Cortés-Ciriano I, Elrick H, Sauer C, Valle-Inclan JE, Trevers K, Tanguy M, Zumalave S, De Noon S, Muyas F, Cascao R, Afonso A, Amary F, Tirabosco R, Giess A, Freeman T, Sosinsky A, Piculell K, Miller D, Faria C, Elgar G, Flanagan A.
Preprint,
2024
doi:10.21203/rs.3.rs-4870639/v1.
Brenton JD, Vias M, Sauer CM, Funingana G, Piskorz AM, Moore E, Chilamakuri C, Hall D, Goranova T, Van Oudenhove E, Earl HM, Goldlust I.
Preprint,
2024
doi:10.1101/2024.08.15.607946.
Elrick H, Sauer CM, Espejo Valle-Inclan J, Trevers K, Tanguy M, Zumalave S, De Noon S, Muyas F, Cascao R, Afonso A, Amary F, Tirabosco R, Giess A, Freeman T, Sosinsky A, Piculell K, Miller DT, Faria CC, Elgar G, Flanagan AM, Cortes-Ciriano I.
Preprint,
2024
doi:10.1101/2024.07.25.604944.
Muyas F, Rodriguez MJG, Cascão R, Afonso A, Sauer CM, Faria CC, Cortés-Ciriano I, Flores I.
Nature communications,
2024
doi:10.1038/s41467-023-44287-8.
Elrick H, Peterson KA, Willis BJ, Lanza DG, Acar EF, Ryder EJ, Teboul L, Kasparek P, Birling MC, Adams DJ, Bradley A, Braun RE, Brown SD, Caulder A, Codner GF, DeMayo FJ, Dickinson ME, Doe B, Duddy G, Gertsenstein M, Goodwin LO, Hérault Y, Lintott LG, Lloyd KCK, Lorenzo I, Mackenzie M, Mallon AM, McKerlie C, Parkinson H, Ramirez-Solis R, Seavitt JR, Sedlacek R, Skarnes WC, Smedley D, Wells S, White JK, Wood JA, International Mouse Phenotyping Consortium, Murray SA, Heaney JD, Nutter LMJ.
Scientific reports,
2024
doi:10.1038/s41598-024-72418-8.
O'Connor D, Valle-Inclán JE, Conde L, Bloye G, Rahman S, Costa JR, Bartram J, Adams S, Wright G, Elrick H, Wall K, Dyer S, Howell C, Jigoulina G, Herrero J, Cortes-Ciriano I, Moorman AV, Mansour MR.
Blood,
2024
doi:10.1182/blood.2023021906.
Rahbari R, Jung H, Yang T, Walker S, Danecek P, Garcia-Salinas O, Neville MDC, Cortés-Ciriano I, Firth H, Scally A, Hurles M, Campbell P.
Preprint,
2024
doi:10.21203/rs.3.rs-4197130/v1.
Hu Q, Espejo Valle-Inclán J, Dahiya R, Guyer A, Mazzagatti A, Maurais EG, Engel JL, Lu H, Davis AJ, Cortés-Ciriano I, Ly P.
Nature communications,
2024
doi:10.1038/s41467-024-49985-5.
Hong SC, Muyas F, Cortés-Ciriano I, Hormoz S.
Preprint,
2024
doi:10.1101/2024.05.14.594208.
Pacini C, Duncan E, Gonçalves E, Gilbert J, Bhosle S, Horswell S, Karakoc E, Lightfoot H, Curry E, Muyas F, Bouaboula M, Pedamallu CS, Cortes-Ciriano I, Behan FM, Zalmas LP, Barthorpe A, Francies H, Rowley S, Pollard J, Beltrao P, Parts L, Iorio F, Garnett MJ.
Cancer cell,
2024
doi:10.1016/j.ccell.2023.12.016.
Nature biotechnology,
2024
doi:10.1038/s41587-023-01883-9.
Marečková M, Garcia-Alonso L, Moullet M, Lorenzi V, Petryszak R, Sancho-Serra C, Oszlanczi A, Icoresi Mazzeo C, Wong FCK, Kelava I, Hoffman S, Krassowski M, Garbutt K, Gaitskell K, Yancheva S, Woon EV, Male V, Granne I, Hellner K, Mahbubani KT, Saeb-Parsy K, Lotfollahi M, Prigmore E, Southcombe J, Dragovic RA, Becker CM, Zondervan KT, Vento-Tormo R.
Nature genetics,
2024
doi:10.1038/s41588-024-01873-w.
Muyas F, Sauer CM, Valle-Inclán JE, Li R, Rahbari R, Mitchell TJ, Hormoz S, Cortés-Ciriano I.
Nature biotechnology,
2023
doi:10.1038/s41587-023-01863-z.
Espejo Valle-Inclan J, De Noon S, Trevers K, Elrick H, Tanguy M, Butters T, Muyas F, Amary F, Tirabosco R, Giess A, Sosinky A, Elgar G, Flanagan AM, Cortes-Ciriano I.
