-
3
-
-
80051688000
-
Field Guide to Next Generation DNA Sequencers
-
Glenn TC. Field Guide to Next Generation DNA Sequencers. Mol Ecol Resour 2011;11:759-69.
-
(2011)
Mol Ecol Resour
, vol.11
, pp. 759-769
-
-
Glenn, T.C.1
-
4
-
-
84954485765
-
-
(accessed July 2015)
-
Glenn TC. http://www.molecularecologist.com/next-gen-fieldguide-2014/ (accessed July 2015), 2014.
-
(2014)
-
-
Glenn, T.C.1
-
5
-
-
84884826911
-
The Next-Generation Sequencing Revolution and Its Impact on Genomics
-
Koboldt DC, Steinberg KM, Larson DE, Wilson RK, Mardis ER. The Next-Generation Sequencing Revolution and Its Impact on Genomics. Cell 2013;155:27-38.
-
(2013)
Cell
, vol.155
, pp. 27-38
-
-
Koboldt, D.C.1
Steinberg, K.M.2
Larson, D.E.3
Wilson, R.K.4
Mardis, E.R.5
-
6
-
-
84882832047
-
A glimpse into past, present, and future DNA sequencing
-
Morey M, Fernandez-Marmiesse A, Castineiras D, Fraga JM, Couce ML, Cocho JA. A glimpse into past, present, and future DNA sequencing. Mol Genet Metab 2013;110:3-24.
-
(2013)
Mol Genet Metab
, vol.110
, pp. 3-24
-
-
Morey, M.1
Fernandez-Marmiesse, A.2
Castineiras, D.3
Fraga, J.M.4
Couce, M.L.5
Cocho, J.A.6
-
7
-
-
84904859627
-
Microbiome analysis -from technical advances to biological relevance
-
Smith MI, Turpin W, Tyler AD, Silverberg MS, Croitoru K. Microbiome analysis -from technical advances to biological relevance. F1000Prime Rep 2014;6:51.
-
(2014)
F1000prime Rep
, vol.6
, pp. 51
-
-
Smith, M.I.1
Turpin, W.2
Tyler, A.D.3
Silverberg, M.S.4
Croitoru, K.5
-
8
-
-
48449094744
-
Alta-Cyclic: A self-optimizing base caller for next-generation sequencing
-
Erlich Y, Mitra PP, de la Bastide M, McCombie WR, Hannon GJ. Alta-Cyclic: a self-optimizing base caller for next-generation sequencing. Nat Methods 2008;5: 679-82.
-
(2008)
Nat Methods
, vol.5
, pp. 679-682
-
-
Erlich, Y.1
Mitra, P.P.2
De La Bastide, M.3
McCombie, W.R.4
Hannon, G.J.5
-
9
-
-
78650911555
-
Torrents of sequence
-
Rusk N. Torrents of sequence. Nature Methods 2011; 8:44.
-
(2011)
Nature Methods
, vol.8
, pp. 44
-
-
Rusk, N.1
-
10
-
-
55549089660
-
Accurate whole human genome sequencing using reversible terminator chemistry
-
Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 2008;456:53-9.
-
(2008)
Nature
, vol.456
, pp. 53-59
-
-
Bentley, D.R.1
Balasubramanian, S.2
Swerdlow, H.P.3
Smith, G.P.4
Milton, J.5
Brown, C.G.6
-
12
-
-
33745351130
-
Amplification of complex gene libraries by emulsion PCR
-
Williams R, Peisajovich SG, Miller OJ, Magdassi S, Tawfik DS, Griffiths AD. Amplification of complex gene libraries by emulsion PCR. Nat Methods 2006; 3:545-50.
-
(2006)
Nat Methods
, vol.3
, pp. 545-550
-
-
Williams, R.1
Peisajovich, S.G.2
Miller, O.J.3
Magdassi, S.4
Tawfik, D.S.5
Griffiths, A.D.6
-
13
-
-
78650775954
-
The $1,000 genome, the $100,000 analysis?
-
Mardis ER. The $1,000 genome, the $100,000 analysis? Genome Med 2010;2:84.
-
(2010)
Genome Med
, vol.2
, pp. 84
-
-
Mardis, E.R.1
-
14
-
-
28944439470
-
Beware of mis-assembled genomes
-
Salzberg SL, Yorke JA. Beware of mis-assembled genomes. Bioinformatics 2005;21:4320-1.
-
(2005)
Bioinformatics
, vol.21
, pp. 4320-4321
-
-
Salzberg, S.L.1
Yorke, J.A.2
-
15
-
-
77955102352
-
Quantifying E. Coli Proteome and Trans-criptome with Single-Molecule Sensitivity in Single Cells
-
Taniguchi Y, Choi PJ, Li GW, Chen H, Babu M, Hearn J, et al. Quantifying E. coli Proteome and Trans-criptome with Single-Molecule Sensitivity in Single Cells. Science 2010;329:533-8.
-
(2010)
Science
, vol.329
, pp. 533-538
-
-
Taniguchi, Y.1
Choi, P.J.2
Li, G.W.3
Chen, H.4
Babu, M.5
Hearn, J.6
-
16
-
-
84868028972
-
Quantitative analysis of fission yeast trans-criptomes and proteomes in proliferating and quiescent cells
-
Marguerat S, Schmidt A, Codlin S, Chen W, Aebersold R, Bähler J. Quantitative analysis of fission yeast trans-criptomes and proteomes in proliferating and quiescent cells. Cell 2012;151:671-83.
-
(2012)
Cell
, vol.151
, pp. 671-683
-
-
Marguerat, S.1
Schmidt, A.2
Codlin, S.3
Chen, W.4
Aebersold, R.5
Bähler, J.6
-
17
-
-
58149313641
-
Absolute quantification of the budding yeast transcriptome by means of competitive PCR between genomic and complementary DNAs
-
Miura F, Kawaguchi N, Yoshida M, Uematsu C, Kito K, Sakaki Y, et al. Absolute quantification of the budding yeast transcriptome by means of competitive PCR between genomic and complementary DNAs. BMC Genomics 2008;9:574.
