ライフサイエンスコーパス: sequence evolution

1 overall rates of gene content evolution and sequence evolution.

2 e unusual in their organization and rates of sequence evolution.

3 that may also affect genome instability and sequence evolution.

4 zations may facilitate virus replication and sequence evolution.

5 ods to the presence of nonneutral convergent sequence evolution.

6 small insertions and subsequent accelerated sequence evolution.

7 ve of CD8 responses capable of selecting for sequence evolution.

8 ults and guides efforts to improve models of sequence evolution.

9 data depends on the use of proper models of sequence evolution.

10 ual genes show little indication of adaptive sequence evolution.

11 butes to the diverse and unpredictable HIV-1 sequence evolution.

12 ion of DNA is one of the forces driving this sequence evolution.

13 e-coding nucleotides will result in atypical sequence evolution.

14 n the links between intron gain and loss and sequence evolution.

15 found that it closely predicts the simulated sequence evolution.

16 we develop an evolutionary model for protein sequence evolution.

17 representing reproductive isolation without sequence evolution.

18 e relationship between protein structure and sequence evolution.

19 election have been the dominant processes of sequence evolution.

20 domains show evidence of significantly slow sequence evolution.

21 ovel genes show accelerated rates of protein sequence evolution.

22 tra stability and an increase in the rate of sequence evolution.

23 n sexuals vs. asexuals, using a model of DNA sequence evolution.

24 n-genetic constraints on the rate of protein sequence evolution.

25 ructures allowed a detailed analysis of rRNA sequence evolution.

26 uch a code enhances the efficacy of adaptive sequence evolution.

27 ide substitution and reticulate processes to sequence evolution.

28 creases with expression level and constrains sequence evolution.

29 emphasis on studies of rates and patterns of sequence evolution.

30 ox clusters that have undergone considerable sequence evolution.

31 d death events and have accelerated rates of sequence evolution.

32 protease gene and, thus, can influence viral sequence evolution.

33 tudinally in conjunction with viral load and sequence evolution.

34 ated loci and in understanding the causes of sequence evolution.

35 karyote tree because of systematic biases in sequence evolution.

36 es in a gene family and the family's rate of sequence evolution.

37 uster architecture and patterns of noncoding sequence evolution.

38 te, 4N(e)r, under an infinite-sites model of sequence evolution.

39 d robust to misspecification of the model of sequence evolution.

40 gene duplication event followed by extensive sequence evolution.

41 he promised advances in the understanding of sequence evolution.

42 Script, with new views for exploring protein sequence evolution.

43 as well as for models of cis-regulatory DNA sequence evolution.

44 variety of biologically realistic models of sequence evolution.

45 s, however, can quickly arrive at a model of sequence evolution.

46 or understanding the mechanisms of molecular sequence evolution.

47 m numerous sequence possibilities as well as sequence evolution.

48 ontribution of retrotransposition to ongoing sequence evolution.

49 ough during chromosome replication to affect sequence evolution.

50 ificant challenge due to their high rates of sequence evolution.

51 ylogenetic test of measurable immunoglobulin sequence evolution.

52 acts as a hotspot of both siRNA matching and sequence evolution.

53 d to study rate acceleration/deceleration in sequence evolution.

54 potheses concerning the process of molecular sequence evolution.

55 ection according to a simple model of random sequence evolution.

56 cture of epistasis in simulations of protein sequence evolution.

57 in our understanding of the patterns of DNA sequence evolution.

58 and report that they have elevated rates of sequence evolution.

59 3D structure prediction and analysis of RNA sequence evolution.

60 xpression patterns show accelerated rates of sequence evolution.

61 notype and is associated with rapid envelope-sequence evolution.

62 he aquatic light environment can shape opsin sequence evolution.

63 archers to compare current and new models of sequence evolution across a large variety of sequences.

64 ns often show correlated changes in rates of sequence evolution across a phylogeny [evolutionary rate

65 rst attempt to detect genome-wide convergent sequence evolution across divergent taxa reveals the phe

66 nce analyses allow us to assess variation in sequence evolution across sites and we apply them to mat

67 ability of a MSA under a stochastic model of sequence evolution along a time axis via substitutions,

68 ithm and software for efficiently simulating sequence evolution along extremely large trees (e.g. > 1

69 However, models of DNA sequence evolution also have important limitations that

70 We report that patterns of nonneutral DNA sequence evolution among published nuclear and mitochond

71 utations, endosymbionts will show (i) faster sequence evolution and (ii) a possible shift in base com

72 lly HIV-1-infected persons were examined for sequence evolution and altered MHC-I downregulatory func

73 We took advantage of rate-constant rDNA sequence evolution and an "external" calibration using p

74 one remarkably frequent bouts of accelerated sequence evolution and architectural changes (e.g. a los

75 nies, we devised computer models to simulate sequence evolution and calculate new phylogenies based o

76 th HCV persistence, we coordinately analyzed sequence evolution and CD8+ T cell responses to epitopes

77 y detected this effect using data on protein sequence evolution and codon usage in Drosophila.

78 cer represents a model for understanding DNA sequence evolution and could reveal causal factors under

79 llenge, particularly in virology where rapid sequence evolution and database expansion confound stati

80 CTT sequences display intermediate levels of sequence evolution and diversity in comparison to the mo

81 sistent correlations between rates of coding-sequence evolution and gene expression levels are appare

82 (HCV) infection is rarely studied, but virus sequence evolution and host-virus dynamics during this e

83 cation persists in EC tissues to allow viral sequence evolution and induce excess immune activation.

84 es compensation of two adverse trends: rapid sequence evolution and loss of genetic information throu

85 tion for new models and methodology to study sequence evolution and may allow general statements abou

86 ht and challenge the conventional picture of sequence evolution and mechanisms of functional and stru

87 We analyzed envelope glycoprotein sequence evolution and neutralization of sequential auto

88 aluation of the impact of metabolism on gene sequence evolution and show that it is possible to predi

89 Correlations between sequence evolution and structural dynamics are of utmost

90 omes revealed differences in the patterns of sequence evolution and the complete inventory of genetic

91 Measurements of HIV-1 sequence evolution and the concentrations of unspliced a

92 ic fragments by simulating within-host HIV-1 sequence evolution and the cycling of viral lineages in

93 virus-specific neutralizing antibodies drive sequence evolution and, in some individuals, play a role

94 d the relationships between organ evolution, sequence evolution, and expression evolution in Arabidop

95 ntly therefore imposed constraints on genome sequence evolution, and since archaeal histones have no

96 re-evaluate the current paradigms of coding-sequence evolution, and that the wide use of K(a)/K(s) a

97 he correlations between chromatin packaging, sequence evolution, and the evolution of gene expression

98 ding AT-biased base composition, accelerated sequence evolution, and, at least sometimes, small genom

99 We suggest that, as with protein sequence evolution, antagonistic co-evolution may be key

100 nts, or a quasispecies, whose complexity and sequence evolution are critical to studies of viral path

101 Our results show that patterns of sequence evolution are driven by a balance between these

102 aw evidence of protein-coding and regulatory sequence evolution as well as the origin of novel genes

103 ough regulatory evolution rather than coding sequence evolution, as CAM-related genes are differentia

104 d as an outgroup, no acceleration in protein sequence evolution associated with chromosomal rearrange

105 Existing mathematical models of DNA sequence evolution assume that all substitutions derive

106 sequencing to examine the dynamics of genome sequence evolution at high temporal resolution in 40 rep

107 We extend these models to track sequence evolution at multiple sites.

108 ression in diverse angiosperms despite rapid sequence evolution at siren loci.

109 Although viral sequence evolution at targeted MHC class I-restricted ep

110 We present two new models of protein sequence evolution based on structural properties of mit

111 Estimates of sequence evolution based on the accumulation of nucleoti

112 ment model with a phylogenetic model for BCR sequence evolution but also naturally accounts for uncer

113 However, in two patients there was sequence evolution but no evidence of drug-resistant vir

114 t orphan loss is not driven by high rates of sequence evolution, but reflects lineage-specific functi

115 ASPM went through an episode of accelerated sequence evolution by positive Darwinian selection after

116 s have demonstrated that adaptive convergent sequence evolution can be detected in vertebrates using

117 tion and provide new insight into how genome sequence evolution can be influenced by adaptation to di

118 he results show that genome-wide patterns of sequence evolution can be influenced by natural selectio

119 Patterns of sequence evolution can be used to identify cis-regulator

120 ion with genetic variation revealed that DNA sequence evolution can explain replication timing variat

121 nction for ATHs and demonstrates that coding sequence evolution can underlie quantitative variation i

122 By integrating sequence evolution, cell phenotypes, developmental conte

123 erved patterns of simple covariation between sequence evolution, codon usage, and mRNA level in E. co

124 Buchnera aphidicola shows elevated rates of sequence evolution compared to free-living relatives, pa

125 ice exhibited dynamic behavior that included sequence evolution, compartmentalization, and the appear

126 One method for diagnosing the mode of sequence evolution considers the ratio of nonsynonymous

127 e-biased genes show elevated rates of coding sequence evolution, consistent with previous reports in

128 efore, interplay between enhancer and coding sequence evolution created a potentially adaptive path f

129 sets, and four uncertain datasets taken from sequence evolution data.

