Publications

Peer-reviewed original papers (@corresponding author, *equal contributions)

Lab members underlined.

          1. 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, Sahm F, Korbel JO, Rutkowski S, Eggermann T, Gajjar A, Northcott P, Elbracht M, Pfister SM, Kontny U, Kurth I. (2019) Germline GPR161 Mutations Predispose to Pediatric Medulloblastoma. J Clin Oncol.  doi: 10.1200/JCO.19.00577. [Epub ahead of print]
          2. Bolognini D,Sanders AKorbel JO, Magi A, Benes V, Rausch T. (2019) VISOR: a versatile haplotype-aware structural variant simulator for short and long read sequencing. Bioinformatics. doi: 10.1093/bioinformatics/btz719. [Epub ahead of print]
          3. 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. 10:1248-1260.
          4. 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, Heringa J, Holub P, Hooyberghs J, Juty N, Keane TM, Korbel JO, Lappalainen I, Leskosek B, Matthijs G, Mayrhofer MT, Metspalu A, Navarro A, Newhouse S, Nyrönen T, Page A, Persson B, Palotie A, Parkinson H, Rambla J, Salgado D, Steinfelder E, Swertz MA, Valencia A, Varma S, Blomberg N, Scollen S. (2019) Leveraging European infrastructures to access 1 million human genomes by 2022. Nat Rev Genet. doi: 10.1038/s41576-019-0156-9. [Epub ahead of print] Review.
          5. Ghavi-Helm Y, Jankowski A, Meiers S, Viales RR, Korbel JO, Furlong EEM. Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression. (2019) Nat Genet. 8:1272-1282.
          6. 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, Kong X, Hormozdiari F, Lee D, Wenger AM, Hastie AR, Antaki D, Anantharaman T, Audano PA, Brand H, Cantsilieris S, Cao H, Cerveira E, Chen C, Chen X, Chin CS, Chong Z, Chuang NT, Lambert CC, Church DM, Clarke L, Farrell A, Flores J, Galeev T, Gorkin DU, Gujral M, Guryev V, Heaton WH, Korlach J, Kumar S, Kwon JY, Lam ET, Lee JE, Lee J, Lee WP, Lee SP, Li S, Marks P, Viaud-Martinez K, Meiers S, Munson KM, Navarro FCP, Nelson BJ, Nodzak C, Noor A, Kyriazopoulou-Panagiotopoulou S, Pang AWC, Qiu Y, Rosanio G, Ryan M, Stütz A, Spierings DCJ, Ward A, Welch AE, Xiao M, Xu W, Zhang C, Zhu Q, Zheng-Bradley X, Lowy E, Yakneen S, McCarroll S, Jun G, Ding L, Koh CL, Ren B, Flicek P, Chen K, Gerstein MB, Kwok PY, Lansdorp PM, Marth GT, Sebat J, Shi X, Bashir A, Ye K, Devine SE, Talkowski ME, Mills RE, Marschall T, Korbel JO, Eichler EE, Lee C. Multi-platform discovery of haplotype-resolved structural variation in human genomes. (2019) Nat Commun. 1:1784.
          7. 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, Sungalee S, Russell RB, Bausinger J, Kretzmer H, Ammerpohl O, Bergmann AK, Binder H, Borkhardt A, Brors B, Claviez A, Doose G, Feuerbach L, Haake A, Hansmann ML, Hoell J, Hummel M, Korbel JO, Lawerenz C, Lenze D, Radlwimmer B, Richter J, Rosenstiel P, Rosenwald A, Schilhabel MB, Stein H, Stilgenbauer S, Stadler PF, Szczepanowski M, Weniger MA, Zapatka M, Eils R, Lichter P, Loeffler M, Möller P, Trümper L, Klapper W; ICGC MMML-Seq Consortium, Hoffmann S, Küppers R, Burkhardt B, Schlesner M, Siebert R. Genomic and transcriptomic changes complement each other in the pathogenesis of sporadic Burkitt lymphoma. (2019) Nat Commun. 1:1459.
          8. 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 TKorbel JO, Nothnagel M, Krawczak M, Gilissen C, Veltman JA, Forster M, Forster P, Lee CC, Fritscher-Ravens A, Schreiber S, Franke A, Rosenstiel P. Missense variants in NOX1 and p22phox in a case of very-early-onset inflammatory bowel disease are functionally linked to NOD2. (2019) Cold Spring Harb Mol Case Stud. 1.
          9. Okonechnikov K, Erkek S, Korbel JO, Pfister SM, Chavez L. InTAD: chromosome conformation guided analysis of enhancer target genes. (2019) BMC Bioinformatics. 1:60.
          10. Li W, Baumbach J, Mohammadnejad A, Brasch-Andersen C, Vandin F, Korbel JO, Tan Q. Enriched power of disease-concordant twin-case-only design in detecting interactions in genome-wide association studies. (2019) Eur J Hum Genet. 4:631-636.
