Identification of novel immune-relevant drug target genes for Alzheimer's Disease by combining ontology inference with network analysis

What Contributes to Serotonin–Norepinephrine Reuptake Inhibitors’ Dual-Targeting Mechanism? The Key Role of Transmembrane Domain 6 in Human Serotonin and Norepinephrine Transporters Revealed by Molecular Dynamics Simulation

(2018) Weiwei Xue et al.   ACS Chemical Neuroscience

Exploring the Binding Mechanism of Metabotropic Glutamate Receptor 5 Negative Allosteric Modulators in Clinical Trials by Molecular Dynamics Simulations

(2018) Tingting Fu et al.   ACS Chemical Neuroscience

Candesartan ameliorates brain inflammation associated with Alzheimer's disease

(2018) Nofar Torika et al.   CNS Neuroscience & Therapeutics

Cholinesterase targeting by polyphenols: A therapeutic approach for the treatment of Alzheimer’s disease

(2018) Nasimudeen R. Jabir et al.   CNS Neuroscience & Therapeutics

Assessing the Performances of Protein Function Prediction Algorithms from the Perspectives of Identification Accuracy and False Discovery Rate

(2018) Chun Yu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Prediction of the binding mode and resistance profile for a dual-target pyrrolyl diketo acid scaffold against HIV-1 integrase and reverse-transcriptase-associated ribonuclease H

(2018) Fengyuan Yang et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Computational identification of the binding mechanism of a triple reuptake inhibitor amitifadine for the treatment of major depressive disorder

(2018) Weiwei Xue et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Clinical Success of Drug Targets Prospectively Predicted by In Silico Study

(2018) Feng Zhu et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Discovery of the Consistently Well-Performed Analysis Chain for SWATH-MS Based Pharmacoproteomic Quantification

(2018) Jianbo Fu et al.   Frontiers in Pharmacology

Comparison of computational model and X-ray crystal structure of human serotonin transporter: potential application for the pharmacology of human monoamine transporters

(2017) Fengyuan Yang et al.   MOLECULAR SIMULATION

NOREVA: normalization and evaluation of MS-based metabolomics data

(2017) Bo Li et al.   NUCLEIC ACIDS RESEARCH

WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research

(2017) Denise N Slenter et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes

(2017) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

The Reactome Pathway Knowledgebase

(2017) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

Revealing vilazodone's binding mechanism underlying its partial agonism to the 5-HT1A receptor in the treatment of major depressive disorder

(2017) Guoxun Zheng et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Anthoxanthin Polyphenols Attenuate AβOligomer-induced Neuronal Responses Associated with Alzheimer's Disease

(2016) Kayla M. Pate et al.   CNS Neuroscience & Therapeutics

The antibody aducanumab reduces Aβ plaques in Alzheimer’s disease

(2016) Jeff Sevigny et al.   NATURE

Suppression of glymphatic fluid transport in a mouse model of Alzheimer's disease

(2016) Weiguo Peng et al.   NEUROBIOLOGY OF DISEASE

Expansion of the Gene Ontology knowledgebase and resources

(2016)   NUCLEIC ACIDS RESEARCH

PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements

(2016) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Identification of the inhibitory mechanism of FDA approved selective serotonin reuptake inhibitors: an insight from molecular dynamics simulation study

(2016) Weiwei Xue et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

SVM-Prot 2016: A Web-Server for Machine Learning Prediction of Protein Functional Families from Sequence Irrespective of Similarity

(2016) Ying Hong Li et al.   PLoS One

IL-33 ameliorates Alzheimer’s disease-like pathology and cognitive decline

(2016) Amy K. Y. Fu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparison of FDA Approved Kinase Targets to Clinical Trial Ones: Insights from Their System Profiles and Drug-Target Interaction Networks

(2016) Jingyu Xu et al.   Biomed Research International

Cell Type-Specific Regulation of Immunological Synapse Dynamics by B7 Ligand Recognition

(2016) Joanna Brzostek et al.   Frontiers in Immunology

The Human Kinome Targeted by FDA Approved Multi-Target Drugs and Combination Products: A Comparative Study from the Drug-Target Interaction Network Perspective

(2016) Ying Hong Li et al.   PLoS One

Exploring the Inhibitory Mechanism of Approved Selective Norepinephrine Reuptake Inhibitors and Reboxetine Enantiomers by Molecular Dynamics Study

(2016) Guoxun Zheng et al.   Scientific Reports

Performance Evaluation and Online Realization of Data-driven Normalization Methods Used in LC/MS based Untargeted Metabolomics Analysis

(2016) Bo Li et al.   Scientific Reports

Boosting translational research on Alzheimer's disease in Europe: The Innovative Medicine Initiative AD research platform

(2015) Elisabetta Vaudano et al.   Alzheimers & Dementia

Genetic Association of CUGBP2 and DNMBP with Alzheimer’ s Disease in the Chinese Han Population

(2015) Ping Yang et al.   Current Alzheimer Research

Short Communication FYB polymorphisms in Brazilian patients with type I diabetes mellitus and autoimmune polyglandular syndrome type III

