Individualized network-based drug repositioning infrastructure for precision oncology in the panomics era.

scientific article published on 12 June 2016

Individualized network-based drug repositioning infrastructure for precision oncology in the panomics era. is …
instance of (P31):
scholarly articleQ13442814

External links are
P8978DBLP publication IDjournals/bib/ChengHYW17
P356DOI10.1093/BIB/BBW051
P698PubMed publication ID27296652

P50authorFeixiong ChengQ47168118
P2093author name stringHuixiao Hong
Yuquan Wei
Shengyong Yang
P2860cites workDigitoxin and its analogs as novel cancer therapeuticsQ21195743
The Sequence of the Human GenomeQ22065842
An integrated encyclopedia of DNA elements in the human genomeQ22122150
Cancer genome landscapesQ22242276
An open investigation of the reproducibility of cancer biology researchQ24273259
NSAID sulindac and its analog bind RXRalpha and inhibit RXRalpha-dependent AKT signalingQ24319576
The Protein Data BankQ24515306
The Reactome pathway knowledgebaseQ24567743
Data, information, knowledge and principle: back to metabolism in KEGGQ24568332
DrugBank 4.0: shedding new light on drug metabolismQ24568341
NCBI GEO: archive for functional genomics data sets--updateQ24595691
International network of cancer genome projectsQ24611474
Pathway Commons, a web resource for biological pathway dataQ24615770
PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouseQ24619841
Itraconazole inhibits angiogenesis and tumor growth in non-small cell lung cancerQ24632703
BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinitiesQ24675698
Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteinsQ24801487
Biomarker-based drug safety assessment in the age of systems pharmacology: from foundational to regulatory scienceQ26778374
PREDICT: a method for inferring novel drug indications with application to personalized medicineQ27137071
Axitinib effectively inhibits BCR-ABL1(T315I) with a distinct binding conformationQ27698001
Immunological Effects of Conventional Chemotherapy and Targeted Anticancer AgentsQ28087754
WikiPathways: building research communities on biological pathwaysQ28090976
Gemcitabine and cisplatin versus methotrexate, vinblastine, doxorubicin, and cisplatin in advanced or metastatic bladder cancer: results of a large, randomized, multinational, multicenter, phase III studyQ28139358
Proteogenomic characterization of human colon and rectal cancerQ28244320
ONCOMINE: a cancer microarray database and integrated data-mining platformQ28255103
Big-data-based edge biomarkers: study on dynamical drug sensitivity and resistance in individuals.Q35789759
Balancing Protein Stability and Activity in Cancer: A New Approach for Identifying Driver Mutations Affecting CBL Ubiquitin Ligase ActivationQ35871171
Developing multi-target therapeutics to fine-tune the evolutionary dynamics of the cancer ecosystemQ36097745
Cyclooxygenase-Dependent Tumor Growth through Evasion of Immunity.Q36134167
Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencingQ36256943
Immunological mechanisms of the antitumor effects of supplemental oxygenationQ36269330
Optimization of dosing for EGFR-mutant non-small cell lung cancer with evolutionary cancer modelingQ36406541
ccmGDB: a database for cancer cell metabolism genesQ36434684
DGIdb 2.0: mining clinically relevant drug-gene interactions.Q36434749
Therapeutic target database update 2016: enriched resource for bench to clinical drug target and targeted pathway informationQ36434850
Mapping the effects of drugs on the immune systemQ36446799
Psmir: a database of potential associations between small molecules and miRNAsQ36463174
ChemProt-2.0: visual navigation in a disease chemical biology databaseQ36491224
InnateDB: systems biology of innate immunity and beyond--recent updates and continuing curationQ36491232
Systematic Prioritization of Druggable Mutations in ∼5000 Genomes Across 16 Cancer Types Using a Structural Genomics-based ApproachQ36539506
Metformin intake is associated with better survival in ovarian cancer: a case-control studyQ36557010
Heterogeneous DNA methylation contributes to tumorigenesis through inducing the loss of coexpression connectivity in colorectal cancerQ36672248
In silico methods for drug repurposing and pharmacologyQ36837816
A randomised controlled phase II trial of pre-operative celecoxib treatment reveals anti-tumour transcriptional response in primary breast cancerQ36903254
The exomes of the NCI-60 panel: a genomic resource for cancer biology and systems pharmacologyQ36971433
Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomesQ37096363
Connecting genomic alterations to cancer biology with proteomics: the NCI Clinical Proteomic Tumor Analysis ConsortiumQ37238264
A drug repositioning approach identifies tricyclic antidepressants as inhibitors of small cell lung cancer and other neuroendocrine tumors.Q37395737
Biomarker-guided repurposing of chemotherapeutic drugs for cancer therapy: a novel strategy in drug development.Q37413146
Computational approaches to identify functional genetic variants in cancer genomesQ37574108
Interaction-based discovery of functionally important genes in cancersQ37574182
Novel modeling of cancer cell signaling pathways enables systematic drug repositioning for distinct breast cancer metastasesQ37733781
Targeting apoptosis pathways by Celecoxib in cancerQ37846306
