Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer’s disease

2014 Alzheimer's disease facts and figures

(2014)   Alzheimers & Dementia

An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex

(2014) Y. Zhang et al.   JOURNAL OF NEUROSCIENCE

Principles of regulatory information conservation between mouse and human

(2014) Yong Cheng et al.   NATURE

Mutant Huntingtin promotes autonomous microglia activation via myeloid lineage-determining factors

(2014) Andrea Crotti et al.   NATURE NEUROSCIENCE

Microglia and brain macrophages in the molecular age: from origin to neuropsychiatric disease

(2014) Marco Prinz et al.   NATURE REVIEWS NEUROSCIENCE

Isolation of glia from Alzheimer's mice reveals inflammation and dysfunction

(2014) Marie Orre et al.   NEUROBIOLOGY OF AGING

Polarization of the Effects of Autoimmune and Neurodegenerative Risk Alleles in Leukocytes

(2014) T. Raj et al.   SCIENCE

Innate Immune Activity Conditions the Effect of Regulatory Variants upon Monocyte Gene Expression

(2014) B. P. Fairfax et al.   SCIENCE

A High-Resolution Enhancer Atlas of the Developing Telencephalon

(2013) Axel Visel et al.   CELL

Integrated Systems Approach Identifies Genetic Nodes and Networks in Late-Onset Alzheimer’s Disease

(2013) Bin Zhang et al.   CELL

Dynamic Analysis of Gene Expression and Genome-wide Transcription Factor Binding during Lineage Specification of Multipotent Progenitors

(2013) Gillian May et al.   Cell Stem Cell

Regulation of Microglial Proliferation during Chronic Neurodegeneration

(2013) D. Gomez-Nicola et al.   JOURNAL OF NEUROSCIENCE

Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease

(2013) Jean-Charles Lambert et al.   NATURE GENETICS

Identification of a unique TGF-β–dependent molecular and functional signature in microglia

(2013) Oleg Butovsky et al.   NATURE NEUROSCIENCE

The microglial sensome revealed by direct RNA sequencing

(2013) Suzanne E Hickman et al.   NATURE NEUROSCIENCE

Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

(2013) Simon Anders et al.   Nature Protocols

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments

(2013) P. Kheradpour et al.   NUCLEIC ACIDS RESEARCH

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

The SH2-domain-containing inositol 5-phosphatase (SHIP) limits the motility of neutrophils and their recruitment to wounds in zebrafish

(2012) P.-y. Lam et al.   JOURNAL OF CELL SCIENCE

Cognitive reserve in ageing and Alzheimer's disease

(2012) Yaakov Stern   LANCET NEUROLOGY

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Integrative annotation of chromatin elements from ENCODE data

(2012) Michael M. Hoffman et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Microarray analyses of laser-captured hippocampus reveal distinct gray and white matter signatures associated with incipient Alzheimer's disease

(2011) Eric M. Blalock et al.   JOURNAL OF CHEMICAL NEUROANATOMY

FACS purification of immunolabeled cell types from adult rat brain

(2011) Danielle Guez-Barber et al.   JOURNAL OF NEUROSCIENCE METHODS

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants

(2011) L. D. Ward et al.   NUCLEIC ACIDS RESEARCH

Mechanisms of specificity in neuronal activity-regulated gene transcription

(2011) Michelle R. Lyons et al.   PROGRESS IN NEUROBIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Deletion of CD14 Attenuates Alzheimer's Disease Pathology by Influencing the Brain's Inflammatory Milieu

(2010) E. G. Reed-Geaghan et al.   JOURNAL OF NEUROSCIENCE

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

(2008) A. J. Vilella et al.   GENOME RESEARCH

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY