Functional regulatory variants implicate distinct transcriptional networks in dementia

A human brain vascular atlas reveals diverse mediators of Alzheimer’s risk

(2022) Andrew C. Yang et al.   NATURE

Genetic analysis of the human microglial transcriptome across brain regions, aging and disease pathologies

(2022) Katia de Paiva Lopes et al.   NATURE GENETICS

17q21.31 sub-haplotypes underlying H1-associated risk for Parkinson’s disease are associated with LRRC37A/2 expression in astrocytes

(2022) Kathryn R. Bowles et al.   Molecular Neurodegeneration

A CRISPRi/a platform in human iPSC-derived microglia uncovers regulators of disease states

(2022) Nina M. Dräger et al.   NATURE NEUROSCIENCE

Long-term maturation of human cortical organoids matches key early postnatal transitions

(2021) Aaron Gordon et al.   NATURE NEUROSCIENCE

Integration of Alzheimer’s disease genetics and myeloid genomics identifies disease risk regulatory elements and genes

(2021) Gloriia Novikova et al.   Nature Communications

Modular, efficient and constant-memory single-cell RNA-seq preprocessing

(2021) Páll Melsted et al.   NATURE BIOTECHNOLOGY

The multiplex model of the genetics of Alzheimer’s disease

(2020) Rebecca Sims et al.   NATURE NEUROSCIENCE

Identification of Conserved Proteomic Networks in Neurodegenerative Dementia

(2020) Vivek Swarup et al.   Cell Reports

Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer’s and Parkinson’s diseases

(2020) M. Ryan Corces et al.   NATURE GENETICS

Genetic architecture of Alzheimer's disease

(2020) Sarah M. Neuner et al.   NEUROBIOLOGY OF DISEASE

The GTEx Consortium atlas of genetic regulatory effects across human tissues

(2020)   SCIENCE

Biological relevance of computationally predicted pathogenicity of noncoding variants

(2019) Li Liu et al.   Nature Communications

Genetic meta-analysis of diagnosed Alzheimer’s disease identifies new risk loci and implicates Aβ, tau, immunity and lipid processing

(2019) Brian W. Kunkle et al.   NATURE GENETICS

A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens

(2019) Molly Gasperini et al.   CELL

gpart: human genome partitioning and visualization of high-density SNP data by identifying haplotype blocks

(2019) Sun Ah Kim et al.   BIOINFORMATICS

Non-coding variability at the APOE locus contributes to the Alzheimer’s risk

(2019) Xiaopu Zhou et al.   Nature Communications

CRISPR Interference-Based Platform for Multimodal Genetic Screens in Human iPSC-Derived Neurons

(2019) Ruilin Tian et al.   NEURON

Dystrophin deficiency leads to dysfunctional glutamate clearance in iPSC derived astrocytes

(2019) Abdulsamie M. Patel et al.   Translational Psychiatry

Emerging Roles of Complement in Psychiatric Disorders

(2019) Mélanie Druart et al.   Frontiers in Psychiatry

Brain cell type–specific enhancer–promoter interactome maps and disease-risk association

(2019) Alexi Nott et al.   SCIENCE

Common Disease Is More Complex Than Implied by the Core Gene Omnigenic Model

(2018) Naomi R. Wray et al.   CELL

From genome-wide associations to candidate causal variants by statistical fine-mapping

(2018) Daniel J. Schaid et al.   NATURE REVIEWS GENETICS

Joint genome-wide association study of progressive supranuclear palsy identifies novel susceptibility loci and genetic correlation to neurodegenerative diseases

(2018) Jason A. Chen et al.   Molecular Neurodegeneration

Identification of evolutionarily conserved gene networks mediating neurodegenerative dementia

(2018) Vivek Swarup et al.   NATURE MEDICINE

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Comprehensive functional genomic resource and integrative model for the human brain

