterberg A, Eils R, Herold-Mende C, Brors B; ICGC MMML-Seq Consortium; Siebert R, Wiemann S, Heppner FL. Radke J, et al. Nat Commun. 2022 May 10;13(1):2558. doi: 10.1038/s41467-022-30050-y. Nat Commun. 2022. PMID: 35538064 Free PMC article.
Author Correction: Genomic footprints of activated telomere maintenance mechanisms in cancer.
Sieverling L, Hong C, Koser SD, Ginsbach P, Kleinheinz K, Hutter B, Braun DM, Cortés-Ciriano I, Xi R, Kabbe R, Park PJ, Eils R, Schlesner M; PCAWG-Structural Variation Working Group; Brors B, Rippe K, Jones DTW, Feuerbach L; PCAWG Consortium. Sieverling L, et al. Nat Commun. 2022 Dec 8;13(1):7574. doi: 10.1038/s41467-022-32328-7. Nat Commun. 2022. PMID: 36481818 Free PMC article. No abstract available.
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