J. Comput. Biol. - Describing the complexity of systems: multivariable set complexity and the information basis of systems biology.

Tópicos

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

Resumo

Context dependence is central to the description of complexity. Keying on the pairwise definition of "set complexity," we use an information theory approach to formulate general measures of systems complexity. We examine the properties of multivariable dependency starting with the concept of interaction information. We then present a new measure for unbiased detection of multivariable dependency, "differential interaction information." This quantity for two variables reduces to the pairwise "set complexity" previously proposed as a context-dependent measure of information in biological systems. We generalize it here to an arbitrary number of variables. Critical limiting properties of the "differential interaction information" are key to the generalization. This measure extends previous ideas about biological information and provides a more sophisticated basis for the study of complexity. The properties of "differential interaction information" also suggest new approaches to data analysis. Given a data set of system measurements, differential interaction information can provide a measure of collective dependence, which can be represented in hypergraphs describing complex system interaction patterns. We investigate this kind of analysis using simulated data sets. The conjoining of a generalized set complexity measure, multivariable dependency analysis, and hypergraphs is our central result. While our focus is on complex biological systems, our results are applicable to any complex system.

Resumo Limpo

context depend central descript complex key pairwis definit set complex use inform theori approach formul general measur system complex examin properti multivari depend start concept interact inform present new measur unbias detect multivari depend differenti interact inform quantiti two variabl reduc pairwis set complex previous propos contextdepend measur inform biolog system general arbitrari number variabl critic limit properti differenti interact inform key general measur extend previous idea biolog inform provid sophist basi studi complex properti differenti interact inform also suggest new approach data analysi given data set system measur differenti interact inform can provid measur collect depend can repres hypergraph describ complex system interact pattern investig kind analysi use simul data set conjoin general set complex measur multivari depend analysi hypergraph central result focus complex biolog system result applic complex system

