The Pathway Coexpression Network: Revealing pathway relationships

Gene set selection via LASSO penalized regression (SLPR)

(2017) H. Robert Frost et al.   NUCLEIC ACIDS RESEARCH

Presenilin-1 mutations and Alzheimer’s disease

(2017) Raymond J. Kelleher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extracellular matrix proteomics in schizophrenia and Alzheimer’s disease

(2016) Manveen K. Sethi et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

VarElect: the phenotype-based variation prioritizer of the GeneCards Suite

(2016) Gil Stelzer et al.   BMC GENOMICS

β-amyloid increases neurocan expression through regulating Sox9 in astrocytes: A potential relationship between Sox9 and chondroitin sulfate proteoglycans in Alzheimer's disease

(2016) Han Yan et al.   BRAIN RESEARCH

Alzheimer's disease

(2016) Philip Scheltens et al.   LANCET

A novel method for crosstalk analysis of biological networks: improving accuracy of pathway annotation

(2016) Christoph Ogris et al.   NUCLEIC ACIDS RESEARCH

Early changes in extracellular matrix in Alzheimer's disease

(2015) F.-X. Lepelletier et al.   NEUROPATHOLOGY AND APPLIED NEUROBIOLOGY

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

A review on Alzheimer's disease pathophysiology and its management: an update

(2015) Anil Kumar et al.   Pharmacological Reports

Structural determinants of Smad function in TGF-β signaling

(2015) Maria J. Macias et al.   TRENDS IN BIOCHEMICAL SCIENCES

Role of TGFβ signaling in the pathogenesis of Alzheimer’s disease

(2015) Rommy von Bernhardi et al.   Frontiers in Cellular Neuroscience

Genome-Wide Detection and Analysis of Multifunctional Genes

(2015) Yuri Pritykin et al.   PLoS Computational Biology

ExAtlas: An interactive online tool for meta-analysis of gene expression data

(2015) Alexei A. Sharov et al.   Journal of Bioinformatics and Computational Biology

Inferring gene ontologies from pairwise similarity data

(2014) M. Kramer et al.   BIOINFORMATICS

Microglial Aβ Receptors in Alzheimer’s Disease

(2014) Yang Yu et al.   CELLULAR AND MOLECULAR NEUROBIOLOGY

The Spleen Tyrosine Kinase (Syk) Regulates Alzheimer Amyloid-β Production and Tau Hyperphosphorylation

(2014) Daniel Paris et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Neurodegeneration by Activation of the Microglial Complement-Phagosome Pathway

(2014) L.-G. Bodea et al.   JOURNAL OF NEUROSCIENCE

Co-expression network analysis of differentially expressed genes associated with metastasis in prolactin pituitary tumors

(2014) WEI ZHANG et al.   Molecular Medicine Reports

Comprehensive analysis of correlation coefficients estimated from pooling heterogeneous microarray data

(2013) Márcia M Almeida-de-Macedo et al.   BMC BIOINFORMATICS

Inferring pathway crosstalk networks using gene set co-expression signatures

(2013) Ting Wang et al.   Molecular BioSystems

The Gene Expression Barcode 3.0: improved data processing and mining tools

(2013) Matthew N. McCall et al.   NUCLEIC ACIDS RESEARCH

Redundancy Control in Pathway Databases (ReCiPa): An Application for Improving Gene-Set Enrichment Analysis in Omics Studies and “Big Data” Biology

(2013) Juan C. Vivar et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Statistical Assessment of Crosstalk Enrichment between Gene Groups in Biological Networks

(2013) Theodore McCormack et al.   PLoS One

Human housekeeping genes, revisited

(2013) Eli Eisenberg et al.   TRENDS IN GENETICS

Pathprinting: An integrative approach to understand the functional basis of disease

(2013) Gabriel M Altschuler et al.   Genome Medicine

Rigorous assessment of gene set enrichment tests

(2012) Haroon Naeem et al.   BIOINFORMATICS

Network enrichment analysis: extension of gene-set enrichment analysis to gene networks

(2012) Andrey Alexeyenko et al.   BMC BIOINFORMATICS

Markov Chain Ontology Analysis (MCOA)

