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Publications 2018

Gregory Davis, Shikui Tu, Joshua W.T. Anderson, Rhys Colson, Menachem Gunzburg, Michelle Francisco, Debashish Ray, Sean Shurbsole, Julia Sobotka, Uri Seroussi, Robert Lao, Tuhin Maity, Monica Wu, Katherine McJunkin, Quaid Morris, Timothy Hughes, Jacqueline Wilce+, Julie Claycomb+, Zhiping Weng+, Peter Boag+.
The TRIM-NHL protein NHL-2 is a co-factor in the nuclear and somatic RNAi pathways in C. elegans.
Elife. 2018 Dec 21;7. pii: e35478. doi: 10.7554/eLife.35478.
+co-corresponding authors 

Daifeng Wang, Shuang Liu, Janathan Warrell, Hyejung Won, Xu Shi, Fabio Navarro, Declan Clarke, Mengting Gu, Prashant Emani, Yucheng Yang, Min Xu, Michael Gandal, Shaoke Lou, Jing Zhang, Jonathan Park, Chengfei Yan, Suhn Kyong Rhie, Kasidet Manakongtreecheep, Holly Zhou, Aparna Nathan, Mette Peters, Eugenio Matte, Dominic Fitzgerald, Tonya Brunetti, Jill Moore, Yan Jiang, Kiran Girdhar, Gabriel Hoffman, Selim Kalayci, Zeynep Gumus, Gregory Crawford, PsychENCODE Consortium, Panos Roussos, Schahram Akbarian, Andrew Jaffe, Kevin White, Zhiping Weng, Nedad Sestan, Daniel Geschwind, James Knowles, Mark Gerstein.
Comprehensive functional genomic resource and integrative model for the human brain.
Science. 2018 Dec 14;362(6420). pii: eaat8464. doi: 10.1126/science.aat8464.  PMID: 30545857 

Prashanth Rajarajan, Tyler Borman, Will Liao, Nadine Schrode, Erin Flaherty, Charlize Casino, Samuel Powell, Chittampalli Yashaswini, Elizabeth LaMarca, Bibi Kassim, Behnam Javidfar, Sergio Espeso-Gil, Aiquin Li, Hyejung Won, Daniel Geschwind, Seok-Man Ho, Matthew MacDonald, Gabriel Hoffman, Panos Roussos, Bin Zhang, Chang-Gyu Hahn, Zhiping Weng, Kristen Brennand, Schahram Akbarian.
Neuron-specific signatures in the chromosomal connectome associated with schizophrenia risk.
Science. 2018 Dec 14;362(6420). pii: eaat4311. doi: 10.1126/science.aat4311  PMID: 30545851 

Gen Zhang, Shikui Tu, Tianxiong Yu, Xiao-Ou Zhang, Swapnil Parhad, Zhiping Weng+, William Theurkauf+.
Co-dependent Assembly of Drosophila piRNA Precursor Complexes and piRNA Cluster Heterochromatin.
Cell Rep. 2018 Sep 25;24(13):3413-3422.e4. doi: 10.1016/j.celrep.2018.08.081. PMID:30257203   +co-corresponding authors 

Xiao-Ou Zhang, Yu Fu, Haiwei Mou, Wen Xue, Zhiping Weng*.
The temporal landscape of recursive splicing during Pol II transcription elongation in human cells.
PLoS Genet. 2018 Aug 27;14(8):e1007579. doi: 10.1371/journal.pgen.1007579. eCollection 2018 Aug.PMID: 30148885  *corresponding author 

Shaliu Fu, Qin Wang, Jill E Moore, Michael J Purcaro, Henry E Pratt, Kaili Fan, Cuihua Gu,Cizhong Jiang, Ruixin Zhu, Anshul Kundaje,  Aiping Lu, Zhiping Weng*.
Differential analysis of chromatin accessibility and histone modifications for predicting mouse developmental enhancers.
Nucleic Acids Res. 2018 Aug 22. doi: 10.1093/nar/gky753.PMID: 30137428
*corresponding author 

Kiran Girdhar, Gabriel E. Hoffman, Yan Jiang, Leanne Brown, Marija Kundakovic, Mads E. Hauberg, Nancy J. Francoeur, Ying-chih Wang, Hardik Shah, David H. Kavanagh, Elizabeth Zharovsky, Rivka Jacobov, Jennifer R. Wiseman, Royce Park, Jessica S. Johnson, Bibi S. Kassim, Laura Sloofman, Eugenio Mattei, Zhiping Weng, Solveig K. Sieberts, Mette A. Peters, Brent T. Harris, Barbara K. Lipska, Pamela Sklar, Panos Roussos, Schahram Akbarian.
Cell-specific histone modification maps in the human frontal lobe link schizophrenia risk to the neuronal epigenome.
Nat Neurosci. 2018 Aug;21(8):1126-1136. doi: 10.1038/s41593-018-0187-0. Epub 2018 Jul 23.PMID:30038276 

Yu Fu, Pei-Hsuan Wu, Timothy Beane, Phillip Zamore+, Zhiping Weng+.
Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers.
BMC Genomics. 2018 Jul 13;19(1):531. doi: 10.1186/s12864-018-4933-1.PMID: 30001700
+co-corresponding authors 

