ライフサイエンスコーパス: genome

1 nsatory mutations occurring across the viral genome.

2 e damage, in particular in the mitochondrial genome.

3 giving insight into the organization of the genome.

4 amplification has been mapped throughout the genome.

5 unity to design probes against any sequenced genome.

6 nts within the massive, ~30kb SARS-CoV-2 RNA genome.

7 cell death to eliminate cells with defective genome.

8 5-hydroxymethylcytosine (5hmC) marks on the genome.

9 chromosome-scale assembly of the T. sinense genome.

10 rhizal species, including 29 new mycorrhizal genomes.

11 iver genes and therapeutic targets in cancer genomes.

12 functional analysis of enhancers in various genomes.

13 fied reference genomes and de novo assembled genomes.

14 ide biosynthetic operons and in other fungal genomes.

15 s harbor a related endogenous virus in their genomes.

16 ut current methods do not scale to mammalian genomes.

17 heus microneptunus, a complete mitochondrial genome (22X coverage) assembled from short Illumina 150

18 More than 125 000 genomes, 516 million genes and almost 100 million unique

19 le in shaping patterns of variability across genomes; accurate predictions of their effects are, ther

20 ed from long terminal repeats during zygotic genome activation.

21 a counterdefense mechanism to protect their genomes against restriction.

22 d C10 domains (18 of 22, 82%, P<0.001 versus Genome Aggregation Database common variants) and were as

23 The resultant IGEs from 2168 genomes, along with integrase phylogenetic analysis and

24 The Yaravirus genome also contained six types of tRNAs that did not ma

25 volutional, and pathological significance in genome analyses.

26 13 has emerged independently in Guyana, with genome analysis indicating an evolutionary origin distin

27 RNA that is currently annotated in the human genome and describe how each class is assigned a standar

28 Studying genome and epigenome led to the fundamentals of developm

29 Whole genome and exome sequencing followed by Sanger confirmat

30 Vs in a pattern similar to those of complete genome and the nucleoprotein (N) gene.

31 wn how the APE2 gene is altered in the human genome and whether APE2 is differentially expressed in c

32 ide TE integration preferences in eukaryotic genomes and by selection following integration.

33 st group of membrane receptors in eukaryotic genomes and collectively they regulate nearly all cellul

34 s) are pervasive in several animal and plant genomes and contribute to shaping genetic diversity.

35 onable compromise between modified reference genomes and de novo assembled genomes.

36 Furthermore, using seed site randomized genomes and evolutionary selection experiments, we found

37 istributed haplotypes from 15,789 SARS-CoV-2 genomes and model their success based on their duration,

38 oes not require prior knowledge of reference genomes and produces highly accurate results, even at a

39 supporting alignment of sequences from both genomes and proteins.

40 r by integrating large-scale prostate cancer genomes and the prostate-specific epigenome.

41 enome collinearity between the two bryophyte genomes and vascular plants is limited, suggesting exten

42 ted virus that transferred an overlength HBV genome-and expressed HB surface antigen at levels releva

43 n mice to determine the epigenetic state, 3D genome architecture and transcriptional landscape of eng

44 Multipartite virus genomes are composed of several segments, each packaged

45 Our results indicate that plant genomes are remarkably plastic, and that dynamic GNs gen

46 Comprehensive, high-quality reference genomes are required for functional characterization and

47 not CPDs, impeded DNA replication across the genome as revealed by microfluidic-assisted replication

48 data sets, as assumptions made by the single genome assembly algorithms do not apply when assembling

49 Hybrid genome assembly has emerged as an important technique in

50 A high quality genome assembly is a vital first step for the study of a

51 Here we present a human genome assembly that surpasses the continuity of GRCh38(

52 Several tools, from base-calling to genome assembly, were ported and benchmarked on an Andro

53 rithms do not apply when assembling multiple genomes at varying levels of abundance.

54 th related origins represented in The Cancer Genome Atlas (TCGA) proteomic data.