          11. 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, Frühwald MC, Northcott PA, Korbel JO, Lichter P, Eils R, Gajjar A, Roberts CWM, Williamson D, Hasselblatt M, Chavez L, Pfister SM, Kool M. Comprehensive Analysis of Chromatin States in Atypical Teratoid/Rhabdoid Tumor Identifies Diverging Roles for SWI/SNF and Polycomb in Gene Regulation. (2019) Cancer Cell. 1:95-110.
          12. Rausch T, Hsi-Yang Fritz M, Korbel JO, Benes V. Alfred: interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencing. (2019) Bioinformatics. 14:2489-2491.
          13. 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, Stütz AM, Weichenhan D, Böttcher LM, Toth R, Hendriksen JD, Koop C, Lutsik P, Matzk S, Warnatz HJ, Amstislavskiy V, Feuerstein C, Raeder B, Bogatyrova O, Schmitz EM, Hube-Magg C, Kluth M, Huland H, Graefen M, Lawerenz C, Henry GH, Yamaguchi TN, Malewska A, Meiners J, Schilling D, Reisinger E, Eils R, Schlesner M, Strand DW, Bristow RG, Boutros PC, von Kalle C, Gordenin D, Sültmann H, Brors B, Sauter G, Plass C, Yaspo ML, Korbel JO, Schlomm T, Weischenfeldt J. Molecular Evolution of Early-Onset Prostate Cancer Identifies Molecular Risk Markers and Clinical Trajectories. (2018) Cancer Cell. 6:996-1011.
          14. Klusmann I, Wohlberedt K, Magerhans A, Teloni F, Korbel JO, Altmeyer M, Dobbelstein M. Chromatin modifiers Mdm2 and RNF2 prevent RNA:DNA hybrids that impair DNA replication. (2018) Proc Natl Acad Sci U S A. 48:E11311-E11320.
          15. Lee AY, Ewing AD, Ellrott K, Hu Y, Houlahan KE, Bare JC, Espiritu SMG, Huang V, Dang K, Chong Z, Caloian C, Yamaguchi TN; ICGC-TCGA DREAM Somatic Mutation Calling Challenge Participants, Kellen MR, Chen K, Norman TC, Friend SH, Guinney J, Stolovitzky G, Haussler D, Margolin AA, Stuart JM, Boutros PC. Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection. (2018) Genome Biol. 1:188.#
          16. 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, Cario G, Escherich G, Bakharevich K, Kirschner-Schwabe R, Eckert C, Muckenthaler MU, Korbel JO, Bourquin JP, Kulozik AE. PDX models recapitulate the genetic and epigenetic landscape of pediatric T-cell leukemia. (2018) EMBO Mol Med. 12. pii: e9443.
          17. Ghareghani M, Porubsky D, Sanders AD, Meiers S, Eichler EE, Korbel JO, Marschall T.  Strand-seq enables reliable separation of long reads by chromosome via expectation maximization. (2018) Bioinformatics. 2018 Jul 1;34(13):i115-i123.
          18. 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. Risk-adapted therapy for young children with medulloblastoma (SJYC07): therapeutic and molecular outcomes from a multicentre, phase 2 trial. (2018) Lancet Oncol. 6:768-784.
          19. 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. Spectrum and prevalence of genetic predisposition in medulloblastoma: a retrospective genetic study and prospective validation in a clinical trial cohort. (2018) Lancet Oncol. pii: S1470-2045(18)30242-0. doi: 10.1016/S1470-2045(18)30242-0. [Epub ahead of print]
          20. 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; ICGC PedBrain-Seq Project; ICGC MMML-Seq Project, 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. The landscape of genomic alterations across childhood cancers. (2018) Nature. 555:321-327.
          21. Porubsky D, Garg S, Sanders ADKorbel JO, Guryev V, Lansdorp PM, Marschall T. Dense and accurate whole-chromosome haplotyping of individual genomes. (2017) Nat Commun. 8:1293.
          22. Segura-Wang M, Onishi-Seebacher M, Stütz AM, Mardin BR@, Korbel JO@. Systematic Identification of Determinants for Single-Strand Annealing-Mediated Deletion Formation in Saccharomyces cerevisiae. (2017) G3 (Bethesda). 27:3269-3279.
          23. 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. The whole-genome landscape of medulloblastoma subtypes. (2017) Nature 547:311-317.
          24. Molnár-Gábor F, Lueck R, Yakneen SKorbel JO@. Computing patient data in the cloud: practical and legal considerations for genetics and genomics research in Europe and internationally. (2017) Genome Med. 9:58.
          25. Buccitelli C, Salgueiro L, Rowald K, Sotillo R, Mardin BR@*, Korbel JO@*. Pan-cancer analysis distinguishes transcriptional changes of aneuploidy from proliferation. (2017) Genome Res 27:501-511.
