Publications

Total: 168 publication(s)

2020

Porubsky D, Sanders AD, Höps W, Hsieh P, Sulovari A, Li R, Mercuri L, Sorensen M, Murali SC, Gordon D, Cantsilieris S, Pollen AA, Ventura M, Antonacci F, Marschall T, Korbel JO, Eichler EE. (2020)

Recurrent inversion toggling and great ape genome evolution.

Nat. Genet. doi: 10.1038/s41588-020-0646-x
Europe PMC | doi

Korbel JO, Stegle O. (2020)

Effects of the COVID-19 pandemic on life scientists.

Genome Biol. 21(1) doi: 10.1186/s13059-020-02031-1
Europe PMC | doi

Schraivogel D, Gschwind AR, Milbank JH, Leonce DR, Jakob P, Mathur L, Korbel JO, Merten CA, Velten L, Steinmetz LM. (2020)

Targeted Perturb-seq enables genome-scale genetic screens in single cells.

Nat. Methods 17(6):629-635. doi: 10.1038/s41592-020-0837-5
Europe PMC | doi

Waszak SM, Robinson GW, Gudenas BL, Smith KS, Forget A, Kojic M, Garcia-Lopez J, Hadley J, Hamilton KV, Indersie E, Buchhalter I, Kerssemakers J, Jäger N, Sharma T, Rausch T, Sturm D, Kool M, Vasilyeva A, Jones DTW, Neale G, Tatevossian RG, Loew D, Lombard B, Rusch M, Nakitandwe J, Bendel A, Bowers DC, Chintagumpala M, Partap S, Gottardo NG, Crawford J, Rutkowski S, Eggen T, Smith A, Dufour C, Feychting M, Lannering B, Wesenberg F, Kjaerheim K, Andersen TV, Röösli M, Schüz J, Johansen C, Remke M, Puget S, Kuehni CE, Grotzer M, Ryzhova M, Witt O, Milde T, Pajtler KW, Brugieres L, Ellison DW, Orr BA, Korshunov A, Wainwright BJ, Gajjar A, Nichols KE, Lichter P, Pfister SM, Northcott PA, Korbel JO, Ayrault O. (2020)

Germline Elongator mutations in Sonic Hedgehog medulloblastoma.

Nature 580(7803):396-401. doi: 10.1038/s41586-020-2164-5
Europe PMC | doi

Drainas AP, Lambuta RA, Ivanova I, Serçin Ö, Sarropoulos I, Smith ML, Efthymiopoulos T, Raeder B, Stütz AM, Waszak SM, Mardin BR, Korbel JO. (2020)

Genome-wide screens implicate loss of cullin ring ligase 3 in persistent proliferation and genome instability in TP53-deficient cells.

Cell Rep 31(1) doi: 10.1016/j.celrep.2020.03.029
Europe PMC | doi

Li Y, Roberts ND, Wala JA, Shapira O, Schumacher SE, Kumar K, Khurana E, Waszak S, Korbel JO, Haber JE, Imielinski M, Imielinski M, Weischenfeldt J, Beroukhim R, Campbell PJ, Campbell PJ. (2020)

Patterns of somatic structural variation in human cancer genomes.

Nature 578(7793):112-121. doi: 10.1038/s41586-019-1913-9
Europe PMC | doi

PCAWG Transcriptome Core Group, Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H; PCAWG Transcriptome Working Group, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z; PCAWG Consortium. (2020)

Genomic basis for RNA alterations in cancer.

Nature 578(7793):129-136. doi: 10.1038/s41586-020-1970-0
Europe PMC | doi

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, Lanzós A, Shuai S, Maruvka YE, Herrmann C, Amin SB, Shen C, Bertl J, Bandopadhayay P, Busanovich J, Boroevich KA, Chakravarty D, Carlevaro-Fita J, Craft D, Chan CWY, Diamanti K, Dhingra P, Guo Q, Hamilton MP, Fonseca NA, Gonzalez-Perez A, Isaev K, Johnson TA, Haradhvala NJ, Hong C, Kahraman A, Kim Y, Juul M, Kahles A, Kumar S, Lee D, Komorowski J, Kumar K, Lochovsky L, Liu EM, Li Y, Lehmann KV, Saksena G, Roberts ND, Pich O, Park K, Sinnott-Armstrong N, Sieverling L, Sidiropoulos N, Schumacher SE, Umer HM, Tubio JMC, Tamborero D, Stewart C, Zhang CZ, Zhang J, Haber JE, Hobolth A, Uusküla-Reimand L, Wadelius C, Wadi L, Yao X, 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. (2020)

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.

Nature 578(7793):102-111. doi: 10.1038/s41586-020-1965-x
Europe PMC | doi

Aarestrup FM, Albeyatti A, Armitage WJ, Auffray C, Augello L, Balling R, Benhabiles N, Bertolini G, Bjaalie JG, Black M, Blomberg N, Bogaert P, Bubak M, Claerhout B, Clarke L, D'Errico G, De Meulder B, Forgo N, Di Meglio A, Gray AE, Gans-Combe C, Gyllenberg A, Gut I, Hjorth L, Hemmrich-Stanisak G, Jarmalaite S, Ioannidis Y, Kherif F, Kel A, Larue C, Korbel JO, Magalhaes L, Manneh-Vangramberen I, Laszlo M, Maas A, Oksvold P, Oxtoby NP, Morley-Fletcher E, Ohmann C, Riess O, Riper H, Perseil I, Pezoulas V, Sabatier P, Sanz F, Roca J, Rosenstiel P, Van den Bulcke M, Van Bussel J, Thomassen G, Tayeb M, Van Oyen H. (2020)

Towards a European health research and innovation cloud (HRIC).

Genome Med 12(1) doi: 10.1186/s13073-020-0713-z
Europe PMC | doi

Molnár-Gábor F, Korbel JO. (2020)

Genomic data sharing in Europe is Stumbling-Could a code of conduct prevent its fall?

EMBO Mol Med 12(3) doi: 10.15252/emmm.201911421
Europe PMC | doi

Lähnemann D, Köster J, Szczurek E, McCarthy DJ, Hicks SC, Robinson MD, Vallejos CA, Campbell KR, Beerenwinkel N, Mahfouz A, Pinello L, Skums P, Stamatakis A, Attolini CS, Aparicio S, Balvert M, Baaijens J, Cappuccio A, Barbanson B, Dutilh BE, Corleone G, Guryev V, Florescu M, Jahn K, Holmer R, Keizer EM, Lobo TJ, Kielbasa SM, Khatri I, Kozlov AM, Korbel JO, Mandoiu II, Marioni JC, Kuo TH, Lelieveldt BPF, Niknejad A, Raczkowski L, Marschall T, Mölder F, Saliba AE, Somarakis A, Reinders M, Ridder J, Yang H, Zelikovsky A, Stegle O, Theis FJ, Schönhuth A, Shah SP, Raphael BJ, McHardy AC. (2020)

Eleven grand challenges in single-cell data science.

Genome Biol. 21(1) doi: 10.1186/s13059-020-1926-6
Europe PMC | doi

Salgueiro L, Buccitelli C, Rowald K, Somogyi K, Kandala S, Korbel JO, Sotillo R. (2020)

Acquisition of chromosome instability is a mechanism to evade oncogene addiction.

EMBO Mol Med 12(3) doi: 10.15252/emmm.201910941
Europe PMC | doi

Cortés-Ciriano I, Lee JJ, Xi R, Jain D, Jung YL, Yang L, Gordenin D, Klimczak LJ, Zhang CZ, Pellman DS, PCAWG Structural Variation Working Group, Park PJ, PCAWG Consortium. (2020)

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing.

Nat. Genet. 52(3):331-341. doi: 10.1038/s41588-019-0576-7
Europe PMC | doi

Rodriguez-Martin B, Alvarez EG, Baez-Ortega A, Zamora J, Supek F, Demeulemeester J, Santamarina M, Ju YS, Temes J, Garcia-Souto D, Detering H, Li Y, Rodriguez-Castro J, Dueso-Barroso A, Bruzos AL, Blanco MG, Dentro SC, Ardeljan D, Contino G, Roberts ND, Tojo M, Edwards PAW, Zumalave S, Puiggròs M, Weischenfeldt J, Chen K, Chong Z, Wala JA, Lee EA, Butler A, Raine K, Schumacher SE, Monlong J, Waszak SM, Navarro FCP, Bourque G, Gerstein M, Maura F, Bolli N, Beroukhim R, Torrents D, Park PJ, Wedge DC, Fitzgerald RC, Van Loo P, Korbel JO, Martincorena I, Campbell PJ, PCAWG Structural Variation Working Group, Burns KH, Kazazian HH, Tubio JMC, PCAWG Consortium. (2020)

Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition.

