• GERMLINE VARIATION CONTRIBUTES TO FALSE NEGATIVE IN CRISPR-BASED CANCER EXPERIMENTS WITH VARYING BURDEN ACROSS ANCESTRIES

Misek SA, Fultineer A, Kalfon J, Noorbakhsh J, Boyle I, Dempster J, Petronio L, Huang K, Saadat A, Green T, Brown A, Doench JG, Root D, McFarland J, Beroukhim R, Boehm JS

bioRxiv. 2022 https://www.biorxiv.org/content/10.1101/2022.11.18.517155v1

  • MASSIVELY PARALLEL PHENOTYPING OF CODING VARIANTS IN CANCER WITH PERTURB-SEQ

Ursu O, Neal JT, Shea E, Thakore PI, Jerby-Arnon L, Nguyen L, Dionne D, Diaz C, Bauman J, Mosaad MM, Fagre C, Lo A, McSharry M, Giacomelli AO, Ly SH, Rozenblatt-Rosen O, Hahn WC, Aguirre AJ, Berger AH, Regev A, Boehm JS

Nature Biotech. 2022. PMID: 35058622

  • Cancer research needs a better map

Boehm JS, Garnett MJ, Adams DJ, Francies HE, Golub TR, Hahn WC, Iorio F, McFarland JM, Parts L, Vazquez F.

Nature. 2021. PMID: 33500573

  • From cell lines to living biosensors: new opportunities to prioritize cancer dependencies using ex vivo cultures

Tseng YY, Boehm JS

Curr Opin Gen Dev. 2019. PMID: 30928774

  • renal medullary carcinomas depend on smarcb1 loss and are sensitive to proteosome inhibition

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.

Elife. 2019. PMID: 30860482

  • NetSIG: network-based discovery from cancer genomes

Horn H, Lawrence, MS, Chouinard CR, Shrestha Y, Hu JX, Worstell E, Shea E, Ilic N, Kim E, Kamburov A, Kashani A, Hahn WC, Campbell JD, Boehm JS*, Getz G*, Lage K*.

Nat Methods. 2018. PMID: 29200198

*These senior authors contributed equally

  • Emerging opportunities for target discovery in rare cancers

Sharifnia T, Hong AL, Painter CA, Boehm JS.

Cell Chem Biol. 2017. PMID: 28938087

Tsherniak A, Vazquez F, Montgomery PG, Weir, BA, Kryukov G, Cowley GS, Gill S, Harrington, WF, Pantel S, Krill-Burger JM, Meyers RM, Ali L, Goodale A, Lee Y, Jiang G, Hsiao J, Gerath, WFJ, Howell S, Merkel E, Ghandi M, Garraway LA, Root DE*, Golub TR*, Boehm JS*, Hahn WC*.

Cell. 2017. PMID: 28753430

*These senior authors contributed equally

  • progress towards precision functional genomics in cancer

Johanessen CM, Boehm JS.

Curr Opin Syst Biol. 2017. 

  • Systematic morphological profiling of human gene and allele function via Cell Painting

Rohban MH, Singh S, Wu X, Berthet JB, Bray MA, Shrestha Y, Varelas X, Boehm JS, Carpenter AE.

Elife. 2017. PMID: 28315521

  • High-throughput Phenotyping of Lung Cancer Somatic Mutations

Berger AH, Brooks AN, Wu X, Shrestha 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 DE, Narayan R, Natoli T, Lahr DL, Tirosh I, Tamayo P, Getz G, Wong B, Doench J, Subramanian A, Golub TR, Meyerson M, Boehm JS.

Cancer Cell. 2016. PMID: 27478040

Hong AL, Tseng YY, Cowley GS, Jonas O, Cheah JH, Kynnap BD, Doshi MB, Oh C, Meyer SC, Church AJ, Gill S, Bielski CM, Keskula P, Imamovic A, Howell S, Kryukov GV, Clemons PA, Tsherniak A, Vazquez F, Crompton BD, Shamji AF, Rodriguez-Galindo C, Janeway KA, Roberts CW, Stegmaier K, van Hummelen P, Cima MJ, Langer RS, Garraway LA, Schreiber SL, Root DE, Hahn WC, Boehm JS.

Nat Commun. 2016. PMID: 27329820

Kim E, Ilic N, Shrestha Y, Zou L, Kamburov A, Zhu C, Yang X, Lubonja R, Tran N, Nguyen C, Lawrence MS, Piccioni F, Bagul M, Doench JG, Chouinard CR, Wu X, Hogstrom L, Natoli T, Tamayo P, Horn H, Corsello SM, Lage K, Root DE, Subramanian A, Golub TR, Getz G, Boehm JS, Hahn WC

Cancer Discov. 2016. PMID: 27147599

  • Genetic and Proteomic Interrogation of Lower Confidence Candidate Genes Reveals Signaling Networks in β-Catenin-Active Cancers.

