Large-scale deep multi-layer analysis of Alzheimer’s disease brain reveals strong proteomic disease-related changes not observed at the RNA level

Restoring metabolism of myeloid cells reverses cognitive decline in ageing

(2021) Paras S. Minhas et al.   NATURE

Integrating human brain proteomes with genome-wide association data implicates new proteins in Alzheimer’s disease pathogenesis

(2021) Aliza P. Wingo et al.   NATURE GENETICS

Deep Multilayer Brain Proteomics Identifies Molecular Networks in Alzheimer’s Disease Progression

(2020) Bing Bai et al.   NEURON

MONET: a toolbox integrating top-performing methods for network modularization

(2020) Mattia Tomasoni et al.   BIOINFORMATICS

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

Targeted mass spectrometry to quantify brain-derived cerebrospinal fluid biomarkers in Alzheimer’s disease

(2020) Maotian Zhou et al.   Clinical Proteomics

Genetics of Gene Expression in the Aging Human Brain Reveal TDP-43 Proteinopathy Pathophysiology

(2020) Hyun-Sik Yang et al.   NEURON

Cortical Proteins Associated With Cognitive Resilience in Community-Dwelling Older Persons

(2020) Lei Yu et al.   JAMA Psychiatry

Phosphorylated tau interactome in the human Alzheimer’s disease brain

(2020) Eleanor Drummond et al.   BRAIN

Large eQTL meta-analysis reveals differing patterns between cerebral cortical and cerebellar brain regions

(2020) Solveig K. Sieberts et al.   Scientific Data

Global quantitative analysis of the human brain proteome and phosphoproteome in Alzheimer’s disease

(2020) Lingyan Ping et al.   Scientific Data

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

Elevated levels of Secreted-Frizzled-Related-Protein 1 contribute to Alzheimer’s disease pathogenesis

(2019) Pilar Esteve et al.   NATURE NEUROSCIENCE

Assessment of network module identification across complex diseases

(2019) Sarvenaz Choobdar et al.   NATURE METHODS

Resistance to autosomal dominant Alzheimer’s disease in an APOE3 Christchurch homozygote: a case report

(2019) Joseph F. Arboleda-Velasquez et al.   NATURE MEDICINE

Longitudinal brain atrophy distribution in advanced Parkinson's disease: What makes the difference in “cognitive status” converters?

(2019) Martin Gorges et al.   HUMAN BRAIN MAPPING

NIA-AA Research Framework: Toward a biological definition of Alzheimer's disease

(2018) Clifford R. Jack et al.   Alzheimers & Dementia

Person-specific contribution of neuropathologies to cognitive loss in old age

(2018) Patricia A. Boyle et al.   ANNALS OF NEUROLOGY

Religious Orders Study and Rush Memory and Aging Project

(2018) David A. Bennett et al.   JOURNAL OF ALZHEIMERS DISEASE

Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography–mass spectrometry

(2018) Philipp Mertins et al.   Nature Protocols

Cortical atrophy patterns in early Parkinson's disease patients using hierarchical cluster analysis

(2018) Carme Uribe et al.   PARKINSONISM & RELATED DISORDERS

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

(2018) Lingyan Ping et al.   Scientific Data

Proteomics analysis identifies new markers associated with capillary cerebral amyloid angiopathy in Alzheimer’s disease

(2018) David C. Hondius et al.   Acta Neuropathologica Communications

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

Deep proteomic network analysis of Alzheimer’s disease brain reveals alterations in RNA binding proteins and RNA splicing associated with disease

(2018) Erik C. B. Johnson et al.   Molecular Neurodegeneration

Integrating Next-Generation Genomic Sequencing and Mass Spectrometry To Estimate Allele-Specific Protein Abundance in Human Brain

(2017) Thomas S. Wingo et al.   JOURNAL OF PROTEOME RESEARCH

Multiscale network modeling of oligodendrocytes reveals molecular components of myelin dysregulation in Alzheimer’s disease

(2017) Andrew T. McKenzie et al.   Molecular Neurodegeneration

A Multi-network Approach Identifies Protein-Specific Co-expression in Asymptomatic and Symptomatic Alzheimer’s Disease

(2017) Nicholas T. Seyfried et al.   Cell Systems

Proteogenomics connects somatic mutations to signalling in breast cancer

(2016) Philipp Mertins et al.   NATURE

Next-generation genotype imputation service and methods

(2016) Sayantan Das et al.   NATURE GENETICS

Late-life depression is not associated with dementia-related pathology.