Resumos Similares

Curr Protoc Bioinformatics - BEDTools: The Swiss-Army Tool for Genome Feature Analysis. ( 0,75411951593836 )
IEEE J Biomed Health Inform - Using evolutional properties of gene networks in understanding survival prognosis of glioblastoma. ( 0,751082233196263 )
Comput Biol Chem - Deciphering histone code of transcriptional regulation in malaria parasites by large-scale data mining. ( 0,749097441251715 )
Comput Biol Chem - Bioinformatic analysis of molecular network of glucosinolate biosynthesis. ( 0,744824425973572 )
J Integr Bioinform - Network expansion and pathway enrichment analysis towards biologically significant findings from microarrays. ( 0,744226594391105 )
J Integr Bioinform - Analysis and construction of pathogenicity island regulatory pathways in Salmonella enterica serovar Typhi. ( 0,741853347928515 )
Wiley Interdiscip Rev Syst Biol Med - Network biology: a direct approach to study biological function. ( 0,737335119531505 )
Brief. Bioinformatics - Alternative applications for distinct RNA sequencing strategies. ( 0,736021421336552 )
J Am Med Inform Assoc - Identifying disease genes and module biomarkers by differential interactions. ( 0,733193319513522 )
J Integr Bioinform - Profiling of genetic switches using boolean implications in expression data. ( 0,732347712532566 )
Wiley Interdiscip Rev Syst Biol Med - Signaling networks in palate development. ( 0,731867411110559 )
Brief. Bioinformatics - Targeted metabolic reconstruction: a novel approach for the characterization of plant-pathogen interactions. ( 0,731808924991397 )
J Biomed Inform - A comparative study of covariance selection models for the inference of gene regulatory networks. ( 0,731128254793135 )
J Integr Bioinform - Towards prediction and prioritization of disease genes by the modularity of human phenome-genome assembled network. ( 0,730796382456595 )
Comput Biol Chem - Exploring the complexity of pathway-drug relationships using latent Dirichlet allocation. ( 0,730530648119476 )
Comput. Biol. Med. - Degrees of separation as a statistical tool for evaluating candidate genes. ( 0,730485804075914 )
J. Comput. Biol. - A topology-based score for pathway enrichment. ( 0,729980100841135 )
Comput Biol Chem - GPEC: a Cytoscape plug-in for random walk-based gene prioritization and biomedical evidence collection. ( 0,725373686591409 )
Curr Protoc Bioinformatics - LipidXplorer: Software for Quantitative Shotgun Lipidomics Compatible with Multiple Mass Spectrometry Platforms. ( 0,72525255686659 )
J Biomed Inform - The detection of risk pathways, regulated by miRNAs, via the integration of sample-matched miRNA-mRNA profiles and pathway structure. ( 0,721193290819887 )
Comput. Biol. Med. - Identification and analysis of the regulatory network of Myc and microRNAs from high-throughput experimental data. ( 0,719164006542637 )
Comput Biol Chem - Using gene expression programming to infer gene regulatory networks from time-series data. ( 0,71839291021042 )
Comput Math Methods Med - Integrating gene expression and protein interaction data for signaling pathway prediction of Alzheimer's disease. ( 0,718169000345229 )
Artif Intell Med - Identifying regulatory relationships among genomic loci, biological pathways, and disease. ( 0,718128063088605 )
Wiley Interdiscip Rev Syst Biol Med - Recent advances in prostate development and links to prostatic diseases. ( 0,717089133619687 )
J. Comput. Biol. - Bioinformatics method to analyze the mechanism of pancreatic cancer disorder. ( 0,716730290225708 )
Brief. Bioinformatics - Revealing the architecture of genetic and epigenetic regulation: a maximum likelihood model. ( 0,716079714440424 )
Comput Biol Chem - Using volcano plots and regularized-chi statistics in genetic association studies. ( 0,715761323333762 )
J. Comput. Biol. - Computational disease gene prioritization: an appraisal. ( 0,71553190337196 )
J Integr Bioinform - Knowledge enrichment analysis for human tissue-specific genes uncover new biological insights. ( 0,712657699959512 )
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. ( 0,712351419632966 )
Wiley Interdiscip Rev Syst Biol Med - Systems biology of adipose tissue metabolism: regulation of growth, signaling and inflammation. ( 0,711681971075271 )
J. Comput. Biol. - An algorithm for efficient identification of branched metabolic pathways. ( 0,71155099248482 )
Comput Biol Chem - Disruption of murine Tcte3-3 induces tissue specific apoptosis via co-expression of Anxa5 and Pebp1. ( 0,711181593673243 )