-
(2008)
BMC Genomics
, vol.9
, pp. 574
-
-
Miura, F.1
Kawaguchi, N.2
Yoshida, M.3
Uematsu, C.4
Kito, K.5
Sakaki, Y.6
-
18
-
-
84879484379
-
Evaluating the Impact of Sequencing Depth on Transcriptome Profiling in Human Adipose
-
Liu Y, Ferguson JF, Xue C, Silverman IM, Gregory B, Reilly MP. Evaluating the Impact of Sequencing Depth on Transcriptome Profiling in Human Adipose. PLoS One 2013;8:e66883.
-
(2013)
Plos One
, vol.8
-
-
Liu, Y.1
Ferguson, J.F.2
Xue, C.3
Silverman, I.M.4
Gregory, B.5
Reilly, M.P.6
-
19
-
-
84920550975
-
A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium
-
SEQC/MAQC-III Consortium
-
SEQC/MAQC-III Consortium. A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nat Biotechnol 2014;32:903-14.
-
(2014)
Nat Biotechnol
, vol.32
, pp. 903-914
-
-
-
20
-
-
84961289698
-
Differential increases of specific FMR1 mRNA isoforms in premutation carriers
-
Pretto DI, Eid JS, Yrigollen CM, Tang HT, Loomis EW, Raske C, et al. Differential increases of specific FMR1 mRNA isoforms in premutation carriers. J Med Genet 2015;52:42-52.
-
(2015)
J Med Genet
, vol.52
, pp. 42-52
-
-
Pretto, D.I.1
Eid, J.S.2
Yrigollen, C.M.3
Tang, H.T.4
Loomis, E.W.5
Raske, C.6
-
21
-
-
84908869950
-
An expanding universe of mRNA modifications
-
Jaffrey SR. An expanding universe of mRNA modifications. Nat Struct Mol Biol 2014;21:945-6.
-
(2014)
Nat Struct Mol Biol
, vol.21
, pp. 945-946
-
-
Jaffrey, S.R.1
-
22
-
-
68549130740
-
Comparison of species richness estimates obtained using nearly complete fragments and simulated pyrosequencing-generated fragments in 16S rRNA gene-based environmental surveys
-
Youssef N, Sheik CS, Krumholz LR, Najar FZ, Roe BA, Elshahed MS. Comparison of species richness estimates obtained using nearly complete fragments and simulated pyrosequencing-generated fragments in 16S rRNA gene-based environmental surveys. Appl Environ Microbiol 2009;75:5227-36.
-
(2009)
Appl Environ Microbiol
, vol.75
, pp. 5227-5236
-
-
Youssef, N.1
Sheik, C.S.2
Krumholz, L.R.3
Najar, F.Z.4
Roe, B.A.5
Elshahed, M.S.6
-
24
-
-
63049092891
-
TerraGenome: A consortium for the sequencing of a soil metagenome
-
Vogel TM, Simonet P, Jansson JK, Hirsch PR, Tiedje JM, van Elsas JD, et al. TerraGenome: a consortium for the sequencing of a soil metagenome. Nat Rev Microbiol 2009;7:252.
-
(2009)
Nat Rev Microbiol
, vol.7
, pp. 252
-
-
Vogel, T.M.1
Simonet, P.2
Jansson, J.K.3
Hirsch, P.R.4
Tiedje, J.M.5
Van Elsas, J.D.6
-
25
-
-
33746061683
-
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
-
DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 2006;72:5069-72.
-
(2006)
Appl Environ Microbiol
, vol.72
, pp. 5069-5072
-
-
Desantis, T.Z.1
Hugenholtz, P.2
Larsen, N.3
Rojas, M.4
Brodie, E.L.5
Keller, K.6
-
26
-
-
50949090204
-
Novelty and uniqueness patterns of rare members of the soil biosphere
-
Elshahed MS, Youssef NH, Spain AM, Sheik C, Najar FZ, Sukharnikov LO, et al. Novelty and uniqueness patterns of rare members of the soil biosphere. Appl Environ Microbiol 2008;74:5422-8.
-
(2008)
Appl Environ Microbiol
, vol.74
, pp. 5422-5428
-
-
Elshahed, M.S.1
Youssef, N.H.2
Spain, A.M.3
Sheik, C.4
Najar, F.Z.5
Sukharnikov, L.O.6
-
29
-
-
68049111391
-
Metatranscriptomics: Eavesdropping on complex microbial communities
-
Moran AM. Metatranscriptomics: eavesdropping on complex microbial communities. Microbe 2009;4:329-35.
-
(2009)
Microbe
, vol.4
, pp. 329-335
-
-
Moran, A.M.1
-
31
-
-
0037474152
-
Zero-mode waveguides for single-molecule analysis at high concentrations
-
Levene MJ, Korlach J, Turner SW, Foquet M, Craighead HG, Webb WW. Zero-mode waveguides for single-molecule analysis at high concentrations. Science 2003; 299:682-6.
-
(2003)
Science
, vol.299
, pp. 682-686
-
-
Levene, M.J.1
Korlach, J.2
Turner, S.W.3
Foquet, M.4
Craighead, H.G.5
Webb, W.W.6
-
32
-
-
58149234737
-
Real-Time DNA sequencing from single polymerase molecules
-
Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, et al. Real-Time DNA sequencing from single polymerase molecules. Science 2009;323:133-8.
-
(2009)
Science
, vol.323
, pp. 133-138
-
-
Eid, J.1
Fehr, A.2
Gray, J.3
Luong, K.4
Lyle, J.5
Otto, G.6
-
33
-
-
77951107295
-
Real-time tRNA transit on single translating ribosomes at codon resolution
-
Uemura S, Aitken CE, Korlach J, Flusberg BA, Turner SW, Puglisi JD. Real-time tRNA transit on single translating ribosomes at codon resolution. Nature 2010; 464:1012-7.
