ライフサイエンスコーパス: nanopore

1 e dynamics of transit of the DNA through the nanopore.

2 tochastic movement of antibiotics inside the nanopore.

3 noise ratio of 21, compared to 11 from a SiS nanopore.

4 hanging how the DNA strand moves through the nanopore.

5 EC) at an electrode as the vesicle exits the nanopore.

6 x that does not fit and cannot traverse this nanopore.

7 delivery and selective sensing of PSA to the nanopore.

8 ding wetting/dewetting in narrow hydrophobic nanopores.

9 ferent complexations taking place inside the nanopores.

10 sembly reactions, thus serving as functional nanopores.

11 uding the double layer formation in confined nanopores.

12 bine the strengths of DNA nanotechnology and nanopores.

13 tion of their use in simulations of water in nanopores.

14 rophobic nanopores than those in hydrophilic nanopores.

15 hat this mechanism is universal for metallic nanopores.

16 methods for identifying macromolecules using nanopores.

17 on through silicon-based truncated pyramidal nanopores.

18 horetically drawn into the cells through the nanopores.

19 ical and artificial membranes, channels, and nanopores.

20 NPs) confined in hydrophilic and hydrophobic nanopores.

21 structures and will aid the design of novel nanopores.

22 odels in describing the behavior of water in nanopores.

23 vestigate the catalytic behavior of metallic nanopores.

24 ) when compared to a silicon-supported (SiS) nanopore (~1.3 nF, and 46-51 pA RMS noise).

25 orts to sequence single protein molecules in nanopores(1-5) have been hampered by the lack of techniq

26 We present ENANO (Encoder for NANOpore), a novel lossless compression algorithm especi

27 uplexes unzipping inside the alpha-hemolysin nanopore (alpha-HL) are presented.

28 of current versus time traces obtained from nanopore analysis at pH 6.5 shows long-lived shallow blo

29 We developed nanopore analysis of co-transcriptional processing (nano

30 uplex unzipping as it takes place inside the nanopore and being preceded by entrapment in the vestibu

31 in the sample also translocating through the nanopore and generating erroneous signals.

32 Compatible with both Oxford Nanopore and PacBio Single-Molecule Real-Time (SMRT) seq

33 by the presence of a DNA molecule inside the nanopore and the DNA translocation speed through it both

34 s of dislocations and is precipitated inside nanopores and also during low-temperature recrystallizat

35 xplores the dynamic behavior of water within nanopores and biological channels in lipid bilayer membr

36 Structures of biological nanopores and channels are reviewed, emphasizing those h

37 l was experimentally validated for different nanopores and DNA molecules with different sizes.

38 effect of hindered adsorbed water in filled nanopores and extends through the capillary range up to

39 Phylogenetic analysis of the nanopore- and Sanger-derived sequences resulted in indis

40 e presence of tangential fluid flow over the nanopore aperture.

41 ed, including porins and beta-barrel protein nanopores, aquaporins and related polar solute pores, an

42 or grafted layers, polymer ordering, polymer nanopores), architecture (branched vs linear), functiona

43 Metallic catalysts with nanopores are advantageous on improving both activity an

44 DNA nanopores are bio-inspired nanostructures that control m

45 e behavior of water in a range of biological nanopores are described, including porins and beta-barre

46 els of molecular simulations of water within nanopores are described, with a focus on molecular dynam

47 These in-plane nanopores are essential in many emerging applications of

48 Nanopores are key in portable sequencing and research gi

49 Nanopore chips with a larger number of nanopores are shown to receive more nanopore blockades f

50 Protein and solid-state nanopores are used for DNA/RNA sequencing as well as for

51 Direct RNA sequencing (direct RNA-seq) using nanopore arrays offers an exciting alternative whereby i

52 to rely on the velocity of fluid flow in the nanopore as well as the nanopore geometry.

53 l greatly improve the utility of solid-state nanopores as sensors of target biomolecule concentration

54 poly-(ethylene terephthalate) nanopore (PET nanopore) as a stochastic sensing element for detection

55 FraC with the aim of remote controlling the nanopore assembly using light.

56 s at pre-designed sites and escort them from nanopores at suitable speeds, thereby greatly enhancing

57 al metamorphosis, leading to the assembly of nanopores at the cell membrane and causing cell death.

