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Korbel Group

From genomic variation to molecular mechanism

Publications

Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas.

Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R

Leukemia 2021

33953289. doi:10.1038/s41375-021-01251-z.

Publisher Correction: LifeTime and improving European healthcare through cell-based interceptive medicine.

Rajewsky N, Almouzni G, Gorski SA, Aerts S, Amit I, Bertero MG, Bock C, Bredenoord AL, Cavalli G, Chiocca S, Clevers H, De Strooper B, Eggert A, Ellenberg J, Fernández XM, Figlerowicz M, Gasser SM, Hubner N, Kjems J, Knoblich JA, Krabbe G, Lichter P, Linnarsson S, Marine JC, Marioni JC, Marti-Renom MA, Netea MG, Nickel D, Nollmann M, Novak HR, Parkinson H, Piccolo S, Pinheiro I, Pombo A, Popp C, Reik W, Roman-Roman S, Rosenstiel P, Schultze JL, Stegle O, Tanay A, Testa G, Thanos D, Theis FJ, Torres-Padilla ME, Valencia A, Vallot C, van Oudenaarden A, Vidal M, Voet T, LifeTime Community Working Groups

Nature 2021

33731935. doi:10.1038/s41586-021-03287-8.

Haplotype-resolved diverse human genomes and integrated analysis of structural variation.

Ebert P, Audano PA, Zhu Q, Rodriguez-Martin B, Porubsky D, Bonder MJ, Sulovari A, Ebler J, Zhou W, Serra Mari R, Yilmaz F, Zhao X, Hsieh P, Lee J, Kumar S, Lin J, Rausch T, Chen Y, Ren J, Santamarina M, Höps W, Ashraf H, Chuang NT, Yang X, Munson KM, Lewis AP, Fairley S, Tallon LJ, Clarke WE, Basile AO, Byrska-Bishop M, Corvelo A, Evani US, Lu TY, Chaisson MJP, Chen J, Li C, Brand H, Wenger AM, Ghareghani M, Harvey WT, Raeder B, Hasenfeld P, Regier AA, Abel HJ, Hall IM, Flicek P, Stegle O, Gerstein MB, Tubio JMC, Mu Z, Li YI, Shi X, Hastie AR, Ye K, Chong Z, Sanders AD, Zody MC, Talkowski ME, Mills RE, Devine SE, Lee C, Korbel JO, Marschall T, Eichler EE

Science (New York, N.Y.) 2021

33632895. doi:10.1126/science.abf7117.

Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility.

Warren WC, Harris RA, Haukness M, Fiddes IT, Murali SC, Fernandes J, Dishuck PC, Storer JM, Raveendran M, Hillier LW, Porubsky D, Mao Y, Gordon D, Vollger MR, Lewis AP, Munson KM, DeVogelaere E, Armstrong J, Diekhans M, Walker JA, Tomlinson C, Graves-Lindsay TA, Kremitzki M, Salama SR, Audano PA, Escalona M, Maurer NW, Antonacci F, Mercuri L, Maggiolini FAM, Catacchio CR, Underwood JG, O'Connor DH, Sanders AD, Korbel JO, Ferguson B, Kubisch HM, Picker L, Kalin NH, Rosene D, Levine J, Abbott DH, Gray SB, Sanchez MM, Kovacs-Balint ZA, Kemnitz JW, Thomasy SM, Roberts JA, Kinnally EL, Capitanio JP, Skene JHP, Platt M, Cole SA, Green RE, Ventura M, Wiseman RW, Paten B, Batzer MA, Rogers J, Eichler EE

Science (New York, N.Y.) 2020

33335035. doi:10.1126/science.abc6617.

Life time and improving European healthcare through cell-based interceptive medicine.

