News and Events
August 31, 2021
Our paper in collaboration with the Struhl lab, "YAP and TAZ are transcriptional co-activators of AP-1 proteins and STAT3 during breast cellular transformation," has been published in eLife. Zlab authors include Henry Pratt, Mingshi Gao, and Zhiping Weng.
Tweet | Article
May 12, 2021
Our paper, "Genetic and epigenetic features of promoters with ubiquitous chromatin accessibility support ubiquitous transcription of cell-essential genes," has been published in Nucleic Acids Research. Zlab authors include Kaili Fan, Jill Moore, Xiao-Ou Zhang, and Zhiping Weng.
Tweet | Article
Apr 1, 2021
Our review, "Investigating the potential roles of SINEs in the human genome," has been published in Annual Review of Genomics and Human Genetics. Zlab authors include Xiao-Ou Zhang, Henry Pratt, and Zhiping Weng.
Tweet | Article
Feb 22, 2021
Our paper, "Annotation of chromatin states in 66 complete mouse epigenomes during development," has been published in Communications Biology. Zlab authors include Arjan van der Velde, Kaili Fan, Junko Tsuji, Jill Moore, Michael Purcaro, Henry Pratt, and Zhiping Weng.
Tweet | Article
Feb 11, 2021
Our paper in collaboration with the Dekker lab, "Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics," has been published in Nature Genetics. Zlab authors include Tyler Borrman and Zhiping Weng.
Tweet | Article
Feb 3, 2021
Our paper in collaboration with the Pierce lab, "An expanded benchmark for antibody-antigen docking and affinity prediction reveals insights into antibody recognition determinants," has been published in Structure. Zlab authors include Thom Vreven and Zhiping Weng.
Tweet | Article
Jan 28, 2021
Our paper in collaboration with the Theurkauf and Lu labs, "A benchmark and an algorithm for detecting germline transposon insertions and measuring de novo transposon insertion frequencies," has been published in Nucleic Acids Research. Zlab authors include Tianxiong Yu and Zhiping Weng.
Tweet | Article | Website
Jan 4, 2021
Our paper in collaboration with the Zamore and Theurkauf labs, "Long first exons and epigenetic marks distinguish conserved pachytene piRNA clusters from other mammalian genes," has been published in Nature Communications. Zlab authors include Tianxiong Yu, Kaili Fan, Yu Fu, and Zhiping Weng.
Tweet | Article
Dec 23, 2020
Our paper in collaboration with the Pierce and Baker labs, "High-throughput modeling and scoring of TCR-pMHC complexes to predict cross-reactive peptides," has been published in Bioinformatics. Zlab authors include Tyler Borrman, Thom Vreven, and Zhiping Weng.
Tweet | Article
Nov 12, 2020
Tyler Borrman successfully defended his PhD thesis, "Measuring stability of 3D chromatin conformations and identifying neuron-specific chromatin loops associated with schizophrenia risk."
Oct 29, 2020
Jill Moore presented cCREs and SCREEN as part of the ENCODE team at the 2020 ASHG meeting.
Tweet | Section II on the Registry of cCREs and SCREEN | All ENCODE presentations
Oct 6, 2020
UCSC released three new ENCODE Public Hubs: DNA, RNA, and Integrative built by Henry Pratt and Michael Purcaro in our lab. These hubs show most genomic and epigenomic data (ChIP, DNase, ATAC, RNA, miRNA, eCLIP) and the Registry of cCREs produced by ENCODE Phase III.
Tweet | UCSC genome browser with the ENCODE DNA, Integrative, and RNA hubs
Oct 1, 2020
Henry Pratt presented a workshop on Factorbook at the ENCODE2020 Users Meeting.
Video of the Factorbook workshop | Factorbook website
Sep 30, 2020
Jill Moore presented a workshop on cCREs and SCREEN at the ENCODE2020 Users Meeting.
Video of the cCREs and SCREEN workshop | SCREEN website | ENCODE3 main paper describing our work on cCREs and SCREEN
Sep 30, 2020
Zhiping Weng presented on an atlas of Pol III transcribed Alu elements at the ENCODE2020 Users Meeting.
Video of the presentation | Our Genome Research paper on this work
Sep 16, 2020
Zhiping Weng presented an ISCBacademy Webinar on our work on the Registry of candidate cis-regulatory elements (cCREs) as part of the ENCODE Project.
Video of the presentation | ENCODE3 main paper describing our work on cCREs and SCREEN
July 29, 2020
ENCODE 3 package was published in Nature.
The ENCODE3 special issue | ENCODE3 main paper describing our work on cCREs and SCREEN