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Publications 2019

Maxwell Libbrecht, Oscar L. Rodriquez, Zhiping Weng, Jeffrey Bilmes, Michael M. Hoffman, William Stafford Noble. 
A Unified Encyclopedia of Human Functional DNA Elements through Fully Automated Annotation of 164 human Cell Types.
Genome Biol. 2019 Aug 28;20(1):180. doi: 10.1186/s13059-019-1784-2.
PMID: 31462275 PMCID: PMC6714098

Xiao-Ou Zhang, Thomas R. Gingeras, Zhiping Weng*.
Genome-wide Analysis of Polymerase III-transcribed Alu Elements Suggests Cell-Type-Specific Enhancer Function. 
Genome Res. 2019 Sep;29(9):1402-1414. doi: 10.1101/gr.249789.119. Epub 2019 Aug 14.
PMID: 31413151
*corresponding author

Sweta Vangaveti, Thom Vreven, Yang Zhang, Zhiping Weng*
Integrating ab initio and Template-Based Algorithms for Protein-Protein Complex Structure Prediction.
Bioinformatics. 2019 Aug 8. pii: btz623. doi: 10.1093/bioinformatics/btz623
PMID: 31393558
*corresponding author

Prashanth Rajarajan, Tyler Borrman, Will Liao, Sergio Espeso-Gil, Sandhya Chandrasekaran, Yan Jiang, Zhiping Weng, Kristen J. Brennand, Schahram Akbarian  
Spatial Genome Exploration in the Context of Cognitive and Neurological Disease.
Curr Opin Neurobiol. 2019 Jun 27;59:112-119. doi:10.1016/j.conb.2019.05.007. 
PMID: 31255842

Suet-Yan Kwan, Ankur Sheel, Chun-Qing Song, Xiao-Ou Zhang, Tingting Jiang, Hien Dang, Yueying Cao, Deniz Ozata, Haiwei Mou, Hao Yin, Zhiping Weng, Xin Wei Wang, Wen Xue.
Depletion of TRRAP induces p53-independent senescence in liver cancer by downregulating mitotic genes.
Hepatology. 2019 Jun 12. doi: 10.1002/hep.30807 
PMID: 31188495

Ge DT, Wang W, Tipping C, Gainetdinov I, Weng Z, Zamore PD.
The RNA-Binding ATPase, Armitage, Couples piRNA Amplification in Nuage to Phased piRNA Production on Mitochondria.
Mol Cell. 2019 Apr 26. pii: S1097-2765(19)30276-X. doi: 10.1016/j.molcel.2019.04.006. [Epub ahead of print]
PMID: 31076285

Fedor E. Gusev, Denis A. Reshetov, Amanda C. Mitchell, Tatiana V. Andreeva, Aslihan Dincer, Anastasia P. Grigorenko, Gennady Fedonin, Tobias Halene, Maria Aliseychik, Andrey Y. Goltsov, Victor Solovyev, Leonid Brizgalov, Elena Filippova, Zhiping Weng, Schahram Akbarian, and Evgeny I. Rogaev
Epigenetic-genetic chromatin footprinting identifies novel and subject-specific genes active in prefrontal cortex neurons.
FASEB J. 2019 Apr 10:fj201802646R. doi: 10.1096/fj.201802646R. [Epub ahead of print]

Timothy Chang, Eugenio Mattei, Ildar Gainetdinov, Cansu Colpan, Zhiping Weng+, Phillip Zamore+.
Maelstrom Represses Canonical Polymerase II Transcription within Bi-directional piRNA Clusters in Drosophila melanogaster.
Mol Cell. 2019 Jan 17;73(2):291-303.e6. doi: 10.1016/j.molcel.2018.10.038  PMID: 30527661 
+co-corresponding authors