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Publications 2023

†: contributed equally, joint first authors
*: corresponding author(s)

Andreas R Gschwind*, Kristy S Mualim*, Alireza Karbalayghareh*, …, Kaili Fan, …, Zhiping Weng, …, Lars M Steinmetz, Anshul Kundaje, and Jesse M Engreitz. An encyclopedia of enhancer-gene regulatory interactions in the human genome. bioRXiv. (2023)

Ailsa M Jeffries*, Tianxiong Yu*, Jennifer S Ziegenfuss, Allie K Tolles, Yerin Kim, Zhiping Weng, Michael A Lodato. Single-cell transcriptomic and genomic changes in the aging human brain. bioRXiv. (2023)

Henry E Pratt, Tong Wu, Shaimae Elhajjajy, Jeffrey Zhou, Kate Fitzgerald, Tom Fazzio, Zhiping Weng, and Daniel S Pratt*. Beyond genome-wide association studies: Investigating the role of noncoding regulatory elements in primary sclerosing cholangitis. Hepatology Communications. (2023)

Samantha Ho, Nicholas P Rice, Tianxiong Yu, Zhiping Weng*, and William E Theurkauf*. Aub, Vasa and Armi localization to phase separated nuage is dispensable for piRNA biogenesis and transposon silencing in Drosophila. bioRXiv. (2023)

Fairlie Reese, Brian Williams, Gabriela Balderrama-Gutierrez, …, Shaimae I. Elhajjajy, …, Zhiping Weng, …, Roderic Guigó, Barbara J. Wold, and Ali Mortazavi. The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity. bioRXiv. (2023)

Gregory Andrews, Kaili Fan, Henry E. Pratt, Nishigandha Phalke, Zoonomia Consortium, Elinor K. Karlsson, Kerstin Lindblad-Toh, Steven Gazal, Jill E. Moore, and Zhiping Weng*Mammalian evolution of human cis-regulatory elements and transcription factor binding sites. Science (2023) (Graphical abstract)

Patrick F. Sullivan, Jennifer R. S. Meadows, Steven Gazal, ..., Gregory Andrews, ..., Zhiping Weng, ..., Karin Forsberg-Nilsson, Elinor K. Karlsson, and Kerstin Lindblad-Toh. Leveraging base-pair mammalian constraint to understand genetic variation and human diseaseScience (2023)

Matthew J. Christmas, Irene M. Kaplow, Diane P. Genereux, ..., Gregory Andrews, ..., Kaili Fan, ..., Zhiping Weng, ..., Andreas R. Pfenning, Kerstin Lindblad-Toh, and Elinor K. Karlsson. Evolutionary constraint and innovation across hundreds of placental mammals. Science (2023)

Joel Rozowsky, Jiahao Gao, Beatrice Borsari, ..., Henry E. Pratt, ..., Zhiping Weng, ..., Roderic Guigó, Thomas R. Gingeras, Mark Gerstein. The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models. Cell (2023). 

Jichuan Cao, Tianxiong Yu, Bo Xu, Zhongren Hu, Xiao-ou Zhang, William E Theurkauf, Zhiping Weng*. Epigenetic and chromosomal features drive transposon insertion in Drosophila melanogaster. Nucleic Acids Research (2023).

Kaili Fan, Edith Pfister, and Zhiping Weng*. Towards a comphrehensize catalog of regulatory elements. Human Genetics (2023)

Soojin Lee, Yong-Woo Jun, Gabriel R. Linares, ..., Zhiping Weng, Justin K. Ichida, and Fen-Biao Gao. Downregulation of Hsp90 and the antimicrobial peptide Mtk suppresses poly(GR)-induced neurotoxicity in C9ORF72-ALS/FTD. Neuron (2023)

Katharine Cecchini, The transcription factor TCFL5 responds to A-MYB to elaborate the male meiotic program in mice. Reproduction (2023)

Hufeng Zhou, Theodore Arapoglou, Xihao Li, ...,  NHGRI Genome Sequencing Program Variant Functional Annotation Working Group, Zhiping Weng, Benjamin Neale, Shamil R Sunyaev and Xihong Lin. FAVOR: functional annotation of variants online resource and annotator for variation across the human genome. Nucleic Acids Research (2023)

Cindy Wen, Michael Margolis, Rujia Dai, …, Henry Pratt, PsychENCODE Consortium, …, Zhiping Weng, Katherine S. Pollard, Chunyu Liu, and Michael J. Gandal. Cross-ancestry, cell-type-informed atlas of gene, isoform, and splicing regulation in the developing human brain. medRXiv (2023).