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Publications 2020

Tyler Borrman, Brian G Pierce, Thom Vreven, Brian M Baker, and Zhiping Weng.
High-throughput modeling and scoring of TCR-pMHC complexes to predict cross-reactive peptides.
Bioinformatics, btaa1050 (2020)

The ENCODE Project Consortium, Jill E. Moore, Michael J. Purcaro, Henry E. Pratt, Charles B. Epstein, Noam Shoresh, Jessika Adrian, Trupti Kawli, Carrie A. Davis, Alexander Dobin, Rajinder Kaul, Jessica Halow, Eric L. Van Nostrand, Peter Freese, David U. Gorkin, Yin Shen, Yupeng He, Mark Mackiewicz, Florencia Pauli-Behn, Brian A. Williams, Ali Mortazavi, Cheryl A. Keller, Xiao-Ou Zhang, Shaimae I. Elhajjajy, Jack Huey, Diane E. Dickel, Valentina Snetkova, Xintao Wei, Xiaofeng Wang, Juan Carlos Rivera-Mulia, Joel Rozowsky, Jing Zhang, Surya B. Chhetri, Jialing Zhang, Alec Victorsen, Kevin P. White, Axel Visel, Gene W. Yeo, Christopher B. Burge, Eric Lécuyer, David M. Gilbert, Job Dekker, John Rinn, Eric M. Mendenhall, Joseph R. Ecker, Manolis Kellis, Robert J. Klein, William S. Noble, Anshul Kundaje, Roderic Guigó, Peggy J. Farnham, J. Michael Cherry, Richard M. Myers, Bing Ren, Brenton R. Graveley, Mark B. Gerstein, Len A. Pennacchio, Michael P. Snyder, Bradley E. Bernstein, Barbara Wold, Ross C. Hardison, Thomas R. Gingeras, John A. Stamatoyannopoulos, and Zhiping Weng.
Expanded encyclopaedias of DNA elements in the human and mouse genomes.
Nature 583, no. 7818 (2020): 699-710.
SCREEN for visualizing cCREs

The ENCODE Project Consortium, Michael P. Snyder, Thomas R. Gingeras, Jill E. Moore, Zhiping Weng, Mark B. Gerstein, Bing Ren, Ross C. Hardison, John A. Stamatoyannopoulos, Brenton R. Graveley, Elise A. Feingold, Michael J. Pazin, Michael Pagan, Daniel A. Gilchrist, Benjamin C. Hitz, J. Michael Cherry, Bradley E. Bernstein, Eric M. Mendenhall, Daniel R. Zerbino, Adam Frankish, Paul Flicek, and Richard M. Myers.
Perspectives on ENCODE.
Nature 583, no. 7818 (2020): 693-698.

Pei-Hsuan Wu, Yu Fu, Katharine Cecchini, Deniz M. Özata, Amena Arif, Tianxiong Yu, Cansu Colpan, Ildar Gainetdinov, Zhiping Weng, and Phillip D. Zamore.
The evolutionarily conserved piRNA-producing locus pi6 is required for male mouse fertility.
Nature Genetics 52, no. 7 (2020): 728-739.

Henry Pratt, Zhiping Weng.
LogoJS: a Javascript package for creating sequence logos and embedding them in web applications.
Bioinformatics 36, no. 11 (2020): 3573-3575.

Jordan L. Smith, Tomás C. Rodríguez, Haiwei Mou, Suet‐Yan Kwan, Henry Pratt, Xiao‐Ou Zhang, Yueying Cao, Shunqing Liang, Deniz M. Ozata, Tianxiong Yu, Qiangzong Yin, Max Hazeltine, Zhiping Weng, Erik J. Sontheimer, and Wen Xue.
YAP1 withdrawal in hepatoblastoma drives therapeutic differentiation of tumor cells to functional hepatocyte‐like cells.
Hepatology (2020).

Henry Pratt, Zhiping Weng, and Daniel Pratt.
Gastroenterology 158, no. 6 (2020): S-1285.

Sergio Espeso-Gil, Tobias Halene, Jaroslav Bendl, Bibi Kassim, Gabriella Ben Hutta, Marina Iskhakova, Neda Shokrian, Pavan Auluck, Behnam Javidfar, Prashanth Rajarajan, Sandhya Chandrasekaran, Cyril J Peter, Alanna Cote, Rebecca Birnbaum, Will Liao, Tyler Borrman, Jennifer Wiseman, Aaron Bell, Michael J Bannon, Panagiotis Roussos, John F Crary, Zhiping Weng, Stefano Marenco, Barbara Lipska, Nadejda M Tsankova, Laura Huckins, Yan Jiang, and Schahram Akbarian.
A chromosomal connectome for psychiatric and metabolic risk variants in adult dopaminergic neurons.
Genome medicine 12, no. 1 (2020): 1-19.

