ライフサイエンスコーパス: annotation

1 lasses, and connection to complete syntactic annotation.

2 n of data sharing capabilities for L1Xplorer annotation.

3 proved to enable fast and automatic function annotation.

4 ous RNAs and summarization based on taxonomy annotation.

5 tional analysis of mRNA-ends to improve gene annotation.

6 of genome alignment and independent of gene annotation.

7 is critical for achieving high-quality gene annotation.

8 ructures from MS/MS spectra missing a manual annotation.

9 rms from 44 968 gene models and updated gene annotation.

10 onomy is required for broad-scale metabolite annotation.

11 104, which is consistent with our functional annotation.

12 unter resembles a workflow of manual spectra annotation.

13 on patterns consistent with the xMSannotator annotation.

14 al 50 MS/MS spectra overlooked during manual annotation.

15 ignificantly enriched for the "liver cancer" annotation.

16 he reads were processed by metagenomic rapid annotation.

17 gmented and are split into more genes during annotation.

18 set annotations, and infers factors without annotation.

19 ges and brain-specific promoter and enhancer annotations.

20 rformed in silico according to Gene Ontology annotations.

21 ally conserved network parts and to transfer annotations.

22 otein domains, beyond our current functional annotations.

23 correlated with different subsets of ENCODE annotations.

24 on of the data to produce unified cell-state annotations.

25 entially causal variants based on functional annotations.

26 tab-separated value format for user-provided annotations.

27 re their MSAs, taxonomic representation, and annotations.

28 ion dependent with respect to the transcript annotations.

29 profiling of genes using highly descriptive annotations.

30 stratified LD score regression to continuous annotations.

31 ss spectral features to confident metabolite annotations.

32 test version of the genomic sequence and its annotations.

33 ity rather than sparse biochemical knowledge annotations.

34 ncer and available pathological and clinical annotations.

35 acteristics of the regions differ across the annotations.

36 nt, and incorporation of functional data and annotations.

37 t risk status can be predicted by functional annotations.

38 approach significantly improves the function annotation accuracy of the former structure-based pipeli

39 otein domains, sharing a specific functional annotation across genomes of given size.

40 logenetics projects, but current methods for annotation, alignment and tree estimation still require

41 Functional annotation analyses indicated that a wide variety of vit

42 e quantified miRNA birth and death using our annotation and a phylogenetic model for estimating rates

43 le analysis pipeline for the high-confidence annotation and acyl composition analysis of oxidized lip

44 explored, particularly in plants where their annotation and characterization are still incomplete.

45 We present GLANET as a comprehensive annotation and enrichment analysis tool which implements

46 me and human effort required for subcellular annotation and feature extraction.

47 a long-standing bottleneck in transcriptome annotation and generates manual-quality full-length tran

48 ertook (1) bioinformatic, functional genomic annotation and human osteoblast expression studies; (2)

49 GWAS is a powerful tool for gene-metabolite annotation and identification, pathways elucidation, and

50 RIC uses this data to improve both subsystem annotation and k-mer classification, and tags new genome

51 seq, DNase hypersensitive site mapping, site annotation and motif identification for DNase-seq, analy

52 Gene ontology annotation and network analysis showed that MALAT1 was h

53 tein structure and function prediction, gene annotation and phylogenetic tree construction.

54 mples from species with and without database annotation and thus has clear advantages over methods th

55 which we explicitly model various functional annotations and allow for linkage disequilibrium estimat

56 ociations based on the quantification of the annotations and allowing for multiple associated variant

57 ntly significant effects of other LD-related annotations and confirmed via forward simulations that t

58 rmal patterns for structuring ontologies and annotations and for linking ontologies to the outputs of

59 discuss the probable error rates in the SRA annotations and introduce a resource assessing SRA data.

60 ity of causality for variants with different annotations and jointly models genome-wide variants to a

61 unctional protein association networks, gene annotations and localization of identified proteins were

62 es, including a comprehensive set of general annotations and more focused annotations for carbohydrat

63 With a linear model that combines chromatin annotations and sequence information, we achieve a Pears

64 and more strongly predictable by both ENCODE annotations and sequence-based models.

65 the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these.

66 vestigators to easily access available brain annotations and thus incorporate this wealth of informat

67 some, minor allele frequency, and functional annotations and to test for enrichment of rare deleterio

68 ficiency of performing data quality control, annotation, and association analysis.