A comprehensive transcriptional portrait of human cancer cell linesQ37854720
Understanding genomic alterations in cancer genomes using an integrative network approachQ38069759
Network-based drug repositioningQ38089597
In silico ADMET prediction: recent advances, current challenges and future trendsQ38107020
Structural Systems Pharmacology: The Role of 3D Structures in Next-Generation Drug DevelopmentQ38109305
Repositioning metformin for cancer prevention and treatmentQ38114964
Cancer systems biology in the genome sequencing era: part 1, dissecting and modeling of tumor clones and their networks.Q38116255
Cancer systems biology in the genome sequencing era: part 2, evolutionary dynamics of tumor clonal networks and drug resistance.Q38116292
Cancer systems biology and modeling: microscopic scale and multiscale approaches.Q38198440
Hot spots in protein-protein interfaces: towards drug discovery.Q38226557
Metformin: from mechanisms of action to therapiesQ38279824
A network-based drug repositioning infrastructure for precision cancer medicine through targeting significantly mutated genes in the human cancer genomes.Q38381789
SM2miR: a database of the experimentally validated small molecules’ effects on microRNA expressionQ38460067
canSAR: updated cancer research and drug discovery knowledgebaseQ38488438
Tumorigenesis: it takes a villageQ38544200
Metformin and prostate cancer stem cells: a novel therapeutic targetQ38555403
Molecularly targeted therapy based on tumour molecular profiling versus conventional therapy for advanced cancer (SHIVA): a multicentre, open-label, proof-of-concept, randomised, controlled phase 2 trialQ38581287
Drug repurposing in oncology--patient and health systems opportunities.Q38611707
Clonotyping for precision oncologyQ38614405
CRISPR/Cas9: molecular tool for gene therapy to target genome and epigenome in the treatment of lung cancerQ38614582
CancerResource--updated database of cancer-relevant proteins, mutations and interacting drugsQ38817942
Stromal contribution to the colorectal cancer transcriptome.Q38906913
SDTNBI: an integrated network and chemoinformatics tool for systematic prediction of drug-target interactions and drug repositioningQ39947451
Dual Targeting of the Autophagic Regulatory Circuitry in Gliomas with Repurposed Drugs Elicits Cell-Lethal Autophagy and Therapeutic BenefitQ41301561
Itraconazole therapy in a pancreatic adenocarcinoma patient: A case reportQ41491252
PROMISCUOUS: a database for network-based drug-repositioningQ41578922
How good can cryo-EM become?Q41603118
Genome-wide analysis of noncoding regulatory mutations in cancerQ41842692
DRUGSURV: a resource for repositioning of approved and experimental drugs in oncology based on patient survival information.Q41979190
Distinguishing binders from false positives by free energy calculations: fragment screening against the flap site of HIV proteaseQ41989179
admetSAR: a comprehensive source and free tool for assessment of chemical ADMET propertiesQ42673952
GlaxoSmithKline opens the door on clinical data sharingQ42678818
PTMcode v2: a resource for functional associations of post-translational modifications within and between proteinsQ43214954
Interactome3D: adding structural details to protein networksQ44525347
In silico drug repositioning – what we need to knowQ44525419
Cancer modeling and network biology: accelerating toward personalized medicineQ44772124
Prediction of human genes and diseases targeted by xenobiotics using predictive toxicogenomic-derived models (PTDMs).Q45746424
Personalized medicine: Time for one-person trialsQ46268988
Prediction of chemical-protein interactions: multitarget-QSAR versus computational chemogenomic methods.Q47428755
Stromal gene expression defines poor-prognosis subtypes in colorectal cancerQ48222476
Adverse drug events: database construction and in silico predictionQ51241453
Individualized systems medicine strategy to tailor treatments for patients with chemorefractory acute myeloid leukemia.Q51781980
Cell competition is a tumour suppressor mechanism in the thymusQ52650208
Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor typesQ54310538
ThalidomideQ56091164
The future of immune checkpoint therapyQ28259862
Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencingQ28275103
Aspirin use, tumor PIK3CA mutation, and colorectal-cancer survivalQ28277824
Detection of chromosomal alterations in the circulation of cancer patients with whole-genome sequencingQ28280303
The BioGRID interaction database: 2013 updateQ28280503
Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortalQ28288215
Discovery and saturation analysis of cancer genes across 21 tumour typesQ28305204
How to improve R&D productivity: the pharmaceutical industry's grand challengeQ28314992
ChEMBL: a large-scale bioactivity database for drug discoveryQ28315179
Using functional signatures to identify repositioned drugs for breast, myelogenous leukemia and prostate cancerQ28480572
Prediction of chemical-protein interactions network with weighted network-based inference methodQ28481329
Prediction of drug-target interactions and drug repositioning via network-based inferenceQ28483634
Towards structural systems pharmacology to study complex diseases and personalized medicineQ28538838
A Gene Gravity Model for the Evolution of Cancer Genomes: A Study of 3,000 Cancer Genomes across 9 Cancer TypesQ28547803
