A High-Resolution Enhancer Atlas of the Developing Telencephalon
Axel Visel,Axel Visel,Leila Taher,Hani Z. Girgis,Dalit May,Olga Golonzhka,Renée V. Hoch,Gabriel L. McKinsey,Kartik Pattabiraman,Shanni N. Silberberg,Matthew J. Blow,David V. Hansen,Alexander Nord,Jennifer A. Akiyama,Amy Holt,Roya Hosseini,Sengthavy Phouanenavong,Ingrid Plajzer-Frick,Malak Shoukry,Veena Afzal,Tommy Kaplan,Tommy Kaplan,Arnold R. Kriegstein,Edward M. Rubin,Edward M. Rubin,Ivan Ovcharenko,Len A. Pennacchio,Len A. Pennacchio,John L.R. Rubenstein +28 more
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TLDR
A digital atlas of in vivo enhancers active in subregions of the developing telencephalon, identifying more than 4,600 candidate embryonic forebrain enhancers and studying the in vivo activity of 329 of these sequences in transgenic mouse embryos is described.About:
This article is published in Cell.The article was published on 2013-02-14 and is currently open access. It has received 249 citations till now. The article focuses on the topics: Forebrain & Enhancer.read more
Citations
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Transcriptional enhancers: from properties to genome-wide predictions.
TL;DR: How properties of enhancer sequences and chromatin are used to predict enhancers in genome-wide studies are discussed and recently developed high-throughput methods that allow the direct testing and identification of enhancers on the basis of their activity are covered.
Journal ArticleDOI
Molecular logic of neocortical projection neuron specification, development and diversity
TL;DR: This work provides substantial insight into the 'molecular logic' underlying cortical development and increasingly supports a model in which individual progenitor-stage and postmitotic regulators are embedded within highly interconnected networks that gate sequential developmental decisions.
Journal ArticleDOI
Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain
Alisa Mo,Eran A. Mukamel,Eran A. Mukamel,Fred P. Davis,Chongyuan Luo,Gilbert L. Henry,Serge Picard,Mark A. Urich,Joseph R. Nery,Terrence J. Sejnowski,Terrence J. Sejnowski,Ryan Lister,Ryan Lister,Sean R. Eddy,Joseph R. Ecker,Jeremy Nathans +15 more
TL;DR: The first affinity purification approach to isolate nuclei from genetically defined cell types in a mammal is developed and this technique is combined with next-generation sequencing to show that three subtypes of neocortical neurons have highly distinctive epigenomic landscapes.
Journal ArticleDOI
The evolution of distributed association networks in the human brain.
TL;DR: A hypothesis about how association networks evolved their prominence and came to possess circuit properties vital to human cognition is offered, as well as its broad implications for understanding critical features of the human brain as a byproduct of size scaling.
Journal ArticleDOI
Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer’s disease
Elizabeta Gjoneska,Andreas R. Pfenning,Hansruedi Mathys,Gerald Quon,Anshul Kundaje,Li-Huei Tsai,Li-Huei Tsai,Manolis Kellis +7 more
TL;DR: This work profiles transcriptional and chromatin state dynamics across early and late pathology in the hippocampus of an inducible mouse model of AD-like neurodegeneration and establishes the mouse as a useful model for functional studies of AD regulatory regions.
References
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Random Forests
TL;DR: Internal estimates monitor error, strength, and correlation and these are used to show the response to increasing the number of features used in the forest, and are also applicable to regression.
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A Map of Human Genome Variation From Population-Scale Sequencing
Gonçalo R. Abecasis,David Altshuler,David Altshuler,Adam Auton,Lisa D Brooks,Richard Durbin,Richard A. Gibbs,Matthew E. Hurles,Gil McVean +8 more
TL;DR: The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype as mentioned in this paper, and the results of the pilot phase of the project, designed to develop and compare different strategies for genomewide sequencing with high-throughput platforms.
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