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Publications 2021

†: contributed equally, joint first authors
*: co-corresponding authors

Gen Zhang^†, Tianxiong Yu^†, Swapnil S. Parhad, Samantha Ho, Zhiping Weng^*, and William E. Theurkauf^*
piRNA-independent transposon silencing by the Drosophila THO complex
Dev. Cell (2021)

Tingting Jiang, Xiao-ou Zhang, Zhiping Weng, and Wen Xue
Deletion and replacement of long genomic sequences using prime editing
Nature Biotechnology (2021)

Lizhi He^†, Henry Pratt^†, Mingshi Gao^†, Fengxiang Wei, Zhiping Weng^*, and Kevin Struhl^*
YAP and TAZ are transcriptional co-activators of AP-1 proteins and STAT3 during breast cellular transformation
eLife (2021)

Weitao Wang, Kyle N. Klein, Karel Proesmans, Hongbo Yang, Claire Marchal, Xiaopeng Zhu, Tyler Borrman, Alex Hastie, Zhiping Weng, John Bechhoefer, Chun-Long Chen, David M. Gilbert, and Nicholas Rhind
Genome-wide mapping of human DNA replication by optical replication mapping supports a stochastic model of eukaryotic replication.
Molecular Cell (2021)

Kaili Fan, Jill E Moore, Xiao-ou Zhang, Zhiping Weng
Genetic and epigenetic features of promoters with ubiquitous chromatin accessibility support ubiquitous transcription of cell-essential genes.
Nucleic Acids Research (2021)
Graphical abstract

Xiao-ou Zhang, Henry Pratt, Zhiping Weng
Investigating the Potential Roles of SINEs in the Human Genome.
Annual Review of Genomics and Human Genetics (2021)

Arjan van der Velde, Kaili Fan, Junko Tsuji, Jill E. Moore, Michael J. Purcaro, Henry E. Pratt, Zhiping Weng
Annotation of chromatin states in 66 complete mouse epigenomes during development.
Communications Biology (2021)
UCSC genome browser for chromatin states

Houda Belaghzal^†, Tyler Borrman^†, Andrew D. Stephens, Denis L. Lafontaine, Sergey V. Venev, Zhiping Weng, John F. Marko, and Job Dekker
Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics.
Nature Genetics (2021): 1-12.

Johnathan D. Guest^†, Thom Vreven^†, Jing Zhou, Iain Moal, Jeliazko R. Jeliazkov, Jeffrey J. Gray, Zhiping Weng^*, and Brian G. Pierce^*
An expanded benchmark for antibody-antigen docking and affinity prediction reveals insights into antibody recognition determinants.
Structure (2021)

Tianxiong Yu, Xiao Huang, Shengqian Dou, Xiaolu Tang, Shiqi Luo, William E Theurkauf^*, Jian Lu^*, and Zhiping Weng^*
A benchmark and an algorithm for detecting germline transposon insertions and measuring de novo transposon insertion frequencies.
Nucleic Acids Research (2021)
Graphical abstract
TEMP2 website | GitHub

Tianxiong Yu^†, Kaili Fan^†, Deniz M. Özata, Gen Zhang, Yu Fu, William E. Theurkauf^*, Phillip D. Zamore^*, and Zhiping Weng^*
Long first exons and epigenetic marks distinguish conserved pachytene piRNA clusters from other mammalian genes.
Nature Communications 12, no. 1 (2021): 1-17.
Graphical abstract