scATAnno: Automated Cell Type Annotation for single-cell ATAC Sequencing Data.
Jiang Y, Hu Z, Lynch AW, Jiang J, Zhu A, Zeng Z, Zhang Y, Wu G, Xie Y, Li R, Zhou N, Meyer C, Cejas P, Brown M, Long HW, Qiu X.
bioRxiv. 2024 Mar 25. PMID: 37333088
Links
Bibliography
Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation.
Singh PNP, Gu W, Madha S, Lynch AW, Cejas P, He R, Bhattacharya S, Gomez MM, Oser MG, Brown M, Long HW, Meyer CA, Zhou Q, Shivdasani RA.
bioRxiv. 2024 Jan 09. PMID: 38260422
Cistrome Data Browser: integrated search, analysis and visualization of chromatin data.
Taing L, Dandawate A, L'Yi S, Gehlenborg N, Brown M, Meyer CA.
Nucleic Acids Res. 2024 Jan 05. 52(D1):D61-D66. PMID: 37971305
Multi-batch single-cell comparative atlas construction by deep learning disentanglement.
Lynch AW, Brown M, Meyer CA.
Nat Commun. 2023 07 12. 14(1):4126. PMID: 37433791
MetaTiME integrates single-cell gene expression to characterize the meta-components of the tumor immune microenvironment.
Zhang Y, Xiang G, Jiang AY, Lynch A, Zeng Z, Wang C, Zhang W, Fan J, Kang J, Gu SS, Wan C, Zhang B, Liu XS, Brown M, Meyer CA.
Nat Commun. 2023 05 06. 14(1):2634. PMID: 37149682
Discovery of Targets for Immune-Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha.
Sahu A, Wang X, Munson P, Klomp JPG, Wang X, Gu SS, Han Y, Qian G, Nicol P, Zeng Z, Wang C, Tokheim C, Zhang W, Fu J, Wang J, Nair NU, Rens JAP, Bourajjaj M, Jansen B, Leenders I, Lemmers J, Musters M, van Zanten S, van Zelst L, Worthington J, Liu JS, Juric D, Meyer CA, Oubrie A, Liu XS, Fisher DE, Flaherty KT.
Cancer Discov. 2023 03 01. 13(3):672-701. PMID: 36745048
Cistrome Explorer: an interactive visual analysis tool for large-scale epigenomic data.
L'Yi S, Keller MS, Dandawate A, Taing L, Chen CH, Brown M, Meyer CA, Gehlenborg N.
Bioinformatics. 2023 02 03. 39(2). PMID: 36688700
A path to translation: How 3D patient tumor avatars enable next generation precision oncology.
Bose S, Barroso M, Chheda MG, Clevers H, Elez E, Kaochar S, Kopetz SE, Li XN, Meric-Bernstam F, Meyer CA, Mou H, Naegle KM, Pera MF, Perova Z, Politi KA, Raphael BJ, Robson P, Sears RC, Tabernero J, Tuveson DA, Welm AL, Welm BE, Willey CD, Salnikow K, Chuang JH, Shen X.
Cancer Cell. 2022 12 12. 40(12):1448-1453. PMID: 36270276
Intrinsic bias estimation for improved analysis of bulk and single-cell chromatin accessibility profiles using SELMA.
Hu SS, Liu L, Li Q, Ma W, Guertin MJ, Meyer CA, Deng K, Zhang T, Zang C.
Nat Commun. 2022 09 21. 13(1):5533. PMID: 36130957
MIRA: joint regulatory modeling of multimodal expression and chromatin accessibility in single cells.
Lynch AW, Theodoris CV, Long HW, Brown M, Liu XS, Meyer CA.
Nat Methods. 2022 09. 19(9):1097-1108. PMID: 36068320