R
R. David Hawkins
Researcher at University of Washington
Publications - 61
Citations - 25698
R. David Hawkins is an academic researcher from University of Washington. The author has contributed to research in topics: Epigenomics & DNA methylation. The author has an hindex of 32, co-authored 57 publications receiving 22872 citations. Previous affiliations of R. David Hawkins include Ludwig Institute for Cancer Research & Åbo Akademi University.
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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.
Journal ArticleDOI
Human DNA methylomes at base resolution show widespread epigenomic differences
Ryan Lister,Mattia Pelizzola,Robert H. Dowen,R. David Hawkins,Gary C. Hon,Julian Tonti-Filippini,Joseph R. Nery,Leonard Lee,Zhen Ye,Que Minh Ngo,Lee Edsall,Jessica Antosiewicz-Bourget,Jessica Antosiewicz-Bourget,Ron Stewart,Ron Stewart,Victor Ruotti,Victor Ruotti,A. Harvey Millar,James A. Thomson,Bing Ren,Bing Ren,Joseph R. Ecker +21 more
TL;DR: The first genome-wide, single-base-resolution maps of methylated cytosines in a mammalian genome, from both human embryonic stem cells and fetal fibroblasts, along with comparative analysis of messenger RNA and small RNA components of the transcriptome, several histone modifications, and sites of DNA-protein interaction for several key regulatory factors were presented in this article.
Journal ArticleDOI
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome.
Nathaniel D. Heintzman,Rhona K. Stuart,Gary C. Hon,Yutao Fu,Christina W. Ching,R. David Hawkins,Leah O. Barrera,Sara Van Calcar,Chunxu Qu,Keith A. Ching,Wei Wang,Zhiping Weng,Roland Green,Gregory E. Crawford,Bing Ren +14 more
TL;DR: Insight is given into the connections between chromatin modifications and transcriptional regulatory activity and a novel functional enhancer for the carnitine transporter SLC22A5 (OCTN2) is uncovered, providing a new tool for the functional annotation of the human genome.
Journal ArticleDOI
Histone modifications at human enhancers reflect global cell-type-specific gene expression
Nathaniel D. Heintzman,Gary C. Hon,R. David Hawkins,Pouya Kheradpour,Alexander Stark,Alexander Stark,Lindsey F. Harp,Zhen Ye,Leonard K. Lee,Rhona K. Stuart,Christina W. Ching,Keith A. Ching,Jessica Antosiewicz-Bourget,Hui Liu,Xinmin Zhang,Roland D. Green,Victor V. Lobanenkov,Ron Stewart,James A. Thomson,James A. Thomson,Gregory E. Crawford,Manolis Kellis,Manolis Kellis,Bing Ren +23 more
TL;DR: The results define over 55,000 potential transcriptional enhancers in the human genome, significantly expanding the current catalogue of human enhancers and highlighting the role of these elements in cell-type-specific gene expression.
Journal Article
Histone Modifications at Human Enhancers Reflect Global Cell-Type-Specific Gene Expression
Nathaniel D. Heintzman,Gary C. Hon,R. David Hawkins,Pouya Kheradpour,Alexander Stark,Lindsey F. Harp,Zhen Ye,Leonard K. Lee,Rhona K. Stuart,Christina W. Ching,Keith A. Ching,Jessica Antosiewicz-Bourget,Hui Liu,Xinmin Zhang,Roland D. Green,Victor V. Lobanenkov,Ron Stewart,James A. Thomson,Gregory E. Crawford,Manolis Kellis,Bing Ren +20 more
TL;DR: In this article, a chromatin-immunoprecipitation-based microarray method (ChIP-chip) was used to locate promoters, enhancers and insulators in the human genome and investigate their roles in cell-type specific gene expression.