Harvard Catalyst Profiles

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Rameen Beroukhim, M.D., Ph.D.

Title
Institution
Department
Address
Phone
Fax

Mentoring
The Tangent copy number inference pipeline for cancer genome analyses
Part Time, 01/23/17 - 01/15/18
Somatic Genetic Biomarkers of Bevacizumab Response in Glioblastoma Multiforme
Summer, 06/01/15 - 08/08/15

Research
The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
  1. R01CA219943 (BEROUKHIM, RAMEEN) Sep 1, 2017 - Aug 31, 2022
    NIH
    Characterizing TP53 and PPM1D mutations as resistance drivers to radiation therapy in Diffuse Intrinsic Pontine Gliomas
    Role: Principal Investigator
  2. R01CA215489 (LIGON, KEITH LLOYD) Apr 1, 2017 - Mar 31, 2022
    NIH
    MYB family alterations in pediatric gliomas
    Role: Co-Principal Investigator
  3. U24CA210978 (BEROUKHIM, RAMEEN) Sep 15, 2016 - Aug 31, 2021
    NIH
    Center for the comprehensive analysis of somatic copy-number alterations in cancer
    Role: Principal Investigator
  4. R01CA188228 (BEROUKHIM, RAMEEN) Apr 1, 2015 - Mar 31, 2020
    NIH
    Genetic evolution of glioblastomas during radiation and temozolomide therapy
    Role: Principal Investigator
  5. K08CA122833 (BEROUKHIM, RAMEEN) Jun 12, 2007 - May 31, 2012
    NIH
    High-resolution genome-wide mapping of structural mutations in prostate cancer
    Role: Principal Investigator

Bibliographic
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Dentro SC, Leshchiner I, Haase K, Tarabichi M, Wintersinger J, Deshwar AG, Yu K, Rubanova Y, Macintyre G, Demeulemeester J, Vázquez-García I, Kleinheinz K, Livitz DG, Malikic S, Donmez N, Sengupta S, Anur P, Jolly C, Cmero M, Rosebrock D, Schumacher SE, Fan Y, Fittall M, Drews RM, Yao X, Watkins TBK, Lee J, Schlesner M, Zhu H, Adams DJ, McGranahan N, Swanton C, Getz G, Boutros PC, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Martincorena I, Markowetz F, Mustonen V, Yuan K, Gerstung M, Spellman PT, Wang W, Morris QD, Wedge DC, Van Loo P. Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes. Cell. 2021 Apr 02. PMID: 33831375.
    Citations:    Fields:    
  2. Carrot-Zhang J, Yao X, Devarakonda S, Deshpande A, Damrauer JS, Silva TC, Wong CK, Choi HY, Felau I, Robertson AG, Castro MAA, Bao L, Rheinbay E, Liu EM, Trieu T, Haan D, Yau C, Hinoue T, Liu Y, Shapira O, Kumar K, Mungall KL, Zhang H, June-Koo Lee J, Berger A, Gao GF, Zhitomirsky B, Liang WW, Zhou M, Moorthi S, Berger AH, Collisson EA, Zody MC, Ding L, Cherniack AD, Getz G, Elemento O, Benz CC, Stuart J, Zenklusen JC, Beroukhim R, Chang JC, Campbell JD, Hayes DN, Yang L, Laird PW, Weinstein JN, Kwiatkowski DJ, Tsao MS, Travis WD, Khurana E, Berman BP, Hoadley KA, Robine N, Meyerson M, Govindan R, Imielinski M. Whole-genome characterization of lung adenocarcinomas lacking alterations in the RTK/RAS/RAF pathway. Cell Rep. 2021 Feb 23; 34(8):108784. PMID: 33626341.
    Citations:    Fields:    
  3. Carrot-Zhang J, Yao X, Devarakonda S, Deshpande A, Damrauer JS, Silva TC, Wong CK, Choi HY, Felau I, Robertson AG, Castro MAA, Bao L, Rheinbay E, Liu EM, Trieu T, Haan D, Yau C, Hinoue T, Liu Y, Shapira O, Kumar K, Mungall KL, Zhang H, Lee JJ, Berger A, Gao GF, Zhitomirsky B, Liang WW, Zhou M, Zhou M, Moorthi S, Berger AH, Collisson EA, Zody MC, Ding L, Cherniack AD, Getz G, Elemento O, Benz CC, Stuart J, Zenklusen JC, Beroukhim R, Chang JC, Campbell JD, Hayes DN, Yang L, Laird PW, Weinstein JN, Kwiatkowski DJ, Tsao MS, Travis WD, Khurana E, Berman BP, Hoadley KA, Robine N, Meyerson M, Govindan R, Imielinski M. Whole-genome characterization of lung adenocarcinomas lacking the RTK/RAS/RAF pathway. Cell Rep. 2021 Feb 02; 34(5):108707. PMID: 33535033.
    Citations:    Fields:    
  4. Cohen-Sharir Y, McFarland JM, Abdusamad M, Marquis C, Bernhard SV, Kazachkova M, Tang H, Ippolito MR, Laue K, Zerbib J, Malaby HLH, Jones A, Stautmeister LM, Bockaj I, Wardenaar R, Lyons N, Nagaraja A, Bass AJ, Spierings DCJ, Foijer F, Beroukhim R, Santaguida S, Golub TR, Stumpff J, Storchová Z, Ben-David U. Aneuploidy renders cancer cells vulnerable to mitotic checkpoint inhibition. Nature. 2021 02; 590(7846):486-491. PMID: 33505028.
    Citations: 1     Fields:    Translation:HumansCells
  5. Chen CCL, Deshmukh S, Jessa S, Hadjadj D, Lisi V, Andrade AF, Faury D, Jawhar W, Dali R, Suzuki H, Pathania M, A D, Dubois F, Woodward E, Hébert S, Coutelier M, Karamchandani J, Albrecht S, Brandner S, De Jay N, Gayden T, Bajic A, Harutyunyan AS, Marchione DM, Mikael LG, Juretic N, Zeinieh M, Russo C, Maestro N, Bassenden AV, Hauser P, Virga J, Bognar L, Klekner A, Zapotocky M, Vicha A, Krskova L, Vanova K, Zamecnik J, Sumerauer D, Ekert PG, Ziegler DS, Ellezam B, Filbin MG, Blanchette M, Hansford JR, Khuong-Quang DA, Berghuis AM, Weil AG, Garcia BA, Garzia L, Mack SC, Beroukhim R, Ligon KL, Taylor MD, Bandopadhayay P, Kramm C, Pfister SM, Korshunov A, Sturm D, Jones DTW, Salomoni P, Kleinman CL, Jabado N. Histone H3.3G34-Mutant Interneuron Progenitors Co-opt PDGFRA for Gliomagenesis. Cell. 2020 Dec 10; 183(6):1617-1633.e22. PMID: 33259802.
