ライフサイエンスコーパス: shotgun

1 ts and use of electronic calls and unplugged shotguns).

2 The objective was to perform whole-genome shotgun 454 pyrosequencing on the same fecal specimens c

3 Fecal samples were subjected to whole-genome shotgun 454 pyrosequencing to identify both fecal bacter

4 A single shotgun analysis produces several hundred of densely pop

5 protein identification (obtained via routine shotgun analysis).

6 n sequences were evaluated by utilizing both shotgun and 16S metagenomic techniques.

7 sequencing projects, including whole-genome shotgun and environmental sampling projects.

8 sequencing projects, including whole-genome shotgun and environmental sampling projects.

9 be accurately phased using a combination of shotgun and proximity ligation sequencing.

10 d an allopolyploid Brassica juncea genome by shotgun and single-molecule reads integrated to genomic

11 Moreover, the fundamental shotgun and storytelling mechanisms of the inherence heu

12 using in silico analyses of the whole-genome shotgun and transcriptome shotgun assembly databases.

13 ban on semiautomatic rifles and pump-action shotguns and rifles and also initiated a program for buy

14 f the whole-genome shotgun and transcriptome shotgun assembly databases.

15 eterochromatic portion, using a whole-genome shotgun assembly, BAC physical mapping, and clone-based

16 n exceeds that of a chromosome-by-chromosome shotgun assembly.

17 ies, Parsons and colleagues launched a risky shotgun-based approach that led ultimately to the cDNA c

18 erotic human aorta sample using whole-genome shotgun bisulfite sequencing.

19 he L2 larval stage, which provided >50-fold "shotgun" cellular coverage of its somatic cell compositi

20 with sequencing data sets with whole-genome shotgun coverage as low as 0.001x.

21 low number of taxa identified when coupling shotgun data with clade-based taxonomic algorithms, prev

22 Low-cost shotgun DNA sequencing is transforming the microbial sci

23 We performed shotgun DNA sequencing on four archived, paraffin-embedd

24 the combination of time-series sampling with shotgun DNA, 16S rRNA gene amplicon, and metatranscripto

25 We demonstrate in simulation that the shotgun experimental design can eliminate the biases ind

26 This work proposes a "shotgun" experimental design, in which we observe multip

27 s ambiguities are common in direct-injection shotgun experiments, where an orthogonal separation (e.g

28 phospholipids in data acquired by LC-MS and shotgun experiments.

29 in bone morphogenetic protein signaling and Shotgun expression only makes a limited contribution to

30 eak intensity-independent noise filtering in shotgun FT MS and FT MS/MS spectra that capitalizes on a

31 folia, genotyped F2 plants using multiplexed shotgun genotyping (MSG), and located MSG markers to the

32 Thus, the natural shotgun glycan microarray of schistosome eggs is useful

33 ized, separated, and used to generate an egg shotgun glycan microarray.

34 were covalently printed to generate pig lung shotgun glycan microarrays.

35 To better define these responses, we used a shotgun glycomics approach in which N-glycans from schis

36 or these studies, we used the technology of "shotgun glycomics" to identify natural receptor glycans.

37 Nonetheless, shotgun has complementary advantages that should be weig

38 -9 for these same HMOs established using the shotgun human milk glycan microarray (HM-SGM-v2) showed

39 This was generated using whole-genome shotgun Illumina reads plus in vitro proximity ligation

40 cation of a combined affinity chromatography shotgun immunoproteomic approach to identify antigens th

41 ing of in vivo covalent chemical capture and shotgun LC-MS/MS (MuDPIT) analysis, we can trap the PPIs

42 has previously been proposed that employs a shotgun-like grid-based approach to systematically cover

43 fication approach can be extended to provide shotgun-like quantification of phospholipids in thin bra

44 een demonstrated with an implementation into shotgun lipid analysis of animal tissues.

45 Although shotgun lipidomics allows for high-throughput analysis,

46 t the protein level, mass spectrometry-based shotgun lipidomics analysis showed significant differenc

47 ability of the lipid concentration levels in shotgun lipidomics analysis was tracked over a period of

48 The assessed shotgun lipidomics approach showed to be remarkably robu

49 Herein, we describe a shotgun lipidomics approach that exploits charge-switch

50 Herein, we describe a shotgun lipidomics approach that utilizes a single-phase

51 Shotgun lipidomics exploits the unique chemical and phys

52 the multidimensional mass-spectrometry-based shotgun lipidomics for global analysis of fatty acids in

53 s of lysophospholipid (LPL) species based on shotgun lipidomics has not been established.