58 We applied nanopore-based direct RNA sequencing to characterize the

59 ntroduce a programmable optofluidic chip for nanopore-based particle analysis: feedback-controlled se

60 To overcome these limitations, we report a nanopore-based sequencing strategy in which short target

61 ng single-molecule, real-time sequencing and nanopore-based sequencing, have provided new opportuniti

62 We describe the characterization of nanopore blockade sensing of PSA by (1) tuning on/off th

63 parameters in determining the performance of nanopore blockade sensing system, where prostate-specifi

64 We have developed a nanopore blockade sensor that alleviates the limitations

65 umber of nanopores are shown to receive more nanopore blockades for a given concentration of analyte.

66 rolled electromagnet, resulting in long-term nanopore blocking events due to the formation of sandwic

67 ium (Ca(++)), and sodium (Na(+)), into these nanopores by electrokinetic flows.

68 nature of the building units, a new type of nanopore can be generated by perforating the basal plane

69 Moreover, based on DNA strand displacement, nanopores can also be utilized to characterize the outpu

70 Nanopores can serve as single molecule sensors.

71 PacBio and the MinION technique from Oxford Nanopore, can generate long, error-prone sequencing read

72 When confined in a microchannel, the nanopore capture and translocation characteristics are a

73 In the present study, we describe nanopore Cas9-targeted sequencing (nCATS), an enrichment

74 For validation, a sapphire-supported (SaS) nanopore chip with a 100 times larger membrane area than

75 ctromagnet, (2) varying nanopore number in a nanopore chip, and (3) deploying the sensor in human pla

76 Nanopore chips with a larger number of nanopores are sho

77 ed by multiple processes: powder compaction, nanopore-collapse, and chemical bond-breakage.

78 Advanced nanopores control transport in response to triggers, but

79 but also may facilitate the design of novel nanopores controlled by hydrophobic gates.

80 which the delivery of biomolecules towards a nanopore controls the method's throughput.

81 Confining water in hydrophobic nanopores could be a way to modulate water solvent prope

82 abling elastic computing for high throughput Nanopore data on HPC cluster as well as multiple cloud p

83 e chromosome X, combined with the ultra-long nanopore data, allowed us to map methylation patterns ac

84 Using Nanopore data, we reliably classified a 20-species mock

85 formance (in both modes) on every considered nanopore dataset, with an average improvement over pigz

86 ompressor pigz on several publicly available nanopore datasets.

87 We exploited the MinION, a portable nanopore device from Oxford Nanopore Technologies, and r

88 ags readable within seconds using a portable nanopore device.

89 A literature review of recent plasmonic nanopore devices is then presented to delineate methods

90 The ReadUntil method allows nanopore devices to selectively eject reads from pores i

91 We conclude that nanopore direct RNA sequencing can reveal the complexity

92 We adapted nanopore direct RNA sequencing to examine RNA from a wil

93 nanopore orifice and is not dependent on the nanopore electric field.

94 anipulation; it simply consists of a generic nanopore-embedded water-filter membrane and a low-voltag

95 th 1k base-pair double-stranded DNA, the SaS nanopore enabled sensing at microsecond speed with a sig

96 modifications, instrumentation advances and nanopore engineering offer a route toward identification

97 r dynamics simulations, that it can charge a nanopore even faster than the corresponding optimized li

98 DFT calculation demonstrates that Co and Cu nanopores exhibit the pincer behavior as well, suggestin

99 nascent RNAs are directly sequenced through nanopores, exposing the dynamics and patterns of RNA spl

100 currents, as the applied voltage across the nanopore facilitated the duplex capture inside the nanop

101 on of ultra-selective membranes with uniform nanopores for precise separation of ions and small solut

102 with this experimental construct when using nanopores for quantitative sensing with low detection li

103 barrel-like DNA pores and larger DNA origami nanopores for targeted applications.

104 incomplete outflow of intruded liquid out of nanopores for the system reusability.

105 However, a detailed nanopore geometry and size characterization or a calibra

106 e alleviates the requirement for knowing the nanopore geometry and size or generating a calibration c

107 of fluid flow in the nanopore as well as the nanopore geometry.