(2016) Robert S. Wilson et al.   NEUROPSYCHOLOGY

Alzheimer’s Disease Risk Genes and Mechanisms of Disease Pathogenesis

(2015) Celeste M. Karch et al.   BIOLOGICAL PSYCHIATRY

How Do Scores on the ADAS-Cog, MMSE, and CDR-SOB Correspond?

(2015) Steve Balsis et al.   CLINICAL NEUROPSYCHOLOGIST

Dickkopf-related protein 3 is a potential Aβ-associated protein in Alzheimer's Disease

(2015) Kim A. Bruggink et al.   JOURNAL OF NEUROCHEMISTRY

Cell type– and brain region–resolved mouse brain proteome

(2015) Kirti Sharma et al.   NATURE NEUROSCIENCE

Arizona Study of Aging and Neurodegenerative Disorders and Brain and Body Donation Program

(2015) Thomas G. Beach et al.   NEUROPATHOLOGY

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

MAGMA: Generalized Gene-Set Analysis of GWAS Data

(2015) Christiaan A. de Leeuw et al.   PLoS Computational Biology

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

Isobaric Labeling-Based Relative Quantification in Shotgun Proteomics

(2014) Navin Rauniyar et al.   JOURNAL OF PROTEOME RESEARCH

Proteogenomic characterization of human colon and rectal cancer

(2014) Bing Zhang et al.   NATURE

Overview and Findings from the Religious Orders Study

(2013) David A. Bennett et al.   Current Alzheimer Research

Overview and Findings from the Rush Memory and Aging Project

(2013) David A. Bennett et al.   Current Alzheimer Research

Removing technical variability in RNA-seq data using conditional quantile normalization

(2012) K. D. Hansen et al.   BIOSTATISTICS

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

National Institute on Aging–Alzheimer’s Association guidelines for the neuropathologic assessment of Alzheimer’s disease: a practical approach

(2011) Thomas J. Montine et al.   ACTA NEUROPATHOLOGICA

Stages of the Pathologic Process in Alzheimer Disease: Age Categories From 1 to 100 Years

(2011) Heiko Braak et al.   JOURNAL OF NEUROPATHOLOGY AND EXPERIMENTAL NEUROLOGY

The Matrisome:In SilicoDefinition andIn VivoCharacterization by Proteomics of Normal and Tumor Extracellular Matrices

(2011) Alexandra Naba et al.   MOLECULAR & CELLULAR PROTEOMICS

MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics

(2011) Lily Ting et al.   NATURE METHODS

SFRPs act as negative modulators of ADAM10 to regulate retinal neurogenesis

(2011) Pilar Esteve et al.   NATURE NEUROSCIENCE

Overview of the Matrisome--An Inventory of Extracellular Matrix Constituents and Functions

(2011) R. O. Hynes et al.   Cold Spring Harbor Perspectives in Biology

Is My Network Module Preserved and Reproducible?

(2011) Peter Langfelder et al.   PLoS Computational Biology

Peptide Labeling with Isobaric Tags Yields Higher Identification Rates Using iTRAQ 4-Plex Compared to TMT 6-Plex and iTRAQ 8-Plex on LTQ Orbitrap

(2010) Peter Pichler et al.   ANALYTICAL CHEMISTRY

Robust relationship inference in genome-wide association studies

(2010) Ani Manichaikul et al.   BIOINFORMATICS

Role of the N- and C-Terminal Domains in Binding of Apolipoprotein E Isoforms to Heparan Sulfate and Dermatan Sulfate: A Surface Plasmon Resonance Study†

(2008) Yuko Yamauchi et al.   BIOCHEMISTRY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Functional organization of the transcriptome in human brain

(2008) Michael C Oldham et al.   NATURE NEUROSCIENCE

Analysis of the structure of complex networks at different resolution levels

(2008) A Arenas et al.   NEW JOURNAL OF PHYSICS