Rosenbluh J, Mercer J, Shrestha Y, Oliver R, Tamayo P, Doench JG, Tirosh I, Piccioni F, Hartenian E, Horn H, Fagbami L, Root DE, Jaffe J, Lage K, Boehm JS, Hahn WC.

Cell Syst. 2016. PMID: 27684187

 

 

Lohr JG, Adalsteinsson VA, Cibulskis K, Choudhury AD, Rosenberg M, Cruz-Gordillo P, Francis JM, Zhang CZ, Shalek AK, Satija R, Trombetta JJ, Lu D, Tallapragada N, Tahirova N, Kim S, Blumenstiel B, Sougnez C, Lowe A, Wong B, Auclair D, Van Allen EM, Nakabayashi M, Lis RT, Lee GS, Li T, Chabot MS, Ly A, Taplin ME, Clancy TE, Loda M, Regev A, Meyerson M, Hahn WC, Kantoff PW, Golub TR, **Getz G, **Boehm JS, **Love JC.

Nat Biotechnol. 2014. PMID: 24752078

**These senior authors contributed equally

Dunn GP, Cheung HW, Agarwalla PK, Thomas S, Zektser Y, Karst AM, Boehm JS, Weir BA, Berlin AM, Zou L, Getz G, Liu JF, Hirsch M, Vazquez F, Root DE, Beroukhim R, Drapkin R, Hahn WC.

Proc Natl Acad Sci U S A. 2014, PMID: 24385586

Yang X, *Boehm JS, Yang X, Salehi-Ashtiani K, Hao T, Shen Y, Lubonja R, Thomas SR, Alkan O, Bhimdi T, Green TM, Johannessen CM, Silver SJ, Nguyen C, Murray RR, Hieronymus H, Balcha D, Fan C, Lin C, Ghamsari L, Vidal M, Hahn WC, Hill DE, Root DE.

Nat Methods. 2011, PMID: 21706014

*These authors contributed equally

*Cheung HW, *Cowley GS, *Weir BA, *Boehm JS, Rusin S, Scott JA, East A, Ali LD, Lizotte PH, Wong TC, Jiang G, Hsiao J, Mermel CH, Getz G, Barretina J, Gopal S, Tamayo P, Gould J, Tsherniak A, Stransky N, Luo B, Ren Y, Drapkin R, Bhatia SN, Mesirov JP, Garraway LA, Meyerson M, Lander ES, Root DE, Hahn WC.

Proc Natl Acad Sci U S A. 2011. PMID: 21746896

*These authors contributed equally

Boehm JS, Hahn WC.

Nat Rev Genet. 2011. PMID: 21681210

*Johannessen CM, *Boehm JS, Kim SY, Thomas SR, Wardwell L, Johnson LA, Emery CM, Stransky N, Cogdill AP, Barretina J, Caponigro G, Hieronymus H, Murray RR, Salehi-Ashtiani K, Hill DE, Vidal M, Zhao JJ, Yang X, Alkan O, Kim S, Harris JL, Wilson CJ, Myer VE, Finan PM, Root DE, Roberts TM, Golub T, Flaherty KT, Dummer R, Weber BL, Sellers WR, Schlegel R, Wargo JA, Hahn WC, Garraway LA.

Nature. 2010. PMID: 21107320

*These authors contributed equally

Moody SE, Boehm JS, Barbie DA, Hahn WC.

Curr Opin Mol Ther. 2010. PMID: 20521217

Barbie DA, Tamayo P, Boehm JS, Kim SY, Moody SE, Dunn IF, Schinzel AC, Sandy P, Meylan E, Scholl C, Fröhling S, Chan EM, Sos ML, Michel K, Mermel C, Silver SJ, Weir BA, Reiling JH, Sheng Q, Gupta PB, Wadlow RC, Le H, Hoersch S, Wittner BS, Ramaswamy S, Livingston DM, Sabatini DM, Meyerson M, Thomas RK, Lander ES, Mesirov JP, Root DE, Gilliland DG, Jacks T, Hahn WC.

Nature. 2009. PMID: 19847166

Boehm JS, Zhao JJ, Yao J, Kim SY, Firestein R, Dunn IF, Sjostrom SK, Garraway LA, Weremowicz S, Richardson AL, Greulich H, Stewart CJ, Mulvey LA, Shen RR, Ambrogio L, Hirozane-Kishikawa T, Hill DE, Vidal M, Meyerson M, Grenier JK, Hinkle G, Root DE, Roberts TM, Lander ES, Polyak K, Hahn WC.

Cell. 2007. PMID: 17574021

Boehm JS, Hession MT, Bulmer SE, Hahn WC.

Mol Cell Biol. 2005. PMID: 16024784

Boehm JS, Hahn WC.

Cytotechnology. 2004. PMID: 19003243