AMIA Annu Symp Proc - A fast algorithm for learning epistatic genomic relationships.

Tópicos

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

Resumo

Genetic epidemiologists strive to determine the genetic profile of diseases. Epistasis is the interaction between two or more genes to affect phenotype. Due to the often non-linearity of the interaction, it is difficult to detect statistical patterns of epistasis. Combinatorial methods for detecting epistasis investigate a subset of combinations of genes without employing a search strategy. Therefore, they do not scale to handling the high-dimensional data found in genome-wide association studies (GWAS). We represent genome-phenome interactions using a Bayesian network rule, which is a specialized Bayesian network. We develop an efficient search algorithm to learn from data a high scoring rule that may contain two or more interacting genes. Our experimental results using synthetic data indicate that this algorithm detects interacting genes as well as a Bayesian network combinatorial method, and it is much faster. Our results also indicate that the algorithm can successfully learn genome-phenome relationships using a real GWAS dataset.

Resumo Limpo

genet epidemiologist strive determin genet profil diseas epistasi interact two gene affect phenotyp due often nonlinear interact difficult detect statist pattern epistasi combinatori method detect epistasi investig subset combin gene without employ search strategi therefor scale handl highdimension data found genomewid associ studi gwas repres genomephenom interact use bayesian network rule special bayesian network develop effici search algorithm learn data high score rule may contain two interact gene experiment result use synthet data indic algorithm detect interact gene well bayesian network combinatori method much faster result also indic algorithm can success learn genomephenom relationship use real gwas dataset

