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Korbel Group

From genomic variation to molecular mechanism

Publications

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Strategies to decrease inequalities in cancer therapeutics, care and prevention.

Ringborg U, von Braun J, Celis J, Baumann M, Berns A, Eggermont A, Heard E, Heitor M, Chandy M, Chen CJ, Costa A, De Lorenzo F, De Robertis EM, Dubee FC, Ernberg I, Gabriel M, Helland Å, Henrique R, Jönsson B, Kallioniemi O, Korbel J, Krause M, Lowy DR, Michielin O, Nagy P, Oberst S, Paglia V, Parker MI, Ryan K, Sawyers CL, Schüz J, Silkaitis K, Solary E, Thomas D, Turkson P, Weiderpass E, Yang H

Molecular oncology, 2023

doi:10.1002/1878-0261.13575.

Assembly of 43 human Y chromosomes reveals extensive complexity and variation.

Hallast P, Ebert P, Loftus M, Yilmaz F, Audano PA, Logsdon GA, Bonder MJ, Zhou W, Höps W, Kim K, Li C, Hoyt SJ, Dishuck PC, Porubsky D, Tsetsos F, Kwon JY, Zhu Q, Munson KM, Hasenfeld P, Harvey WT, Lewis AP, Kordosky J, Hoekzema K, Human Genome Structural Variation Consortium (HGSVC), O'Neill RJ, Korbel JO, Tyler-Smith C, Eichler EE, Shi X, Beck CR, Marschall T, Konkel MK, Lee C

Nature, 2023

doi:10.1038/s41586-023-06425-6.

A draft human pangenome reference.

Martin FJ, Billis K, Fairley S, Frankish A, Giron CG, Haggerty L, Hourlier T, Korbel JO, Tricomi FF, Flicek P

Nature, 2023

doi:10.1038/s41586-023-05896-x.

Inversion polymorphism in a complete human genome assembly.

Porubsky D, Harvey WT, Rozanski AN, Ebler J, Höps W, Ashraf H, Hasenfeld P, Human Pangenome Reference Consortium (HPRC), Human Genome Structural Variation Consortium (HGSVC), Paten B, Sanders AD, Marschall T, Korbel JO, Eichler EE

Genome biology, 2023

doi:10.1186/s13059-023-02919-8.

Author Correction: 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, Dentro SC, Blanco MG, Contino G, Ardeljan D, Tojo M, Roberts ND, Zumalave S, Edwards PA, Weischenfeldt J, Puiggròs M, Chong Z, Chen K, Lee EA, Wala JA, Raine KM, Butler A, Waszak SM, Navarro FCP, Schumacher SE, Monlong J, Maura F, Bolli N, Bourque G, Gerstein M, Park PJ, Wedge DC, Beroukhim R, Torrents D, Korbel JO, Martincorena I, Fitzgerald RC, Van Loo P, Kazazian HH, Burns KH, PCAWG Structural Variation Working Group, Campbell PJ, Tubio JMC, PCAWG Consortium

Nature genetics, 2023

doi:10.1038/s41588-023-01319-9.

Author correction: 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, 2023

doi:10.1038/s41586-022-05596-y.

Author correction: 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, 2023

doi:10.1038/s41586-022-05599-9.

Semi-automated assembly of high-quality diploid human reference genomes.

Jarvis ED, Formenti G, Rhie A, Guarracino A, Yang C, Wood J, Tracey A, Thibaud-Nissen F, Vollger MR, Porubsky D, Cheng H, Asri M, Logsdon GA, Carnevali P, Chaisson MJP, Chin CS, Cody S, Collins J, Ebert P, Escalona M, Fedrigo O, Fulton RS, Fulton LL, Garg S, Gerton JL, Ghurye J, Granat A, Green RE, Harvey W, Hasenfeld P, Hastie A, Haukness M, Jaeger EB, Jain M, Kirsche M, Kolmogorov M, Korbel JO, Koren S, Korlach J, Lee J, Li D, Lindsay T, Lucas J, Luo F, Marschall T, Mitchell MW, McDaniel J, Nie F, Olsen HE, Olson ND, Pesout T, Potapova T, Puiu D, Regier A, Ruan J, Salzberg SL, Sanders AD, Schatz MC, Schmitt A, Schneider VA, Selvaraj S, Shafin K, Shumate A, Stitziel NO, Stober C, Torrance J, Wagner J, Wang J, Wenger A, Xiao C, Zimin AV, Zhang G, Wang T, Li H, Garrison E, Haussler D, Hall I, Zook JM, Eichler EE, Phillippy AM, Paten B, Howe K, Miga KH, Human Pangenome Reference Consortium

Nature, 2022

doi:10.1038/s41586-022-05325-5.

Rare germline variants are associated with rapid biochemical recurrence after radical prostate cancer treatment: a pan prostate cancer group study.