-
(2010)
Nature
, vol.464
, pp. 1012-1017
-
-
Uemura, S.1
Aitken, C.E.2
Korlach, J.3
Flusberg, B.A.4
Turner, S.W.5
Puglisi, J.D.6
-
34
-
-
77955463346
-
Sequencing: Pacific Biosciences' single molecule real time technology
-
McCarthy A. Third Generation DNA Sequencing: Pacific Biosciences' single molecule real time technology. Chem Biol 2010;17:675-6.
-
(2010)
Chem Biol
, vol.17
, pp. 675-676
-
-
McCarthy, A.1
Third Generation, D.2
-
36
-
-
77956125365
-
A flexible and efficient template format for circular consensus sequencing and SNP detection
-
Travers KJ, Chin CS, Rank DR, Eid JS, Turner SW. A flexible and efficient template format for circular consensus sequencing and SNP detection. Nucleic Acids Res 2010;38:e159.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Travers, K.J.1
Chin, C.S.2
Rank, D.R.3
Eid, J.S.4
Turner, S.W.5
-
37
-
-
84869814079
-
Mind the gap: Upgrading genomes with Pacific Biosciences RS long-read sequencing technology
-
English AC, Richards S, Han Y, Wang M, Vee V, Qu J, et al. Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology. PLoS One 2012;7:e47768.
-
(2012)
Plos One
, vol.7
-
-
English, A.C.1
Richards, S.2
Han, Y.3
Wang, M.4
Vee, V.5
Qu, J.6
-
38
-
-
84868327508
-
Finished bacterial genomes from shotgun sequence data
-
Ribeiro FJ, Przybylski D, Yin S, Sharpe T, Gnerre S, Abouelleil A, et al. Finished bacterial genomes from shotgun sequence data. Genome Res 2012;22:2270-7.
-
(2012)
Genome Res
, vol.22
, pp. 2270-2277
-
-
Ribeiro, F.J.1
Przybylski, D.2
Yin, S.3
Sharpe, T.4
Gnerre, S.5
Abouelleil, A.6
-
39
-
-
84863651532
-
Hybrid error correction and de novo assembly of single-molecule sequencing reads
-
Koren S, Schatz MC, Walenz BP, Martin J, Howard JT, Ganapathy G, et al. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat Biotechnol 2012;30:693-700.
-
(2012)
Nat Biotechnol
, vol.30
, pp. 693-700
-
-
Koren, S.1
Schatz, M.C.2
Walenz, B.P.3
Martin, J.4
Howard, J.T.5
Ganapathy, G.6
-
40
-
-
84883664726
-
Reducing assembly complexity of microbial genomes with single-molecule sequencing
-
Koren S, Harhay GP, Smith TP, Bono JL, Harhay DM, Mcvey SD, et al. Reducing assembly complexity of microbial genomes with single-molecule sequencing. Genome Biol 2013;14: 101.
-
(2013)
Genome Biol
, vol.14
, pp. 101
-
-
Koren, S.1
Harhay, G.P.2
Smith, T.P.3
Bono, J.L.4
Harhay, D.M.5
McVey, S.D.6
-
41
-
-
84925497196
-
Resolving the complexity of the human genome using single-molecule sequencing
-
Chaisson MJ, Huddleston J, Dennis MY, Sudmant PH, Malig M, Hormozdiari F, et al. Resolving the complexity of the human genome using single-molecule sequencing. Nature 2015;517:608-11.
-
(2015)
Nature
, vol.517
, pp. 608-611
-
-
Chaisson, M.J.1
Huddleston, J.2
Dennis, M.Y.3
Sudmant, P.H.4
Malig, M.5
Hormozdiari, F.6
-
42
-
-
77952967431
-
Direct detection of DNA meth-ylation during single-molecule, real-time sequencing
-
Flusberg FA, Webster DR, Lee JH, Travers KJ, Olivares EC, Clark TA, et al. Direct detection of DNA meth-ylation during single-molecule, real-time sequencing. Nat Methods 2010;7:461-5.
-
(2010)
Nat Methods
, vol.7
, pp. 461-465
-
-
Flusberg, F.A.1
Webster, D.R.2
Lee, J.H.3
Travers, K.J.4
Olivares, E.C.5
Clark, T.A.6
-
43
-
-
84870880581
-
Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing
-
Fang G, Munera D, Friedman DI, Mandlik A, Chao MC, Banerjee O, et al. Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing. Nat Biotechnol 2012;30:1232-9.
-
(2012)
Nat Biotechnol
, vol.30
, pp. 1232-1239
-
-
Fang, G.1
Munera, D.2
Friedman, D.I.3
Mandlik, A.4
Chao, M.C.5
Banerjee, O.6
-
44
-
-
84887412533
-
A single-molecule long-read survey of the human transcriptome
-
Sharon D, Tilgner H, Grubert F, Snyder M. A single-molecule long-read survey of the human transcriptome. Nat Biotechnol 2013;31:1009-14.
-
(2013)
Nat Biotechnol
, vol.31
, pp. 1009-1014
-
-
Sharon, D.1
Tilgner, H.2
Grubert, F.3
Snyder, M.4
-
45
-
-
84904016056
-
Defining a personal, allele-specific, and single-molecule long-read transcriptome
-
Tilgner H, Grubert F, Sharon D, Snyder MP. Defining a personal, allele-specific, and single-molecule long-read transcriptome. Proc Natl Acad Sci U S A 2014; 111:9869-74.
-
(2014)
Proc Natl Acad Sci U S A
, vol.111
, pp. 9869-9874
-
-
Tilgner, H.1
Grubert, F.2
Sharon, D.3
Snyder, M.P.4
-
46
-
-
84926486633
-
Successful test launch for nano-pore sequencing
-
Loman NJ, Watson M. Successful test launch for nano-pore sequencing. Nat Methods 2015;12:303-4.
-
(2015)
Nat Methods
, vol.12
, pp. 303-304
-
-
Loman, N.J.1
Watson, M.2
-
47
-
-
0034177819
-
Nanopores and nucleic acids: Prospects for ultrarapid sequencing
-
Deamer DW, Akeson M. Nanopores and nucleic acids: prospects for ultrarapid sequencing. Trends Biotechnol 2000;18:147-51.
