ライフサイエンスコーパス: sequence evolution

1 small insertions and subsequent accelerated sequence evolution.

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

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

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

5 ual genes show little indication of adaptive sequence evolution.

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

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

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

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

10 found that it closely predicts the simulated sequence evolution.

11 we develop an evolutionary model for protein sequence evolution.

12 representing reproductive isolation without sequence evolution.

13 e relationship between protein structure and sequence evolution.

14 election have been the dominant processes of sequence evolution.

15 domains show evidence of significantly slow sequence evolution.

16 ovel genes show accelerated rates of protein sequence evolution.

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

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

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

20 ructures allowed a detailed analysis of rRNA sequence evolution.

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

22 ide substitution and reticulate processes to sequence evolution.

23 creases with expression level and constrains sequence evolution.

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

25 ox clusters that have undergone considerable sequence evolution.

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

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

28 tudinally in conjunction with viral load and sequence evolution.

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

30 karyote tree because of systematic biases in sequence evolution.

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

32 uster architecture and patterns of noncoding sequence evolution.

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

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

35 gene duplication event followed by extensive sequence evolution.

36 he promised advances in the understanding of sequence evolution.

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

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

39 variety of biologically realistic models of sequence evolution.

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

41 or understanding the mechanisms of molecular sequence evolution.

42 m numerous sequence possibilities as well as sequence evolution.

43 ontribution of retrotransposition to ongoing sequence evolution.

44 ough during chromosome replication to affect sequence evolution.

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

46 potheses concerning the process of molecular sequence evolution.

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

48 cture of epistasis in simulations of protein sequence evolution.

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

50 3D structure prediction and analysis of RNA sequence evolution.

51 xpression patterns show accelerated rates of sequence evolution.

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

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

54 he aquatic light environment can shape opsin sequence evolution.

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

56 that may also affect genome instability and sequence evolution.

57 zations may facilitate virus replication and sequence evolution.

58 ods to the presence of nonneutral convergent sequence evolution.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

80 Correlations between sequence evolution and structural dynamics are of utmost

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

98 Estimates of sequence evolution based on the accumulation of nucleoti

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

138 Viral sequence evolution has previously been shown to mediate

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

156 Highly elevated rates of sequence evolution in Geraniaceae mitochondrial genomes

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

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

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

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

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

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

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

164 Tracing their sequence evolution in the Drosophila lineage suggests th

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

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

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

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

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

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

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

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

173 Analyses of sequence evolution indicate that regulation of social or

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

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

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

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

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

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

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

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

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

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

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

185 We develop a sequence evolution model that leverages substantially mo

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

208 orrelation between gene expression level and sequence evolution rate.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

257 Sequence evolution was significantly correlated with lev

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

259 Viral phylogenetic changes and sequence evolution were analyzed.

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

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

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

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

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

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

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

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

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

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

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

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