A Pan-Cancer Catalogue of Cancer Driver Protein Interaction InterfacesQ28550391
The Genotype-Tissue Expression (GTEx) projectQ28657968
Suppression of KRas-mutant cancer through the combined inhibition of KRAS with PLK1 and ROCKQ28833740
PubChem: a public information system for analyzing bioactivities of small moleculesQ28842768
Human Protein Reference Database--2009 updateQ29547392
The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and diseaseQ29547614
The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivityQ29547693
Clonal evolution in cancerQ29547696
STRING v9.1: protein-protein interaction networks, with increased coverage and integrationQ29614691
Drug repositioning: identifying and developing new uses for existing drugsQ29614779
Integrative analysis of 111 reference human epigenomesQ29615565
COSMIC: exploring the world's knowledge of somatic mutations in human cancerQ29615725
STITCH 5: augmenting protein–chemical interaction networks with tissue and affinity dataQ30002336
Harnessing Connectivity in a Large-Scale Small-Molecule Sensitivity Dataset.Q30384542
Computational repositioning of the anticonvulsant topiramate for inflammatory bowel diseaseQ30526431
TCPA: a resource for cancer functional proteomics dataQ30666936
Predictive genomics: a cancer hallmark network framework for predicting tumor clinical phenotypes using genome sequencing dataQ30804500
TCGA-assembler: open-source software for retrieving and processing TCGA dataQ30827501
Learning from big health care dataQ30828982
IDEA: Integrated Drug Expression Analysis-Integration of Gene Expression and Clinical Data for the Identification of Therapeutic CandidatesQ30990059
Genetics: Big hopes for big dataQ31025594
TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA dataQ31034005
Data gaps limit the translational potential of preclinical researchQ31035567
Toward better drug repositioning: prioritizing and integrating existing methods into efficient pipelinesQ33611069
Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancerQ33667666
Identification of small molecules enhancing autophagic function from drug network analysisQ33712703
LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signaturesQ33860855
Pharmaco-miR: linking microRNAs and drug effectsQ33920265
Studying tumorigenesis through network evolution and somatic mutational perturbations in the cancer interactomeQ33923533
Quantitative network mapping of the human kinome interactome reveals new clues for rational kinase inhibitor discovery and individualized cancer therapyQ33977022
Discovery and preclinical validation of drug indications using compendia of public gene expression dataQ33995422
PharmGKB: the Pharmacogenetics Knowledge BaseQ34010656
Systematic identification of novel protein domain families associated with nuclear functionsQ34108188
RNAi therapies: drugging the undruggableQ34131220
Diagnosing the decline in pharmaceutical R&D efficiencyQ34257771
Identification of Drugs Including a Dopamine Receptor Antagonist that Selectively Target Cancer Stem CellsQ34282943
Genomics of Drug Sensitivity in Cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cellsQ34313686
Repurposing itraconazole as a treatment for advanced prostate cancer: a noncomparative randomized phase II trial in men with metastatic castration-resistant prostate cancer.Q34323756
Itraconazole suppresses the growth of glioblastoma through induction of autophagy: involvement of abnormal cholesterol traffickingQ34373100
Diurnal suppression of EGFR signalling by glucocorticoids and implications for tumour progression and treatmentQ34385041
mTOR-targeted therapy of cancer with rapamycin derivativesQ34397003
EGFR-mutated lung cancer: a paradigm of molecular oncologyQ34406334
Functional consequences of somatic mutations in cancer using protein pocket-based prioritization approachQ34423170
Biological and therapeutic impact of intratumor heterogeneity in cancer evolutionQ34457994
In silico prescription of anticancer drugs to cohorts of 28 tumor types reveals targeting opportunitiesQ34466574
Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humansQ34475541
Applications of the CRISPR-Cas9 system in cancer biologyQ34479139
Drug repositioning by structure-based virtual screeningQ34536280
Metformin selectively targets cancer stem cells, and acts together with chemotherapy to block tumor growth and prolong remissionQ34611836
An atlas of active enhancers across human cell types and tissuesQ34660689
New uses for old drugsQ34661227
SoNar, a Highly Responsive NAD+/NADH Sensor, Allows High-Throughput Metabolic Screening of Anti-tumor AgentsQ35593948
PINA v2.0: mining interactome modules.Q35630696
A Novel Method of Transcriptional Response Analysis to Facilitate Drug Repositioning for Cancer TherapyQ35652903
Elucidating Compound Mechanism of Action by Network Perturbation Analysis.Q35694439
Identification of links between small molecules and miRNAs in human cancers based on transcriptional responsesQ35767380
P433issue4
P921main subjectinfrastructureQ121359
drug repositioningQ5308921
P304page(s)682-697
P577publication date2017-07-01
P13046publication type of scholarly workreview articleQ7318358
P1433published inBriefings in BioinformaticsQ4967031
P1476titleIndividualized network-based drug repositioning infrastructure for precision oncology in the panomics era
P478volume18