-
(2000)
Trends Biotechnol
, vol.18
, pp. 147-151
-
-
Deamer, D.W.1
Akeson, M.2
-
48
-
-
0036797062
-
Characterization of nucleic acids by nanopore analysis
-
Deamer DW, Branton D. Characterization of nucleic acids by nanopore analysis. Acc Chem Res 2002;35: 817-25.
-
(2002)
Acc Chem Res
, vol.35
, pp. 817-825
-
-
Deamer, D.W.1
Branton, D.2
-
50
-
-
84860435798
-
Genome sequencing. Search for pore-fection
-
Pennisi E. Genome sequencing. Search for pore-fection. Science 2012;336:534-7.
-
(2012)
Science
, vol.336
, pp. 534-537
-
-
Pennisi, E.1
-
51
-
-
84920506933
-
Nanopore Sequencing: From imagination to reality
-
Bayley H. Nanopore Sequencing: From imagination to reality. Clin Chem 2015;61:25-31.
-
(2015)
Clin Chem
, vol.61
, pp. 25-31
-
-
Bayley, H.1
-
52
-
-
84863470343
-
Nanopores: A journey towards DNA sequencing
-
Wanunu M. Nanopores: A journey towards DNA sequencing. Phys Life Rev 2012;9:125-58.
-
(2012)
Phys Life Rev
, vol.9
, pp. 125-158
-
-
Wanunu, M.1
-
53
-
-
58549116498
-
Detection with an engineered MspA protein nanopore
-
Butler TZ, Pavlenok M, Derrington IM, Niederweis M, Gundlach JH. Single-molecule DNA detection with an engineered MspA protein nanopore. Proc Natl Acad Sci U S A 2008;105:20647-52.
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, pp. 20647-20652
-
-
Butler, T.Z.1
Pavlenok, M.2
Derrington, I.M.3
Niederweis, M.4
Gundlach, J.H.5
Single-Molecule, D.6
-
54
-
-
70449556810
-
Translocation of double-stranded DNA through membrane-adapted phi29 motor protein nanopores
-
Wendell D, Jing P, Geng J, Subramaniam V, Lee TJ, Montemagno C, et al. Translocation of double-stranded DNA through membrane-adapted phi29 motor protein nanopores. Nat Nanotechnol 2009;4:765-72.
-
(2009)
Nat Nanotechnol
, vol.4
, pp. 765-772
-
-
Wendell, D.1
Jing, P.2
Geng, J.3
Subramaniam, V.4
Lee, T.J.5
Montemagno, C.6
-
55
-
-
0030447720
-
Structure of staphylococcal a-hemolysin, a heptameric transmembrane pore
-
Song L, Hobaugh MR, Shustak C, Cheley S, Bayley H, Gouaux JE. Structure of staphylococcal a-hemolysin, a heptameric transmembrane pore. Science 1996;274: 1859-66.
-
(1996)
Science
, vol.274
, pp. 1859-1866
-
-
Song, L.1
Hobaugh, M.R.2
Shustak, C.3
Cheley, S.4
Bayley, H.5
Gouaux, J.E.6
-
56
-
-
0019850449
-
On the mechanism of membrane damage by Staphylococcus aureus a-toxin
-
Füssle R, Bhakdi S, Sziegoleit A, Tranum-Jensen J, Kranz T, Wellensiek HJ. On the mechanism of membrane damage by Staphylococcus aureus a-toxin. J Cell Biol 1981;91:83-94.
-
(1981)
J Cell Biol
, vol.91
, pp. 83-94
-
-
Füssle, R.1
Bhakdi, S.2
Sziegoleit, A.3
Tranum-Jensen, J.4
Kranz, T.5
Wellensiek, H.J.6
-
57
-
-
0031877366
-
A-Hemolysin from Staphylococcus aureus: An archetype of ß-barrel, channel-forming toxins
-
Gouaux E. a-Hemolysin from Staphylococcus aureus: an archetype of ß-barrel, channel-forming toxins. J Struct Biol 1998;21:110-22.
-
(1998)
J Struct Biol
, vol.21
, pp. 110-122
-
-
Gouaux, E.1
-
58
-
-
0036674122
-
Single molecule measurements of DNA transport through a nanopore
-
Meller A, Branton D. Single molecule measurements of DNA transport through a nanopore. Electrophoresis 2002;23:2583-91.
-
(2002)
Electrophoresis
, vol.23
, pp. 2583-2591
-
-
Meller, A.1
Branton, D.2
-
59
-
-
0032762996
-
Microsecond time-scale discrimination among polycytidylic acid, polyadenylic acid and poly-uridylic acid as homopolymers or as segments within single RNA molecules
-
Akeson M, Branton D, Kasianwicz JJ, Brandin E, Deamer DW. Microsecond time-scale discrimination among polycytidylic acid, polyadenylic acid and poly-uridylic acid as homopolymers or as segments within single RNA molecules. Biophys J 1999;77:3227-33.
-
(1999)
Biophys J
, vol.77
, pp. 3227-3233
-
-
Akeson, M.1
Branton, D.2
Kasianwicz, J.J.3
Brandin, E.4
Deamer, D.W.5
-
60
-
-
0033980542
-
Rapid nanopore discrimination between single polynucleotide molecules
-
Meller A, Nivon L, Brandin E, Golovchenko J, Branton D. Rapid nanopore discrimination between single polynucleotide molecules. Proc Natl Acad Sci U S A 2000;97:1079-84.
-
(2000)
Proc Natl Acad Sci U S A
, vol.97
, pp. 1079-1084
-
-
Meller, A.1
Nivon, L.2
Brandin, E.3
Golovchenko, J.4
Branton, D.5
-
61
-
-
60849133617
-
Controlling the translocation of single-stranded DNA through alpha-hemolysin ion channels using viscosity
-
Kawano R, Schibel AE, Cauley C, White HS. Controlling the translocation of single-stranded DNA through alpha-hemolysin ion channels using viscosity. Langmuir 2009;25:1233-7.