Nat. Genet. 52(3):306-319. doi: 10.1038/s41588-019-0562-0
Europe PMC | doi

Yakneen S, Waszak SM, PCAWG Technical Working Group, Gertz M, Korbel JO, PCAWG Consortium. (2020)

Butler enables rapid cloud-based analysis of thousands of human genomes.

Nat. Biotechnol. 38(3):288-292. doi: 10.1038/s41587-019-0360-3
Europe PMC | doi

Yakneen S, Waszak SM, PCAWG Technical Working Group, Gertz M, Korbel JO; PCAWG Consortium. (2020)

Publisher Correction: Butler enables rapid cloud-based analysis of thousands of human genomes.

Nat. Biotechnol. doi: 10.1038/s41587-020-0448-9
Europe PMC | doi

Begemann M, Waszak SM, Robinson GW, Jäger N, Sharma T, Knopp C, Kraft F, Moser O, Mynarek M, Guerrini-Rousseau L, Brugieres L, Varlet P, Pietsch T, Bowers DC, Chintagumpala M, Korbel JO, Sahm F, Eggermann T, Rutkowski S, Northcott P, Gajjar A, Pfister SM, Elbracht M, Kurth I, Kontny U. (2020)

Germline GPR161 mutations predispose to pediatric medulloblastoma.

J. Clin. Oncol. 38(1):43-50. doi: 10.1200/JCO.19.00577
Europe PMC | doi


2019

Sanders AD, Meiers S, Ghareghani M, Porubsky D, Jeong H, van Vliet MACC, Rausch T, Richter-Pechańska P, Kunz JB, Jenni S, Bolognini D, Longo GMC, Raeder B, Kinanen V, Zimmermann J, Schrappe M, Benes V, Kulozik AE, Mardin BR, Bourquin JP, Bornhauser B, Korbel JO, Marschall T. (2019)

Single-cell analysis of structural variations and complex rearrangements with tri-channel processing.

Nat. Biotechnol. 38(3):343-354. doi: 10.1038/s41587-019-0366-x
Europe PMC | doi

Lambo S, Gröbner SN, Rausch T, Waszak SM, Schmidt C, Gorthi A, Romero JC, Mauermann M, Brabetz S, Krausert S, Buchhalter I, Koster J, Zwijnenburg DA, Sill M, Hübner JM, Schwalm B, Mack N, Hovestadt V, Ryzhova M, Chan JA, Papillon-Cavanagh S, Ho B, Landgraf P, Witt O, Milde T, Sahm F, Ecker J, Ellison DW, Sumerauer D, Darabi A, Orr BA, Wesseling P, Schittenhelm J, Haberler C, Figarella-Branger D, Gil-da-Costa MJ, Łastowska M, Remke M, Taylor MD, Hauser P, Pietsch T, Grajkowska W, Hasselblatt M, Masliah-Planchon J, Rigau V, Uro-Coste E, Bourdeaut F, Schüller U, Li XN, Wolf S, Alexandrescu S, Jabado N, Giangaspero F, Karajannis MA, Snuderl M, von Hoff K, Korbel JO, Jones DTW, von Deimling A, Pfister SM, Bishop AJR, Huang A, Lichter P, Korshunov A, Kool M. (2019)

The molecular landscape of ETMR at diagnosis and relapse.

Nature 576(7786):274-280. doi: 10.1038/s41586-019-1815-x
Europe PMC | doi

Sulovari A, Li R, Audano PA, Porubsky D, Vollger MR, Logsdon GA, Logsdon GA, Warren WC, Pollen AA, Chaisson MJP, Eichler EE. (2019)

Human-specific tandem repeat expansion and differential gene expression during primate evolution.

Proc. Natl. Acad. Sci. U.S.A. 116(46):23243-23253. doi: 10.1073/pnas.1912175116
Europe PMC | doi

Karoutas A, Szymanski W, Rausch T, Guhathakurta S, Rog-Zielinska EA, Peyronnet R, Seyfferth J, Chen HR, de Leeuw R, Herquel B, Kimura H, Mittler G, Kohl P, Medalia O, Korbel JO, Akhtar A. (2019)

The NSL complex maintains nuclear architecture stability via lamin A/C acetylation.

Nat. Cell Biol. 21(10):1248-1260. doi: 10.1038/s41556-019-0397-z
Europe PMC | doi

Bolognini D, Sanders A, Korbel JO, Magi A, Benes V, Rausch T. (2019)

VISOR: a versatile haplotype-aware structural variant simulator for short and long read sequencing.

Bioinformatics 36(4) doi: 10.1093/bioinformatics/btz719
Europe PMC | doi

Saunders G, Baudis M, Becker R, Beltran S, Béroud C, Birney E, Brooksbank C, Brunak S, Van den Bulcke M, Drysdale R, Capella-Gutierrez S, Flicek P, Florindi F, Goodhand P, Gut I, Holub P, Heringa J, Juty N, Hooyberghs J, Korbel JO, Keane TM, Leskosek B, Lappalainen I, Mayrhofer MT, Matthijs G, Navarro A, Metspalu A, Nyrönen T, Newhouse S, Persson B, Page A, Rambla J, Salgado D, Palotie A, Parkinson H, Valencia A, Varma S, Steinfelder E, Swertz MA, Blomberg N, Scollen S. (2019)

Author Correction: Leveraging European infrastructures to access 1 million human genomes by 2022.

Nat Rev Genet 20(11) doi: 10.1038/s41576-019-0178-3
Europe PMC | doi

Saunders G, Baudis M, Becker R, Beltran S, Béroud C, Birney E, Brooksbank C, Brunak S, Van den Bulcke M, Drysdale R, Capella-Gutierrez S, Flicek P, Florindi F, Goodhand P, Gut I, Holub P, Heringa J, Juty N, Hooyberghs J, Korbel JO, Keane TM, Leskosek B, Lappalainen I, Mayrhofer MT, Matthijs G, Navarro A, Metspalu A, Nyrönen T, Newhouse S, Persson B, Page A, Rambla J, Salgado D, Palotie A, Parkinson H, Valencia A, Varma S, Steinfelder E, Swertz MA, Blomberg N, Scollen S. (2019)

Leveraging European infrastructures to access 1 million human genomes by 2022.

Nat. Rev. Genet. 20(11):693-701. doi: 10.1038/s41576-019-0156-9
Europe PMC | doi

Ghavi-Helm Y, Jankowski A, Meiers S, Viales RR, Korbel JO, Furlong EEM. (2019)

Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression.

Nat. Genet. 51(8) doi: 10.1038/s41588-019-0462-3
Europe PMC | doi

Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez OL, Guo L, Collins RL, Fan X, Wen J, Handsaker RE, Fairley S, Kronenberg ZN, Hormozdiari F, Kong X, Wenger AM, Lee D, Antaki D, Hastie AR, Audano PA, Anantharaman T, Cantsilieris S, Brand H, Cerveira E, Cao H, Chen X, Chen C, Chong Z, Chin CS, Church DM, Clarke L, Chuang NT, Lambert CC, Galeev T, Gorkin DU, Farrell A, Flores J, Heaton WH, Korlach J, Gujral M, Guryev V, Lam ET, Lee JE, Kumar S, Kwon JY, Li S, Lee SP, Lee WP, Lee J, Munson KM, Meiers S, Viaud-Martinez K, Marks P, Noor A, Nodzak C, Nelson BJ, Navarro FCP, Rosanio G, Qiu Y, Pang AWC, Kyriazopoulou-Panagiotopoulou S, Welch AE, Xiao M, Xu W, Zhang C, Ryan M, Stütz A, Spierings DCJ, Ward A, McCarroll S, Jun G, Ding L, Koh CL, Zhu Q, Zheng-Bradley X, Lowy E, Yakneen S, Lansdorp PM, Kwok PY, Sebat J, Marth GT, Flicek P, Ren B, Gerstein MB, Chen K, Mills RE, Talkowski ME, Korbel JO, Marschall T, Bashir A, Shi X, Devine SE, Ye K, Eichler EE, Lee C. (2019)

Multi-platform discovery of haplotype-resolved structural variation in human genomes.

