Brief. Bioinformatics - Design and validation issues in RNA-seq experiments.

Tópicos

{ sequenc(1873) structur(1644) protein(1328) }
{ research(1085) discuss(1038) issu(1018) }
{ gene(2352) biolog(1181) express(1162) }
{ framework(1458) process(801) describ(734) }
{ general(901) number(790) one(736) }
{ studi(1410) differ(1259) use(1210) }
{ design(1359) user(1324) use(1319) }
{ model(3480) simul(1196) paramet(876) }
{ health(1844) social(1437) communiti(874) }
{ model(3404) distribut(989) bayesian(671) }
{ bind(1733) structur(1185) ligand(1036) }
{ method(1219) similar(1157) match(930) }
{ network(2748) neural(1063) input(814) }
{ imag(2675) segment(2577) method(1081) }
{ assess(1506) score(1403) qualiti(1306) }
{ algorithm(1844) comput(1787) effici(935) }
{ data(1714) softwar(1251) tool(1186) }
{ search(2224) databas(1162) retriev(909) }
{ howev(809) still(633) remain(590) }
{ data(3963) clinic(1234) research(1004) }
{ health(3367) inform(1360) care(1135) }
{ monitor(1329) mobil(1314) devic(1160) }
{ ehr(2073) health(1662) electron(1139) }
{ model(2656) set(1616) predict(1553) }
{ can(774) often(719) complex(702) }
{ imag(1947) propos(1133) code(1026) }
{ data(1737) use(1416) pattern(1282) }
{ inform(2794) health(2639) internet(1427) }
{ system(1976) rule(880) can(841) }
{ measur(2081) correl(1212) valu(896) }
{ imag(1057) registr(996) error(939) }
{ featur(3375) classif(2383) classifi(1994) }
{ imag(2830) propos(1344) filter(1198) }
{ 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) }
{ 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) }
{ extract(1171) text(1153) clinic(932) }
{ method(1557) propos(1049) approach(1037) }
{ control(1307) perform(991) simul(935) }
{ model(2220) cell(1177) simul(1124) }
{ care(1570) inform(1187) nurs(1089) }
{ method(984) reconstruct(947) comput(926) }
{ 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) }
{ visual(1396) interact(850) tool(830) }
{ compound(1573) activ(1297) structur(1058) }
{ perform(1367) use(1326) method(1137) }
{ studi(1119) effect(1106) posit(819) }
{ blood(1257) pressur(1144) flow(957) }
{ spatial(1525) area(1432) region(1030) }
{ record(1888) medic(1808) patient(1693) }
{ state(1844) use(1261) util(961) }
{ research(1218) medic(880) student(794) }
{ patient(2837) hospit(1953) medic(668) }
{ 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) }
{ sampl(1606) size(1419) use(1276) }
{ 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) }
{ 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) }
{ drug(1928) target(777) effect(648) }
{ result(1111) use(1088) new(759) }
{ implement(1333) system(1263) develop(1122) }
{ survey(1388) particip(1329) question(1065) }
{ estim(2440) model(1874) function(577) }
{ 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) }
{ detect(2391) sensit(1101) algorithm(908) }

Resumo

The next-generation sequencing technologies are being rapidly applied in biological research. Tens of millions of short sequences generated in a single experiment provide us enormous information on genome composition, genetic variants, gene expression levels and protein binding sites depending on the applications. Various methods are being developed for analyzing the data generated by these technologies. However, the relevant experimental design issues have rarely been discussed. In this review, we use RNA-seq as an example to bring this topic into focus and to discuss experimental design and validation issues pertaining to next-generation sequencing in the quantification of transcripts.

Resumo Limpo

nextgener sequenc technolog rapid appli biolog research ten million short sequenc generat singl experi provid us enorm inform genom composit genet variant gene express level protein bind site depend applic various method develop analyz data generat technolog howev relev experiment design issu rare discuss review use rnaseq exampl bring topic focus discuss experiment design valid issu pertain nextgener sequenc quantif transcript