(2012) H Frost et al.   BMC BIOINFORMATICS

Extracellular matrix modulator lysyl oxidase colocalizes with amyloid-beta pathology in Alzheimer's disease and hereditary cerebral hemorrhage with amyloidosis—Dutch type

(2012) Micha M.M. Wilhelmus et al.   EXPERIMENTAL GERONTOLOGY

A gene ontology inferred from molecular networks

(2012) Janusz Dutkowski et al.   NATURE BIOTECHNOLOGY

Reuse of public genome-wide gene expression data

(2012) Johan Rung et al.   NATURE REVIEWS GENETICS

Tissue transglutaminase colocalizes with extracellular matrix proteins in cerebral amyloid angiopathy

(2012) Mieke de Jager et al.   NEUROBIOLOGY OF AGING

Gene Expression Commons: An Open Platform for Absolute Gene Expression Profiling

(2012) Jun Seita et al.   PLoS One

Pathway analysis of genomic data: concepts, methods, and prospects for future development

(2012) Vijay K. Ramanan et al.   TRENDS IN GENETICS

Alzheimer disease and platelets: how’s that relevant

(2012) Silvia Catricala et al.   Immunity & Ageing

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

Assessing affymetrix GeneChip microarray quality

(2011) Matthew N McCall et al.   BMC BIOINFORMATICS

Involvement of Perineuronal and Perisynaptic Extracellular Matrix in Alzheimer's Disease Neuropathology

(2011) Markus Morawski et al.   BRAIN PATHOLOGY

Gene set enrichment analysis: performance evaluation and usage guidelines

(2011) J.-H. Hung et al.   BRIEFINGS IN BIOINFORMATICS

Deficient brain insulin signalling pathway in Alzheimer's disease and diabetes

(2011) Ying Liu et al.   JOURNAL OF PATHOLOGY

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

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

How APC/C–Cdc20 changes its substrate specificity in mitosis

(2011) Daisuke Izawa et al.   NATURE CELL BIOLOGY

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

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

Cross-species queries of large gene expression databases

(2010) Hai-Son Le et al.   BIOINFORMATICS

Frozen robust multiarray analysis (fRMA)

(2010) M. N. McCall et al.   BIOSTATISTICS

Detection of characteristic sub pathway network for angiogenesis based on the comprehensive pathway network

(2010) Yezhou Huang et al.   BMC BIOINFORMATICS

A global map of human gene expression

(2010) Margus Lukk et al.   NATURE BIOTECHNOLOGY

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

GOing Bayesian: model-based gene set analysis of genome-scale data

(2010) Sebastian Bauer et al.   NUCLEIC ACIDS RESEARCH

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function

(2010) David Warde-Farley et al.   NUCLEIC ACIDS RESEARCH

Reactome: a database of reactions, pathways and biological processes

(2010) D. Croft et al.   NUCLEIC ACIDS RESEARCH

Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation

(2010) Daniele Merico et al.   PLoS One

Unveiling the role of network and systems biology in drug discovery

(2010) Albert Pujol et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Unite and conquer: univariate and multivariate approaches for finding differentially expressed gene sets

(2009) Galina V. Glazko et al.   BIOINFORMATICS

Selecting control genes for RT-QPCR using public microarray data

(2009) Vlad Popovici et al.   BMC BIOINFORMATICS

Global networks of functional coupling in eukaryotes from comprehensive data integration

(2009) A. Alexeyenko et al.   GENOME RESEARCH

A global pathway crosstalk network

(2008) Yong Li et al.   BIOINFORMATICS

A probabilistic generative model for GO enrichment analysis

(2008) Yong Lu et al.   NUCLEIC ACIDS RESEARCH

PID: the Pathway Interaction Database

(2008) Carl F. Schaefer et al.   NUCLEIC ACIDS RESEARCH

Reactome knowledgebase of human biological pathways and processes

(2008) L. Matthews et al.   NUCLEIC ACIDS RESEARCH

Using Ribosomal Protein Genes as Reference: A Tale of Caution

(2008) Lieven Thorrez et al.   PLoS One