          26. Weischenfeldt J*, Dubash T*, Drainas AP*, Mardin BR, Chen Y, Stütz AM, Waszak SM, Bosco G, Halvorsen AR, Raeder B, Efthymiopoulos T, Erkek S, Siegl C, Brenner H, Brustugun OT, Dieter SM, Northcott PA, Petersen I, Pfister SM, Schneider M, Solberg SK, Thunissen E, Weichert W, Zichner T, Thomas R, Peifer M, Helland A, Ball CR, Jechlinger M, Sotillo R, Glimm H@*Korbel JO@*. Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking. (2017) Nat Genet 1:65-74.
          27. Ratnaparkhe M, Hlevnjak M, Kolb T, Jauch A, Maass KK, Devens F, Rode A, Hovestadt V, Korshunov A, Pastorczak A, Mlynarski W, Sungalee SKorbel 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. Genomic profiling of Acute lymphoblastic leukemia in ataxia telangiectasia patients reveals tight link between ATM mutations and chromothripsis. (2017) Leukemia doi: 10.1038/leu.2017.55. [Epub ahead of print]
          28. 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. Identification of a genetically defined ultra-high-risk group in relapsed pediatric T-lymphoblastic leukemia. (2017) Blood Cancer J 7(2):e523
          29. 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, Rappsilbe, J, Jechlinger M, Korbel JO, Berger I, Braese S, Lemke EA. Genetic code expansion for multiprotein complex engineering. (2016) Nat Methods 12:997-1000.
          30. Cannavo E, Khoueiry P, Garfield DA, Geeleher P, Zichner T, Gustafson EH, Ciglar L, Korbel JO, and Furlong EE. Shadow Enhancers Are Pervasive Features of Developmental Regulatory Networks. (2016) Curr Biol 26:38-51.
          31. Gatz SA, Salles D, Jacobsen EM, Dork T, Rausch T, Aydin S, Surowy H, Volcic M, Vogel W, Debatin KM, Stutz AM, Schwarz K, Pannicke U, Hess T, Korbel JO, Schulz AS, Schumacher J, and Wiesmuller L. MCM3AP and POMP Mutations Cause a DNA-Repair and DNA-Damage-Signaling Defect in an Immunodeficient Child. (2016) Hum Mutat 37, 257-68.
          32. Molnar-Gabor F, Korbel JO. Processing of patient data in the cloud. (2016) Zeitschrift für Datenschutz 6:274.
          33. 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 K, Amstislavskiy V, Lehrach H, Yaspo ML, Eils R, Lichter P, Korbel JO, Pfister SM, Bradner JE, Northcott P. Active medulloblastoma enhancers reveal subgroup-specific cellular origins. (2016) Nature 530:57-62.
          34. 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. Atypical Teratoid/Rhabdoid Tumors Are Comprised of Three Epigenetic Subgroups with Distinct Enhancer Landscapes. (2016) Cancer Cell 29:379-93.
          35. Schütze DM, ,Krijgsman O, Snijders PJF, Ylstra B, Weischenfeldt J, Mardin BR, Stütz AM, Korbel JO, de Winter JP, Meijer CJLM, Quint W, Bosch L, Wilting SM, Steenbergen RDM. Immortalization capacity of HPV types is inversely related to chromosomal instability. (2016) Oncotarget 25:37608-37621.
          36. 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. No correlation between NF1 mutation position and risk of optic pathway glioma in 77 unrelated NF1 patients. (2016) Hum Genet 5:469-75.
          37. Rowald K, Mantovan M, Passos J, Buccitelli C, Mardin BR, Korbel JO, Jechlinger M, Sotillo R. Negative Selection and Chromosome Instability Induced by Mad2 Overexpression Delay Breast Cancer but Facilitate Oncogene-Independent Outgrowth. (2016) Cell Rep 12:2679-2691.
          38. Coccé MC, Mardin BR, Bens S, Stütz AM, Lubieniecki F, Vater I, Korbel JO, Siebert, R, Alonso CN, Gallego MS. Identification of ZCCHC8 as Fusion Partner of ROS1 in a case of Congenital Glioblastoma Multiforme with a t(6;12)(q21;q24.3). (2016) Genes Chromosomes Cancer 9:677-87.
          39. 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.
          40. Tica J, Lee E, Untergasser A, Meiers S, Garfield DA, Gokcumen O, Furlong EE, Park PJ, Stütz AM, Korbel, JO@. Next-generation sequencing-based detection of germline L1-mediated transductions. (2016) BMC Genomics 1:342.
          41. Sudmant P, Rausch T, Gardner E, Handsaker R, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Fritz M, Konkel M, Malhotra A, Stütz A, Shi X, Casale F, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson M, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam H, 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 J, Kong Y, Lameijer E, McCarthy S, Flicek P, Gibbs R, Marth G, Mason C, Menelaou A, Muzny D, Nelson B, Noor A, Parrish N, Pendleton M, Quitadamo A, Raeder B, Schadt E, Romanovitch M, Schlattl A, Sebra R, Shabalin A, Untergasser A, Walker J, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer M, McCarroll S, The 1000 Genomes Project Consortium, Mills R*, Gerstein M*, 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 526:75-81
          42. 1000 Genomes Consortium (2015). A global reference for human genetic variation. Nature, 526:68-74 (consortium paper with >400 authors, including Korbel JO, as a member of the paper writing group, the steering committee, and a co-chair of the SV Analysis Group).
          43. 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 11:828
          44. 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 100:1442-50
          45. 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 47:1020-9.
          46. George J, Lim JS, Jang SJ, Cun Y, Ozretić L, Kong G, Leenders F, Lu X, Fernández-Cuesta L, Bosco G, Müller 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, Pützer B, Bos M, Michels S, Vlasic I, Seidel D, Pinther B, Schaub P, Becker C, Altmüller 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, Castaños-Vélez E, Roz L, Pastorino U, Brustugun OT, Lund-Iversen M, Thunnissen E, Köhler J, Schuler M, Botling J, Sandelin M, Sanchez-Cespedes M, Salvesen HB, Achter V, Lang U, Bogus M, Schneider PM, Zander T, Ansén S, Hallek M, Wolf J, Vingron M, Yatabe Y, Travis WD, Nürnberg P, Reinhardt C, Perner S, Heukamp L, Büttner R, Haas SA, Brambilla E, Peifer M, Sage J, Thomas RK (2015). Comprehensive genomic profiles of small cell lung cancer. Nature. 524:47-53.
          47. 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 12:780-6.
          48. 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 68:348-50.
          49. 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. Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms (2015). Nat Commun. 6:7256.
          50. 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 JO, Schlomm T, Sauter G, Eils R, Plass C, Santoro R. BAZ2A (TIP5) is involved in epigenetic alterations in prostate cancer and its overexpression predicts disease recurrence (2015). Nat Genet. 47:22-30.
          51. Kluth M, Galal R, Krohn A, Weischenfeldt J, Tsourlakis C, Paustian L, Ahrary R, Ahmed M, Scherzai S, Meyer A, Sirma H, Korbel JO, Sauter G, Schlomm T, Simon R, Minner S (2015) Prevalence of chromosomal rearrangements involving non-ETS genes in prostate cancer. Int J Oncol. 46:1637-42.
          52. 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. Comprehensive characterization of complex structural variations in cancer by directly comparing genome sequence reads (2014). Nat Biotechnol. 32:1106-12.
          53. Northcott P, Lee C, Zichner T, Stütz A, Erkek S, Kawauchi D, Shih D, Hovestadt V, Zapatka M, Sturm D, Jones D, Kool M, Remke M, Cavalli F, Zuyderduyn S, Bader G, VandenBerg S, Adriana Esparza L, Ryzhova M, Wang W, Wittmann A, Stark S, Sieber L, Seker-Cin H, Linke L, Kratochwil F, Jäger N, Buchhalter I, Imbusch C, Zipprich G, Raeder B, Schmidt S, Diess N, Wolf S, Wiemann S, Brors B, Lawerenz C, Eils J, Warnatz H, Risch T, Yaspo M.-L., Weber U, Bartholomae C, 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 M, Ebinger M, Grimes H, Robinson G, Gajjar A, Mynarek M, von Hoff K, Rutkowski S, Pietsch T, Scheurlen W, Felsberg J, Reifenberger G, Kulozik A, von Deimling A, Witt O, Eils R, Gilbertson R, Korshunov A, Taylor M, Lichter P@,*, Korbel JO@,*, Wechsler-Reya R@,* & Pfister S@,* on behalf of the ICGC PedBrain Tumor Project (2014). Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma. Nature 511:428-34.
          54. Mack S, Witt H, Piro R, Gu L, Zuyderduyn S, Stütz A, Wang X, Gallo M, Garzia L, Zayne K, Zhang X, Ramaswamy V, Jäger N, Jones D, Sill M, Pugh T, Ryzhova M, Wani K, Shih D, Head R, Remke M, Bailey S, Zichner T, Faria C, Barszczyk M, Stark S, Seker-Cin H, Hutter S, Johann P, Bender S, Hovestadt V, Tzaridis T, Dubuc AM, Northcott P, Peacock J, Bertrand K, Agnihotri S, Cavalli F, Clarke I, Nethery-Brokx K, Creasy CL, Verma S, Koster J, Wu X, Yao Y, Milde T, Sin-Chan P, Zuccaro J, Lau L, Pereira S, Castelo-Branco P, Hirst M, Marra M, Roberts SS, Fults D, Massimi L, Cho Y, Van Meter T, Grajkowska W, Lach B, Kulozik A, von Deimling A, Witt O, Scherer S, Fan X, Muraszko K, Kool M, Pomeroy S, Gupta N, Phillips J, Huang A, Tabori U, Hawkins C, Malkin D, Kongkham P, Weiss WA, Jabado N, Rutka JT, Bouffet E, Korbel JO, Lupien M, Aldape K, Bader G, Eils R, Lichter P, Dirks PB, Pfister S, Korshunov A & Taylor M (2014). Epigenomic alterations define lethal CIMP-positive ependymomas of infancy. Nature 506:445-50.
          55. 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 M, Schüller U, Korshunov A, Eils R, Wechsler-Reya R, Lichter P & Pfister S, for the ICGC PedBrain Tumor Project (2014). Genome Sequencing of SHH Medulloblastoma Predicts Genotype-Related Response to Smoothened Inhibition. Cancer Cell 25:393-405.
          56. 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:e188-92.
          57. 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 JO, 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 66:978-81
          58. 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 JO, Schlomm T, Tanay A, Sauter G, Gerhäuser C & Plass C, for the ICGC Early Onset Prostate Cancer Project (2014). Intratumor DNA methylation heterogeneity reflects clonal evolution in aggressive prostate cancer. Cell Rep 8:798-806.
          59. 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 JO, 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, 135:1369-80.
          60. 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 15:190-4
          61. 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 JO, 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. 16:764-8
          62. 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. 24:1193-208.
          63. 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. PNAS 110:15764-9.
          64. Zichner T, Garfield DA, Rausch T, Stütz AM, Cannavó E, Braun M, Furlong EE & Korbel JO@ (2013). Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing. Genome Res 23:568-79.
          65. Weischenfeldt J, Simon R, Feuerbach L, Schlangen K, Weichenhan D, Minner S, Wuttig D, Warnatz HJ, Stehr H, Rausch T, Jäger N, Gu L, Bogatyrova O, Stütz AM, Claus R, Eils J, Eils R, Gerhäuser C, Huang PH, Hutter B, Kabbe R, Lawerenz C, Radomski S, Bartholomae CC, Fälth M, Gade S, Schmidt M, Amschler N, Haß T, Galal R, Gjoni J, Kuner R, Baer C, Masser S, von Kalle C, Zichner T, Benes V, Raeder B, Mader M, Amstislavskiy V, Avci M, Lehrach H, Parkhomchuk D, Sultan M, Burkhardt L, Graefen M, Huland H, Kluth M, Krohn A, Sirma H, Stumm L, Steurer S, Grupp K, Sültmann H*, Sauter G*, Plass C*, Brors B*, Yaspo ML*, Korbel JO@,* & Schlomm T* (2013). Integrative genomic analyses reveal an androgen-driven somatic alteration landscape in early-onset prostate cancer. Cancer Cell 23:159-70.
          66. Greil J, Rausch T, Giese T, Bandapalli OR, Daniel V, Bekeredjian-Ding I, Stütz AM, Drees C, Roth S, Ruland J, Korbel JO@ & Kulozik AE@ (2013). Whole-exome sequencing links caspase recruitment domain 11 (CARD11) inactivation to severe combined immunodeficiency. JACI 131:1376-83.
          67. Jones DT, Hutter B, Jäger N, Korshunov A, Kool M, Warnatz HJ, Zichner T, Lambert SR, Ryzhova M, Quang DA, Fontebasso AM, Stütz AM, Hutter S, Zuckermann M, Sturm D, Gronych J, Lasitschka B, Schmidt S, Seker-Cin H, Witt H, Sultan M, Ralser M, Northcott PA, Hovestadt V, Bender S, Pfaff E, Stark S, Faury D, Schwartzentruber J, Majewski J, Weber UD, Zapatka M, Raeder B, Schlesner M, Worth CL, Bartholomae CC, von Kalle C, Imbusch CD, Radomski S, Lawerenz C, van Sluis P, Koster J, Volckmann R, Versteeg R, Lehrach H, Monoranu C, Winkler B, Unterberg A, Herold-Mende C, Milde T, Kulozik AE, Ebinger M, Schuhmann MU, Cho YJ, Pomeroy SL, von Deimling A, Witt O, Taylor MD, Wolf S, Karajannis MA, Eberhart CG, Scheurlen W, Hasselblatt M, Ligon KL, Kieran MW, Korbel JO, Yaspo ML, Brors B, Felsberg J, Reifenberger G, Collins VP, Jabado N, Eils R, Lichter P & Pfister SM, for the International Cancer Genome Consortium PedBrain Tumor Project (2013). Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma. Nat Genet 45:927-32.
          68. Kluth M, Hesse J, Heinl A, Krohn A, Steurer S, Sirma H, Simon R, Mayer PS, Schumacher U, Grupp K, Izbicki JR, Pantel K, Dikomey E, Korbel JO, Plass C, Sauter G, Schlomm T & Minner S. (2013). Genomic deletion of MAP3K7 at 6q12-22 is associated with early PSA recurrence in prostate cancer and absence of TMPRSS2:ERG Mod Pathol 26:975-83.
          69. Grosch M, Grüner B, Spranger S, Stütz AM, Rausch T, Korbel JO, Seelow D, Nürnberg P, Sticht H, Lausch E, Zabel B, Winterpacht A & Tagariello A (2013). Identification of a Ninein (NIN) mutation in a family with spondyloepimetaphyseal dysplasia with joint laxity (leptodactylic type)-like phenotype. Matrix Biol 32:387-92.
          70. Landry JJ, Pyl PT, Rausch T, Zichner T, Tekkedil MM, Stütz AM, Jauch A, Aiyar RS, Pau G, Delhomme N, Gagneur J, Korbel JO, Huber W, Steinmetz LM (2013). The Genomic and Transcriptomic Landscape of a HeLa Cell Line. G3 (Bethesda) 3:1213-24.
          71. Rausch T, Jones DT, Zapatka M, Stütz AM, Zichner T, Weischenfeldt J, Jäger N, Remke M, Shih D, Northcott PA, Pfaff E, Tica J, Wang Q, Massimi L, Witt H, Bender S, Pleier S, Cin H, Hawkins C, Beck C, von Deimling A, Hans V, Brors B, Eils R, Scheurlen W, Blake J, Benes V, Kulozik AE, Witt O, Martin D, Zhang C, Porat R, Merino DM, Wasserman J, Jabado N, Fontebasso A, Bullinger L, Rücker FG, Döhner K, Döhner H, Koster J, Molenaar JJ, Versteeg R, Kool M, Tabori U, Malkin D, Korshunov A, Taylor MD, Lichter P@,*, Pfister SM@,* & Korbel JO@,* (2012). Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 Cell 148:59-71.
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          75. Richter J, Schlesner M, Hoffmann S, Kreuz M, Leich E, Burkhardt B, Rosolowski M, Ammerpohl O, Wagener R, Bernhart SH, Lenze D, Szczepanowski M, Paulsen M, Lipinski S, Russell RB, Adam-Klages S, Apic G, Claviez A, Hasenclever D, Hovestadt V, Hornig N, Korbel JO, Kube D, Langenberger D, Lawerenz C, Lisfeld J, Meyer K, Picelli S, Pischimarov J, Radlwimmer B, Rausch T, Rohde M, Schilhabel M, Scholtysik R, Spang R, Trautmann H, Zenz T, Borkhardt A, Drexler HG, Möller P, MacLeod RA, Pott C, Schreiber S, Trümper L, Loeffler M, Stadler PF, Lichter P, Eils R, Küppers R, Hummel M, Klapper W, Rosenstiel P, Rosenwald A, Brors B & Siebert R; for the ICGC MMML-Seq Project (2012). Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated genome, exome and transcriptome sequencing. Nat Genet 44:1316-20.
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          77. Haemmerling S, Behnisch W, Doerks T, Korbel JO, Bork P, Moog U, Hentze S, Grasshoff U, Bonin M, Rieß O, Janssen JW, Jauch A, Bartram CR, Reinhardt D, Koch KA, Bandapalli OR & Kulozik AE (2012). A 15q24 microdeletion in transient myeloproliferative disease (TMD) and acute megakaryoblastic leukaemia (AMKL) implicates PML and SUMO3 in the leukaemogenesis of TMD/AMKL. Br J Haematol 157:180-187.
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          80. Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stütz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE*, Gerstein MB*, Hurles ME*, Lee C*, McCarroll SA* & Korbel JO@,*; 1000 Genomes Project (2011). Mapping copy number variation by population-scale genome sequencing. Nature 470:59-65.
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          82. Stewart C, Kural D, Strömberg MP, Walker JA, Konkel MK, Stütz AM, Urban AE, Grubert F, Lam HY, Lee WP, Busby M, Indap AR, Garrison E, Huff C, Xing J, Snyder MP, Jorde LB, Batzer MA, Korbel JO & Marth GT; 1000 Genomes Project (2011). A comprehensive map of mobile element insertion polymorphisms in humans. PLoS Genet 7:e1002236.
          83. Waszak SM, Hasin Y, Zichner T, Olender T, Keydar I, Khen M, Stütz AM, Schlattl A, Lancet D, Korbel JO@ (2010). Systematic inference of copy-number genotypes from personal genome sequencing data reveals extensive olfactory receptor gene content diversity. PLoS Comput Biol6:e1000988.