108 mics simulations revealed that the aerolysin nanopore has a built-in single-molecule trap that fully

109 In terms of geometry, MoS(2) nanopores have a well-defined vertical profile due to th

110 Single nanopores have attracted much scientific interest becaus

111 Solid-state nanopores have broad applications from single-molecule b

112 the behavior of water in idealized models of nanopores have revealed aspects of the organization and

113 orter chromosome size from the hybrid Oxford Nanopore-Illumina platform were noted.

114 The first is getting the analyte to the nanopore in a reasonable time frame and the second is ot

115 pores, model peptide nanopores, track-etched nanopores in polymer membranes, and hydroxylated and fun

116 e-stranded DNA molecules through solid-state nanopores in the presence of tangential fluid flow over

117 on in the electrical current detected at the nanopore, increased translocation rates and decreased sa

118 e and transport across a voltage-biased OmpF nanopore is dominated by the electroosmotic flow rather

119 fluidic channel where the voltage across the nanopore is turned off after a user-defined number of si

120 ule long-read DNA sequencing with biological nanopores is fast and high-throughput but suffers reduce

121 mulation studies in a range of nonbiological nanopores is presented, including carbon nanotubes, synt

122 ron microscopy reveals that plasma membrane "nanopore-like" structures (~100-nm diameter) form rapidl

123 combines an Illumina shotgun library, Oxford nanopore long reads, and chromosome conformation capture

124 De novo assembly of a human genome using nanopore long-read sequences has been reported, but it u

125 Here, using raw electric signals of Oxford Nanopore long-read sequencing data, we design DeepMod, a

126 emerges, whereby the behavior of water in a nanopore may be predicted as a function of its hydrophob

127 nderstanding of tRNA structural dynamics and nanopore measurements, we apply molecular dynamics simul

128 plasma membranes, calibrated by severity of nanopore-mediated local calcium influx for lysosome fusi

129 on to their use in DNA sequencing, ultrathin nanopore membranes have potential applications in detect

130 A new approach is proposed here for forming nanopore membranes on insulating sapphire wafers to prom

131 anoscale reaction centres, for example using nanopore membranes.

132 ed, and reproducible pipelines for analyzing Nanopore metagenomic sequencing data are still lacking.

133 Nanopore metagenomics can rapidly and accurately charact

134 earch contributing to efforts for developing nanopore methods associated with DNA nanotechnology.

135 We use PacBio, Oxford Nanopore, methylated DNA immunoprecipitation sequencing

136 d k-mer matching, which, when used on Oxford Nanopore MinION data, can run in real time.

137 the amplified genomes on the portable Oxford Nanopore MinION platform and analyzed the data using a n

138 nced the genome of C. bovis using the Oxford Nanopore MinION platform in a nearby field laboratory an

139 ed to assess the feasibility of using Oxford Nanopore MinION whole-genome sequencing data of Mycobact

140 Applying SMURF-seq using the Oxford Nanopore MinION yields up to 30 fragments per read, prov

141 ented, including carbon nanotubes, synthetic nanopores, model peptide nanopores, track-etched nanopor

142 tatic compression experiments on a series of nanopores/nonwetting liquid material systems have been p

143 tuning on/off the electromagnet, (2) varying nanopore number in a nanopore chip, and (3) deploying th

144 ed to directly detect ion movements into the nanopores of a conductive metal-organic framework (MOF)

145 soluble molecules and water into hydrophobic nanopores of a host material where the lowered polarity

146 olid-liquid interactions with functionalized nanopores or/and liquids.

147 ested that liposome disruption occurs at the nanopore orifice and is not dependent on the nanopore el

148 conical shaped poly-(ethylene terephthalate) nanopore (PET nanopore) as a stochastic sensing element

149 ining resistive pulse (RP) measurements in a nanopore pipet and vesicle impact electrochemical cytome

150 Sequencing using the nanopore platform could be completed in less than an hou

151 We observed that inside the voltage-biased nanopore, polyarginine-conjugated DNA-PNA duplexes dehyb

152 outflow of confined liquid from hydrophobic nanopores, potentially useful for devising emerging nano

153 This SaS nanopore presents a manufacturable nanoelectronic platfo

154 These findings may pave the way to nanopore protein sequencing.

155 We explore the use of lossy compression for nanopore raw data using two state-of-the-art lossy time-

156 a target-specific DNA aptamer coupled with a nanopore read-out to enable individual biomarker detecti

157 identity (Phred quality score QV = 30) with nanopore reads alone.