55 ncer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA)(5).

56 ncer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), which aggregated whole-genome seque

57 rge-scale cancer studies, such as The Cancer Genome Atlas (TCGA), with both RNA-Seq and array-based p

58 three different tumor types from the Cancer Genome Atlas (TCGA).

59 ndreds to thousands of samples in the Cancer Genome Atlas (TCGA).

60 es and matched healthy tissues in The Cancer Genome Atlas database were analyzed to select shared FSP

61 ith high accuracy when applied to the Cancer Genome Atlas datasets.

62 ing Archive and genomic data from The Cancer Genome Atlas from 110 patients from five institutions wi

63 xomes across 14 cancer types from The Cancer Genome Atlas.

64 s, some functions that are trivial on linear genomes become much more difficult in genome graphs.

65 The recovery of genomes belonging to uncultured groups from the environm

66 By studying whole-exome sequencing and whole-genome bisulfite sequencing of cell free DNA (cfDNA) and

67 archers to explore this data set easily in a genome browser.

68 ases are present in Phytophthora and Pythium genomes, but only UP2 is seen in Saprolegnia spp. which

69 ed reads mapping to the Bacteroides fragilis genome by 48- and 154-fold in mucus and tissue, respecti

70 The three-dimensional conformation of a genome can be profiled using Hi-C, a technique that comb

71 We analyzed 453 SARS-CoV-2 genomes collected between 20 February and 15 March 2020

72 Specifically, genome collinearity between the two bryophyte genomes an

73 is regulation occurs in the context of large genomes condensed by histone proteins into chromatin.

74 CAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TC

75 CAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TC

76 de novo assembled O. nubilalis mitochondrial genomes contained 82 intraspecific substitution and inse

77 milder cases and a higher proportion of the genome contributing to this shared genetic liability wit

78 A mean depth of 15 achieved >99% 5-fold genome coverage (in 9/20 clinical samples).

79 -deficient cells, a second, subsequent whole-genome CRISPR-Cas9 screen identified the LITAF-like prot

80 enabled processing of a 725-terabyte cancer genome dataset from the Pan-Cancer Analysis of Whole Gen

81 Whole-genome deep sequencing-based analysis has revealed unexp

82 an by autotetraploidization (that is, direct genome doubling).

83 s with yeast paralogs derived from the whole-genome duplication event.

84 V-1 RNA from a large pool of mRNAs as virion genome during virus assembly.

85 Genome-edited donor-derived allogeneic anti-CD19 chimeri

86 eadouts from functional experiments, such as genome editing and reporter assays.

87 The ODInCas9 mouse allows robust and tunable genome editing granting flexibility, speed and uniformit

88 CRISPR/Cas9 genome editing has revolutionized functional genomics in

89 nation of human association analysis, CRISPR genome editing in mice, animal behavioural analysis and

90 9), an alternative to the most commonly used genome editing protein Streptococcus pyogenes Cas9 (SpyC

91 y, disruption of GAL5.1 in mice using CRISPR genome editing significantly reduced GAL expression in t

92 We then use genome editing to disrupt the coding sequence of a S. ro

93 ment of cobalamin metabolic enzymes, we used genome editing to study the loss of mmachc function and

94 The development of new CRISPR-Cas genome editing tools continues to drive major advances i

95 technologies have revealed that more of the genome encodes proteins than originally thought possible

96 The Arabidopsis genome encodes six TIR1/AFB proteins representing three

97 l (hiPSC)-based technology with CRISPR-based genome engineering facilitates precise isogenic comparis

98 Transposable elements (TEs) drive genome evolution and are a notable source of pathogenesi

99 owerful tool for gaining novel insights into genome evolution.