Burns D, Anokian E, Saunders EJ, Bristow RG, Fraser M, Reimand J, Schlomm T, Sauter G, Brors B, Korbel J, Weischenfeldt J, Waszak SM, Corcoran NM, Jung CH, Pope BJ, Hovens CM, Cancel-Tassin G, Cussenot O, Loda M, Sander C, Hayes VM, Dalsgaard Sorensen K, Lu YJ, Hamdy FC, Foster CS, Gnanapragasam V, Butler A, Lynch AG, Massie CE, CR-UK/Prostate Cancer UK, ICGC, The PPCG, Woodcock DJ, Cooper CS, Wedge DC, Brewer DS, Kote-Jarai Z, Eeles RA

European urology, 2022

doi:10.1016/j.eururo.2022.05.007.

Focal structural variants revealed by whole genome sequencing disrupt the histone demethylase KDM4C in B cell lymphomas.

Lopez C, Schleussner N, Bernhart SH, Kleinheinz K, Sungalee S, Sczakiel HL, Kretzmer H, Toprak UH, Glaser S, Wagener R, Ammerpohl O, Bens S, Giefing M, Sanchez JCG, Apic G, Hubschmann D, Janz M, Kreuz M, Mottok A, Muller JM, Seufert J, Hoffmann S, Korbel JO, Russell RB, Schule R, Trumper L, Klapper W, Radlwimmer B, Lichter P, Kuppers R, Schlesner M, Mathas S, Siebert R

Haematologica, 2022

doi:10.3324/haematol.2021.280005.

Familial long-read sequencing increases yield of de novo mutations.

Noyes MD, Harvey WT, Porubsky D, Sulovari A, Li R, Rose NR, Audano PA, Munson KM, Lewis AP, Hoekzema K, Mantere T, Graves-Lindsay TA, Sanders AD, Goodwin S, Kramer M, Mokrab Y, Zody MC, Hoischen A, Korbel JO, McCombie WR, Eichler EE

American journal of human genetics, 2022

doi:10.1016/j.ajhg.2022.02.014.

The Porto European Cancer Research Summit 2021.

Ringborg U, Berns A, Celis JE, Heitor M, Tabernero J, Schüz J, Baumann M, Henrique R, Aapro M, Basu P, Beets-Tan R, Besse B, Cardoso F, Carneiro F, van den Eede G, Eggermont A, Fröhling S, Galbraith S, Garralda E, Hanahan D, Hofmarcher T, Jönsson B, Kallioniemi O, Kásler M, Kondorosi E, Korbel J, Lacombe D, Carlos Machado J, Martin-Moreno JM, Meunier F, Nagy P, Nuciforo P, Oberst S, Oliveiera J, Papatriantafyllou M, Ricciardi W, Roediger A, Ryll B, Schilsky R, Scocca G, Seruca R, Soares M, Steindorf K, Valentini V, Voest E, Weiderpass E, Wilking N, Wren A, Zitvogel L

Molecular oncology, 2021

doi:10.1002/1878-0261.13078.

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

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

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

doi:10.1126/science.abf7117.

The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research.

Salgado D, Armean IM, Baudis M, Beltran S, Capella-Gutierrez S, Carvalho-Silva D, Dominguez Del Angel V, Dopazo J, Furlong LI, Gao B, Garcia L, Gerloff D, Gut I, Gyenesei A, Habermann N, Hancock JM, Hanauer M, Hovig E, Johansson LF, Keane T, Korbel J, Lauer KB, Laurie S, Leskošek B, Lloyd D, Marques-Bonet T, Mei H, Monostory K, Piñero J, Poterlowicz K, Rath A, Samarakoon P, Sanz F, Saunders G, Sie D, Swertz MA, Tsukanov K, Valencia A, Vidak M, Yenyxe González C, Ylstra B, Béroud C

F1000Research, 2020

doi:10.12688/f1000research.24887.1.

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

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

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

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

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

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

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

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

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

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

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

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

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

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BMC GENOMICS, 2020

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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

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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

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

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Nature reviews. Genetics, 2019

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Nature reviews. Genetics, 2019

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Nature communications, 2019

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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

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EMBO molecular medicine, 2018

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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

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

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Nature, 2018

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

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The Lancet. Oncology, 2018

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The Lancet. Oncology, 2018

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Nature, 2018

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

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Leukemia, 2017

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Mitochondrial mutations drive prostate cancer aggression.

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Nature communications, 2017

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Nature, 2017

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Nature Genetics, 2016

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Recurrent MET fusion genes represent a drug target in pediatric glioblastoma

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NATURE MEDICINE, 2016

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Haematologica, 2016

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Nature methods, 2016

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

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Cancer cell, 2016

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Nature, 2016

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Nature, 2015

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Nature genetics, 2015

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Toward understanding and exploiting tumor heterogeneity.

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NATURE MEDICINE, 2015

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Science (New York, N.Y.), 2010

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

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Proceedings of the National Academy of Sciences of the United States of America, 2009

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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

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Nature, 2007

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Structured RNAs in the ENCODE selected regions of the human genome

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

Genome research, 2007

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Novel transcribed regions in the human genome

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

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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