Preprint,
2023
doi:10.1101/2023.12.29.573403.
van Belzen IA, van Tuil M, Badloe S, Janse A, Verwiel ET, Santoso M, de Vos S, Baker-Hernandez J, Kerstens HH, Solleveld-Westerink N, Meister MT, Drost J, van den Heuvel-Eibrink MM, Merks JHM, Molenaar JJ, Peng WC, Tops BB, Holstege FC, Kemmeren P, Hehir-Kwa JY.
Preprint,
2023
doi:10.1101/2023.09.19.558241.
Haefliger S, Bubbear J, Davies C, Cottone L, Amary F, Tirabosco R, Cortes-Ciriano I, O'Donnell P, Flanagan AM.
Skeletal radiology,
2023
doi:10.1007/s00256-023-04369-6.
Espejo Valle-Inclán J, Cortés-Ciriano I.
Bioinformatics (Oxford, England),
2023
doi:10.1093/bioinformatics/btad719.
Chu C, Lin EW, Tran A, Jin H, Ho NI, Veit A, Cortes-Ciriano I, Burns KH, Ting DT, Park PJ.
Nucleic acids research,
2023
doi:10.1093/nar/gkad821.
Westcott PMK, Muyas F, Hauck H, Smith OC, Sacks NJ, Ely ZA, Jaeger AM, Rideout WM, Zhang D, Bhutkar A, Beytagh MC, Canner DA, Jaramillo GC, Bronson RT, Naranjo S, Jin A, Patten JJ, Cruz AM, Shanahan SL, Cortes-Ciriano I, Jacks T.
Nature genetics,
2023
doi:10.1038/s41588-023-01499-4.
Heidegger S, Stritzke F, Dahl S, Daßler-Plenker J, Joachim L, Buschmann D, Fan K, Sauer CM, Ludwig N, Winter C, Enssle S, Li S, Perl M, Görgens A, Haas T, Orberg ET, Göttert S, Wölfel C, Engleitner T, Cortés-Ciriano I, Rad R, Herr W, Giebel B, Ruland J, Bassermann F, Coch C, Hartmann G, Poeck H.
Cell reports. Medicine,
2023
doi:10.1016/j.xcrm.2023.101171.
Lee JJ, Jung YL, Cheong TC, Espejo Valle-Inclan J, Chu C, Gulhan DC, Ljungström V, Jin H, Viswanadham VV, Watson EV, Cortés-Ciriano I, Elledge SJ, Chiarle R, Pellman D, Park PJ.
Nature,
2023
doi:10.1038/s41586-023-06057-w.
Lin YF, Hu Q, Mazzagatti A, Valle-Inclán JE, Maurais EG, Dahiya R, Guyer A, Sanders JT, Engel JL, Nguyen G, Bronder D, Bakhoum SF, Cortés-Ciriano I, Ly P.
Nature,
2023
doi:10.1038/s41586-023-05974-0.
Cortés-Ciriano I, Lee JJ, Xi R, Jain D, Jung YL, Yang L, Gordenin D, Klimczak LJ, Zhang CZ, Pellman DS, PCAWG Structural Variation Working Group, Park PJ, PCAWG Consortium.
Nature genetics,
2023
doi:10.1038/s41588-023-01315-z.
Espejo Valle-Inclan J, Cortes-Ciriano I.
Preprint,
2023
doi:10.1101/2023.02.24.529890.
Scotto di Carlo F, Russo S, Muyas F, Mangini M, Garribba L, Pazzaglia L, Genesio R, Biamonte F, De Luca AC, Santaguida S, Scotlandi K, Cortés-Ciriano I, Gianfrancesco F.
Communications biology,
2023
doi:10.1038/s42003-022-04392-8.
Cortes-Ciriano I, Steele CD, Piculell K, Al-Ibraheemi A, Eulo V, Bui MM, Chatzipli A, Dickson BC, Borcherding DC, Feber A, Galor A, Hart J, Jones KB, Jordan JT, Kim RH, Lindsay D, Miller C, Nishida Y, Proszek PZ, Serrano J, Sundby RT, Szymanski JJ, Ullrich NJ, Viskochil D, Wang X, Snuderl M, Park PJ, Flanagan AM, Hirbe AC, Pillay N, Miller DT, Genomics of MPNST (GeM) Consortium.
Cancer discovery,
2023
doi:10.1158/2159-8290.cd-22-0786.
Cortés-Ciriano I, Lee JJ, Xi R, Jain D, Jung YL, Yang L, Gordenin D, Klimczak LJ, Zhang CZ, Pellman DS, PCAWG Structural Variation Working Group, Park PJ, PCAWG Consortium.
Nature genetics,
2023
doi:10.1038/s41588-020-0634-1.
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.