Wiley Interdiscip Rev Syst Biol Med - Hierarchical approaches for systems modeling in cardiac development. ( 0,709088042228314 )
Comput Biol Chem - Expression patterns of photoperiod and temperature regulated heading date genes in Oryza sativa. ( 0,707019460206561 )
Comput Math Methods Med - First comprehensive in silico analysis of the functional and structural consequences of SNPs in human GalNAc-T1 gene. ( 0,706510435666017 )
J Am Med Inform Assoc - Complex-disease networks of trait-associated single-nucleotide polymorphisms (SNPs) unveiled by information theory. ( 0,706506625723156 )
J Am Med Inform Assoc - Extracting coordinated patterns of DNA methylation and gene expression in ovarian cancer. ( 0,705989872496718 )
Wiley Interdiscip Rev Syst Biol Med - Using variability in gene expression as a tool for studying gene regulation. ( 0,705253725217654 )
J Biomed Inform - Where we stand, where we are moving: Surveying computational techniques for identifying miRNA genes and uncovering their regulatory role. ( 0,703143951641299 )
J Am Med Inform Assoc - Advantages of genomic complexity: bioinformatics opportunities in microRNA cancer signatures. ( 0,702833348044551 )
J Integr Bioinform - An integrative bioinformatics framework for genome-scale multiple level network reconstruction of rice. ( 0,701722416863453 )
Comput. Biol. Med. - Mathematical modeling and sensitivity analysis of the integrated TNFa-mediated apoptotic pathway for identifying key regulators. ( 0,700945552328408 )
Brief. Bioinformatics - Affymetrix GeneChip microarray preprocessing for multivariate analyses. ( 0,700702652973766 )
Artif Intell Med - An extensive analysis of disease-gene associations using network integration and fast kernel-based gene prioritization methods. ( 0,700685887255472 )
Wiley Interdiscip Rev Syst Biol Med - Diverse functional networks of Tbx3 in development and disease. ( 0,700589638926906 )
Wiley Interdiscip Rev Syst Biol Med - Regulatory variation: an emerging vantage point for cancer biology. ( 0,698781379155276 )
J Integr Bioinform - Assembling cell context-specific gene sets: a case in cardiomyopathy. ( 0,695189984955558 )
J Integr Bioinform - Bioinformatics tools help molecular characterization of Perkinsus olseni differentially expressed genes. ( 0,694667473609419 )
J. Comput. Biol. - Vavien: an algorithm for prioritizing candidate disease genes based on topological similarity of proteins in interaction networks. ( 0,694532631895209 )
Comput Biol Chem - Identifying novel prostate cancer associated pathways based on integrative microarray data analysis. ( 0,694003464543655 )
Wiley Interdiscip Rev Syst Biol Med - Integrating omics into the cardiac differentiation of human pluripotent stem cells. ( 0,692312057466835 )
J Am Med Inform Assoc - An integrated approach to identify causal network modules of complex diseases with application to colorectal cancer. ( 0,690917174008409 )
Brief. Bioinformatics - An open-pollinated design for mapping imprinting genes in natural populations. ( 0,690255750876777 )
Comput. Biol. Med. - A molecular prospective provides new insights into implication of PDYN and OPRK1 genes in alcohol dependence. ( 0,688924401217083 )
J Biomed Inform - Gene pathways and subnetworks distinguish between major glioma subtypes and elucidate potential underlying biology. ( 0,687391343300541 )
Brief. Bioinformatics - Literature-aided interpretation of gene expression data with the weighted global test. ( 0,685314303455147 )
Brief. Bioinformatics - Learning transcriptional regulation on a genome scale: a theoretical analysis based on gene expression data. ( 0,684099642048506 )
Comput. Biol. Med. - A review on the computational approaches for gene regulatory network construction. ( 0,683831191439383 )
Comput Math Methods Med - Understanding the pathogenesis of Kawasaki disease by network and pathway analysis. ( 0,68304282255681 )
Comput Methods Programs Biomed - Warehousing re-annotated cancer genes for biomarker meta-analysis. ( 0,682154281100927 )
J Biomed Inform - Independent component analysis: mining microarray data for fundamental human gene expression modules. ( 0,680922156285667 )
Brief. Bioinformatics - Identification of aberrant pathways and network activities from high-throughput data. ( 0,679846814825779 )
J Biomed Inform - Prioritization of potential candidate disease genes by topological similarity of protein-protein interaction network and phenotype data. ( 0,678863148094315 )
