Searching journal content for Z. Jeffrey Chen in author.

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  1. Resource: A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq
    • Sophia C. Gaynor-Gillett,
    • Lijun Cheng,
    • Manman Shi,
    • Jason Liu,
    • Gaoyuan Wang,
    • Megan Spector,
    • Qiuyu Guo,
    • Le Qi,
    • Mary Flaherty,
    • Martha Wall,
    • Ahyeon Hwang,
    • Mengting Gu,
    • Zhanlin Chen,
    • Yuhang Chen,
    • PsychENCODE Consortium,
    • Jennifer R. Moran,
    • Jing Zhang,
    • Donghoon Lee,
    • Mark Gerstein,
    • Daniel Geschwind,
    • and Kevin P. White
    Genome Res. August 2025 35: 1887-1901; Published in Advance July 11, 2025, doi:10.1101/gr.279584.124
  2. Research: Plasma cell-free RNA characteristics in COVID-19 patients
    • Yanqun Wang,
    • Jie Li,
    • Lu Zhang,
    • Hai-Xi Sun,
    • Zhaoyong Zhang,
    • Jinjin Xu,
    • Yonghao Xu,
    • Yu Lin,
    • Airu Zhu,
    • Yuxue Luo,
    • Haibo Zhou,
    • Yan Wu,
    • Shanwen Lin,
    • Yuzhe Sun,
    • Fei Xiao,
    • Ruiying Chen,
    • Liyan Wen,
    • Wei Chen,
    • Fang Li,
    • Rijing Ou,
    • Yanjun Zhang,
    • Tingyou Kuo,
    • Yuming Li,
    • Lingguo Li,
    • Jing Sun,
    • Kun Sun,
    • Zhen Zhuang,
    • Haorong Lu,
    • Zhao Chen,
    • Guoqiang Mai,
    • Jianfen Zhuo,
    • Puyi Qian,
    • Jiayu Chen,
    • Huanming Yang,
    • Jian Wang,
    • Xun Xu,
    • Nanshan Zhong,
    • Jingxian Zhao,
    • Junhua Li,
    • Jincun Zhao,
    • and Xin Jin
    Genome Res. February 2022 32: 228-241; Published in Advance January 21, 2022, doi:10.1101/gr.276175.121
    OPEN ACCESS ARTICLE
  3. Erratum: Erratum: Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information
    • Zhoutao Chen,
    • Long Pham,
    • Tsai-Chin Wu,
    • Guoya Mo,
    • Yu Xia,
    • Peter L. Chang,
    • Devin Porter,
    • Tan Phan,
    • Huu Che,
    • Hao Tran,
    • Vikas Bansal,
    • Justin Shaffer,
    • Pedro Belda-Ferre,
    • Greg Humphrey,
    • Rob Knight,
    • Pavel Pevzner,
    • Son Pham,
    • Yong Wang,
    • and Ming Lei
    Genome Res. May 2021 31: 934; doi:10.1101/gr.275614.121
    OPEN ACCESS ARTICLE
  4. Method: Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information
    • Zhoutao Chen,
    • Long Pham,
    • Tsai-Chin Wu,
    • Guoya Mo,
    • Yu Xia,
    • Peter L. Chang,
    • Devin Porter,
    • Tan Phan,
    • Huu Che,
    • Hao Tran,
    • Vikas Bansal,
    • Justin Shaffer,
    • Pedro Belda-Ferre,
    • Greg Humphrey,
    • Rob Knight,
    • Pavel Pevzner,
    • Son Pham,
    • Yong Wang,
    • and Ming Lei
    Genome Res. June 2020 30: 898-909; Published in Advance June 15, 2020, doi:10.1101/gr.260380.119
  5. Research: An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells
    • Zhizhuo Zhang,
    • Kern Rei Chng,
    • Shreyas Lingadahalli,
    • Zikai Chen,
    • Mei Hui Liu,
    • Huy Hoang Do,
    • Shaojiang Cai,
    • Nicola Rinaldi,
    • Huay Mei Poh,
    • Guoliang Li,
    • Ying Ying Sung,
    • Charlie L. Heng,
    • Leighton J. Core,
    • Si Kee Tan,
    • Xiaoan Ruan,
    • John T. Lis,
    • Manolis Kellis,
    • Yijun Ruan,
    • Wing-Kin Sung,
    • and Edwin Cheung
    Genome Res. February 2019 29: 223-235; Published in Advance January 3, 2019, doi:10.1101/gr.230243.117
  6. Research: Widespread roles of enhancer-like transposable elements in cell identity and long-range genomic interactions
