ライフサイエンスコーパス: bacterial genome

1 ed from the intergenic regions (IGRs) of the bacterial genome.

2 to distinguish plasmids from each other in a bacterial genome.

3 ind to eight different operator sites in the bacterial genome.

4 Red outperformed the related tools on a bacterial genome.

5 study the evolution of prophages within the bacterial genome.

6 essentiality of each genetic component in a bacterial genome.

7 rage intergenic regions in the corresponding bacterial genome.

8 ccumulated burden of coding mutations in the bacterial genome.

9 ct that they analyzed different parts of the bacterial genome.

10 ission cycles in shaping and maintaining the bacterial genome.

11 ed into, and replicated as part of, the host bacterial genome.

12 because of phage-mediated degradation of the bacterial genome.

13 rophages are abundant residents of sequenced bacterial genomes.

14 esponses and therapeutic interventions-shape bacterial genomes.

15 can play an outsized role in shaping extant bacterial genomes.

16 the many unannotated short ORFs expressed in bacterial genomes.

17 and combined to make a non-redundant set of bacterial genomes.

18 l constraints shaping the gene repertoire of bacterial genomes.

19 enchmark its performance on a diverse set of bacterial genomes.

20 onuclease and 34 BisI homologs identified in bacterial genomes.

21 specific DNA sequences into a population of bacterial genomes.

22 component tools for assembling and finishing bacterial genomes.

23 s central to the adaptation and evolution of bacterial genomes.

24 s (long and short) were found in each of the bacterial genomes.

25 e key forces that shape genetic diversity in bacterial genomes.

26 e homologues in a survey of sequenced marine bacterial genomes.

27 fficiently distribute variability throughout bacterial genomes.

28 k models using a phylogenomic dataset of 211 bacterial genomes.

29 l sequences in previously published complete bacterial genomes.

30 ch-mediated mechanisms are ubiquitous across bacterial genomes.

31 egulatory RNAs, are vital components of many bacterial genomes.

32 embling, engineering and transplanting whole bacterial genomes.

33 ss-kingdom comparative analysis of plant and bacterial genomes.

34 n properties from such summary statistics in bacterial genomes.

35 r viruses, biochemical pathways and assemble bacterial genomes.

36 d-binding proteins found in 72% of sequenced bacterial genomes.

37 , which aligns with encoded gene clusters in bacterial genomes.

38 iboswitches in DNA sequences on the scale of bacterial genomes.

39 teins are conserved across a large number of bacterial genomes.

40 tant role in the plasticity and evolution of bacterial genomes.

41 and a global driving force for the coding of bacterial genomes.

42 cy of lantipeptide biosynthetic machinery in bacterial genomes.

43 its that integrate into and excise from host bacterial genomes.

44 bsent from eukaryotic genomes in contrast to bacterial genomes.

45 ues and thresholds of the Refseq-97 complete bacterial genomes.

46 diverse defense systems that are abundant in bacterial genomes.

47 types highlight our limited understanding of bacterial genomes.

48 e and conjugative element in several ruminal bacterial genomes.

49 s molybdo/tungsto-enzymes in a wide range of bacterial genomes.

50 the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist ge

51 racteristically present in several copies in bacterial genomes (7 in E. coli), play a central role in

52 adaptive response" protein that protects the bacterial genome against alkylation damage.

53 ave carried out a computational study on 725 bacterial genomes, aiming to elucidate other factors tha

54 Several bacterial genomes also contain putative MCU homologs tha

55 The marine Roseobacter clade bacterial genomes also encode full sets of genes providi

56 f prophages (phage DNA integrated within the bacterial genome) among pneumococci isolated over the pa

57 complete repertoire of proteins encoded by a bacterial genome and demonstrates fundamentally differen

58 is common in microbes, with ~5% of sequenced bacterial genomes and 7% of genome equivalents in metage

59 identified in currently available reference bacterial genomes and a few other collections of sequenc

60 ce to simultaneously detect recombination in bacterial genomes and account for it in phylogenetic rec