Resumos Similares

Brief. Bioinformatics - Methodological aspects of whole-genome bisulfite sequencing analysis. ( 0,779836057254388 )
Brief. Bioinformatics - Environmental bio-monitoring with high-throughput sequencing. ( 0,732467020764714 )
J Integr Bioinform - Identification of common carp innate immune genes with whole-genome sequencing and RNA-Seq data. ( 0,723709941421033 )
Wiley Interdiscip Rev Syst Biol Med - Genome network medicine: innovation to overcome huge challenges in cancer therapy. ( 0,718020316806558 )
Brief. Bioinformatics - A review of statistical methods for prediction of proteolytic cleavage. ( 0,712781002873083 )
Wiley Interdiscip Rev Syst Biol Med - Quantitative analysis of phosphorylation-based protein signaling networks in the immune system by mass spectrometry. ( 0,712058308236149 )
Brief. Bioinformatics - Bioinformatics for personal genome interpretation. ( 0,707015799526737 )
Brief. Bioinformatics - Experimental evidence validating the computational inference of functional associations from gene fusion events: a critical survey. ( 0,705809478407338 )
Wiley Interdiscip Rev Syst Biol Med - Subdiffractive microscopy: techniques, applications, and challenges. ( 0,703484032899793 )
J. Comput. Biol. - Reconstructing the history of large-scale genomic changes: biological questions and computational challenges. ( 0,701145124521501 )
Comput Biol Chem - Gene expression regulation of the PF00480 or PF14340 domain proteins suggests their involvement in sulfur metabolism. ( 0,696934557076064 )
Brief. Bioinformatics - Introduction into the analysis of high-throughput-sequencing based epigenome data. ( 0,684672300727797 )
Comput Biol Chem - Large replication skew domains delimit GC-poor gene deserts in human. ( 0,684137847538702 )
Brief. Bioinformatics - Probabilistic graphical models for genetic association studies. ( 0,682973437166738 )
Comput Biol Chem - New insights on gene regulation in archaea. ( 0,681972388511651 )
J Chem Inf Model - Computational prediction of metabolism: sites, products, SAR, P450 enzyme dynamics, and mechanisms. ( 0,676319409514333 )
Brief. Bioinformatics - Toward microRNA-mediated gene regulatory networks in plants. ( 0,675167227042821 )
Brief. Bioinformatics - The genomic and functional characteristics of disease genes. ( 0,67375753381011 )
J Integr Bioinform - Prediction of thioredoxin and glutaredoxin target proteins by identifying reversibly oxidized cysteinyl residues. ( 0,668823663580444 )
J Integr Bioinform - Integrating sequence analysis with biophysical modelling for accurate transcription start site prediction. ( 0,667423812471915 )
Brief. Bioinformatics - Sequencing technologies and tools for short tandem repeat variation detection. ( 0,661461496550292 )
Comput Biol Chem - ProCoCoA: A quantitative approach for analyzing protein core composition. ( 0,661216758062004 )
Comput Biol Chem - In silico characterization and evolutionary analyses of CCAAT binding proteins in the lycophyte plant Selaginella moellendorffii genome: a growing comparative genomics resource. ( 0,660707113455955 )
Brief. Bioinformatics - Reconciliation of metabolites and biochemical reactions for metabolic networks. ( 0,659764237498481 )
Wiley Interdiscip Rev Syst Biol Med - The zebrafish: scalable in vivo modeling for systems biology. ( 0,65966585773003 )
Wiley Interdiscip Rev Syst Biol Med - Large-scale mouse knockouts and phenotypes. ( 0,656415888577721 )
Brief. Bioinformatics - Evolution of gene regulation--on the road towards computational inferences. ( 0,654344442647252 )
Wiley Interdiscip Rev Syst Biol Med - Mechanisms controlling hematopoietic stem cell functions during normal hematopoiesis and hematological malignancies. ( 0,653554335472689 )
J. Comput. Biol. - A probabilistic model of neutral and selective dynamics of protein network evolution. ( 0,651646280127217 )
Comput Math Methods Med - Analyzing effects of naturally occurring missense mutations. ( 0,651016936759753 )
Comput Biol Chem - In silico identification of conserved microRNAs and their target transcripts from expressed sequence tags of three earthworm species. ( 0,648195093206013 )
Brief. Bioinformatics - Information theory applications for biological sequence analysis. ( 0,647750275631296 )
Brief. Bioinformatics - Application of second-generation sequencing to cancer genomics. ( 0,646628970466139 )
