Publications

2022 2021 20202019 | 20182017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010

2022

Moorthi S, Berger AH. All about that Ras: Novel fusion drives Ras pathway activation in lung cancer. Clinical Cancer Research. 2022 May 5; Online ahead of print

Caicedo JC, Arevalo J, Piccioni F, Bray MA, Hartland CL, Wu X, Brooks AN, Berger AH, Boehm JS, Carpenter AE, Singh S. Cell Painting predicts impact of lung cancer variants. Molecular Biology of the Cell. 2022 Mar 30; In Press

Ursu O, Neal JT, Shea E, Thakore PI, Jerby-Arnon L, Nguyen L, Dionne D, Diaz C, Bauman J, Mounir Mosaad M, Fagre C, Lo A, McSharry M, Giacomelli AO, Ly SH, Rozenblatt-Rosen O, Hanh WC, Aguirre AJ, Berger AH, Regev A, Boehm JS. Massively parallel phenotyping of coding variants in cancer with Perturb-seq. Nature Biotechnology. 2022 Jan 20

2021

Lo A*, Holmes K*, Kamlapurkar S, Mund  F, Moorthi S, Fung I, Fereshetian S, Watson J, Carr SA, Mertins P, Berger AH. Multiomic characterization of oncogenic signaling mediated by wild-type and mutant RIT1. Science Signaling. 2021 Nov 30;14(711):eabc4520. *equal contribution

Riley AK, Berger AH. Genome-wide CRISPR screening reveals novel therapeutic targets in RIT1-driven lung cancer. Molecular and Cellular Oncology. 2021 Nov 16; 8:6

Parrish PCR*, Thomas JD*, Gabel AM, Kamlapurkar S, Bradley RK, Berger AH. Discovery of synthetic lethal and tumor suppressor paralog pairs in the human genome. Cell Reports. 2021 Aug 31;36(9):109597.*equal contribution

Vichas A*, Riley AK*, Nkinsi NT Kamlapurkar S, Parrish PCR, Lo A, Fujiko D, Chen J, Fung I, Watson J, Rees M, Gabel AM, Thomas JD, Bradley RK, Lee JK, Hatch EM, Baine MK, Rekhtman N, Ladanyi M, Piccioni F, Berger AHIntegrative oncogene-dependency mapping identifies RIT1 vulnerabilities and synergies in lung cancerNature Communications. 2021 Aug 9;(12): 4789.*equal contribution

Mathsyaraja H, Catchpole J, Freie B, Eastwood E, Babaeva E, Beuenich M, Cheng PF, Ayers J, Yu M, Wu N, Moorthi S, Poudel KR, Koehne A, Grady W, Houghton AM, Berger AH, Shiio Y, MacPherson D, Eisenman RN. Loss of MGA repression mediated by an atypical polycomb complex promotes tumor progression and invasiveness. Elife. 2021 Jul 8;10:e64212.

Thornton AM, Fang L, Lo A, McSharry M, Haan D, O’Brien C, Berger AH, Giannakis M, Brooks AN. eVIP: Expression-based variant impact phenotyping to predict the function of gene variants. PLoS Computational Biology. 2021 Jul 2;17(7):e10091312.

Carrot-Zhang J, Yao X, Devarakonda S, Deshpande A, Damrauer JS, Chedraoui Silva T, Wong CK, Young Choi H, Felau I, Gordon Robertson A, Castro MAA, Bao L, Rheinbay E, Minwei Liu E, 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, TCGA Research Network; Meyerson M, Govindan R, Imielinski M. Whole-genome characterization of lung adenocarcinomas lacking the RTK/RAS/RAF pathwayCell Reports. 2021 Feb 23;34(5):108707.

Parrish PCR, Berger AH. CRISPR base editor screens identify variant function at scale. Molecular Cell. 2021 Feb 18;81(4):647-648.

2020

Thomas JD, Polaski JT, Feng Q, De Neef EJ, Hoppe ER, McSharry MV, Pangallo J, Gabel AM, Belleville AE, Watson J, Nkinsi NT, Berger AH, Bradley RK. RNA isoform screens uncover the essentiality and tumor-suppressor activity of ultraconserved poison exons. Nature Genetics. 2020 Jan 7, (52): 84–94.

