Transformative Network Modeling of Multi-omics Data Reveals Detailed Circuits, Key Regulators, and Potential Therapeutics for Alzheimer’s Disease

Large-scale proteomic analysis of Alzheimer’s disease brain and cerebrospinal fluid reveals early changes in energy metabolism associated with microglia and astrocyte activation

(2020) Erik C. B. Johnson et al.   NATURE MEDICINE

Structure of V-ATPase from the mammalian brain

(2020) Yazan M. Abbas et al.   SCIENCE

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

(2019) Iris E. Jansen 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

Single-cell transcriptomic analysis of Alzheimer’s disease

(2019) Hansruedi Mathys et al.   NATURE

Covalent targeting of the vacuolar H+-ATPase activates autophagy via mTORC1 inhibition

(2019) Clive Yik-Sham Chung et al.   Nature Chemical Biology

Synergistic effects of common schizophrenia risk variants

(2019) Nadine Schrode et al.   NATURE GENETICS

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

(2019) Ruilin Tian et al.   NEURON

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

(2018) Mariet Allen et al.   Alzheimers & Dementia

2018 Alzheimer's disease facts and figures

(2018)   Alzheimers & Dementia

EMUDRA: Ensemble of Multiple Drug Repositioning Approaches to improve prediction accuracy

(2018) Xianxiao Zhou et al.   BIOINFORMATICS

De novo mutations of the ATP6V1A gene cause developmental encephalopathy with epilepsy

(2018) Anna Fassio et al.   BRAIN

Disease-Associated Microglia: A Universal Immune Sensor of Neurodegeneration

(2018) Aleksandra Deczkowska et al.   CELL

GABAA receptor subunit expression changes in the human Alzheimer's disease hippocampus, subiculum, entorhinal cortex and superior temporal gyrus

(2018) Andrea Kwakowsky et al.   JOURNAL OF NEUROCHEMISTRY

The V-ATPase V1 subunit A1 is required for rhodopsin anterograde trafficking in Drosophila

(2018) Haifang Zhao et al.   MOLECULAR BIOLOGY OF THE CELL

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

Randomized Trial of Verubecestat for Mild-to-Moderate Alzheimer’s Disease

(2018) Michael F. Egan et al.   NEW ENGLAND JOURNAL OF MEDICINE

Trial of Solanezumab for Mild Dementia Due to Alzheimer’s Disease

(2018) Lawrence S. Honig et al.   NEW ENGLAND JOURNAL OF MEDICINE

Brain Cell Type Specific Gene Expression and Co-expression Network Architectures

(2018) Andrew T. McKenzie et al.   Scientific Reports

Combining NGN2 Programming with Developmental Patterning Generates Human Excitatory Neurons with NMDAR-Mediated Synaptic Transmission

(2018) Ralda Nehme et al.   Cell Reports

GWAS on family history of Alzheimer’s disease

(2018) Riccardo E. Marioni et al.   Translational Psychiatry

The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations

(2018) Alexandra B. Keenan et al.   Cell Systems

Global quantitative analysis of the human brain proteome in Alzheimer’s and Parkinson’s Disease

(2018) Lingyan Ping et al.   Scientific Data

Aging in a Dish: iPSC-Derived and Directly Induced Neurons for Studying Brain Aging and Age-Related Neurodegenerative Diseases

(2018) Jerome Mertens et al.   Annual Review of Genetics

The Mount Sinai cohort of large-scale genomic, transcriptomic and proteomic data in Alzheimer's disease

(2018) Minghui Wang et al.   Scientific Data

A multi-omic atlas of the human frontal cortex for aging and Alzheimer’s disease research

(2018) Philip L. De Jager et al.   Scientific Data

Childhood-Onset Schizophrenia: Insights from Induced Pluripotent Stem Cells

(2018) Anke Hoffmann et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Integrative approach to sporadic Alzheimer’s disease: deficiency of TYROBP in cerebral Aβ amyloidosis mouse normalizes clinical phenotype and complement subnetwork molecular pathology without reducing Aβ burden

(2018) Jean-Vianney Haure-Mirande et al.   MOLECULAR PSYCHIATRY

Drug repurposing: progress, challenges and recommendations

(2018) Sudeep Pushpakom et al.   NATURE REVIEWS DRUG DISCOVERY

An xQTL map integrates the genetic architecture of the human brain's transcriptome and epigenome

(2017) Bernard Ng et al.   NATURE NEUROSCIENCE

Evaluating Synthetic Activation and Repression of Neuropsychiatric-Related Genes in hiPSC-Derived NPCs, Neurons, and Astrocytes

(2017) Seok-Man Ho et al.   Stem Cell Reports

Alzheimer's Disease and the Amyloid-β Peptide

(2017) M. Paul Murphy et al.   JOURNAL OF ALZHEIMERS DISEASE

variancePartition: interpreting drivers of variation in complex gene expression studies

