ライフサイエンスコーパス: annotation

1 s essential to the development of systematic annotation.

2 to have) experimentally verified functional annotation.

3 ies and controlled vocabularies are used for annotation.

4 mation from cross-species genotype-phenotype annotation.

5 nd browse test statistics and perform genome annotation.

6 The Sepsis-3 criterion is applied for annotation.

7 res a loss function that tolerates errors in annotation.

8 e isoforms not present in the WormBase WS265 annotation.

9 changes for adduct peaks, facilitating their annotation.

10 , it may be advantageous to use a customized annotation.

11 mily sequence homology hinder their accurate annotation.

12 cluding those without substantial functional annotations.

13 ty assignment and use of more sequence-based annotations.

14 er conditioning on a broad set of functional annotations.

15 he relative paucity of negative experimental annotations.

16 onstraint and genes with disease-appropriate annotations.

17 ES events, we performed multiple functional annotations.

18 uch as linkage disequilibrium and functional annotations.

19 ced functions for the flexible extraction of annotations.

20 rable to differences between two physicians' annotations.

21 n of multiple molecular datasets and pathway annotations.

22 sis and compare the accuracy of existing TSS annotations.

23 from their accuracy in predicting regulatory annotations.

24 vely low RAR usually correspond to incorrect annotations.

25 tion analysis with in silico genomic feature annotations.

26 specifications via Python scripts or Genbank annotations.

27 tidimensional summaries of in silico variant annotations.

28 al associations, metadata terms and ontology annotations.

29 ter, sequencer), keywords and other provided annotations.

30 a balanced test set of positive and negative annotations.

31 ips with PPI networks using anatomy ontology annotations.

32 tatives, and 40% of the UHGP lack functional annotations.

33 establish objectivity in fluorescent feature annotations.

34 road set of coding, conserved and regulatory annotations.

35 tational cost allowing for large data volume annotations.

36 protein sequences with additional functional annotations.

37 acts without a large training set of labeled annotations.

38 round truth to gene function predictions and annotations?

39 candidates with putative function and family annotations; (2) a large-scale M. truncatula RNA-sequenc

40 we performed a large number of expert-based annotations, 72,722 in total.

41 However, these in-source annotation algorithms are limited by ESI sources that ar

42 ta and sequencing variants, existing variant annotation algorithms lack the efficiency and scalabilit

43 e visibility of both the annotation data and annotation algorithms.

44 Furthermore, we show how our annotation allows us to place oncogenic transformations

45 cted quantitative trait locus and functional annotation analyses.

46 ble and multipurpose, with uses ranging from annotation and classification of individual signals or s

47 ion, batch correction, clustering, cell type annotation and differential gene expression analysis.

48 uctor package tximeta that performs numerous annotation and metadata gathering tasks automatically on

49 placing critical importance on the accurate annotation and quantification of their Ig and TCR repert

50 lic resource that focuses on simplifying the annotation and submission process of data with its corre

51 , so their analysis requires careful variant annotation and very large sample sizes(1).

52 were evaluated jointly by various functional annotations and 4-kb sliding windows.

53 s to four datasets with experimental doublet annotations and find that our methods perform at least a

54 Functional annotations and genome-scale metabolic modelling of sele

55 pports both region-based and allele-specific annotations and introduces advanced functions for the fl

56 References, annotations and layout of the CellDesigner molecular map

57 a suitable framework for tracking functional annotations and linking to complex human pathology.

58 annotation versions, and to access P. patens annotations and related resources, a lookup database and

59 sets derived from gene ontology and pathway annotations and showed that NetPAS uncovered functional

60 terfaces hosting genomic resources with gene annotations and transcriptomic and proteomic data for si

61 eral pathway databases to enhance functional annotation, and elastic net and a gene expression compos

62 ghting shortcomings of sequencing, assembly, annotation, and reconstruction that prevent predictions

63 earch Experiences (CUREs) centered on genome annotation, and students to participate in genomics rese

64 causal relationship between images and their annotations, and offer step-by-step recommendations for

65 tools for genome browsing (JBrowse), genome annotation (Apollo), data mining (BovineMine) and sequen

66 imputation reference panels, and functional annotation approaches.

67 e across species, automated TE discovery and annotation are challenging and time-consuming tasks.

68 Published algorithms for automatic cell annotation are limited to known cell types and fail to c

69 pts, reconstructed GRN, modules and detailed annotations are all available as Supplementary Files.

70 olipid species is challenging, and incorrect annotations are common.

