ライフサイエンスコーパス: bacterial genome

1 study the evolution of prophages within the bacterial genome.

2 rage intergenic regions in the corresponding bacterial genome.

3 ccumulated burden of coding mutations in the bacterial genome.

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

5 ission cycles in shaping and maintaining the bacterial genome.

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

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

8 lution, in situ ordered restriction map of a bacterial genome.

9 nce genes that can incorporate into the host bacterial genome.

10 ts mediate large-scale rearrangements of the bacterial genome.

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

12 Red outperformed the related tools on a bacterial genome.

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

14 embling, engineering and transplanting whole bacterial genomes.

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

16 n properties from such summary statistics in bacterial genomes.

17 r viruses, biochemical pathways and assemble bacterial genomes.

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

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

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

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

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

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

24 cy of lantipeptide biosynthetic machinery in bacterial genomes.

25 n the set of highly expressed genes for 300+ bacterial genomes.

26 wn about the complement of dNKs in different bacterial genomes.

27 resence of homologous gene clusters in other bacterial genomes.

28 eing discovered in the noncoding portions of bacterial genomes.

29 ation events that affected a given sample of bacterial genomes.

30 b the coordinated regulation of the host and bacterial genomes.

31 The DedA family genes are found in most bacterial genomes.

32 both artificial chimeric genomes and genuine bacterial genomes.

33 >1,500 proteins identified by sequencing of bacterial genomes.

34 yoeB toxin-antitoxin system found in various bacterial genomes.

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

36 We conducted a large-scale analysis of 133 bacterial genomes.

37 l constraints shaping the gene repertoire of bacterial genomes.

38 es new data on the evolution of multipartite bacterial genomes.

39 rks is essential for complete duplication of bacterial genomes.

40 e has profound evolutionary consequences for bacterial genomes.

41 rved HyP genes account for >30% of sequenced bacterial genomes.

42 bust process to CGH microarray studies using bacterial genomes.

43 t promotes better-than-random segregation of bacterial genomes.

44 cifically to understand the mosaic nature of bacterial genomes.

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

46 onuclease and 34 BisI homologs identified in bacterial genomes.

47 specific DNA sequences into a population of bacterial genomes.

48 component tools for assembling and finishing bacterial genomes.

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

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

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

52 rophages are abundant residents of sequenced bacterial genomes.

53 fficiently distribute variability throughout bacterial genomes.

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

55 esponses and therapeutic interventions-shape bacterial genomes.

56 ch-mediated mechanisms are ubiquitous across bacterial genomes.

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

58 ructural stability typical of highly reduced bacterial genomes [4, 9, 10].

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

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

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

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

63 The increased availability of sequenced bacterial genomes allows application of an alternative e

64 Several bacterial genomes also contain putative MCU homologs tha

65 Many bacterial genomes also encode a parallel PTS pathway tha

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

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

68 previously known and novel MITEs in the two bacterial genomes, Anabaena variabilis ATCC 29413 and Ha

69 They are integrated into the bacterial genome and are capable of conjugative transfer

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

71 tetS followed by clustering)], involving 624 bacterial genomes and >2 million genes.

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

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

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

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

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

77 nown mitochondrial genomes, larger than most bacterial genomes and even some nuclear genomes.

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

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

80 Bacterial genomes and large-scale computer software proj

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

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

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

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

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

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

87 e for controlling the expression of genes in bacterial genomes and when visualized on a genomic scale

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

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

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

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

92 lves according to polar sequences present in bacterial genomes, and perform various additional roles

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

94 Accurate replication and segregation of the bacterial genome are essential for cell cycle progressio

95 and location of novel genomic elements in a bacterial genome are not straightforward, unless the who

96 Bacterial genomes are characterized by a high gene densi

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

98 The physical properties of most bacterial genomes are largely unexplored.

99 Bacterial genomes are mosaics with fragments showing dis

100 genes comprising the ubiquitous backbone of bacterial genomes are not subject to frequent horizontal

101 Bacterial genomes are organized by structural and functi

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

103 ply an alternative 'top-down' approach where bacterial genomes are recursively divided into progressi

104 Sequenced bacterial genomes are routinely found to contain gene cl

105 Bacterial genomes are simpler than mammalian ones, and y

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

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

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

109 ultiple genomes comparison and assistance of bacterial genome assembly.

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

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

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

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

114 haemoprotein sensors that are widespread in bacterial genomes, but limited information is available

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

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

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

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

119 The intergenic regions in bacterial genomes can contain regulatory leader sequence

120 but also that the orphan SBP genes common to bacterial genomes can encode functional SBPs.

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

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

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 However, many bacterial genomes contain several genes coding for these

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

127 tion also plays an important role in shaping bacterial genome content.

128 Similar bacterial genome copy numbers were detected in control a

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

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

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

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

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

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

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

136 Although bacterial genome editing is a relatively unexplored and

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

138 ases generated from sequences of hundreds of bacterial genomes enables various statistical approaches

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

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

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

142 Many bacterial genomes encode several copies of proteins cont

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

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

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

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

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

148 etween species is an important mechanism for bacterial genome evolution.

149 atic bias from applying simplified models to bacterial genome evolution.