Nat Commun 10(1) doi: 10.1038/s41467-018-08148-z
Europe PMC | doi

López C, Kleinheinz K, Aukema SM, Rohde M, Bernhart SH, Hübschmann D, Wagener R, Toprak UH, Raimondi F, Kreuz M, Waszak SM, Huang Z, Sieverling L, Paramasivam N, Seufert J, Russell RB, Sungalee S, Kretzmer H, Bausinger J, Bergmann AK, Ammerpohl O, Borkhardt A, Binder H, Claviez A, Brors B, Feuerbach L, Doose G, Hansmann ML, Haake A, Hummel M, Hoell J, Lenze D, Radlwimmer B, Korbel JO, Lawerenz C, Rosenwald A, Schilhabel MB, Richter J, Rosenstiel P, Stadler PF, Szczepanowski M, Stein H, Stilgenbauer S, Eils R, Lichter P, Weniger MA, Zapatka M, Klapper W, Trümper L, Möller P, Loeffler M, Burkhardt B, Küppers R, Hoffmann S, Klapper W, Siebert R, Schlesner M. (2019)

Genomic and transcriptomic changes complement each other in the pathogenesis of sporadic Burkitt lymphoma.

Nat Commun 10(1) doi: 10.1038/s41467-019-08578-3
Europe PMC | doi

Lipinski S, Petersen BS, Barann M, Piecyk A, Tran F, Mayr G, Jentzsch M, Aden K, Stengel ST, Klostermeier UC, Sheth V, Ellinghaus D, Rausch T, Korbel JO, Nothnagel M, Gilissen C, Krawczak M, Forster M, Veltman JA, Lee CC, Forster P, Schreiber S, Fritscher-Ravens A, Rosenstiel P, Franke A. (2019)

Missense variants in NOX1 and p22phox in a case of very-early-onset inflammatory bowel disease are functionally linked to NOD2.

Cold Spring Harb Mol Case Stud 5(1) doi: 10.1101/mcs.a002428
Europe PMC | doi

Okonechnikov K, Erkek S, Korbel JO, Pfister SM, Chavez L. (2019)

InTAD: chromosome conformation guided analysis of enhancer target genes.

BMC Bioinformatics 20(1) doi: 10.1186/s12859-019-2655-2
Europe PMC | doi

Li W, Baumbach J, Mohammadnejad A, Brasch-Andersen C, Vandin F, Korbel JO, Tan Q. (2019)

Enriched power of disease-concordant twin-case-only design in detecting interactions in genome-wide association studies.

Eur. J. Hum. Genet. 27(4):631-636. doi: 10.1038/s41431-018-0320-2
Europe PMC | doi


2018

Richter-Pechańska P, Kunz JB, Bornhauser B, von Knebel Doeberitz C, Rausch T, Erarslan-Uysal B, Assenov Y, Frismantas V, Marovca B, Waszak SM, Zimmermann M, Seemann J, Happich M, Stanulla M, Schrappe M, Escherich G, Cario G, Kirschner-Schwabe R, Bakharevich K, Muckenthaler MU, Eckert C, Bourquin JP, Korbel JO, Kulozik AE. (2018)

PDX models recapitulate the genetic and epigenetic landscape of pediatric T-cell leukemia.

EMBO Mol Med 10(12) doi: 10.15252/emmm.201809443
Europe PMC | doi

Erkek S, Johann PD, Finetti MA, Drosos Y, Chou HC, Zapatka M, Sturm D, Jones DTW, Korshunov A, Rhyzova M, Wolf S, Mallm JP, Beck K, Witt O, Kulozik AE, Northcott PA, Frühwald MC, Lichter P, Korbel JO, Gajjar A, Eils R, Williamson D, Roberts CWM, Chavez L, Hasselblatt M, Kool M, Pfister SM. (2018)

Comprehensive analysis of chromatin states in atypical teratoid/rhabdoid tumor identifies diverging roles for SWI/SNF and polycomb in gene regulation.

Cancer Cell 35(1):95-110.e8. doi: 10.1016/j.ccell.2018.11.014
Europe PMC | doi

Gerhauser C, Favero F, Risch T, Simon R, Feuerbach L, Assenov Y, Heckmann D, Sidiropoulos N, Waszak SM, Hübschmann D, Urbanucci A, Girma EG, Kuryshev V, Klimczak LJ, Saini N, Weichenhan D, Stütz AM, Toth R, Böttcher LM, Koop C, Hendriksen JD, Matzk S, Lutsik P, Amstislavskiy V, Warnatz HJ, Raeder B, Feuerstein C, Schmitz EM, Bogatyrova O, Kluth M, Hube-Magg C, Lawerenz C, Henry GH, Huland H, Graefen M, Meiners J, Schilling D, Yamaguchi TN, Malewska A, Schlesner M, Strand DW, Reisinger E, Eils R, von Kalle C, Gordenin D, Bristow RG, Boutros PC, Plass C, Sauter G, Brors B, Sültmann H, Yaspo ML, Korbel JO, Schlomm T, Weischenfeldt J. (2018)

Molecular evolution of early-onset prostate cancer identifies molecular risk markers and clinical trajectories.

Cancer Cell 34(6):996-1011.e8. doi: 10.1016/j.ccell.2018.10.016
Europe PMC | doi

Rausch T, Fritz MH, Korbel JO, Benes V. (2018)

Alfred: Interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencing.

Bioinformatics 35(14):2489-2491. doi: 10.1093/bioinformatics/bty1007
Europe PMC | doi

Klusmann I, Wohlberedt K, Magerhans A, Teloni F, Korbel JO, Altmeyer M, Dobbelstein M. (2018)

Chromatin modifiers Mdm2 and RNF2 prevent RNA:DNA hybrids that impair DNA replication.

Proc. Natl. Acad. Sci. U.S.A. 115(48) doi: 10.1073/pnas.1809592115
Europe PMC | doi

Ghareghani M, Porubsk D, Sanders AD, Meiers S, Eichler EE, Korbel JO, Marschall T. (2018)

Strand-seq enables reliable separation of long reads by chromosome via expectation maximization.

Bioinformatics 34(13):i115-i123. doi: 10.1093/bioinformatics/bty290
Europe PMC | doi

Gröbner SN, Worst BC, Weischenfeldt J, Buchhalter I, Kleinheinz K, Rudneva VA, Johann PD, Balasubramanian GP, Segura-Wang M, Brabetz S, Bender S, Hutter B, Sturm D, Pfaff E, Hübschmann D, Heinold M, Zipprich G, Lawerenz C, Eils J, Lambo S, Erkek S, Blattmann C, Waszak S, Kuhlen M, Borkhardt A, Fulda S, Eggert A, Wegert J, Gessler M, Baumhoer D, Kappler R, Kontny U, Kulozik AE, Burdach S, Kirschner-Schwabe R, Eckert C, Bielack S, Lohmann D, Hettmer S, Richter GH, Schulte J, Nathrath M, Niemeyer C, Molenaar JJ, Vassal G, Siebert R, Westermann F, Witt O, Kratz CP, Burkhardt B, Witt H, Dirksen U, Fleischhack G, Kramm CM, van Tilburg CM, Wolf S, von Hoff K, Frühwald M, Rutkowski S, Koster J, Landgraf P, Koscielniak E, Klingebiel T, Waanders AJ, Zwijnenburg DA, Raman P, Brors B, Resnick AC, Zhang J, Liu Y, Zhou X, Piro RM, Korbel JO, Schlesner M, Eils R, Weber UD, Northcott PA, Pajtler KW, Kool M, Lichter P, Pfister SM, Eils R, Weber U, Lichter P, Jones DTW, Zapatka M, Chavez L, von Kalle C, Felsberg J, Bartholomä C, Schmidt M, Witt O, Korshunov A, Reifenberger G, Pfister S, Korbel J, Stütz A, Jäger N, Buchhalter I, Jones D, Lichter P, Taylor M, Pfister S, Borkhardt A, Brors B, Warnatz HJ, Landgraf P, Yaspo ML, Lehrach H, Rausch T, Radlwimmer B, Haake A, Wagner S, Siebert R, Lawerenz C, Eils J, Eils R, Eils R, Zapatka M, Scholz I, Jaeger-Schmidt C, Kerssemakers J, Eils J, Lawerenz C, Eils R, Richter G, Richter J, Hansmann ML, Haas S, Kneba M, Karsch D, Mantovani-Löffler L, Lisfeld J, Ott G, Rohde M, Borst C, Bergmann AK, Claviez A, Burkhardt B, Eberth S, Dreyling M, Frickhofen N, Einsele H, Weniger M, Hummel M, Klapper W, Kostezka U, Lenze D, Möller P, Rosenwald A, Ott G, Stadler C, Staib P, Stilgenbauer S, Trümper L, Zenz T, Hansmann ML, Kube D, Küppers R, Pischimariov J, Nagel I, López C, Lichter P, Rosenwald A, Rosenstiel P, Richter J, Radlwimmer B, Binder V, Aukema SM, Ammerpohl O, Szczepanowski M, Leich E, Hoell JI, Haake A, Borkhardt A, Hoffmann S, Hopp L, Doose G, Eils R, Kretzmer H, Kreuz M, Hübschmann D, Kleinheinz K, Vater I, Wagener R, Schilhabel M, Schreiber S, Binder H, Brors B, Siebert R, Bernhart SH, Stadler PF, Schlesner M, Langenberger D, Korbel J, Rosolowski M, Loeffler M, Sungalee S. (2018)

Author Correction: The landscape of genomic alterations across childhood cancers.

