N
Neil D. Clarke
Researcher at Genome Institute of Singapore
Publications - 59
Citations - 9003
Neil D. Clarke is an academic researcher from Genome Institute of Singapore. The author has contributed to research in topics: Transcription factor & Binding site. The author has an hindex of 34, co-authored 58 publications receiving 8575 citations. Previous affiliations of Neil D. Clarke include Johns Hopkins University & National University of Singapore.
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Journal ArticleDOI
Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells
Xi Chen,Han Xu,Ping Yuan,Fang Fang,Fang Fang,Mikael Huss,Vinsensius B. Vega,Eleanor Wong,Yuriy L. Orlov,Weiwei Zhang,Weiwei Zhang,Jianming Jiang,Jianming Jiang,Yuin-Han Loh,Yuin-Han Loh,Hock Chuan Yeo,Zhen Xuan Yeo,Vipin Narang,Kunde R Govindarajan,Bernard Leong,Atif Shahab,Yijun Ruan,Guillaume Bourque,Wing-Kin Sung,Neil D. Clarke,Chia-Lin Wei,Huck-Hui Ng,Huck-Hui Ng +27 more
TL;DR: This study uses chromatin immunoprecipitation coupled with ultra-high-throughput DNA sequencing to map the locations of TF-binding sites and identifies important features of the transcriptional regulatory networks that define ES-cell identity.
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Resolution of Cell Fate Decisions Revealed by Single-Cell Gene Expression Analysis from Zygote to Blastocyst
Guoji Guo,Mikael Huss,Guo Qing Tong,Chaoyang Wang,Li Li Sun,Neil D. Clarke,Paul Robson,Paul Robson +7 more
TL;DR: It is shown that in the morula, blastomeres coexpress transcription factors specific to different lineages, but by the 64-cell stage three cell types can be clearly distinguished according to their quantitative expression profiles.
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Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity
Lingyun Song,Zhancheng Zhang,Linda L. Grasfeder,Alan P. Boyle,Paul G. Giresi,Bum Kyu Lee,Nathan C. Sheffield,Stefan Gräf,Mikael Huss,Damian Keefe,Zheng Liu,Darin London,Ryan M. McDaniell,Yoichiro Shibata,Kimberly A. Showers,Jeremy M. Simon,Teresa Vales,Tianyuan Wang,Deborah R. Winter,Zhuzhu Zhang,Neil D. Clarke,Ewan Birney,Vishwanath R. Iyer,Gregory E. Crawford,Jason D. Lieb,Terrence S. Furey +25 more
TL;DR: Gene expression and RNA Pol II binding data support the hypothesis that COREs control gene activity required for the maintenance of cell-type identity, and it is shown that open chromatin regions bound by CTCF are potent insulators.
Journal ArticleDOI
A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters.
Gwenael Badis,Esther T. Chan,Harm van Bakel,Lourdes Peña-Castillo,Desiree Tillo,Kyle Tsui,Clayton D. Carlson,Andrea J. Gossett,Michael J. Hasinoff,Christopher L. Warren,Marinella Gebbia,Shaheynoor Talukder,Ally Yang,Sanie Mnaimneh,Dimitri Terterov,David Coburn,Ai Li Yeo,Zhen Xuan Yeo,Neil D. Clarke,Jason D. Lieb,Aseem Z. Ansari,Corey Nislow,Timothy P. Hughes +22 more
TL;DR: Systematic determination of yeast transcription factor DNA-binding specificities shows that Rsc3 plays a broad role in targeting nucleosome exclusion at yeast promoters, suggesting a role in promoter architecture.
Journal ArticleDOI
Towards a Rigorous Assessment of Systems Biology Models: The DREAM3 Challenges
Robert J. Prill,Daniel Marbach,Julio Saez-Rodriguez,Julio Saez-Rodriguez,Peter K. Sorger,Peter K. Sorger,Leonidas G. Alexopoulos,Xiaowei Xue,Neil D. Clarke,Grégoire Altan-Bonnet,Gustavo Stolovitzky +10 more
TL;DR: Ass assessments of the four challenges associated with the third DREAM conference, which came to be known as the DREAM3 challenges, show that combining the predictions of multiple teams can in some cases improve predictive power beyond that of any single method.