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Integrative Omics for Informed Drug Repurposing: Targeting CNS Disorders

https://doi.org/10.1101/2020.04.24.060392

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Association of Hydroxylmethyl Glutaryl Coenzyme A Reductase Inhibitors, L-Type Calcium Channel Antagonists, and Biguanides With Rates of Psychiatric Hospitalization and Self-Harm in Individuals With Serious Mental Illness

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ZINC — A Free Database of Commercially Available Compounds for Virtual Screening.

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Comparative evaluation of eight docking tools for docking and virtual screening accuracy

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The promise and challenges of drug repurposing in psychiatry

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Fast Molecular Docking Methods

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Systematic Drug Repurposing Through Text Mining

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Text Mining for Drug Discovery

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Molecular Docking

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Extremely randomized trees

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Adverse Drug Reactions

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Deficient Hippocampal Neuron Expression of Proteasome, Ubiquitin, and Mitochondrial Genes in Multiple Schizophrenia Cohorts

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High-throughput Phenotyping of Lung Cancer Somatic Mutations

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Genetic Heterogeneity in Human Disease

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An Expanded View of Complex Traits: From Polygenic to Omnigenic

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A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles

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The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations

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Cheminformatics Tools for Analyzing and Designing Optimized Small Molecule Collections and Libraries

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State-of-the-art in ligand-based virtual screening

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Transcriptional data: a new gateway to drug repositioning?

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Re-thinking Alzheimer's disease therapeutic targets using gene-based tests

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Update on NCI in vitro drug screen utilities

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Computer-guided drug repurposing: Identification of trypanocidal activity of clofazimine, benidipine and saquinavir

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An update on vinpocetine: New discoveries and clinical implications

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RosettaLigand Docking with Full Ligand and Receptor Flexibility

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A “mitochondrial cascade hypothesis” for sporadic Alzheimer's disease

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Improving and Accelerating Drug Development for Nervous System Disorders

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Identification of relevant hub genes for early intervention at gene coexpression modules with altered predicted expression in schizophrenia

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Adverse drug reactions: definitions, diagnosis, and management

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On the allelic spectrum of human disease

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The essence of SNPs

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Text-mining approaches in molecular biology and biomedicine

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Treatment resistant depression and Axis I co-morbidity

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ZINC − A Free Database of Commercially Available Compounds for Virtual Screening

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Consensus Scoring Criteria for Improving Enrichment in Virtual Screening

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Classics in Chemical Neuroscience: Fluoxetine (Prozac)

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Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy

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A Critical Assessment of Docking Programs and Scoring Functions

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Lithium in the treatment of bipolar disorder: pharmacology and pharmacogenetics

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Analysis of genome-wide association data highlights candidates for drug repositioning in psychiatry

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Neuron-specific deficits of bioenergetic processes in the dorsolateral prefrontal cortex in schizophrenia

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A Bayesian machine learning approach for drug target identification using diverse data types

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SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules

inferredcites →https://doi.org/10.1039/c3mb25382aopenalex-snapshot

Network-based drug repositioning

inferredcites →https://doi.org/10.1039/c3mb70554dopenalex-snapshot

Drug repositioning by applying ‘expression profiles’ generated by integrating chemical structure similarity and gene semantic similarity

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Kinase network dysregulation in a human induced pluripotent stem cell model of DISC1 schizophrenia

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HPO-Shuffle: an associated gene prioritization strategy and its application in drug repurposing for the treatment of canine epilepsy

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Brain-on-a-chip: A history of development and future perspective

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Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

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Toward performance-diverse small-molecule libraries for cell-based phenotypic screening using multiplexed high-dimensional profiling

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inferredcites →https://doi.org/10.1093/bib/bbx017openalex-snapshot

A review of network-based approaches to drug repositioning

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Drug repositioning by integrating target information through a heterogeneous network model

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inferredcites →https://doi.org/10.1093/bioinformatics/btw228openalex-snapshot

Drug repositioning based on comprehensive similarity measures and Bi-Random walk algorithm

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EMUDRA: Ensemble of Multiple Drug Repositioning Approaches to improve prediction accuracy

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ORegAnno: an open-access community-driven resource for regulatory annotation

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ModBase, a database of annotated comparative protein structure models, and associated resources

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The SIDER database of drugs and side effects

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Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data

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PubChem 2019 update: improved access to chemical data

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Rapid Reversal of Psychotic Depression Using Mifepristone

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Comparing gene expression similarity metrics for connectivity map

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INDIVIDUAL AND ORGANIZATIONAL DETERMINANTS OF ALCOHOL SCREENING AND BRIEF INTERVENTION IMPLEMENTATION IN EMERGENCY DEPARTMENTS (SIPS-ED)

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The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease

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Data-Driven Prediction of Drug Effects and Interactions

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Ketamine for treatment-resistant depression: recent developments and clinical applications

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The Merck Index: 12th edition 1996

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Drug Repurposing Is a New Opportunity for Developing Drugs against Neuropsychiatric Disorders

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Valsartan lowers brain β-amyloid protein levels and improves spatial learning in a mouse model of Alzheimer disease

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A Comparison of Mirtazapine and Nortriptyline Following Two Consecutive Failed Medication Treatments for Depressed Outpatients: A STAR*D Report

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Gene-set analysis based on the pharmacological profiles of drugs to identify repurposing opportunities in schizophrenia

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Transcriptomic profiling of human hippocampal progenitor cells treated with antidepressants and its application in drug repositioning

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sscMap: An extensible Java application for connecting small-molecule drugs using gene-expression signatures

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Pathway-based drug repositioning using causal inference

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A simple and robust method for connecting small-molecule drugs using gene-expression signatures

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A method for high-throughput gene expression signature analysis

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Medicinal chemical properties of successful central nervous system drugs

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Drug resistance in cancer: molecular evolution and compensatory proliferation

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Valproic Acid and Epilepsy: From Molecular Mechanisms to Clinical Evidences

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Pathway-Based Drug Repositioning for Breast Cancer Molecular Subtypes

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Advances and Challenges in Protein-Ligand Docking

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A History of the Pharmacological Treatment of Bipolar Disorder

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A Structure-Based Drug Discovery Paradigm

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Precision Psychiatry Applications with Pharmacogenomics: Artificial Intelligence and Machine Learning Approaches

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Anticonvulsant Use in the Treatment of Bipolar Disorder

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Review of Drug Repositioning Approaches and Resources

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Adverse drug reactions: An Overview

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