(2018) Daifeng Wang et al.   SCIENCE

Optimized libraries for CRISPR-Cas9 genetic screens with multiple modalities

(2018) Kendall R. Sanson et al.   Nature Communications

Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data

(2017) Yi-Fei Huang et al.   NATURE GENETICS

Pooled CRISPR screening with single-cell transcriptome readout

(2017) Paul Datlinger et al.   NATURE METHODS

Settling the score: variant prioritization and Mendelian disease

(2017) Karen Eilbeck et al.   NATURE REVIEWS GENETICS

Clinical Neurology and Epidemiology of the Major Neurodegenerative Diseases

(2017) Michael G. Erkkinen et al.   Cold Spring Harbor Perspectives in Biology

A Highly Efficient Human Pluripotent Stem Cell Microglia Model Displays a Neuronal-Co-culture-Specific Expression Profile and Inflammatory Response

(2017) Walther Haenseler et al.   Stem Cell Reports

BBMerge – Accurate paired shotgun read merging via overlap

(2017) Brian Bushnell et al.   PLoS One

Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits

(2016) Jacob C. Ulirsch et al.   CELL

Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay

(2016) Ryan Tewhey et al.   CELL

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9

(2016) John G Doench et al.   NATURE BIOTECHNOLOGY

SNP2TFBS – a database of regulatory SNPs affecting predicted transcription factor binding site affinity

(2016) Sunil Kumar et al.   NUCLEIC ACIDS RESEARCH

Human whole genome genotype and transcriptome data for Alzheimer’s and other neurodegenerative diseases

(2016) Mariet Allen et al.   Scientific Data

motifbreakR: an R/Bioconductor package for predicting variant effects at transcription factor binding sites: Fig. 1.

(2015) Simon G. Coetzee et al.   BIOINFORMATICS

PLEKHM1 Regulates Autophagosome-Lysosome Fusion through HOPS Complex and LC3/GABARAP Proteins

(2015) David G. McEwan et al.   MOLECULAR CELL

Regulation of human MAPT gene expression

(2015) Marie-Laure Caillet-Boudin et al.   Molecular Neurodegeneration

Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo

(2015) Matthew T Maurano et al.   NATURE GENETICS

Partitioning heritability by functional annotation using genome-wide association summary statistics

(2015) Hilary K Finucane et al.   NATURE GENETICS

ENCODE data at the ENCODE portal

(2015) Cricket A. Sloan et al.   NUCLEIC ACIDS RESEARCH

A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

Functional annotation of noncoding sequence variants

(2014) Graham R S Ritchie et al.   NATURE METHODS

Massively Parallel Reporter Assays in Cultured Mammalian Cells

(2014) Alexandre Melnikov et al.   Jove-Journal of Visualized Experiments

Glial and Neuronal Tau Pathology in Tauopathies

(2013) Isidre Ferrer et al.   JOURNAL OF NEUROPATHOLOGY AND EXPERIMENTAL NEUROLOGY

Tau pathology and neurodegeneration

(2013) Maria Grazia Spillantini et al.   LANCET NEUROLOGY

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

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

Comprehensive Search for Alzheimer Disease Susceptibility Loci in the APOE Region

(2012) Gyungah Jun et al.   ARCHIVES OF NEUROLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Structural and functional characterization of H2 haplotype MAPT promoter: Unique neurospecific domains and a hypoxia-inducible element would enhance rationally targeted tauopathy research for Alzheimer's disease

(2012) Bryan Maloney et al.   GENE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Interpreting noncoding genetic variation in complex traits and human disease

(2012) Lucas D Ward et al.   NATURE BIOTECHNOLOGY

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

(2012) Alexandre Melnikov et al.   NATURE BIOTECHNOLOGY

Massively parallel functional dissection of mammalian enhancers in vivo

(2012) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Identification of common variants influencing risk of the tauopathy progressive supranuclear palsy

(2011) Günter U Höglinger et al.   NATURE GENETICS

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

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Sp1 Phosphorylation and Its Regulation of Gene Transcription

(2009) N. Y. Tan et al.   MOLECULAR AND CELLULAR BIOLOGY

Transcription factor Sp1 dysregulation in Alzheimer's disease

(2008) Bruce A. Citron et al.   JOURNAL OF NEUROSCIENCE RESEARCH

Blocking TGF-β–Smad2/3 innate immune signaling mitigates Alzheimer-like pathology

(2008) Terrence Town et al.   NATURE MEDICINE