Brief. Bioinformatics - A survey of sequence alignment algorithms for next-generation sequencing. ( 0,645953439364847 )
Brief. Bioinformatics - Network inference from AP-MS data: computational challenges and solutions. ( 0,640227810842393 )
Comput. Biol. Med. - Impact of TGF-b on breast cancer from a quantitative proteomic analysis. ( 0,636108762037557 )
Brief. Bioinformatics - Next generation sequencing in functional genomics. ( 0,635264223563441 )
Comput Biol Chem - Identical sequence patterns in the ends of exons and introns of human protein-coding genes. ( 0,634320443724569 )
Comput Biol Chem - Analysis of the relationships between evolvability, thermodynamics, and the functions of intrinsically disordered proteins/regions. ( 0,632082487268455 )
Comput Biol Chem - Identification of potential drug targets by subtractive genome analysis of Bacillus anthracis A0248: An in silico approach. ( 0,631696286119636 )
J. Comput. Biol. - Biological network querying techniques: analysis and comparison. ( 0,631202510723437 )
Brief. Bioinformatics - Systematic identification of Class I HDAC substrates. ( 0,630747484465314 )
J Am Med Inform Assoc - Ethical and practical challenges to studying patients who opt out of large-scale biorepository research. ( 0,628148634537008 )
Comput Biol Chem - Global expression analysis of miRNA gene cluster and family based on isomiRs from deep sequencing data. ( 0,62736623561393 )
Brief. Bioinformatics - Rich annotation of DNA sequencing variants by leveraging the Ensembl Variant Effect Predictor with plugins. ( 0,626559175574975 )
Brief. Bioinformatics - The what, where, how and why of gene ontology--a primer for bioinformaticians. ( 0,626309548329072 )
Wiley Interdiscip Rev Syst Biol Med - Mass spectrometry-based proteomics: qualitative identification to activity-based protein profiling. ( 0,626145513101011 )
J Chem Inf Model - Proteins as sponges: a statistical journey along protein structure organization principles. ( 0,625511874827984 )
BMC Med Inform Decis Mak - Improved method for protein complex detection using bottleneck proteins. ( 0,625346845177108 )
Brief. Bioinformatics - New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing. ( 0,62383568114704 )
Brief. Bioinformatics - Alternative applications for distinct RNA sequencing strategies. ( 0,621128952894451 )
Brief. Bioinformatics - A practical guide for the computational selection of residues to be experimentally characterized in protein families. ( 0,620077828522192 )
Wiley Interdiscip Rev Syst Biol Med - Promise of personalized omics to precision medicine. ( 0,619499646347027 )
Comput Math Methods Med - Uses of phage display in agriculture: sequence analysis and comparative modeling of late embryogenesis abundant client proteins suggest protein-nucleic acid binding functionality. ( 0,617816241525466 )
Wiley Interdiscip Rev Syst Biol Med - Postgenomic technologies targeting the Wnt signaling network. ( 0,615457454896664 )
Brief. Bioinformatics - Advances in network-based metabolic pathway analysis and gene expression data integration. ( 0,614638913004928 )
Sci Data - Comprehensive analysis of the venom gland transcriptome of the spider Dolomedes fimbriatus. ( 0,61025829098629 )
J Integr Bioinform - Construction of coffee transcriptome networks based on gene annotation semantics. ( 0,608833448633111 )
Brief. Bioinformatics - The challenges of delivering bioinformatics training in the analysis of high-throughput data. ( 0,60806899210506 )
Comput Methods Programs Biomed - Pinda: a web service for detection and analysis of intraspecies gene duplication events. ( 0,606122276409271 )
Wiley Interdiscip Rev Syst Biol Med - Recent approaches to the prioritization of candidate disease genes. ( 0,605894098581958 )
Brief. Bioinformatics - Congruency in the prediction of pathogenic missense mutations: state-of-the-art web-based tools. ( 0,605154877755753 )
AMIA Annu Symp Proc - Similarity-based disease risk assessment for personal genomes: proof of concept. ( 0,605098881053673 )
Brief. Bioinformatics - Positional orthology: putting genomic evolutionary relationships into context. ( 0,604847035404034 )
Comput Biol Chem - Structural characteristics of genomic islands associated with GMP synthases as integration hotspot among sequenced microbial genomes. ( 0,60046262211345 )
J Integr Bioinform - BacillusRegNet: a transcriptional regulation database and analysis platform for Bacillus species. ( 0,600004272028537 )
