Selected Publications & Preprints

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A genome-wide atlas of human cell morphology
A genome-wide atlas of human cell morphology

Ramezani M*, Bauman J*, Singh A*, Weisbart E*, Yong J, Lozada ME, Way GP, Kavari SL, Diaz C, Haghighi M, Perez-Schindler J, Batista TM, Claussnitzer M, Singh S, Cimini BA, Blainey PC^, Carpenter AE^, Jan CH^, Neal JT^. Nature Methods [in press] 2024 Oct 25. *equal contribution ^joint co-senior authors

Genome-wide analysis of somatic noncoding mutation patterns in cancer
Genome-wide analysis of somatic noncoding mutation patterns in cancer

Dietlein F, Wang AB, Fagre C, Tang A, Besselink N, Cuppen E, Li C, Sunyaev SR, Neal JT*, Van Allen EM*. Science. 2022 Apr 8;376(6589):eabg5601. PMID: 35389777. *joint co-senior authors

Massively parallel phenotyping of variant impact in cancer with Perturb-seq reveals a shift in the spectrum of cell states induced by somatic mutations
Massively parallel phenotyping of variant impact in cancer with Perturb-seq reveals a shift in the spectrum of cell states induced by somatic mutations

Ursu O*, Neal JT*, Shea E, Thakore PI, Jerby-Arnon L, Diaz C, Bauman J, Mosaad MM, Fagre C, Giacomelli AO, Ly SH, Hahn WC, Aguirre AJ, Berger AH, Regev A, Boehm JS. Nature Biotechnology. 2022 Jan 20. PMID: 35058622. *equal contribution

Massively parallel assessment of human variants with base editor screens
Massively parallel assessment of human variants with base editor screens

Hanna RE, Hegde M, Fagre CR, DeWeirdt PC, Sangree AK, Szegletes Z, Griffith A, Feeley MN, Sanson KR, Baidi Y, Koblan LW, Liu DR, Neal JT, Doench JG. Cell . 2021 Feb 18; 184(4):1064-1080

Using protein interaction networks to identify cancer dependencies from tumor genome data
Using protein interaction networks to identify cancer dependencies from tumor genome data

Horn H, Fagre C, Gupta A, Tsafou K, Fornelos N, Neal JT*, Lage K*. bioRxiv preprint. *joint co-senior authors

Organoid Modeling of the Tumor Immune Microenvironment
Organoid Modeling of the Tumor Immune Microenvironment

Neal JT*, Li X*, Zhu J, Giangarra V, Grzeskowiak CL, Ju J, Liu IH, Chiou SH, Salahudeen AA, Smith AR, Deutsch BC, Liao L, Zemek AJ, Zhao F, Karlsson K, Schultz LM, Metzner TJ, Nadauld LD, Tseng YY, Alkhairy S, Oh C, Keskula P, Mendoza- Villanueva D, De La Vega FM, Kunz PL, Liao JC, Leppert JT, Sunwoo JB, Sabatti C, Boehm JS, Hahn WC, Zheng GXY, Davis MM, Kuo CJ. Cell. 2018 Dec 13;175(7):1972-1988 PMID: 30550791

Organoids as models of neoplastic transformation
Organoids as models of neoplastic transformation

Neal JT, Kuo CJ. Annu Rev Pathol. 2016 May 23; 11:199-220. PMID: 26907527