Rajewsky N, Almouzni G, Gorski SA, Aerts S, Amit I, Bertero MG, Bock C, Bredenoord AL, Cavalli G, Chiocca S, Clevers H, De Strooper B, Eggert A, Ellenberg J, Fernández XM, Figlerowicz M, Gasser SM, Hubner N, Kjems J, Knoblich JA, Krabbe G, Lichter P, Linnarsson S, Marine JC, Marioni J, Marti-Renom MA, Netea MG, Nickel D, Nollmann M, Novak HR, Parkinson H, Piccolo S, Pinheiro I, Pombo A, Popp C, Reik W, Roman-Roman S, Rosenstiel P, Schultze JL, Stegle O, Tanay A, Testa G, Thanos D, Theis FJ, Torres-Padilla ME, Valencia A, Vallot C, van Oudenaarden A, Vidal M, Voet T

Nature 2020

32894860. doi:10.1038/s41586-020-2715-9.

Recurrent inversion toggling and great ape genome evolution.

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

Nature genetics 2020

32541924. doi:10.1038/s41588-020-0646-x.

Germline Elongator mutations in Sonic Hedgehog medulloblastoma.

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, Kool M, Sturm D, Jones DTW, Vasilyeva A, Tatevossian RG, Neale G, Lombard B, Loew D, Nakitandwe J, Rusch M, Bowers DC, Bendel A, Partap S, Chintagumpala M, Crawford J, Gottardo NG, Smith A, Dufour C, Rutkowski S, Eggen T, Wesenberg F, Kjaerheim K, Feychting M, Lannering B, Schüz J, Johansen C, Andersen TV, Röösli M, Kuehni CE, Grotzer M, Remke M, Puget S, Pajtler KW, Milde T, Witt O, Ryzhova M, Korshunov A, Orr BA, Ellison DW, Brugieres L, Lichter P, Nichols KE, Gajjar A, Wainwright BJ, Ayrault O, Korbel JO, Northcott PA, Pfister SM

Nature 2020

32296180. doi:10.1038/s41586-020-2164-5.

Genomic basis for RNA alterations in cancer.

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

Nature 2020

32025019. doi:10.1038/s41586-020-1970-0.

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

Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, 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

Nature 2020

32025015. doi:10.1038/s41586-020-1965-x.

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

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

Genome medicine 2020

32075696. doi:10.1186/s13073-020-0713-z.

Eleven grand challenges in single-cell data science.

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

Genome biology 2020

32033589. doi:10.1186/s13059-020-1926-6.

Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer

Akdemir KC, Le VTT, Chandran S, Li YL, Verhaak RG, Beroukhim R, Campbell PJ, Chin L, Dixon JR, Futreal PA, Alvarez EG, Baez-Ortega A, Beroukhim R, Boutros PC, Bowtell DDL, Brors B, Burns KH, Chan K, Chen K, Cortes-Ciriano I, Dueso-Barroso A, Dunford AJ, Edwards PA, Estivill X, Etemadmoghadam D, Feuerbach L, Fink JL, Frenkel-Morgenstern M, Garsed DW, Gerstein M, Gordenin DA, Haan D, Haber JE, Hess JM, Hutter B, Imielinski M, Jones DTW, Ju YS, Kazanov MD, Klimczak LJ, Koh Y, Korbel JO, Kumar K, Lee EA, Lee JJK, Lynch AG, Macintyre G, Markowetz F, Martincorena I, Martinez-Fundichely A, Meyerson M, Miyano S, Nakagawa H, Navarro FCP, Ossowski S, Park PJ, Pearson JV, Puiggros M, Rippe K, Roberts ND, Roberts SA, Rodriguez-Martin B, Schumacher SE, Scully R, Shackleton M, Sidiropoulos N, Sieverling L, Stewart C, Torrents D, Tubio JMC, Villasante I, Waddell N, Wala JA, Weischenfeldt J, Yang LX, Yao XT, Yoon SS, Zamora J, Zhang CZ

NATURE GENETICS 2020

32024999. doi:10.1038/s41588-019-0564-y.

Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis.