    Citations:    Fields:    
  6. Spurr LF, Touat M, Taylor AM, Dubuc AM, Shih J, Meredith DM, Pisano WV, Meyerson ML, Ligon KL, Cherniack AD, Li YY, Beroukhim R. Quantification of aneuploidy in targeted sequencing data using ASCETS. Bioinformatics. 2020 Nov 28. PMID: 33247715.
    Citations:    Fields:    
  7. Feldman D, Tsai F, Garrity AJ, O'Rourke R, Brenan L, Ho P, Gonzalez E, Konermann S, Johannessen CM, Beroukhim R, Bandopadhayay P, Blainey PC. CloneSifter: enrichment of rare clones from heterogeneous cell populations. BMC Biol. 2020 11 24; 18(1):177. PMID: 33234154.
    Citations:    Fields:    
  8. Hadi K, Yao X, Behr JM, Deshpande A, Xanthopoulakis C, Tian H, Kudman S, Rosiene J, Darmofal M, DeRose J, Mortensen R, Adney EM, Shaiber A, Gajic Z, Sigouros M, Eng K, Wala JA, Wrzeszczynski KO, Arora K, Shah M, Emde AK, Felice V, Frank MO, Darnell RB, Ghandi M, Huang F, Dewhurst S, Maciejowski J, de Lange T, Setton J, Riaz N, Reis-Filho JS, Powell S, Knowles DA, Reznik E, Mishra B, Beroukhim R, Zody MC, Robine N, Oman KM, Sanchez CA, Kuhner MK, Smith LP, Galipeau PC, Paulson TG, Reid BJ, Li X, Wilkes D, Sboner A, Mosquera JM, Elemento O, Imielinski M. Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs. Cell. 2020 Oct 01; 183(1):197-210.e32. PMID: 33007263.
    Citations: 7     Fields:    
  9. Enache OM, Rendo V, Abdusamad M, Lam D, Davison D, Pal S, Currimjee N, Hess J, Pantel S, Nag A, Thorner AR, Doench JG, Vazquez F, Beroukhim R, Golub TR, Ben-David U. Author Correction: Cas9 activates the p53 pathway and selects for p53-inactivating mutations. Nat Genet. 2020 Jul; 52(7):748-749. PMID: 32587373.
    Citations: 2     Fields:    
  10. Mineo M, Lyons SM, Zdioruk M, von Spreckelsen N, Ferrer-Luna R, Ito H, Alayo QA, Kharel P, Giantini Larsen A, Fan WY, Auduong S, Grauwet K, Passaro C, Khalsa JK, Shah K, Reardon DA, Ligon KL, Beroukhim R, Nakashima H, Ivanov P, Anderson PJ, Lawler SE, Chiocca EA. Tumor Interferon Signaling Is Regulated by a lncRNA INCR1 Transcribed from the PD-L1 Locus. Mol Cell. 2020 06 18; 78(6):1207-1223.e8. PMID: 32504554.
    Citations: 3     Fields:    Translation:HumansAnimalsCells
  11. Oak N, Cherniack AD, Mashl RJ, Hirsch FR, Ding L, Beroukhim R, Gümüs ZH, Plon SE, Huang KL. Ancestry-specific predisposing germline variants in cancer. Genome Med. 2020 05 29; 12(1):51. PMID: 32471518.
    Citations: 1     Fields:    
  12. Nichols CA, Gibson WJ, Brown MS, Kosmicki JA, Busanovich JP, Wei H, Urbanski LM, Curimjee N, Berger AC, Gao GF, Cherniack AD, Dhe-Paganon S, Paolella BR, Beroukhim R. Loss of heterozygosity of essential genes represents a widespread class of potential cancer vulnerabilities. Nat Commun. 2020 05 20; 11(1):2517. PMID: 32433464.
    Citations: 5     Fields:    Translation:Humans
  13. Enache OM, Rendo V, Abdusamad M, Lam D, Davison D, Pal S, Currimjee N, Hess J, Pantel S, Nag A, Thorner AR, Doench JG, Vazquez F, Beroukhim R, Golub TR, Ben-David U. Cas9 activates the p53 pathway and selects for p53-inactivating mutations. Nat Genet. 2020 07; 52(7):662-668. PMID: 32424350.
    Citations: 11     Fields:    Translation:HumansCells
  14. Lu Z, Paolella BR, Truex NL, Loftis AR, Liao X, Rabideau AE, Brown MS, Busanovich J, Beroukhim R, Pentelute BL. Targeting Cancer Gene Dependencies with Anthrax-Mediated Delivery of Peptide Nucleic Acids. ACS Chem Biol. 2020 06 19; 15(6):1358-1369. PMID: 32348107.
    Citations: 1     Fields:    
  15. Carrot-Zhang J, Chambwe N, Damrauer JS, Knijnenburg TA, Robertson AG, Yau C, Zhou W, Berger AC, Huang KL, Newberg JY, Mashl RJ, Romanel A, Sayaman RW, Demichelis F, Felau I, Frampton GM, Han S, Hoadley KA, Kemal A, Laird PW, Lazar AJ, Le X, Oak N, Shen H, Wong CK, Zenklusen JC, Ziv E, Cherniack AD, Beroukhim R. Comprehensive Analysis of Genetic Ancestry and Its Molecular Correlates in Cancer. Cancer Cell. 2020 05 11; 37(5):639-654.e6. PMID: 32396860.
    Citations: 10     Fields:    Translation:HumansCells
  16. 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. Mechanisms and therapeutic implications of hypermutation in gliomas. Nature. 2020 04; 580(7804):517-523. PMID: 32322066.
    Citations: 36     Fields:    Translation:HumansAnimalsCells
  17. Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vázquez-García I, Haase K, Jerman L, Sengupta S, Macintyre G, Malikic S, Donmez N, Livitz DG, Cmero M, Demeulemeester J, Schumacher S, Fan Y, Yao X, Lee J, Schlesner M, Boutros PC, Bowtell DD, Zhu H, Getz G, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Markowetz F, Mustonen V, Yuan K, Wang W, Morris QD, Spellman PT, Wedge DC, Van Loo P. The evolutionary history of 2,658 cancers. Nature. 2020 02; 578(7793):122-128. PMID: 32025013.
    Citations: 78     Fields:    Translation:HumansCells
  18. Sethi NS, Kikuchi O, Duronio GN, Stachler MD, McFarland JM, Ferrer-Luna R, Zhang Y, Bao C, Bronson R, Patil D, Sanchez-Vega F, Liu JB, Sicinska E, Lazaro JB, Ligon KL, Beroukhim R, Bass AJ. Early TP53 alterations engage environmental exposures to promote gastric premalignancy in an integrative mouse model. Nat Genet. 2020 02; 52(2):219-230. PMID: 32025000.