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

151 highlight the way in which the plasticity of bacterial genomes facilitates the emergence of new patho

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

153 (ADAM), a technology that searches an entire bacterial genome for mutations that contribute to select

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

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

156 Here, we detail how collections of bacterial genomes from a particular species (population

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

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

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

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

161 he maintenance of this genome and of complex bacterial genomes generally.

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

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

164 Most bacterial genomes harbor restriction-modification system

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

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

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

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

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

170 he main chromosome, approximately one in ten bacterial genomes have a 'second chromosome' or 'megapla

171 Most bacterial genomes have five to nine distinct genes predi

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

173 100 base pair lengths occupy more than 1% of bacterial genomes; however, commitment to strand exchang

174 Phage DNA may also constitute 20% of bacterial genomes; however, its role is ill defined.

175 A search of five thermophilic bacterial genomes identified a coded amino acid sequence

176 A recent analysis of bacterial genomes identified many alpha-macroglobulin-li

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

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

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

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

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

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

183 port a method that can seamlessly modify the bacterial genome in yeast with high efficiency.

184 emical synthesis, assembly, and cloning of a bacterial genome in yeast.

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

186 Here we report the cloning of whole bacterial genomes in the yeast Saccharomyces cerevisiae

187 ifferent directions: 'top-down' reduction of bacterial genomes in vivo and 'bottom-up' integration of

188 derived from horizontal transfer events from bacterial genomes include components of transporters ass

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

190 An analysis of 992 fully sequenced bacterial genomes, including both Gram-positive and Gram

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

192 pontaneously decay, genetic analysis of some bacterial genomes indicates that an aminotransferase may

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

194 ogs with various sequence identities in some bacterial genomes indicates that there may be multiple p

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

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

197 that the global arrangement of operons in a bacterial genome is largely influenced by the tendency t

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

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

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

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

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

203 The recent explosion in newly sequenced bacterial genomes is outpacing the capacity of researche

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

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

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

207 cleotide identity) genes found in 2,235 full bacterial genomes, is shaped principally by ecology rath

208 erformance of the system by sequencing three bacterial genomes, its robustness and scalability by pro

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

210 es derived from spontaneous deletions of the bacterial genome maintained in yeast.

211 Bacterial genome mining indicates three tandem ORFs that

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

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

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

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

216 ractive browsing and comparative analysis of bacterial genomes online.

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

218 Analysis of newly sequenced bacterial genomes points to the existence of a much broa

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

220 reliable functions to enzymes discovered in bacterial genome projects; in this Current Topic, we rev

221 Sequenced bacterial genomes provide a wealth of information but li

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

223 Establishing that oligos can recombine with bacterial genomes provides a link to similar observation

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

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

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

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

228 produce long DNA fragments (up to 0.5 Mb) of bacterial genome restriction digest and perform DNA tagg

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

230 oinformatic analysis of ORF sequences in 816 bacterial genomes revealed that these features show dist

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

232 The availability of bacterial genome sequence databases has facilitated the

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

234 REIS one of the most plastic and repetitive bacterial genomes sequenced to date.

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

236 The availability of whole bacterial genome sequences has enabled us to perform com

237 The availability of bacterial genome sequences has ushered in an era of post

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

239 ing technologies have made the production of bacterial genome sequences increasingly easy, and it can

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

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

242 en in Perl, used for the rapid annotation of bacterial genome sequences.

243 nly a few hours on alignments of hundreds of 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 most challenging and time-consuming tasks in bacterial genome sequencing projects, especially with th

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

248 Bacterial genome sequencing, functional assays, and in v

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

250 However, bacterial genomes show diverse arrays of P(1B)-type ATPa

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

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

253 Extensive experiments with bacterial genomes showed that the proposed scoring schem

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

255 olution, namely the phage Modular Theory and bacterial genome stability in obligate intracellular spe

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

257 have provided insight into the evolution of bacterial genome structures; revealing the impact of mob

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

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

260 = 1consecutive genes on the same strand of a bacterial genome that are transcribed into a single mRNA

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

262 mic data from insect symbionts have revealed bacterial genomes that are incredibly small-two to four

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 ans-acting regulatory RNAs commonly occur in bacterial genomes, they have been better characterized i

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

269 ve PSI-BLAST and TBLASTN searches across 774 bacterial genomes to identify homologs of known type I t

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

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

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

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

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

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

276 ify choline utilization clusters in numerous bacterial genomes, underscoring the importance and preva

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

278 and present experimental results on several bacterial genomes using next-generation sequencing techn

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

280 Bacterial genomes vary extensively in terms of both gene

281 Bacterial genomes vary in size over two orders of magnit

282 Since the first complete sequence for a bacterial genome was reported, the emphasis has switched

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

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

285 rrent arrangements of operons in most of the bacterial genomes we studied tend to minimize the overal

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

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

288 and homologs of R1 are found in 11 sequenced bacterial genomes, where they are paired with specificit

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

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

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

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

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

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

295 ted by the need to improve the annotation of bacterial genomes with GO and to improve how prokaryotic

296 equence data to identify differences between bacterial genomes with high sensitivity and specificity.

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

298 Sequencing whole bacterial genomes with single-nucleotide resolution demo

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

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