100 ERT mRNA expression by RNA-sequencing, whole-genome/exome sequencing, and clinical covariates in 134

101 pact of DNA damage response and repair on 3D genome folding using Hi-C experiments on wild type cells

102 we present a combined analysis of 135 fungal genomes from 73 saprotrophic, endophytic and pathogenic

103 Sequencing of 1,314 SARS-CoV-2 viral genomes from available patient samples enabled us to est

104 sis in a collection of over 10,000 bacterial genomes from both cultured isolates and metagenomic data

105 There is a need for reference genomes from multiple human populations to avoid potenti

106 Prior to this study, complete mitochondrial genomes from Order Thysanoptera were restricted to a sin

107 highlights the challenge of assembling viral genomes from short-read metagenomes.

108 obal insights into cellular organization and genome function require comprehensive understanding of t

109 However, due to the greater complexity of genome graphs relative to linear genomes, some functions

110 linear genomes become much more difficult in genome graphs.

111 These new genomes greatly expanded the known pangenomes of many or

112 lved gonococci into discrete and stable core genome groups, some of which persisted for multiple deca

113 This lack of full-length genomes hampers our ability to understand the molecular

114 he extant distributions of TEs in eukaryotic genomes have been shaped by both bona fide TE integratio

115 Mitochondria harboring wild-type genomes have functional electron transport chains and pr

116 Interrogation of the F. alocis genome identified the HMPREF0389_00796 gene that encodes

117 Training on both genomes improves gene expression prediction accuracy on

118 An analysis of the coding regions of the genome in 886 index cases of PID found that disease-caus

119 nces with a large database of complete viral genomes, including 76,262 identified from a systematic s

120 We therefore used the 3D genome information along with an ensemble pMHC-I coding

121 ss of HR sub-pathways, with implications for genome instability and cancer.

122 process that produces gene amplification and genome instability.

123 he formation of micronuclei, a clear sign of genome instability.

124 macroautophagy must be inhibited to maintain genome integrity.

125 s, suggesting a role for zinc in maintaining genome integrity.

126 d genome replication, as well as maintaining genome integrity.

127 ggest that the epigenetic state of the viral genome is an important determinant of reactivation that

128 -1 reverse transcription, in which viral RNA genome is converted into double-stranded DNA, is that it

129 Accessibility of the human genome is modulated by the ATP-driven SWI/SNF chromatin

130 After a new genome is sequenced and assembled, structural gene annot

131 s telomere-to-telomere assemblies of complex genomes is one of the ultimate challenges in genomics.

132 target by genomic editing most areas of the genome, is producing important preliminary therapeutic r

133 Barr virus (EBV) switches between four viral genome latency and lytic programmes to navigate the B-ce

134 d alpha3 capsids are nearly identical, their genome lengths vary widely from 5,386 ( X174) to 6,067 (

135 al sequences when aligned with the reference genome, limiting the potential of whole metagenomics.

136 e fertilization precedes maternal (egg cell) genome loss.

137 it origin activation, which is important for genome maintenance.

138 olymerase II transcribing the circular viral genome more than once.

139 These mutations in cancer genomes occur due to internal and external mutagenesis f

140 rization were not possible until a reference genome of autotetraploid wild type sugarcane specie, Sac

141 We sequenced the genome of C. bovis using the Oxford Nanopore MinION plat

142 The genome of Escherichia coli O157:H7 bacteriophage vB_EcoM

143 cing has become a powerful tool to study the genome of individual cells for the detection of mosaic m

144 By sequencing the whole genome of MERS-CoV from persistently infected bat cells,

145 s been employed to define the core essential genome of this bacterium and genes conditionally essenti

146 10-y period, we collected and sequenced the genomes of 110 VREfm isolates from gastrointestinal and

147 Here, we sequenced the whole genomes of 24 individual pigs representing 22 breeds dis

148 extent of structural changes experienced by genomes of eukaryotic cells can be dramatic and spans se

149 cells, with the exception of the specialized genomes of mitochondria and plastids, all genetic inform

150 R-loops are common in the genomes of pro- and eukaryotes, including humans, and ma

151 l (CoMM) was proposed to jointly interrogate genome on complex traits by integrating both the GWAS da

152 and limited inflammation or detectable viral genome or antigen was noted in lungs of animals in eithe

153 fy seamlessly due to their recurrence in the genome or essentiality for cell function.