Marečková M, Garcia-Alonso L, Moullet M, Lorenzi V, Petryszak R, Sancho-Serra C, Oszlanczi A, Mazzeo CI, Hoffman S, Krassowski M, Garbutt K, Kelava I, Gaitskell K, Yancheva S, Woon EV, Male V, Granne I, Hellner K, Mahbubani KT, Saeb-Parsy K, Lotfollahi M, Prigmore E, Southcombe J, Dragovic RA, Becker CM, Zondervan KT, Vento-Tormo R.
Preprint,
2023
doi:10.1101/2023.11.03.564728.
Irie N, Lee SM, Lorenzi V, Xu H, Chen J, Inoue M, Kobayashi T, Sancho-Serra C, Drousioti E, Dietmann S, Vento-Tormo R, Song CX, Surani MA.
Nature cell biology,
2023
doi:10.1038/s41556-023-01224-7.
Goh I, Botting RA, Rose A, Webb S, Engelbert J, Gitton Y, Stephenson E, Quiroga Londoño M, Mather M, Mende N, Imaz-Rosshandler I, Yang L, Horsfall D, Basurto-Lozada D, Chipampe NJ, Rook V, Lee JTH, Ton ML, Keitley D, Mazin P, Vijayabaskar MS, Hannah R, Gambardella L, Green K, Ballereau S, Inoue M, Tuck E, Lorenzi V, Kwakwa K, Alsinet C, Olabi B, Miah M, Admane C, Popescu DM, Acres M, Dixon D, Ness T, Coulthard R, Lisgo S, Henderson DJ, Dann E, Suo C, Kinston SJ, Park JE, Polanski K, Marioni J, van Dongen S, Meyer KB, de Bruijn M, Palis J, Behjati S, Laurenti E, Wilson NK, Vento-Tormo R, Chédotal A, Bayraktar O, Roberts I, Jardine L, Göttgens B, Teichmann SA, Haniffa M.
Science (New York, N.Y.),
2023
doi:10.1126/science.add7564.
Garcia-Alonso L, Handfield LF, Roberts K, Nikolakopoulou K, Fernando RC, Gardner L, Woodhams B, Arutyunyan A, Polanski K, Hoo R, Sancho-Serra C, Li T, Kwakwa K, Tuck E, Lorenzi V, Massalha H, Prete M, Kleshchevnikov V, Tarkowska A, Porter T, Mazzeo CI, van Dongen S, Dabrowska M, Vaskivskyi V, Mahbubani KT, Park JE, Jimenez-Linan M, Campos L, Kiselev VY, Lindskog C, Ayuk P, Prigmore E, Stratton MR, Saeb-Parsy K, Moffett A, Moore L, Bayraktar OA, Teichmann SA, Turco MY, Vento-Tormo R.
Nature genetics,
2023
doi:10.1038/s41588-022-01287-6.
Smith P, Bradley T, Gavarró LM, Goranova T, Ennis D, Mirza H, De Silva D, Piskorz A, Al-Khalidi S, Sauer C, Funingana I, Reinius M, Giannone G, Lewsley L, Stobo J, McQueen J, Bryson G, Eldridge M, The BriTROC Investigators, Macintyre G, Markowetz F, Brenton J, McNeish I.
Preprint,
2022
doi:10.1101/2022.10.21.22280992.
Sauer CM, Hall JA, Couturier D, Bradley T, Piskorz AM, Griffiths J, Sawle A, Eldridge MD, Smith P, Hosking K, Reinius MA, Gavarró LM, Mes-Masson A, Ennis D, Millan D, Hoyle A, McNeish IA, Jimenez-Linan M, Martins FC, Tischer J, Vias M, Brenton JD.
Preprint,
2022
doi:10.1101/2022.09.13.507750.
Chen H, Mueller N, Stott K, Rivers E, Kapeni C, Sauer CM, Beke F, Walsh S, Ashman N, O’Brien L, Fard AR, Godsinia A, Joud F, Giger O, Zlobec I, Olan I, Aitken SJ, Hoare M, Mair R, Serrao E, Brenton JD, Garcia-Gimenez A, Richardson SE, Huntly B, Spring DR, Skjødt M, Skjødt K, de la Roche M, de la Roche M.
Preprint,
2022
doi:10.1101/2022.09.01.506182.
Vias M, Morrill Gavarró L, Sauer CM, Sanders D, Piskorz AM, Couturier D, Ballereau S, Hernando B, Hall J, Correia-Martins F, Markowetz F, Macintyre G, Brenton JD.
Preprint,
2022
doi:10.1101/2022.09.01.506155.
Sauer CM, Heider K, Belic J, Boyle SE, Hall JA, Couturier D, An A, Vijayaraghavan A, Reinius MA, Hosking K, Vias M, Rosenfeld N, Brenton JD.
Preprint,
2022
doi:10.1101/2022.01.15.476442.
Barker CG, Petsalaki E, Giudice G, Sero J, Ekpenyong EN, Bakal C, Petsalaki E.