Nature 559(7714) doi: 10.1038/s41586-018-0167-2
Europe PMC | doi

Robinson GW, Rudneva VA, Buchhalter I, Billups CA, Waszak SM, Smith KS, Bowers DC, Bendel A, Fisher PG, Partap S, Crawford JR, Hassall T, Indelicato DJ, Boop F, Klimo P, Sabin ND, Patay Z, Merchant TE, Stewart CF, Orr BA, Korbel JO, Jones DTW, Sharma T, Lichter P, Kool M, Korshunov A, Pfister SM, Gilbertson RJ, Sanders RP, Onar-Thomas A, Ellison DW, Gajjar A, Northcott PA. (2018)

Risk-adapted therapy for young children with medulloblastoma (SJYC07): therapeutic and molecular outcomes from a multicentre, phase 2 trial.

Lancet Oncol 19(6) doi: 10.1016/S1470-2045(18)30204-3
Europe PMC | doi

Waszak SM, Northcott PA, Buchhalter I, Robinson GW, Sutter C, Groebner S, Grund KB, Brugières L, Jones DTW, Pajtler KW, Morrissy AS, Kool M, Sturm D, Chavez L, Ernst A, Brabetz S, Hain M, Zichner T, Segura-Wang M, Weischenfeldt J, Rausch T, Mardin BR, Zhou X, Baciu C, Lawerenz C, Chan JA, Varlet P, Guerrini-Rousseau L, Fults DW, Grajkowska W, Hauser P, Jabado N, Ra YS, Zitterbart K, Shringarpure SS, De La Vega FM, Bustamante CD, Ng HK, Perry A, MacDonald TJ, Hernáiz Driever P, Bendel AE, Bowers DC, McCowage G, Chintagumpala MM, Cohn R, Hassall T, Fleischhack G, Eggen T, Wesenberg F, Feychting M, Lannering B, Schüz J, Johansen C, Andersen TV, Röösli M, Kuehni CE, Grotzer M, Kjaerheim K, Monoranu CM, Archer TC, Duke E, Pomeroy SL, Shelagh R, Frank S, Sumerauer D, Scheurlen W, Ryzhova MV, Milde T, Kratz CP, Samuel D, Zhang J, Solomon DA, Marra M, Eils R, Bartram CR, von Hoff K, Rutkowski S, Ramaswamy V, Gilbertson RJ, Korshunov A, Taylor MD, Lichter P, Malkin D, Gajjar A, Korbel JO, Pfister SM. (2018)

Spectrum and prevalence of genetic predisposition in medulloblastoma: a retrospective genetic study and prospective validation in a clinical trial cohort.

Lancet Oncol 19(6) doi: 10.1016/S1470-2045(18)30242-0
Europe PMC | doi

Gröbner SN, Worst BC, Weischenfeldt J, Buchhalter I, Kleinheinz K, Rudneva VA, Johann PD, Balasubramanian GP, Segura-Wang M, Brabetz S, Bender S, Hutter B, Sturm D, Pfaff E, Hübschmann D, Zipprich G, Heinold M, Eils J, Lawerenz C, Erkek S, Lambo S, Waszak S, Blattmann C, Borkhardt A, Kuhlen M, Eggert A, Fulda S, Gessler M, Wegert J, Kappler R, Baumhoer D, Burdach S, Kirschner-Schwabe R, Kontny U, Kulozik AE, Lohmann D, Hettmer S, Eckert C, Bielack S, Nathrath M, Niemeyer C, Richter GH, Schulte J, Siebert R, Westermann F, Molenaar JJ, Vassal G, Witt H, Witt H, Witt H, Burkhardt B, Kratz CP, Witt O, van Tilburg CM, Kramm CM, Fleischhack G, Dirksen U, Rutkowski S, Frühwald M, von Hoff K, Wolf S, Klingebiel T, Koscielniak E, Landgraf P, Koster J, Resnick AC, Zhang J, Liu Y, Zhou X, Waanders AJ, Zwijnenburg DA, Raman P, Brors B, Weber UD, Northcott PA, Pajtler KW, Kool M, Piro RM, Korbel JO, Schlesner M, Eils R, Jones DTW, Lichter P, Chavez L, Zapatka M, Pfister SM. (2018)

The landscape of genomic alterations across childhood cancers.

Nature 555(7696) doi: 10.1038/nature25480
Europe PMC | doi

Computational Pan-Genomics Consortium. (2018)

Computational pan-genomics: status, promises and challenges.

Brief. Bioinformatics 19(1):118-135. doi: 10.1093/bib/bbw089
Europe PMC | doi

Haas J, Mester S, Lai A, Frese KS, Sedaghat-Hamedani F, Kayvanpour E, Rausch T, Nietsch R, Boeckel JN, Carstensen A, Völkers M, Dietrich C, Pils D, Amr A, Holzer DB, Martins Bordalo D, Oehler D, Weis T, Mereles D, Buss S, Riechert E, Wirsz E, Wuerstle M, Korbel JO, Keller A, Katus HA, Posch AE, Meder B. (2018)

Genomic structural variations lead to dysregulation of important coding and non-coding RNA species in dilated cardiomyopathy.

EMBO Mol Med 10(1) doi: 10.15252/emmm.201707838
Europe PMC | doi


2017

Kluth M, Jung S, Habib O, Eshagzaiy M, Heinl A, Amschler N, Masser S, Mader M, Runte F, Barow P, Frogh S, Omari J, Möller-Koop C, Hube-Magg C, Weischenfeldt J, Korbel J, Steurer S, Krech T, Huland H, Graefen M, Minner S, Sauter G, Schlomm T, Simon R. (2017)

Deletion lengthening at chromosomes 6q and 16q targets multiple tumor suppressor genes and is associated with an increasingly poor prognosis in prostate cancer.

Oncotarget 8(65):108923-108935. doi: 10.18632/oncotarget.22408
Europe PMC | doi

Porubsky D, Garg S, Sanders AD, Korbel JO, Guryev V, Lansdorp PM, Marschall T. (2017)

Dense and accurate whole-chromosome haplotyping of individual genomes.

Nat Commun 8(1) doi: 10.1038/s41467-017-01389-4
Europe PMC | doi

Segura-Wang M, Onishi-Seebacher M, Stütz AM, Mardin BR, Korbel JO. (2017)

Systematic Identification of Determinants for Single Strand Annealing Mediated Deletion Formation in Saccharomyces cerevisiae.

G3 (Bethesda) 7(10) doi: 10.1534/g3.117.300165
Europe PMC | doi

Ratnaparkhe M, Hlevnjak M, Kolb T, Jauch A, Maass KK, Devens F, Rode A, Hovestadt V, Korshunov A, Pastorczak A, Mlynarski W, Sungalee S, Korbel J, Hoell J, Fischer U, Milde T, Kramm C, Nathrath M, Chrzanowska K, Tausch E, Takagi M, Taga T, Constantini S, Loeffen J, Meijerink J, Zielen S, Gohring G, Schlegelberger B, Maass E, Siebert R, Kunz J, Kulozik AE, Worst B, Jones DT, Pfister SM, Zapatka M, Lichter P, Ernst A. (2017)

Genomic profiling of Acute lymphoblastic leukemia in ataxia telangiectasia patients reveals tight link between ATM mutations and chromothripsis.

