Publications

Fu, H; Zheng, H; Muglia, L; Wang, L; Liu, Y. GTAGMe-seq: joint profiling of genetic variants, DNA methylation, GpC methyltransferase footprints, and 3D genome in the same DNA molecules. 2022.

Liu, Y. At the dawn: cell-free DNA fragmentomics and gene regulation. British Journal of Cancer. 2022; 126:379-390.

Zheng, H; Zhu, MS; Liu, Y. FinaleDB: a browser and database of cell-free DNA fragmentation patterns. Computer Applications in the Biosciences. 2021; 37:2502-2503.

Abascal, F; Acosta, R; Addleman, NJ; Adrian, J; Afzal, V; Aken, B; Akiyama, JA; Jammal, OA; Amrhein, H; Anderson, SM; et al. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 2020; 583:699-710.

Abascal, F; Acosta, R; Addleman, NJ; Adrian, J; Afzal, V; Aken, B; Akiyama, JA; Jammal, OA; Amrhein, H; Anderson, SM; et al. Perspectives on ENCODE. Nature. 2020; 583:693-698.

Zhou, X; Zheng, H; Fu, H; Dillehay McKillip, K; Pinney, S; Liu, Y. CRAG: De novo characterization of cell-free DNA fragmentation hotspots in plasma whole-genome sequencing. 2020.

Wan, N; Weinberg, D; Liu, TY; Niehaus, K; Ariazi, EA; Delubac, D; Kannan, A; White, B; Bailey, M; Bertin, M; et al. Machine learning enables detection of early-stage colorectal cancer by whole-genome sequencing of plasma cell-free DNA. BMC Cancer. 2019; 19.

Li, G; Liu, Y; Zhang, Y; Kubo, N; Yu, M; Fang, R; Kellis, M; Ren, B. Joint profiling of DNA methylation and chromatin architecture in single cells. Nature Methods. 2019; 16:991-993.

Gamazon, ER; Segrè, AV; van de Bunt, M; Wen, X; Xi, HS; Hormozdiari, F; Ongen, H; Konkashbaev, A; Derks, EM; Aguet, F; et al. Using an atlas of gene regulation across 44 human tissues to inform complex disease- and trait-associated variation. Nature Genetics. 2018; 50:956-967.