    Citations: 3     Fields:    Translation:HumansAnimalsCellsPHPublic Health
  19. 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 PAW, Weischenfeldt J, Puiggròs M, Chong Z, Chen K, Lee EA, Wala JA, Raine K, 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, Campbell PJ, Tubio JMC. Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Nat Genet. 2020 03; 52(3):306-319. PMID: 32024998.
    Citations: 31     Fields:    Translation:HumansCells
  20. Li Y, Roberts ND, Wala JA, Shapira O, Schumacher SE, Kumar K, Khurana E, Waszak S, Korbel JO, Haber JE, Imielinski M, Weischenfeldt J, Beroukhim R, Campbell PJ. Patterns of somatic structural variation in human cancer genomes. Nature. 2020 02; 578(7793):112-121. PMID: 32025012.
    Citations: 46     Fields:    Translation:Humans
  21. 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, Weischenfeldt J, Beroukhim R, Martincorena I, Pedersen JS, Getz G. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature. 2020 02; 578(7793):102-111. PMID: 32025015.
    Citations: 48     Fields:    Translation:Humans
  22. Akdemir KC, Le VT, Chandran S, Li Y, Verhaak RG, Beroukhim R, Campbell PJ, Chin L, Dixon JR, Futreal PA. Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer. Nat Genet. 2020 03; 52(3):294-305. PMID: 32024999.
    Citations: 14     Fields:    Translation:HumansCells
  23. Kurppa KJ, Liu Y, To C, Zhang T, Fan M, Vajdi A, Knelson EH, Xie Y, Lim K, Cejas P, Portell A, Lizotte PH, Ficarro SB, Li S, Chen T, Haikala HM, Wang H, Bahcall M, Gao Y, Shalhout S, Boettcher S, Shin BH, Thai T, Wilkens MK, Tillgren ML, Mushajiang M, Xu M, Choi J, Bertram AA, Ebert BL, Beroukhim R, Bandopadhayay P, Awad MM, Gokhale PC, Kirschmeier PT, Marto JA, Camargo FD, Haq R, Paweletz CP, Wong KK, Barbie DA, Long HW, Gray NS, Jänne PA. Treatment-Induced Tumor Dormancy through YAP-Mediated Transcriptional Reprogramming of the Apoptotic Pathway. Cancer Cell. 2020 01 13; 37(1):104-122.e12. PMID: 31935369.
    Citations: 21     Fields:    Translation:HumansAnimalsCells
  24. Barthel FP, Johnson KC, Varn FS, Moskalik AD, Tanner G, Kocakavuk E, Anderson KJ, Abiola O, Aldape K, Alfaro KD, Alpar D, Amin SB, Ashley DM, Bandopadhayay P, Barnholtz-Sloan JS, Beroukhim R, Bock C, Brastianos PK, Brat DJ, Brodbelt AR, Bruns AF, Bulsara KR, Chakrabarty A, Chakravarti A, Chuang JH, Claus EB, Cochran EJ, Connelly J, Costello JF, Finocchiaro G, Fletcher MN, French PJ, Gan HK, Gilbert MR, Gould PV, Grimmer MR, Iavarone A, Ismail A, Jenkinson MD, Khasraw M, Kim H, Kouwenhoven MCM, LaViolette PS, Li M, Lichter P, Ligon KL, Lowman AK, Malta TM, Mazor T, McDonald KL, Molinaro AM, Nam DH, Nayyar N, Ng HK, Ngan CY, Niclou SP, Niers JM, Noushmehr H, Noorbakhsh J, Ormond DR, Park CK, Poisson LM, Rabadan R, Radlwimmer B, Rao G, Reifenberger G, Sa JK, Schuster M, Shaw BL, Short SC, Smitt PAS, Sloan AE, Smits M, Suzuki H, Tabatabai G, Van Meir EG, Watts C, Weller M, Wesseling P, Westerman BA, Widhalm G, Woehrer A, Yung WKA, Zadeh G, Huse JT, De Groot JF, Stead LF, Verhaak RGW. Longitudinal molecular trajectories of diffuse glioma in adults. Nature. 2019 12; 576(7785):112-120. PMID: 31748746.
    Citations: 43     Fields:    Translation:HumansCells
  25. Lee EQ, Muzikansky A, Duda DG, Gaffey S, Dietrich J, Nayak L, Chukwueke UN, Beroukhim R, Doherty L, Laub CK, LaFrankie D, Fontana B, Stefanik J, Ruland S, Caruso V, Bruno J, Ligon K, Reardon DA, Wen PY. Phase II trial of ponatinib in patients with bevacizumab-refractory glioblastoma. Cancer Med. 2019 10; 8(13):5988-5994. PMID: 31444999.
    Citations: 4     Fields:    Translation:HumansCTClinical Trials
  26. Reitman ZJ, Paolella BR, Bergthold G, Pelton K, Becker S, Jones R, Sinai CE, Malkin H, Huang Y, Grimmet L, Herbert ZT, Sun Y, Weatherbee JL, Alberta JA, Daley JF, Rozenblatt-Rosen O, Condurat AL, Qian K, Khadka P, Segal RA, Haas-Kogan D, Filbin MG, Suva ML, Regev A, Stiles CD, Kieran MW, Goumnerova L, Ligon KL, Shalek AK, Bandopadhayay P, Beroukhim R. Mitogenic and progenitor gene programmes in single pilocytic astrocytoma cells. Nat Commun. 2019 08 19; 10(1):3731. PMID: 31427603.
    Citations: 4     Fields:    Translation:HumansAnimalsCells
  27. Miklja Z, Pasternak A, Stallard S, Nicolaides T, Kline-Nunnally C, Cole B, Beroukhim R, Bandopadhayay P, Chi S, Ramkissoon SH, Mullan B, Bruzek AK, Gauthier A, Garcia T, Atchison C, Marini B, Fouladi M, Parsons DW, Leary S, Mueller S, Ligon KL, Koschmann C. Molecular profiling and targeted therapy in pediatric gliomas: review and consensus recommendations. Neuro Oncol. 2019 08 05; 21(8):968-980. PMID: 30805642.