Genome research,
2022
doi:10.1101/gr.276059.121.
van Belzen IA, van Tuil M, Badloe S, Strengman E, Janse A, Verwiel ET, van der Leest DF, de Vos S, Baker-Hernandez J, Groenendijk A, de Krijger R, Kerstens HH, Drost J, van den Heuvel-Eibrink MM, Tops BB, Holstege FC, Kemmeren P, Hehir-Kwa JY.
Preprint,
2022
doi:10.1101/2022.08.12.503742.
Muyas F, Li R, Rahbari R, Mitchell T, Hormoz S, Cortes-Ciriano I.
Preprint,
2022
doi:10.21203/rs.3.rs-2306461/v1.
Kildisiute G, Kalyva M, Elmentaite R, van Dongen S, Thevanesan C, Piapi A, Ambridge K, Prigmore E, Haniffa M, Teichmann SA, Straathof K, Cortés-Ciriano I, Behjati S, Young MD.
Preprint,
2022
doi:10.1101/2022.11.28.518191.
Muyas F, Li R, Rahbari R, Mitchell TJ, Hormoz S, Cortés-Ciriano I.
Preprint,
2022
doi:10.1101/2022.11.22.517567.
Oliver TRW, Chappell L, Sanghvi R, Deighton L, Ansari-Pour N, Dentro SC, Young MD, Coorens THH, Jung H, Butler T, Neville MDC, Leongamornlert D, Sanders MA, Hooks Y, Cagan A, Mitchell TJ, Cortes-Ciriano I, Warren AY, Wedge DC, Heer R, Coleman N, Murray MJ, Campbell PJ, Rahbari R, Behjati S.
Nature communications,
2022
doi:10.1038/s41467-022-31375-4.
Cortes-Ciriano I, Steele C, Piculell K, Al-Ibraheemi A, Eulo V, Bui M, Chatzipli A, Dickson B, Borcherding D, Feber A, Galor A, Hart J, Jones K, Jordan J, Kim R, Lindsay D, Miller C, Nishida Y, Proszek P, Serrano J, Sundby R, Szymanski J, Ullrich N, Viskochil D, Wang X, Genomics of MPNST (GeM) Consortium, Snuderl M, Park P, Flanagan A, Hirbe A, Pillay N, Miller D.
Preprint,
2022
doi:10.1101/2022.05.03.490481.
Scotto di Carlo F, Russo S, Muyas F, Mangini M, Pazzaglia L, Biamonte F, De Luca AC, Scotlandi K, Cortés-Ciriano I, Gianfrancesco F.
Preprint,
2022
doi:10.1101/2022.02.01.478160.
Muyas F, Gómez Rodriguez MJ, Cortes-Ciriano I, Flores I.
Preprint,
2022
doi:10.1101/2022.01.25.477771.
Lorenzi V, Vento-Tormo R, Garcia-Alonso L.
Clinical and translational medicine,
2022
doi:10.1002/ctm2.1123.
Botting RA, Goh I, Rose A, Webb S, Engelbert J, Gitton Y, Stephenson E, Quiroga Londoño M, Mather M, Mende N, Imaz-Rosshandler I, Horsfall D, Basurto-Lozada D, Chipampe N, Rook V, Mazin P, Vijayabaskar M, Hannah R, Gambardella L, Green K, Ballereau S, Inoue M, Tuck L, Lorenzi V, Kwakwa K, Alsinet C, Olabi B, Miah M, Admane C, Popescu D, Acres M, Dixon D, Coulthard R, Lisgo S, Henderson DJ, Dann E, Suo C, Kinston SJ, Park J, Polanski K, Van Dongen S, Meyer KB, de Bruijn M, Palis J, Behjati S, Laurenti E, Wilson NK, Vento-Tormo R, Chédotal A, Bayraktar O, Roberts I, Jardine L, Göttgens B, Teichmann SA, Haniffa M.
Preprint,
2022
doi:10.1101/2022.08.03.502475.
Kilpatrick AM, Rahman F, Anjum A, Shome S, Andalib KMS, Banik S, Chowdhury SF, Coombe P, Astroz YC, Douglas JM, Eranti P, Kiran AD, Kumar S, Lim H, Lorenzi V, Lubiana T, Mahmud S, Puche R, Rybarczyk A, Al Sium SM, Twesigomwe D, Zok T, Orengo CA, Friedberg I, Kelso JF, Welch L.
Bioinformatics (Oxford, England),
2022
doi:10.1093/bioinformatics/btac236.
Sauer CM, Eldridge MD, Vias M, Hall JA, Boyle S, Macintyre G, Bradley T, Markowetz F, Brenton JD.
Preprint,
2021
doi:10.1101/2021.07.19.452658.
Ochoa D, Hercules A, Carmona M, Suveges D, Gonzalez-Uriarte A, Malangone C, Miranda A, Fumis L, Carvalho-Silva D, Spitzer M, Baker J, Ferrer J, Raies A, Razuvayevskaya O, Faulconbridge A, Petsalaki E, Mutowo P, Machlitt-Northen S, Peat G, McAuley E, Ong CK, Mountjoy E, Ghoussaini M, Pierleoni A, Papa E, Pignatelli M, Koscielny G, Karim M, Schwartzentruber J, Hulcoop DG, Dunham I, McDonagh EM.
Nucleic acids research,
2021
doi:10.1093/nar/gkaa1027.
Elrick H, Peterson KA, Willis BJ, Lanza DG, Acar EF, Ryder EJ, Teboul L, Kasparek P, Birling M, Adams DJ, Bradley A, Braun RE, Brown SD, Caulder A, Codner GF, DeMayo FJ, Dickinson ME, Doe B, Duddy G, Gertsenstein M, Goodwin LO, Hérault Y, Lintott LG, Lloyd KCK, Lorenzo I, Mackenzie M, Mallon A, McKerlie C, Parkinson H, Ramirez-Solis R, Seavitt JR, Sedlacek R, Skarnes WC, Smedley D, Wells S, White JK, Wood JA, International Mouse Phenotyping Consortium, Murray SA, Heaney JD, Nutter LMJ.
Preprint,
2021
doi:10.1101/2021.10.06.463037.
van Belzen IA, Cai C, van Tuil M, Badloe S, Strengman E, Janse A, Verwiel ET, van der Leest DF, Kester L, Molenaar JJ, Meijerink J, Drost J, Peng WC, Kerstens HH, Tops BB, Holstege FC, Kemmeren P, Hehir-Kwa JY.
Preprint,
2021
doi:10.1101/2021.08.31.458342.
Van Egeren D, Escabi J, Nguyen M, Liu S, Reilly CR, Patel S, Kamaz B, Kalyva M, DeAngelo DJ, Galinsky I, Wadleigh M, Winer ES, Luskin MR, Stone RM, Garcia JS, Hobbs GS, Camargo FD, Michor F, Mullally A, Cortes-Ciriano I, Hormoz S.
Cell stem cell,
2021
doi:10.1016/j.stem.2021.02.001.
Bender A, Cortes-Ciriano I.
Drug discovery today,
2021
doi:10.1016/j.drudis.2020.11.037.
Garcia-Alonso L, Handfield LF, Roberts K, Nikolakopoulou K, Fernando RC, Gardner L, Woodhams B, Arutyunyan A, Polanski K, Hoo R, Sancho-Serra C, Li T, Kwakwa K, Tuck E, Lorenzi V, Massalha H, Prete M, Kleshchevnikov V, Tarkowska A, Porter T, Mazzeo CI, van Dongen S, Dabrowska M, Vaskivskyi V, Mahbubani KT, Park JE, Jimenez-Linan M, Campos L, Kiselev VY, Lindskog C, Ayuk P, Prigmore E, Stratton MR, Saeb-Parsy K, Moffett A, Moore L, Bayraktar OA, Teichmann SA, Turco MY, Vento-Tormo R.
Nature genetics,
2021
doi:10.1038/s41588-021-00972-2.
Alsinet C, Primo M, Lorenzi V, Knights AJ, Sancho-Serra C, Park J, Wyspianska BS, Tough DF, Alvarez-Errico D, Gaffney DJ, Vento-Tormo R.
Preprint,
2021
doi:10.1101/2021.11.17.469005.
Martins FC, Couturier D, Santiago Id, Sauer CM, Vias M, Angelova M, Sanders D, Piskorz A, Hall J, Hosking K, Amirthanayagam A, Cosulich S, Carnevalli L, Davies B, Watkins TBK, Funingana G, Bolton H, Haldar K, Latimer J, Baldwin P, Crawford R, Eldridge M, Basu B, Jimenez-Linan M, McGranahan N, Litchfield K, Shah SP, McNeish I, Caldas C, Evan G, Swanton C, Brenton JD.
Preprint,
2020
doi:10.1101/2020.10.04.325365.
Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J, Kaake RM, Weckstein AR, Owens TW, Gupta M, Pourmal S, Titus EW, Cakir M, Soucheray M, McGregor M, Cakir Z, Jang G, O'Meara MJ, Tummino TA, Zhang Z, Foussard H, Rojc A, Zhou Y, Kuchenov D, Hüttenhain R, Xu J, Eckhardt M, Swaney DL, Fabius JM, Ummadi M, Tutuncuoglu B, Rathore U, Modak M, Haas P, Haas KM, Naing ZZC, Pulido EH, Shi Y, Barrio-Hernandez I, Memon D, Petsalaki E, Dunham A, Marrero MC, Burke D, Koh C, Vallet T, Silvas JA, Azumaya CM, Billesbølle C, Brilot AF, Campbell MG, Diallo A, Dickinson MS, Diwanji D, Herrera N, Hoppe N, Kratochvil HT, Liu Y, Merz GE, Moritz M, Nguyen HC, Nowotny C, Puchades C, Rizo AN, Schulze-Gahmen U, Smith AM, Sun M, Young ID, Zhao J, Asarnow D, Biel J, Bowen A, Braxton JR, Chen J, Chio CM, Chio US, Deshpande I, Doan L, Faust B, Flores S, Jin M, Kim K, Lam VL, Li F, Li J, Li YL, Li Y, Liu X, Lo M, Lopez KE, Melo AA, Moss FR, Nguyen P, Paulino J, Pawar KI, Peters JK, Pospiech TH, Safari M, Sangwan S, Schaefer K, Thomas PV, Thwin AC, Trenker R, Tse E, Tsui TKM, Wang F, Whitis N, Yu Z, Zhang K, Zhang Y, Zhou F, Saltzberg D, QCRG Structural Biology Consortium, Hodder AJ, Shun-Shion AS, Williams DM, White KM, Rosales R, Kehrer T, Miorin L, Moreno E, Patel AH, Rihn S, Khalid MM, Vallejo-Gracia A, Fozouni P, Simoneau CR, Roth TL, Wu D, Karim MA, Ghoussaini M, Dunham I, Berardi F, Weigang S, Chazal M, Park J, Logue J, McGrath M, Weston S, Haupt R, Hastie CJ, Elliott M, Brown F, Burness KA, Reid E, Dorward M, Johnson C, Wilkinson SG, Geyer A, Giesel DM, Baillie C, Raggett S, Leech H, Toth R, Goodman N, Keough KC, Lind AL, Zoonomia Consortium, Klesh RJ, Hemphill KR, Carlson-Stevermer J, Oki J, Holden K, Maures T, Pollard KS, Sali A, Agard DA, Cheng Y, Fraser JS, Frost A, Jura N, Kortemme T, Manglik A, Southworth DR, Stroud RM, Alessi DR, Davies P, Frieman MB, Ideker T, Abate C, Jouvenet N, Kochs G, Shoichet B, Ott M, Palmarini M, Shokat KM, García-Sastre A, Rassen JA, Grosse R, Rosenberg OS, Verba KA, Basler CF, Vignuzzi M, Peden AA, Beltrao P, Krogan NJ.
Science (New York, N.Y.),
2020
doi:10.1126/science.abe9403.
Elrick H, Nelakuditi V, Clark G, Brudno M, Ramani AK, Nutter LM.
Preprint,
2020
doi:10.1101/2020.04.21.053090.
van Belzen I, Deutekom ES, Snel B.
Preprint,
2020
doi:10.1101/2020.02.14.947036.
Bender A, Cortés-Ciriano I.
Drug discovery today,
2020
doi:10.1016/j.drudis.2020.12.009.
Cortés-Ciriano I, Škuta C, Bender A, Svozil D.
Journal of cheminformatics,
2020
doi:10.1186/s13321-020-00444-5.
Goldman MJ, Zhang J, Fonseca NA, Cortés-Ciriano I, Xiang Q, Craft B, Piñeiro-Yáñez E, O'Connor BD, Bazant W, Barrera E, Muñoz-Pomer A, Petryszak R, Füllgrabe A, Al-Shahrour F, Keays M, Haussler D, Weinstein JN, Huber W, Valencia A, Park PJ, Papatheodorou I, Zhu J, Ferretti V, Vazquez M.
Nature communications,
2020
doi:10.1038/s41467-020-16785-6.
Touat M, Li YY, Boynton AN, Spurr LF, Iorgulescu JB, Bohrson CL, Cortes-Ciriano I, Birzu C, Geduldig JE, Pelton K, Lim-Fat MJ, Pal S, Ferrer-Luna R, Ramkissoon SH, Dubois F, Bellamy C, Currimjee N, Bonardi J, Qian K, Ho P, Malinowski S, Taquet L, Jones RE, Shetty A, Chow KH, Sharaf R, Pavlick D, Albacker LA, Younan N, Baldini C, Verreault M, Giry M, Guillerm E, Ammari S, Beuvon F, Mokhtari K, Alentorn A, Dehais C, Houillier C, Laigle-Donadey F, Psimaras D, Lee EQ, Nayak L, McFaline-Figueroa JR, Carpentier A, Cornu P, Capelle L, Mathon B, Barnholtz-Sloan JS, Chakravarti A, Bi WL, Chiocca EA, Fehnel KP, Alexandrescu S, Chi SN, Haas-Kogan D, Batchelor TT, Frampton GM, Alexander BM, Huang RY, Ligon AH, Coulet F, Delattre JY, Hoang-Xuan K, Meredith DM, Santagata S, Duval A, Sanson M, Cherniack AD, Wen PY, Reardon DA, Marabelle A, Park PJ, Idbaih A, Beroukhim R, Bandopadhayay P, Bielle F, Ligon KL.
Nature,
2020
doi:10.1038/s41586-020-2209-9.
Miller DT, Cortés-Ciriano I, Pillay N, Hirbe AC, Snuderl M, Bui MM, Piculell K, Al-Ibraheemi A, Dickson BC, Hart J, Jones K, Jordan JT, Kim RH, Lindsay D, Nishida Y, Ullrich NJ, Wang X, Park PJ, Flanagan AM.