Brief. Bioinformatics - Protein inference: a review. ( 0,599685515281644 )
Artif Intell Med - Predicting malaria interactome classifications from time-course transcriptomic data along the intraerythrocytic developmental cycle. ( 0,598479921910822 )
Brief. Bioinformatics - De novo assembly of short sequence reads. ( 0,598076654288738 )
Comput Biol Chem - Genomic studies on nitrogen metabolism in Halomonas boliviensis: metabolic pathway, biochemistry and evolution. ( 0,59675083535877 )
Comput. Biol. Med. - Accelerating in silico research with workflows: a lesson in Simplicity. ( 0,595254139583361 )
J. Comput. Biol. - Node fingerprinting: an efficient heuristic for aligning biological networks. ( 0,594435519873055 )
Brief. Bioinformatics - Identification of aberrant pathways and network activities from high-throughput data. ( 0,594414430525721 )
Brief. Bioinformatics - A survey of tools for variant analysis of next-generation genome sequencing data. ( 0,594361485128962 )
Comput Math Methods Med - Mathematical model of dynamic protein interactions regulating p53 protein stability for tumor suppression. ( 0,594340962261089 )
Brief. Bioinformatics - Integrative approaches for predicting protein function and prioritizing genes for complex phenotypes using protein interaction networks. ( 0,593809341477097 )
Brief. Bioinformatics - Machine learning approaches for the discovery of gene-gene interactions in disease data. ( 0,591804575046095 )
Brief. Bioinformatics - Motif discovery and transcription factor binding sites before and after the next-generation sequencing era. ( 0,591551384564792 )
Comput Biol Chem - Conserved patterns in bacterial genomes: a conundrum physically tailored by evolutionary tinkering. ( 0,591442397616682 )
Wiley Interdiscip Rev Syst Biol Med - Noncoding RNAs in gene regulation. ( 0,5908977687893 )
J. Comput. Biol. - Gene prediction based on DNA spectral analysis: a literature review. ( 0,58948914016617 )
Comput. Biol. Med. - Evolution of the mir-181 microRNA family. ( 0,588501238269571 )
Comput Biol Chem - lncRNAMap: a map of putative regulatory functions in the long non-coding transcriptome. ( 0,588202748048444 )
Curr Protoc Bioinformatics - Using Weeder, Pscan, and PscanChIP for the Discovery of Enriched Transcription Factor Binding Site Motifs in Nucleotide Sequences. ( 0,588001445345163 )
Brief. Bioinformatics - Reference databases for taxonomic assignment in metagenomics. ( 0,587725116830377 )
Comput Biol Chem - Computational insight into nitration of human myoglobin. ( 0,587414653900381 )
Brief. Bioinformatics - Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies. ( 0,587383974885884 )
Brief. Bioinformatics - Advantages of mixing bioinformatics and visualization approaches for analyzing sRNA-mediated regulatory bacterial networks. ( 0,586873370520596 )
Wiley Interdiscip Rev Syst Biol Med - The molecular circuitry underlying pluripotency in embryonic stem cells. ( 0,586685930662581 )
Brief. Bioinformatics - Base-calling for next-generation sequencing platforms. ( 0,586673594672461 )
Comput Biol Chem - All-atomic molecular dynamic studies of human CDK8: insight into the A-loop, point mutations and binding with its partner CycC. ( 0,586672902207946 )
Brief. Bioinformatics - Learning transcriptional regulation on a genome scale: a theoretical analysis based on gene expression data. ( 0,586047389293755 )
Comput Biol Chem - Gene cloning, homology comparison and analysis of the main functional structure domains of beta estrogen receptor in Jining Gray goat. ( 0,58590508106388 )
Comput Biol Chem - Computational intelligence techniques in bioinformatics. ( 0,583191126509596 )
Comput. Biol. Med. - Computer-aided techniques for chromogenic immunohistochemistry: status and directions. ( 0,582832428484929 )
J. Comput. Biol. - Sequence alignment of viral channel proteins with cellular ion channels. ( 0,58262725666805 )
Brief. Bioinformatics - Visualizing time-related data in biology, a review. ( 0,582071797034365 )
Comput Biol Chem - Menzerath-Altmann law in mammalian exons reflects the dynamics of gene structure evolution. ( 0,580288457473997 )
Comput Math Methods Med - First comprehensive in silico analysis of the functional and structural consequences of SNPs in human GalNAc-T1 gene. ( 0,579922185408541 )
J. Comput. Biol. - IDBA-MTP: A Hybrid Metatranscriptomic Assembler Based on Protein Information. ( 0,578619927628327 )