J Chem Inf Model - Drug-disease association and drug-repositioning predictions in complex diseases using causal inference-probabilistic matrix factorization.

Tópicos

{ data(2317) use(1299) case(1017) }
{ drug(1928) target(777) effect(648) }
{ model(2341) predict(2261) use(1141) }
{ compound(1573) activ(1297) structur(1058) }
{ sequenc(1873) structur(1644) protein(1328) }
{ method(2212) result(1239) propos(1039) }
{ model(3404) distribut(989) bayesian(671) }
{ high(1669) rate(1365) level(1280) }
{ network(2748) neural(1063) input(814) }
{ data(3008) multipl(1320) sourc(1022) }
{ method(1219) similar(1157) match(930) }
{ risk(3053) factor(974) diseas(938) }
{ gene(2352) biolog(1181) express(1162) }
{ cancer(2502) breast(956) screen(824) }
{ use(1733) differ(960) four(931) }
{ import(1318) role(1303) understand(862) }
{ group(2977) signific(1463) compar(1072) }
{ activ(1138) subject(705) human(624) }
{ data(1737) use(1416) pattern(1282) }
{ imag(1057) registr(996) error(939) }
{ featur(3375) classif(2383) classifi(1994) }
{ patient(2315) diseas(1263) diabet(1191) }
{ framework(1458) process(801) describ(734) }
{ search(2224) databas(1162) retriev(909) }
{ use(976) code(926) identifi(902) }
{ result(1111) use(1088) new(759) }
{ survey(1388) particip(1329) question(1065) }
{ assess(1506) score(1403) qualiti(1306) }
{ problem(2511) optim(1539) algorithm(950) }
{ extract(1171) text(1153) clinic(932) }
{ method(1557) propos(1049) approach(1037) }
{ control(1307) perform(991) simul(935) }
{ method(984) reconstruct(947) comput(926) }
{ spatial(1525) area(1432) region(1030) }
{ record(1888) medic(1808) patient(1693) }
{ health(3367) inform(1360) care(1135) }
{ research(1218) medic(880) student(794) }
{ age(1611) year(1155) adult(843) }
{ cost(1906) reduc(1198) effect(832) }
{ intervent(3218) particip(2042) group(1664) }
{ time(1939) patient(1703) rate(768) }
{ analysi(2126) use(1163) compon(1037) }
{ structur(1116) can(940) graph(676) }
{ decis(3086) make(1611) patient(1517) }
{ process(1125) use(805) approach(778) }
{ activ(1452) weight(1219) physic(1104) }
{ can(774) often(719) complex(702) }
{ imag(1947) propos(1133) code(1026) }
{ inform(2794) health(2639) internet(1427) }
{ system(1976) rule(880) can(841) }
{ measur(2081) correl(1212) valu(896) }
{ bind(1733) structur(1185) ligand(1036) }
{ imag(2830) propos(1344) filter(1198) }
{ imag(2675) segment(2577) method(1081) }
{ take(945) account(800) differ(722) }
{ studi(2440) review(1878) systemat(933) }
{ motion(1329) object(1292) video(1091) }
{ treatment(1704) effect(941) patient(846) }
{ surgeri(1148) surgic(1085) robot(1054) }
{ error(1145) method(1030) estim(1020) }
{ chang(1828) time(1643) increas(1301) }
{ learn(2355) train(1041) set(1003) }
{ concept(1167) ontolog(924) domain(897) }
{ clinic(1479) use(1117) guidelin(835) }
{ algorithm(1844) comput(1787) effici(935) }
{ data(1714) softwar(1251) tool(1186) }
{ design(1359) user(1324) use(1319) }
{ model(2220) cell(1177) simul(1124) }
{ care(1570) inform(1187) nurs(1089) }
{ general(901) number(790) one(736) }
{ featur(1941) imag(1645) propos(1176) }
{ case(1353) use(1143) diagnosi(1136) }
{ howev(809) still(633) remain(590) }
{ data(3963) clinic(1234) research(1004) }
{ studi(1410) differ(1259) use(1210) }
{ perform(999) metric(946) measur(919) }
{ research(1085) discuss(1038) issu(1018) }
{ system(1050) medic(1026) inform(1018) }
{ visual(1396) interact(850) tool(830) }
{ perform(1367) use(1326) method(1137) }
{ studi(1119) effect(1106) posit(819) }
{ blood(1257) pressur(1144) flow(957) }
{ model(3480) simul(1196) paramet(876) }
{ monitor(1329) mobil(1314) devic(1160) }
{ ehr(2073) health(1662) electron(1139) }
{ state(1844) use(1261) util(961) }
{ patient(2837) hospit(1953) medic(668) }
{ model(2656) set(1616) predict(1553) }
{ medic(1828) order(1363) alert(1069) }
{ signal(2180) analysi(812) frequenc(800) }
{ sampl(1606) size(1419) use(1276) }
{ first(2504) two(1366) second(1323) }
{ patient(1821) servic(1111) care(1106) }
{ use(2086) technolog(871) perceiv(783) }
{ can(981) present(881) function(850) }
{ health(1844) social(1437) communiti(874) }
{ implement(1333) system(1263) develop(1122) }
{ estim(2440) model(1874) function(577) }
{ method(1969) cluster(1462) data(1082) }
{ detect(2391) sensit(1101) algorithm(908) }

Resumo