Leukemia 31(10) doi: 10.1038/leu.2017.55
Europe PMC | doi

Hopkins JF, Sabelnykova VY, Weischenfeldt J, Simon R, Aguiar JA, Alkallas R, Heisler LE, Zhang J, Watson JD, Chua MLK, Fraser M, Favero F, Lawerenz C, Plass C, Sauter G, McPherson JD, van der Kwast T, Korbel J, Schlomm T, Bristow RG, Boutros PC. (2017)

Mitochondrial mutations drive prostate cancer aggression.

Nat Commun 8(1) doi: 10.1038/s41467-017-00377-y
Europe PMC | doi

Weischenfeldt J, Korbel JO. (2017)

Genomes of early onset prostate cancer.

Curr Opin Urol 27(5) doi: 10.1097/MOU.0000000000000422
Europe PMC | doi

Northcott PA, Buchhalter I, Morrissy AS, Hovestadt V, Weischenfeldt J, Ehrenberger T, Gröbner S, Segura-Wang M, Zichner T, Rudneva VA, Warnatz HJ, Sidiropoulos N, Phillips AH, Schumacher S, Kleinheinz K, Waszak SM, Erkek S, Jones DTW, Worst BC, Kool M, Zapatka M, Jäger N, Chavez L, Hutter B, Bieg M, Paramasivam N, Heinold M, Gu Z, Ishaque N, Jäger-Schmidt C, Imbusch CD, Jugold A, Hübschmann D, Risch T, Amstislavskiy V, Gonzalez FGR, Weber UD, Wolf S, Robinson GW, Zhou X, Wu G, Finkelstein D, Liu Y, Cavalli FMG, Luu B, Ramaswamy V, Wu X, Koster J, Ryzhova M, Cho YJ, Pomeroy SL, Herold-Mende C, Schuhmann M, Ebinger M, Liau LM, Mora J, McLendon RE, Jabado N, Kumabe T, Chuah E, Ma Y, Moore RA, Mungall AJ, Mungall KL, Thiessen N, Tse K, Wong T, Jones SJM, Witt O, Milde T, Von Deimling A, Capper D, Korshunov A, Yaspo ML, Kriwacki R, Gajjar A, Zhang J, Beroukhim R, Fraenkel E, Korbel JO, Brors B, Schlesner M, Eils R, Marra MA, Pfister SM, Taylor MD, Lichter P. (2017)

The whole-genome landscape of medulloblastoma subtypes.

Nature 547(7663):311-317. doi: 10.1038/nature22973
Europe PMC | doi

Molnar-Gabor F, Lueck R, Yakneen S, Korbel JO. (2017)

Computing patient data in the cloud: practical and legal considerations for genetics and genomics research in Europe and internationally

Genome Med 9(1) doi: 10.1186/s13073-017-0449-6
Europe PMC | doi

Buccitelli C, Salgueiro L, Rowald K, Sotillo R, Mardin BR, Korbel JO. (2017)

Pan-cancer analysis distinguishes transcriptional changes of aneuploidy from proliferation.

Genome Res. 27(4):501-511. doi: 10.1101/gr.212225.116
Europe PMC | doi

Richter-Pechańska P, Kunz JB, Hof J, Zimmermann M, Rausch T, Bandapalli OR, Orlova E, Scapinello G, Sagi JC, Stanulla M, Schrappe M, Cario G, Kirschner-Schwabe R, Eckert C, Benes V, Korbel JO, Muckenthaler MU, Kulozik AE. (2017)

Identification of a genetically defined ultra-high-risk group in relapsed pediatric T-lymphoblastic leukemia.

Blood Cancer J 7(2):e523. doi: 10.1038/bcj.2017.3
Europe PMC | doi

Weischenfeldt J., Dubash T., Drainas A., Mardin B., Chen Y., Stütz A., Waszak S., Bosco G., Halvorsen A., Raeder B., Efthymiopoulos T., Erkek S., Siegl C., Brenner H., Brustugun O., Dieter S., Northcott P., Petersen I., Pfister S., Schneider M., Solberg S., Thunissen E., Weichert W., Zichner T., Thomas R., Peifer M., Helland A., Ball C., Jechlinger M., Sotillo R., Glimm H., Korbel J.. (2017)

Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking

Nat Genet. 49(1):65-74. doi: 10.1038/ng.3722
Europe PMC | doi


2016

Bender S, Gronych J, Warnatz HJ, Hutter B, Grobner S, Ryzhova M, Pfaff E, Hovestadt V, Weinberg F, Halbach S, Kool M, Northcott PA, Sturm D, Bjerke L, Zichner T, Stutz AM, Schramm K, Huang B, Buchhalter I, Heinold M, Risch T, Worst BC, van Tilburg CM, Weber UD, Zapatka M, Raeder B, Milford D, Heiland S, von Kalle C, Previti C, Lawerenz C, Kulozik AE, Unterberg A, Witt O, von Deimling A, Capper D, Truffaux N, Grill J, Jabado N, Sehested AM, Sumerauer D, Hmida-Ben Brahim D, Trabelsi S, Ng HK, Zagzag D, Allen JC, Karajannis MA, Gottardo NG, Jones C, Korbel J, Schmidt S, Wolf S, Reifenberger G, Felsberg J, Brors B, Herold-Mende C, Lehrach H, Brummer T, Korshunov A, Eils R, Yaspo ML, Pfister SM, Lichter P, Jones DTW. (2016)

Recurrent MET fusion genes represent a drug target in pediatric glioblastoma

Nat. Med. 22(11):1314-1320. doi: 10.1038/nm.4204
Europe PMC | doi

Hezaveh K, Kloetgen A, Bernhart SH, Mahapatra KD, Lenze D, Richter J, Haake A, Bergmann AK, Brors B, Burkhardt B, Claviez A, Drexler HG, Eils R, Haas S, Hoffmann S, Karsch D, Klapper W, Kleinheinz K, Korbel J, Kretzmer H, Kreuz M, Küppers R, Lawerenz C, Leich E, Loeffler M, Mantovani-Loeffler L, López C, McHardy AC, Möller P, Rohde M, Rosenstiel P, Rosenwald A, Schilhabel M, Schlesner M, Scholz I, Stadler PF, Stilgenbauer S, Sungalee S, Szczepanowski M, Trümper L, Weniger MA, Siebert R, Borkhardt A, Hummel M, Hoell JI. (2016)

Alterations of microRNA and microRNA-regulated messenger RNA expression in germinal center B-cell lymphomas determined by integrative sequencing analysis.

Haematologica 101(11):671-678. doi: 10.3324/haematol.2016.143891
Europe PMC | doi

Koehler C, Sauter PF, Wawryszyn M, Girona GE, Gupta K, Landry JJ, Fritz MH, Radic K, Hoffmann JE, Chen ZA, Zou J, Tan PS, Galik B, Junttila S, Stolt-Bergner P, Pruneri G, Gyenesei A, Schultz C, Biskup MB, Besir H, Benes V, Rappsilber J, Jechlinger M, Korbel JO, Berger I, Braese S, Lemke EA. (2016)

Genetic code expansion for multiprotein complex engineering.

Nat. Methods 13(12) doi: 10.1038/nmeth.4032
Europe PMC | doi

Coccé M., Mardin B., Bens S., Stütz A., Lubieniecki F., Vater I., Korbel J., Siebert R., Alonso C., Gallego M.. (2016)

Identification of ZCCHC8 as fusion partner of ROS1 in a case of congenital glioblastoma multiforme with a t(6;12)(q21;q24.3)

Genes Chromosomes Cancer 55(9):677-687. doi: 10.1002/gcc.22369
Europe PMC | doi

Tsourlakis MC, Stender A, Quaas A, Kluth M, Wittmer C, Haese A, Graefen M, Steurer S, Simon R, Korbel J, Weischenfeldt J, Huland H, Sauter G, Schlomm T, Minner S. (2016)

Heterogeneity of ERG expression in prostate cancer: a large section mapping study of entire prostatectomy specimens from 125 patients.

BMC Cancer 16:641. doi: 10.1186/s12885-016-2674-6
Europe PMC | doi

Habermann N, Mardin BR, Yakneen S, Korbel JO. (2016)

Using large-scale genome variation cohorts to decipher the molecular mechanism of cancer.

C. R. Biol. 339(7-8):308-313. doi: 10.1016/j.crvi.2016.05.008
Europe PMC | doi

Rowald K, Mantovan M, Passos J, Buccitelli C, Mardin BR, Korbel JO, Jechlinger M, Sotillo R. (2016)

Negative Selection and Chromosome Instability Induced by Mad2 Overexpression Delay Breast Cancer but Facilitate Oncogene-Independent Outgrowth.