Carlevaro-Fita J, Lanzos A, Feuerbach L, Hong C, Mas-Ponte D, Pedersen JS, Johnson R, Abascal F, Amin SB, Bader GD, Barenboim J, Beroukhim R, Bertl J, Boroevich KA, Brunak S, Campbell PJ, Carlevaro-Fita J, Chakravarty D, Chan CWY, Chen K, Choi JK, Deu-Pons J, Dhingra P, Diamanti K, Feuerbach L, Fink JL, Fonseca NA, Frigola J, Gambacorti-Passerini C, Garsed DW, Gerstein M, Getz G, Gonzalez-Perez A, Guo QY, Gut IG, Haan D, Hamilton MP, Haradhvala NJ, Harmanci AO, Helmy M, Herrmann C, Hess JM, Hobolth A, Hodzic E, Hong C, Hornshoj H, Isaev K, Izarzugaza JMG, Johnson TA, Juul M, Juul RI, Kahles A, Kahraman A, Kellis M, Khurana E, Kim J, Kim JK, Kim Y, Komorowski J, Korbel JO, Kumar S, Lanzos A, Larsson E, Lawrence MS, Lee D, Lehmann KV, Li ST, Li XT, Lin Z, Liu EM, Lochovsky L, Lou SK, Madsen T, Marchal K, Martincorena I, Martinez-Fundichely A, Maruvka YE, McGillivray PD, Meyerson W, Muinos F, Mularoni L, Nakagawa H, Nielsen MM, Paczkowska M, Park K, Park K, Pedersen JS, Pich O, Pons T, Pulido-Tamayo S, Raphael BJ, Reimand J, Reyes-Salazar I, Reyna MA, Rheinbay E, Rubin MA, Rubio-Perez C, Sabarinathan R, Sahinalp SC, Saksena G, Salichos L, Sander C, Schumacher SE, Shackleton M, Shapira O, Shen CY, Shrestha R, Shuai SM, Sidiropoulos N, Sieverling L, Sinnott-Armstrong N, Stein LD, Stuart JM, Tamborero D, Tiao GC, Tsunoda T, Umer HM, Uuskula-Reimand L, Valencia A, Vazquez M, Verbeke LPC, Wadelius C, Wadi L, Wang JY, Warrell J, Waszak SM, Weischenfeldt J, Wheeler DA, Wu GM, Yu J, Zhang J, Zhang XP, Zhang Y, Zhao ZM, Zou LH, von Mering C

COMMUNICATIONS BIOLOGY 2020

32024996. doi:10.1038/s42003-019-0741-7.

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

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

Nature genetics 2020

32024998. doi:10.1038/s41588-019-0562-0.

The effects of common structural variants on 3D chromatin structure.

Shanta O, Noor A, Sebat J, Chaisson MJP, Sanders AD, Zhao XF, 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 XM, Hormozdiari F, Lee DL, Wenger AM, Hastie AR, Antaki D, Anantharaman T, Audano PA, Brand H, Cantsilieris S, Cao H, Cerveira E, Chen C, Chen XT, Chin CS, Chong ZC, Chuang NST, Lambert CC, Church DM, Clarke L, Farrell A, Flores J, Galeey T, Gujral M, Guryev V, Heaton WH, Korlach J, Kumar S, Kwon JY, Lam ET, Lee JE, Lee JC, Lee WP, Lee SP, Li ST, Marks P, Viaud-Martinez K, Meiers S, Munson KM, Navarro FCP, Nelson BJ, Nodzak C, Kyriazopoulou-Panagiotopoulou S, Pang AWC, Rosanio G, Ryan M, Stutz A, Spierings DCJ, Ward A, Welch AME, Xiao M, Xu W, Zhang CS, Zhu QH, Zheng-Bradley X, Lowy E, Yakneen S, McCarroll S, Jun G, Ding L, Koh CL, Flicek P, Chen K, Gerstein MB, Kwok PY, Lansdorp PM, Marth GT, Shi XH, Bashir A, Ye K, Devine SE, Talkowski ME, Mills RE, Marschall T, Korbel JO, Eichler EE, Lee CL

BMC GENOMICS 2020

32000688. doi:10.1186/s12864-020-6516-1.

Germline GPR161 mutations predispose to pediatric medulloblastoma.

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

Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2019

31609649. doi:10.1200/JCO.19.00577.

The molecular landscape of ETMR at diagnosis and relapse.

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

Nature 2019

31802000. doi:10.1038/s41586-019-1815-x.

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

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

Nature reviews. Genetics 2019

31520075. doi:10.1038/s41576-019-0178-3.