Reverse relations

cites work (P2860)
Q47343676Accurate prediction and elucidation of drug resistance based on the robust and reproducible chemoresponse communities
Q47948290Drug repurposing for the treatment of glioblastoma multiforme.
Q98626411Emerging strategies on in silico drug development against COVID-19: challenges and opportunities
Q52564950Gender Dimorphism Creates Divergent Cancer Susceptibilities
Q37701286IODNE: An integrated optimization method for identifying the deregulated subnetwork for precision medicine in cancer
Q91855356Identifying Cancer Driver lncRNAs Bridged by Functional Effectors through Integrating Multi-omics Data in Human Cancers
Q47168067In silico prediction of chemical mechanism of action via an improved network-based inference method
Q90482543Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2
Q41084007Precision medicine for hepatocelluar carcinoma using molecular pattern diagnostics: results from a preclinical pilot study.
Q47731882Quantitative and Systems Pharmacology. 1. In Silico Prediction of Drug-Target Interactions of Natural Products Enables New Targeted Cancer Therapy
Q47397587Systems Bioinformatics: increasing precision of computational diagnostics and therapeutics through network-based approaches
Q27468694Systems Biology-Based Investigation of Cellular Antiviral Drug Targets Identified by Gene-Trap Insertional Mutagenesis
Q37708902Systems Pharmacology-Based Discovery of Natural Products for Precision Oncology Through Targeting Cancer Mutated Genes.
Q39257898Transcriptome- and proteome-oriented identification of dysregulated eIF4G, STAT3, and Hippo pathways altered by PIK3CA H1047R in HER2/ER-positive breast cancer

Search more.