ライフサイエンスコーパス: annotate

1 gene to a 620 kb region where 19 genes were annotated.

2 fever virus (ASFV) genomes have been poorly annotated.

3 ne catalog is functionally and taxonomically annotated.

4 etabolomic analysis and 192 metabolites were annotated.

5 Using this tool, we completely annotated 201 adduct and fragment ions from 10 metabolit

6 novo variants (DNVs) in connectome genes, we annotated 229 published NDD genes for connectome status

7 ng to its haploid chromosome complement, and annotated 27 969 protein-coding genes and 6747 non-codin

8 and provided evidence for correction of mis-annotated 28 C-terminal residues within the NADH dehydro

9 a shift of upstream polyadenylation sites to annotated 3' ends.

10 These issues were due, in part, to variably annotated 3' untranslated regions and thousands of gene

11 ing based on UHPLC-QTOF metabolomics allowed annotating 316 compounds, comprising mainly polyphenols

12 7 Gb genome sequence into 24 chromosomes and annotate 32,690 protein-coding genes.

13 ed-reads and optical mapping to assemble and annotate a nearly chromosome-quality genome of the corn

14 ave demonstrated to be effective approach to annotate a set of genes, the same idea can be extended t

15 tative trait loci (eQTL) information to help annotate a set of genomic intervals in terms of transcri

16 The ability to visualize and annotate acoustic events efficiently can enhance scienti

17 y tools have been developed to recognize and annotate adduct ions.

18 enables researchers to easily and accurately annotate an entire phage genome.

19 ptomes, and a single resource to best share, annotate and analyze the massive m7G data generated rece

20 Here, we describe ORFquant, a method to annotate and quantify translation at the level of single

21 b application combining multiple features to annotate and visualize genomic variant data.

22 total of 2854 images from 201 LC videos were annotated and 402 images were further segmented.

23 arbDB, the complete carbohydrate ligands are annotated and all their interactions are displayed.

24 cade, researchers have deposited hundreds of annotated and curated datasets on both normal and disord

25 ing duplicates, each of the 158 variants was annotated and independently classified by two additional

26 mammalian genome, including both previously annotated and novel iCGI/host gene pairs.

27 bacteria as more AasS enzymes continue to be annotated and provides a platform for potential antibiot

28 users with access to over 250 000 uniformly annotated and publicly available genomes with curated me

29 Here, we present 94 newly annotated and re-annotated genomes, bringing the total n

30 rine, algal and plant biological samples, we annotated and semiquantified 8,051 lipids using MS-DIAL

31 While the human genome has been extensively annotated and studied, model organisms have been less ex

32 ment with reference sequences, MPs have been annotated and their sequences made available for search,

33 All the nanostructures are annotated and transformed into protein data bank files,

34 derscores the importance of considering both annotated and unannotated splicing events.

35 These publicly accessible data can be annotated and updated with the GNPS infrastructure keepi

36 oing study (Ethics Ref 13/SC/0250), manually annotated and used for model training and evaluation.

37 tional resources, we envision the process of annotating and interpreting models as an open-ended proc

38 By consistently annotating and naming 10,899 microRNA genes in these org

39 . gene and regulatory elements) to discover, annotate, and visualize recurrent SVs and their targeted

40 137 unique urinary metabolites were annotated, and several identified that were higher in ca

41 how that the STK19 gene has been incorrectly annotated, and that the expressed protein is 110 amino a

42 a zDHHC20 S-acyltransferase interactor, and annotated as a potential thioesterase.

43 nosa harbors three paralogous zinc proteases annotated as AmpD, AmpDh2, and AmpDh3, which turn over t

44 report that the Mycobacterium smegmatis gene annotated as encoding Tam, an O-methyltransferase that m

45 Lymph nodes were segmented and annotated as ENE-positive or ENE-negative on the basis o

46 ly annotated transcripts in RTR, 34 213 were annotated as high confident coding transcripts and 24 72

47 Seventeen DEGs, annotated as R genes, were shared by both introgression

48 rt enhancers; 12 395 had not been previously annotated as strong enhancers.