    Citations: 9     Fields:    
  28. Bandopadhayay P, Piccioni F, O'Rourke R, Ho P, Gonzalez EM, Buchan G, Qian K, Gionet G, Girard E, Coxon M, Rees MG, Brenan L, Dubois F, Shapira O, Greenwald NF, Pages M, Balboni Iniguez A, Paolella BR, Meng A, Sinai C, Roti G, Dharia NV, Creech A, Tanenbaum B, Khadka P, Tracy A, Tiv HL, Hong AL, Coy S, Rashid R, Lin JR, Cowley GS, Lam FC, Goodale A, Lee Y, Schoolcraft K, Vazquez F, Hahn WC, Tsherniak A, Bradner JE, Yaffe MB, Milde T, Pfister SM, Qi J, Schenone M, Carr SA, Ligon KL, Kieran MW, Santagata S, Olson JM, Gokhale PC, Jaffe JD, Root DE, Stegmaier K, Johannessen CM, Beroukhim R. Neuronal differentiation and cell-cycle programs mediate response to BET-bromodomain inhibition in MYC-driven medulloblastoma. Nat Commun. 2019 06 03; 10(1):2400. PMID: 31160565.
    Citations: 5     Fields:    Translation:HumansAnimalsCells
  29. Chakraborty AA, Laukka T, Myllykoski M, Ringel AE, Booker MA, Tolstorukov MY, Meng YJ, Meier SR, Jennings RB, Creech AL, Herbert ZT, McBrayer SK, Olenchock BA, Jaffe JD, Haigis MC, Beroukhim R, Signoretti S, Koivunen P, Kaelin WG. Histone demethylase KDM6A directly senses oxygen to control chromatin and cell fate. Science. 2019 03 15; 363(6432):1217-1222. PMID: 30872525.
    Citations: 65     Fields:    Translation:HumansAnimalsCells
  30. Hong AL, Tseng YY, Wala JA, Kim WJ, Kynnap BD, Doshi MB, Kugener G, Sandoval GJ, Howard TP, Li J, Yang X, Tillgren M, Ghandi M, Sayeed A, Deasy R, Ward A, McSteen B, Labella KM, Keskula P, Tracy A, Connor C, Clinton CM, Church AJ, Crompton BD, Janeway KA, Van Hare B, Sandak D, Gjoerup O, Bandopadhayay P, Clemons PA, Schreiber SL, Root DE, Gokhale PC, Chi SN, Mullen EA, Roberts CW, Kadoch C, Beroukhim R, Ligon KL, Boehm JS, Hahn WC. Renal medullary carcinomas depend upon SMARCB1 loss and are sensitive to proteasome inhibition. Elife. 2019 03 12; 8. PMID: 30860482.
    Citations: 11     Fields:    Translation:HumansAnimalsCells
  31. Hong AL, Guerriero JL, Doshi MB, Kynnap BD, Kim WJ, Schinzel AC, Modiste R, Schlauch AJ, Adam RM, Kwiatkowski DJ, Beroukhim R, Letai A, Rosenberg JE, Hahn WC. MCL1 and DEDD Promote Urothelial Carcinoma Progression. Mol Cancer Res. 2019 06; 17(6):1294-1304. PMID: 30777879.
    Citations: 1     Fields:    Translation:HumansAnimalsCells
  32. Wen PY, Touat M, Alexander BM, Mellinghoff IK, Ramkissoon S, McCluskey CS, Pelton K, Haidar S, Basu SS, Gaffey SC, Brown LE, Martinez-Ledesma JE, Wu S, Kim J, Wei W, Park MA, Huse JT, Kuhn JG, Rinne ML, Colman H, Agar NYR, Omuro AM, DeAngelis LM, Gilbert MR, de Groot JF, Cloughesy TF, Chi AS, Roberts TM, Zhao JJ, Lee EQ, Nayak L, Heath JR, Horky LL, Batchelor TT, Beroukhim R, Chang SM, Ligon AH, Dunn IF, Koul D, Young GS, Prados MD, Reardon DA, Yung WKA, Ligon KL. Buparlisib in Patients With Recurrent Glioblastoma Harboring Phosphatidylinositol 3-Kinase Pathway Activation: An Open-Label, Multicenter, Multi-Arm, Phase II Trial. J Clin Oncol. 2019 03 20; 37(9):741-750. PMID: 30715997.
    Citations: 21     Fields:    Translation:HumansCellsCTClinical Trials
  33. Ben-David U, Beroukhim R, Golub TR. Genomic evolution of cancer models: perils and opportunities. Nat Rev Cancer. 2019 02; 19(2):97-109. PMID: 30578414.
    Citations: 35     Fields:    Translation:HumansAnimals
  34. Cui T, Bell EH, McElroy J, Becker AP, Gulati PM, Geurts M, Mladkova N, Gray A, Liu K, Yang L, Liu Z, Fleming JL, Haque SJ, Barnholtz-Sloan JS, Ligon KL, Beroukhim R, Robe P, Chakravarti A. miR-4516 predicts poor prognosis and functions as a novel oncogene via targeting PTPN14 in human glioblastoma. Oncogene. 2019 04; 38(16):2923-2936. PMID: 30559405.
    Citations: 11     Fields:    Translation:HumansCells
  35. Iniguez AB, Alexe G, Wang EJ, Roti G, Patel S, Chen L, Kitara S, Conway A, Robichaud AL, Stolte B, Bandopadhayay P, Goodale A, Pantel S, Lee Y, Cheff DM, Hall MD, Guha R, Davis MI, Menard M, Nasholm N, Weiss WA, Qi J, Beroukhim R, Piccioni F, Johannessen C, Stegmaier K. Resistance to Epigenetic-Targeted Therapy Engenders Tumor Cell Vulnerabilities Associated with Enhancer Remodeling. Cancer Cell. 2018 12 10; 34(6):922-938.e7. PMID: 30537514.
    Citations: 9     Fields:    Translation:HumansAnimalsCells
  36. Holst F, Werner HMJ, Mjøs S, Hoivik EA, Kusonmano K, Wik E, Berg A, Birkeland E, Gibson WJ, Halle MK, Trovik J, Cherniack AD, Kalland KH, Mills GB, Singer CF, Krakstad C, Beroukhim R, Salvesen HB. PIK3CA Amplification Associates with Aggressive Phenotype but Not Markers of AKT-MTOR Signaling in Endometrial Carcinoma. Clin Cancer Res. 2019 01 01; 25(1):334-345. PMID: 30442683.
    Citations: 3     Fields:    Translation:HumansCells
  37. Wong GS, Zhou J, Bin Liu J, Wu Z, Xu X, Li T, Xu D, Schumacher SE, Puschhof J, McFarland J, Zou C, Dulak A, Henderson L, Xu P, O'Day E, Rendak R, Liao WL, Cecchi F, Hembrough T, Schwartz S, Szeto C, Rustgi AK, Wong KK, Diehl JA, Jensen K, Graziano F, Ruzzo A, Fereshetian S, Mertins P, Carr SA, Beroukhim R, Nakamura K, Oki E, Watanabe M, Baba H, Imamura Y, Catenacci D, Bass AJ. Author Correction: Targeting wild-type KRAS-amplified gastroesophageal cancer through combined MEK and SHP2 inhibition. Nat Med. 2018 Oct; 24(10):1627. PMID: 30093730.
