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Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer.
Becker WR, Nevins SA, Chen DC, Chiu R, Horning AM, Guha TK, Laquindanum R, Mills M, Chaib H, Ladabaum U, Longacre T, Shen J, Esplin ED, Kundaje A, Ford JM, Curtis C, Snyder MP, Greenleaf WJ. Becker WR, et al. Among authors: shen j. Nat Genet. 2022 Jul;54(7):985-995. doi: 10.1038/s41588-022-01088-x. Epub 2022 Jun 20. Nat Genet. 2022. PMID: 35726067 Free PMC article.
MITI minimum information guidelines for highly multiplexed tissue images.
Schapiro D, Yapp C, Sokolov A, Reynolds SM, Chen YA, Sudar D, Xie Y, Muhlich J, Arias-Camison R, Arena S, Taylor AJ, Nikolov M, Tyler M, Lin JR, Burlingame EA; Human Tumor Atlas Network; Chang YH, Farhi SL, Thorsson V, Venkatamohan N, Drewes JL, Pe'er D, Gutman DA, Herrmann MD, Gehlenborg N, Bankhead P, Roland JT, Herndon JM, Snyder MP, Angelo M, Nolan G, Swedlow JR, Schultz N, Merrick DT, Mazzili SA, Cerami E, Rodig SJ, Santagata S, Sorger PK. Schapiro D, et al. Nat Methods. 2022 Mar;19(3):262-267. doi: 10.1038/s41592-022-01415-4. Nat Methods. 2022. PMID: 35277708 Free PMC article.
Global loss of promoter-enhancer connectivity and rebalancing of gene expression during early colorectal cancer carcinogenesis.
Zhu Y, Lee H, White S, Weimer AK, Monte E, Horning A, Nevins SA, Esplin ED, Paul K, Krieger G, Shipony Z, Chiu R, Laquindanum R, Karathanos TV, Chua MWY, Mills M, Ladabaum U, Longacre T, Shen J, Jaimovich A, Lipson D, Kundaje A, Greenleaf WJ, Curtis C, Ford JM, Snyder MP. Zhu Y, et al. Among authors: shen j. Nat Cancer. 2024 Oct 30. doi: 10.1038/s43018-024-00823-z. Online ahead of print. Nat Cancer. 2024. PMID: 39478119
Multiomic analysis of familial adenomatous polyposis reveals molecular pathways associated with early tumorigenesis.
Esplin ED, Hanson C, Wu S, Horning AM, Barapour N, Nevins SA, Jiang L, Contrepois K, Lee H, Guha TK, Hu Z, Laquindanum R, Mills MA, Chaib H, Chiu R, Jian R, Chan J, Ellenberger M, Becker WR, Bahmani B, Khan A, Michael B, Weimer AK, Esplin DG, Shen J, Lancaster S, Monte E, Karathanos TV, Ladabaum U, Longacre TA, Kundaje A, Curtis C, Greenleaf WJ, Ford JM, Snyder MP. Esplin ED, et al. Among authors: shen j. Nat Cancer. 2024 Oct 30. doi: 10.1038/s43018-024-00831-z. Online ahead of print. Nat Cancer. 2024. PMID: 39478120
A spatial map of human macrophage niches reveals context-dependent macrophage functions in colon and breast cancer.
Matusiak M, Hickey JW, Luca B, Lu G, Kidziński L, Zhu S, Colburg DRC, Phillips DJ, Brubaker SW, Charville GW, Shen J, Nolan GP, Newman AM, West RB, van de Rijn M. Matusiak M, et al. Among authors: shen j. Res Sq [Preprint]. 2023 Jan 10:rs.3.rs-2393443. doi: 10.21203/rs.3.rs-2393443/v1. Res Sq. 2023. PMID: 36711732 Free PMC article. Preprint.
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