-
(2009)
Langmuir
, vol.25
, pp. 1233-1237
-
-
Kawano, R.1
Schibel, A.E.2
Cauley, C.3
White, H.S.4
-
62
-
-
49649084921
-
Chemical tags facilitate the sensing of individual DNA strands with nanopores
-
Mitchell N, Howorka S. Chemical tags facilitate the sensing of individual DNA strands with nanopores. Angew Chem Int Ed Engl 2008;47:5565-8.
-
(2008)
Angew Chem Int Ed Engl
, vol.47
, pp. 5565-5568
-
-
Mitchell, N.1
Howorka, S.2
-
63
-
-
84878748248
-
Nanopore detection of DNA molecules in magnesium chloride solutions
-
Zhang Y, Liu L, Sha J, Ni Z, Yi H, Chen Y. Nanopore detection of DNA molecules in magnesium chloride solutions. Nanoscale Res Lett 2013;8:245.
-
(2013)
Nanoscale Res Lett
, vol.8
, pp. 245
-
-
Zhang, Y.1
Liu, L.2
Sha, J.3
Ni, Z.4
Yi, H.5
Chen, Y.6
-
64
-
-
58149402384
-
Enhanced translocation of single DNA molecules through alpha-hemolysin nanopores by manipulation of internal charge
-
Maglia G, Restrepo MR, Mikhailova E, Bayley H. Enhanced translocation of single DNA molecules through alpha-hemolysin nanopores by manipulation of internal charge. Proc Natl Acad Sci U S A 2008; 105:19720-5.
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, pp. 19720-19725
-
-
Maglia, G.1
Restrepo, M.R.2
Mikhailova, E.3
Bayley, H.4
-
65
-
-
79851485457
-
Controlled translocation of individual DNA molecules through protein nanopores with engineered molecular brakes
-
Rincon-Restrepo M, Mikhailova E, Bayley H, Maglia G. Controlled translocation of individual DNA molecules through protein nanopores with engineered molecular brakes. Nano Lett 2011;11:746-50.
-
(2011)
Nano Lett
, vol.11
, pp. 746-750
-
-
Rincon-Restrepo, M.1
Mikhailova, E.2
Bayley, H.3
Maglia, G.4
-
66
-
-
84859175970
-
Automated Forward and Reverse Ratcheting of DNA in a Nanopore at Five Angstrom Precision
-
Cherf GM, Lieberman KR, Rashid H, Lam CE, Karplus K, Akeson M. Automated Forward and Reverse Ratcheting of DNA in a Nanopore at Five Angstrom Precision. Nat Biotechnol 2012;30:344-8.
-
(2012)
Nat Biotechnol
, vol.30
, pp. 344-348
-
-
Cherf, G.M.1
Lieberman, K.R.2
Rashid, H.3
Lam, C.E.4
Karplus, K.5
Akeson, M.6
-
67
-
-
78650280872
-
Processive replication of single DNA molecules in a nanopore catalyzed by phi29 DNA polymerase
-
Lieberman KR, Cherf GM, Doody MJ, Olasagasti F, Kolodji Y, Akeson M. Processive replication of single DNA molecules in a nanopore catalyzed by phi29 DNA polymerase. J Am Chem Soc 2010;132:17961-72.
-
(2010)
J am Chem Soc
, vol.132
, pp. 17961-17972
-
-
Lieberman, K.R.1
Cherf, G.M.2
Doody, M.J.3
Olasagasti, F.4
Kolodji, Y.5
Akeson, M.6
-
68
-
-
84922311054
-
DNA stretching and optimization of nucleobase recognition in enzymatic nanopore sequencing
-
Stoddart D, Franceschini L, Heron A, Bayley H, Maglia G. DNA stretching and optimization of nucleobase recognition in enzymatic nanopore sequencing. Nano-technology 2015;26:084002.
-
(2015)
Nano-Technology
, vol.26
-
-
Stoddart, D.1
Franceschini, L.2
Heron, A.3
Bayley, H.4
Maglia, G.5
-
69
-
-
78149408624
-
Replication of individual DNA molecules under electronic control using a protein nanopore
-
Olasagasti F, Lieberman KR, Benner S, Cherf GM, Dahl JM, Deamer DW, et al. Replication of individual DNA molecules under electronic control using a protein nanopore. Nat Nanotechnol 2010;5:798-806.
-
(2010)
Nat Nanotechnol
, vol.5
, pp. 798-806
-
-
Olasagasti, F.1
Lieberman, K.R.2
Benner, S.3
Cherf, G.M.4
Dahl, J.M.5
Deamer, D.W.6
-
70
-
-
53649108801
-
The potential and challenges of nanopore sequencing
-
Branton D, Deamer DW, Marziali A, Bayley H, Benner SA, Butler T, et al. The potential and challenges of nanopore sequencing. Nat Biotechnol 2008;26:1146-53.
-
(2008)
Nat Biotechnol
, vol.26
, pp. 1146-1153
-
-
Branton, D.1
Deamer, D.W.2
Marziali, A.3
Bayley, H.4
Benner, S.A.5
Butler, T.6
-
71
-
-
66049132042
-
Single-nucleotide discrimination in immobilized DNA oligonucleotides with a biological nanopore
-
)
-
Stoddart D, Heron AJ, Mikhailova E, Maglia G, Bayley H. Single-nucleotide discrimination in immobilized DNA oligonucleotides with a biological nanopore. Proc Natl Acad Sci U S A 2009;106:7702-7.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 7702-7707
-
-
Stoddart, D.1
Heron, A.J.2
Mikhailova, E.3
Maglia, G.4
Bayley, H.5
-
72
-
-
84917736997
-
Creating a single sensing zone within an alpha-hemolysin pore via site-directed mutagenesis
-
Ervin EN, Barrall GA, Pal P, Bean MK, Schibel AE, Hibbs AD. Creating a single sensing zone within an alpha-hemolysin pore via site-directed mutagenesis. Bionanoscience 2014;4:78-84.