The high incidence of complex diseases has become a worldwide threat to human health. Multiple targets and pathways are perturbed during the pathological process of complex diseases. Systematic investigation of complex relationship between drugs and diseases is necessary for new association discovery and drug repurposing. For this purpose, three causal networks were constructed herein for cardiovascular diseases, diabetes mellitus, and neoplasms, respectively. A causal inference-probabilistic matrix factorization (CI-PMF) approach was proposed to predict and classify drug-disease associations, and further used for drug-repositioning predictions. First, multilevel systematic relations between drugs and diseases were integrated from heterogeneous databases to construct causal networks connecting drug-target-pathway-gene-disease. Then, the association scores between drugs and diseases were assessed by evaluating a drug's effects on multiple targets and pathways. Furthermore, PMF models were learned based on known interactions, and associations were then classified into three types by trained models. Finally, therapeutic associations were predicted based upon the ranking of association scores and predicted association types. In terms of drug-disease association prediction, modified causal inference included in CI-PMF outperformed existing causal inference with a higher AUC (area under receiver operating characteristic curve) score and greater precision. Moreover, CI-PMF performed better than single modified causal inference in predicting therapeutic drug-disease associations. In the top 30% of predicted associations, 58.6% (136/232), 50.8% (31/61), and 39.8% (140/352) hit known therapeutic associations, while precisions obtained by the latter were only 10.2% (231/2264), 8.8% (36/411), and 9.7% (189/1948). Clinical verifications were further conducted for the top 100 newly predicted therapeutic associations. As a result, 21, 12, and 32 associations have been studied and many treatment effects of drugs on diseases were investigated for cardiovascular diseases, diabetes mellitus, and neoplasms, respectively. Related chains in causal networks were extracted for these 65 clinical-verified associations, and we further illustrated the therapeutic role of etodolac in breast cancer by inferred chains. Overall, CI-PMF is a useful approach for associating drugs with complex diseases and provides potential values for drug repositioning.

Resumo Limpo

high incid complex diseas becom worldwid threat human health multipl target pathway perturb patholog process complex diseas systemat investig complex relationship drug diseas necessari new associ discoveri drug repurpos purpos three causal network construct herein cardiovascular diseas diabet mellitus neoplasm respect causal inferenceprobabilist matrix factor cipmf approach propos predict classifi drugdiseas associ use drugreposit predict first multilevel systemat relat drug diseas integr heterogen databas construct causal network connect drugtargetpathwaygenediseas associ score drug diseas assess evalu drug effect multipl target pathway furthermor pmf model learn base known interact associ classifi three type train model final therapeut associ predict base upon rank associ score predict associ type term drugdiseas associ predict modifi causal infer includ cipmf outperform exist causal infer higher auc area receiv oper characterist curv score greater precis moreov cipmf perform better singl modifi causal infer predict therapeut drugdiseas associ top predict associ hit known therapeut associ precis obtain latter clinic verif conduct top newli predict therapeut associ result associ studi mani treatment effect drug diseas investig cardiovascular diseas diabet mellitus neoplasm respect relat chain causal network extract clinicalverifi associ illustr therapeut role etodolac breast cancer infer chain overal cipmf use approach associ drug complex diseas provid potenti valu drug reposit

Resumos Similares

Brief. Bioinformatics - Database identifies FDA-approved drugs with potential to be repurposed for treatment of orphan diseases. ( 0,788173682536712 )
Comput. Biol. Med. - Cladograms with Path to Event (ClaPTE): a novel algorithm to detect associations between genotypes or phenotypes using phylogenies. ( 0,760952275082218 )
Wiley Interdiscip Rev Syst Biol Med - Emerging clinical applications in cardiovascular pharmacogenomics. ( 0,754241283834257 )
J Chem Inf Model - Data mining of protein-binding profiling data identifies structural modifications that distinguish selective and promiscuous compounds. ( 0,736779805478786 )
J Chem Inf Model - Compound pathway model to capture SAR progression: comparison of activity cliff-dependent and -independent pathways. ( 0,695613459934695 )