69 f published data, provide standardization of annotation, and improve accessibility, we created denovo

70 HC class II region with rigorous manual gene annotation, and it will serve as an important resource f

71 such as: narrow and broad peak calling, peak annotation, and motif identification for ChIP-seq, diffe

72 total of 39,902 putative genes were assigned annotations, and 936 and 220 genes involved in salt resp

73 data associated with the regions across the annotations, and across annotation intersections, provid

74 ance of individual factors, refines gene set annotations, and infers factors without annotation.

75 One widely used annotation approach is to search spectral libraries in r

76 y this shortcoming, we present a new genetic annotation approach termed Codon Consequence Scanner (CO

77 degenerate features", using a context-driven annotation approach.

78 Current annotation approaches report the impact of such variants

79 their local genomic context, accurate genome annotations are essential.

80 Databases collecting drug targets and gene annotations are growing and can be harnessed to shed a n

81 Importantly, when functional annotations are not predictive of risk status, the propo

82 Direct incorporation of one functional annotation as weight in existing dispersion and burden t

83 t loci (cis-eQTLs) using a set of 92 genomic annotations as predictive features.

84 Functional annotations as well as correlations with specific experi

85 em to gain an integrated overview of protein annotations available to aid their knowledge gain on pro

86 e autophagy and proteosomal systems, and the annotation based on the MEROPS nomenclature of peptidase

87 ation method, termed Biologically Consistent Annotation (BioCAn), that combines the results from data

88 algorithms, sequence gap-filled gene feature annotation, bit-block encoded genotypes and sectional fa

89 Annotations by two human radiologists were made for thre

90 how that targeted sequencing plus functional annotation can identify potentially causative variants,

91 ality genomes whose sequences and consistent annotations can be retrieved individually or by taxonomi

92 Our new annotation combines strand-specific Illumina RNA-seq and

93 formulations, indexing drugs and drug label annotations, complementing similar resources available o

94 Maintaining the accuracy of the annotation continues to be a prerequisite for future pro

95 egrating genetic fine-mapping and epigenomic annotation data and performing promoter-reporter and chr

96 includes population frequency and functional annotation data as well as short read support for the ca

97 This annotation data can be especially useful for studying ne

98 terpretation, we included various functional annotation data, especially brain eQTL, methylation QTL,

99 in simulations that by leveraging functional annotation data, fastPAINTOR increases fine-mapping reso

100 oss correlated traits, as well as functional annotation data, to improve fine-mapping accuracy at ple

101 omparative genomic database or multi-layered annotation database.

102 pts (35.52%) based on BLAST searches against annotation databases including GO and KEGG.

103 Comprehensive transcription factor (TF) annotation discovered 978 TFs in 62 families, among whic

104 These applications include functional annotation, disease gene prioritization, comparative ana

105 for human nuclear genome variant calling and annotation do not handle mitochondrial genome data appro

106 approach that incorporates functional genome annotations (e.g., exon or 5'UTR), total linkage disequi

107 in spite of potential risk of false positive annotations emerging from automation.

108 he visualization and retrieval of functional annotations, estimates of nucleotide diversity metrics,

109 ods, and we show that many erroneous variant annotations exist in human reference data.

110 de novo transcriptome assemblies: incomplete annotation, exon level differences, transcript fragmenta

111 or lower and 101-1000 ng/mL; and the PRETEXT annotation factors metastatic disease (M), macrovascular

112 and network reconstruction, with network and annotation files created for visualization in Cytoscape.

113 nformatics, machine learning, and functional annotation filters in order to provide interaction data

114 r findings provide additional candidate-gene annotation for 37 disease susceptibility loci for human

115 circulation, we also created a gene ontology annotation for circulating miRNAs using the gene ontolog

116 s these signatures to generate a genome-wide annotation for each cell type by calculating the most pr

117 nd spatial mark patterns to infer a complete annotation for each cell type.

118 SynEM removes the burden of manual synapse annotation for large densely mapped connectomes.

119 set of general annotations and more focused annotations for carbohydrate-active enzymes and antibiot

120 tely, current PDB files do not provide exact annotations for most carbohydrate derivatives and more t

121 selection of sgSTOPs, our resource includes annotations for off-target propensity, percentage of iso

122 l sub-paths per phenotype and dynamic linked annotations for the engaged genes and molecular relation

123 ng the model, dubbed Maximum Entropy Genomic Annotation from Biomarkers Associated to Structural Ense

124 Our model clearly distinguished true annotation from random annotation with Bayesian annotati

125 hSEQ to provide reliable and rapid ethnicity annotation from whole exome sequencing individual's data

126 Another issue is that annotations from different tools often disagree.

127 in cell resolution by the lack of functional annotations from difficult-to-characterize or rare cell

128 ry information from ENSEMBL, with functional annotations from the Encyclopaedia of DNA Elements conso

129 de evidence-based gene and regulatory region annotation, genome variation and gene trees.