71 Several of the resulting annotations are informative for common disease, even aft

72 g the position of the measurement and manual annotations are not practical for large population studi

73 In contrast, transposable element (TE) annotations are rudimentary, consisting of information o

74 re able to generate assemblies whose protein annotations are statistically enriched for specific gene

75 neuroimaging datasets with clinical outcome annotations are typically limited, especially in neonate

76 High-quality annotations are unfortunately expensive as they require

77 implement the submission of these structural annotations as an automated part of existing internal wo

78 c databases universally store the functional annotations at the gene level.

79 ional genomic databases uniformly record the annotations at the gene-level, and rarely record the ann

80 ons at the gene-level, and rarely record the annotations at the isoform-level, differentiating isofor

81 ion in xenograft experiments, and functional annotation based on in vitro cell viability assays we de

82 rns in the protein 3D structures, literature annotation based on OncoKB, TP53 mutations based on thei

83 eannotation; extending or truncating default annotations based on RNA-Seq read evidence and (ii) filt

84 as fine-mapping resolution and cell-specific annotations become richer.

85 can be shown as tracks in the 1D sequence/annotation browser.

86 Here, we develop such a custom annotation by leveraging advanced assays, such as eCLIP,

87 ect potentially incorrect Gene Ontology (GO) annotations by comparing the ratio of annotation rates (

88 uated using 10-fold cross-validation against annotations by expert surgeons.

89 ing LabxDB's programmatic access (REST API), annotations can be easily integrated into bioinformatics

90 IMPACT annotations captured consistent SNP heritability between

91 ataWeb links targets to KEGG pathways and GO annotations, completing the bridge from drugs/chemicals

92 ent a new dataset, EVICAN-Expert visual cell annotation, comprising partially annotated grayscale ima

93 Overall, our assembly and annotation constitute a high-quality genomic resource th

94 erlying eQTL data used, the directed genomic annotations could predict up to 1.5% of the variance obs

95 With greatly improved spectral annotation, coupled with the speed of index-based scorin

96 thereby widening the visibility of both the annotation data and annotation algorithms.

97 With the growing volume of functional annotation data and sequencing variants, existing varian

98 ugment quantity and diversity of genome-wide annotation data for the latest reference genome to promo

99 ying PAS, the need for tremendous amounts of annotation data hinder applications of existing methods

100 ne-mapping studies, some approaches leverage annotation data to prioritize likely functional polymorp

101 more are deleterious based on their Combined Annotation Dependent Depletion (CADD) scores.

102 oth additional training sequences and unique annotations describing tissue and cell states unavailabl

103 Gene annotations, different transcript isoforms, nucleotide s

104 etworks with application to protein function annotation, disease gene prediction, and drug discovery.

105 guish nonfunctional genes from genes missing annotation due to sequencing and assembly artifacts.

106 hat lie within regions of functional genomic annotation (e.g. insulator and chromatin accessible site

107 analyses and Apollo, a collaborative genome annotation editor, visualizes the results of these analy

108 this study, enhanced in-source fragmentation annotation (eISA) was created by tuning the ISF conditio

109 d loss-of-function variants are enriched for annotation errors, and tend to be found at extremely low

110 ering for artefacts caused by sequencing and annotation errors.

111 uated the combination of cancer-related gene annotations, evolutionary conservation and pre-computed

112 For wheat, these include gene model annotations, expression atlases and gene networks that p

113 this problem is the use of incomplete genome annotation files.

114 KB contains 6496 UniRule rules which provide annotation for 53 million proteins, accounting for 30% o

115 tegrates RNA-seq read support with extensive annotation for candidate ranking.

116 annoFuse provides standardized filtering and annotation for gene fusion calls from STAR-Fusion and Ar

117 l networks, updating databases and providing annotation for new pathways.

118 GFF files) while being able to retrieve all annotations for a given identifier or a range of coordin

119 o integrate SVs, gene expression, and genome annotations for discovering biologically relevant SVs al

120 roMatch had wide coverage, returning 27 PFAS annotations for landfill leachate samples, explaining 71

121 enerating high-quality genome assemblies and annotations for many aquatic species still presents sign

122 s with accurate voxel-level mandibular canal annotations for model evaluation.

123 including de novo genome assemblies and gene annotations for the population founders, have allowed th

124 We pre-compute smORF annotations for thousands of RefSeq isolate genomes and

125 We used existing Uberon anatomical entity annotations for zebrafish and mouse genes to construct g

126 Here, we present ASCOT, a resource that uses annotation-free methods to rapidly analyze and visualize

127 RefSeq they are most similar to, and feature annotation from the RefSeq is mapped based on a nucleoti

128 s annotations from Gene Ontology and disease annotations from DisGeNET are captured.