-
(2014)
Bionanoscience
, vol.4
, pp. 78-84
-
-
Ervin, E.N.1
Barrall, G.A.2
Pal, P.3
Bean, M.K.4
Schibel, A.E.5
Hibbs, A.D.6
-
73
-
-
84859629295
-
Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase
-
Manrao EA, Derrington IM, Laszlo AH, Langford KW, Hopper MK, Gillgren N, et al. Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase. Nat Biotechnol 2012;30: 349-53.
-
(2012)
Nat Biotechnol
, vol.30
, pp. 349-353
-
-
Manrao, E.A.1
Derrington, I.M.2
Laszlo, A.H.3
Langford, K.W.4
Hopper, M.K.5
Gillgren, N.6
-
74
-
-
80053530116
-
Nucleotide discrimination with DNA immobilized in the MspA nanopore
-
Manrao EA, Derrington IM, Pavlenok M, Niederweis M, Gundlach JH. Nucleotide discrimination with DNA immobilized in the MspA nanopore. PLoS One 2011; 6:e25723.
-
(2011)
Plos One
, vol.6
-
-
Manrao, E.A.1
Derrington, I.M.2
Pavlenok, M.3
Niederweis, M.4
Gundlach, J.H.5
-
75
-
-
77956424842
-
Nucleobase recognition in ssDNA at the central constriction of the a-hemolysin pore
-
Stoddart D, Heron AJ, Klingelhoefer J, Mikhailova E, Maglia G, Bayley H. Nucleobase recognition in ssDNA at the central constriction of the a-hemolysin pore. Nano Lett 2010;10:3633-7.
-
(2010)
Nano Lett
, vol.10
, pp. 3633-3637
-
-
Stoddart, D.1
Heron, A.J.2
Klingelhoefer, J.3
Mikhailova, E.4
Maglia, G.5
Bayley, H.6
-
76
-
-
74549164354
-
Multiple base-recognition sites in a biological nanopore: Two heads are better than one
-
Stoddart D, Maglia G, Mikhailova E, Heron AJ, Bayley H. Multiple base-recognition sites in a biological nanopore: two heads are better than one. Angew Chem Int Ed Engl 2010;49:556-9.
-
(2010)
Angew Chem Int Ed Engl
, vol.49
, pp. 556-559
-
-
Stoddart, D.1
Maglia, G.2
Mikhailova, E.3
Heron, A.J.4
Bayley, H.5
-
77
-
-
77958487369
-
Identification of epi-genetic DNA modifications with a protein nanopore
-
Wallace EV, Stoddart D, Heron AJ, Mikhailova E, Maglia G, Donohoe TJ, et al. Identification of epi-genetic DNA modifications with a protein nanopore. Chem Commun 2010;46:8195-7.
-
(2010)
Chem Commun
, vol.46
, pp. 8195-8197
-
-
Wallace, E.V.1
Stoddart, D.2
Heron, A.J.3
Mikhailova, E.4
Maglia, G.5
Donohoe, T.J.6
-
79
-
-
84931044183
-
Analysis of nanopore data using Hidden Markov Models
-
Schreiber J, Karplus K. Analysis of nanopore data using Hidden Markov Models. Bioinformatics 2015; 31:1897-903.
-
(2015)
Bioinformatics
, vol.31
, pp. 1897-1903
-
-
Schreiber, J.1
Karplus, K.2
-
80
-
-
84905723571
-
Decoding long nanopore sequencing reads of natural DNA
-
Laszlo AH, Derrington IM, Ross BC, Brinkerhoff H, Adey A, Nova IC, et al. Decoding long nanopore sequencing reads of natural DNA. Nat Biotechnol 2014; 32:829-33.
-
(2014)
Nat Biotechnol
, vol.32
, pp. 829-833
-
-
Laszlo, A.H.1
Derrington, I.M.2
Ross, B.C.3
Brinkerhoff, H.4
Adey, A.5
Nova, I.C.6
-
81
-
-
84861149539
-
DNA base-calling from a nanopore using a Viterbi algorithm
-
Timp W, Comer J, Aksimentiev A. DNA base-calling from a nanopore using a Viterbi algorithm. Biophys J 2012;102:L37-9.
-
(2012)
Biophys J
, vol.102
, pp. 37-39
-
-
Timp, W.1
Comer, J.2
Aksimentiev, A.3
-
82
-
-
84935113569
-
Error bounds for convolutional codes and an asymptotically optimum decoding algorithm
-
Viterbi AJ. Error bounds for convolutional codes and an asymptotically optimum decoding algorithm. Inf Theory IEEE Trans 1967;3:260-9.
-
(1967)
Inf Theory IEEE Trans
, vol.3
, pp. 260-269
-
-
Viterbi, A.J.1
-
84
-
-
84907952658
-
A first look at the Oxford Nanopore MinION sequencer
-
Mikheyev AS, Tin MM. A first look at the Oxford Nanopore MinION sequencer. Mol Ecol Resour 2014; 14:1097-102.
-
(2014)
Mol Ecol Resour
, vol.14
, pp. 1097-1102
-
-
Mikheyev, A.S.1
Tin, M.M.2
-
85
-
-
85019264879
-
Genome assembly using nanopore-guided long and error-free DNA reads
-
Madoui MA, Engelen S, Cruaud C, Belser C, Bertrand L, Alberti A, et al. Genome assembly using nanopore-guided long and error-free DNA reads. BMC Genomics 2015;16:327.
-
(2015)
BMC Genomics
, vol.16
, pp. 327
-
-
Madoui, M.A.1
Engelen, S.2
Cruaud, C.3
Belser, C.4
Bertrand, L.5
Alberti, A.6
-
86
-
-
84938421951
-
A complete bacterial genome assembled de novo using only nanopore sequencing data
-
Loman NJ, Quick J, Simpson JT. A complete bacterial genome assembled de novo using only nanopore sequencing data. Nat Methods 2015;12:733-5.