154 ndrial DNA are also reflected in the nuclear genome or, alternatively, are the product of limited fem

155 ond nucleocytoplasmic trafficking, including genome organization and gene expression.

156 replication stress in the context of the 3D genome organization.

157 e first pharmaceutical strongly affecting 3D genome organization.

158 Compared to the reference genome, our de novo assembled O. nubilalis mitochondrial

159 Referred to as the "guardian of the genome", p53 is the most frequently mutated protein in c

160 The genome packaging motor of tailed bacteriophages and herp

161 tant role in Gag:RNA interactions leading to genome packaging.

162 eractions occur at multiple RNA sites during genome packaging; furthermore, there are functionally re

163 8 donors of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer G

164 as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer G

165 ataset from the Pan-Cancer Analysis of Whole Genomes (PCAWG) project in a time-efficient and uniform

166 analysis of methylation, transcriptome, and genome profiles of more than 400 BE and EAC tissues, alo

167 It is built on the foundation of the 1000 Genomes Project, which created the largest openly access

168 es, substantiating the need for multi-ethnic genome references.

169 we analyze the folding stability of this RNA genome relative to the structural landscape of other wel

170 Genome replication is initiated from specific origin sit

171 leus plays a key role in gene regulation and genome replication, as well as maintaining genome integr

172 We show that using a graph personalized genome represents a reasonable compromise between modifi

173 Jellyfish genomes reveal a mosaic of conserved and divergent genom

174 Our analysis of other oomycete genomes revealed that both uridine phosphorylases are pr

175 ng with the increasing quantity of available genome-scale data across the tree of life.

176 Genome-scale technologies have enabled mapping of the co

177 n composition that allow OGT prediction from genome sequence alone.

178 cing technologies, we provide a high-quality genome sequence of a cultivated accession of white lupin

179 The reported first genome sequence of a tropical rubber tree pathogen R. mi

180 ve evolved through cis-regulatory changes in genome sequence that influence the magnitude, timing and

181 e recent publication of a high-quality wheat genome sequence, alongside gene expression atlases, vari

182 he data to generate a chromosome-scale draft genome sequence.

183 tegrated vector sequence and the neighboring genome sequence.

184 We present 929 high-coverage genome sequences from 54 diverse human populations, 26 o

185 Analysis of chromosome-scale mango genome sequences reveals photosynthesis and lipid metabo

186 Here, we use 490 Argentinian V. cholerae genome sequences to characterise the variation within, a

187 The availability of whole genome sequences was expected to supply essentially unli

188 Multilocus Sequence Typing (MLST) and Whole Genome Sequencing (WGS) analysis.

189 me wards within 7 days were chosen for whole-genome sequencing (WGS) and a phylogenetic analysis was

190 enomic landscape of myeloma using deep whole-genome sequencing (WGS) and develop a model that identif

191 ew sequencing approaches, particularly whole-genome sequencing (WGS), have dramatically changed the l

192 Whole genome sequencing data did not identify a strain genotyp

193 Genome Atlas (TCGA), which aggregated whole-genome sequencing data from 2,658 cancers across 38 tumo

194 As access to whole-genome sequencing has grown, greater amounts of molecula

195 Whole genome sequencing in multiplex families, proband-parent

196 ccurring on palms, soles or nail beds, whole genome sequencing of 87 tumors with matching transcripto

197 Whole genome sequencing of select transformants demonstrated t

198 However, genome sequencing of specimens is challenging because of

199 MIC, pDST and whole genome sequencing of the pncA, rpsA and panD genes were

200 Whole genome sequencing revealed differences in putative virul

201 APOR retrieved references for 257 real whole-genome sequencing samples with a mean of >99.8% identity

202 Viral genome sequencing showed that the majority of HCWs had t

203 lonization on NF admission, we applied whole-genome sequencing to track the spread of 4 ARO species a

204 mic data, particularly when annotating whole-genome sequencing variants against a huge database with

205 Whole genome sequencing was performed on 20 matched blood and

206 Whole genome sequencing was used to uncover a frame-shift inse

207 Using whole genome sequencing, we identified a heterozygous frameshi

208 diabetes, six by exome sequencing and one by genome sequencing.