129 al perspective, trends in biological process annotations from Gene Ontology and disease annotations f

130 ction is generally predicted by transferring annotations from homologous genes or proteins for which

131 We use experimental annotations from over 40 000 proteins, drawn from over 8

132 Here, we evaluate genome-wide SNP annotations from two previous deep learning models, Deep

133 a local database providing pre-processed PTM annotations from Uniport/Swiss-Prot for users to downloa

134 This substantial annotation gap can be reduced with the help of accurate

135 usly identified in human plasma samples with annotations generated by three similar tools, we found t

136 s, generating a high-quality genome assembly/annotation has become an indispensable tool for better u

137 The scope for data annotation has been substantially expanded to enhance bi

138 Integration of GWAS signals with epigenomic annotations has demonstrated that AD risk variants are e

139 Current transcriptome annotations have largely relied on short read lengths in

140 nhancers have been nominated via biochemical annotations; however, only a handful of these have been

141 Annotation identified 20,157 protein-coding genes, of wh

142 for CAZyme and enzyme EC classification and annotation; (ii) the k-mer-based tools (including PPR-Ho

143 Our annotation improves detection of cell type-specific gene

144 Preliminary compound identification and peak annotation in gas chromatography-mass spectrometry is us

145 enhancer landscapes and super-enhancer (SE) annotation in numerous archived FFPE samples from distin

146 went further and eliminated subjective human annotation in the training step by training a weakly sup

147 UniRule provides scalable enrichment of annotation in UniProtKB.

148 ge to reveal associations between functional annotations in an Arabidopsis thaliana gene network.

149 re diversity and is applicable for improving annotations in any model organism.

150 Both these variants have conflicting annotations in ClinVar and are of low penetrance (TNNI3:

151 ng resources, has ensured that the number of annotations in Genome3D has nearly doubled since the las

152 ple comparison correction; (ii) employ brain annotation information to enable biologically meaningful

153 TAAR (variant-set test for association using annotation information), a scalable and powerful RV asso

154 egrates and displays the mRNA and miRNA gene annotation information, signaling cascade pathways and d

155 evel signals and integrates brain anatomical annotation information.

156 Genome annotation is an important step for all in-depth bioinfo

157 is sequenced and assembled, structural gene annotation is often the first step in analysis.

158 This annotation is propagated to unreviewed records in UniPro

159 At the CPT, genome annotation is separated into two robust segments that ar

160 a Viewer (GDV), displays our in-house RefSeq annotation; is integrated with other NCBI resources such

161 s could not be explained by other functional annotations known to be associated with psychiatric diso

162 ncing data are often summarized at different annotation levels for further analysis, generally using

163 y used tool, multimarker analysis of genomic annotation (MAGMA), addresses this issue by aggregating

164 mong collaborators with incorrect or missing annotation metadata, it becomes difficult or impossible

165 s a control, we used the same sequencing and annotation methods to show that a closely related myxozo

166 nctive categories of defense system with the annotation of 6 600 264 genes retrieved from 63,701 geno

167 The annotation of 6 mA marks in genome is the first crucial

168 of recent N-glycoproteomics data resulted in annotation of 80% more glycopeptide spectrum matches (gl

169 Here, we report genome sequence and annotation of a South African QPM line K0326Y, which is

170 ry motor cortex, providing a morpho-electric annotation of almost all transcriptomically defined neur

171 Common tools used for annotation of antibody sequences are often limited in fu

172 pe I modular PKSs, featuring a comprehensive annotation of available docking domains information in b

173 operator and suggest the first protocol for annotation of compartmental domains in sparse single cel

174 3' end of each RNA, TIF-Seq2 can improve the annotation of complex genomes, facilitate accurate assig

175 competitive approach that allows for doublet annotation of datasets with thousands of cells in a matt

176 We believe the new annotation of enhancers in EnhancerAtlas 2.0 will facili

177 However, manual annotation of fluorescent features with a low signal-to-

178 Full annotation of fusion genes aided by the visualization to

179 s driving the need for improved unsupervised annotation of genome components such as transposable ele

180 in our GWAS using the Functional Mapping and Annotation of GWAS platform, and did colocalisation anal

181 emerging role in human diseases, a thorough annotation of human viral transcriptional regulators (vT

182 The dense anatomical annotation of medical images may improve their use for a

183 Here, we present DRAM (Distilled and Refined Annotation of Metabolism), a framework to translate the

184 ur dataset for vaccine design and functional annotation of mutations observed during viral surveillan

185 annotation of the entire plant (EP) and (2) annotation of partial sections of the leaf blade (LB).