130 The OntoNotes annotation guidelines, with minor adaptations, were used

131 Approximately 31% of the genes in the v.2.1 annotation have been tagged in this population.

132 Functional annotations highlight lipid metabolism and a change in t

133 act in computational function prediction and annotation in databases.

134 ense have not yet been exploited for lack of annotation in public databases.

135 strates the importance of effective sequence annotation in unlocking the potential diversity that Nat

136 -of-function mutagenesis for functional gene annotation in vertebrate models, including zebrafish, mi

137 Our method exploits various genomic annotations in addition to sequence data.

138 e types of genomic and epigenomic functional annotations in genetic risk prediction for complex disea

139 ol that leverages a limited number of manual annotations in order to train a classifier and segment t

140 led tissue-specific enrichment of regulatory annotations in pancreatic islet enhancers for loci influ

141 apped to reference genome or sets of genomic annotations in that reference genome.

142 to distinguish them from the homology-based annotations in the remainder of the SCOPe hierarchy.

143 vide a variety of criteria behind metabolite annotation including peak shapes, intensities in differe

144 Partitioning by genic annotation indicated a greater contribution of SNPs in p

145 Functional annotation indicated that SKAP1 regulates expression of

146 Sequence annotations indicated dominance of Sulfurospirillum, Rhi

147 ings demonstrate the boost in power with the annotation-informed FDR method, and provide insight into

148 bioinformatics analyses typically including annotation, intersection, and merging of data from multi

149 e regions across the annotations, and across annotation intersections, providing insight into how cha

150 e analysis that incorporates such functional annotations into sequencing studies can aid the discover

151 Structural and functional annotation is carried out by JGI's genome and metagenome

152 ubstantial loss of power when the functional annotation is not predictive of the risk status of a var

153 t sequence features are associated with each annotation label.

154 c variants, their sizeable number and poorer annotation make prioritization challenging.

155 regions, an artificial one-to-one region-to-annotation mapping, a lack of visualization options to e

156 ortium has published whole-genome functional annotation maps in 127 human cell types by integrating d

157 This paper presents a novel LC-MS data annotation method, termed Biologically Consistent Annota

158 peline and other state-of-the-art functional annotation methods, particularly for targets that have n

159 A) tracts, a common problem with current PAS annotation methods.

160 rable to other lipid identification software annotations, MS-DIAL and Greazy.

161 f this effect can be explained by functional annotations negatively correlated with LLD, such as DNas

162 e large numbers of structures and functional annotations now available, we have investigated how prot

163 ucted a platform 'TFBSbank' which houses the annotation of 1870 chromatin immunoprecipitation (ChIP)

164 C. elegans Overall, we provide experimental annotation of 26,644 putative CRMs in the embryo contain

165 and straightforward approach for genome-wide annotation of 5- and 3-RNA ends.

166 directly from the density map, analysis and annotation of a cryo-EM density map still primarily rely

167 The workflow provided rapid annotation of a diversity of endogenous and gut microbia

168 ediction details and in their consistency of annotation of a given genomic position across cell types

169 Here we report the assembly and annotation of a reference genome of maize, a genetic and

170 Functional annotation of a set of 106 genes with the highest effect

171 These include the annotation of assays and targets using ontologies, the i

172 Functional annotation of bacterial genomes is an obligatory and cru

173 Taking human annotation of cAT EM data as ground truth, we show that

174 es and 119 of 1602 (7.4%) antibodies with no annotation of catalytic activity.

175 Using annoBTD, Verdant provides accurate annotation of chloroplast genomes without manual interve

176 showing them to be useful for improving the annotation of CRISPR-Cas systems.

177 se-CRISPRs could be used to reduce the false annotation of CRISPRs, therefore showing them to be usef

178 Annotation of differentially expressed genes revealed di

179 LE greatly improves upon current methods for annotation of enhancers across a variety of cell and tis

180 an now be also grouped according to KOG (The annotation of Eukaryotic Orthologous Groups) and KO (KEG

181 ocess could be made easier by automating the annotation of gene fusion products and generating easily

182 Functional annotation of gene models identified orthologous familie

183 Accurate annotation of genes and their transcripts is a foundatio

184 ial progress has been made in the functional annotation of genetic variation in the human genome.

185 achieve near complete assembly and accurate annotation of genomes.

186 mbination events by similarity plots and (v) annotation of genomic regions.

187 nal tool that allows for variant calling and annotation of human mtDNA data coming from NGS experimen

188 a large-scale identification and structural annotation of lncRNAs in the S. mansoni genome.

189 se-causing potential of LoF variants, ALoFT (annotation of Loss-of-Function Transcripts) and show its

190 es across samples MS2LDA+ aids in structural annotation of metabolites and guides prioritization of a

191 mputational tool that facilitates structural annotation of metabolites not described in databases.

192 Structural annotation of metabolites relies mainly on tandem mass s

193 Functional annotation of metagenomic and metatranscriptomic data se

194 of large tumour numbers has also allowed the annotation of more than 13 million non-coding mutations,

195 data could enable more accurate assembly and annotation of newly sequenced genomes.

196 tiles 0-2 per map) or as artifact because of annotation of noise or interpolation in areas of incompl

197 As a proxy for the structural annotation of novel metabolites, we tested 148 metabolit

198 nology allows the high-throughput functional annotation of putative regulatory elements in their nati

199 mated command-line tool for the analysis and annotation of RNA tertiary structures.

200 /MS-based approach allows identification and annotation of S-sulfonated peptides across complex mixtu

201 nition of markables, connection to extensive annotation of several domain-relevant semantic classes,

202 to modern criteria; clinical information and annotation of somatic mutations in both driver and selec

203 Furthermore, manual annotation of the data remains intractable due to the la

204 mes clonal variance by permitting functional annotation of the genome directly in sister cells.

205 We generated a draft assembly and annotation of the genome of the free-living nematode Osc

206 le high-throughput, reproducible, functional annotation of the genome.

207 tation pipeline, we were able to improve the annotation of the Oryza sativa genome compared to using

208 atches identified by iMet enables the proper annotation of the unknown metabolites.

209 er of apparent discrepancies in assembly and annotation of these genomes.

210 expression analysis provided the functional annotation of these lncRNAs in humans and rats.

211 mics methods including metabolite detection, annotation of unknown metabolites, and comparative quant

212 substructure using an internal database, (v) annotation of unknowns with chemical and spectral databa

213 using RegulomeDB, haploreg, and Genome-Wide Annotation of Variants.

214 (rice) supported by published literature and annotation of well-characterized genes.

215 As our analyses concerned bio-annotations of both high-quality protein coding genes an

216 The few reported annotations of branch site are imprecise as reverse tran

217 stand relationship and similarity between GO annotations of genes, it is important to have a convenie

218 experimental characterization and functional annotations of IDPs/IDRs, and is intended to provide an

219 future research efforts; and build molecular annotations of network perturbations.

220 These data also greatly improve the annotations of P. vivax gene untranslated regions, provi

221 data, predictions of novel variant proteins, annotations of phenotype-associated sequence markers and

222 Functional annotations of regulated proteins and measurement of pho

223 ere indirectly evaluated through the concept annotations on a gold standard corpus and also by docume

224 approaches will struggle to provide reliable annotations or accurate matches to mass spectral librari

225 s functions for quality control, filtration, annotation, pathogenic prediction and statistical tests.

226 We did gene annotation, pathway, and gene-set-enrichment analyses an

227 Here, we present a new IS elements annotation pipeline to address these issues.

228 Using an integrative annotation pipeline, we assembled tissue-specific RNA-Se

229 d using the programs within the MAKER genome annotation pipeline, we were able to improve the annotat

230 s carried out by JGI's genome and metagenome annotation pipelines.

231 ties associated with more than 2,000 disease annotations, placing numerous candidate disease genes in

232 Functional genome annotation predicts that at least 66 potential PME genes

233 The M. sympodialis genome assembly and annotation presented here is at a quality yet achieved o

234 completed in 1.5 hr, included loading data, annotation, principal component analysis, and single var

235 otation from random annotation with Bayesian annotation probability >0.95.

236 encing and assembly have become trivial, its annotation procedure has not been standardized yet.

237 ential of the CCS matching in supporting the annotation procedure.

238 an enhanced version of the protein alignment annotation program JoY, formats a submitted multiple-seq

239 and database built to take advantage a novel annotation program, annoBTD.

240 o progress of the Gene Ontology Phylogenetic Annotation Project.

241 to annotate such genomic regions to genomic annotations (promoters, exons, enhancers, etc.).

242 We present a new GC-specific MAKER annotation protocol to predict new and improved gene mod

243 genome compared to using the standard MAKER annotation protocol.