(2015) C.J.C. Addobbati et al.   GENETICS AND MOLECULAR RESEARCH

Reconstructed Ancestral Enzymes Impose a Fitness Cost upon Modern Bacteria Despite Exhibiting Favourable Biochemical Properties

(2015) Joanne K. Hobbs et al.   JOURNAL OF MOLECULAR EVOLUTION

HLA-B polymorphisms and intracellular assembly modes

(2015) Malini Raghavan et al.   MOLECULAR IMMUNOLOGY

Structural and functional features of central nervous system lymphatic vessels

(2015) Antoine Louveau et al.   NATURE

Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer’s disease

(2015) Elizabeta Gjoneska et al.   NATURE

Il10 Deficiency Rebalances Innate Immunity to Mitigate Alzheimer-Like Pathology

(2015) Marie-Victoire Guillot-Sestier et al.   NEURON

Pathways with PathWhiz

(2015) Allison Pon et al.   NUCLEIC ACIDS RESEARCH

Therapeutic target database update 2016: enriched resource for bench to clinical drug target and targeted pathway information

(2015) Hong Yang et al.   NUCLEIC ACIDS RESEARCH

Co-targeting cancer drug escape pathways confers clinical advantage for multi-target anticancer drugs

(2015) Lin Tao et al.   PHARMACOLOGICAL RESEARCH

Genetic analysis of the RELN gene: Gender specific association with Alzheimer’s disease

(2015) Ágnes Fehér et al.   PSYCHIATRY RESEARCH

Innate Immunity Fights Alzheimer's Disease

(2015) Marie-Victoire Guillot-Sestier et al.   TRENDS IN NEUROSCIENCES

Risk prediction for sporadic Alzheimer’s disease using genetic risk score in the Han Chinese population

(2015) Qianyi Xiao et al.   Oncotarget

Alzheimer's disease, enzyme targets and drug discovery struggles: From natural products to drug prototypes

(2014) Tiago Silva et al.   AGEING RESEARCH REVIEWS

The BioGRID interaction database: 2015 update

(2014) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

Microglial TNF-α-Dependent Elevation of MHC Class I Expression on Brain Endothelium Induced by Amyloid-Beta Promotes T Cell Transendothelial Migration

(2013) Yi-Ming Yang et al.   NEUROCHEMICAL RESEARCH

Robust rank aggregation for gene list integration and meta-analysis

(2012) Raivo Kolde et al.   BIOINFORMATICS

A pathway profile-based method for drug repositioning

(2012) Hao Ye et al.   CHINESE SCIENCE BULLETIN

Reelin and its complex involvement in brain development and function

(2012) Silvia Lakatosova et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation

(2012) Karin Breuer et al.   NUCLEIC ACIDS RESEARCH

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Drug Discovery Prospect from Untapped Species: Indications from Approved Natural Product Drugs

(2012) Feng Zhu et al.   PLoS One

A Paravascular Pathway Facilitates CSF Flow Through the Brain Parenchyma and the Clearance of Interstitial Solutes, Including Amyloid  

(2012) J. J. Iliff et al.   Science Translational Medicine

Therapeutic target database update 2012: a resource for facilitating target-oriented drug discovery

(2011) F. Zhu et al.   NUCLEIC ACIDS RESEARCH

Clustered patterns of species origins of nature-derived drugs and clues for future bioprospecting

(2011) F. Zhu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DrugBank 3.0: a comprehensive resource for 'Omics' research on drugs

(2010) C. Knox et al.   NUCLEIC ACIDS RESEARCH

Discovery of drug mode of action and drug repositioning from transcriptional responses

(2010) F. Iorio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Novel opportunities for computational biology and sociology in drug discovery

(2010) Lixia Yao et al.   TRENDS IN BIOTECHNOLOGY

NetPath: a public resource of curated signal transduction pathways

(2010) Kumaran Kandasamy et al.   GENOME BIOLOGY

Trends in the Exploration of Anticancer Targets and Strategies in Enhancing the Efficacy of Drug Targeting

(2010) F. Zhu et al.   Current Molecular Pharmacology

Identifying druggable disease-modifying gene products

(2009) Scott J Dixon et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Roles of phosphatidylinositol 3-kinase and p38 mitogen-activated protein kinase in the regulation of protein kinase C-α activation in interferon-γ-stimulated macrophages

(2009) Pierre-Olivier Hardy et al.   IMMUNOLOGY

What Are Next Generation Innovative Therapeutic Targets? Clues from Genetic, Structural, Physicochemical, and Systems Profiles of Successful Targets

(2009) F. Zhu et al.   JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS

Update of TTD: Therapeutic Target Database

(2009) Feng Zhu et al.   NUCLEIC ACIDS RESEARCH

Human Disease-Drug Network Based on Genomic Expression Profiles

(2009) Guanghui Hu et al.   PLoS One

Reelin signaling antagonizes  -amyloid at the synapse

(2009) M. S. Durakoglugil et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Homology-Free Prediction of Functional Class of Proteins and Peptides by Support Vector Machines

(2008) Y. Chen et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

PID: the Pathway Interaction Database

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

Drug Target Identification Using Side-Effect Similarity

(2008) M. Campillos et al.   SCIENCE