    Citations: 1     Fields:    
  38. Ben-David U, Siranosian B, Ha G, Tang H, Oren Y, Hinohara K, Strathdee CA, Dempster J, Lyons NJ, Burns R, Nag A, Kugener G, Cimini B, Tsvetkov P, Maruvka YE, O'Rourke R, Garrity A, Tubelli AA, Bandopadhayay P, Tsherniak A, Vazquez F, Wong B, Birger C, Ghandi M, Thorner AR, Bittker JA, Meyerson M, Getz G, Beroukhim R, Golub TR. Genetic and transcriptional evolution alters cancer cell line drug response. Nature. 2018 08; 560(7718):325-330. PMID: 30089904.
    Citations: 140     Fields:    Translation:HumansCells
  39. Chapuy B, Stewart C, Dunford AJ, Kim J, Kamburov A, Redd RA, Lawrence MS, Roemer MGM, Li AJ, Ziepert M, Staiger AM, Wala JA, Ducar MD, Leshchiner I, Rheinbay E, Taylor-Weiner A, Coughlin CA, Hess JM, Pedamallu CS, Livitz D, Rosebrock D, Rosenberg M, Tracy AA, Horn H, van Hummelen P, Feldman AL, Link BK, Novak AJ, Cerhan JR, Habermann TM, Siebert R, Rosenwald A, Thorner AR, Meyerson ML, Golub TR, Beroukhim R, Wulf GG, Ott G, Rodig SJ, Monti S, Neuberg DS, Loeffler M, Pfreundschuh M, Trümper L, Getz G, Shipp MA. Publisher Correction: Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 Aug; 24(8):1292. PMID: 29955181.
    Citations:    Fields:    
  40. Chapuy B, Stewart C, Dunford AJ, Kim J, Kamburov A, Redd RA, Lawrence MS, Roemer MGM, Li AJ, Ziepert M, Staiger AM, Wala JA, Ducar MD, Leshchiner I, Rheinbay E, Taylor-Weiner A, Coughlin CA, Hess JM, Pedamallu CS, Livitz D, Rosebrock D, Rosenberg M, Tracy AA, Horn H, van Hummelen P, Feldman AL, Link BK, Novak AJ, Cerhan JR, Habermann TM, Siebert R, Rosenwald A, Thorner AR, Meyerson ML, Golub TR, Beroukhim R, Wulf GG, Ott G, Rodig SJ, Monti S, Neuberg DS, Loeffler M, Pfreundschuh M, Trümper L, Getz G, Shipp MA. Author Correction: Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 Aug; 24(8):1290-1291. PMID: 29955182.
    Citations: 6     Fields:    
  41. Ricketts CJ, De Cubas AA, Fan H, Smith CC, Lang M, Reznik E, Bowlby R, Gibb EA, Akbani R, Beroukhim R, Bottaro DP, Choueiri TK, Gibbs RA, Godwin AK, Haake S, Hakimi AA, Henske EP, Hsieh JJ, Ho TH, Kanchi RS, Krishnan B, Kwiatkowski DJ, Lui W, Merino MJ, Mills GB, Myers J, Nickerson ML, Reuter VE, Schmidt LS, Shelley CS, Shen H, Shuch B, Signoretti S, Srinivasan R, Tamboli P, Thomas G, Vincent BG, Vocke CD, Wheeler DA, Yang L, Kim WY, Robertson AG, Spellman PT, Rathmell WK, Linehan WM. The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma. Cell Rep. 2018 Jun 19; 23(12):3698. PMID: 29925010.
    Citations: 42     Fields:    
  42. Viswanathan SR, Ha G, Hoff AM, Wala JA, Carrot-Zhang J, Whelan CW, Haradhvala NJ, Freeman SS, Reed SC, Rhoades J, Polak P, Cipicchio M, Wankowicz SA, Wong A, Kamath T, Zhang Z, Gydush GJ, Rotem D, Love JC, Getz G, Gabriel S, Zhang CZ, Dehm SM, Nelson PS, Van Allen EM, Choudhury AD, Adalsteinsson VA, Beroukhim R, Taplin ME, Meyerson M. Structural Alterations Driving Castration-Resistant Prostate Cancer Revealed by Linked-Read Genome Sequencing. Cell. 2018 07 12; 174(2):433-447.e19. PMID: 29909985.
    Citations: 61     Fields:    Translation:HumansCells
  43. Glioma through the looking GLASS: molecular evolution of diffuse gliomas and the Glioma Longitudinal Analysis Consortium. Neuro Oncol. 2018 06 18; 20(7):873-884. PMID: 29432615.
    Citations: 24     Fields:    Translation:Humans
  44. Forget MA, Haymaker C, Hess KR, Meng YJ, Creasy C, Karpinets T, Fulbright OJ, Roszik J, Woodman SE, Kim YU, Sakellariou-Thompson D, Bhatta A, Wahl A, Flores E, Thorsen ST, Tavera RJ, Ramachandran R, Gonzalez AM, Toth CL, Wardell S, Mansaray R, Patel V, Carpio DJ, Vaughn C, Farinas CM, Velasquez PG, Hwu WJ, Patel SP, Davies MA, Diab A, Glitza IC, Tawbi H, Wong MK, Cain S, Ross MI, Lee JE, Gershenwald JE, Lucci A, Royal R, Cormier JN, Wargo JA, Radvanyi LG, Torres-Cabala CA, Beroukhim R, Hwu P, Amaria RN, Bernatchez C. Prospective Analysis of Adoptive TIL Therapy in Patients with Metastatic Melanoma: Response, Impact of Anti-CTLA4, and Biomarkers to Predict Clinical Outcome. Clin Cancer Res. 2018 09 15; 24(18):4416-4428. PMID: 29848573.
    Citations: 19     Fields:    Translation:HumansCells
  45. Wong GS, Zhou J, Liu JB, Wu Z, Xu X, Li T, Xu D, Schumacher SE, Puschhof J, McFarland J, Zou C, Dulak A, Henderson L, Xu P, O'Day E, Rendak R, Liao WL, Cecchi F, Hembrough T, Schwartz S, Szeto C, Rustgi AK, Wong KK, Diehl JA, Jensen K, Graziano F, Ruzzo A, Fereshetian S, Mertins P, Carr SA, Beroukhim R, Nakamura K, Oki E, Watanabe M, Baba H, Imamura Y, Catenacci D, Bass AJ. Targeting wild-type KRAS-amplified gastroesophageal cancer through combined MEK and SHP2 inhibition. Nat Med. 2018 07; 24(7):968-977. PMID: 29808010.