158 Nanopore reads can be used to implement a straightforwar

159 ark it on the set of long error-prone Oxford Nanopore reads generated by the Telomere-to-Telomere con

160 Using nanopore reads, we demonstrate differential 3' splice si

161 Intact oligos traverse the MinION's nanopore relatively quickly compared to the device's acq

162 location of biomolecules through solid-state nanopores represents a label-free single-molecule techni

163 In summary, DNA assembly-based nanopore research can pave the way for the realization o

164 subsequent cDNA strand insertion inside the nanopore's beta-barrel past the constriction site, its c

165 transport by convection and reduction in the nanopore's capture volume with increased flow velocity.

166 re facilitated the duplex capture inside the nanopore's vestibule against the constriction region, su

167 tegration of optical detection techniques on nanopore-selected particles.

168 Our developed PET nanopore sensing strategy not only provides a general pl

169 ble solutions to current obstacles hindering nanopore sensing technologies.

170 ar species, on-demand chemical reactions and nanopore sensing.

171 ulating sapphire wafers to promote low-noise nanopore sensing.

172 We demonstrate that the PET nanopore sensor is not only sensitive and selective, but

173 The detection principle of nanopore sensors relies on measuring changes in electric

174 Integrating nanopore sensors within microfluidic architectures is ke

175 ing short-read Illumina and long-read Oxford Nanopore sequence data circumvented the expected error r

176 using SPAdes, combining Illumina and Oxford Nanopore sequence reads.

177 d bioinformatics workflows using a long-read nanopore sequencer (MinION) for Y. pestis (6.5 h) and B.

178 pooled for liquid storage, and read using a nanopore sequencer and a novel, minimal preparation prot

179 Using a single PromethION nanopore sequencer and our toolkit, we assembled 11 high

180 Nanopore sequencers can be used to selectively sequence

181 nd deployable on either benchtop or portable nanopore sequencers, making this method directly applica

182 The median identity of consensus nanopore sequences with Sanger or Illumina sequences fro

183 R-Cas9 genome editing tool combined with the Nanopore Sequencing (ONT) we showed that the 7-deazaguan

184 Here we present RNA structure analysis using nanopore sequencing (PORE-cupine), which combines struct

185 combination of isothermal amplification and Nanopore sequencing also offers appealing potential to d

186 To address these gaps, we use long-read nanopore sequencing and assemble the genomes of two circ

187 Here, we use nanopore sequencing and Hi-C scaffolding to produce de n

188 MYCN amplicon structure using short-read and Nanopore sequencing and its chromatin landscape using Ch

189 We applied nanopore sequencing and our workflow, named Lathe, which

190 developed an assembly-free, single-molecule nanopore sequencing approach, enabling direct recovery o

191 We also demonstrate the potential of nanopore sequencing assemblies for rapid preliminary phy

192 Our results indicate that nanopore sequencing can be a suitable alternative to, or

193 We investigated if Nanopore sequencing can detect sufficient Neisseria gono

194 Our findings show that metagenomic Nanopore sequencing can provide reliable diagnostic info

195 suggest that sequencing the IGS region using nanopore sequencing could be a potential new molecular d

196 separate species, which we wanted to see if nanopore sequencing could detect.

197 and cloud compatible pipeline for analyzing Nanopore sequencing data.

198 e algorithm and tested it on both PacBio and Nanopore sequencing datasets.

199 using lossy compression, potentially on the nanopore sequencing device itself, to achieve significan

200 Nanopore sequencing errors were predominantly in regions

201 ompression algorithm especially designed for nanopore sequencing FASTQ files.

202 r work demonstrates the potential utility of nanopore sequencing for cancer and splicing research.

203 ic spacer (IGS) sequence in combination with nanopore sequencing for fungal identification.