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

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

Nature reviews. Genetics 2019

31455890. doi:10.1038/s41576-019-0156-9.

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

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

Nature communications 2019

30992455. doi:10.1038/s41467-018-08148-z.

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

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

Nature communications 2019

30926794. doi:10.1038/s41467-019-08578-3.

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

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

EMBO molecular medicine 2018

30389682. doi:10.15252/emmm.201809443.

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

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

Cancer cell 2018

30595504. doi:10.1016/j.ccell.2018.11.014.

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

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

Cancer cell 2018

30537516. doi:10.1016/j.ccell.2018.10.016.

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

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Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma

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, International Cancer Genome Consortium PedBrain Tumor Project

Nature genetics 2013

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Recurrent FGFR1 hotspot mutations represent a novel therapeutic target in childhood astrocytorna

Jones DTW, Hutter B, Jager N, Korshunov A, Kool M, Lambert SR, Quang DAK, Fontebasso AM, Ryzhova M, Warnatz HJ, Zichner T, Korbel JO, Wolf S, Yaspo ML, Ligon KL, Kieran MW, Brors B, Feisberg J, Reifenberger G, Collins VP, Jabado N, Elis R, Lichter P, Pfister SM

CANCER RESEARCH 2013

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Northcott P, Zichner T, Jones D, Kool M, Jager N, Feychting M, Lannering B, Tynes T, Wesenberg F, Hauser P, Ra YS, Zitterbart K, Jabado N, Chan J, Fults D, Mueller S, Grajkowska W, Lichter P, Korbel J, Pfister S

NEURO-ONCOLOGY 2013

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Integrative genomic analyses reveal an androgen-driven somatic alteration landscape in early-onset prostate cancer

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Cancer cell 2013

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Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated genome, exome and transcriptome sequencing

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Nature genetics 2012

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Dissecting the genomic complexity underlying medulloblastoma

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Nature 2012

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Subgroup-specific structural variation across 1,000 medulloblastoma genomes

Northcott PA, Shih DJ, Peacock J, Garzia L, Morrissy AS, Zichner T, Stütz AM, Korshunov A, Reimand J, Schumacher SE, Beroukhim R, Ellison DW, Marshall CR, Lionel AC, Mack S, Dubuc A, Yao Y, Ramaswamy V, Luu B, Rolider A, Cavalli FM, Wang X, Remke M, Wu X, Chiu RY, Chu A, Chuah E, Corbett RD, Hoad GR, Jackman SD, Li Y, Lo A, Mungall KL, Nip KM, Qian JQ, Raymond AG, Thiessen NT, Varhol RJ, Birol I, Moore RA, Mungall AJ, Holt R, Kawauchi D, Roussel MF, Kool M, Jones DT, Witt H, Fernandez-L A, Kenney AM, Wechsler-Reya RJ, Dirks P, Aviv T, Grajkowska WA, Perek-Polnik M, Haberler CC, Delattre O, Reynaud SS, Doz FF, Pernet-Fattet SS, Cho BK, Kim SK, Wang KC, Scheurlen W, Eberhart CG, Fèvre-Montange M, Jouvet A, Pollack IF, Fan X, Muraszko KM, Gillespie GY, Di Rocco C, Massimi L, Michiels EM, Kloosterhof NK, French PJ, Kros JM, Olson JM, Ellenbogen RG, Zitterbart K, Kren L, Thompson RC, Cooper MK, Lach B, McLendon RE, Bigner DD, Fontebasso A, Albrecht S, Jabado N, Lindsey JC, Bailey S, Gupta N, Weiss WA, Bognár L, Klekner A, Van Meter TE, Kumabe T, Tominaga T, Elbabaa SK, Leonard JR, Rubin JB, Liau LM, Van Meir EG, Fouladi M, Nakamura H, Cinalli G, Garami M, Hauser P, Saad AG, Iolascon A, Jung S, Carlotti CG, Vibhakar R, Ra YS, Robinson S, Zollo M, Faria CC, Chan JA, Levy ML, Sorensen PH, Meyerson M, Pomeroy SL, Cho YJ, Bader GD, Tabori U, Hawkins CE, Bouffet E, Scherer SW, Rutka JT, Malkin D, Clifford SC, Jones SJ, Korbel JO, Pfister SM, Marra MA, Taylor MD