Cell Rep 15(12):2679-2691. doi: 10.1016/j.celrep.2016.05.048
Europe PMC | doi

Schütze DM, Krijgsman O, Snijders PJ, Ylstra B, Weischenfeldt J, Mardin BR, Stütz AM, Korbel JO, de Winter JP, Meijer CJ, Quint WG, Bosch L, Wilting SM, Steenbergen RD. (2016)

Immortalization capacity of HPV types is inversely related to chromosomal instability.

Oncotarget 7(25) doi: 10.18632/oncotarget.8058
Europe PMC | doi

Tica J, Lee E, Untergasser A, Meiers S, Garfield DA, Gokcumen O, Furlong EE, Park PJ, Stütz AM, Korbel JO. (2016)

Next-generation sequencing-based detection of germline L1-mediated transductions.

BMC Genomics 17(1) doi: 10.1186/s12864-016-2670-x
Europe PMC | doi

Johann PD, Erkek S, Zapatka M, Kerl K, Buchhalter I, Hovestadt V, Jones DT, Sturm D, Hermann C, Segura Wang M, Korshunov A, Rhyzova M, Gröbner S, Brabetz S, Chavez L, Bens S, Gröschel S, Kratochwil F, Wittmann A, Sieber L, Geörg C, Wolf S, Beck K, Oyen F, Capper D, van Sluis P, Volckmann R, Koster J, Versteeg R, von Deimling A, Milde T, Witt O, Kulozik AE, Ebinger M, Shalaby T, Grotzer M, Sumerauer D, Zamecnik J, Mora J, Jabado N, Taylor MD, Huang A, Aronica E, Bertoni A, Radlwimmer B, Pietsch T, Schüller U, Schneppenheim R, Northcott PA, Korbel JO, Siebert R, Frühwald MC, Lichter P, Eils R, Gajjar A, Hasselblatt M, Pfister SM, Kool M. (2016)

Atypical Teratoid/Rhabdoid Tumors Are Comprised of Three Epigenetic Subgroups with Distinct Enhancer Landscapes.

Cancer Cell 29(3):379-393. doi: 10.1016/j.ccell.2016.02.001
Europe PMC | doi

Hutter S, Piro RM, Waszak SM, Kehrer-Sawatzki H, Friedrich RE, Lassaletta A, Witt O, Korbel JO, Lichter P, Schuhmann MU, Pfister SM, Tabori U, Mautner VF, Jones DT. (2016)

No correlation between NF1 mutation position and risk of optic pathway glioma in 77 unrelated NF1 patients.

Hum. Genet. 135(5) doi: 10.1007/s00439-016-1646-x
Europe PMC | doi

Lin CY, Erkek S, Tong Y, Yin L, Federation AJ, Zapatka M, Haldipur P, Kawauchi D, Risch T, Warnatz HJ, Worst BC, Ju B, Orr BA, Zeid R, Polaski DR, Segura-Wang M, Waszak SM, Jones DT, Kool M, Hovestadt V, Buchhalter I, Sieber L, Johann P, Chavez L, Gröschel S, Ryzhova M, Korshunov A, Chen W, Chizhikov VV, Millen KJ, Amstislavskiy V, Lehrach H, Yaspo ML, Eils R, Lichter P, Korbel JO, Pfister SM, Bradner JE, Northcott PA. (2016)

Active medulloblastoma enhancers reveal subgroup-specific cellular origins.

Nature 530(7588) doi: 10.1038/nature16546
Europe PMC | doi

Cannavò E, Khoueiry P, Garfield DA, Geeleher P, Zichner T, Gustafson EH, Ciglar L, Korbel JO, Furlong EE. (2016)

Shadow Enhancers Are Pervasive Features of Developmental Regulatory Networks.

Curr. Biol. 26(1):38-51. doi: 10.1016/j.cub.2015.11.034
Europe PMC | doi


2015

Gatz SA, Salles D, Jacobsen EM, Dörk T, Rausch T, Aydin S, Surowy H, Volcic M, Vogel W, Debatin KM, Stütz AM, Schwarz K, Pannicke U, Hess T, Korbel JO, Schulz AS, Schumacher J, Wiesmüller L. (2015)

MCM3AP and POMP Mutations Cause a DNA-Repair and DNA-Damage-Signaling Defect in an Immunodeficient Child.

Hum Mutat 37(3):257-268. doi: 10.1002/humu.22939
Europe PMC | doi

Kovac M, Blattmann C, Ribi S, Smida J, Mueller NS, Engert F, Castro-Giner F, Weischenfeldt J, Kovacova M, Krieg A, Andreou D, Tunn PU, Dürr HR, Rechl H, Schaser KD, Melcher I, Burdach S, Kulozik A, Specht K, Heinimann K, Fulda S, Bielack S, Jundt G, Tomlinson I, Korbel JO, Nathrath M, Baumhoer D. (2015)

Exome sequencing of osteosarcoma reveals mutation signatures reminiscent of BRCA deficiency.

Nat Commun 6 doi: 10.1038/ncomms9940
Europe PMC | doi

Stockklausner C, Raffel S, Klermund J, Bandapalli OR, Beier F, Brümmendorf TH, Bürger F, Sauer SW, Hoffmann GF, Lorenz H, Tagliaferri L, Nowak D, Hofmann WK, Buergermeister R, Kerber C, Rausch T, Korbel JO, Luke B, Trumpp A, Kulozik AE. (2015)

A novel autosomal recessive TERT T1129P mutation in a dyskeratosis congenita family leads to cellular senescence and loss of CD34+ hematopoietic stem cells not reversible by mTOR-inhibition.

Aging (Albany NY) 7(11):911-927. doi: 10.18632/aging.100835
Europe PMC | doi

1000 Genomes Project Consortium. (2015)

A global reference for human genetic variation.

Nature 526(7571):68-74. doi: 10.1038/nature15393
Europe PMC | doi

Abyzov A, Li S, Kim DR, Mohiyuddin M, Stütz AM, Parrish NF, Mu XJ, Clark W, Chen K, Hurles M, Korbel JO, Lam HY, Lee C. (2015)

Erratum: Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms.

Nat Commun 6:8389. doi: 10.1038/ncomms9389
Europe PMC | doi

Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Hsi-Yang Fritz M, Konkel MK, Malhotra A, Stütz AM, Shi X, Paolo Casale F, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJ, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HY, Jasmine Mu X, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA, 1000 Genomes Project Consortium, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO. (2015)

An integrated map of structural variation in 2,504 human genomes.

Nature 526(7571):75-81. doi: 10.1038/nature15394
Europe PMC | doi

Mardin BR, Drainas AP, Waszak SM, Weischenfeldt J, Isokane M, Stütz AM, Raeder B, Efthymiopoulos T, Buccitelli C, Segura-Wang M, Northcott P, Pfister SM, Lichter P, Ellenberg J, Korbel JO. (2015)

A cell-based model system links chromothripsis with hyperploidy.

Mol. Syst. Biol. 11(9):828. doi: 10.15252/msb.20156505
Europe PMC | doi

Fischer U*, Forster M*, Rinaldi A*, Risch T*, Sungalee S*, Warnatz HJ*, Bornhauser B, Gombert M, Kratsch C, Stütz AM, Sultan M, Tchinda J, Worth CL, Amstislavskiy V, Badarinarayan N, Baruchel A, Bartram T, Basso G, Canpolat C, Cario G, Cavé H, Dakaj D, Delorenzi M, Dobay MP, Eckert C, Ellinghaus E, Eugster S, Frismantas V, Ginzel S, Haas OA, Heidenreich O, Hemmrich-Stanisak G, Hezaveh K, Höll JI, Hornhardt S, Husemann P, Kachroo P, Kratz CP, Kronnie GT, Marovca B, Niggli F, McHardy AC, Moorman AV, Panzer-Grümayer R, Petersen BS, Raeder B, Ralser M, Rosenstiel P, Schäfer D, Schrappe M, Schreiber S, Schütte M, Stade B, Thiele R, Weid NV, Vora A, Zaliova M, Zhang L, Zichner T, Zimmermann M, Lehrach H, Borkhardt A, Bourquin JP, Franke A, Korbel JO, Stanulla M, Yaspo ML. (2015)

Genomics and drug profiling of fatal TCF3-HLF-positive acute lymphoblastic leukemia identifies recurrent mutation patterns and therapeutic options.