61 nalyze how noncoding RNAs are distributed in bacterial genomes and also shows conserved features of i

62 unt for ~30% of genes in both eukaryotic and bacterial genomes and are predicted to encode what are o

63 icted prophage regions within self-targeting bacterial genomes and discovered two previously unknown

64 )-NQR and other FMN-binding flavoproteins in bacterial genomes and encode proteins with previously un

65 NRPS biosynthetic gene clusters from 39 232 bacterial genomes and established the first IMLs databas

66 size, contents, and compact organization of bacterial genomes and have allowed the establishment of

67 Application of our approach to bacterial genomes and human microbiome datasets allowed

68 Their genes have been found in nearly all bacterial genomes and in some organelles.

69 Bacterial genomes and large-scale computer software proj

70 orthia This GRE is widely distributed in gut bacterial genomes and may represent a novel target for c

71 on simulated read libraries of 3810 complete bacterial genomes and plasmids in GenBank and were capab

72 ransport, lipoproteins constitute 2 to 3% of bacterial genomes and play critical roles in bacterial p

73 ins limited when compared with the number of bacterial genomes and regulatory systems to be discovere

74 lowed by hierarchical synthesis of wild-type bacterial genomes and subsequently on transplantation of

75 enabled the identification of Mbn operons in bacterial genomes and the prediction of diverse Mbn stru

76 ps proteins are found almost ubiquitously in bacterial genomes and there is now an appreciation of th

77 ntitoxin (TA) systems are near ubiquitous in bacterial genomes and they play key roles in important a

78 intergenic regions (IGRs) compose 10-15% of bacterial genomes, and contain many regulatory elements

79 or function together are often clustered in bacterial genomes, and it has been proposed that this cl

80 resource has scaled up its representation of bacterial genomes, and now includes the genomes of over

81 thetic pathway is conserved in several other bacterial genomes, and our study reveals a redox-balanci

82 antitoxin (TA) systems are ubiquitous within bacterial genomes, and the mechanisms of many TA systems

83 Bacterial genomes are being sequenced at an exponentiall

84 parative phylogenomic analyses of fungal and bacterial genomes are consistent with an ancient origin

85 Although bacterial genomes are generally considered to be optimiz

86 Bacterial genomes are mosaics with fragments showing dis

87 Although these new bacterial genomes are partitioned into discrete cell typ

88 Sequenced bacterial genomes are routinely found to contain gene cl

89 vasion and nutrient acquisition, but as more bacterial genomes are sequenced, we are beginning to dis

90 Bacterial genomes are simpler than mammalian ones, and y

91 eotides are rare in bacteria, likely because bacterial genomes are under strong evolutionary pressure

92 ally improved the assemblies of many isolate bacterial genomes as compared to fragmented short-read a

93 demonstrate direct cell-to-cell transfer of bacterial genomes as large as 1.8 megabases (Mb) into ye

94 However, bacterial genomes assembled from short-read sequencing a

95 n extensive list of contaminant sequences in bacterial genome assemblies and the proteins associated

96 Thus, to date, about 1800 bacterial genome assemblies have been "finished" at grea

97 after 2016, identify the most commonly used bacterial genome assembly program, and address how anima

98 Open-source bacterial genome assembly remains inaccessible to many b

99 lecule, real-time sequencing to map (5m)C in bacterial genomes at base resolution.

100 chnologies have made it possible to generate bacterial genomes at clinically relevant timescales and

101 With the large number of complete bacterial genomes available, we now have the opportunity

102 omesticated elements end up deleted from the bacterial genome because they are replaced by analogous

103 t time to methylate recognition sites in the bacterial genome before the toxic restriction endonuclea

104 With increasing bacterial genomes being sequenced, similar host mining s

105 port family, which are widely distributed in bacterial genomes but for which details of structure-fun

106 obacterium virulence genes are found in many bacterial genomes, but only one non-Agrobacterium bacter

107 en a frequent subject of investigation using bacterial genomes, but previous approaches have not yet

108 ) systems are ubiquitous genetic elements in bacterial genomes, but their functions are controversial