Resumos Similares

Comput Biol Chem - Fast detection of high-order epistatic interactions in genome-wide association studies using information theoretic measure. ( 0,80611956397295 )
J. Comput. Biol. - Biological cluster evaluation for gene function prediction. ( 0,746751410494926 )
Comput. Biol. Med. - Multi-stage filtering for improving confidence level and determining dominant clusters in clustering algorithms of gene expression data. ( 0,741634739765686 )
J. Comput. Biol. - Markov logic networks in the analysis of genetic data. ( 0,733714801607687 )
J Integr Bioinform - Profiling of genetic switches using boolean implications in expression data. ( 0,728282745116171 )
Sci Data - Assessment of lipidomic species in hepatocyte lipid droplets from stressed mouse models. ( 0,725233196496247 )
Comput Biol Chem - Mode of action classification of chemicals using multi-concentration time-dependent cellular response profiles. ( 0,711491094919923 )
Comput. Biol. Med. - Nonlinear dimensionality reduction of gene expression data for visualization and clustering analysis of cancer tissue samples. ( 0,704184038998346 )
Brief. Bioinformatics - GO-function: deriving biologically relevant functions from statistically significant functions. ( 0,701827696010706 )
Comput Biol Chem - Ped_Outlier software for automatic identification of within-family outliers. ( 0,691194004724981 )
J Integr Bioinform - Discovery of miR-mRNA interactions via simultaneous Bayesian inference of gene networks and clusters using sequence-based predictions and expression data. ( 0,689578788877701 )
J Biomed Inform - Average correlation clustering algorithm (ACCA) for grouping of co-regulated genes with similar pattern of variation in their expression values. ( 0,688805502432383 )
Comput Biol Chem - Analysis of the NCI-60 dataset for cancer-related microRNA and mRNA using expression profiles. ( 0,68150307222326 )
Comput Biol Chem - Meta-analysis of microarray data: The case of imatinib resistance in chronic myelogenous leukemia. ( 0,679215865303077 )
J. Comput. Biol. - A stationary wavelet entropy-based clustering approach accurately predicts gene expression. ( 0,671710738570998 )
J. Comput. Biol. - A topology-based score for pathway enrichment. ( 0,671303113232898 )
J Integr Bioinform - Parallel Niche Pareto AlineaGA--an evolutionary multiobjective approach on multiple sequence alignment. ( 0,660136507219476 )
Brief. Bioinformatics - A quantitative model of transcriptional differentiation driving host-pathogen interactions. ( 0,649659088473992 )
J Biomed Inform - Enabling enrichment analysis with the Human Disease Ontology. ( 0,646033743720637 )
J Integr Bioinform - Clustering of gene expression profiles: creating initialization-independent clusterings by eliminating unstable genes. ( 0,643209245435375 )
J Biomed Inform - Statistical file matching of flow cytometry data. ( 0,640333712435994 )
Wiley Interdiscip Rev Syst Biol Med - Mechanisms of genetic regulation in gene expression: examples from drug metabolizing enzymes and transporters. ( 0,636965076005027 )
Brief. Bioinformatics - Similarity of markers identified from cancer gene expression studies: observations from GEO. ( 0,634105932387056 )
Artif Intell Med - Hybrid genetic algorithm-neural network: feature extraction for unpreprocessed microarray data. ( 0,633757328674274 )
Comput. Biol. Med. - Impact of TGF-b on breast cancer from a quantitative proteomic analysis. ( 0,630930974324097 )
Comput Biol Chem - Using volcano plots and regularized-chi statistics in genetic association studies. ( 0,63057021581391 )
Artif Intell Med - An extensive analysis of disease-gene associations using network integration and fast kernel-based gene prioritization methods. ( 0,629554977331413 )
J Integr Bioinform - Using variable precision rough set for selection and classification of biological knowledge integrated in DNA gene expression. ( 0,622491491047515 )
Brief. Bioinformatics - Bayesian inference for genomic imprinting underlying developmental characteristics. ( 0,622393384685837 )
Comput. Biol. Med. - An ant colony optimization based algorithm for identifying gene regulatory elements. ( 0,618894077747005 )
Comput. Biol. Med. - CAM: a web tool for combining array CGH and microarray gene expression data from multiple samples. ( 0,61869724070239 )
Comput Biol Chem - Genomic studies on nitrogen metabolism in Halomonas boliviensis: metabolic pathway, biochemistry and evolution. ( 0,618552741931304 )
J Biomed Inform - Using semantic predications to uncover drug-drug interactions in clinical data. ( 0,618135208075583 )