Nat Genet. 47(9):1020-1029. doi: 10.1038/ng.3362
Europe PMC | doi

Kunz JB, Rausch T, Bandapalli OR, Eilers J, Pechanska P, Schuessele S, Assenov Y, Stütz AM, Kirschner-Schwabe R, Hof J, Eckert C, von Stackelberg A, Schrappe M, Stanulla M, Koehler R, Avigad S, Elitzur S, Handgretinger R, Benes V, Weischenfeldt J, Korbel JO, Muckenthaler MU, Kulozik AE. (2015)

Pediatric T-lymphoblastic leukemia evolves into relapse by clonal selection, acquisition of mutations and promoter hypomethylation.

Haematologica 100(11) doi: 10.3324/haematol.2015.129692
Europe PMC | doi

Alizadeh AA, Aranda V, Bardelli A, Blanpain C, Bock C, Borowski C, Caldas C, Califano A, Doherty M, Elsner M, Esteller M, Fitzgerald R, Korbel JO, Lichter P, Mason CE, Navin N, Pe'er D, Polyak K, Roberts CWM, Siu L, Snyder A, Stower H, Swanton C, Verhaak RGW, Zenklusen JC, Zuber J, Zucman-Rossi J. (2015)

Toward understanding and exploiting tumor heterogeneity.

Nat Med 21(8):846-853. doi: 10.1038/nm.3915
Europe PMC | doi

George J, Lim JS, Jang SJ, Cun YP, Ozretic L, Kong G, Leenders F, Lu X, Fernandez-Cuesta L, Bosco G, Muller C, Dahmen I, Jahchan NS, Park KS, Yang D, Karnezis AN, Vaka D, Torres A, Wang MS, Korbel JO, Menon R, Chun SM, Kim D, Wilkerson M, Hayes N, Engelmann D, Putzer B, Bos M, Michels S, Vlasic I, Seidel D, Pinther B, Schaub P, Becker C, Altmuller J, Yokota J, Kohno T, Iwakawa R, Tsuta K, Noguchi M, Muley T, Hoffmann H, Schnabel PA, Petersen I, Chen Y, Soltermann A, Tischler V, Choi CM, Kim YH, Massion PP, Zou Y, Jovanovic D, Kontic M, Wright GM, Russell PA, Solomon B, Koch I, Lindner M, Muscarella LA, la Torre A, Field JK, Jakopovic M, Knezevic J, Castanos-Velez E, Roz L, Pastorino U, Brustugun OT, Lund-Iversen M, Thunnissen E, Kohler J, Schuler M, Botling J, Sandelin M, Sanchez-Cespedes M, Salvesen HB, Achter V, Lang U, Bogus M, Schneider PM, Zander T, Ansen S, Hallek M, Wolf J, Vingron M, Yatabe Y, Travis WD, Nurnberg P, Reinhardt C, Perner S, Heukamp L, Buttner R, Haas SA, Brambilla E, Peifer M, Sage J, Thomas RK. (2015)

Comprehensive genomic profiles of small cell lung cancer.

Nature 524(7563):47-53. doi: 10.1038/nature14664
Europe PMC | doi

Forster M, Szymczak S, Ellinghaus D, Hemmrich G, Rühlemann M, Kraemer L, Mucha S, Wienbrandt L, Stanulla M, UFO Sequencing Consortium within I-BFM Study Group, Franke A. (2015)

Vy-PER: eliminating false positive detection of virus integration events in next generation sequencing data.

Sci Rep 5:11534. doi: 10.1038/srep11534
Europe PMC | doi

Stein LD, Knoppers BM, Campbell P, Getz G, Korbel JO. (2015)

Data analysis: Create a cloud commons.

Nature 523(7559):149-151. doi: 10.1038/523149a
Europe PMC | doi

Pendleton M, Sebra R, Pang AW, Ummat A, Franzen O, Rausch T, Stütz AM, Stedman W, Anantharaman T, Hastie A, Dai H, Fritz MH, Cao H, Cohain A, Deikus G, Durrett RE, Blanchard SC, Altman R, Chin CS, Guo Y, Paxinos EE, Korbel JO, Darnell RB, McCombie WR, Kwok PY, Mason CE, Schadt EE, Bashir A. (2015)

Assembly and diploid architecture of an individual human genome via single-molecule technologies.

Nat. Methods 12(8) doi: 10.1038/nmeth.3454
Europe PMC | doi

Abyzov A, Li S, Kim DR, Mohiyuddin M, Stütz AM, Parrish NF, Mu XJ, Clark W, Chen K, Hurles M, Korbel JO, Lam HY, Lee C, Gerstein MB. (2015)

Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms.

Nat Commun 6:7256. doi: 10.1038/ncomms8256
Europe PMC | doi

Schlomm T, Weischenfeldt J, Korbel J, Sauter G. (2015)

The Aging Prostate Is Never "Normal": Implications from the Genomic Characterization of Multifocal Prostate Cancers.

Eur. Urol. 68(3) doi: 10.1016/j.eururo.2015.04.012
Europe PMC | doi

Kluth M, Galal R, Krohn A, Weischenfeldt J, Tsourlakis C, Paustian L, Ahrary R, Ahmed M, Scherzai S, Meyer A, Sirma H, Korbel J, Sauter G, Schlomm T, Simon R, Minner S. (2015)

Prevalence of chromosomal rearrangements involving non-ETS genes in prostate cancer.

Int. J. Oncol. 46(4):1637-1642. doi: 10.3892/ijo.2015.2855
Europe PMC | doi

Gu L, Frommel SC, Oakes CC, Simon R, Grupp K, Gerig CY, Bär D, Robinson MD, Baer C, Weiss M, Gu Z, Schapira M, Kuner R, Sültmann H, Provenzano M, ICGC Project on Early Onset Prostate Cancer, Yaspo ML, Brors B, Korbel J, Schlomm T, Sauter G, Eils R, Plass C, Santoro R. (2015)

BAZ2A (TIP5) is involved in epigenetic alterations in prostate cancer and its overexpression predicts disease recurrence.

Nat. Genet. 47(1) doi: 10.1038/ng.3165
Europe PMC | doi


2014

Steurer S, Mayer PS, Adam M, Krohn A, Koop C, Ospina-Klinck D, Tehrani AA, Simon R, Tennstedt P, Graefen M, Wittmer C, Brors B, Plass C, Korbel J, Weischenfeldt J, Sauter G, Huland H, Tsourlakis MC, Minner S, Schlomm T. (2014)

TMPRSS2-ERG Fusions Are Strongly Linked to Young Patient Age in Low-grade Prostate Cancer

Eur. Urol. 66(6):978-981. doi: 10.1016/j.eururo.2014.06.027
Europe PMC | doi

Hammer C, Degenhardt F, Priebe L, Stütz AM, Heilmann S, Waszak SM, Schlattl A, Mangold E, Hoffmann P, Nöthen MM, Rietschel M, Rappold G, Korbel J, Cichon S, Niesler B. (2014)

A common microdeletion affecting a hippocampus- and amygdala-specific isoform of tryptophan hydroxylase 2 is not associated with affective disorders.

Bipolar Disord 16(7):764-768. doi: 10.1111/bdi.12207
Europe PMC | doi

Moncunill V, Gonzalez S, Beà S, Andrieux LO, Salaverria I, Royo C, Martinez L, Puiggròs M, Segura-Wang M, Stütz AM, Navarro A, Royo R, Gelpí JL, Gut IG, López-Otín C, Orozco M, Korbel JO, Campo E, Puente XS, Torrents D. (2014)

Comprehensive characterization of complex structural variations in cancer by directly comparing genome sequence reads.

Nat. Biotechnol. 32(11):1106-1112. doi: 10.1038/nbt.3027
Europe PMC | doi

Willems T, Gymrek M, Highnam G, 1000 Genomes Project Consortium, Mittelman D, Erlich Y. (2014)

The landscape of human STR variation.

Genome Res. 24(11):1894-1904. doi: 10.1101/gr.177774.114
Europe PMC | doi

Kluth M, Harasimowicz S, Burkhardt L, Grupp K, Krohn A, Prien K, Gjoni J, Haß T, Galal R, Graefen M, Haese A, Simon R, Hühne-Simon J, Koop C, Korbel J, Weischenfeld J, Huland H, Sauter G, Quaas A, Wilczak W, Tsourlakis MC, Minner S, Schlomm T. (2014)

Clinical significance of different types of p53 gene alteration in surgically treated prostate cancer.