(2016) Gabriel E. Hoffman et al.   BMC BIOINFORMATICS

Identification of CD112R as a novel checkpoint for human T cells

(2016) Yuwen Zhu et al.   JOURNAL OF EXPERIMENTAL MEDICINE

FK506, an Immunosuppressive Drug, Induces Autophagy by Binding to the V-ATPase Catalytic Subunit A in Neuronal Cells

(2016) Dongyoung Kim et al.   JOURNAL OF PROTEOME RESEARCH

Rapid Ngn2-induction of excitatory neurons from hiPSC-derived neural progenitor cells

(2016) Seok-Man Ho et al.   METHODS

Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets

(2016) Zhihong Zhu et al.   NATURE GENETICS

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

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

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

(2016) B. B. Lake et al.   SCIENCE

EPRS is a critical regulator of cell proliferation and estrogen signaling in ER+ breast cancer

(2016) Igor Katsyv et al.   Oncotarget

Integrative network analysis of nineteen brain regions identifies molecular signatures and networks underlying selective regional vulnerability to Alzheimer’s disease

(2016) Minghui Wang et al.   Genome Medicine

Stabilization of Microtubule-Unbound Tau via Tau Phosphorylation at Ser262/356 by Par-1/MARK Contributes to Augmentation of AD-Related Phosphorylation and Aβ42-Induced Tau Toxicity

(2016) Kanae Ando et al.   PLoS Genetics

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

(2016) Mariet Allen et al.   Scientific Data

CRISPR-ERA: a comprehensive design tool for CRISPR-mediated gene editing, repression and activation: Fig. 1.

(2015) Honglei Liu et al.   BIOINFORMATICS

Leveraging existing data sets to generate new insights into Alzheimer’s disease biology in specific patient subsets

(2015) Kevin D. Fowler et al.   Scientific Reports

Efficient Test and Visualization of Multi-Set Intersections

(2015) Minghui Wang et al.   Scientific Reports

Multiscale Embedded Gene Co-expression Network Analysis

(2015) Won-Min Song et al.   PLoS Computational Biology

Genome-wide eQTLs and heritability for gene expression traits in unrelated individuals

(2014) Shengjie Yang et al.   BMC GENOMICS

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation

(2014) Luke A. Gilbert et al.   CELL

RNA-Seq Data Mining: Downregulation of NeuroD6 Serves as a Possible Biomarker for Alzheimer’s Disease Brains

(2014) Jun-ichi Satoh et al.   DISEASE MARKERS

Transcriptional landscape of the prenatal human brain

(2014) Jeremy A. Miller et al.   NATURE

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

A Systems Biology Framework Identifies Molecular Underpinnings of Coronary Heart Disease

(2013) Tianxiao Huan et al.   ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Digital sorting of complex tissues for cell type-specific gene expression profiles

(2013) Yi Zhong et al.   BMC BIOINFORMATICS

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

(2013) Bin Zhang et al.   CELL

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

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

Rapid Single-Step Induction of Functional Neurons from Human Pluripotent Stem Cells

(2013) Yingsha Zhang et al.   NEURON

Alzheimer’s Disease: Analyzing the Missing Heritability

(2013) Perry G. Ridge et al.   PLoS One

Genes and pathways underlying regional and cell type changes in Alzheimer's disease

(2013) Jeremy A Miller et al.   Genome Medicine

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

(2012) A. A. Shabalin   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Structure, Function, and Modulation of GABAAReceptors

(2012) Erwin Sigel et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Loss of functional GABAA receptors in the Alzheimer diseased brain

(2012) A. Limon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

mTORC1 Senses Lysosomal Amino Acids Through an Inside-Out Mechanism That Requires the Vacuolar H+-ATPase

(2011) R. Zoncu et al.   SCIENCE

Is My Network Module Preserved and Reproducible?

(2011) Peter Langfelder et al.   PLoS Computational Biology

Gene expression reveals overlap between normal aging and Alzheimer's disease genes

(2010) Dimitrios Avramopoulos et al.   NEUROBIOLOGY OF AGING

Genetic Control of Human Brain Transcript Expression in Alzheimer Disease

(2009) Jennifer A. Webster et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

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

Disentangling molecular relationships with a causal inference test

(2009) Joshua Millstein et al.   BMC GENETICS

Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks

(2008) Jun Zhu et al.   NATURE GENETICS

Altered neuronal gene expression in brain regions differentially affected by Alzheimer's disease: a reference data set

(2008) Winnie S. Liang et al.   PHYSIOLOGICAL GENOMICS

Transcriptional vulnerability of brain regions in Alzheimer's disease and dementia

(2007) Vahram Haroutunian et al.   NEUROBIOLOGY OF AGING