54 en together, by exploiting the principles of shotgun lipidomics in combination with a novel strategy

55 Shotgun lipidomics relies on the direct infusion of tota

56 combination with a dedicated high-resolution shotgun lipidomics routine enables both quantification a

57 Shotgun lipidomics showed that MUFAs were significantly

58 bining GC-MS based fatty acid profiling with shotgun lipidomics strategy.

59 m 8 different lipid classes were profiled by shotgun lipidomics with the use of a triple-quadrupole m

60 benefit of the DMS separation in this unique shotgun lipidomics workflow is its ability to separate m

61 nd predictable separation technique within a shotgun lipidomics workflow, with a special focus on pho

62 sobaric and isomeric lipids that by standard shotgun lipidomics workflows are difficult to assess pre

63 ass spectrometry, either by direct infusion (shotgun lipidomics) or coupled with liquid chromatograph

64 ss spectrometry after direct infusion (i.e., shotgun lipidomics).

65 regioisomers, particularly in an approach of shotgun lipidomics, are still missing.

66 the diet on the brain lipidome, we performed Shotgun Lipidomics.

67 of multidimensional mass spectrometry-based shotgun lipidomics.

68 ajor bottleneck in high-throughput bottom-up shotgun lipidomics.

69 y RNA sequencing, targeted metabolomics, and shotgun lipidomics.

70 to-noise ratio in direct-MS analyses (e.g., "shotgun" lipidomics and MS imaging).

71 We employed shotgun liquid chromatography-mass spectrometry (LC-MS)

72 esent in a sample are sequenced in a random, shotgun manner.

73 roach based on the computational querying of shotgun mass spectra by LipidXplorer software.

74 emains challenging to detect and quantify by shotgun mass spectrometry (MS) where it is time-consumin

75 P (Liver-Perchloric acid-soluble protein) by shotgun mass spectrometry analysis and gene identificati

76 Enabled by a shotgun mass spectrometry analysis founded on tissue cul

77 Currently, shotgun mass spectrometry is the primary technology for

78 RNase A-treated nuclear extracts followed by shotgun mass spectrometry revealed the presence of hnRNP

79 MS studies of membrane-protein complexes and shotgun membrane proteomics studies.

80 a combination of 16S rRNA gene profiling and shotgun metagenome analysis of the microbiota associated

81 and use them to guide the development of the Shotgun Metagenome Annotation Pipeline (ShotMAP).

82 According to 16S rRNA pyrosequencing and shotgun metagenome sequencing analyses, the most abundan

83 addition to the detection of MDR bacteria by shotgun metagenome sequencing as a novel method that mig

84 We investigated shotgun metagenome sequencing for the detection of methi

85 Shotgun metagenome sequencing has become a fast, cheap a

86 combination of 16S rRNA amplicon sequencing, shotgun metagenome sequencing, and liquid chromatography

87 bial taxonomic and functional diversity with shotgun metagenome sequencing.

88 ommon within viral genomes and virioplankton shotgun metagenomes (viromes), and estimated to occur wi

89 nts one of the largest resources of analysed shotgun metagenomes.

90 single-nucleotide polymorphisms (SNPs), from shotgun metagenomes.

91 Shotgun metagenomic analysis identified a variety of Mic

92 Shotgun metagenomic analysis of the human associated mic

93 By mining the shotgun metagenomic data from the Human Microbiome Proje

94 Using shotgun metagenomic data from wild baboons, we found tha

95 rvum sp. RIFRC-1, via assembly of short-read shotgun metagenomic data using a complexity reduction ap

96 e for detecting such variation directly from shotgun metagenomic data.

97 Shotgun metagenomic DNA sequencing is a widely applicabl

98 e the best thresholds based on how simulated shotgun metagenomic reads of known composition map onto

99 prevalence of all gene families in the >700 shotgun metagenomic samples of the Human Microbiome Proj

100 Meisel et al. show that while whole genome shotgun metagenomic sequences were most similar to expec

101 sative disease agents in human patients from shotgun metagenomic sequencing (SMS) presents a powerful

102 16S rRNA and shotgun metagenomic sequencing identified the principle

103 In this issue, Dudek et al. show that shotgun metagenomic sequencing of a less-well-studied en

104 hnologies (ranging from 16S ribosomal RNA to shotgun metagenomic sequencing) in enumerating the commu

105 Using shotgun metagenomic sequencing, we analyzed fecal sample

106 ogenating enzymes in a German forest soil by shotgun metagenomic sequencing.

107 d eukaryotic communities via marker gene and shotgun metagenomic sequencing.

108 ent identification of viral pathogens using 'shotgun' metagenomic sequencing is an emerging approach

109 poration of DNA methylation information into shotgun metagenomics analyses will complement existing m

110 Shotgun metagenomics and computational analysis are used

111 ogenetic analysis of fungi and bacteria with shotgun metagenomics and extracellular enzyme assays.

112 lar challenges, we advocate for the use of a shotgun metagenomics approach in ancient microbiome reco

113 We used a shotgun metagenomics approach to investigate the taxonom

114 ect guts, providing a powerful complement to shotgun metagenomics in microbial community studies.

115 y focused on a handful of known species, and shotgun metagenomics is limited in the ability to detect

116 A major challenge in the field of shotgun metagenomics is the accurate identification of o

117 Shotgun metagenomics is widely used to investigate these

118 Shotgun metagenomics methods enable characterization of

119 putational pipelines have been combined into shotgun metagenomics methods that have transformed micro

120 es using a mass ratio approach and conducted shotgun metagenomics on purified viral samples collected

121 DNA was extracted and shotgun metagenomics performed.

122 ool (SMART), a novel searching heuristic for shotgun metagenomics sequencing results.

123 We utilized shotgun metagenomics to provide a first description of t

124 In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better under

125 tadpole surface microbiome was assessed with shotgun metagenomics.

126 High-resolution shotgun metaproteomics confirmed many of these responses

127 We have provided a fast "shotgun" method for chemical truncation of a membrane pr

128 rk as an alternative approach to established shotgun MS or high-performance liquid chromatography-MS.

129 Alanine scanning-based shotgun mutagenesis epitope mapping studies revealed div

130 Epitope mapping using a comprehensive shotgun mutagenesis library of 910 mutants with E2/E1 al

131 sing a high-throughput screening technology (shotgun mutagenesis) to create and evaluate 852 variants

132 comprehensive alanine-scanning mutagenesis (shotgun mutagenesis), neutralization escape, and whole v

133 eration sequencing techniques - amplicon and shotgun - on water samples across four of Brazil's major

134 high fidelity, using amplicon, whole genome shotgun or single molecule sequencing approaches.

135 t part of any proteomics experiment, whether shotgun or top-down approaches are used.

136 asma samples, which enables the untargeted ("shotgun") or targeted profiling of hydrophilic, amphipat

137 al and fast method that represents the first shotgun polyphenomics analysis of wine.

138 dynamic range of full-lipidome quantitative shotgun profiling.

139 uenced both short and long RNA and conducted shotgun proteomic analyses.

140 mined the analytical figures of merit of our shotgun proteomic approach regarding proteome coverage c

141 Here, we used a shotgun proteomic approach to characterize the proteins

142 iously published modules for the analysis of shotgun proteomic data.

143 On the other hand, different gel-based and shotgun proteomic methods have been utilized to assign g

144 Proteome data were based on label-free shotgun proteomics (spectral counting) and transcript da

145 e proposed approach may be incorporated into shotgun proteomics algorithms and allows for the develop

146 dimension of separation in multidimensional shotgun proteomics analysis, with a potential for fully

147 nrichment protocol was included in a typical shotgun proteomics analytical workflow based on nanoHPLC

148 Using shotgun proteomics and ChIP sequencing, we demonstrate t

149 of the remnants of a previous blood meal via shotgun proteomics and spectral matching.

150 We used standardized shotgun proteomics and targeted protein quantitation pla

151 A combination of shotgun proteomics and whole-cell matrix-assisted laser

152 We applied an improved label-free shotgun proteomics approach to evaluate the global prote

153 tion procedure using trypsin digestion and a shotgun proteomics approach.

154 t least 36 novel proteins were detected from shotgun proteomics data of 41 breast samples.

155 This approach can be applied to any shotgun proteomics data set acquired with high mass accu

156 Quantitative label-free shotgun proteomics demonstrated that both proapoptotic p

157 ass spectrometry (MS/MS) spectra acquired in shotgun proteomics experiments are typically matched to

158 Shotgun proteomics experiments integrate a complex seque

159 d used to control the acquisition process of shotgun proteomics experiments.

160 In this study, we applied shotgun proteomics for the identification and quantifica

161 romatography mass spectrometry (LC-MS) based shotgun proteomics has evolved as a sensitive and inform

162 ntary use of immunofluorescence labeling and shotgun proteomics has substantially resolved the cellul

163 Shotgun proteomics is a powerful analytic method to char

164 Analysis pipelines that assign peptides to shotgun proteomics mass spectra often discard identified

165 Our aim is to develop an accurate and rapid shotgun proteomics method for the identification of beta

166 Shotgun proteomics of 12 collected fractions from each o

167 el protein fractionation in conjunction with shotgun proteomics on fractions containing N-lactoyl-Phe

168 Complex shotgun proteomics peptide profiles obtained in quantita

169 Here, we present large-scale shotgun proteomics profiling of tomato fruit across two

170 Shotgun proteomics technique was used to understand degr

171 e protocol utilizes quantitative, bottom-up, shotgun proteomics technologies (isobaric mass tags for

172 cal analysis of redox active components, and shotgun proteomics to study elements of the organohalide

173 Shotgun proteomics using liquid chromatography-tandem ma

174 peaks of peptides adducted by NAPQI and for shotgun proteomics via tandem mass spectrometry (MS/MS).

175 Immunofluorescence labeling and shotgun proteomics were used to establish the cell type-

176 Quantitative 2D gel-based and shotgun proteomics, 1D and 2D immunoblotting, and quanti

177 Here, we used shotgun proteomics, OxICAT and RNA-seq transcriptomics t

178 T2B (PCAF), we determined their acetylome by shotgun proteomics.

179 ion (PTM) from complex biological samples by shotgun proteomics.

180 sulting in a powerful computational tool for shotgun proteomics.

181 MUMAL2, provides a two-fold contribution to shotgun proteomics.

182 -MS instruments such as those widely used in shotgun proteomics.

183 peptides provides a streamlined approach to shotgun proteomics.

184 s recently attracted attention as a tool for shotgun proteomics.

185 disease biology than do peptides created in shotgun proteomics.

186 es in the proteome were assessed by LC-MS/MS shotgun proteomics.

187 entified as major urinary proteins (MUPs) by shotgun proteomics.

188 vein endothelial cells and HeLa cells using shotgun proteomics.

189 igestion of an E. coli membrane fraction for shotgun proteomics.

190 interpret expression data in microarray and shotgun proteomics.

191 id chromatography-tandem MS (LC-MS/MS)-based shotgun proteomics; and (v) computational data analysis.

192 m mass spectrometry to generate an unbiased, shotgun-proteomics view of protein identities and abunda

193 In summary, shotgun pyrosequencing metagenomic analyses of agricultu

194 In this study, we performed shotgun pyrosequencing metagenomic analyses of DNA from

195 sequence alignment showed that 19% or 62% of shotgun pyrosequencing metagenomic DNA sequence reads fr

196 geographic locations and then conducted 454 shotgun pyrosequencing procedures to obtain 16-24 x cove

197 terize complex satellites using whole-genome shotgun read datasets.

198 al species, of which 51 were not found using shotgun reads alone.

199 sembled genome sequences and unassembled NGS shotgun reads as input, and wraps the output in a standa

200 Binning environmental shotgun reads is one of the most fundamental tasks in me

201 These metagenomic shotgun reads of mammalian origin were excluded from our

202 ering information obtained from whole-genome shotgun reads to model two haploid human satellite array

203 robiome, the analysis was first performed on shotgun reads without considering a reference metagenome

204 TM-1 genome by integrating whole-genome shotgun reads, bacterial artificial chromosome (BAC)-end

205 ased on Clustering) to cluster environmental shotgun reads, by considering k-mer frequency in reads a

206 asispecies spectra from the NGS amplicon and shotgun reads, respectively.

207 clearly challenging the dogma that mid-depth shotgun recovers more diversity than amplicon-based appr

208 We have generated a new wheat whole-genome shotgun sequence assembly using a combination of optimiz

209 rces for the species, we generated 600 Gb of shotgun sequence data and developed methods for sequenci

210 opment in many studies by using whole genome shotgun sequence data directly.

211 e results from new low-coverage whole-genome shotgun sequence data from five hunter-gatherers and fiv

212 We integrated whole-genome shotgun sequence data from the individuals of two mappin

213 novo assembly of genomes from whole- genome shotgun sequence data is a computationally intensive, mu

214 divulgatum isolates from different sites and shotgun sequence data of Parys Mountain samples suggests

215 bination with the comprehensive whole-genome shotgun sequence data sets allowed us to independently v

216 e telomere length from whole genome or exome shotgun sequence data.

217 astaci and A. invadans from the whole genome shotgun sequence reads (PRJNA187372; PRJNA258292, respec

218 6S rRNA (16S) gene database with metagenomic shotgun sequences promises unbiased identification of kn

219 released a resource integrating whole-genome shotgun sequences with a physical and genetic framework.

220 benchmarking against the synthetic and real shotgun sequences, we demonstrated that full-length 16S

221 ences in the near-terabase-scale metagenomic shotgun sequences, which markedly improve metagenomic da

222 lete pipeline for the analysis of metagenome shotgun sequences.

223 Environmental shotgun sequencing (ESS) has potential to give greater i

224 y, 16S rRNA gene sequencing, and metagenomic shotgun sequencing (MSS) for Clostridium difficile ident

225 Metagenomic shotgun sequencing (MSS) is an important tool for charac

226 Whole-transcriptome shotgun sequencing (RNA-Seq) provides new possibilities

227 We used whole-transcriptome shotgun sequencing (RNA-seq) to compare the S. pneumonia

228 We carried out metagenomic shotgun sequencing and a metagenome-wide association stu

229 On the basis of shotgun sequencing and genomic comparisons to Balsas teo

230 -variety arowana using a combination of deep shotgun sequencing and high-resolution linkage mapping.

231 we discuss how the integration of microbiome shotgun sequencing and metabolic modeling approaches suc

232 AFS uses metagenomic shotgun sequencing and sequence read counting to infer s

233 Whole-genome shotgun sequencing and sequencing analysis of the gene e

234 This first large-scale survey of HPV using a shotgun sequencing approach yielded a comprehensive map

235 pon the contiguity observed from traditional shotgun sequencing approaches, with scaffold N50 values

236 at, ordering of whole-genome or hierarchical shotgun sequencing contigs is primarily based on recombi

237 plete workflow processes whole transcriptome shotgun sequencing data files by trimming reads and remo

238 Our approach can also reduce error in shotgun sequencing data generated from libraries with sm

239 an subjects, by metagenomics analysis of the shotgun sequencing data generated from the NIH Human Mic

240 ng STR markers directly from high-throughput shotgun sequencing data without a reference genome, and

241 o classify microorganisms using whole-genome shotgun sequencing data, comprehensive comparisons of th

242 cumulation lines by analysis of whole genome shotgun sequencing data.

243 nts from paired amplicon (V3 U341F/534R) and shotgun sequencing datasets, we demonstrate that extensi

244 Shotgun sequencing enables the reconstruction of genomes

245 of DNA for many uses, including metagenomic shotgun sequencing for infection diagnosis.

246 Metagenomic shotgun sequencing is a new tool to identify organisms u

247 Whole metagenome shotgun sequencing is a powerful approach for assaying t

248 t advances in NGS technologies, whole-genome shotgun sequencing is cost-prohibitive for species with

249 rase chain reaction, and whole transcriptome shotgun sequencing is critically dependent on RNA qualit

250 Combined with deep shotgun sequencing of all stools, we find that multidrug

251 Through massive shotgun sequencing of circulating cell-free DNA from the

252 Sanger shotgun sequencing of clone inserts, however, has now be

253 Shotgun sequencing of DNA from the input pooled VLP prep

254 We used shotgun sequencing of genomic DNA, using an Illumina MiS

255 A from the input pooled VLP preparation plus shotgun sequencing of gut microbiota samples and purifie

256 low levels of endogenous DNA, precluding the shotgun sequencing of many interesting samples because o

257 Prior to capture, shotgun sequencing of these libraries yielded an average

258 encing overcomes this drawback by untargeted shotgun sequencing of whole metagenomes at affordable co

259 umatoid arthritis patients and controls, and shotgun sequencing on a subset of 44 such samples.

260 Deep shotgun sequencing on next generation sequencing (NGS) p

261 We first employ a metagenomic shotgun sequencing protocol on a total of 93 clinical sa

262 Unlike culture, shotgun sequencing quantitatively characterizes the burd

263 le of a microbial community from unannotated shotgun sequencing reads is one of the important goals i

264 taset of 17,676 viral contigs assembled from shotgun sequencing reads of VLP DNAs, we identified viru

265 s (0.03% and 0.08% alignable high-throughput shotgun sequencing reads) of their respective DNA conten

266 Whole-genome shotgun sequencing results revealed that fiber consumpti

267 Based on the shotgun sequencing results, there was no evidence of a f

268 gle-molecule real-time (Pacific Biosciences) shotgun sequencing to assemble the six chromosomal regio

269 lied 16S rRNA gene amplicon and whole-genome shotgun sequencing to examine the microbial diversity in

270 uantitative metagenomics study based on deep shotgun sequencing was performed, using gut microbial DN

271 mic (16S ribosomal RNA gene and whole-genome shotgun sequencing) approaches to 144 nasopharyngeal air

272 rdered-clone genome sequencing, whole-genome shotgun sequencing, and BioNano optical genome mapping,

273 Using deep shotgun sequencing, chemical dietary analysis, and chlor

274 via amplicon sequencing were recovered from shotgun sequencing, clearly challenging the dogma that m

275 There is increasing interest in employing shotgun sequencing, rather than amplicon sequencing, to

276 By ultra-deep metagenomic shotgun sequencing, we revealed higher relative abundanc

277 irome profile was analyzed using metagenomic shotgun sequencing.

278 te for hierarchical clone-by-clone map-based shotgun sequencing.

279 m applications such as PCR amplification and shotgun sequencing.

280 ubjected them to high-coverage, whole-genome shotgun sequencing.

281 the 16S rRNA gene coupled with direct whole shotgun sequencing.

282 tally healthy individuals using whole genome shotgun sequencing.

283 Here we describe the shotgun-sequencing of ancient DNA from five specimens of

284 moved more than 95% of signals detectable in shotgun spectra without compromising the accuracy and sc

285 A new method, based on shotgun spectral matching of peptide tandem mass spectra

286 nt causal configurations of the region via a shotgun stochastic search algorithm.

287 on fosmid pooling together with whole-genome shotgun strategies, based solely on next-generation sequ

288 ptors using the "SimpleCell" O-glycoproteome shotgun strategy.

289 ation of PCs in a bovine liver extract via a shotgun strategy.

290 We employed metabolic (15)N labeling and shotgun ultra-high-resolution mass spectrometry (sUHR) t

291 sequencing projects, including whole genome shotgun (WGS) and environmental sampling projects.

292 cultivar IT97K-499-35 include a whole-genome shotgun (WGS) assembly, a bacterial artificial chromosom

293 f TE families from low-coverage whole-genome shotgun (WGS) data, enabling the rapid identification of

294 De novo assembly of whole genome shotgun (WGS) next-generation sequencing (NGS) data bene

295 ed BAC clones and 100x Illumina whole-genome shotgun (WGS) sequence coverage.

296 as a model system, we analyzed whole genome shotgun (WGS) sequences for the two maize inbred lines B

297 The method can be used for whole genome shotgun (WGS) sequencing data.

298 t ( approximately 10,000 cells) whole-genome shotgun (WGS) sequencing of Mycobacterium tuberculosis a

299 s, sequencing depth, data type (whole genome shotgun (WGS) vs.16S rRNA gene sequence data), and 16S r

300 ibosomal RNA (rRNA) gene or whole metagenome shotgun (WMS) sequencing provides more precise microbial