Nature 2012

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Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma (vol 482, pg 226, 2012)

Schwartzentruber J, Korshunov A, Liu XY, Jones DTW, Pfaff E, Jacob K, Sturm D, Fontebasso AM, Quang DAK, Tonjes M, Hovestadt V, Albrecht S, Kool M, Nantel A, Konermann C, Lindroth A, Jager N, Rausch T, Ryzhova M, Korbel JO, Hielscher T, Hauser P, Garami M, Klekner A, Bognar L, Ebinger M, Schuhmann MU, Scheurlen W, Pekrun A, Fruhwald MC, Roggendorf W, Kramm C, Durken M, Atkinson J, Lepage P, Montpetit A, Zakrzewska M, Zakrzewski K, Liberski PP, Dong ZF, Siegel P, Kulozik AE, Zapatka M, Guha A, Malkin D, Felsberg J, Reifenberger G, von Deimling A, Ichimura K, Collins VP, Witt H, Milde T, Witt O, Zhang C, Castelo-Branco P, Lichter P, Faury D, Tabori U, Plass C, Majewski J, Pfister SM, Jabado N

NATURE 2012

doi:10.1038/nature11026.

Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma

Schwartzentruber J, Korshunov A, Liu XY, Jones DT, Pfaff E, Jacob K, Sturm D, Fontebasso AM, Quang DA, Tönjes M, Hovestadt V, Albrecht S, Kool M, Nantel A, Konermann C, Lindroth A, Jäger N, Rausch T, Ryzhova M, Korbel JO, Hielscher T, Hauser P, Garami M, Klekner A, Bognar L, Ebinger M, Schuhmann MU, Scheurlen W, Pekrun A, Frühwald MC, Roggendorf W, Kramm C, Dürken M, Atkinson J, Lepage P, Montpetit A, Zakrzewska M, Zakrzewski K, Liberski PP, Dong Z, Siegel P, Kulozik AE, Zapatka M, Guha A, Malkin D, Felsberg J, Reifenberger G, von Deimling A, Ichimura K, Collins VP, Witt H, Milde T, Witt O, Zhang C, Castelo-Branco P, Lichter P, Faury D, Tabori U, Plass C, Majewski J, Pfister SM, Jabado N

Nature 2012

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Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations

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

Cell 2012

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Mapping copy number variation by population-scale genome sequencing

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

Nature 2011

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The functional spectrum of low-frequency coding variation

Marth GT, Yu F, Indap AR, Garimella K, Gravel S, Leong WF, Tyler-Smith C, Bainbridge M, Blackwell T, Zheng-Bradley X, Chen Y, Challis D, Clarke L, Ball EV, Cibulskis K, Cooper DN, Fulton B, Hartl C, Koboldt D, Muzny D, Smith R, Sougnez C, Stewart C, Ward A, Yu J, Xue Y, Altshuler D, Bustamante CD, Clark AG, Daly M, DePristo M, Flicek P, Gabriel S, Mardis E, Palotie A, Gibbs R, 1000 Genomes Project

Genome biology 2011

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Nature 2010

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Variation in transcription factor binding among humans

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

Science (New York, N.Y.) 2010

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Potential and challenges of personalized genomics and the 1000 Genome Project

Stutz AM, Korbel JO

Medizinische Genetik : Mitteilungsblatt des Berufsverbandes Medizinische Genetik e.V 2010

doi:10.1007/s11825-010-0220-5.

The genetic architecture of Down syndrome phenotypes revealed by high-resolution analysis of human segmental trisomies

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

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Nature 2007

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Structured RNAs in the ENCODE selected regions of the human genome

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Genome research 2007

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Novel transcribed regions in the human genome

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Cold Spring Harbor symposia on quantitative biology 2006

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The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources

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Bioinformatics (Oxford, England) 2004

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Compositional asymmetries and predicted origins of replication of the Saccharomyces Cerevisiae genome

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