130 Although the rate of protein sequence evolution depends primarily on the level of fun

131 The underlying model of sequence evolution describes indels and substitutions.

132 lutionary pressures, and models of molecular sequence evolution developed using other kinds of sequen

133 molecular mechanisms of mtDNA control region sequence evolution differ among acipenserids.

134 correspond to the extremes in a continuum of sequence evolution displayed in a SCYLV superpopulation

135 some skepticism over the degree that neutral sequence evolution drives overall patterns of diversity.

136 NA structures exhibit correlated patterns of sequence evolution due to constraints imposed by the int

137 duals, to distinguish changes resulting from sequence evolution due to possible superinfection.

138 HVR1 can undergo rapid sequence evolution during acute infection, and the varia

139 T-cell responses and their effects on viral sequence evolution during chronic infection in order to

140 ion factor binding as two separable modes of sequence evolution, each of which is a direct target of

141 traint and accelerates an organism's protein sequence evolution, especially for genes from early deve

142 Both experimental as well as sequence evolution evidence suggests that transcription

143 oding element divergence, accelerated coding sequence evolution, expression divergence associated wit

144 n use a variety of biological data including sequence-, evolution-, expression-, and structure-based

145 ve revealed the importance of cis-regulatory sequence evolution, few examples exist where the downstr

146 enomes to characterize rates and patterns of sequence evolution for a broad sampling of photosyntheti

147 The model of sequence evolution for each of the eight categories is a

148 Nav channels show adaptive sequence evolution for increasing diversity in communica

149 sequence comparison showed a higher rate of sequence evolution for the rapid progressors in three of

150 xtensive knowledge about the rate of protein sequence evolution for thousands of genes in hundreds of

151 HIV-1 envelope sequence evolution from CCR5 to CXCR4 use is constrained

152 en gene family; this pipeline can model gene sequence evolution, gene duplication-loss, gene transfer

153 synteny, transposable element (TE) dynamics, sequence evolution, gene family evolution, and temporal

154 This process was distinct from more-recent sequence evolution generating diversity within picornavi

155 n that of C. elegans or Drosophila, and that sequence evolution has occurred at a typical rate.

156 Viral sequence evolution has previously been shown to mediate

157 The rate and mechanism of protein sequence evolution have been central questions in evolut

158 enetic analyses based on models of molecular sequence evolution have driven to industrial scale the g

159 High rates of amino-acid sequence evolution have sometimes been considered to be

160 Empirical models of sequence evolution have spurred progress in the field of

161 We examined rates of DNA sequence evolution in 12 populations of Escherichia coli

162 We analyzed plasma virus sequence evolution in 5.2-kb hemigenomes from multiple l

163 Systematic analyses of convergent sequence evolution in 805,053 amino acids within 2,326 o

164 ned, unpartitioned and mixture models of DNA sequence evolution in a Bayesian context.

165 ic T cells, and antibodies, as well as viral sequence evolution in a white male who spontaneously cle

166 Our goals were to compare rates of sequence evolution in Blochmannia with related bacteria,

167 ved noncoding regions, and relative rates of sequence evolution in both coding and noncoding tracts.

168 Previous studies demonstrated accelerated sequence evolution in Buchnera compared to free-living b

169 duced N(e) as a primary cause of accelerated sequence evolution in Buchnera.

170 uences of long-term asexual reproduction for sequence evolution in diploid or polyploid eukaryotic or

171 ted by anecdotal accounts of higher rates of sequence evolution in disordered protein than in ordered

172 e results to obtain insights into regulatory sequence evolution in Drosophila and humans.

173 of transposed genes, we detected accelerated sequence evolution in duplicated genes that transposed w

174 Highly elevated rates of sequence evolution in Geraniaceae mitochondrial genomes

175 However, selection could have skewed sequence evolution in introns and exons.

176 isons to investigate the impact of the IR on sequence evolution in plastids.

177 genes display an accelerated rate of protein sequence evolution in primates relative to rodents or ca

178 ies showed evidence of convergent amino acid sequence evolution in salivary-expressed members.

179 Here we report patterns of mitochondrial sequence evolution in South American marsh rats (genus H

180 nes experiencing more rapid rates of protein sequence evolution in T. dactyloides.

181 In analyzing patterns of cis-sequence evolution in the 5' part of the clusters, we ex

182 We examined viral sequence evolution in the C2V3C3 region of the viral env

183 Tracing their sequence evolution in the Drosophila lineage suggests th

184 Our finding supports the concept that sequence evolution in the extracellular domain may be re

185 res, mechanisms, and specificities of recent sequence evolution in the indica and japonica subspecies

186 understanding the mutational mechanisms and sequence evolution in the mammalian genomes.