109 ke it easy to generate very high coverage of bacterial genomes, but these advances mean that DNA prep

110 Much has been learnt about bacterial genomes by creating large mutant libraries and

111 dependent targets that subtle changes in the bacterial genome can be recovered at efficiencies rangin

112 A single bacterial genome can encode > 100 ECF sigma factors, and

113 Our previous study showed that bacterial genomes can be identified using 16S rRNA seque

114 Single-nucleotide polymorphism changes in bacterial genomes can cause significant changes in pheno

115 Bacterial genomes can contain traces of a complex evolut

116 ages (viral genomes integrated within a host bacterial genome) can confer various phenotypic traits t

117 Although the vast majority of bacterial genomes carry the genes involved in natural tr

118 enetic diversity of S. enterica, all ancient bacterial genomes clustered in a single previously uncha

119 ponsible for triuret decomposition (trtA) in bacterial genomes, clustered with biuH, which encodes bi

120 eve two complementary goals: recovering more bacterial genomes compared to binning a single sample as

121 ke receptor-9 (TLR9) has been shown to sense bacterial genome components (CpG DNA) and to play an ant

122 acter ethensis-2.0 (C. eth-2.0), a rewritten bacterial genome composed of the most fundamental functi

123 s of unordered contig or scaffold sequences, bacterial genomes consisting of a single complete chromo

124 Most bacterial genomes contain different types of toxin-antit

125 Predictably, the dark matter of bacterial genomes contains a wealth of genetic gold.

126 Similar bacterial genome copy numbers were detected in control a

127 RecBCD and the distribution of Chi sites in bacterial genomes could allow the RecBCD pathway to avoi

128 logenetic and machine-learning approaches to bacterial genome data to quantify the roles of badgers a

129 Despite the enormous proliferation of bacterial genome data, surprisingly persistent collectio

130 The rise in the availability of bacterial genomes defines a need for synthesis: abstract

131 ce evaluation based on the Rfam database and bacterial genomes demonstrate that RNAdetect can accurat

132 The HBC increases the number of bacterial genomes derived from human gastrointestinal mi

133 onships within large sequence collections of bacterial genomes derived from the same microbial specie

134 nical progress, options and applications for bacterial genome design, assembly and activation are dis

135 ogenetic and molecular clock analyses of the bacterial genome, detailed archaeological information, a

136 ignificance--identification of alien DNAs in bacterial genomes, detection of structural variants in c

137 icating that nuclear, mitochondrial, and gut bacterial genomes diversified in concert during hominid

138 Bacterial genome duplication and transcription require s

139 tion with these extrachromosomal elements on bacterial genome dynamics in host-dependent microbes.

140 iosynthetic gene clusters were identified in bacterial genomes, each containing a gene encoding a pro

141 This review summarizes recent progress in bacterial genome editing and identifies fundamental gene

142 Although bacterial genome editing is a relatively unexplored and

143 ed to as CRISPR/Cas, are the components of a bacterial genome editing system that can be used to pert

144 m Photorhabdus luminescens incorporated into bacterial genomes, elicits the production of biological

145 ng pathogens that can lead to changes in the bacterial genome enabling the pathogen to escape host re

146 Many bacterial genomes encode dynamin-like proteins, but the

147 y, we explore the logic behind the fact that bacterial genomes encode multiple Mg(2+) transporters an

148 Currently available tools for multiplex bacterial genome engineering are optimized for a few lab

149 Allelic exchange is an efficient method of bacterial genome engineering.

150 esting the versatility of this technique for bacterial genome engineering.

151 web service to extract prophage genomes from bacterial genomes, evaluate the activity of the prophage

152 gene providers is central for understanding bacterial genome evolution by horizontal transfer.

153 ed computational demand compared to previous bacterial genome evolution simulators, FastSimBac provid

154 for a faster approach to model and simulate bacterial genome evolution.