Genes,
2020
doi:10.3390/genes11040387.
ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium.
Nature,
2020
doi:10.1038/s41586-020-1969-6.
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.
Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, Shuai S, Lanzós A, Herrmann C, Maruvka YE, Shen C, Amin SB, Bandopadhayay P, Bertl J, Boroevich KA, Busanovich J, Carlevaro-Fita J, Chakravarty D, Chan CWY, Craft D, Dhingra P, Diamanti K, Fonseca NA, Gonzalez-Perez A, Guo Q, Hamilton MP, Haradhvala NJ, Hong C, Isaev K, Johnson TA, Juul M, Kahles A, Kahraman A, Kim Y, Komorowski J, Kumar K, Kumar S, Lee D, Lehmann KV, Li Y, Liu EM, Lochovsky L, Park K, Pich O, Roberts ND, Saksena G, Schumacher SE, Sidiropoulos N, Sieverling L, Sinnott-Armstrong N, Stewart C, Tamborero D, Tubio JMC, Umer HM, Uusküla-Reimand L, Wadelius C, Wadi L, Yao X, Zhang CZ, Zhang J, Haber JE, Hobolth A, Imielinski M, Kellis M, Lawrence MS, von Mering C, Nakagawa H, Raphael BJ, Rubin MA, Sander C, Stein LD, Stuart JM, Tsunoda T, Wheeler DA, Johnson R, Reimand J, Gerstein M, Khurana E, Campbell PJ, López-Bigas N, PCAWG Drivers and Functional Interpretation Working Group, PCAWG Structural Variation Working Group, Weischenfeldt J, Beroukhim R, Martincorena I, Pedersen JS, Getz G, PCAWG Consortium.
Nature,
2020
doi:10.1038/s41586-020-1965-x.
Li Y, Roberts ND, Wala JA, Shapira O, Schumacher SE, Kumar K, Khurana E, Waszak S, Korbel JO, Haber JE, Imielinski M, PCAWG Structural Variation Working Group, Weischenfeldt J, Beroukhim R, Campbell PJ, PCAWG Consortium.
Nature,
2020
doi:10.1038/s41586-019-1913-9.
Cortés-Ciriano I, Lee JJ, Xi R, Jain D, Jung YL, Yang L, Gordenin D, Klimczak LJ, Zhang CZ, Pellman DS, PCAWG Structural Variation Working Group, Park PJ, PCAWG Consortium.
Nature genetics,
2020
doi:10.1038/s41588-019-0576-7.
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,
2020
doi:10.1038/s41588-019-0562-0.
Zhang Y, Chen F, Fonseca NA, He Y, Fujita M, Nakagawa H, Zhang Z, Brazma A, PCAWG Transcriptome Working Group, PCAWG Structural Variation Working Group, Creighton CJ, PCAWG Consortium.
Nature communications,
2020
doi:10.1038/s41467-019-13885-w.
Dou Y, Kwon M, Rodin RE, Cortés-Ciriano I, Doan R, Luquette LJ, Galor A, Bohrson C, Walsh CA, Park PJ.
Nature biotechnology,
2020
doi:10.1038/s41587-019-0368-8.
Jiménez-Sánchez A, Cybulska P, Mager KL, Koplev S, Cast O, Couturier DL, Memon D, Selenica P, Nikolovski I, Mazaheri Y, Bykov Y, Geyer FC, Macintyre G, Gavarró LM, Drews RM, Gill MB, Papanastasiou AD, Sosa RE, Soslow RA, Walther T, Shen R, Chi DS, Park KJ, Hollmann T, Reis-Filho JS, Markowetz F, Beltrao P, Vargas HA, Zamarin D, Brenton JD, Snyder A, Weigelt B, Sala E, Miller ML.
Nature genetics,
2020
doi:10.1038/s41588-020-0630-5.
Lawson ARJ, Abascal F, Coorens THH, Hooks Y, O'Neill L, Latimer C, Raine K, Sanders MA, Warren AY, Mahbubani KTA, Bareham B, Butler TM, Harvey LMR, Cagan A, Menzies A, Moore L, Colquhoun AJ, Turner W, Thomas B, Gnanapragasam V, Williams N, Rassl DM, Vöhringer H, Zumalave S, Nangalia J, Tubío JMC, Gerstung M, Saeb-Parsy K, Stratton MR, Campbell PJ, Mitchell TJ, Martincorena I.
Science (New York, N.Y.),
2020
doi:10.1126/science.aba8347.
Menden MP, Wang D, Mason MJ, Szalai B, Bulusu KC, Guan Y, Yu T, Kang J, Jeon M, Wolfinger R, Nguyen T, Zaslavskiy M, AstraZeneca-Sanger Drug Combination DREAM Consortium, Jang IS, Ghazoui Z, Ahsen ME, Vogel R, Neto EC, Norman T, Tang EKY, Garnett MJ, Veroli GYD, Fawell S, Stolovitzky G, Guinney J, Dry JR, Saez-Rodriguez J.
Nature communications,
2019
doi:10.1038/s41467-019-09799-2.
Cortés-Ciriano I, Lee J, Xi R, Jain D, Jung YL, Yang L, Gordenin D, Klimczak LJ, Zhang C, Pellman DS, Park PJ, on behalf of the PCAWG Structural Variation Working Group, the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network.
Preprint,
2018
doi:10.1101/333617.
Cortés-Ciriano I, Murrell DS, Chetrit B, Bender A, Malliavin T, Ballester PJ.
Preprint,
2017
doi:10.1101/105478.
Sieverling L, Hong C, Koser SD, Ginsbach P, Kleinheinz K, Hutter B, Braun DM, Cortés-Ciriano I, Xi R, Kabbe R, Park PJ, Eils R, Schlesner M, Rippe K, Jones DT, Brors B, Feuerbach L, on behalf of the PCAWG Structural Variation Working Group, PCAWG SNV Calling Working Group, PCAWG Drivers and Functional Interpretation Group, PCAWG Evolution and Heterogeneity Working Group, PCAWG Technical Working Group, and the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network.
Preprint,
2017
doi:10.1101/157560.
Goldman M, Zhang J, Fonseca NA, Cortés-Ciriano I, Xiang Q, Craft B, Piñeiro-Yáñez E, O’Connor BD, Bazant W, Barrera E, Muñoz-Pomer A, Petryszak R, Füllgrabe A, Al-Shahrour F, Keays M, Haussler D, Weinstein JN, Huber W, Valencia A, Park PJ, Papatheodorou I, Zhu J, Ferretti V, Vazquez M, on behalf of the PCAWG Portals and Visualization Working Group, the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network.
Preprint,
2017
doi:10.1101/163907.
McConnell MJ, Moran JV, Abyzov A, Akbarian S, Bae T, Cortes-Ciriano I, Erwin JA, Fasching L, Flasch DA, Freed D, Ganz J, Jaffe AE, Kwan KY, Kwon M, Lodato MA, Mills RE, Paquola ACM, Rodin RE, Rosenbluh C, Sestan N, Sherman MA, Shin JH, Song S, Straub RE, Thorpe J, Weinberger DR, Urban AE, Zhou B, Zhou B, Gage FH, Lehner T, Senthil G, Walsh CA, Chess A, Courchesne E, Gleeson JG, Kidd JM, Park PJ, Pevsner J, Vaccarino FM, Brain Somatic Mosaicism Network.
Science (New York, N.Y.),
2017
doi:10.1126/science.aal1641.
Perna D, Karreth FA, Rust AG, Perez-Mancera PA, Rashid M, Iorio F, Alifrangis C, Arends MJ, Bosenberg MW, Bollag G, Tuveson DA, Adams DJ.
Proceedings of the National Academy of Sciences of the United States of America,
2015
doi:10.1073/pnas.1418163112.
Cortés-Ciriano I, van Westen GJ, Bouvier G, Nilges M, Overington JP, Bender A, Malliavin TE.
Bioinformatics (Oxford, England),
2015
doi:10.1093/bioinformatics/btv529.
Murrell DS, Cortes-Ciriano I, van Westen GJP, Stott IP, Bender A, Malliavin TE, Glen RC.
Journal of cheminformatics,
2015
doi:10.1186/s13321-015-0086-2.
Cortes-Ciriano I, van Westen G, Murrell D, Lenselink E, Bender A, Malliavin T.
BMC bioinformatics,
2015
doi:10.1186/1471-2105-16-s3-a4.
Cortes-Ciriano I, Murrell DS, van Westen GJ, Bender A, Malliavin TE.
Journal of cheminformatics,
2015
doi:10.1186/s13321-014-0049-z.
Cortes-Ciriano I, van Westen GJ, Lenselink EB, Murrell DS, Bender A, Malliavin T.
Journal of cheminformatics,
2014
doi:10.1186/1758-2946-6-35.
van Westen GJ, Swier RF, Cortes-Ciriano I, Wegner JK, Overington JP, Ijzerman AP, van Vlijmen HW, Bender A.
Journal of cheminformatics,
2013
doi:10.1186/1758-2946-5-42.
Rust AG, Mongin E, Birney E.
Drug discovery today,
2002
doi:10.1016/s1359-6446(02)02289-4.
Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, Durbin R, Eyras E, Gilbert J, Hammond M, Huminiecki L, Kasprzyk A, Lehvaslaiho H, Lijnzaad P, Melsopp C, Mongin E, Pettett R, Pocock M, Potter S, Rust A, Schmidt E, Searle S, Slater G, Smith J, Spooner W, Stabenau A, Stalker J, Stupka E, Ureta-Vidal A, Vastrik I, Clamp M.
Nucleic acids research,
2002
doi:10.1093/nar/30.1.38.