J Biomed Inform - Towards probabilistic decision support in public health practice: predicting recent transmission of tuberculosis from patient attributes. ( 0,689765909553063 )
Comput. Biol. Med. - Comparative structural modeling and docking studies of uricase: possible implication in enzyme supplementation therapy for hyperuricemic disorders. ( 0,664936135004828 )
Comput. Biol. Med. - Preclinical evaluation and molecular docking of 4-phenyl-1-Napthyl phenyl acetamide (4P1NPA) from Streptomyces sp. DPTB16 as a potent antifungal compound. ( 0,652597247130336 )
J Chem Inf Model - Performance evaluation of 2D fingerprint and 3D shape similarity methods in virtual screening. ( 0,649375412652776 )
J Integr Bioinform - In silico strain optimization by adding reactions to metabolic models. ( 0,618476799442182 )
J Am Med Inform Assoc - Using administrative medical claims data to supplement state disease registry systems for reporting zoonotic infections. ( 0,61474750760669 )
J. Med. Internet Res. - An internet-based epidemiological investigation of the outbreak of H7N9 Avian influenza A in China since early 2013. ( 0,61070302924278 )
J Clin Monit Comput - Anesthetic agent vapor analyzers and propellants of pressurized meter-dose inhalers. ( 0,61044571231904 )
BMC Med Inform Decis Mak - A Bayesian spatio-temporal approach for real-time detection of disease outbreaks: a case study. ( 0,604685357889267 )
BMC Med Inform Decis Mak - Establishing a web-based integrated surveillance system for early detection of infectious disease epidemic in rural China: a field experimental study. ( 0,595643308637147 )
J Biomed Inform - Mining patterns in disease classification forests. ( 0,594556742169454 )
J Chem Inf Model - Classification of cytochrome P450 inhibitors and noninhibitors using combined classifiers. ( 0,591968052608491 )
BMC Med Inform Decis Mak - Development of ClickClinica: a novel smartphone application to generate real-time global disease surveillance and clinical practice data. ( 0,590834087910728 )
J Chem Inf Model - GES polypharmacology fingerprints: a novel approach for drug repositioning. ( 0,590366933370415 )
Spat Spatiotemporal Epidemiol - Review of methods for space-time disease surveillance. ( 0,58827430145237 )
Int J Health Geogr - Modeling tools for dengue risk mapping - a systematic review. ( 0,587622446734244 )
J. Med. Internet Res. - Postmarket drug surveillance without trial costs: discovery of adverse drug reactions through large-scale analysis of web search queries. ( 0,585429731900603 )
Int J Health Geogr - Advancements in web-database applications for rabies surveillance. ( 0,584231200457241 )
J Chem Inf Model - Prediction of polypharmacological profiles of drugs by the integration of chemical, side effect, and therapeutic space. ( 0,578889495228683 )
J Am Med Inform Assoc - Machine learning-based prediction of drug-drug interactions by integrating drug phenotypic, therapeutic, chemical, and genomic properties. ( 0,576369739462645 )
Int J Health Geogr - Estimating the geographic distribution of human Tanapox and potential reservoirs using ecological niche modeling. ( 0,574983250246615 )
Brief. Bioinformatics - Drug repositioning for orphan diseases. ( 0,569726230365968 )
J Biomed Inform - Exploring the associations between drug side-effects and therapeutic indications. ( 0,56914469289002 )
AMIA Annu Symp Proc - Exploring the relationship between drug side-effects and therapeutic indications. ( 0,568743850441603 )
J Integr Bioinform - An integrated dataset for in silico drug discovery. ( 0,567609114427987 )
J Chem Inf Model - Curation and analysis of multitargeting agents for polypharmacological modeling. ( 0,566477753082092 )
J Chem Inf Model - Development of a comprehensive, validated pharmacophore hypothesis for anthrax toxin lethal factor (LF) inhibitors using genetic algorithms, Pareto scoring, and structural biology. ( 0,566369670670274 )
BMC Med Inform Decis Mak - Identifying work related injuries: comparison of methods for interrogating text fields. ( 0,564500340928928 )
J Chem Inf Model - Fighting obesity with a sugar-based library: discovery of novel MCH-1R antagonists by a new computational-VAST approach for exploration of GPCR binding sites. ( 0,564052001951556 )
IEEE Trans Image Process - Eye-tracking database for a set of standard video sequences. ( 0,563137584006735 )
Comput Math Methods Med - Antibody Drug Conjugate bioinformatics: drug delivery through the letterbox. ( 0,561779118754445 )