Comput. Biol. Med. - Inferring functional miRNA-mRNA regulatory modules in epithelial-mesenchymal transition with a probabilistic topic model. ( 0,616743962481058 )
J Biomed Inform - A machine-learned knowledge discovery method for associating complex phenotypes with complex genotypes. Application to pain. ( 0,614676396287228 )
Methods Inf Med - Application of microarray analysis on computer cluster and cloud platforms. ( 0,612587470681225 )
J Am Med Inform Assoc - Advantages of genomic complexity: bioinformatics opportunities in microRNA cancer signatures. ( 0,611422397876818 )
J Biomed Inform - Comparative analysis of a novel disease phenotype network based on clinical manifestations. ( 0,609876492254586 )
Comput Methods Programs Biomed - Development and application of efficient pathway enumeration algorithms for metabolic engineering applications. ( 0,609779271865363 )
Brief. Bioinformatics - Accounting for noise when clustering biological data. ( 0,608495236836731 )
BMC Med Inform Decis Mak - Finding type 2 diabetes causal single nucleotide polymorphism combinations and functional modules from genome-wide association data. ( 0,607723468864131 )
J Integr Bioinform - An integrative bioinformatics framework for genome-scale multiple level network reconstruction of rice. ( 0,606765555465923 )
J. Comput. Biol. - Stochastic simulation of notch signaling reveals novel factors that mediate the differentiation of neural stem cells. ( 0,605809572084981 )
J. Comput. Biol. - Vavien: an algorithm for prioritizing candidate disease genes based on topological similarity of proteins in interaction networks. ( 0,605350070345774 )
Comput Methods Programs Biomed - MCF: a tool to find multi-scale community profiles in biological networks. ( 0,603133176259201 )
J Am Med Inform Assoc - Integrated morphologic analysis for the identification and characterization of disease subtypes. ( 0,603062530655651 )
Comput Biol Chem - Deciphering histone code of transcriptional regulation in malaria parasites by large-scale data mining. ( 0,599895564463365 )
J Biomed Inform - Analysis of functional and pathway association of differential co-expressed genes: a case study in drug addiction. ( 0,599855166095397 )
IEEE Trans Vis Comput Graph - GPU-based Multilevel Clustering. ( 0,599106584179951 )
J Am Med Inform Assoc - Network models of genome-wide association studies uncover the topological centrality of protein interactions in complex diseases. ( 0,598496169271326 )
Comput Math Methods Med - Understanding the pathogenesis of Kawasaki disease by network and pathway analysis. ( 0,593712336118844 )
J Biomed Inform - Mining patterns in disease classification forests. ( 0,593627127447342 )
J Integr Bioinform - Towards prediction and prioritization of disease genes by the modularity of human phenome-genome assembled network. ( 0,590524574353998 )
J Am Med Inform Assoc - Complex-disease networks of trait-associated single-nucleotide polymorphisms (SNPs) unveiled by information theory. ( 0,589231319159722 )
J. Comput. Biol. - Narratives in the network: interactive methods for mining cell signaling networks. ( 0,588770802231879 )
J Am Med Inform Assoc - Utility of gene-specific algorithms for predicting pathogenicity of uncertain gene variants. ( 0,588531454987767 )
Comput Biol Chem - lncRNAMap: a map of putative regulatory functions in the long non-coding transcriptome. ( 0,58637801181386 )
J Am Med Inform Assoc - Identifying disease genes and module biomarkers by differential interactions. ( 0,584572989011704 )
Brief. Bioinformatics - Pharmaco-miR: linking microRNAs and drug effects. ( 0,583725206492828 )
Brief. Bioinformatics - Extracting reaction networks from databases-opening Pandora's box. ( 0,58341195596274 )
Comput Biol Chem - Sparse regularized discriminant analysis with application to microarrays. ( 0,582185027402637 )
Comput Math Methods Med - Novel harmonic regularization approach for variable selection in Cox's proportional hazards model. ( 0,580576336587418 )
Wiley Interdiscip Rev Syst Biol Med - Using variability in gene expression as a tool for studying gene regulation. ( 0,579448260179805 )
J Biomed Inform - A comparative study of covariance selection models for the inference of gene regulatory networks. ( 0,575542203603824 )
Comput Biol Chem - In silico analysis of cis-acting regulatory elements in 5' regulatory regions of sucrose transporter gene families in rice (Oryza sativa Japonica) and Arabidopsis thaliana. ( 0,575114538021216 )
Comput Methods Programs Biomed - Fuzzy and hard clustering analysis for thyroid disease. ( 0,574899410943582 )