Aiping Lu, Maren Watkins, Qing Li, Samuel D. Robinson, Gisela P. Concepcion, Mark Yandell, Zhiping Weng, Baldomero M. Olivera, Helena Safavi-Hemami, and Alexander E. Fedosov.
Transcriptomic profiling reveals extraordinary diversity of venom peptides in unexplored predatory gastropods of the genus Clavus.
Genome biology and evolution 12, no. 5 (2020): 684-700.

Tingting Jiang, Jordana M. Henderson, Kevin Coote, Yi Cheng, Hillary C. Valley, Xiao-Ou Zhang, Qin Wang, Luke H. Rhym, Yueying Cao, Gregory A. Newby, Hermann Bihler, Martin Mense, Zhiping Weng, Daniel G. Anderson, Anton P. McCaffrey, David R. Liu, and Wen Xue.
Chemical modifications of adenine base editor mRNA and guide RNA expand its application scope.
Nature Communications 11, no. 1 (2020): 1-9.

Peng Zhang, Xiao-Ou Zhang, Tingting Jiang, Lingling Cai, Xiao Huang, Qi Liu, Dan Li, Aiping Lu, Yan Liu, Wen Xue, Peng Zhang, and Zhiping Weng
Comprehensive identification of alternative back-splicing in human tissue transcriptomes. 
Nucleic Acids Research 48, no. 4 (2020): 1779-1789.

Swapnil S. Parhad, Tianxiong Yu, Gen Zhang, Nicholas P. Rice, Zhiping Weng, and William E. Theurkauf.
Adaptive Evolution Targets a piRNA Precursor Transcription Network. 
Cell Rep. 30, no. 8 (2020): 2672-2685.

Brian Baker, Lance Hellman, Brian Pierce, and Zhiping Weng.
Molecular constructs and uses thereof.
US Patent 10,526,391

Thom Vreven, Sweta Vangaveti, Tyler M. Borrman, Jennifer C. Gaines, and Zhiping Weng.
Performance of ZDOCK and IRAD in CAPRI rounds 39‐45.
Proteins: Structure, Function, and Bioinformatics (2020).

Sweta Vangaveti, Thom Vreven, Yang Zhang, and Zhiping Weng.
Integrating ab initio and template-based algorithms for protein-protein complex structure prediction. 
Bioinformatics. 36, no. 3 (2020): 751-757.

Alison P. Casserly, Junko Tsuji, Rubing Zhao-Shea, Ciearra B. Smith, Susanna Molas, Andrew R. Tapper, Zhiping Weng, and Paul D. Gardner.
Integrated miRnA-/mRnA-Seq of the Habenulo-interpeduncular circuit During Acute nicotine Withdrawal.
Scientific Reports 10, no. 1 (2020): 1-14.

Junko Tsuji, Travis Thomson, Elizabeth Chan, Christine K. Brown, Julia Oppenheimer, Carol Bigelow, Xianjun Dong, William E. Theurkauf, Zhiping Weng, and Lawrence M. Schwartz.
High resolution analysis of differential gene expression during skeletal muscle atrophy and programmed cell death.
Physiological Genomics (2020).

Suet‐Yan Kwan, Ankur Sheel, Chun‐Qing Song, Xiao‐Ou Zhang, Tingting Jiang, Hien Dang, Yueying Cao, Deniz M. Ozata, Haiwei Mou, Hao Yin, Zhiping Weng, Xin Wei Wang, and Wen Xue.
Depletion of TRRAP Induces p53-Independent Senescence in Liver Cancer by Down-Regulating Mitotic Genes
Hepatology. 71, no. 1 (2020): 275-290.

Yu H. Sun, Jiang Zhu, Li Huitong Xie, Ziwei Li, Rajyalakshmi Meduri, Xiaopeng Zhu, Chi Song, Chen Chen, Emiliano P. Ricci, Zhiping Weng, and Xin Zhiguo Li.
Ribosomes guide pachytene piRNA formation on long intergenic piRNA precursors.
Nature Cell Biology 22, no. 2 (2020): 200-212.

Deniz M. Özata, Tianxiong Yu, Haiwei Mou, Ildar Gainetdinov, Cansu Colpan, Katharine Cecchini, Yasin Kaymaz, Pei-Hsuan Wu, Kaili Fan, Alper Kucukural, Zhiping Weng, and Phillip D. Zamore.
Evolutionarily conserved pachytene piRNA loci are highly divergent among modern humans.
Nature Ecology & Evolution 4, no. 1 (2020): 156-168.

Jill E. Moore, Henry E. Pratt, Michael J. Purcaro, Zhiping Weng.
A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods. 
Genome Biol. 21, no. 1 (2020): 17.