          84. Kasowski M, Grubert F, Heffelfinger C, Hariharan M, Asabere A, Waszak SM, Habegger L, Rozowsky J, Shi M, Urban AE, Hong MY, Karczewski KJ, Huber W, Weissman SM, Gerstein MB, Korbel JO@ & Snyder M@ (2010). Variation in transcription factor binding among humans. Science 328:232-5.
          85. Lam HY*, Mu XJ*, Stütz AM, Tanzer A, Cayting PD, Snyder M, Kim PM, Korbel JO@,* & Gerstein MB@ (2010). Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library. Nat Biotechnol 28:47-55.
          86. The 1000 Genomes Project Consortium (2010). A map of human genome variation from population-scale sequencing. Nature 467:1061-73 [consortium paper, 361 authors, including Korbel JO].
          87. Nishant KT, Wei W, Mancera E, Argueso JL, Schlattl A, Delhomme N, Ma X, Bustamante CD, Korbel JO, Gu Z, Steinmetz LM & Alani E (2010). The Baker’s Yeast Diploid Genome Is Remarkably Stable in Vegetative Growth and Meiosis. PLoS Genet 6: e1001109.
          88. Korbel JO@, Abyzov A, Mu XJ, Carriero N, Cayting P, Zhang Z, Snyder M & Gerstein MB (2009). PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biol10:R23.
          89. Korbel JO*, Tirosh-Wagner T*, Urban AE*, Chen XN, Kasowski M, Dai L, Grubert F, Erdman C, Gao MC, Lange K, Sobel EM, Barlow GM, Aylsworth AS, Carpenter NJ, Clark RD, Cohen MY, Doran E, Falik-Zaccai T, Lewin SO, Lott IT, McGillivray BC, Moeschler JB, Pettenati MJ, Pueschel SM, Rao KW, Shaffer LG, Shohat M, Van Riper AJ, Warburton D, Weissman S, Gerstein MB, Snyder M & Korenberg JR (2009). The genetic architecture of Down syndrome phenotypes revealed by high-resolution analysis of human segmental trisomies. PNAS 106:12031-6.
          90. Demichelis F, Setlur SR, Beroukhim R, Perner S, Korbel JO, Lafargue CJ, Pflueger D, Pina C, Hofer MD, Sboner A, Svensson MA, Rickman DS, Urban A, Snyder M, Meyerson M, Lee C, Gerstein MB, Kuefer R & Rubin MA (2009). Distinct genomic aberrations associated with ERG rearranged prostate cancer. Genes Chromosomes Cancer 48:366-80.
          91. Gianoulis TA, Raes J, Patel PV, Bjornson R, Korbel JO, Letunic I, Yamada T, Paccanaro A, Jensen LJ, Snyder M, Bork P & Gerstein MB (2009). Quantifying environmental adaptation of metabolic pathways in metagenomics. PNAS 106:1374-9. (
          92. Wang LY, Abyzov A, Korbel JO, Snyder M & Gerstein M (2009). MSB: a mean-shift-based approach for the analysis of structural variation in the genome. Genome Res 19:106-17.
          93. Hasin Y, Olender T, Khen M, Gonzaga-Jauregui C, Kim PM, Urban AE, Snyder M, Gerstein MB, Lancet D & Korbel JO@ (2008). High-resolution copy-number variation map reflects human olfactory receptor diversity and evolution. PLoS Genet 4:e1000249.
          94. Kim PM, Lam HY, Urban AE, Korbel JO, Affourtit J, Grubert F, Chen X, Weissman S, Snyder M & Gerstein MB (2008). Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history. Genome Res 18:1865-74.
          95. Lee AS, Gutiérrez-Arcelus M, Perry GH, Vallender EJ, Johnson WE, Miller GM, Korbel JO & Lee C (2008). Analysis of copy number variation in the rhesus macaque genome identifies candidate loci for evolutionary and human disease studies. Hum Mol Genet 17:1127-36.
          96. Korbel JO*, Urban AE*, Affourtit JP*, Godwin B, Grubert F, Simons JF, Kim PM, Palejev D, Carriero NJ, Du L, Taillon BE, Chen Z, Tanzer A, Saunders AC, Chi J, Yang F, Carter NP, Hurles ME, Weissman SM, Harkins TT, Gerstein MB, Egholm M & Snyder M (2007). Paired-end mapping reveals extensive structural variation in the human genome. Science 318:420-6.
          97. Korbel JO*, Urban AE*, Grubert F, Du J, Royce TE, Starr P, Zhong G, Emanuel BS, Weissman SM, Snyder M & Gerstein MB (2007). Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome. PNAS 104:10110-5.
          98. Kim PM@,*, Korbel JO@,* & Gerstein MB@ (2007). Positive selection at the protein network periphery: evaluation in terms of structural constraints and cellular context. PNAS 104:20274-9.