2019

Gelman H, Dines JN, Berg J, Berger AH, Brnich S, Hisama FM, James RG, Rubin AF, Shendure J, Shirts B, Fowler DM, Starita LM, Brotman Baty Institute Mutational Scanning Working Group. Recommendations for the collection and use of multiplexed functional data for clinical variant interpretation. Genome Medicine. 2019 Dec 20;11(1):85.

Chen M, Zhang J, Berger AH, Diolombi MS, Ng C, Fung J, Bronson RT, Castillo-Martin M, Thin TH, Cordon-Cardo C, Plevin R, Pandolfi PP. Compound haploinsufficiency of Dok2 and Dusp4 promotes lung tumorigenesis. J Clin Invest. 2019 Jan 2;129(1):215-222.

2018

Sanchez-Vega F, Mina M, Armenia J, Chatila WK, Luna A, La KC, Dimitriadoy S, Liu DL, Kantheti HS, Saghafinia S, Chakravarty D, Daian F, Gao Q, Bailey MH, Liang WW, Foltz SM, Shmulevich I, Ding L, Heins Z, Ochoa A, Gross B, Gao J, Zhang H, Kundra R, Kandoth C, Bahceci I, Dervishi L, Dogrusoz U, Zhou W, Shen H, Laird PW, Way GP, Greene CS, Liang H, Xiao Y, Wang C, Iavarone A, Berger AH, Bivona TG, Lazar AJ, Hammer GD, Giordano T, Kwong LN, McArthur G, Huang C, Tward AD, Frederick MJ, McCormick F, Meyerson M; Cancer Genome Atlas Research Network, Van Allen EM, Cherniack AD, Ciriello G, Sander C, Schultz N. Oncogenic Signaling Pathways in The Cancer Genome Atlas. Cell. 2018 Apr 5;173(2):321-337.

2017

Subramanian A, Narayan R, Corsello SM, Peck DD, Natoli TE, Lu X, Gould J, Davis JF, Tubelli AA, Asiedu JK, Lahr DL, Hirschman JE, Liu Z, Donahue M, Julian B, Khan M, Wadden D, Smith IC, Lam D, Liberzon A, Toder C, Bagul M, Orzechowski M, Enache OM, Piccioni F, Johnson SA, Lyons NJ, Berger AH, Shamji AF, Brooks AN, Vrcic A, Flynn C, Rosains J, Takeda DY, Hu R, Davison D, Lamb J, Ardlie K, Hogstrom L, Greenside P, Gray NS, Clemons PA, Silver S, Wu X, Zhao WN, Read-Button W, Wu X, Haggarty SJ, Ronco LV, Boehm JS, Schreiber SL, Doench JG, Bittker JA, Root DE, Wong B, Golub TR. 2017. A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles. Cancer Cell 11;32(6):884.

2016

Sholl LM, Do K, Shivdasani P, Cerami E, Dubuc AM, Kuo FC, Garcia EP, Jia Y, Davineni P, Abo RP, Pugh TJ, van Hummelen P, Thorner AR, Ducar M, Berger AH, Nishino M, Janeway KA, Church A, Harris M, Ritterhouse LL, Campbell JD, Rojas-Rudilla V, Ligon AH, Ramkissoon S, Cleary JM, Matulonis U, Oxnard GR, Chao R, Tassell V, Christensen J, Hahn WC, Kantoff PW, Kwiatkowski DJ, Johnson BE, Meyerson M, Garraway LA, Shapiro GI, Rollins BJ, Lindeman NI, MacConaill LE. 2016. Institutional implementation of clinical tumor profiling on an unselected cancer population. JCI Insight 1(19):e87062.

Lu X, Peled N, Greer J, Wu W, Choi P, Berger AH, Wong S, Jen KY, Seo Y, Hann B, Brooks A, Meyerson M, Collisson EA. 2017. MET Exon 14 Mutation Encodes an Actionable Therapeutic Target in Lung Adenocarcinoma. Cancer Research 77(16):4498-4505.