187 ding sequences revealed accelerated rates of sequence evolution in this group.

188 valuated the ability of our model to capture sequence evolution in vivo by comparing our simulated se

189 re from neutralizing antibodies drives viral sequence evolution in vivo.

190 greatly facilitates comparative research on sequence evolution including changes in gene content, co

191 istory of transfer and evaluated for rate of sequence evolution, including minicircle genes (presumab

192 Analyses of sequence evolution indicate that regulation of social or

193 y variation is significantly associated with sequence evolution, inheritance of parental expression p

194 e findings reveal two distinct mechanisms of sequence evolution involved in HCV persistence: viral es

195 relationship between protein and regulatory sequence evolution is a central question in molecular ev

196 ndous among-protein variation in the rate of sequence evolution is a central subject of molecular evo

197 matoda, and they show that rapid homeodomain sequence evolution is a general feature of nematode Hox

198 Thus, sequence evolution is delayed compared to genome evoluti

199 restimated (due to primer mismatch) and that sequence evolution is misperceived due to unrecognized c

200 hat, even under purifying selection, protein sequence evolution is often contingent on history and so

201 Sequence evolution is viewed as a means to drive the sys

202 rect evidence to link this response to viral sequence evolution, ISG regulation, and selection of the

203 se, because despite having experienced rapid sequence evolution, its HI properties are a shared funct

204 ces between dsx mimicry alleles, and protein sequence evolution may also have a role.

205 Patterns of sequence evolution may provide evidence of positive sele

206 of magnitude lower than the rate of protein sequence evolution measured by the number of amino acid

207 We develop a sequence evolution model that leverages substantially mo

208 phylogenetic information only as independent sequence evolution models for each position of a multipl

209 ogeny, histones and histone-dependent genome sequence evolution most likely evolved after the bacteri

210 hat the structural influences on the rate of sequence evolution observed in earlier simulations can b

211 onal analysis reveals positive selection for sequence evolution of elements in the Swi/Snf chromatin

212 oposed that there was widespread accelerated sequence evolution of genes functioning in the nervous s

213 examine the influence of host genetics upon sequence evolution of highly variable pathogens.

214 ion (gBGC) predominates over mutation in the sequence evolution of hotspots.

215 Here we explore DNA sequence evolution of orthologous and paralogous copies

216 packing is a crucial determinant guiding the sequence evolution of protein cores.

217 actors that have been proposed to affect the sequence evolution of TAG members.

218 stone methylation patterns, and analyzed the sequence evolution of the genes.

219 We show that a higher rate of protein sequence evolution of the neo-X-linked copy of Cyclin B

220 In this paper, we analyze the sequence evolution of three influenza A genes over the p

221 ion relates inversely to the rate of protein sequence evolution on a genomic scale.

222 ysis highlights conserved features of coding sequence evolution on the X and the autosomes and illumi

223 es used for maximum likelihood estimation of sequence evolution parameters.

224 ing to acceleration of an organism's protein-sequence evolution, particularly for genes expressed at

225 ublocalization happened through two types of sequence evolution patterns.

226 Models of sequence evolution play an important role in molecular e

227 statistical physics to simulate in vivo HIV sequence evolution, predicting the relative rate of esca

228 likely moved to their present locations via sequence evolution processes involving gene duplication

229 ion, we examined the connections between the sequence evolution rate and other genomic features.

230 iables that describe gene evolution, such as sequence evolution rate and propensity for gene loss.

231 orrelation between gene expression level and sequence evolution rate.

232 icantly, but positively, correlates with the sequence evolution rate.

233 interactivity is much stronger than that for sequence evolution rate.

234 ificant negative correlation with the coding-sequence evolution rate; intron loss rate also significa

235 ent, these changes usually are the result of sequence evolution, rather than superinfection.

236 ses behind the selective pressures on coding-sequence evolution remain controversial.

237 However, the role of coding sequence evolution remains unresolved.

238 Maximum likelihood models of coding sequence evolution reveal that a high proportion (approx

239 her a clock-like or a variable rate model of sequence evolution, sampling from the internal nodes and

240 ence to test the hypothesis that subtelomere sequence evolution shapes recurrent innovation of telome

241 Bayesian models of sequence evolution showed that only the sialidase of M.

242 This study uses sequences simulated by a sequence-evolution simulation program that compares pars

243 frequency in the MSAs created via a genuine sequence evolution simulator, Dawg.