155 e-nucleotide polymorphisms (SNPs) in ancient bacterial genomes, facilitating qualitative analyses of

156 st of peptidases from a completely sequenced bacterial genome for a particular strain of the organism

157 hese inhibitors, we searched cas9-containing bacterial genomes for the co-existence of a CRISPR space

158 evious dataset of 820 bacteriophage and 2699 bacterial genomes, [Formula: see text] host prediction a

159 an yield high-quality contiguous or circular bacterial genomes from a complex human gut sample in app

160 ultiple genome assembly programs to assemble bacterial genomes from a single, deep-coverage library.

161 calculated quality scores for around 100,000 bacterial genomes from all major genome repositories and

162 biosynthesis in a collection of over 10,000 bacterial genomes from both cultured isolates and metage

163 rt-read error correction, to assemble closed bacterial genomes from complex microbiomes.

164 arge (170 GB) reference collection of 43 552 bacterial genomes from Ensembl.

165 eved by combining a manually curated list of bacterial genomes from human faecal samples with over 21

166 All ancient bacterial genomes from prehistoric (agro-)pastoralists f

167 In our experimentation with bacterial genomes from the Human Oral Microbiome Databas

168 Six bacterial genomes, Geobacter metallireducens GS-15, Chro

169 tion on non-palindromic TAGGAG motifs in the bacterial genome guides self/non-self discrimination and

170 Most bacterial genomes harbor restriction-modification system

171 ents using meiotic recombination between the bacterial genomes harbored in yeast.

172 nthetic biology aims to design and construct bacterial genomes harboring the minimum number of genes

173 Almost all bacterial genomes harbour prophages, yet it remains unkn

174 ears as the ubiquitous nature of TA genes on bacterial genomes has been revealed.

175 oughput technologies, the cost of sequencing bacterial genomes has been vastly reduced.

176 ubiquity of genes encoding GGDEF proteins in bacterial genomes has established the dominance of cdiG

177 heir wide prevalence and amplification among bacterial genomes has led to sub-group classification an

178 y and distribution of methylated residues in bacterial genomes has prevented a full understanding of

179 Full genome sequencing of bacterial genomes has revealed the presence of numerous

180 Bioinformatic analysis of sequenced bacterial genomes has uncovered an increasing number of

181 Bacterial genomes have been shown to be partitioned into

182 Because bacterial genomes have high gene content, forces that op

183 n that sequencing and analysis of historical bacterial genomes have made to a wide variety of fields.

184 100 base pair lengths occupy more than 1% of bacterial genomes; however, commitment to strand exchang

185 A systematic search of 54,875 bacterial genomes identified 4686 intergenic invertible

186 f cellulose synthase operon found in various bacterial genomes, identify additional bcs genes that en

187 scuss the automatic and manual annotation of bacterial genomes, identify common problems introduced b

188 Expanding the comparison to 894 distinct bacterial genomes illustrates fractional conservation an

189 This puts the bacterial genome in a state of continuous flux of acquis

190 The ability to sequence a bacterial genome in less than 1 day represents a step ch

191 ation and maintenance of this 1.66 Mb intact bacterial genome in S. cerevisiae.

192 rms; (vii) EcoTools access to >2000 complete bacterial genomes in EcoGene-RefSeq; (viii) establishmen

193 nding of the dynamic spatial organization of bacterial genomes in live cells.

194 as an analysis tool for the 15,000+ complete bacterial genomes in NCBI's Refseq library.

195 to construct 469 draft metagenome-assembled bacterial genomes, including 460 novel strains, 283 nove

196 anol synthase (Ths) is found in a variety of bacterial genomes, including aerobic methanotrophs, nitr

197 ge resistance systems has been identified in bacterial genomes, including restriction-modification sy

198 Bioinformatic analysis of bacterial genomes indicates that the production of metha

199 bsequently on transplantation of synthesized bacterial genomes into closely related recipient strains

200 on of transcription units (TUs) encoded in a bacterial genome is essential to elucidation of transcri

201 Moreover, the numbers of dps genes per bacterial genome is variable; even amongst closely relat

202 classification of M. tuberculosis and other bacterial genomes is a core analysis for studying evolut

203 Editing bacterial genomes is an essential tool in research and s

204 Functional annotation of bacterial genomes is an obligatory and crucially importa

205 oftware combined with targeted sequencing of bacterial genomes is needed to understand the contributi

206 conformations and the details of how DNA in bacterial genomes is rapidly searched until homologous a

207 and that the distribution of DksA and i6 in bacterial genomes is strongly concordant.