186 However, the automated annotation of prokaryotic genomes is imperfect, and erro

187 Consistent with the annotation of rhamnogalacturonan lyase in Stammera, cass

188 The annotation of short-reads metagenomes is an essential pr

189 Functional annotation of shotgun metagenomic data has become an inc

190 methods are needed for supervised cell type annotation of single-cell RNA sequencing data.

191 To facilitate the annotation of specific smORFs, we introduce SmORFinder.

192 Due to this complexity, the automated annotation of sphingolipid species is challenging, and i

193 address the challenges inherent to automated annotation of sphingolipid structures from MS/MS data, w

194 ation of breast cancer through more accurate annotation of targetable pathways and biological feature

195 For example, batch annotation of TCR repertoire sequencing samples allows f

196 The repetitiveness and limited annotation of TEs prevent the ability to distinguish bet

197 MirCure can also curate and adjust the annotation of the 5p and 3p arms based on user-provided

198 For example, in the annotation of the Caenorhabditis elegans transcriptome,

199 corroborating biological significance of our annotation of the chromatin compartmental domains in sin

200 Our annotation of the cv Purple Kush reference genome identi

201 wo annotation techniques were evaluated: (1) annotation of the entire plant (EP) and (2) annotation o

202 However, the annotation of the genome by chromatin proteins, histone

203 ng, quality assurance and enhancing accurate annotation of the genome-encoded proteome.

204 tural strains, calculated after assembly and annotation of the genomes of 20 isolates.

205 ates the power of precision cytogenetics for annotation of the infertile genome, suggests that these

206 Mendelian Inheritance in Man, the Functional Annotation of the Mammalian genome 5, the Genotype-Tissu

207 An in-depth annotation of the newly discovered coronavirus (2019-nCo

208 utomatic pipelines, we present a genome-wide annotation of the pseudogenes in the mouse reference gen

209 Our functional annotation of the risk alleles within 15q24.3 coupled wi

210 Further annotation of top-ranking metabolic features nominated b

211 Here we report a genome-wide annotation of transcriptional regulators in A. fumigatus

212 nearly 90% accuracy and deployed it for the annotation of understudied GTs.

213 itional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolut

214 pipeline to produce comprehensive sRNA locus annotations of 47 diverse plants, yielding more than 2.7

215 When we compared Binner annotations of 75 compounds previously identified in hum

216 c targets. To date, systematic and intensive annotations of ES events based on the skipped exon units

217 Annotations of evolutionary sequence constraint based on

218 e approaches implicitly assume the collected annotations of genes are complete and only integrate mul

219 gene-term data matrix (storing Gene Ontology annotations of genes) into low-rank matrices to simultan

220 ated enrichment of heritability within 2,868 annotations of genome-wide transcription factor occupanc

221 Experimental annotations of intrinsic disorder are available for 0.1%

222 The main bottleneck is that functional annotations of isoforms are generally unavailable and fu

223 rms, thus accomplishing the prediction of GO annotations of isoforms.

224 set with the structure- and disorder-derived annotations of PBRs (to analyze the cross-over) and the

225 g is prohibitively expensive, and only rough annotations of the entire tissues are typically availabl

226 This dataset is composed of annotations of the five hemorrhage subtypes (subarachnoi

227 Interestingly, the functional annotations of this core set center around response to e

228 comprehensive manner, including detailed PTM annotation on the 3D structure and biological informatio

229 m/z values that support the correct peptide annotation or can be used for de novo sequencing.

230 ic and three real datasets with ground truth annotation or manually labeling, SynQuant was demonstrat

231 roteins and confirming up to 98% of existing annotations per virus.

232 Here we introduce MetaLAFFA, a functional annotation pipeline designed to take unfiltered shotgun

233 priate sequencing and software platforms and annotation pipelines for a new genome project can be dau

234 es are frequently overlooked, because genome annotation pipelines generally ignore small open reading

235 at were previously neglected by conventional annotation pipelines.

236 To deal with inaccurate pixelwise manual annotations, prediction accuracy was also evaluated agai

237 sues allows decisions about data collection, annotation, preprocessing, and learning strategies to be

238 For the latter, we introduce 'annotation principal components', multidimensional summa

239 Conditional analysis and functional annotation prioritized the missense variant rs147647315

240 Functional annotations prioritized several dozen genes where signif

241 Furthermore, the nanostructure annotation procedure generates 2142 nanodescriptors for

242 ual updates to expand the range and depth of annotations provided.