Berger AH*, Brooks AN*, Wu X*, Shretha Y, Chouinard C, Piccioni F, Bagul M, Kamburov A, Imielinski M, Hogstrom L, Zhu C, Yang X, Pantel S, Sakai R, Watson J, Kaplan N, Campbell JD, Singh S, Root D, Narayan R, Natoli T, Lahr D, Tirosh I, Tamayo P, Getz G, Wong B, Doench J, Subramanian A, Golub T, Meyerson M, and Boehm J. 2016. High-throughput phenotyping of lung cancer somatic mutations. Cancer Cell 30(2): 214-228. *equal contribution

Campbell JD, Alexandrov A, Kim J, Wala J, Berger AH, Pedamallu CS, Shukla SA, Guo G, Brooks AN, Murray BA, Imielinski M, Hu X, Ling S, Akbani R, Rosenberg M, Cibulskis C, Ramachandran A, Collisson EA, Kwiatkowski DJ, Lawrence MS, Weinstein JN, Verhaak RG, Wu CJ, Hammerman PS, Cherniack AD, Getz G; Cancer Genome Atlas Research Network, Artyomov MN, Schreiber R, Govindan R, Meyerson M. 2016. Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas. Nat Genet 48(6):607-16.

2015

Lunardi A, Varmeh S, Chen M, Taulli R, Guarnerio J, Ala U, Seitzer N, Ishikawa T, Carver BS, Hobbs RM, Quarantotti V, Ng C, Berger AH, Nardella C, Poliseno L, Montironi R, Castillo-Martin M, Cordon-Cardo C, Signoretti S, Pandolfi PP. 2015. Suppression of CHK1 by ETS family members promotes DNA Damage response bypass and tumorigenesis. Cancer Discovery 5(5):550-63.

2014

The Cancer Genome Atlas Network (including Berger AH). 2014. Comprehensive Molecular Profiling of Lung Adenocarcinoma. Nature 511(7511):543-50.

Berger AH, Imielinski M, Duke F, Wala J, Kaplan N, Shi G, Andres D, Meyerson M. 2014. Oncogenic RIT1 mutations in lung adenocarcinoma. Oncogene 33(35):4418-23.

Morotti A, Panuzzo C, Crivellaro S, Pergolizzi B, Familiari U, Berger AH, Saglio G, Pandolfi, PP. 2014. BCR-ABL disrupts PTEN nuclear-cytoplasmic shuttling through phosphorylation-dependent activation of HAUSP. Leukemia 28(6):1326-33.

2013

Berger AH, Chen M, Morotti A, Janas JA, Niki M, Bronson RT, Taylor BS, Ladanyi M, Van Aelst L, Politi K, Varmus HE, Pandolfi, PP. 2013. DOK2 inhibits EGFR-mutated lung adenocarcinoma. PLOS One 8(11):e79526.

2012

Imielinski, M*, Berger AH*, Hammerman PS*, Hernandez B*, Pugh TJ*, Hodis E, Cho J, Suh J, Capelletti M, Sivachenko A, Sougnez C, Auclair D, Lawrence MS, Stojanov P, Cibulski K, Choi K, de Waal L, Sharifnia T, Brooks A, Greulich H, Banerji S, Zander T, Seidel D, Leenders F, Ansén S, Ludwig C, Engel-Riedel W, Stoelben E, Wolf J, Goparju C, Thompson K, Winckler W, Kwiatkowski D, Johnson BE, Janne P, Miller VA, Pao W, Travis WD, Pass HI, Gabriel SB, Lander ES, Thomas RK, Garraway LA, Getz G, Meyerson M. 2012. Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing. Cell 150(6):1107-20. *equal contribution

Greulich H, Kaplan B, Mertins P, Chen TH, Tanaka KE, Yun CH, Zhang X, Lee SH, Cho J, Ambrogio L, Liao R, Imielinski M, Banerji S, Berger AH, Lawrence MS, Zhang J, Pho NH, Walker SR, Winckler W, Getz G, Frank D, Hahn WC, Eck MJ, Mani DR, Jaffe JD, Carr SA, Wong KK, Meyerson M. 2012. Functional analysis of receptor tyrosine kinase mutations in lung cancer identifies oncogenic extracellular domain mutations of ERBB2. PNAS 109(36): 14476-81.

2011

Berger AH, Knudson AG, Pandolfi PP. 2011. A continuum model for tumour suppression. Nature 476(7359):163-9.

Berger AH, Pandolfi PP. 2011. Haplo-insufficiency: a driving force in cancer. J Pathol. 223(2): 137-46.

2010

Berger AH*, Niki M*, Morotti A, Taylor BS, Socci ND, Viale A, Brennan C, Szoke J, Motoi N, Rothman PB, Teruya-Feldstein J, Gerald WL, Ladanyi M, Pandolfi PP. 2010. Identification of DOK genes as lung tumor suppressors. Nature Genetics 42(3):216-23. *equal contribution