Analytical Strategy to Prioritize Alzheimer’s Disease Candidate Genes in Gene Regulatory Networks Using Public Expression Data

Higher brainBDNFgene expression is associated with slower cognitive decline in older adults

(2016) Aron S. Buchman et al.   NEUROLOGY

Brain-derived neurotrophic factor and its clinical implications

(2015) Siresha Bathina et al.   Archives of Medical Science

Differential co-expression and regulation analyses reveal different mechanisms underlying major depressive disorder and subsyndromal symptomatic depression

(2015) Fan Xu et al.   BMC BIOINFORMATICS

Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data

(2015) Ricardo de Matos Simoes et al.   BMC Systems Biology

Cascading network failure across the Alzheimer’s disease spectrum

(2015) David T. Jones et al.   BRAIN

Using prior knowledge from cellular pathways and molecular networks for diagnostic specimen classification

(2015) Enrico Glaab   BRIEFINGS IN BIOINFORMATICS

Prevention of sporadic Alzheimer's disease: lessons learned from clinical trials and future directions

(2015) Sandrine Andrieu et al.   LANCET NEUROLOGY

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

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

GTEx detects genetic effects

(2015) G. Gibson   SCIENCE

An RNA biosensor for imaging the first round of translation from single cells to living animals

(2015) J. M. Halstead et al.   SCIENCE

NeuroTransDB: highly curated and structured transcriptomic metadata for neurodegenerative diseases

(2015) Shweta Bagewadi et al.   Database-The Journal of Biological Databases and Curation

Differential co-expression network centrality and machine learning feature selection for identifying susceptibility hubs in networks with scale-free structure

(2015) Caleb A Lareau et al.   BioData Mining

Impairment of the activity of the plasma membrane Ca2+-ATPase in Alzheimer's disease

(2015) Ana M. Mata et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

2014 Alzheimer's disease facts and figures

(2014)   Alzheimers & Dementia

Genetic network identifies novel pathways contributing to atherosclerosis susceptibility in the innominate artery

(2014) Jody Albright et al.   BMC Medical Genomics

Inference and validation of predictive gene networks from biomedical literature and gene expression data

(2014) Catharina Olsen et al.   GENOMICS

Whole-genome haplotyping using long reads and statistical methods

(2014) Volodymyr Kuleshov et al.   NATURE BIOTECHNOLOGY

Alzheimer’s disease drug-development pipeline: few candidates, frequent failures

(2014) Jeffrey L Cummings et al.   Alzheimers Research & Therapy

The amyloid cascade-inflammatory hypothesis of Alzheimer disease: implications for therapy

(2013) Patrick L. McGeer et al.   ACTA NEUROPATHOLOGICA

Identification of active transcription factor and miRNA regulatory pathways in Alzheimer’s disease

(2013) Wei Jiang et al.   BIOINFORMATICS

Co-expression network analysis identifies Spleen Tyrosine Kinase (SYK) as a candidate oncogenic driver in a subset of small-cell lung cancer

(2013) Akshata R Udyavar et al.   BMC Systems Biology

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

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

(2013) Bin Zhang et al.   CELL

Dynamic trans-Acting Factor Colocalization in Human Cells

(2013) Dan Xie et al.   CELL

GWAS Central: a comprehensive resource for the comparison and interrogation of genome-wide association studies

(2013) Tim Beck et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Synthetic Aβ oligomers (Aβ1–42 globulomer) modulate presynaptic calcium currents: Prevention of Aβ-induced synaptic deficits by calcium channel blockers

(2013) David Hermann et al.   EUROPEAN JOURNAL OF PHARMACOLOGY

Avoiding pitfalls in gene (co)expression meta-analysis

(2013) Gabriel Östlund et al.   GENOMICS

MHC class I immune proteins are critical for hippocampus-dependent memory and gate NMDAR-dependent hippocampal long-term depression

(2013) P. A. Nelson et al.   LEARNING & MEMORY

Overcoming barriers and thresholds -- signaling of oligomeric Abeta through the prion protein to Fyn

(2013) Hansen Wang et al.   Molecular Neurodegeneration

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

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

Amyloid-β25–35 induces impairment of cognitive function and long-term potentiation through phosphorylation of collapsin response mediator protein 2

(2013) Toshinari Isono et al.   NEUROSCIENCE RESEARCH

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

(2013) Danielle Welter et al.   NUCLEIC ACIDS RESEARCH

Adaptor complex AP2/PICALM, through interaction with LC3, targets Alzheimer's APP-CTF for terminal degradation via autophagy

(2013) Y. Tian et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Generation and Characterization of Spiking and Nonspiking Oligodendroglial Progenitor Cells from Embryonic Stem Cells

(2013) Peng Jiang et al.   STEM CELLS

Intracellular Itinerary of Internalised β-Secretase, BACE1, and Its Potential Impact on β-Amyloid Peptide Biogenesis

(2013) Pei Zhi Cheryl Chia et al.   TRAFFIC

Dissection of Regulatory Networks that Are Altered in Disease via Differential Co-expression

(2013) David Amar et al.   PLoS Computational Biology

Alzheimer's therapeutics: Continued clinical failures question the validity of the amyloid hypothesis—but what lies beyond?