J Am Med Inform Assoc - Network models of genome-wide association studies uncover the topological centrality of protein interactions in complex diseases. ( 0,678744630472738 )
Wiley Interdiscip Rev Syst Biol Med - Engineered genetic information processing circuits. ( 0,678004190566672 )
Wiley Interdiscip Rev Syst Biol Med - Genome network medicine: innovation to overcome huge challenges in cancer therapy. ( 0,676908246730026 )
J Biomed Inform - Hemojuvelin-hepcidin axis modeled and analyzed using Petri nets. ( 0,676631740450036 )
Wiley Interdiscip Rev Syst Biol Med - Mediators and dynamics of DNA methylation. ( 0,67443803672526 )
Comput Math Methods Med - Identification and functional annotation of genome-wide ER-regulated genes in breast cancer based on ChIP-Seq data. ( 0,673190848400573 )
Wiley Interdiscip Rev Syst Biol Med - miRNA regulation in the context of functional protein networks: principles and applications. ( 0,673031484407243 )
Brief. Bioinformatics - How to cluster gene expression dynamics in response to environmental signals. ( 0,67236028964258 )
Comput Biol Chem - Revealing weak differential gene expressions and their reproducible functions associated with breast cancer metastasis. ( 0,671896702451951 )
AMIA Annu Symp Proc - Mining disease fingerprints from within genetic pathways. ( 0,671810655016795 )
Brief. Bioinformatics - Identifying miRNAs, targets and functions. ( 0,671659884421039 )
Wiley Interdiscip Rev Syst Biol Med - Sex and the circuitry: progress toward a systems-level understanding of vertebrate sex determination. ( 0,671100534390587 )
Brief. Bioinformatics - Evolution of gene regulation--on the road towards computational inferences. ( 0,670792067049955 )
J. Comput. Biol. - Optimally orienting physical networks. ( 0,670066573583668 )
Wiley Interdiscip Rev Syst Biol Med - Postgenomic technologies targeting the Wnt signaling network. ( 0,669913825437874 )
Sci Data - DNA methylation temporal profiling following peripheral versus central nervous system axotomy. ( 0,668702034259718 )
Wiley Interdiscip Rev Syst Biol Med - Reverse-engineering human regulatory networks. ( 0,668146413715244 )
Comput Math Methods Med - State observer design for delayed genetic regulatory networks. ( 0,666140257084438 )
Wiley Interdiscip Rev Syst Biol Med - Establishing the stem cell state: insights from regulatory network analysis of blood stem cell development. ( 0,664495618225334 )
Perspect Health Inf Manag - Flexible approaches for teaching computational genomics in a health information management program. ( 0,663819087900409 )
Comput Math Methods Med - Dynamic regulatory network reconstruction for Alzheimer's disease based on matrix decomposition techniques. ( 0,663150345453447 )
Methods Inf Med - Pathway based microarray analysis, utilising enzyme compounds and cascade events. ( 0,662410804014231 )
Brief. Bioinformatics - Principal component analysis based methods in bioinformatics studies. ( 0,661693336467113 )
Brief. Bioinformatics - Visualizing time-related data in biology, a review. ( 0,660828564569186 )
J Biomed Inform - Comparative analysis of a novel disease phenotype network based on clinical manifestations. ( 0,660648960917333 )
Brief. Bioinformatics - Toward microRNA-mediated gene regulatory networks in plants. ( 0,66031520864682 )
J Am Med Inform Assoc - Using systems and structure biology tools to dissect cellular phenotypes. ( 0,659996499547993 )
Wiley Interdiscip Rev Syst Biol Med - Where gene discovery turns into systems biology: genome-scale RNAi screens in Drosophila. ( 0,659434796367568 )
J Am Med Inform Assoc - Knowledge boosting: a graph-based integration approach with multi-omics data and genomic knowledge for cancer clinical outcome prediction. ( 0,658446077685479 )
Comput Methods Programs Biomed - TMT-HCC: a tool for text mining the biomedical literature for hepatocellular carcinoma (HCC) biomarkers identification. ( 0,658212404551191 )
AMIA Annu Symp Proc - Towards mechanism classifiers: expression-anchored Gene Ontology signature predicts clinical outcome in lung adenocarcinoma patients. ( 0,657355777068437 )
Brief. Bioinformatics - A brief introduction to web-based genome browsers. ( 0,657352968849792 )
AMIA Annu Symp Proc - An ontology-neutral framework for enrichment analysis. ( 0,655910295190869 )
Brief. Bioinformatics - A guide to web tools to prioritize candidate genes. ( 0,655377691323075 )
Wiley Interdiscip Rev Syst Biol Med - Using a systems biology approach to understand and study the mechanisms of metastasis. ( 0,654569143236329 )