209 Established methods for whole-genome-sequencing (WGS) technology allow for the detecti

210 , interrogation of sequenced E. coli O157:H7 genomes showed a high level of CycA conservation, highli

211 lion years ago contributed compellingly to A-genome size expansion, speciation and evolution.

212 ) whose length enigmatically correlates with genome size.

213 ch isolate, representing ~64% of the average genome size.

214 mplexity of genome graphs relative to linear genomes, some functions that are trivial on linear genom

215 leotide polymorphisms (SNPs) in the pathogen genomes sourced from host samples.

216 applied to specific research fields such as genome stability and developmental biology and to test c

217 The maintenance of genome stability is essential for the cell as the integr

218 nd whether it plays a role in maintenance of genome stability remain to be determined.

219 ys roles in transcription and maintenance of genome stability.

220 te the presence of a mechanism to protect 3D genome structure integrity during DNA damage repair.

221 tegrates transcription factor binding and 3D genome structure to reflect "transcriptional niche" in t

222 This revealed 44,652 high-quality viral genomes (that is, >90% complete), although the vast majo

223 In the C. papaya chloroplast genome, there are 46 RNA editing loci with an average RN

224 his study was conducted to explore the enset genome to develop molecular markers, genomics resources,

225 involving uncoating and delivery of the RNA genome to the cytoplasm.

226 d a diverse set of 58 complete P. aeruginosa genomes to curate a set of 4,440 core genes found in eac

227 Developmental plasticity allows genomes to encode multiple distinct phenotypes that can

228 icular cardiomyocytes and interrogated whole genome transcriptional responses.

229 Our analyses of the genome, transcriptome, and functional assays advance gen

230 pathway genes are impacted by a recent whole-genome triplication event.

231 ction model and selection for G418 resistant genomes, we demonstrated that Y138 is a critical residue

232 blastoma pathogenesis, here we analyze whole-genome, whole-exome and/or transcriptome data from 702 n

233 A genome wide association study demonstrated that both die

234 Our genome-wide analyses identified one novel gene (NDUFB9)

235 may be relevant for future population-scale genome-wide analyses of blueberry.

236 The PRP was constructed from a genome-wide analysis of BBxgenotype interaction predicti

237 However, unbiased methods to profile GxE genome-wide are nascent and, as we show, cannot accommod

238 based on summary statistics from the largest genome-wide association analysis of MD (n = 135,458 case

239 Previous genome-wide association studies (GWAS) have identified 1

240 ct of unmeasured geographical confounding on genome-wide association studies (GWAS) of complex human

241 predictive polygenic risk scores (PRS) from genome-wide association studies (GWASs) including 55,105

242 analyses of findings from a meta-analysis of genome-wide association studies (meta-GWASs) of the broa

243 Genome-wide association studies have revolutionized our

244 In recent years, genome-wide association studies have shed light on the g

245 Genome-wide association studies have shown many variants

246 Data from genome-wide association studies in up to 215,551 partici

247 GKQ locus is the 3rd strongest risk locus in genome-wide association studies of Parkinson disease (PD

248 A polygenic risk score (PRS) derived from genome-wide association studies of posttraumatic stress

249 Rationale: GWAS (Genome-Wide Association Studies) have identified hundred

250 s that can be used to interpret results from genome-wide association studies, and we discuss current

251 and evaluated heritability enrichment in 64 genome-wide association studies, emphasizing schizophren

252 enes associated with type 2 diabetes risk in genome-wide association studies.

253 forming meta-analyses with 2 independent EoE genome-wide association studies.

254 located within a PD risk locus identified by genome-wide association studies.

255 g 17 mouse organs with body mass index (BMI) genome-wide association study (GWAS) data from >457,000

256 Our genome-wide association study (GWAS) identified one nove

257 We performed a genome-wide association study and analysed the most rece

258 We performed a genome-wide association study in Arabidopsis (Arabidopsi

259 In addition, we used a genome-wide association study to identify loci that are

260 like Zld, influences chromatin accessibility genome-wide at cellularization, suggesting both are pion

261 is currently available that has investigated genome-wide changes in gene expression during the normal

262 Thus, ANP32E dramatically influences genome-wide chromatin accessibility through subtle refin

263 Genome-wide chromatin interaction mapping, using Hi-C, r

264 Genome-wide CNV breakpoint association showed not only s

265 Here we performed genome-wide CRISPR screens in Vero-E6 cells with SARS-Co

266 The genome-wide cross-trait analysis features in several ana

267 hitherto there is no comprehensive survey of genome-wide CTCF binding patterns across different human

268 the history of these movements, we generated genome-wide data for 11 ancient individuals from the isl

269 Genome-wide DNA methylation and gene expression are comm

270 ave addressed these questions in a series of genome-wide experiments coupled to a novel bioinformatic

271 , but only modest (1.4-7.8%) perturbation in genome-wide expression was observed.

272 of immune cells and inhibitory checkpoints, genome-wide frequencies of copy number alterations, muta

273 Cellular integrity, migration, and genome-wide gene expression changes were examined in 16H

274 Here, we integrate estimates of genome-wide genetic variation with demographic and niche

275 multiple gene regulatory processes including genome-wide histone modification, transcriptional regula

276 Our results suggest a general strategy for genome-wide identification and characterization of silen

277 etic diversity analysis revealed significant genome-wide losses of variation among the three stages a

278 arching for statistically enriched dots on a genome-wide map.

279 Here, we integrate genome-wide measures of mRNA expression, miRNA expressio

280 r than recently published approaches, making genome-wide multilocus analysis of longitudinal traits p

281 This screen utilized the most extensive genome-wide ORF collection to date, covering 90% of huma

282 Using genome-wide profiling of the H3K27ac histone modificatio

283 lations largely manifested as differences in genome-wide recombination rate rather than remodeling of

284 tunes transcription factor availability via genome-wide redistribution and couples BRAF to tumorigen

285 ff-target effects in KID-KCs, as detected by genome-wide RNA sequencing.

286 e generated during development, we performed genome-wide RNA tomography sequencing on zebrafish, chic

287 However, the genome-wide role of CSB/Rad26 in TC-NER, particularly in

288 Here, using genome-wide screening, we find that SAT1 selectively con

289 associated with the reproductive subtype at genome-wide significance (PRDM2/KAZN, P = 2.2 x 10-10; I

290 agnosis as well as aggressiveness; 183 reach genome-wide significance.

291 ructed weighted polygenic scores using known genome-wide significant associations for T2D, fasting gl

292 The authors identified novel genome-wide significant associations near genes involved

293 ubgenera (Amygdalus, Prunus and Cerasus) for genome-wide SNP identification and to assess genetic div

294 Genome-wide spatial transcriptomics analysis provides an

295 Genome-wide transcriptomic analyses have revealed abunda

296 use passage of Pol II through +1 nucleosomes genome-wide would obligate H2A.Z turnover, we propose th

297 and GWAX, based on the number of independent genome-wide-significant loci across all diseases (for ex

298 s very extensive transcriptional readthrough genome-wide.

299 ophages comprise many architecturally mosaic genomes with distinct DNA sequences.

300 enetic analysis places the majority of these genomes with viruses sequenced from Washington state.