208 -resolution ordered restriction mapping of a bacterial genome, is a relatively new genomic tool that

209 Although hipBA operons are widespread in bacterial genomes, it is unknown if this mechanism is co

210 ge resistance systems has been identified in bacterial genomes (Labrie et al, 2010), including restri

211 On eight bacterial genomes, Look4TRs outperformed the second and

212 tion of signal transduction protein genes in bacterial genomes made them the first to be amenable to

213 In bacterial genomes, methylation occurs on adenosine and c

214 h-resolution time-lapse imaging to peer into bacterial genome (nucleoid) structure.

215 e currently available for many core genes in bacterial genomes of significant global public health im

216 e demonstrate that, with these improvements, bacterial genomes often can be assembled in a few contig

217 systems may direct significant evolution of bacterial genomes on a population level, influencing gen

218 ractive browsing and comparative analysis of bacterial genomes online.

219 ion algorithm to all available Gram-negative bacterial genomes (over 600 chromosomes) and have constr

220 Structural integrity of the bacterial genome plays an important role in bacterial su

221 the number of ribosomal RNA operons (rrn) in bacterial genomes predicts two important components of r

222 ing and labor cost reductions in large-scale bacterial genome projects.

223 Analysis of HK sequences in bacterial genomes provided evidence that the selective p

224 y, there are approximately 140 000 assembled bacterial genomes publicly available, more than 8500 of

225 A majority of large-scale bacterial genome rearrangements involve mobile genetic e

226 ed metabolic capabilities of four uncultured bacterial genomes (reconstructed using metagenomic assem

227 n vivo and their distribution throughout the bacterial genome remain unknown.

228 Understanding the extreme variation among bacterial genomes remains an unsolved challenge in evolu

229 n and secretion of proteins predominate over bacterial genome replication and cell division.

230 Historical bacterial genomes represent a unique source of genetic i

231 bing a collection of 1239 publicly available bacterial genomes, representing cultured and uncultivate

232 diverse properties of different genes within bacterial genomes results in a lack of standard reproduc

233 A search of bacterial genomes revealed the presence of sequences tha

234 A survey of bacterial genomes reveals that genes encoding Ssp6-like

235 combination with other metrics to establish bacterial genome sequence accuracy.

236 ument can generate data required for a draft bacterial genome sequence in days, making them attractiv

237 sequencing, we have produced the first whole bacterial genome sequences direct from clinical samples.

238 Over the past decade, bacterial genome sequences have revealed an immense rese

239 apidly construct phylogenetic trees of draft bacterial genome sequences on a standard desktop compute

240 ia for experimental validation and reference bacterial genome sequences to interpret metagenome datas

241 from the growing base of publicly available bacterial genome sequences, we developed pan-PCR.

242 nly a few hours on alignments of hundreds of bacterial genome sequences.

243 valuated with three datasets from fungal and bacterial genome sequences.

244 clinical trial to obtain comprehensive fecal bacterial genome sequencing coverage and explore the ful

245 Large-scale bacterial genome sequencing efforts to date have provide

246 PCR primers that exploited this rapid draft bacterial genome sequencing to distinguish between E. co

247 Bacterial genome sequencing, functional assays, and in v

248 lly increased throughput and reduced cost of bacterial genome sequencing.

249 Our simulations on bacterial genomes show that AGORA is effective at produc

250 Analyses of the extant bacterial genomes showed that bioH is absent from many b

251 l settings, as well as their role in shaping bacterial genome size and composition.

252 determined, in part, by a trade-off between bacterial genome size and local variation in climatic co

253 Mean bacterial genome size, GC content, total number of tRNA

254 rthologs have been identified in 3% to 5% of bacterial genomes, spanning the majority of phyla.