    Citations: 44     Fields:    Translation:HumansAnimalsCells
  46. Chapuy B, Stewart C, Dunford AJ, Kim J, Kamburov A, Redd RA, Lawrence MS, Roemer MGM, Li AJ, Ziepert M, Staiger AM, Wala JA, Ducar MD, Leshchiner I, Rheinbay E, Taylor-Weiner A, Coughlin CA, Hess JM, Pedamallu CS, Livitz D, Rosebrock D, Rosenberg M, Tracy AA, Horn H, van Hummelen P, Feldman AL, Link BK, Novak AJ, Cerhan JR, Habermann TM, Siebert R, Rosenwald A, Thorner AR, Meyerson ML, Golub TR, Beroukhim R, Wulf GG, Ott G, Rodig SJ, Monti S, Neuberg DS, Loeffler M, Pfreundschuh M, Trümper L, Getz G, Shipp MA. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 05; 24(5):679-690. PMID: 29713087.
    Citations: 221     Fields:    Translation:Humans
  47. Filbin MG, Tirosh I, Hovestadt V, Shaw ML, Escalante LE, Mathewson ND, Neftel C, Frank N, Pelton K, Hebert CM, Haberler C, Yizhak K, Gojo J, Egervari K, Mount C, van Galen P, Bonal DM, Nguyen QD, Beck A, Sinai C, Czech T, Dorfer C, Goumnerova L, Lavarino C, Carcaboso AM, Mora J, Mylvaganam R, Luo CC, Peyrl A, Popovic M, Azizi A, Batchelor TT, Frosch MP, Martinez-Lage M, Kieran MW, Bandopadhayay P, Beroukhim R, Fritsch G, Getz G, Rozenblatt-Rosen O, Wucherpfennig KW, Louis DN, Monje M, Slavc I, Ligon KL, Golub TR, Regev A, Bernstein BE, Suvà ML. Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq. Science. 2018 04 20; 360(6386):331-335. PMID: 29674595.
    Citations: 87     Fields:    Translation:HumansCells
  48. Ricketts CJ, De Cubas AA, Fan H, Smith CC, Lang M, Reznik E, Bowlby R, Gibb EA, Akbani R, Beroukhim R, Bottaro DP, Choueiri TK, Gibbs RA, Godwin AK, Haake S, Hakimi AA, Henske EP, Hsieh JJ, Ho TH, Kanchi RS, Krishnan B, Kwiatkowski DJ, Lui W, Merino MJ, Mills GB, Myers J, Nickerson ML, Reuter VE, Schmidt LS, Shelley CS, Shen H, Shuch B, Signoretti S, Srinivasan R, Tamboli P, Thomas G, Vincent BG, Vocke CD, Wheeler DA, Yang L, Kim WY, Robertson AG, Spellman PT, Rathmell WK, Linehan WM. The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma. Cell Rep. 2018 04 03; 23(1):313-326.e5. PMID: 29617669.
    Citations: 85     Fields:    Translation:Humans
  49. Taylor AM, Shih J, Ha G, Gao GF, Zhang X, Berger AC, Schumacher SE, Wang C, Hu H, Liu J, Lazar AJ, Cherniack AD, Beroukhim R, Meyerson M. Genomic and Functional Approaches to Understanding Cancer Aneuploidy. Cancer Cell. 2018 04 09; 33(4):676-689.e3. PMID: 29622463.
    Citations: 131     Fields:    Translation:HumansCells
  50. Wala JA, Bandopadhayay P, Greenwald NF, O'Rourke R, Sharpe T, Stewart C, Schumacher S, Li Y, Weischenfeldt J, Yao X, Nusbaum C, Campbell P, Getz G, Meyerson M, Zhang CZ, Imielinski M, Beroukhim R. SvABA: genome-wide detection of structural variants and indels by local assembly. Genome Res. 2018 04; 28(4):581-591. PMID: 29535149.
    Citations: 63     Fields:    Translation:Humans
  51. Coroller TP, Bi WL, Huynh E, Abedalthagafi M, Aizer AA, Greenwald NF, Parmar C, Narayan V, Wu WW, Miranda de Moura S, Gupta S, Beroukhim R, Wen PY, Al-Mefty O, Dunn IF, Santagata S, Alexander BM, Huang RY, Aerts HJWL. Radiographic prediction of meningioma grade by semantic and radiomic features. PLoS One. 2017; 12(11):e0187908. PMID: 29145421.
    Citations: 21     Fields:    Translation:Humans
  52. Greenwald NF, Bandopadhayay P, Beroukhim R. Open data: Spot data glitches before publication. Nature. 2017 10 18; 550(7676):333. PMID: 29052624.
    Citations:    Fields:    Translation:Humans
  53. Ben-David U, Ha G, Tseng YY, Greenwald NF, Oh C, Shih J, McFarland JM, Wong B, Boehm JS, Beroukhim R, Golub TR. Patient-derived xenografts undergo mouse-specific tumor evolution. Nat Genet. 2017 Nov; 49(11):1567-1575. PMID: 28991255.
    Citations: 158     Fields:    Translation:HumansAnimalsCells
  54. Bi WL, Greenwald NF, Abedalthagafi M, Wala J, Gibson WJ, Agarwalla PK, Horowitz P, Schumacher SE, Esaulova E, Mei Y, Chevalier A, A Ducar M, Thorner AR, van Hummelen P, O Stemmer-Rachamimov A, Artyomov M, Al-Mefty O, Dunn GP, Santagata S, Dunn IF, Beroukhim R. Erratum: Genomic landscape of high-grade meningiomas. NPJ Genom Med. 2017; 2:26. PMID: 29263836.
    Citations: 5     
  55. 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. Nature. 2017 07 19; 547(7663):311-317. PMID: 28726821.
    Citations: 180     Fields:    Translation:HumansCells
  56. Bi WL, Greenwald NF, Ramkissoon SH, Abedalthagafi M, Coy SM, Ligon KL, Mei Y, MacConaill L, Ducar M, Min L, Santagata S, Kaiser UB, Beroukhim R, Laws ER, Dunn IF. Clinical Identification of Oncogenic Drivers and Copy-Number Alterations in Pituitary Tumors. Endocrinology. 2017 07 01; 158(7):2284-2291. PMID: 28486603.