Jian Hu, Liang Gu, Youqiong Ye, Meizhu Zheng, Zhu Xu, Jing Lin, Yanhua Du, Mengxue Tian, Lifang Luo, Beibei Wang, Xiaobai Zhang, Zhiping Weng, Chizhong Jiang.
Dynamic placement of the linker histone H1 associated with nucleosome arrangement and gene transcription in early Drosophila embryonic development.
Cell Death Dis. 2018 Jul 9;9(7):765. doi: 10.1038/s41419-018-0819-z. PMID: 29988149 

Wei-Sheng Wu, Wei-Che Huang, Jordan S Brown, Donglei Zhang, Xiaoyan Song, Hao Chen, Shikui Tu, Zhiping Weng, Heng-Chi Lee.
pirScan: a webserver to predict piRNA targeting sites and to avoid transgene silencing in C. elegans.
Nucleic Acids Res. 2018 Jul 2;46(W1):W43-W48. doi: 10.1093/nar/gky277. PMID: 29897582 

Weijun Chen, Jill Moore, Hakan Ozadam, Hennady Shulha, Nicholas Rhind, Zhiping Weng, Melissa Moore.
Transcriptome-wide Interrogation of the Functional Intronome by Spliceosome Profiling.
Cell. 2018 May 3;173(4):1031-1044.e13. doi: 10.1016/j.cell.2018.03.062.PMID:29727662 

Thom Vreven+, Devin Schweppe, Juan Chavez, Chad Weisbrod, Sayaka Shibata, Chunxiang Zheng, James Bruce, Zhiping Weng+
Integrating Cross-Linking Experiments with Ab Initio Protein-Protein Docking.
J Mol Biol. 2018 Jun 8;430(12):1814-1828. doi:  10.1016/j.jmb.2018.04.010. Epub 2018 Apr 14. PMID: 29665372
+co-corresponding authors 

Chun-Qing Song, Dan Wang, Tingting Jiang, Kevin O’Conner, Qiushi Tang, Lingling Cai, Xiangrui Li, Zhiping Weng, Hao Yin, Guangping Gao, Christian Mueller, Terance Flotte, Wen Xue.
In vivo Genome Editing Partially Restores Alpha 1-Antitrypsin in a Murine Model of AAT Deficiency.
Hum Gene Ther. 2018 Aug;29(8):853-860. doi: 10.1089/hum.2017.225. Epub 2018 May 14. PMID: 29597895 

Wen Tang, Meetu Seth, Shikui Tu, En-zhi Shen, Qian Le, Masaki Shirayama, Zhiping Weng, Craig Mello.
A Sex Chromosome piRNA Promotes Robust Dosage Compensation and Sex Determination in C. elegans.
Dev Cell. 2018 Mar 26;44(6):762-770.e3. doi:10.1016/j.devcel.2018.01.025. Epub 2018 Feb 15. PMID:29456136 

Meetu Seth, Masaki Shirauama, Wen Tang, En-Zhi Shen, Shikui Tu, Heng-Chi Lee, Zhiping Weng, Craig Mello.
The Coding Regions of Germline mRNAs Confer Sensitivity to Argonaute Regulation in C. elegans.
Cell Rep. 2018 Feb 27;22(9):2254-2264. doi: 10.1016/j.celrep.2018.02.009. Epub 2018 Feb 15.PMID: 29456100 

En-Zhi Shen*, Hao Chen*, Ahmet R Ozturk, Shikui Tu, Masaki Shirayama, Wen Tang, Yue-He Ding, Si-Yuan Dai, Zhiping Weng, Craig C Mello.
Identification of piRNA binding sites reveals the Argonaute regulatory landscape of the C. elegans germline.
Cell. (Published on Feb 15).
*Joint first authors. 

Donglei Zhang, Shikui Tu, Michael Stubna, Wei-Sheng Wu, Wei-Che Huang, Zhiping Weng, Heng-Chi Lee.
The piRNA targeting rules and the resistance to piRNA silencing in endogenous genes.
Science. 359(6375):587-592. 

Yu Fu, Yujing Yang, Han Zhang, Gwen Farley, Junling Wang, Kaycee A Quarles, Zhiping Weng+, Phillip D Zamore+.
The genome of the Hi5 germ cell line from Trichoplusia ni, an agricultural pest and novel model for small RNA biology.
eLife. 7:e31638.
+Co-corresponding authors. 

Julianna Bozler, Balint Z Kacsoh, Hao Chen, William E Theurkauf, Zhiping Weng, Giovanni Bosco.
A systems level approach to temporal expression dynamics in Drosophila reveals clusters of long-term memory genes.
PLoS Genetics. 13(10):e1007054. 

Nishant K Singh, Timothy P Riley, Sarah Catherine B Baker, Tyler Borrman, Zhiping Weng, Brian M Baker.
Emerging Concepts in TCR Specificity: Rationalizing and (Maybe) Predicting Outcomes.
The Journal of Immunology. 199(7):2203-2213.

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