All Publications

A full list of publications can be retrieved from one of the following sources:


Featured First/Corresponding-author Publications

Gerami P*#, Tandukar B*, Deivendran D, Olivares S, Chen L, Tang J, Tan T, Sharma H, Bandari AK, Cruz-Pacheco N, Chang D, Marty A, Olshen A, Murad NF, Song J, Lee J, Yeh I, Shain AH#. Molecular effects of indoor tanning. bioRxiv. June 2024. Available Here. * jointly led the project. #co-senior author.

Chen L, Chang D, Tandukar B, Deivendran D, Pozniak J, Cruz-Pacheco N, Cho R, Cheng J, Yeh I, Marine C, Bastian BC, Ji AL, Shain AH. STmut: a framework for visualizing somatic alterations in spatial transcriptomics data of cancer. Genome Biology. November 2023. Available Here.

Chang D, Shain AH. The landscape of driver mutations in cutaneous squamous cell carcinoma. npj Genomic Medicine. July 2021. Available Here.

Tang J, Fewing, Chang D, Zeng H, Liu S, Jorapur A, Belote RL, McNeal AS, Tan T, Yeh I, Arron ST, Judson-Torres RL, Bastian BC, Shain AH. The genomic landscapes of individual melanocytes from human skin. Nature. October 2020. Available Here.

Shain AH*#, Bagger MM#, Yu R, Chang D, Liu S, Vemula S, Weier JF, Wadt K, Heegaard S, Bastian BC*, Kiilgaard JF*. The genetic evolution of metastatic uveal melanoma. Nature Genetics. July 2019. Available Here.

Shain AH*, Joseph NM, Yu R, Benhamida J, Liu S, Prow T, Ruben B, North J, Pincus L, Yeh I, Judson R, Bastian BC*. Genomic and transcriptomic analysis reveal incremental disruption of key signaling pathways during melanoma evolution. Cancer Cell. July 2018. Available Here.

Shain AH, Bastian BC. From melanocytes to melanomas. Nature Reviews Cancer. June 2016. Available Here.

  • Over 900 citations

Shain AH, Yeh I, Kovalyshyn I, Sriharan A, Talevich E, Gagnon A, Dummer R, North J, Pincus L, Ruben B, Rickaby W, D'Arrigo C, Robson A, Bastian BC. The genetic evolution of melanoma from precursor lesions. The New England Journal of Medicine. November 2015. Available Here.

Shain AH, Garrido M, Botton T, Talevich E, Yeh I, Sanborn JZ, Chung J, Wang NJ, Kakavand H, Mann GJ, Thompson JF, Wiesner T, Roy R, Olshen AB, Gagnon A, Gray JW, Huh N, Hur JS, Busam KJ, Scolyer RA, Cho RJ, Murali R, Bastian BC. Exome sequencing of desmoplastic melanoma identifies recurrent NFKBIE promoter mutations and diverse activating mutations in the MAPK pathway. Nature Genetics. October 2015. Available Here.

Shain AH, Pollack JR. The spectrum of SWI/SNF mutations, ubiquitous in human cancers. PLoS One. January 2013. Available Here.

  • Over 600 citations

Shain AH, Giacomini CP, Matsukuma K, Karikari CA, Bashyam MD, Hidalgo M, Maitra A, Pollack JR. Convergent structural alterations define SWItch/Sucrose NonFermentable (SWI/SNF) chromatin remodeler as a central tumor suppressive complex in pancreatic cancer. PNAS. January 2012. Available Here.


Featured collaborative studies

Cao W, Lee H, Wu W, Zaman A, McCorkle S, Yan M, Chen J, Xing Q, Sinnott-Armstrong N, Xu H, Sailani MR, Tang W, Cui Y, Liu J, Guan H, Lv P, Sun X, Sun L, Han P, Lou Y, Chang J, Wang J, Gao Y, Guo J, Schenk G, Shain AH, Biddle FG, Collisson E, Synder M, Bivona TG. Multi-faceted epigenetic dysregulation of gene expression promotes esophageal squamous cell carcinoma. Nature Communications. July 2020.

Zeng H, Jorapur A, Shain AH, Lang UE, Torres R, Zhang Y, McNeal AS, Botton T, Lin J, Donne M, Bastian IN, Yu R, North JP, Pincus L, Ruben BS, Joseph NM, Yeh I, Bastian BC, Judson RL. Bi-allelic loss of CDKN2A initiates melanoma invasion via BRN2 activation. Cancer Cell. July 2018.

Chiba K, Lorbeer FK, Shain AH, McSwiggen DT, Schruf E, Oh A, Ryu J, Darzacq X, Bastian BC, Hockenmeyer D. Mutations in the promoter of telomerase gene TERT contribute to tumorigenesis by a two-step mechanism. Science. September 2017.

Yeh I, Lang UE, Durieux E, Tee MK, Jorapur A, Shain AH, Haddad V, Pissaloux D, Chen X, Cerroni L, Judson RL, LeBoit PE, McCalmont TH, Bastian BC, de la Fouchardiere A. Nature Communications. September 2017.

Yeh I, Botton T, Talevich E, Shain AH, Sparatta AJ, de la Fouchardiere A, Mully TW, North JP, Garrido MC, Gagnon A, Vemula SS, McCalmont TH, LeBoit PE, Bastian BC. Nature Communications. May 2015.



The Shain lab is grateful for the following sources of active funding: NIH National Cancer Institute (R01 CA265786), NIH NIAMS (AR080626), Department of Defense Melanoma Research Program, Melanoma Research Alliance, the LEO Foundation, and UCSF Department of Dermatology, and Tracy and Guy Jacquier charity to fight squamous cell carcinoma.

We also thank the following sources of former funding: American Cancer Society Research Scholar Grant, National Cancer Institute (K22 CA217997), Melanoma Research Foundation, American Federation of Aging Research, George and Judy Marcus Precision Medicine Fund, UCSF Institute of Human Genetics, University of California Cancer Research Coordinating Committee, PhRMA Foundation, Dermatology Foundation, Mt. Zion Health Research Fund, UCSF Program in Breakthrough Biomedical Research, National Cancer Institute (T32 CA177555), National Science Foundation Graduate Fellowship Research Program, Stanford Graduate Fellows program