204 -sample sequencing cost and hands-on time of Nanopore sequencing for hybrid assembly by at least 50%

205 ning inverted duplicated DNA sequences using nanopore sequencing identified recurrent aberrant behavi

206 analysis enabled pathogen identification by nanopore sequencing in a median 50-min sequencing and 6-

207 ial resistance determinants from error-prone Nanopore sequencing is a substantial bioinformatics chal

208 We report nanopore sequencing of full-length cDNA from CLL samples

209 We performed nanopore sequencing of nucleosome occupancy and methylom

210 as enabled by high-coverage, ultra-long-read nanopore sequencing of the complete hydatidiform mole CH

211 Using Nanopore sequencing of urine samples from men with ureth

212 We present a nested PCR and nanopore sequencing protocol that allows rapid (<3 days)

213 Quasi-metagenomics with nanopore sequencing provided thousands of high-contiguit

214 Nanopore sequencing provides a real-time and portable so

215 However, nanopore sequencing technologies are rapidly gaining pop

216 circumvented the expected error rate of the nanopore sequencing technology, producing a genome seque

217 ast, to overcome the high error rates of the nanopore sequencing technology.

218 l role in overcoming the high error rates of nanopore sequencing technology.

219 We used long-read nanopore sequencing to capture 238,490 SVs in 100 divers

220 apply new computational tools and long-read nanopore sequencing to directly infer CpG methylation of

221 m(6)A) methyltransferase, and the ability of nanopore sequencing to directly read DNA modifications.

222 In this study, we use nanopore sequencing to evaluate CpG methylation and chro

223 ra-fast 84-second LC-MS method, and barcoded nanopore sequencing to rapidly isolate and characterise

224 Here, we report the use of long-read nanopore sequencing to simultaneously sequence the entir

225 this challenge, combining long-range PCR and nanopore sequencing with a novel bioinformatics pipeline

226 We find that nanopore sequencing with Hi-C scaffolding produces highl

227 in biotechnological applications such as DNA nanopore sequencing(2-4), resulting in considerable inte

228 One such method is nanopore sequencing, in which the delivery of biomolecul

229 idization, whole-genome, target-enriched and nanopore sequencing, sequence alignment and variant dete

230 ng methods eliminate many of the benefits of nanopore sequencing, such as the ability to accurately d

231 nces at a median accuracy of 97.9% using our nanopore sequencing-based Rolling Circle Amplification t

232 us generation for closely related genes with nanopore sequencing.

233 obtained from clinical samples using R9.4.1 Nanopore sequencing.

234 and 91 and 100% for fungi, respectively, by nanopore sequencing.

235 ng, and demonstrate retrieval with streaming nanopore sequencing.

236 mosomal DNA with Cas9 to ligate adapters for nanopore sequencing.

237 ecoded from the Oxford Nanopore Technologies nanopore-sequencing ionic current signals.

238 the number of nucleotide modifications from nanopore-sequencing readouts.

239 h various algorithms have been developed for nanopore-sequencing-based modification analysis, more de

240 protein translocation processes through the nanopores show that the tri-color fluorescence time-trac

241 We classify molbits directly from raw nanopore signal, avoiding basecalling.

242 Recently, solid-state plasmonic and nanopore structures have been integrated within monolith

243 The fundamental point vacancy and nanopore structures in PbI(2) monolayers are directly im

244 hnologies, and constructing novel biomimetic nanopore systems.

245 side experimental evaluation of more complex nanopore systems.

246 Oxford Nanopore technologies (ONT) add miniaturization and real

247 The Oxford Nanopore Technologies (ONT) MinION is used for sequencin

248 ssemblies of high-coverage, ultralong Oxford Nanopore Technologies (ONT) reads in terms of both accur

249 and bioinformatics concepts using the Oxford Nanopore Technologies (ONT) sequencing platform.

250 cs, Pacific Biosciences (PacBio), and Oxford Nanopore Technologies (ONT) sequencing.