          99. The ENCODE Project Consortium (2007). Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799-816 [consortium paper with 311 authors, including Korbel JO].
          100. Washietl S, Pedersen JS, Korbel JO, Stocsits C, Gruber AR, Hackermüller J, Hertel J, Lindemeyer M, Reiche K, Tanzer A, Ucla C, Wyss C, Antonarakis SE, Denoeud F, Lagarde J, Drenkow J, Kapranov P, Gingeras TR, Guigó R, Snyder M, Gerstein MB, Reymond A, Hofacker IL & Stadler PF (2007). Structured RNAs in the ENCODE selected regions of the human genome. Genome Res 17:852-64.
          101. Rozowsky JS, Newburger D, Sayward F, Wu J, Jordan G, Korbel JO, Nagalakshmi U, Yang J, Zheng D, Guigó R, Gingeras TR, Weissman S, Miller P, Snyder M & Gerstein MB (2007). The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci. Genome Res 17:732-45.
          102. Raes J*, Korbel JO*, Lercher MJ, von Mering C, Bork P. (2007). Prediction of effective genome size in metagenomic samples. Genome Biol 8: R10.
          103. Pachkov M, Dandekar T, Korbel JO, Bork P, Schuster S (2007). Use of pathway analysis and genome context methods for functional genomics of Mycoplasma pneumoniae nucleotide metabolism. Gene 396:215-25.
          104. Li L, Wang X, Sasidharan R, Stolc V, Deng W, He H, Korbel JO, Chen X, Tongprasit W, Ronald P, Chen R, Gerstein M & Deng XW. (2007). Global identification and characterization of transcriptionally active regions in the rice genome. PLoS One 2:e294.
          105. Yanai I, Korbel JO, Boue S, McWeeney SK, Bork P & Lercher MJ (2006). Similar gene expression profiles do not imply similar tissue functions. Trends Genet 22:132-8.
          106. Urban AE*, Korbel JO*, Selzer R, Richmond T, Hacker A, Popescu GV, Cubells JF, Green R, Emanuel BS, Gerstein MB, Weissman SM & Snyder M (2006). High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays. PNAS 103:4534-4539.
          107. Du J, Rozowsky JS, Korbel JO, Zhang ZD, Royce TE, Schultz MH, Snyder M & Gerstein M. (2006). A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and ChIP-chip experiments: systematically incorporating validated biological knowledge. Bioinformatics 22:3016-24.
          108. Rozowsky J, Wu J, Lian Z, Nagalakshmi U, Korbel JO, Kapranov P, Zheng D, Dyke S, Newburger P, Miller P, Gingeras TR, Weissman S, Gerstein M, Snyder M (2006). Novel transcribed regions in the human genome. Cold Spring Harb Symp Quant Biol. 71:111-6.
          109. Korbel JO*, Doerks T*, Jensen LJ, Perez-Iratxeta C, Kaczanowski S, Hooper SD, Andrade MA & Bork P (2005). Systematic association of genes to phenotypes by genome and literature mining. PLoS Biol 3:e134.
          110. Korbel JO, Jensen LJ, von Mering C, Bork P (2004). Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs. Nat Biotechnol 22:911-917.
          111. Pena RN, Webster J, Kwan S, Korbel JO, Whitelaw BA (2004). Transgene methylation in mice reflects copy number but not expression level. Mol Biotechnol 26:215-20.
          112. Crass T, Antes I, Basekow R, Bork P, Buning C, Christensen M, Claussen H, Ebeling C, Ernst P, Gailus-Durner V, Glatting KH, Gohla R, Gössling F, Grote K, Heidtke K, Herrmann A, O’Keeffe S, Kiesslich O, Kolibal S, Korbel JO, Lengauer T, Liebich I, van der Linden M, Luz H, Meissner K, von Mering C, Mevissen HT, Mewes HW, Michael H, Mokrejs M, Müller T, Pospisil H, Rarey M, Reich JG, Schneider R, Schomburg D, Schulze-Kremer S, Schwarzer K, Sommer I, Springstubbe S, Suhai S, Thoppae G, Vingron M, Warfsmann J, Werner T, Wetzler D, Wingender E & Zimmer R (2004). The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources. Bioinformatics 20:268-70.
          113. Morett E*, Korbel JO*, Rajan E, Saab-Rincon G, Olvera L, Olvera M, Schmidt S, Snel B & Bork P (2003). Systematic discovery of analogous enzymes in thiamin biosynthesis. Nat Biotechnol
            21:790-5.
          114. Korbel JO*, Snel B*, Huynen MA & Bork P. (2002). SHOT: a web server for the construction of genome phylogenies. Trends Genet 18:158-62.
          115. Kiełbasa S*, Korbel JO*, Beule D, Schuchhardt J, Herzel H (2001). Combining frequency and positional information to predict transcription factor binding sites. Bioinformatics 17:1019-26.