255 functions in multiple pathways that promote bacterial genome stability including the suppression of

256 age, and distant homologs in other phage and bacterial genomes, suggesting that dG(+) is not a rare m

257 rtial PT modification of consensus motifs in bacterial genomes suggests an unusual mechanism of PT-de

258 A survey of bacterial genomes suggests that the diversity within rec

259 = 1consecutive genes on the same strand of a bacterial genome that are transcribed into a single mRNA

260 ystem has been used to select changes in the bacterial genome that cannot be directly detected by oth

261 een and select putative novel effectors from bacterial genomes that can be validated by a smaller num

262 enomes from thousands of genetically diverse bacterial genomes that represent the diversity of an ent

263 are for finding gene clusters in hundreds of bacterial genomes, that comes with an easy-to-use graphi

264 logous regulators in several closely related bacterial genomes, that were reconstructed by comparativ

265 es in the speed of sequencing and annotating bacterial genomes, the identification and categorisation

266 orthologues of these enzymes are present in bacterial genomes, their biological functions remain lar

267 ions to additional copies of PmoC encoded in bacterial genomes, thus contributing to growth on methan

268 by which integrases dramatically manipulate bacterial genomes to allow cotransfer of disparate chrom

269 at allows comparative analysis across entire bacterial genomes to identify regions of genomic similar

270 We then compared 3,837 bacterial genomes to identify thousands of plant-associa

271 tween DNA sequences in the bacteriophage and bacterial genomes to integrate or excise the phage DNA.

272 nology have been reported ranging from small bacterial genomes to large plant and animal genomes.

273 Over 80% of the bacterial genomes transferred in this way are complete,

274 been found scattered in several archaeal and bacterial genomes, unassociated with CRISPR loci or othe

275 Application of DeepBGC to bacterial genomes uncovered previously undetectable puta

276 able genetic modification and engineering of bacterial genomes using homologous recombination methods

277 search for gene clusters in a dataset of 678 bacterial genomes using Synechocystis sp. PCC 6803 as a

278 Bacterial genomes vary extensively in terms of both gene

279 prised of nearly all proteins encoded by the bacterial genome was used to determine the kinetics of t

280 Here, Shannon's index of complete phage and bacterial genomes was examined.

281 ive understanding of dynamics of MGEs in the bacterial genome, we engineered the genome of V. cholera

282 Using over thirteen hundred sequenced bacterial genomes, we built a novel function-based micro

283 rst, the entire 2628-annotated genes of this bacterial genome were categorized into essential, non-es

284 Operons are a hallmark of bacterial genomes, where they allow concerted expression

285 te cell lysis for virion release, and within bacterial genomes, where they serve a diversity of poten

286 GC skew is a phenomenon observed in many bacterial genomes, wherein the two replication strands o

287 poses additional evolutionary constraints on bacterial genomes, which go beyond preservation of struc

288 Bacterial genome-wide association studies (GWAS) can ide

289 s evolutionary importance, only a handful of bacterial, genome-wide cytosine studies have been conduc

290 obacterium SAR324 genome, which is the first bacterial genome with a comprehensive single-cell genome

291 rediction of 94% of prophages in 50 complete bacterial genomes with a 6% false-negative rate and a 0.

292 At PATRIC, we have been collecting bacterial genomes with AMR metadata for several years.

293 e demonstrate a rapid approach for rewriting bacterial genomes with modified synthetic DNA.

294 Sequencing whole bacterial genomes with single-nucleotide resolution demo

295 excellent sequence coverage over the entire bacterial genome, with >99% alignment to the reference g

296 haea, and represented in approximately 5% of bacterial genomes, with an over-representation among pat

297 used UNCALLED to deplete sequencing of known bacterial genomes within a metagenomics community, enric

298 o reconstruct 63 complete or nearly complete bacterial genomes within single contigs.

299 they instead package fragments of the entire bacterial genome without preference for their own genes.

300 of the human gut microbiome can yield draft bacterial genomes without isolation and culture.