J Biomed Inform - Size matters: how population size influences genotype-phenotype association studies in anonymized data. ( 0,560642479966948 )
BMC Med Inform Decis Mak - Prediction of gastrointestinal disease with over-the-counter diarrheal remedy sales records in the San Francisco Bay Area. ( 0,5599425570779 )
Int J Health Geogr - Selection for resistance to oseltamivir in seasonal and pandemic H1N1 influenza and widespread co-circulation of the lineages. ( 0,5581400240494 )
J Chem Inf Model - How do metabolites differ from their parent molecules and how are they excreted? ( 0,55780328067232 )
J Chem Inf Model - Adverse drug events: database construction and in silico prediction. ( 0,553957644386494 )
Int J Med Inform - Reporting systems, reporting rates and completeness of data reported from primary healthcare to a Swedish quality register--the National Diabetes Register. ( 0,552690863437576 )
Spat Spatiotemporal Epidemiol - Companion animal disease surveillance: a new solution to an old problem? ( 0,552445260054378 )
Artif Intell Med - Discovering human immunodeficiency virus mutational pathways using temporal Bayesian networks. ( 0,551048895290866 )
Comput Math Methods Med - Structural equation modeling for analyzing erythrocyte fatty acids in Framingham. ( 0,550879208805563 )
J Am Med Inform Assoc - Mining local climate data to assess spatiotemporal dengue fever epidemic patterns in French Guiana. ( 0,549789623137709 )
J Chem Inf Model - XenoSite: accurately predicting CYP-mediated sites of metabolism with neural networks. ( 0,54775194783763 )
J Chem Inf Model - Exploring polypharmacology using a ROCS-based target fishing approach. ( 0,546545882646013 )
J Am Med Inform Assoc - Dictionary construction and identification of possible adverse drug events in Danish clinical narrative text. ( 0,545289018545375 )
AMIA Annu Symp Proc - Towards drug repositioning: a unified computational framework for integrating multiple aspects of drug similarity and disease similarity. ( 0,545098591084165 )
J. Med. Internet Res. - The complex relationship of realspace events and messages in cyberspace: case study of influenza and pertussis using tweets. ( 0,544123505387477 )
AMIA Annu Symp Proc - A neighborhood susceptibility index for planning of local physical interventions in response to pandemic influenza outbreaks. ( 0,543411553263722 )
J Biomed Inform - Using chief complaints for syndromic surveillance: a review of chief complaint based classifiers in North America. ( 0,543394324023198 )
J. Comput. Biol. - Elucidating influenza inhibition pathways via network reconstruction. ( 0,543244581987167 )
J Chem Inf Model - A computational approach to design and evaluate enzymatic reaction pathways: application to 1-butanol production from pyruvate. ( 0,540450629137429 )
BMC Med Inform Decis Mak - HERALD (health economics using routine anonymised linked data). ( 0,540357249011116 )
J Chem Inf Model - Chemogenomics approaches to rationalizing the mode-of-action of traditional Chinese and Ayurvedic medicines. ( 0,540315031951868 )
J Chem Inf Model - Predictive models for cytochrome p450 isozymes based on quantitative high throughput screening data. ( 0,539054828740707 )
J. Med. Internet Res. - Scoping review on search queries and social media for disease surveillance: a chronology of innovation. ( 0,538735209932915 )
J Biomed Inform - Disambiguation of PharmGKB drug-disease relations with NDF-RT and SPL. ( 0,538385716148181 )
J Am Med Inform Assoc - Assessment of administrative claims data for public health reporting of Salmonella in Tennessee. ( 0,537801603417576 )
Comput. Biol. Med. - Time-series analysis in the medical domain: a study of Tacrolimus administration and influence on kidney graft function. ( 0,537641350707904 )
Int J Health Geogr - Using Google Street View for systematic observation of the built environment: analysis of spatio-temporal instability of imagery dates. ( 0,537432076592449 )
J Chem Inf Model - DrugLogit: logistic discrimination between drugs and nondrugs including disease-specificity by assigning probabilities based on molecular properties. ( 0,537407544110443 )
AMIA Annu Symp Proc - Predicting adverse drug events from personal health messages. ( 0,535287470078206 )
J Biomed Inform - LabeledIn: cataloging labeled indications for human drugs. ( 0,534648626945986 )
J. Med. Internet Res. - Patient-reported outcomes as a source of evidence in off-label prescribing: analysis of data from PatientsLikeMe. ( 0,534309977824037 )
