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Publications 2019

Zhang XO, Gingeras TR, Weng Z. 
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. PubMed PMID: 31413151; PubMed Central PMCID: PMC6724667.

Gusev FE, Reshetov DA, Mitchell AC, Andreeva TV, Dincer A, Grigorenko AP, Fedonin G, Halene T, Aliseychik M, Filippova E, Weng Z, Akbarian S, Rogaev EI. 
Chromatin profiling of cortical neurons identifies individual epigenetic signatures in schizophrenia. 
Transl Psychiatry. 2019 Oct 17;9(1):256. doi: 10.1038/s41398-019-0596-1. PubMed PMID: 31624234; PubMed Central PMCID: PMC6797775.

Yu T, Koppetsch BS, Pagliarani S, Johnston S, Silverstein NJ, Luban J, Chappell K, Weng Z, Theurkauf WE. 
The piRNA Response to Retroviral Invasion of the Koala Genome. 
Cell. 2019 Oct 17;179(3):632-643.e12. doi: 10.1016/j.cell.2019.09.002. Epub 2019 Oct 10. PubMed PMID: 31607510; PubMed Central PMCID: PMC6800666.

Rajarajan P, Borrman T, Liao W, Espeso-Gil S, Chandrasekaran S, Jiang Y, Weng Z, Brennand KJ, Akbarian S. 
Spatial genome exploration in the context of cognitive and neurological disease. 
Curr Opin Neurobiol. 2019 Dec;59:112-119. doi: 10.1016/j.conb.2019.05.007. Epub 2019 Jun 27. Review. PubMed PMID: 31255842; PubMed Central PMCID: PMC6889018.

Lensink MF, Brysbaert G, Nadzirin N, Velankar S, Chaleil RAG, Gerguri T, Bates PA, Laine E, Carbone A, Grudinin S, Kong R, Liu RR, Xu XM, Shi H, Chang S, Eisenstein M, Karczynska A, Czaplewski C, Lubecka E, Lipska A, Krupa P, Mozolewska M, Golon Ł, Samsonov S, Liwo A, Crivelli S, Pagès G, Karasikov M, Kadukova M, Yan Y, Huang SY, Rosell M, Rodríguez-Lumbreras LA, Romero-Durana M, Díaz-Bueno L, Fernandez-Recio J, Christoffer C, Terashi G, Shin WH, Aderinwale T, Maddhuri Venkata Subraman SR, Kihara D, Kozakov D, Vajda S, Porter K, Padhorny D, Desta I, Beglov D, Ignatov M, Kotelnikov S, Moal IH, Ritchie DW, Chauvot de Beauchêne I, Maigret B, Devignes MD, Ruiz Echartea ME, Barradas-Bautista D, Cao Z, Cavallo L, Oliva R, Cao Y, Shen Y, Baek M, Park T, Woo H, Seok C, Braitbard M, Bitton L, Scheidman-Duhovny D, Dapkūnas J, Olechnovič K, Venclovas Č, Kundrotas PJ, Belkin S, Chakravarty D, Badal VD, Vakser IA, Vreven T, Vangaveti S, Borrman T, Weng Z, Guest JD, Gowthaman R, Pierce BG, Xu X, Duan R, Qiu L, Hou J, Ryan Merideth B, Ma Z, Cheng J, Zou X, Koukos PI, Roel-Touris J, Ambrosetti F, Geng C, Schaarschmidt J, Trellet ME, Melquiond ASJ, Xue L, Jiménez-García B, van Noort CW, Honorato RV, Bonvin AMJJ, Wodak SJ. 
Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment. 
Proteins. 2019 Dec;87(12):1200-1221. doi: 10.1002/prot.25838. Epub 2019 Oct 25. PubMed PMID: 31612567.

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