243 ine brain samples revealed a highly improved annotation quality as measured by sensitivity and reliab

244 data curation of all entries to improve the annotation quality of our repository.

245 y (GO) annotations by comparing the ratio of annotation rates (RAR) for the same GO term across diffe

246 h sources of gene expression data exist, but annotation rates are poor and the ability to carry out t

247 and are significantly enriched in functional annotations related to gene regulation.

248 Interreader variability in semantic feature annotation remains a challenge and affects the reproduci

249 a crucial need to generate appropriate gene annotation repositories and resources.

250 However, human annotation requires considerable time, effort and expert

251 However, existing annotation resources can present challenges as many lack

252 ale variants in large and complex functional annotation resources.

253 Annotation results revealed 31 quantitative trait loci (

254 Genome-wide annotations revealed 1,516 nucleotide-level variations a

255 and a user-friendly interface convenient for annotation review and inter-annotator disagreement resol

256 as used for data collection, a multi-faceted annotation scheme was developed, and a user-friendly sea

257 We demonstrate that expression-based annotation selectively filters 22.8% of falsely annotate

258 We propose a novel annotation source, sequence-dependent DNA topology, as a

259 in turnover.IMPORTANCE We extended the known annotation space for the NCLDV by 46%, revealing high-pr

260 sequenced genomes and a variety of different annotation strategies, comes the potential for ambiguous

261 ted MEGARes, a hand-curated AMR database and annotation structure developed to facilitate the analysi

262 for discovering LCRs and provides functional annotations such as domain detection, transmembrane segm

263 External annotations such as ENCODE data or DeepSea predictions c

264 Functional annotation suggested the role of inflammation, specifica

265 The annotation system is based on the analysis of the input

266 our integrative and discriminative epigenome annotation system, we identified and assigned epigenetic

267 Two annotation techniques were evaluated: (1) annotation of

268 a more comprehensive zebrafish transcriptome annotation that addresses these deficiencies.

269 re constructed based on the anatomy ontology annotations that were obtained from the experimental dat

270 tories, scientists must rely on inconsistent annotation to identify and interpret meaningful data.

271 We utilized these high-quality annotations to assess gene family evolution within Jugla

272 is and takes advantage of probabilistic eQTL annotations to delineate and tackle the unique challenge

273 estigators to contribute additional data and annotations to this resource to accelerate research and

274 published the miRNA enrichment analysis and annotation tool (miEAA) for human precursor and mature m

275 Currently, no existing annotation tool systematically incorporates information

276 ssification, motif identification and genome annotation tool using a bipartite network algorithm.

277 Existing genome annotation tools focus on annotating intact genes and do

278 ools, linking them with advanced binning and annotation tools, and maintaining provenance of the proc

279 the viral genome and grouped together into "annotation tracks" where they can be visualized along th

280 allows live messaging, notifications for new annotation tracks, heavy-duty analyses initiated by the

281 nd, eQTL allows us to provide the regulatory annotation under the context of specific tissue types.

282 ermore, MAESTRO supports automatic cell-type annotation using predefined cell type marker genes and i

283 ted with detected sources of variation, gene annotation using publicly available databases and gene s

284 ariant categories and multiple complementary annotations using a dynamic weighting scheme.

285 ms and demonstrated the accuracy of selected annotations using MS/MS.

286 openly available BAGLS dataset using manual annotations, utilized both, simulations and annotated en

287 ene expression queries across different gene annotation versions, and to access P. patens annotations

288 ervice), that integrates the identification, annotation, visualization, and interrogation of multisca

289 To improve genome annotations, we linearly integrate these sequences into

290 rtitioning heritability across 28 functional annotations, we observe enrichment of heritability in FA

291 A chromosome-level genome assembly and annotation were established for one of the most sensitiv

292 The annotations were highly enriched for disease heritabilit

293 Annotations were performed by four high-volume surgeons.

294 t enables weak supervision from tissue-level annotations when classifying subtissue locations.

295 enomes, longer contigs and better functional annotations when compared to culture-independent methods

296 community resource, any user can add manual annotations which are quality checked and shared publicl

297 This type of annotation, which is currently missing in other drug ban

298 or performance in the number and accuracy of annotations while simultaneously minimizing the number o

299 to integrate data-driven primary transcript annotations with transcriptional unit coordinates identi

300 This is followed by a functional annotation workflow that combines sequence comparisons a