Int J Health Geogr - Identifying malaria vector breeding habitats with remote sensing data and terrain-based landscape indices in Zambia. ( 0,533661638462549 )
Comput Biol Chem - Pharmacoepidemiological characterization of drug-induced adverse reaction clusters towards understanding of their mechanisms. ( 0,533560154504331 )
J Am Med Inform Assoc - Data use and effectiveness in electronic surveillance of healthcare associated infections in the 21st century: a systematic review. ( 0,531974795800495 )
J Chem Inf Model - A mechanistic hypothesis for the cytochrome P450-catalyzed cis-trans isomerization of 4-hydroxytamoxifen: an unusual redox reaction. ( 0,531145807681499 )
J Am Med Inform Assoc - A methodology for a minimum data set for rare diseases to support national centers of excellence for healthcare and research. ( 0,530134363175966 )
IEEE Trans Pattern Anal Mach Intell - Identifying Rare and Subtle Behaviours: A Weakly Supervised Joint Topic Model. ( 0,525074494089502 )
J Chem Inf Model - Drug side-effect prediction based on the integration of chemical and biological spaces. ( 0,524942695162205 )
J. Med. Internet Res. - Guess who's not coming to dinner? Evaluating online restaurant reservations for disease surveillance. ( 0,523469470798681 )
AMIA Annu Symp Proc - Syndromic surveillance in an ICD-10 world. ( 0,522773684351889 )
J Chem Inf Model - Virtual libraries of tetrapyrrole macrocycles. Combinatorics, isomers, product distributions, and data mining. ( 0,521925360485592 )
J Chem Inf Model - Accurate atom-mapping computation for biochemical reactions. ( 0,521590119438264 )
BMC Med Inform Decis Mak - Summary of data reported to CDC's national automated biosurveillance system, 2008. ( 0,521197622618603 )
J Chem Inf Model - Modular architecture of metabolic pathways revealed by conserved sequences of reactions. ( 0,521098504875643 )
BMC Med Inform Decis Mak - Designing concept maps for a precise and objective description of pharmaceutical innovations. ( 0,520823520475649 )
J. Comput. Biol. - Increasing power of groupwise association test with likelihood ratio test. ( 0,520808273816818 )
Med Decis Making - Survival analysis and extrapolation modeling of time-to-event clinical trial data for economic evaluation: an alternative approach. ( 0,520096940763887 )
Health Informatics J - Development of a pseudo/anonymised primary care research database: Proof-of-concept study. ( 0,519685827165912 )
Comput. Biol. Med. - Systems pharmacology-based approach for dissecting the addition and subtraction theory of traditional Chinese medicine: An example using Xiao-Chaihu-Decoction and Da-Chaihu-Decoction. ( 0,518283787036746 )
Spat Spatiotemporal Epidemiol - Assessment of land use factors associated with dengue cases in Malaysia using Boosted Regression Trees. ( 0,517529889386589 )
J Chem Inf Model - Enumeration of ring-chain tautomers based on SMIRKS rules. ( 0,516962724554405 )
Artif Intell Med - Detecting disease genes based on semi-supervised learning and protein-protein interaction networks. ( 0,516189768837964 )
J Am Med Inform Assoc - A novel signal detection algorithm for identifying hidden drug-drug interactions in adverse event reports. ( 0,515889645224139 )
J Chem Inf Model - Development of an informatics platform for therapeutic protein and peptide analytics. ( 0,515041561881449 )
J Chem Inf Model - Making sense of large-scale kinase inhibitor bioactivity data sets: a comparative and integrative analysis. ( 0,514481290424096 )
Telemed J E Health - A new paradigm for disease surveillance in Vietnam. ( 0,512367702712979 )
J Chem Inf Model - Virtual affinity fingerprints for target fishing: a new application of Drug Profile Matching. ( 0,509229300519251 )
Wiley Interdiscip Rev Syst Biol Med - Drug repurposing and adverse event prediction using high-throughput literature analysis. ( 0,507933939632 )
J Chem Inf Model - CLCA: maximum common molecular substructure queries within the MetRxn database. ( 0,506842047183482 )
J Chem Inf Model - Insights into molecular basis of cytochrome p450 inhibitory promiscuity of compounds. ( 0,506655992419642 )
J Chem Inf Model - New benchmark for chemical nomenclature software. ( 0,505586208970506 )
J Chem Inf Model - Probing the bioactivity-relevant chemical space of robust reactions and common molecular building blocks. ( 0,505356195410179 )
Brief. Bioinformatics - Old friends in new guise: repositioning of known drugs with structural bioinformatics. ( 0,504491756400015 )
J Chem Inf Model - Predicting drug-target interactions using probabilistic matrix factorization. ( 0,50372476763673 )