J
John W. Whitaker
Researcher at University of California, San Diego
Publications - 32
Citations - 7810
John W. Whitaker is an academic researcher from University of California, San Diego. The author has contributed to research in topics: DNA methylation & Epigenetics. The author has an hindex of 20, co-authored 29 publications receiving 6584 citations. Previous affiliations of John W. Whitaker include Johnson & Johnson & University of Leeds.
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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
Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells
Wei Xie,Matthew D. Schultz,Ryan Lister,Zhonggang Hou,Nisha Rajagopal,Pradipta R. Ray,John W. Whitaker,Shulan Tian,R. David Hawkins,Danny Leung,Hongbo Yang,Tao Wang,Ah Young Lee,Scott Swanson,Jiuchun Zhang,Jiuchun Zhang,Yun Zhu,Audrey Kim,Joseph R. Nery,Mark A. Urich,Samantha Kuan,Chia-An Yen,Sarit Klugman,Pengzhi Yu,Kran Suknuntha,Nicholas E. Propson,Huaming Chen,Lee Edsall,Ulrich Wagner,Yan Li,Zhen Ye,Ashwinikumar Kulkarni,Zhenyu Xuan,Wen Yu Chung,Neil C. Chi,Jessica Antosiewicz-Bourget,Igor I. Slukvin,Ron Stewart,Michael Q. Zhang,Michael Q. Zhang,Wei Wang,James A. Thomson,James A. Thomson,James A. Thomson,Joseph R. Ecker,Bing Ren,Bing Ren +46 more
TL;DR: It is found that promoters that are active in early developmental stages tend to be CG rich and mainly engage H3K27me3 upon silencing in nonexpressing lineages, while promoters for genes expressed preferentially at later stages are often CG poor and primarily employ DNA methylation upon repression.
Journal ArticleDOI
Human body epigenome maps reveal noncanonical DNA methylation variation
Matthew D. Schultz,Yupeng He,John W. Whitaker,Manoj Hariharan,Eran A. Mukamel,Danny Leung,Nisha Rajagopal,Joseph R. Nery,Mark A. Urich,Huaming Chen,Shin Lin,Yiing Lin,Inkyung Jung,Anthony D. Schmitt,Siddarth Selvaraj,Bing Ren,Terrence J. Sejnowski,Wei Wang,Joseph R. Ecker +18 more
TL;DR: High coverage methylomes are reported that catalogue cytosine methylation in all contexts for the major human organ systems, integrated with matched transcriptomes and genomic sequence.
Journal ArticleDOI
DNA methylome signature in rheumatoid arthritis
TL;DR: DNA methylation of critical genes suggests that RA FLS are imprinted and implicate epigenetic contributions to inflammatory arthritis.
Journal ArticleDOI
Predicting enhancer transcription and activity from chromatin modifications
TL;DR: A logistic regression model is developed that provides a powerful tool to identify active enhancers and reveal the relationship between chromatin modifications, eRNA production and enhancer activity.