D
Daofeng Li
Researcher at Washington University in St. Louis
Publications - 77
Citations - 10186
Daofeng Li is an academic researcher from Washington University in St. Louis. The author has contributed to research in topics: DNA methylation & Epigenomics. The author has an hindex of 32, co-authored 63 publications receiving 7999 citations. Previous affiliations of Daofeng Li include University of Minnesota & University of Washington.
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Journal ArticleDOI
Integrative analysis of 111 reference human epigenomes
Anshul Kundaje,Wouter Meuleman,Wouter Meuleman,Jason Ernst,Misha Bilenky,Angela Yen,Angela Yen,Alireza Heravi-Moussavi,Pouya Kheradpour,Pouya Kheradpour,Zhizhuo Zhang,Zhizhuo Zhang,Jianrong Wang,Jianrong Wang,Michael J. Ziller,Viren Amin,John W. Whitaker,Matthew D. Schultz,Lucas D. Ward,Lucas D. Ward,Abhishek Sarkar,Abhishek Sarkar,Gerald Quon,Gerald Quon,Richard Sandstrom,Matthew L. Eaton,Matthew L. Eaton,Yi-Chieh Wu,Yi-Chieh Wu,Andreas R. Pfenning,Andreas R. Pfenning,Xinchen Wang,Xinchen Wang,Melina Claussnitzer,Melina Claussnitzer,Yaping Liu,Yaping Liu,Cristian Coarfa,R. Alan Harris,Noam Shoresh,Charles B. Epstein,Elizabeta Gjoneska,Elizabeta Gjoneska,Danny Leung,Wei Xie,R. David Hawkins,Ryan Lister,Chibo Hong,Philippe Gascard,Andrew J. Mungall,Richard A. Moore,Eric Chuah,Angela Tam,Theresa K. Canfield,R. Scott Hansen,Rajinder Kaul,Peter J. Sabo,Mukul S. Bansal,Mukul S. Bansal,Mukul S. Bansal,Annaick Carles,Jesse R. Dixon,Kai How Farh,Soheil Feizi,Soheil Feizi,Rosa Karlic,Ah Ram Kim,Ah Ram Kim,Ashwinikumar Kulkarni,Daofeng Li,Rebecca F. Lowdon,Ginell Elliott,Tim R. Mercer,Shane Neph,Vitor Onuchic,Paz Polak,Paz Polak,Nisha Rajagopal,Pradipta R. Ray,Richard C Sallari,Richard C Sallari,Kyle Siebenthall,Nicholas A Sinnott-Armstrong,Nicholas A Sinnott-Armstrong,Michael Stevens,Robert E. Thurman,Jie Wu,Bo Zhang,Xin Zhou,Arthur E. Beaudet,Laurie A. Boyer,Philip L. De Jager,Philip L. De Jager,Peggy J. Farnham,Susan J. Fisher,David Haussler,Steven J.M. Jones,Steven J.M. Jones,Wei Li,Marco A. Marra,Michael T. McManus,Shamil R. Sunyaev,Shamil R. Sunyaev,James A. Thomson,Thea D. Tlsty,Li-Huei Tsai,Li-Huei Tsai,Wei Wang,Robert A. Waterland,Michael Q. Zhang,Lisa Helbling Chadwick,Bradley E. Bernstein,Bradley E. Bernstein,Bradley E. Bernstein,Joseph F. Costello,Joseph R. Ecker,Martin Hirst,Alexander Meissner,Aleksandar Milosavljevic,Bing Ren,John A. Stamatoyannopoulos,Ting Wang,Manolis Kellis,Manolis Kellis +123 more
TL;DR: It is shown that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease.
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The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions.
Yanli Wang,Fan Song,Bo Zhang,Lijun Zhang,Jie Xu,Da Kuang,Daofeng Li,Mayank N. K. Choudhary,Yun Li,Ming Hu,Ross C. Hardison,Ting Wang,Feng Yue +12 more
TL;DR: The 3D Genome Browser is introduced, which provides multiple methods linking distal cis-regulatory elements with their potential target genes and a new binary data format for Hi-C data that reduces the file size by at least a magnitude and allows users to visualize chromatin interactions over millions of base pairs within seconds.
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Widespread contribution of transposable elements to the innovation of gene regulatory networks
Vasavi Sundaram,Yong Cheng,Zhihai Ma,Daofeng Li,Xiaoyun Xing,Peter Edge,Michael Snyder,Ting Wang +7 more
TL;DR: Transposable elements have significantly and continuously shaped gene regulatory networks during mammalian evolution, and are an important driving force for regulatory innovation.
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PMRD: plant microRNA database
Zhenhai Zhang,Jingyin Yu,Daofeng Li,Zuyong Zhang,Fengxia Liu,Xin Zhou,Tao Wang,Yi Ling,Zhen Su +8 more
TL;DR: The plant miRNA database (PMRD) integrates available plant miRNAs data deposited in public databases, gleaned from the recent literature, and data generated in-house, and contains sequence information, secondary structure, target genes, expression profiles and a genome browser.
Journal ArticleDOI
The Human Epigenome Browser at Washington University
Xin Zhou,Brett B Maricque,Mingchao Xie,Daofeng Li,Vasavi Sundaram,Eric A Martin,Brian C. Koebbe,Cydney B. Nielsen,Martin Hirst,Peggy J. Farnham,Robert M. Kuhn,Jingchun Zhu,Ivan Smirnov,W. James Kent,David Haussler,David Haussler,Pamela A. F. Madden,Joseph F. Costello,Ting Wang +18 more
TL;DR: The Human Epigenome Browser is web-based, and it extends the seminal concept introduced by the University of California Santa Cruz Cancer Genomics Browser to support large, sequencing-based datasets.