    Citations: 17     Fields:    Translation:HumansCells
  57. Ramkissoon SH, Bandopadhayay P, Hwang J, Ramkissoon LA, Greenwald NF, Schumacher SE, O'Rourke R, Pinches N, Ho P, Malkin H, Sinai C, Filbin M, Plant A, Bi WL, Chang MS, Yang E, Wright KD, Manley PE, Ducar M, Alexandrescu S, Lidov H, Delalle I, Goumnerova LC, Church AJ, Janeway KA, Harris MH, MacConaill LE, Folkerth RD, Lindeman NI, Stiles CD, Kieran MW, Ligon AH, Santagata S, Dubuc AM, Chi SN, Beroukhim R, Ligon KL. Clinical targeted exome-based sequencing in combination with genome-wide copy number profiling: precision medicine analysis of 203 pediatric brain tumors. Neuro Oncol. 2017 Jul 01; 19(7):986-996. PMID: 28104717.
    Citations: 20     Fields:    Translation:Humans
  58. Tanguturi SK, Trippa L, Ramkissoon SH, Pelton K, Knoff D, Sandak D, Lindeman NI, Ligon AH, Beroukhim R, Parmigiani G, Wen PY, Ligon KL, Alexander BM. Leveraging molecular datasets for biomarker-based clinical trial design in glioblastoma. Neuro Oncol. 2017 Jul 01; 19(7):908-917. PMID: 28339723.
    Citations: 7     Fields:    Translation:HumansCells
  59. Holst F, Hoivik EA, Gibson WJ, Taylor-Weiner A, Schumacher SE, Asmann YW, Grossmann P, Trovik J, Necela BM, Thompson EA, Meyerson M, Beroukhim R, Salvesen HB, Cherniack AD. Corrigendum: Recurrent hormone-binding domain truncated ESR1 amplifications in primary endometrial cancers suggest their implication in hormone independent growth. Sci Rep. 2017 06 30; 7:46873. PMID: 28664899.
    Citations:    Fields:    
  60. Mei Y, Bi WL, Greenwald NF, Agar NY, Beroukhim R, Dunn GP, Dunn IF. Genomic profile of human meningioma cell lines. PLoS One. 2017; 12(5):e0178322. PMID: 28552950.
    Citations: 11     Fields:    Translation:HumansCells
  61. Godlewski J, Ferrer-Luna R, Rooj AK, Mineo M, Ricklefs F, Takeda YS, Nowicki MO, Salinska E, Nakano I, Lee H, Weissleder R, Beroukhim R, Chiocca EA, Bronisz A. MicroRNA Signatures and Molecular Subtypes of Glioblastoma: The Role of Extracellular Transfer. Stem Cell Reports. 2017 06 06; 8(6):1497-1505. PMID: 28528698.
    Citations: 25     Fields:    Translation:HumansAnimalsCells
  62. Bi WL, Greenwald NF, Abedalthagafi M, Wala J, Gibson WJ, Agarwalla PK, Horowitz P, Schumacher SE, Esaulova E, Mei Y, Chevalier A, Ducar M, Thorner AR, van Hummelen P, Stemmer-Rachamimov A, Artyomov M, Al-Mefty O, Dunn GP, Santagata S, Dunn IF, Beroukhim R. Genomic landscape of high-grade meningiomas. NPJ Genom Med. 2017; 2. PMID: 28713588.
    Citations: 24     
  63. Schumacher SE, Shim BY, Corso G, Ryu MH, Kang YK, Roviello F, Saksena G, Peng S, Shivdasani RA, Bass AJ, Beroukhim R. Somatic copy number alterations in gastric adenocarcinomas among Asian and Western patients. PLoS One. 2017; 12(4):e0176045. PMID: 28426752.
    Citations: 11     Fields:    Translation:Humans
  64. Shankar GM, Abedalthagafi M, Vaubel RA, Merrill PH, Nayyar N, Gill CM, Brewster R, Bi WL, Agarwalla PK, Thorner AR, Reardon DA, Al-Mefty O, Wen PY, Alexander BM, van Hummelen P, Batchelor TT, Ligon KL, Ligon AH, Meyerson M, Dunn IF, Beroukhim R, Louis DN, Perry A, Carter SL, Giannini C, Curry WT, Cahill DP, Barker FG, Brastianos PK, Santagata S. Germline and somatic BAP1 mutations in high-grade rhabdoid meningiomas. Neuro Oncol. 2017 04 01; 19(4):535-545. PMID: 28170043.
    Citations: 36     Fields:    Translation:Humans
  65. Wala J, Beroukhim R. SeqLib: a C?++ API for rapid BAM manipulation, sequence alignment and sequence assembly. Bioinformatics. 2017 03 01; 33(5):751-753. PMID: 28011768.
    Citations: 2     Fields:    Translation:Cells
  66. Paolella BR, Gibson WJ, Urbanski LM, Alberta JA, Zack TI, Bandopadhayay P, Nichols CA, Agarwalla PK, Brown MS, Lamothe R, Yu Y, Choi PS, Obeng EA, Heckl D, Wei G, Wang B, Tsherniak A, Vazquez F, Weir BA, Root DE, Cowley GS, Buhrlage SJ, Stiles CD, Ebert BL, Hahn WC, Reed R, Beroukhim R. Copy-number and gene dependency analysis reveals partial copy loss of wild-type SF3B1 as a novel cancer vulnerability. Elife. 2017 02 08; 6. PMID: 28177281.
    Citations: 26     Fields:    Translation:HumansCells
  67. Beroukhim R, Zhang X, Meyerson M. Copy number alterations unmasked as enhancer hijackers. Nat Genet. 2016 12 28; 49(1):5-6. PMID: 28029156.
    Citations: 13     Fields:    Translation:HumansCells
  68. Gong Y, Schumacher SE, Wu WH, Tang F, Beroukhim R, Chan TA. Pan-Cancer Analysis Links PARK2 to BCL-XL-Dependent Control of Apoptosis. Neoplasia. 2017 02; 19(2):75-83. PMID: 28038320.
    Citations: 12     Fields:    Translation:HumansCells
  69. Taylor-Weiner A, Zack T, O'Donnell E, Guerriero JL, Bernard B, Reddy A, Han GC, AlDubayan S, Amin-Mansour A, Schumacher SE, Litchfield K, Turnbull C, Gabriel S, Beroukhim R, Getz G, Carter SL, Hirsch MS, Letai A, Sweeney C, Van Allen EM. Genomic evolution and chemoresistance in germ-cell tumours. Nature. 2016 11 30; 540(7631):114-118. PMID: 27905446.
    Citations: 42     Fields:    Translation:HumansCells
  70. Dunford A, Weinstock DM, Savova V, Schumacher SE, Cleary JP, Yoda A, Sullivan TJ, Hess JM, Gimelbrant AA, Beroukhim R, Lawrence MS, Getz G, Lane AA. Tumor-suppressor genes that escape from X-inactivation contribute to cancer sex bias. Nat Genet. 2017 01; 49(1):10-16. PMID: 27869828.