Artif Intell Med - Identifying regulatory relationships among genomic loci, biological pathways, and disease. ( 0,572969600081948 )
Wiley Interdiscip Rev Syst Biol Med - Where gene discovery turns into systems biology: genome-scale RNAi screens in Drosophila. ( 0,572752209192808 )
J Chem Inf Model - Investigation of the use of spectral clustering for the analysis of molecular data. ( 0,570567300213294 )
Int J Neural Syst - A cluster merging method for time series microarray with production values. ( 0,570350763977721 )
Comput Biol Chem - Disruption of murine Tcte3-3 induces tissue specific apoptosis via co-expression of Anxa5 and Pebp1. ( 0,570301411175586 )
IEEE Trans Neural Netw Learn Syst - Improved Fault Classification in Series Compensated Transmission Line: Comparative Evaluation of Chebyshev Neural Network Training Algorithms. ( 0,569631461726882 )
J. Comput. Biol. - An algorithm for efficient identification of branched metabolic pathways. ( 0,569597808682387 )
Comput Biol Chem - Identification of all trinucleotide circular codes. ( 0,569286003496958 )
Brief. Bioinformatics - Identifying miRNAs, targets and functions. ( 0,568970028438913 )
Brief. Bioinformatics - Revealing the architecture of genetic and epigenetic regulation: a maximum likelihood model. ( 0,568023291780461 )
Wiley Interdiscip Rev Syst Biol Med - Recent advances in prostate development and links to prostatic diseases. ( 0,567281145948985 )
Comput Biol Chem - Identifying novel prostate cancer associated pathways based on integrative microarray data analysis. ( 0,565444375166381 )
Comput. Biol. Med. - Revealing pathway maps of renal cell carcinoma by gene expression change. ( 0,565098403914018 )
J. Comput. Biol. - Bioinformatics method to analyze the mechanism of pancreatic cancer disorder. ( 0,564337986869302 )
J Am Med Inform Assoc - An integrated approach to identify causal network modules of complex diseases with application to colorectal cancer. ( 0,563104445170901 )
Wiley Interdiscip Rev Syst Biol Med - Using systems approaches to address challenges for clinical implementation of pharmacogenomics. ( 0,562710036521932 )
Comput Biol Chem - Expression patterns of photoperiod and temperature regulated heading date genes in Oryza sativa. ( 0,56176640977722 )
AMIA Annu Symp Proc - Towards mechanism classifiers: expression-anchored Gene Ontology signature predicts clinical outcome in lung adenocarcinoma patients. ( 0,561353147960934 )
J Chem Inf Model - ThermoData Engine (TDE): software implementation of the dynamic data evaluation concept. 6. Dynamic web-based data dissemination through the NIST Web Thermo Tables. ( 0,561325202564627 )
J Biomed Inform - Drug target identification in sphingolipid metabolism by computational systems biology tools: metabolic control analysis and metabolic pathway analysis. ( 0,561167253754031 )
AMIA Annu Symp Proc - Mining disease fingerprints from within genetic pathways. ( 0,560904519437817 )
Comput. Biol. Med. - Computational gene network study on antibiotic resistance genes of Acinetobacter baumannii. ( 0,560626762642777 )
Comput. Biol. Med. - Meta analysis of gene expression changes upon treatment of A549 cells with anti-cancer drugs to identify universal responses. ( 0,560411820205511 )
Comput. Biol. Med. - Degrees of separation as a statistical tool for evaluating candidate genes. ( 0,559410860532759 )
J Chem Inf Model - Modular architecture of metabolic pathways revealed by conserved sequences of reactions. ( 0,5593241306599 )
AMIA Annu Symp Proc - Exploring schizophrenia drug-gene interactions through molecular network and pathway modeling. ( 0,559161815184091 )
Wiley Interdiscip Rev Syst Biol Med - Noncoding RNAs in gene regulation. ( 0,559075393100024 )
Wiley Interdiscip Rev Syst Biol Med - Integrating omics into the cardiac differentiation of human pluripotent stem cells. ( 0,558728007995108 )
Comput Biol Chem - Statistical analysis of combinatorial transcriptional regulatory motifs in human intron-containing promoter sequences. ( 0,557328991754099 )
Comput. Biol. Med. - Identification and analysis of the regulatory network of Myc and microRNAs from high-throughput experimental data. ( 0,556502732121529 )
Comput. Biol. Med. - Prediction of microRNA-regulated protein interaction pathways in Arabidopsis using machine learning algorithms. ( 0,556300808265793 )
Wiley Interdiscip Rev Syst Biol Med - Diverse functional networks of Tbx3 in development and disease. ( 0,556097152985805 )
Comput. Biol. Med. - An evolutionary approach for searching metabolic pathways. ( 0,55608062190915 )
Methods Inf Med - Pathway based microarray analysis, utilising enzyme compounds and cascade events. ( 0,555056064443669 )