Int. J. Cancer 135(6):1369-1380. doi: 10.1002/ijc.28784
Europe PMC | doi

Brocks D, Assenov Y, Minner S, Bogatyrova O, Simon R, Koop C, Oakes C, Zucknick M, Lipka DB, Weischenfeldt J, Feuerbach L, Cowper-Sal Lari R, Lupien M, Brors B, Korbel J, Schlomm T, Tanay A, Sauter G, Gerhäuser C, Plass C. (2014)

Intratumor DNA Methylation Heterogeneity Reflects Clonal Evolution in Aggressive Prostate Cancer

Cell Rep 8(3):798-806. doi: 10.1016/j.celrep.2014.06.053
Europe PMC | doi

Northcott PA, Lee C, Zichner T, Stütz AM, Erkek S, Kawauchi D, Shih DJ, Hovestadt V, Zapatka M, Sturm D, Jones DT, Kool M, Remke M, Cavalli FM, Zuyderduyn S, Bader GD, VandenBerg S, Esparza LA, Ryzhova M, Wang W, Wittmann A, Stark S, Sieber L, Seker-Cin H, Linke L, Kratochwil F, Jäger N, Buchhalter I, Imbusch CD, Zipprich G, Raeder B, Schmidt S, Diessl N, Wolf S, Wiemann S, Brors B, Lawerenz C, Eils J, Warnatz HJ, Risch T, Yaspo ML, Weber UD, Bartholomae CC, von Kalle C, Turányi E, Hauser P, Sanden E, Darabi A, Siesjö P, Sterba J, Zitterbart K, Sumerauer D, van Sluis P, Versteeg R, Volckmann R, Koster J, Schuhmann MU, Ebinger M, Grimes HL, Robinson GW, Gajjar A, Mynarek M, von Hoff K, Rutkowski S, Pietsch T, Scheurlen W, Felsberg J, Reifenberger G, Kulozik AE, von Deimling A, Witt O, Eils R, Gilbertson RJ, Korshunov A, Taylor MD, Lichter P, Korbel JO, Wechsler-Reya RJ, Pfister SM. (2014)

Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma

Nature 511(7510):428-434. doi: 10.1038/nature13379
Europe PMC | doi

Huang W, Massouras A, Inoue Y, Peiffer J, Ràmia M, Tarone AM, Turlapati L, Zichner T, Zhu D, Lyman RF, Magwire MM, Blankenburg K, Carbone MA, Chang K, Ellis LL, Fernandez S, Han Y, Highnam G, Hjelmen CE, Jack JR, Javaid M, Jayaseelan J, Kalra D, Lee S, Lewis L, Munidasa M, Ongeri F, Patel S, Perales L, Perez A, Pu L, Rollmann SM, Ruth R, Saada N, Warner C, Williams A, Wu YQ, Yamamoto A, Zhang Y, Zhu Y, Anholt RR, Korbel JO, Mittelman D, Muzny DM, Gibbs RA, Barbadilla A, Johnston JS, Stone EA, Richards S, Deplancke B, Mackay TF. (2014)

Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines.

Genome Res. 24(7):1193-1208. doi: 10.1101/gr.171546.113
Europe PMC | doi

Delaneau O, Marchini J, 1000 Genomes Project Consortium. (2014)

Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel.

Nat Commun 5 doi: 10.1038/ncomms4934
Europe PMC | doi

Bandapalli OR, Schuessele S, Kunz JB, Rausch T, Stütz AM, Tal N, Geron I, Gershman N, Izraeli S, Eilers J, Vaezipour N, Kirschner-Schwabe R, Hof J, von Stackelberg A, Schrappe M, Stanulla M, Zimmermann M, Koehler R, Avigad S, Handgretinger R, Frismantas V, Bourquin JP, Bornhauser B, Korbel JO, Muckenthaler MU, Kulozik AE. (2014)

The activating STAT5B N642H mutation is a common abnormality in pediatric T-cell acute lymphoblastic leukemia and confers a higher risk of relapse

Haematologica 99(10):e188-92. doi: 10.3324/haematol.2014.104992
Europe PMC | doi

Bens S, Zichner T, Stütz AM, Caliebe A, Wagener R, Hoff K, Korbel JO, von Bismarck P, Siebert R. (2014)

SPAG7 is a candidate gene for the periodic fever, aphthous stomatitis, pharyngitis and adenopathy (PFAPA) syndrome

Genes Immun. 15(3):190-194. doi: 10.1038/gene.2013.73
Europe PMC | doi

Kool M, Jones DT, Jäger N, Northcott PA, Pugh TJ, Hovestadt V, Piro RM, Esparza LA, Markant SL, Remke M, Milde T, Bourdeaut F, Ryzhova M, Sturm D, Pfaff E, Stark S, Hutter S, Seker-Cin H, Johann P, Bender S, Schmidt C, Rausch T, Shih D, Reimand J, Sieber L, Wittmann A, Linke L, Witt H, Weber UD, Zapatka M, König R, Beroukhim R, Bergthold G, van Sluis P, Volckmann R, Koster J, Versteeg R, Schmidt S, Wolf S, Lawerenz C, Bartholomae CC, von Kalle C, Unterberg A, Herold-Mende C, Hofer S, Kulozik AE, von Deimling A, Scheurlen W, Felsberg J, Reifenberger G, Hasselblatt M, Crawford JR, Grant GA, Jabado N, Perry A, Cowdrey C, Croul S, Zadeh G, Korbel JO, Doz F, Delattre O, Bader GD, McCabe MG, Collins VP, Kieran MW, Cho YJ, Pomeroy SL, Witt O, Brors B, Taylor MD, Schüller U, Korshunov A, Eils R, Wechsler-Reya RJ, Lichter P, Pfister SM, ICGC PedBrain Tumor Project. (2014)

Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition

Cancer Cell 25(3):393-405. doi: 10.1016/j.ccr.2014.02.004
Europe PMC | doi

Mack SC, Witt H, Piro RM, Gu L, Zuyderduyn S, Stütz AM, Wang X, Gallo M, Garzia L, Zayne K, Zhang X, Ramaswamy V, Jäger N, Jones DT, Sill M, Pugh TJ, Ryzhova M, Wani KM, Shih DJ, Head R, Remke M, Bailey SD, Zichner T, Faria CC, Barszczyk M, Stark S, Seker-Cin H, Hutter S, Johann P, Bender S, Hovestadt V, Tzaridis T, Dubuc AM, Northcott PA, Peacock J, Bertrand KC, Agnihotri S, Cavalli FM, Clarke I, Nethery-Brokx K, Creasy CL, Verma SK, Koster J, Wu X, Yao Y, Milde T, Sin-Chan P, Zuccaro J, Lau L, Pereira S, Castelo-Branco P, Hirst M, Marra MA, Roberts SS, Fults D, Massimi L, Cho YJ, Van Meter T, Grajkowska W, Lach B, Kulozik AE, von Deimling A, Witt O, Scherer SW, Fan X, Muraszko KM, Kool M, Pomeroy SL, Gupta N, Phillips J, Huang A, Tabori U, Hawkins C, Malkin D, Kongkham PN, Weiss WA, Jabado N, Rutka JT, Bouffet E, Korbel JO, Lupien M, Aldape KD, Bader GD, Eils R, Lichter P, Dirks PB, Pfister SM, Korshunov A, Taylor MD. (2014)

Epigenomic alterations define lethal CIMP-positive ependymomas of infancy

Nature 506(7489):445-450. doi: 10.1038/nature13108
Europe PMC | doi


2013

Korbel JO, Lee C. (2013)

Genome assembly and haplotyping with Hi-C

Nat. Biotechnol. 31(12):1099-1101. doi: 10.1038/nbt.2764
Europe PMC | doi

Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüs ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GR, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F, 1000 Genomes Project Consortium, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M. (2013)

Integrative annotation of variants from 1092 humans: application to cancer genomics

Science 342(6154):1235587. doi: 10.1126/science.1235587
Europe PMC | doi

Gokcumen O, Tischler V, Tica J, Zhu Q, Iskow RC, Lee E, Fritz MH, Langdon A, Stütz AM, Pavlidis P, Benes V, Mills RE, Park PJ, Lee C, Korbel JO. (2013)

Primate genome architecture influences structural variation mechanisms and functional consequences

Proc. Natl. Acad. Sci. U.S.A. 110(39):15764-15769. doi: 10.1073/pnas.1305904110
Europe PMC | doi