    Citations: 67     Fields:    Translation:HumansCells
  71. Gibson WJ, Ruan DT, Paulson VA, Barletta JA, Hanna GJ, Kraft S, Calles A, Nehs MA, Moore FD, Taylor-Weiner A, Wala JA, Zack TI, Lee TC, Fennessy FM, Alexander EK, Thomas T, Janne PA, Garraway LA, Carter SL, Beroukhim R, Lorch JH, Van Allen EM. Genomic Heterogeneity and Exceptional Response to Dual Pathway Inhibition in Anaplastic Thyroid Cancer. Clin Cancer Res. 2017 May 01; 23(9):2367-2373. PMID: 27797976.
    Citations: 10     Fields:    Translation:HumansCells
  72. Agnihotri S, Jalali S, Wilson MR, Danesh A, Li M, Klironomos G, Krieger JR, Mansouri A, Khan O, Mamatjan Y, Landon-Brace N, Tung T, Dowar M, Li T, Bruce JP, Burrell KE, Tonge PD, Alamsahebpour A, Krischek B, Agarwalla PK, Bi WL, Dunn IF, Beroukhim R, Fehlings MG, Bril V, Pagnotta SM, Iavarone A, Pugh TJ, Aldape KD, Zadeh G. The genomic landscape of schwannoma. Nat Genet. 2016 11; 48(11):1339-1348. PMID: 27723760.
    Citations: 26     Fields:    Translation:HumansAnimalsCells
  73. Bi WL, Horowitz P, Greenwald NF, Abedalthagafi M, Agarwalla PK, Gibson WJ, Mei Y, Schumacher SE, Ben-David U, Chevalier A, Carter S, Tiao G, Brastianos PK, Ligon AH, Ducar M, MacConaill L, Laws ER, Santagata S, Beroukhim R, Dunn IF. Landscape of Genomic Alterations in Pituitary Adenomas. Clin Cancer Res. 2017 Apr 01; 23(7):1841-1851. PMID: 27707790.
    Citations: 22     Fields:    Translation:HumansCells
  74. Ni J, Xie S, Ramkissoon SH, Luu V, Sun Y, Bandopadhayay P, Beroukhim R, Roberts TM, Stiles CD, Segal RA, Ligon KL, Hahn WC, Zhao JJ. Tyrosine receptor kinase B is a drug target in astrocytomas. Neuro Oncol. 2017 01; 19(1):22-30. PMID: 27402815.
    Citations: 15     Fields:    Translation:HumansAnimalsCells
  75. Gibson WJ, Hoivik EA, Halle MK, Taylor-Weiner A, Cherniack AD, Berg A, Holst F, Zack TI, Werner HM, Staby KM, Rosenberg M, Stefansson IM, Kusonmano K, Chevalier A, Mauland KK, Trovik J, Krakstad C, Giannakis M, Hodis E, Woie K, Bjorge L, Vintermyr OK, Wala JA, Lawrence MS, Getz G, Carter SL, Beroukhim R, Salvesen HB. The genomic landscape and evolution of endometrial carcinoma progression and abdominopelvic metastasis. Nat Genet. 2016 08; 48(8):848-55. PMID: 27348297.
    Citations: 60     Fields:    Translation:Humans
  76. Holst F, Hoivik EA, Gibson WJ, Taylor-Weiner A, Schumacher SE, Asmann YW, Grossmann P, Trovik J, Necela BM, Thompson EA, Meyerson M, Beroukhim R, Salvesen HB, Cherniack AD. Corrigendum: Recurrent hormone-binding domain truncated ESR1 amplifications in primary endometrial cancers suggest their implication in hormone independent growth. Sci Rep. 2016 06 24; 6:27960. PMID: 27338572.
    Citations:    Fields:    
  77. Miller MB, Bi WL, Ramkissoon LA, Kang YJ, Abedalthagafi M, Knoff DS, Agarwalla PK, Wen PY, Reardon DA, Alexander BM, Laws ER, Dunn IF, Beroukhim R, Ligon KL, Ramkissoon SH. MAPK activation and HRAS mutation identified in pituitary spindle cell oncocytoma. Oncotarget. 2016 Jun 14; 7(24):37054-37063. PMID: 27175596.
    Citations: 6     Fields:    Translation:HumansCells
  78. Holst F, Hoivik EA, Gibson WJ, Taylor-Weiner A, Schumacher SE, Asmann YW, Grossmann P, Trovik J, Necela BM, Thompson EA, Meyerson M, Beroukhim R, Salvesen HB, Cherniack AD. Recurrent hormone-binding domain truncated ESR1 amplifications in primary endometrial cancers suggest their implication in hormone independent growth. Sci Rep. 2016 05 10; 6:25521. PMID: 27160768.
    Citations: 3     Fields:    
  79. Kim JW, Botvinnik OB, Abudayyeh O, Birger C, Rosenbluh J, Shrestha Y, Abazeed ME, Hammerman PS, DiCara D, Konieczkowski DJ, Johannessen CM, Liberzon A, Alizad-Rahvar AR, Alexe G, Aguirre A, Ghandi M, Greulich H, Vazquez F, Weir BA, Van Allen EM, Tsherniak A, Shao DD, Zack TI, Noble M, Getz G, Beroukhim R, Garraway LA, Ardakani M, Romualdi C, Sales G, Barbie DA, Boehm JS, Hahn WC, Mesirov JP, Tamayo P. Characterizing genomic alterations in cancer by complementary functional associations. Nat Biotechnol. 2016 05; 34(5):539-46. PMID: 27088724.
    Citations: 27     Fields:    Translation:HumansCells
  80. Bi WL, Mei Y, Agarwalla PK, Beroukhim R, Dunn IF. Genomic and Epigenomic Landscape in Meningioma. Neurosurg Clin N Am. 2016 Apr; 27(2):167-79. PMID: 27012381.
    Citations: 7     Fields:    Translation:HumansAnimalsCells
  81. Wala J, Beroukhim R. CANCER. The oncogene makes its escape. Science. 2016 Mar 25; 351(6280):1398-9. PMID: 27013717.
    Citations: 1     Fields:    Translation:Humans
  82. Dodgshun AJ, SantaCruz N, Hwang J, Ramkissoon SH, Malkin H, Bergthold G, Manley P, Chi S, MacGregor D, Goumnerova L, Sullivan M, Ligon K, Beroukhim R, Herrington B, Kieran MW, Hansford JR, Bandopadhayay P. Disseminated glioneuronal tumors occurring in childhood: treatment outcomes and BRAF alterations including V600E mutation. J Neurooncol. 2016 06; 128(2):293-302. PMID: 26994902.
    Citations: 13     Fields:    Translation:Humans
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