244 model) and the model used by Dawg, a genuine sequence evolution simulator.

245 were used to obtain a substitution model of sequence evolution specific for HIV-1 subtype B env by e

246 ds did not account for major features of DNA sequence evolution such as transition/transversion rate

247 test was used to test hypotheses concerning sequence evolution, such as rate constancy among lineage

248 ins have an unusually high rate of molecular sequence evolution, suggesting either a high rate of neu

249 hus decoupled from the global rate of genome sequence evolution, suggesting that a small fraction of

250 between sexual selection and rates of coding sequence evolution, suggesting that expression changes m

251 This unusual pattern of sequence evolution suggests the hypothesis that purifyin

252 with the significant deviations from neutral sequence evolution, suggests a role for balancing select

253 ide) and have two times or greater impact on sequence evolution than point mutations.

254 ucts show a very different tempo and mode of sequence evolution than star products.

255 e have recently begun to implement models of sequence evolution that account for heterogeneity across

256 We introduce a model of amino acid sequence evolution that accounts for the statistical beh

257 ly striking in the face of the rapid protein sequence evolution that characterizes many reproductive

258 enetic analyses frequently rely on models of sequence evolution that detail nucleotide substitution r

259 ethylation is enabled by a regime of genomic sequence evolution that enriches CG dinucleotides and dr

260 sequently, they fail to account for modes of sequence evolution that involve frequent insertions or d

261 replication apparently have little impact on sequence evolution, the effects of transcription are obs

262 we find no effect of preformation on protein sequence evolution, the evolutionary rates of early-stag

263 detect positive selection in protein-coding sequence evolution, the ratio of the nonsynonymous to sy

264 tion rates for Ebola virus given its natural sequence evolution, these treatment strategies are likel

265 to their hosts by facilitating localized DNA sequence evolution through a specialized error-prone rev

266 to reliably calculate the probability of the sequence evolution through indel processes.

267 ombined analysis of protein biochemistry and sequence evolution to characterize the structural and fu

268 binding site (TFBS) turnover, which relates sequence evolution to epigenetic conservation or diverge

269 We compared the observed sequence evolution to predictions based on different sce

270 r methods by incorporating a simple model of sequence evolution to test the effect of introducing seq

271 hensive software system for relating protein sequence evolution to the evolution of specific protein

272 programs designed for biological analysis of sequence evolution to uncover the relationships between

273 a powerful probabilistic method for studying sequence evolution, to analyze patterns of substitutions

274 gical dissimilarities, as well as fitness to sequence evolution under a maximum parsimony criterion;

275 ated with ethnic groups, likely due to viral sequence evolution under environmental influences.

276 on-based TZM-bl cell assay and monitored env sequence evolution using single-genome amplification in

277 ssed the prevalence of low-level viremia and sequence evolution, using ultrasensitive viral load (<6.

278 We show that rates of sequence evolution vary nearly as much within vertebrate

279 ities under biologically realistic models of sequence evolution via indels.

280 ate that both gene gain and loss and protein sequence evolution via positive selection are important

281 icating between 1964 and 1995, their rate of sequence evolution was at least 10-fold lower than that

282 Although some proviral sequence evolution was demonstrable in >50% of these pat

283 Finally, the rate of sequence evolution was observed to decline over the cour

284 Sequence evolution was significantly correlated with lev

285 However, in contrast to powerful models of sequence evolution, we lack a consensus model of gene ex

286 extent, kinetics, and driving forces of HCV sequence evolution, we sequenced the entire HCV genome l

287 Viral phylogenetic changes and sequence evolution were analyzed.

288 identifies sets of genes sharing patterns of sequence evolution, which suggests shared function.

289 ets with a way to quickly compute a model of sequence evolution, while the nucleotide substitution mo

290 ransferred genes have a more typical rate of sequence evolution, while those whose history was wholly

291 equately model the process of protein-coding sequence evolution with a resulting increase in phylogen

292 These studies reveal hotspots for sequence evolution with implications for targeting and s

293 nt genes, optimality criteria, and models of sequence evolution with previous studies encompassing fe

294 omparing true alignments from simulations of sequence evolution with reconstructed alignments.

295 duct of a dynamic mix of gene loss and rapid sequence evolution, with the most derived state observed

296 Furthermore, rates of sequence evolution within grasses are lower, indicating

297 esent comparisons of genome organization and sequence evolution within Poales.

298 and D. virilis yellow genes, indicating that sequence evolution within the yellow gene underlies the

299 rogeneous, then examining patterns of coding sequence evolution without taking these underlying varia

300 eT-A(yak), TART(yak) is undergoing concerted sequence evolution, yet they retain the unusual features