49 cellulolytic clostridia do not contain genes annotated as transaldolase.

50 2 and B3 produced four compounds, which were annotated as two EOM and two (+)-catechin-4-O-methyl (CO

51 issions passing all tests to be accepted and annotated automatically, without the need for any human

52 Phylogenetic analysis of more than 4000 annotated bacterial acid phosphatases was carried out.

53 d PTS permease (EIIC) genes in MGAS5005, the annotated beta-glucoside PTS transporter (bglP) was foun

54 CE is an unsupervised method that accurately annotates binding sites for specific TFs automatically w

55 nome sequencing effort, we have included 363 annotated bird genomes in addition to other publicly ava

56 Application to mouse liver data annotated both known metabolite and known adduct peaks w

57 Annotating both gene sets with data from multiple genome

58 MicroRNA loci are relatively well-annotated but compose only a small minority of the total

59 y antigens are not monophyletic as currently annotated, but rather can be categorized into two evolut

60 uses an attention mechanism on tumoral areas annotated by a pathologist whereas the second ("CHOWDER"

61 one laparoscopic cholecystectomy videos were annotated by AI for disease severity (Parkland Scale), C

62 lides were digitized, and the urothelium was annotated by expert observers.

63 es and veins on their CT scans were manually annotated by five experienced observers.

64 ining five new compounds were identified and annotated by high-resolution mass spectrometry.

65 A total of 88 compounds were annotated by mass spectrometry and included a diverse se

66 lumes, with mandibular canals being coarsely annotated by radiologists, and using a dataset of 15 vol

67 another 20 patients, independently partially annotated by three radiologist readers.

68 gnificant content increase and the number of annotated causal interactions have almost doubled.

69 SIGNOR 2.0 now stores almost 23 000 manually-annotated causal relationships between proteins and othe

70 These structurally annotated CDRs provide unprecedented insights into both

71 We use ACTIONet to integrate and annotate cells across three human cortex data sets.

72 The manual labor of hand annotating cells can be significantly accelerated by usi

73 The network was trained with the fully annotated cerebral vessel artery-vein maps from 60 patie

74 inct Carnegie stages (13-14, 16-21, and 23), annotated chromatin states, and compared these maps to o

75 ChromA annotates chromatin landscape by integrating information

76 circ-MDM2, an annotated circRNA from the MDM2 locus, was one of the ha

77 extensive research to predict, quantify, and annotate circRNAs, our understanding of their functions

78 In a highly annotated cohort of older adults with HLH we found that

79 able the community to store, process, share, annotate, compare and perform molecular networking of GC

80 racellular organization, gene expression and annotated contextual knowledge.

81 network (AtlasNet) was trained on 6888 fully annotated CT images (80% for training and 20% for valida

82 Three radiologists annotated CT images obtained during the arterial and por

83 In addition, CancerGeneNet annotates curated pathways that are relevant to rational

84 Surprisingly, only half of the annotated cysteines were identified by both iodoacetamid

85 or medical imaging: scarcity of high-quality annotated data and mismatch between the development data

86 We further made the annotated data and protein structures readily downloadab

87 Annotated data include predicted and validated immune ep

88 Manually annotated data is key to developing text-mining and info

89 a augmentation, crowdsourcing for generating annotated data sets, and unsupervised learning with mole

90 s a challenge due to the lack of large, well-annotated data sets, which are typically required for th

91 ications may be trained on a large amount of annotated data to be able to match the highest expectati

92 strict evaluation of SemRep on our manually annotated dataset yields 0.55 precision, 0.34 recall, an

93 stems of readily accessible, structured, and annotated datasets that can be dynamically queried and a

94 new drug class and have used it initially to annotate drugs relevant to cardiovascular disease.

95 publicly available a large dataset of 10,030 annotated echocardiogram videos.

96 annotations, utilized both, simulations and annotated endoscopic images, to train deep neural networ

97 Strikingly, 217 LG4s overlap annotated enhancers, and we find the promoters regulated

98 t thousands of proteins have DFLs, they were annotated experimentally in <200 proteins.