(2012) Kevin Mullane et al.   BIOCHEMICAL PHARMACOLOGY

Calmodulin antagonizes amyloid-β peptides-mediated inhibition of brain plasma membrane Ca2+-ATPase

(2012) Maria Berrocal et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

Pathway-based classification of cancer subtypes

(2012) Shinuk Kim et al.   Biology Direct

Mining biomarker information in biomedical literature

(2012) Erfan Younesi et al.   BMC Medical Informatics and Decision Making

Organizational structure and the periphery of the gene regulatory network in B-cell lymphoma

(2012) Ricardo de Matos Simoes et al.   BMC Systems Biology

Alzheimer's disease, β-amyloid, glutamate, NMDA receptors and memantine - searching for the connections

(2012) Wojciech Danysz et al.   BRITISH JOURNAL OF PHARMACOLOGY

Multiple roles for the actin cytoskeleton during regulated exocytosis

(2012) Natalie Porat-Shliom et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Annotation of functional variation in personal genomes using RegulomeDB

(2012) A. P. Boyle et al.   GENOME RESEARCH

The early events of Alzheimer's disease pathology: from mitochondrial dysfunction to BDNF axonal transport deficits

(2012) Xuan Ye et al.   NEUROBIOLOGY OF AGING

Comprehensive literature review and statistical considerations for microarray meta-analysis

(2012) George C. Tseng et al.   NUCLEIC ACIDS RESEARCH

Bagging Statistical Network Inference from Large-Scale Gene Expression Data

(2012) Ricardo de Matos Simoes et al.   PLoS One

Concerted Perturbation Observed in a Hub Network in Alzheimer’s Disease

(2012) Dapeng Liang et al.   PLoS One

The NIH Roadmap Epigenomics Program data resource

(2012) Lisa Helbling Chadwick   Epigenomics

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

Curcumin nanoformulations: a future nanomedicine for cancer

(2011) Murali M. Yallapu et al.   DRUG DISCOVERY TODAY

GWASdb: a database for human genetic variants identified by genome-wide association studies

(2011) Mulin Jun Li et al.   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants

(2011) L. D. Ward et al.   NUCLEIC ACIDS RESEARCH

Network Based Consensus Gene Signatures for Biomarker Discovery in Breast Cancer

(2011) Holger Fröhlich   PLoS One

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

(2010) William McLaren et al.   BIOINFORMATICS

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

Functional Genomics of Brain Aging and Alzheimers Disease: Focus on Selective Neuronal Vulnerability

(2010) Xinkun Wang et al.   CURRENT GENOMICS

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

(2010) A. P. Boyle et al.   GENOME RESEARCH

11C-PiB PET assessment of change in fibrillar amyloid-β load in patients with Alzheimer's disease treated with bapineuzumab: a phase 2, double-blind, placebo-controlled, ascending-dose study

(2010) Juha O Rinne et al.   LANCET NEUROLOGY

Novel mechanism of increased Ca2+ release following oxidative stress in neuronal cells involves type 2 inositol-1,4,5-trisphosphate receptors

(2010) S. Kaja et al.   NEUROSCIENCE

ConsensusPathDB: toward a more complete picture of cell biology

(2010) Atanas Kamburov et al.   NUCLEIC ACIDS RESEARCH

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

(2010) Vân Anh Huynh-Thu et al.   PLoS One

Calcium signaling in neurodegeneration

(2009) Philippe Marambaud et al.   Molecular Neurodegeneration

The dysbindin-containing complex (BLOC-1) in brain: developmental regulation, interaction with SNARE proteins and role in neurite outgrowth

(2009) C A Ghiani et al.   MOLECULAR PSYCHIATRY

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Quantitation of glycogen synthase kinase-3 sensitive proteins in neuronal membrane rafts

(2009) Andrew J. Thompson et al.   PROTEOMICS

Role of Axonal Transport in Neurodegenerative Diseases

(2008) Kurt J. De Vos et al.   Annual Review of Neuroscience

arrayQualityMetrics—a bioconductor package for quality assessment of microarray data

(2008) Audrey Kauffmann et al.   BIOINFORMATICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Seeded Bayesian Networks: Constructing genetic networks from microarray data

(2008) Amira Djebbari et al.   BMC Systems Biology

Association between the interleukin-1β polymorphisms and Alzheimer's disease: A systematic review and meta-analysis

(2008) Danilo Di Bona et al.   BRAIN RESEARCH REVIEWS

Linking Calcium to Aβ and Alzheimer's Disease

(2008) Kim N. Green et al.   NEURON

Network inference using informative priors

(2008) S. Mukherjee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Neuronal calcium mishandling and the pathogenesis of Alzheimer's disease

(2008) Ilya Bezprozvanny et al.   TRENDS IN NEUROSCIENCES

Meta-analysis for ranked discovery datasets: Theoretical framework and empirical demonstration for microarrays

(2007) Elias Zintzaras et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY