Systematic review and meta-analysis of human transcriptomics reveals neuroinflammation, deficient energy metabolism, and proteostasis failure across neurodegeneration

An atlas of the protein-coding genes in the human, pig, and mouse brain

(2020) Evelina Sjöstedt et al.   SCIENCE

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

Meta-analysis of mouse transcriptomic studies supports a context-dependent astrocyte reaction in acute CNS injury versus neurodegeneration

(2020) Sudeshna Das et al.   Journal of Neuroinflammation

Meta-Analysis of the Alzheimer’s Disease Human Brain Transcriptome and Functional Dissection in Mouse Models

(2020) Ying-Wooi Wan et al.   Cell Reports

Astrocytes and microglia play orchestrated roles and respect phagocytic territories during neuronal corpse removal in vivo

(2020) Eyiyemisi C. Damisah et al.   Science Advances

Tau PTM Profiles Identify Patient Heterogeneity and Stages of Alzheimer’s Disease

(2020) Hendrik Wesseling et al.   CELL

Gene expression meta-analysis of Parkinson’s disease and its relationship with Alzheimer’s disease

(2019) Jack Kelly et al.   Molecular Brain

A Meta-Analysis of Alzheimer’s Disease Brain Transcriptomic Data

(2019) Hamel Patel et al.   JOURNAL OF ALZHEIMERS DISEASE

Single-cell transcriptomic analysis of Alzheimer’s disease

(2019) Hansruedi Mathys et al.   NATURE

Characterization of the 18 kDa translocator protein (TSPO) expression in post‐mortem normal and Alzheimer's disease brains

(2019) Yaxing Gui et al.   BRAIN PATHOLOGY

The landscape of multiscale transcriptomic networks and key regulators in Parkinson’s disease

(2019) Qian Wang et al.   Nature Communications

Integrated MRI and [11 C]-PBR28 PET Imaging in Amyotrophic Lateral sclerosis

(2018) Mohamad J. Alshikho et al.   ANNALS OF NEUROLOGY

Evidence for a Pan-Neurodegenerative Disease Response in Huntington's and Parkinson's Disease Expression Profiles

(2018) Adam Labadorf et al.   Frontiers in Molecular Neuroscience

Selective autophagy as a potential therapeutic target for neurodegenerative disorders

(2018) Aurora Scrivo et al.   LANCET NEUROLOGY

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

The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

Diagnosis and management of dementia with Lewy bodies

(2017) Ian G. McKeith et al.   NEUROLOGY

ATP as a biological hydrotrope

(2017) Avinash Patel et al.   SCIENCE

Robust hyperparameter estimation protects against hypervariable genes and improves power to detect differential expression

(2016) Belinda Phipson et al.   Annals of Applied Statistics

Structured States of Disordered Proteins from Genomic Sequences

(2016) Agnes Toth-Petroczy et al.   CELL

Purification and Characterization of Progenitor and Mature Human Astrocytes Reveals Transcriptional and Functional Differences with Mouse

(2016) Ye Zhang et al.   NEURON

A transcriptional signature of Alzheimer’s disease is associated with a metastable subproteome at risk for aggregation

(2016) Prajwal Ciryam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Influence of microglial activation on neuronal function in Alzheimer's and Parkinson's disease dementia

(2015) Zhen Fan et al.   Alzheimers & Dementia

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

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

The role of protein clearance mechanisms in organismal ageing and age-related diseases

(2014) David Vilchez et al.   Nature Communications

Integrated multi-cohort transcriptional meta-analysis of neurodegenerative diseases

(2014) Matthew D Li et al.   Acta Neuropathologica Communications

The Hallmarks of Aging

(2013) Carlos López-Otín et al.   CELL

The C9orf72 GGGGCC Repeat Is Translated into Aggregating Dipeptide-Repeat Proteins in FTLD/ALS

(2013) K. Mori et al.   SCIENCE

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

Detecting disease-associated genes with confounding variable adjustment and the impact on genomic meta-analysis: With application to major depressive disorder

(2012) Xingbin Wang et al.   BMC BIOINFORMATICS

The diagnosis of dementia due to Alzheimer’s disease: Recommendations from the National Institute on Aging-Alzheimer’s Association workgroups on diagnostic guidelines for Alzheimer's disease

(2011) Guy M. McKhann et al.   Alzheimers & Dementia

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

Sensitivity of revised diagnostic criteria for the behavioural variant of frontotemporal dementia

(2011) Katya Rascovsky et al.   BRAIN

Optimally weighted Z-test is a powerful method for combining probabilities in meta-analysis

(2011) D. V. ZAYKIN   JOURNAL OF EVOLUTIONARY BIOLOGY

A framework for oligonucleotide microarray preprocessing

(2010) Benilton S. Carvalho et al.   BIOINFORMATICS

Microarray data quality control improves the detection of differentially expressed genes

(2010) Audrey Kauffmann et al.   GENOMICS

Microglial Cx3cr1 knockout prevents neuron loss in a mouse model of Alzheimer's disease

(2010) Martin Fuhrmann et al.   NATURE NEUROSCIENCE

PGC-1 , A Potential Therapeutic Target for Early Intervention in Parkinson's Disease

(2010) B. Zheng et al.   Science Translational Medicine

Mutations in the FUS/TLS Gene on Chromosome 16 Cause Familial Amyotrophic Lateral Sclerosis

(2009) T. J. Kwiatkowski et al.   SCIENCE

arrayQualityMetrics—a bioconductor package for quality assessment of microarray data

(2008) Audrey Kauffmann et al.   BIOINFORMATICS