99 l types that have never been seen before and annotate experiments that are as yet unannotated.

100 rs can interactively visualize data details, annotate findings and export resultant diagrams in high-

101 olates from seven lineages paired with fully-annotated, finished, de novo assembled genomes.

102 ine-tuned on a small dataset of 438 CT scans annotated for appendicitis.

103 fragments in Escherichia coli, has not been annotated for most intracellular pathogens.

104 ing of approximately 500,000 video clips and annotated for one of 600 human action classes, and then

105 ity, glycosylation, and alkylation, manually annotated for substance classes, the relative mass defec

106 ssessment of hand movements done by manually annotating frames.

107 rmation (PHI) in 2503 radiology reports were annotated from a large multihospital academic health sys

108 Major challenges remain in annotating function, given the dearth of functional data

109 Previous attempts to annotate gene losses have required significant manual cu

110 eaction in histidine biosynthesis lacking an annotated gene and highlight metabolic modules with poor

111 vided for each species includes functionally-annotated gene and transcript models with orthology rela

112 traits of plants from the subset gene other annotated gene models which are unlikely to play a role

113 with known phenotypes and the overall set of annotated gene models.

114 performed previous methods and nearly 19,000 annotated gene sets for resolving 52 experimentally dete

115 e PFAM database, assesses reciprocality, and annotates gene partners for kinase domain retention.

116 classified based on their putative effect on annotated genes and KOG analysis was carried out to prov

117 The annotated genes associated with identified genomic regio

118 Function well annotated genes in the list include ADORA2B, ARNT, S100G

119 apped expression quantitative trait loci for annotated genes, novel transcribed regions, transposable

120 oly(A) sites could not be linked with known, annotated genes, suggestive of the existence of numerous

121 was the metabolic pathway containing 101,427 annotated genes, which consisted of 51.4% of all annotat

122 tated genes, which consisted of 51.4% of all annotated genes.

123 34 predicted deleterious mutations in 10,642 annotated genes.

124 required for global detection of translated annotated genes.

125 Here, we develop VarNote to rapidly annotate genome-scale variants in large and complex func

126 The increasing availability of annotated genome sequences enables construction of genom

127 Here, we present 94 newly annotated and re-annotated genomes, bringing the total number of genomes

128 t generates and publicly releases clinically annotated genomic data on tumor and germline specimens o

129 ilized a machine learning model trained with annotated genotypic data to classify variants as benign

130 visual cell annotation, comprising partially annotated grayscale images of 30 different cell lines fr

131 to evaluate the model performance versus the annotated ground truth.

132 p learning algorithms requires a plethora of annotated (ground truth) data.

133 Geneset enrichment is a popular method for annotating high-throughput sequencing data.

134 une 2019) are presented in alignment with an annotated histological atlas and can be browsed down to

135 Evolutionary analyses of well-annotated HIV sequence data can provide insights into vi

136 To extend our ability to annotate human disease processes, we have implemented a

137 literature and other atlases to identify and annotate hundreds of cell types and subtypes, both withi

138 This paper provides original, annotated images demarcating the ventral intermediate nu

139 r data augmentation via 3D-reconstruction of annotated images to train a robust view-invariant deep n

140 utional network using a dataset of 4,339,879 annotated images, consisting of 103 subjects with divers

141 f these studies, whereas they were correctly annotated in 15 more recent studies.

142 lls toward specific fates, including several annotated in an existing scRNA-seq gastrulation atlas, a

143 ing (piling-up) of peaks, or other features, annotated in high-resolution datasets, to measure their

144 s contributed up to 12% of all viromic reads annotated in the analysed viromes.

145 erlap with cancer-related mutation positions annotated in the COSMIC database.

146 each major class of ncRNA that is currently annotated in the human genome and describe how each clas

147 on the catalytic residues of 648 enzymes, as annotated in the Mechanism and Catalytic Site Atlas (M-C

148 sly made available a tool for validating and annotating influenza virus sequences that is used to che

149 esults across different experiments, without annotated information of genomes or prior knowledge from

150 Existing genome annotation tools focus on annotating intact genes and do not attempt to distinguis

151 931,698 reads were annotated into 11,676 coding sequences (CDS), which were

152 nces in the S. spontaneum genome, which were annotated into 63 genes, including 6 (9.5%) genes with f

153 AI-annotated intraoperative events were associated with bot

154 Surgeons agreed with 99% of AI-annotated intraoperative events.

155 the assembly of the D. suzukii genome and to annotate it in a way that facilitates comparisons with D

156 creases the sequence contiguity 120-fold and annotate it using 6.5 million full-length transcripts, t

157 a meta-learning approach for identifying and annotating known as well as new cell types.

158 TCR repertoire sequencing samples allows for annotating large datasets on-line.

159 sue, using an image-based screen to assay an annotated library of compounds.

160 el, conserved small protein encoded by a mis-annotated lncRNA that regulates apoptosis and tumorigeni

161 While the number of annotated lncRNAs in mammalian genomes has greatly expan

162 We also annotate loops associated with the SMC component of the

163 haromyces cerevisiae) system to functionally annotate maize (Zea mays) auxin signaling components, fo

164 erminal Mu insertions covering 16,392 of the annotated maize genes (37% of the B73v4 genome).

165 labeling, and present data in the context of annotated metabolic pathways.

166 sugar alcohols were the most representative annotated metabolite classes that were increased in milk

167 eted metabolomic analyses detect 129 and 199 annotated metabolites that are differentially accumulate

168 siders primary read coverage information and annotated metadata.

169 me Atlas (TCGA) and found 12,141 incorrectly annotated MNVs.

170 ed to detect related phages, or functionally annotate most of the genes, subsequent reanalysis with p

171 s alignment of this cell cluster with a well-annotated mouse classification shows strong homology to

172 rable portion of their transcripts share the annotated mRNA 3' end.

173 At least 1000 of these overlap with annotated mRNA TSSs and a considerable portion of their

174 data with sample information (metadata) and annotated MS(2) spectra.

175 g targeted RNA sequencing, we systematically annotated multi-exonic non-coding RNA (mencRNA) genes tr

176 of a large nanomaterial database containing annotated nanostructures suited for modeling research.

177 ach subfamily, and thus were further used to annotate new genomes for CAZymes.

178 cal tumor-specific HLA peptides derived from annotated non-coding regions could elicit anti-tumor imm

179 s and the capability to detect and correctly annotate novel sphingolipid species make LDA broadly app

180 ast and colon cancer images with pathologist-annotated nuclei, finding that both cellular and interce

181 was developed to accelerate the editing and annotating of automated detections from extensive acoust

182 Eleven intracranial structures were manually annotated on the axial oblique series.

183 d integrate stable isotope tracing data into annotated or custom-built metabolic networks.

184 They use either structure-annotated or disorder-annotated training datasets, poten

185 , from alternative start sites nested within annotated ORFs and from RNAs previously considered nonco

186 ated ORFs encoded upstream and downstream of annotated ORFs, from alternative start sites nested with

187 Cenote-Taker, was developed to automatically annotate over 2500 complete genomes in a GenBank-complia

188 basis of SCA2 SC phenotypes and demonstrates annotated pathways shared with TDP-43 and SOD1 ALS mice

189 o accurately predict disorder- and structure-annotated PBRs.

190 stromal content of PDA samples from numerous annotated PDA data sets and correlating stromal content

191 es was very useful to increase the number of annotated peptide peaks with their corresponding amino a

192 viding a unique patient-derived, molecularly annotated pharmacologic resource that is reflective of T

193 otation selectively filters 22.8% of falsely annotated pLoF variants found in haploinsufficient disea

194 Pockets are represented by pharmacophore-annotated point clouds mimicking ideal ligands or fragme

195 ne expression changes using RNA-seq data and annotated polyadenylation sites in the PolyA_DB database

196 Detailed clinically annotated population-based data and further molecular ch

197 velopmental dataset, we were able to rapidly annotate previously unidentified clusters from existing

198 neously minimizing the number of incorrectly annotated principal ions.

199 d shinyFuse, a companion web application, to annotate, prioritize, and explore biologically-relevant

200 CCS values provide additional confidence of annotating prioritized features in untargeted screening

201 we examine the distributions of over 50,000 annotated prophage genes identified in 1384 prophage seq

202 algorithms, and all are highly dependent on annotated protein features.

203 n, we examined the extent to which different annotated protein pathways and complexes showed similari

204 nts identified by peak calling correspond to annotated protein-binding sites and/or have stable predi

205 Of these, 618 genes have >=5 annotated protein-isoforms.

206 annoFuse annotates protein domains using the PFAM database, asses

207 omics') has been studied for many years, but annotating protein subcellular locations and understandi

208 t PBRs, except for SCRIBER for the structure-annotated proteins and disoRDPbind for the disorder-anno

209 ults that cross-over structure- and disorder-annotated proteins and produces relatively low amount of

210 s make accurate predictions on the structure-annotated proteins.

211 ined predictors predict well on the disorder-annotated proteins.

212 ed proteins and disoRDPbind for the disorder-annotated proteins.

213 ular disorder predictors using 6200 disorder-annotated proteins.

214 n of an insertional mutant library of all 14 annotated PTS permease (EIIC) genes in MGAS5005, the ann

215 Screening this library of well-annotated, published kinase inhibitors has yielded a ple

216 ns using state-of-the-art tools to assemble, annotate, quantify, and bin metagenome data.

217 e homologous against all currently available annotated reference sequences of 22 C. albicans strains,

218 xpression effects of rare CNVs and use it to annotate regulatory disruption of CNVs from 14,891 indep

219 nscription factor occupancy data are used to annotate regulatory factors, such as combinatorial trans

220 l analysis based on expression of previously annotated rejection-related transcripts identified 4 gro

221 validated or predicted RNA motifs from gene-annotated RNA regions.

222 ow the utility of RTK-targeted immuno-PET to annotate RTK changes in protein expression and inform tu

223 ses are limited to small numbers of manually annotated samples from a single cerebral hemisphere, mea

224 Benchmarking using expert-annotated scRNA-seq datasets shows that our method autom

225 commendations regarding the requirements for annotating sequences as new subtypes.

226 We built and evaluated our system on small annotated sets of chemical reaction relationships from t

227 cers, defined by homeobox family motifs, and annotated several cardiovascular disease susceptibility

228 leviviral genomes, but most of these lack an annotated sgl, mainly due to the small size, lack of seq

229 n 1 [SERBP1] in mammals), and recently, late-annotated short open reading frame 2 (Lso2; coiled-coil

230 On the other hand, manually annotating single cell clusters by examining the express

231 The current solutions for annotating single cell clusters generally lack a graphic

232 as good or potentially better than manually annotated stages by cancer pathologists.

233 density cost-calculator-simulator' and fully-annotated statistical examples/code, this themed-framewo

234 re is a comprehensive study of all currently annotated Stig cyclases, revealing that these proteins c

235 In one evaluation, we use a manually annotated test collection and perform a comprehensive er

236 We investigate approaches to annotate TF binding, including directly measured chromat

237 lyses and conserved domain identification to annotate the apoptotic pathway in A. pisum and found low

238 ing has become a key method to visualize and annotate the chemical space in non-targeted mass spectro

239 ition method called "archetypal analysis" to annotate the dashboard.

240 Here, we use chemo-proteomics to annotate the degradable kinome.

241 Second, a U-net model segmented images to annotate the location of each left ventricular wall.

242 We annotate the position of PopZ with single-molecule local

243 fered for coding and non-coding regions that annotate the potential impact of putative off-target sit

244 To annotate the precise cellular composition of distinct ti

245 We assembled and annotated the genome of the cultivated variety "Big Star

246 During the analysis of scRNAseq data, annotating the biological identity of cell clusters is a

247 un time, serving as an ideal alternative for annotating the clinical significance of cancer-associate

248 We illustrate the workflow by annotating the positions of three proteins in the bacter

249 i-omics features facilitated identifying and annotating the predicted loops.

250 AnnoGen is capable of annotating the proprietary pragmatic features for variab

251 provides a simple approach for functionally annotating the regulatory consequences of CNVs.

252 files that are dense information sources for annotating the regulatory elements.

253 MiSplice will be useful for automatically annotating the splicing impact of coding and non-coding

254 ure of resources in the follow-up process of annotating the variants in the credible set to determine

255 blicly available for researchers who wish to annotate their own sequences.

256 has demanded new computational approaches to annotate their roles.

257 tribute to many disorders, yet, functionally annotating them remains a major challenge.

258 ged cell types defined by gene expression to annotate these data and cataloged hundreds of thousands

259 This package is also capable of annotating these variants to identify the most impactful

260 v model to classify regulatory elements, and annotated this model with matched gene expression data.

261 d well-characterized tool compounds manually annotated to 218 unique MoAs, and we profiled each compo

262 For testing, a dataset of 50 scans was annotated to assess the segmentation accuracy and was co

263 n chromosome 11 (chr11:2,322,050-2,323,247), annotated to C11orf2; TSPAN32 genes.

264 identified, only 214 have been functionally annotated to date, and 40 unique structures are represen

265 In this training set, 2740 frames were annotated to develop the segmentation model, which achie

266 Each publication was annotated to identify study topic, methodology and stati

267 protein domain movements comprises sequences annotated to indicate whether the amino acid residue is

268 significant for both Cd and current smoking (annotated to PRSS23, AHRR, F2RL3, RARA, and 2q37.1), we

269 Methylation at one DMP (cg18587484), annotated to the gene TJAP1, was associated with perfluo

270 Among genes annotated to these 188 CpGs, we found enrichment in targ

271 y use either structure-annotated or disorder-annotated training datasets, potentially creating a dich

272 We then used these inferred coordinates to annotate transcriptional units identified de novo.

273 (Accession: PRJNA398984), the assembled and annotated transcriptome can be viewed and downloaded fro

274 n disease mechanisms and treatments, but its annotated transcriptome is far from complete.

275 Of all 73 074 newly annotated transcripts in RTR, 34 213 were annotated as h

276 PAGE signatures similar to those of recently annotated transcripts.

277 ) of the matrix (temporal wise) were used to annotate trends of relevant wastewater contaminants.

278 r CNNs are able to classify TCGA pathologist-annotated tumor/normal status of whole slide images (WSI

279 CIPR facilitates scRNAseq data analysis by annotating unknown cell clusters in an objective and eff

280 74.45% of these were annotated using UNIPROT.

281 et of reference populations, and downloading annotated variant lists.

282 Functionally annotated variant subgroups were used to re-evaluate gen

283 ion status, can be leveraged to functionally annotate variants and map them to genes.

284 enchmarked against a dataset of about 20 000 annotated variants, the methodology is shown to outperfo

285 In this work, we annotated viral mRNAs and non-coding transcripts, and a

286 Viral Annotation DefineR) that validates and annotates viral sequences in GenBank submissions.

287 nces and target sequences were integrated to annotate VISs.

288 Out of a total of 298 metabolites that were annotated we report here 185 that showed a technical var

289 od more than doubled the number of glycoPSMs annotated when searching the same glycans as the origina

290 A transcripts, some of which were previously annotated while others are identified in this study.

291 process big genomic data, particularly when annotating whole-genome sequencing variants against a hu

292 aking it possible for any variant file to be annotated with any isoform expression dataset, and will

293 the CDR dataset, a standard benchmark corpus annotated with causal chemical-disease relationships.

294 Still images from LC videos were annotated with CVS criteria and hepatocystic anatomy seg

295 Acylcarnitine tandem spectra were annotated with fragments from carnitine and acyl moietie

296 selective sweeps in P. fuscatus contain loci annotated with functions in long-term memory formation,

297 ersion of the human reference genome, and is annotated with highly similar gene content.

298 _Corpus) and a more general set of abstracts annotated with MeSH (Medical Subject Headings) term Bact

299 A collection of 33,953 subpockets annotated with their bound fragments was screened for lo

300 e and convenient chromatography modification annotated yeast metabolomics data with similar effective