    • Yaqiang Cao,
    • Guoyu Chen,
    • Gang Wu,
    • Xiaoli Zhang,
    • Joseph McDermott,
    • Xingwei Chen,
    • Chi Xu,
    • Quanlong Jiang,
    • Zhaoxiong Chen,
    • Yingying Zeng,
    • Daosheng Ai,
    • Yi Huang,
    • and Jing-Dong J. Han
    Genome Res. January 2019 29: 40-52; Published in Advance November 19, 2018, doi:10.1101/gr.235747.118
    OPEN ACCESS ARTICLE
  7. Research: LTRs activated by Epstein-Barr virus–induced transformation of B cells alter the transcriptome
    • Amy Leung,
    • Candi Trac,
    • Hiroyuki Kato,
    • Kevin R. Costello,
    • Zhaoxia Chen,
    • Rama Natarajan,
    • and Dustin E. Schones
    Genome Res. December 2018 28: 1791-1798; Published in Advance October 31, 2018, doi:10.1101/gr.233585.117
  8. Research: The gene repressor complex NuRD interacts with the histone variant H3.3 at promoters of active genes
    • Daniel C. Kraushaar,
    • Zuozhou Chen,
    • Qingsong Tang,
    • Kairong Cui,
    • Junfang Zhang,
    • and Keji Zhao
    Genome Res. November 2018 28: 1646-1655; Published in Advance September 25, 2018, doi:10.1101/gr.236224.118
  9. Resource: Comparative validation of the D. melanogaster modENCODE transcriptome annotation
    • Zhen-Xia Chen,
    • David Sturgill,
    • Jiaxin Qu,
    • Huaiyang Jiang,
    • Soo Park,
    • Nathan Boley,
    • Ana Maria Suzuki,
    • Anthony R. Fletcher,
    • David C. Plachetzki,
    • Peter C. FitzGerald,
    • Carlo G. Artieri,
    • Joel Atallah,
    • Olga Barmina,
    • James B. Brown,
    • Kerstin P. Blankenburg,
    • Emily Clough,
    • Abhijit Dasgupta,
    • Sai Gubbala,
    • Yi Han,
    • Joy C. Jayaseelan,
    • Divya Kalra,
    • Yoo-Ah Kim,
    • Christie L. Kovar,
    • Sandra L. Lee,
    • Mingmei Li,
    • James D. Malley,
    • John H. Malone,
    • Tittu Mathew,
    • Nicolas R. Mattiuzzo,
    • Mala Munidasa,
    • Donna M. Muzny,
    • Fiona Ongeri,
    • Lora Perales,
    • Teresa M. Przytycka,
    • Ling-Ling Pu,
    • Garrett Robinson,
    • Rebecca L. Thornton,
    • Nehad Saada,
    • Steven E. Scherer,
    • Harold E. Smith,
    • Charles Vinson,
    • Crystal B. Warner,
    • Kim C. Worley,
    • Yuan-Qing Wu,
    • Xiaoyan Zou,
    • Peter Cherbas,
    • Manolis Kellis,
    • Michael B. Eisen,
    • Fabio Piano,
    • Karin Kionte,
    • David H. Fitch,
    • Paul W. Sternberg,
    • Asher D. Cutter,
    • Michael O. Duff,
    • Roger A. Hoskins,
    • Brenton R. Graveley,
    • Richard A. Gibbs,
    • Peter J. Bickel,
    • Artyom Kopp,
    • Piero Carninci,
    • Susan E. Celniker,
    • Brian Oliver,
    • and Stephen Richards
    Genome Res. July 2014 24: 1209-1223; Published in Advance July 1, 2014, doi:10.1101/gr.159384.113
    OPEN ACCESS ARTICLE
  10. Resource: Genome-wide high resolution parental-specific DNA and histone methylation maps uncover patterns of imprinting regulation in maize
    • Mei Zhang,
    • Shaojun Xie,
    • Xiaomei Dong,
    • Xin Zhao,
    • Biao Zeng,
    • Jian Chen,
    • Hui Li,
    • Weilong Yang,
    • Hainan Zhao,
    • Gaokui Wang,
    • Zongliang Chen,
    • Silong Sun,
    • Andrew Hauck,
    • Weiwei Jin,
    • and Jinsheng Lai
    Genome Res. January 2014 24: 167-176; Published in Advance October 16, 2013, doi:10.1101/gr.155879.113
    OPEN ACCESS ARTICLE
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