244 Complete and accurate reference genomes and annotations provide fundamental tools for characterizati

245 rojects and enriches their data with variant annotation provided by CellBase, a rich and fast annotat

246 These developments enrich the annotations provided by InterPro, increase the overall n

247 eukaryotic genomes are available, and genome annotation remains a major challenge.

248 Functional annotation results revealed that both SNPs might be invo

249 tal databases to assign confidence levels to annotation results.

250 g RNA structure analysis, RNA alignment, RNA annotation, RNA-protein interaction, ribosome profiling,

251 tion and differential evolution based global annotation score optimization, and (vi) network graph vi

252 g linkage disequilibrium (LD)-weighted genic annotation scores, total LD scores and heterozygosity.

253 d tests that can utilize multiple functional annotations simultaneously for integrative association a

254 tation provided by CellBase, a rich and fast annotation solution.

255 Existing tools are limited by a lack of annotation sources and flexible options, the time it tak

256 that many authors do not adhere to existing annotation standards when describing models.

257 the enforcement of nomenclature and related annotation standards, MTB supports aggregation of data a

258 ine information mined from text with curated annotations stored in ChEMBL to investigate the patterns

259 introduce a principled framework to estimate annotation-stratified genetic covariance between traits

260 urated antimicrobial resistance database and annotation structure that provides a foundation for the

261 The method combines user-supplied functional annotation such as expression quantitative trait loci (e

262 this study, we introduce the Bee Behavioral Annotation System (BBAS), which enables the automated de

263 in we report the design of a structure-based annotation system for the identification of functionally

264 s a foundation of genomics, but currently no annotation technique combines throughput and accuracy.

265 vity, Uniclust contains 17% more Pfam domain annotations than UniProt.

266 udies (GWAS) using functional and regulatory annotations that relate to the cells, tissues, and patho

267 To accelerate lncRNA annotation, the GENCODE consortium has developed RNA Cap

268 s, such as the multiple approaches for motif annotation, the need for frequent database updating, and

269 eved high sensitivity and accuracy in domain annotation, the sensitivity of HMMER on short reads decl

270 um to substantially expand the canine genome annotation to include 10 374 novel lncRNAs and 58 640 mR

271 icted, and rapidly give additional layers of annotation to predicted genes.

272 ice using exome sequencing and bioinformatic annotation to prioritize mutations in genes of unknown f

273 nsive filtering functions and cancer-related annotations to better interpret mutation effects and the

274 tomated enrichment analysis of the resulting annotations to facilitate the functional interpretations

275 real time, and connecting literature-derived annotations to the latest version of the genomic sequenc

276 b application and added protein modification annotations to the sequence diagram and structure displa

277 nto chemical structures and their subsequent annotation together with text mining applications for li

278 For the new version of L1Base, a LINE-1 annotation tool, L1Xplorer, has been used to mine potent

279 grated with transcriptomics data in standard annotation tools.

280 JBrowse now displays BAM, VCF and other annotation tracks, the additional genome assemblies and

281 er studied species, ODG can perform syntenic annotation translations or rapidly identify characterist

282 The TAIR10 annotation update had a profound impact on Arabidopsis r

283 e to facilitate rapid, comprehensive feature annotation using a peak-picker-output and MS(2) data fil

284 nical information and additional open-source annotations using accessible databases via ANNOVAR.

285 bility sensor output versus manual physician annotation was 0.86 (95% CI, 0.72-1.00).

286 L. tarentolae and L. major genome annotation was transferred and these gene models were ma

287 sed proteomics approach together with manual annotation, we are able to provide, to our knowledge, th

288 e number of genes without current functional annotation were among direct targets providing a rich re

289 MS/MS spectra available for 828 of these annotations were analyzed by translating experimentally

290 revealed that about two-thirds of the novel annotations were indeed supported by the available ribos

291 Gene annotations were updated using 111,000 full-length trans

292 These reference annotations were used to project pathways for 62 model,

293 a greater portion of the lipidome and using annotation which does not over-report biologically relev

294 transcript fragmentation and incorrect gene annotation, which we suggest that de novo assembly is be

295 uality genomes with comprehensive functional annotations will promote advances in clinical microbial

296 This updated Arabidopsis genome annotation with a substantially increased resolution of

297 ly distinguished true annotation from random annotation with Bayesian annotation probability >0.95.

298 Annotation with ontology terms can play an important rol

299 Structured annotation with ontology terms provides a potential solu

300 Annotation with predicted chemical formulas is also not