251 A comparison of Oxford Nanopore Technologies and Pacific Biosciences phased ass

252 h as Pacific Biosciences (PacBio) and Oxford Nanopore Technologies can potentially overcome this limi

253 next generation sequencer MinION from Oxford Nanopore Technologies had significant Spearman rank corr

254 enic members of this genus, using the Oxford Nanopore Technologies MinION device and Sanger sequencin

255 After sequencing on the Oxford Nanopore Technologies MinION platform, the resulting rep

256 -TB, for use on the compact, low-cost Oxford Nanopore Technologies MinION sequencer.

257 Here, we demonstrate the use of the Oxford Nanopore Technologies MinION to detect 11 different thym

258 read sequencing (LRS) techniques, the Oxford Nanopore Technologies MinION, and the LoopSeq synthetic

259 cation status can be decoded from the Oxford Nanopore Technologies nanopore-sequencing ionic current

260 latforms from Pacific Biosciences and Oxford Nanopore Technologies to profile the vaccinia virus (VAC

261 d from non-cultivated locations using Oxford Nanopore Technologies' MinION.

262 nION, a portable nanopore device from Oxford Nanopore Technologies, and repurposed it to detect any D

263 RNA sequencing strategy developed by Oxford Nanopore Technologies.

264 e-genome sequencing data generated by Oxford Nanopore Technologies.

265 RNA Sequencing (DRS) using the latest Oxford Nanopore Technology (ONT) with exceptional read length.

266 Metagenomic sequencing combined with Oxford Nanopore Technology has the potential to become a point-

267 Nanopore technology is a promising label-free detection

268 Solid-state nanopore technology presents an emerging single-molecule

269 a miniature DNA sequencer based on versatile nanopore technology that could be implemented on future

270 using Oxford Nanopore Technology.

271 and higher activation energy in hydrophobic nanopores than those in hydrophilic nanopores.

272 oss a Mycobacterium smegmatis porin A (MspA) nanopore, thus changing how the DNA strand moves through

273 the development and application of the MspA nanopore to sequence DNA containing the dTPT3-dNaM UBP.

274 l by reversing the voltage across individual nanopores to reject specific sequences, enabling enrichm

275 y engineer the structure and function of DNA nanopores to synergistically combine the strengths of DN

276 Achieving precise nanopore topologies in graphene using top-down lithograp

277 anotubes, synthetic nanopores, model peptide nanopores, track-etched nanopores in polymer membranes,

278 Accordingly, differences in nanopore translocation times and distributions may be us

279 t unfolding of the terminal RNA helix during nanopore translocation.

280 We use single-molecule picometer-resolution nanopore tweezers (SPRNT) to measure the kinetics of tra

281 rescence resonance energy transfer (smFRET), nanopore tweezers, and hybrid techniques that increase t

282 from sample to an array of antibody-modified nanopores under a controlled electromagnet, resulting in

283 died ionic and fluidic movement through thin nanopores under viscosity gradients both experimentally

284 he modulation of the ion current through the nanopore upon the DNA origami translocation strongly dep

285 We evaluated three Nanopore variant callers and developed a random forest c

286 he procedure covers the self-assembly of DNA nanopores via thermal annealing, their characterization

287 ions reveal that the grafted silyl chains on nanopore wall surfaces will promote the hydrophobic conf

288 times larger membrane area than conventional nanopores was tested, which showed 130 times smaller cap

289 of the product molecules in the two types of nanopores were deduced from the single-molecule imaging

290 of understanding allows for the design of a nanopore which promotes wetting over dewetting or vice v

291 However, to design a novel nanopore, which enables fast, selective, and gated flow

292 Of particular interest are molecular nanopores, which transport cargo across membranes, as in

293 We now combine the CsgG nanopore with the 35-residue N-terminal region of its ex

294 ty proteinogenic amino acids in an aerolysin nanopore with the help of a short polycationic carrier.

295 by a factor of 26 times by creating in-plane nanopores with an average diameter of ~3 nm and a high d

296 spontaneous liquid outflow from hydrophobic nanopores with high and stable efficiency can be achieve

297 Wider nanopores with hydrophobic linings favor water flow wher

298 d cleaning procedure (24 h), the creation of nanopores within MoS(2) (30 min) and performing DNA tran

299 tion of probe molecules through water-filled nanopores without steric or electrostatic hindrance from

300 analyses reveal that the concave surface of nanopores works like a pincer to capture and clamp CO(2)