-
(2015)
Nat Methods
, vol.12
, pp. 733-735
-
-
Loman, N.J.1
Quick, J.2
Simpson, J.T.3
-
87
-
-
84942520038
-
A reference bacterial genome dataset generated on the MinION(TM) portable single-molecule nanopore sequencer
-
Quick J, Quinlan AR, Loman NJ. A reference bacterial genome dataset generated on the MinION(TM) portable single-molecule nanopore sequencer. Gigascience 2014;3:22.
-
(2014)
Gigascience
, vol.3
, pp. 22
-
-
Quick, J.1
Quinlan, A.R.2
Loman, N.J.3
-
88
-
-
84926047262
-
DNA Damage -the major cause of missing pieces from the DNA puzzle
-
Evans TC. DNA Damage -the major cause of missing pieces from the DNA puzzle. NEB Expressions 2007; 2:1.
-
(2007)
NEB Expressions
, vol.2
, pp. 1
-
-
Evans, T.C.1
-
89
-
-
84926472171
-
Improved data analysis for the MinION nanopore sequencer
-
Jain M, Fiddes IT, Miga KH, Olsen HE, Paten B, Akeson M. Improved data analysis for the MinION nanopore sequencer. Nat Methods 2015;12:351-6.
-
(2015)
Nat Methods
, vol.12
, pp. 351-356
-
-
Jain, M.1
Fiddes, I.T.2
Miga, K.H.3
Olsen, H.E.4
Paten, B.5
Akeson, M.6
-
90
-
-
84954476048
-
-
The HDF Group, version 5, 1997-2015, (accessed Aug 2015)
-
The HDF Group. Hierarchical Data Format, version 5, 1997-2015. http://www.hdfgroup.org/HDF5/ (accessed Aug 2015), 2015.
-
(2015)
Hierarchical Data Format
-
-
-
91
-
-
84924426384
-
Poretools: A toolkit for analyzing nanopore sequence data
-
Loman NJ, Quinlan AR. Poretools: a toolkit for analyzing nanopore sequence data. Bioinformatics 2014; 30:3399-401.
-
(2014)
Bioinformatics
, vol.30
, pp. 3399-3401
-
-
Loman, N.J.1
Quinlan, A.R.2
-
92
-
-
84922368174
-
Pore: An R package for the visualization and analysis of nanopore sequencing data
-
Watson M, Thomson M, Risse J, Talbot R, Santoyo-Lopez J, Gharbi K, et al. pore: an R package for the visualization and analysis of nanopore sequencing data. Bioinformatics 2015;31:114-5.
-
(2015)
Bioinformatics
, vol.31
, pp. 114-115
-
-
Watson, M.1
Thomson, M.2
Risse, J.3
Talbot, R.4
Santoyo-Lopez, J.5
Gharbi, K.6
-
94
-
-
79952256999
-
Adaptive seeds tame genomic sequence comparison
-
Kielbasa SM, Wan R, Sato K, Horton P, Frith MC. Adaptive seeds tame genomic sequence comparison. Genome Res 2011;21:487-93.
-
(2011)
Genome Res
, vol.21
, pp. 487-493
-
-
Kielbasa, S.M.1
Wan, R.2
Sato, K.3
Horton, P.4
Frith, M.C.5
-
95
-
-
84992382190
-
-
bioRxiv
-
Sovic I, Sikic M, Wilm A, Fenlon SN, Chen S, Nagarajan N. Fast and sensitive mapping of error-prone nanopore sequencing reads with GraphMap. bioRxiv 2015. doi: http://dx.doi.org/10.1101/020719.
-
(2015)
Fast and Sensitive Mapping of Error-Prone Nanopore Sequencing Reads with Graphmap
-
-
Sovic, I.1
Sikic, M.2
Wilm, A.3
Fenlon, S.N.4
Chen, S.5
Nagarajan, N.6
-
96
-
-
84979584495
-
LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads
-
Warren RL, Yang C, Vandervalk BP, Behsaz B, Lagman A, Jones SJ, et al. LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads. Giga-Science 2015;4:35.
-
(2015)
Giga-Science
, vol.4
, pp. 35
-
-
Warren, R.L.1
Yang, C.2
Vandervalk, B.P.3
Behsaz, B.4
Lagman, A.5
Jones, S.J.6
-
97
-
-
84913554630
-
One chromosome, one contig: Complete microbial genomes from long-read sequencing and assembly
-
Koren S, Phillippy AM. One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly. Curr Opin Microbiol 2015;23:110-20.
-
(2015)
Curr Opin Microbiol
, vol.23
, pp. 110-120
-
-
Koren, S.1
Phillippy, A.M.2
-
98
-
-
84936764311
-
Scaffolding of a bacterial genome using MinION nanopore sequencing
-
Karlsson E, Lärkeryd A, Sjödin A, Forsman M, Stenberg P. Scaffolding of a bacterial genome using MinION nanopore sequencing. Sci Rep 2015;5:11996.
-
(2015)
Sci Rep
, vol.5
, pp. 11996
-
-
Karlsson, E.1
Lärkeryd, A.2
Sjödin, A.3
Forsman, M.4
Stenberg, P.5
-
99
-
-
84902707563
-
SSPACE-LongRead: Scaffolding bacterial draft genomes using long read sequence information
-
Boetzer M, Pirovano W. SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information. BMC Bioinformatics 2014;15:211.
-
(2014)
BMC Bioinformatics
, vol.15
, pp. 211
-
-
Boetzer, M.1
Pirovano, W.2
-
100
-
-
84866266717
-
Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): Application and theory
-
Chaisson MJ, Tesler G. Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. BMC Bioinformatics 2012;13:238.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 238
-
-
Chaisson, M.J.1
Tesler, G.2
-
101
-
-
85033345115
-
A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data
-
Risse J, Thomson M, Blakely G, Koutsovoulos G, Blaxter M, Watson M. A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data. BioRxiv 2015. doi: http://dx.doi.org/10.1101/024323.
-
(2015)
Biorxiv
-
-
Risse, J.1
Thomson, M.2
Blakely, G.3
Koutsovoulos, G.4
Blaxter, M.5
Watson, M.6
-
102
-
-
84925353483
-
-
bioRxiv
-
Goodwin S, Gurtowski J, Ethe-Sayers S, Deshpande P, Schatz M, McCombie WR. Oxford Nanopore Sequencing and de novo Assembly of a Eukaryotic Genome. bioRxiv 2015. doi: http://dx.doi.org/10.1101/013490.
-
(2015)
Oxford Nanopore Sequencing and De Novo Assembly of a Eukaryotic Genome
-
-
Goodwin, S.1
Gurtowski, J.2
Ethe-Sayers, S.3
Deshpande, P.4
Schatz, M.5
McCombie, W.R.6
-
103
-
-
84924388692
-
MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island
-
Ashton PM, Nair S, Dallman T, Rubino S, Rabsch W, Mwaigwisya S, et al. MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island. Nat Biotechnol 2015;33:296-300.
-
(2015)
Nat Biotechnol
, vol.33
, pp. 296-300
-
-
Ashton, P.M.1
Nair, S.2
Dallman, T.3
Rubino, S.4
Rabsch, W.5
Mwaigwisya, S.6
-
104
-
-
84931292033
-
Long read nanopore sequencing for detection of HLA and CYP2D6 variants and haplotypes
-
Ammar R, Paton TA, Torti D, Shlien A, Bader GD. Long read nanopore sequencing for detection of HLA and CYP2D6 variants and haplotypes. F1000Res 2015; 4:17.
-
(2015)
F1000res
, vol.4
, pp. 17
-
-
Ammar, R.1
Paton, T.A.2
Torti, D.3
Shlien, A.4
Bader, G.D.5
-
106
-
-
84890387605
-
Nanopore-Based Identification of Individual Nucleotides for Direct RNA Sequencing
-
Ayub M, Hardwick SW, Luisi BF, Bayley H. Nanopore-Based Identification of Individual Nucleotides for Direct RNA Sequencing. Nano Lett 2013;13:6144-50.
-
(2013)
Nano Lett
, vol.13
, pp. 6144-6150
-
-
Ayub, M.1
Hardwick, S.W.2
Luisi, B.F.3
Bayley, H.4
-
107
-
-
84888101866
-
Error rates for nanopore discrimination among cytosine, methylcytosine, and hydroxymethylcytosine along individual DNA strands
-
Schreiber J, Wescoe ZL, Abu-Shumays R, Vivian JT, Baatar B, Karplus K, et al. Error rates for nanopore discrimination among cytosine, methylcytosine, and hydroxymethylcytosine along individual DNA strands. Proc Natl Acad Sci U S A 2013;110:18910-5.
-
(2013)
Proc Natl Acad Sci U S A
, vol.110
, pp. 18910-18915
-
-
Schreiber, J.1
Wescoe, Z.L.2
Abu-Shumays, R.3
Vivian, J.T.4
Baatar, B.5
Karplus, K.6
-
110
-
-
84954501560
-
-
BioRxiv
-
Cao MD, Ganesamoorthy D, Elliott A, Zhang H, Cooper M, Coin L. Real-time strain typing and analysis of antibiotic resistance potential using Nanopore MinION sequencing. BioRxiv 2015. doi: http://dx.doi.org/ 10.1101/019356.
-
(2015)
Real-Time Strain Typing and Analysis of Antibiotic Resistance Potential Using Nanopore Minion Sequencing
-
-
Cao, M.D.1
Ganesamoorthy, D.2
Elliott, A.3
Zhang, H.4
Cooper, M.5
Coin, L.6
-
111
-
-
84934284959
-
Rapid draft sequencing and real-time nanopore sequencing in a hospital out break of Salmonella
-
Quick J, Ashton P, Calus S, Chatt C, Gossain S, Hawker J, et al. Rapid draft sequencing and real-time nanopore sequencing in a hospital out break of Salmonella. Genome Biol 2015;16:114.
-
(2015)
Genome Biol
, vol.16
, pp. 114
-
-
Quick, J.1
Ashton, P.2
Calus, S.3
Chatt, C.4
Gossain, S.5
Hawker, J.6
-
112
-
-
84938851187
-
MinION nanopore sequencing of an influenza genome
-
Wang J, Moore NE, Deng YM, Eccles DA, Hall RJ. MinION nanopore sequencing of an influenza genome. Front Microbiol 2015;6:766.
-
(2015)
Front Microbiol
, vol.6
, pp. 766
-
-
Wang, J.1
Moore, N.E.2
Deng, Y.M.3
Eccles, D.A.4
Hall, R.J.5
-
113
-
-
84962672508
-
-
bioRxiv
-
Greninger AL, Naccache SN, Federman S, Yu G, Mbala P, Bres V, et al. Rapid metagenomic identification of viral pathogens in clinical samples by realtime nanopore sequencing analysis. bioRxiv 2015. doi: http://dx.doi.org/10.1101/020420.
-
(2015)
Rapid Metagenomic Identification of Viral Pathogens in Clinical Samples by Realtime Nanopore Sequencing Analysis
-
-
Greninger, A.L.1
Naccache, S.N.2
Federman, S.3
Yu, G.4
Mbala, P.5
Bres, V.6
-
114
-
-
84938850442
-
Bacterial and viral identification and differentiation by amplicon sequencing on the MinION nanopore sequencer
-
Kilianski A, Haas JL, Cornveau EJ, Liem AT, Willis KL, Kadavy DR, et al. Bacterial and viral identification and differentiation by amplicon sequencing on the MinION nanopore sequencer. Gigascience 2015;4:12.
-
(2015)
Gigascience
, vol.4
, pp. 12
-
-
Kilianski, A.1
Haas, J.L.2
Cornveau, E.J.3
Liem, A.T.4
Willis, K.L.5
Kadavy, D.R.6
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