Liu Lab

Zheng, H; Zhu, MS; Liu, Y. FinaleDB: a browser and database of cell-free DNA fragmentation patterns. Computer Applications in the Biosciences. 2020.

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: New biology. 2020; 583:699-710.

ENCODE Project Consortium, ; Snyder, MP; Gingeras, TR; Moore, JE; Weng, Z; Gerstein, MB; Ren, B; Hardison, RC; Stamatoyannopoulos, JA; Graveley, BR; et al. Perspectives on ENCODE. Nature: New biology. 2020; 583:693-698.

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.

Liu, Y; Sarkar, A; Kheradpour, P; Ernst, J; Kellis, M. Evidence of reduced recombination rate in human regulatory domains. Genome Biology. 2017; 18.

Stranger, BE; Brigham, LE; Hasz, R; Hunter, M; Johns, C; Johnson, M; Kopen, G; Leinweber, WF; Lonsdale, JT; McDonald, A; et al. Enhancing GTEx by bridging the gaps between genotype, gene expression, and disease. Nature Genetics. 2017; 49:1664-1670.

Ongen, H; Brown, AA; Delaneau, O; Panousis, NI; Nica, AC; GTEx Consortium, ; Dermitzakis, ET. Estimating the causal tissues for complex traits and diseases. Nature Genetics. 2017; 49:1676-1683.

Luo, H; Xi, Y; Li, W; Li, J; Li, Y; Dong, S; Peng, L; Liu, Y; Yu, W. Cell identity bookmarking through heterogeneous chromatin landscape maintenance during the cell cycle. Human Molecular Genetics. 2017; 26:4231-4243.

Yang, F; Wang, J; Pierce, BL; Chen, LS; Aguet, F; Ardlie, KG; Cummings, BB; Gelfand, ET; Getz, G; Hadley, K; et al. Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis. PCR Methods and Applications. 2017; 27:1859-1871.

Saha, A; Kim, Y; Gewirtz, AD H; Jo, B; Gao, C; McDowell, IC; Aguet, F; Ardlie, KG; Cummings, BB; Gelfand, ET; et al. Co-expression networks reveal the tissue-specific regulation of transcription and splicing. PCR Methods and Applications. 2017; 27:1843-1858.

Aguet, F; Brown, AA; Castel, SE; Davis, JR; He, Y; Jo, B; Mohammadi, P; Park, YS; Parsana, P; Segrè, AV; et al. Genetic effects on gene expression across human tissues. Nature: New biology. 2017; 550:204-213.

Tukiainen, T; Villani, AC; Yen, A; Rivas, MA; Marshall, JL; Satija, R; Aguirre, M; Gauthier, L; Fleharty, M; Kirby, A; et al. Landscape of X chromosome inactivation across human tissues. Nature: New biology. 2017; 550:244-248.

Tan, MH; Li, Q; Shanmugam, R; Piskol, R; Kohler, J; Young, AN; Liu, KI; Zhang, R; Ramaswami, G; Ariyoshi, K; et al. Dynamic landscape and regulation of RNA editing in mammals. Nature: New biology. 2017; 550:249-254.

Kim, Y; Tsang, EK; Davis, JR; Damani, FN; Chiang, C; Hess, GT; Zappala, Z; Strober, BJ; Scott, AJ; Li, A; et al. The impact of rare variation on gene expression across tissues. Nature: New biology. 2017; 550:239-243.