Single-nucleus chromatin accessibility and transcriptomic characterization of Alzheimer’s disease

Molecular characterization of selectively vulnerable neurons in Alzheimer’s disease

(2021) Kun Leng et al.   NATURE NEUROSCIENCE

ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis

(2021) Jeffrey M. Granja et al.   NATURE GENETICS

Human and mouse single-nucleus transcriptomics reveal TREM2-dependent and TREM2-independent cellular responses in Alzheimer’s disease

(2020) Yingyue Zhou et al.   NATURE MEDICINE

CTCF mediates chromatin looping via N-terminal domain-dependent cohesin retention

(2020) Elena M. Pugacheva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Disease-associated astrocytes in Alzheimer’s disease and aging

(2020) Naomi Habib et al.   NATURE NEUROSCIENCE

Identification of Conserved Proteomic Networks in Neurodegenerative Dementia

(2020) Vivek Swarup et al.   Cell Reports

Integrative genomics approach identifies conserved transcriptomic networks in Alzheimer’s disease

(2020) Samuel Morabito et al.   HUMAN MOLECULAR GENETICS

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

Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer’s disease risk

(2019) Iris E. Jansen et al.   NATURE GENETICS

Interrogation of human hematopoiesis at single-cell and single-variant resolution

(2019) Jacob C. Ulirsch et al.   NATURE GENETICS

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

Spatial and temporal heterogeneity of mouse and human microglia at single-cell resolution

(2019) Takahiro Masuda et al.   NATURE

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Altered human oligodendrocyte heterogeneity in multiple sclerosis

(2019) Sarah Jäkel et al.   NATURE

Single-cell transcriptomic analysis of Alzheimer’s disease

(2019) Hansruedi Mathys et al.   NATURE

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity

(2019) Joshua D. Welch et al.   CELL

Conserved cell types with divergent features in human versus mouse cortex

(2019) Rebecca D. Hodge et al.   NATURE

A single-nuclei RNA sequencing study of Mendelian and sporadic AD in the human brain

(2019) Jorge L. Del-Aguila et al.   Alzheimers Research & Therapy

A single-cell atlas of entorhinal cortex from individuals with Alzheimer’s disease reveals cell-type-specific gene expression regulation

(2019) Alexandra Grubman et al.   NATURE NEUROSCIENCE

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

(2019) Alexi Nott et al.   SCIENCE

Conserved brain myelination networks are altered in Alzheimer's and other neurodegenerative diseases

(2018) Mariet Allen et al.   Alzheimers & Dementia

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection

(2018) Antonio F. Pardiñas et al.   NATURE GENETICS

Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types

(2018) Hilary K. Finucane et al.   NATURE GENETICS

A molecular network of the aging human brain provides insights into the pathology and cognitive decline of Alzheimer’s disease

(2018) Sara Mostafavi et al.   NATURE NEUROSCIENCE

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

(2018) Darren A. Cusanovich et al.   CELL

Molecular Architecture of the Mouse Nervous System

(2018) Amit Zeisel et al.   CELL

Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data

(2018) Hannah A. Pliner et al.   MOLECULAR CELL

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

Aβ inhibits SREBP-2 activation through Akt inhibition

(2017) Amany Mohamed et al.   JOURNAL OF LIPID RESEARCH

Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain

(2017) Blue B Lake et al.   NATURE BIOTECHNOLOGY

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

(2017) Alicia N Schep et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

SREBP-regulated lipid metabolism: convergent physiology — divergent pathophysiology

(2017) Hitoshi Shimano et al.   Nature Reviews Endocrinology

Detecting Activated Cell Populations Using Single-Cell RNA-Seq

(2017) Ye Emily Wu et al.   NEURON

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

Novel genetic loci associated with hippocampal volume

(2017) Derrek P. Hibar et al.   Nature Communications

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Adult mouse cortical cell taxonomy revealed by single cell transcriptomics

(2016) Bosiljka Tasic et al.   NATURE NEUROSCIENCE

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system

(2016) S. Marques et al.   SCIENCE

Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain

(2016) B. B. Lake et al.   SCIENCE

Novel multiple sclerosis susceptibility loci implicated in epigenetic regulation

(2016) T. F. M. Andlauer et al.   Science Advances

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations

(2015) Jimmy Z Liu et al.   NATURE GENETICS

Frontotemporal dementia and its subtypes: a genome-wide association study

(2014) Raffaele Ferrari et al.   LANCET NEUROLOGY

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Defining the role of common variation in the genomic and biological architecture of adult human height

(2014) Andrew R Wood et al.   NATURE GENETICS

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

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

(2013) Bin Zhang et al.   CELL

Discovery and refinement of loci associated with lipid levels

(2013) Cristen J Willer et al.   NATURE GENETICS

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

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

Common variants at ABCA7, MS4A6A/MS4A4E, EPHA1, CD33 and CD2AP are associated with Alzheimer's disease

(2011) Paul Hollingworth et al.   NATURE GENETICS

A flexible R package for nonnegative matrix factorization

(2010) Renaud Gaujoux et al.   BMC BIOINFORMATICS

Genetic variation in PCDH11X is associated with susceptibility to late-onset Alzheimer's disease

(2009) Minerva M Carrasquillo et al.   NATURE GENETICS

Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimer's disease

(2009) Denise Harold et al.   NATURE GENETICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS