Please find our full publication list @ our google scholar site

Selected papers/preprints

  • Chen Z, Zhang J, Liu J, Dai Y, Lee D, Min MR, Xu M, Gerstein M: DECODE: A Deep-learning Framework for Condensing Enhancers and Refining Boundaries with Large-scale Functional Assays. (ISMB 2021, co-first and co-corresponding author) bioRxiv 2021:2021.2001.2027.428477.
  • Cao Y, Fu L, Wu J, Peng Q, Nie Q, Zhang J, Xie X: SAILER: Scalable and Accurate Invariant Representation Learning for Single-Cell ATAC-Seq Processing and Integration. (ISMB 2021, co-corresponding author) bioRxiv 2021:2021.2001.2028.428689.
  • Chen Z, Zhang J, Liu J, Zhang Z, Zhu J, Lee D, Xu M, Gerstein M: SCAN-ATAC-Sim: a scalable and efficient method for simulating single-cell ATAC-seq data from bulk-tissue experiments. Bioinformatics 2021. (co-first and co-corresponding author)
  • Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshoj H, Hess JM, Juul RI, Lin Z et al: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature 2020, 578(7793):102-111.
  • Lee D, Shi M, Moran J, Wall M, Zhang J, Liu J, Fitzgerald D, Kyono Y, Ma L, White KP et al: STARRPeaker: uniform processing and accurate identification of STARR-seq active regions. Genome Biol 2020, 21(1):298.
  • Consortium ITP-CAoWG: Pan-cancer analysis of whole genomes. Nature 2020, 578(7793):82-93.
  • Consortium EP, Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A et al: Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature 2020, 583(7818):699-710.
  • Zhang J, Liu J, Lee D, Feng JJ, Lochovsky L, Lou S, Rutenberg-Schoenberg M, Gerstein M: RADAR: annotation and prioritization of variants in the post-transcriptional regulome of RNA-binding proteins. Genome Biol 2020, 21(1):151.
  • Zhang J, Lee D, Dhiman V, Jiang P, Xu J, McGillivray P, Yang H, Liu J, Meyerson W, Clarke D et al: An integrative ENCODE resource for cancer genomics. Nat Commun 2020, 11(1):3696.
  • Wang D, Liu S, Warrell J, Won H, Shi X, Navarro FCP, Clarke D, Gu M, Emani P, Yang YT et al: Comprehensive functional genomic resource and integrative model for the human brain. Science 2018, 362(6420).
  • Psych EC: Revealing the brain’s molecular architecture. Science 2018, 362(6420):1262-1263.
  • Lochovsky L, Zhang J, Gerstein M: MOAT: efficient detection of highly mutated regions with the Mutations Overburdening Annotations Tool. Bioinformatics 2018, 34(6):1031-1033.
  • Zhang J, Kuo CC, Chen L: WemIQ: an accurate and robust isoform quantification method for RNA-seq data. Bioinformatics 2015, 31(6):878-885.
  • Lochovsky L, Zhang J, Fu Y, Khurana E, Gerstein M: LARVA: an integrative framework for large-scale analysis of recurrent variants in noncoding annotations. Nucleic Acids Res 2015, 43(17):8123-8134.
  • Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Fritz MH et al: An integrated map of structural variation in 2,504 human genomes. Nature 2015, 526(7571):75-81.
  • Genomes Project C, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA et al: A global reference for human genetic variation. Nature 2015, 526(7571):68-74.