-
1
-
-
84941755547
-
Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses
-
Mendoza MLZ, Sicheritz-Ponten T, Gilbert MTP. Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses. Briefings in Bioinformatics 2015;1-14. doi: 10.1093/bib/bbv001
-
(2015)
Briefings in Bioinformatics
, pp. 1-14
-
-
Mendoza, M.L.Z.1
Sicheritz-Ponten, T.2
Gilbert, M.T.P.3
-
3
-
-
0030465241
-
Characterization of individual polynucleotide molecules using a membrane channel
-
Kasianowicz JJ, Brandin E, Branton D et al. Characterization of individual polynucleotide molecules using a membrane channel. Proc Natl Acad Sci 1996;93:13770-3
-
(1996)
Proc Natl Acad Sci
, vol.93
-
-
Kasianowicz, J.J.1
Brandin, E.2
Branton, D.3
-
4
-
-
84859643160
-
Oxford Nanopore announcement sets sequencing sector abuzz
-
Eisenstein M. Oxford Nanopore announcement sets sequencing sector abuzz. Nat Biotechnol 2012;30:295-6
-
(2012)
Nat Biotechnol
, vol.30
, pp. 295-296
-
-
Eisenstein, M.1
-
5
-
-
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
-
6
-
-
84977828810
-
Oxford Nanopore sequencing and de novo assembly of a eukaryotic genome
-
Goodwin S, Gurtowski J, Ethe-Sayers S, Deshpande P, Schatz M, McCombie WR. Oxford Nanopore sequencing and de novo assembly of a eukaryotic genome. Genome Res 2015a;25:1-7
-
(2015)
Genome Res
, vol.25
, pp. 1-7
-
-
Goodwin, S.1
Gurtowski, J.2
Ethe-Sayers, S.3
Deshpande, P.4
Schatz, M.5
McCombie, W.R.6
-
7
-
-
84991528128
-
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. GigaScience 2015;4:60
-
(2015)
GigaScience
, vol.4
, pp. 60
-
-
Risse, J.1
Thomson, M.2
Blakely, G.3
Koutsovoulos, G.4
Blaxter, M.5
Watson, M.6
-
8
-
-
84934284959
-
Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella
-
Quick J, Ashton P, Calus S, Chatt C, Gossain S et al. Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak 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
-
9
-
-
85019264879
-
Genome assembly using nanopore-guided long and error-free DNA reads
-
Madoui M-A, Engelen S, Cruaud C 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
-
10
-
-
84975137357
-
The evaluation on molecular techniques of reverse transcription loop-mediated isothermal amplification (RT-LAMP), reverse transcription polymerase chain reaction (RT-PCR), and their diagnostic results on MinIONTM nanopore sequencer for the detection of dengue virus serotypes
-
Mongan AE, Yusuf I, Wahid I et al. The evaluation on molecular techniques of reverse transcription loop-mediated isothermal amplification (RT-LAMP), reverse transcription polymerase chain reaction (RT-PCR), and their diagnostic results on MinIONTM nanopore sequencer for the detection of dengue virus serotypes. Am J Microbiol Res 2015;3:118-24
-
(2015)
Am J Microbiol Res
, vol.3
, pp. 118-124
-
-
Mongan, A.E.1
Yusuf, I.2
Wahid, I.3
-
11
-
-
84949664420
-
Snake venom gland cDNA sequencing using the Oxford nanopore MinION portable DNA sequencer
-
eCollection 2015
-
Hargreaves AD, Mulley JF. Snake venom gland cDNA sequencing using the Oxford nanopore MinION portable DNA sequencer. PeerJ 2015 Nov 24;3:e1441. doi: 10.7717/peerj.1441. eCollection 2015
-
PeerJ 2015 Nov 24
, vol.3
-
-
Hargreaves, A.D.1
Mulley, J.F.2
-
12
-
-
84942602825
-
Determining exon connectivity in complex mRNAs by nanopore sequencing
-
Bolisetty MT, Rajadinakaran G, Graveley BR. Determining exon connectivity in complex mRNAs by nanopore sequencing. Genome Biol 2015;16:204
-
(2015)
Genome Biol
, vol.16
, pp. 204
-
-
Bolisetty, M.T.1
Rajadinakaran, G.2
Graveley, B.R.3
-
13
-
-
84954501560
-
Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinION sequencing
-
Cao MD, Ganesamoorthy D, Elliott A et al. Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinION sequencing. bioRxiv 2015; doi: http://dx.doi.org/10.1101/019356
-
(2015)
bioRxiv
-
-
Cao, M.D.1
Ganesamoorthy, D.2
Elliott, A.3
-
14
-
-
84943806095
-
Early insights into the potential of the Oxford Nanopore MinION for the detection of antimicrobial resistance genes
-
Judge K, Harris SR, Reuter S et al. Early insights into the potential of the Oxford Nanopore MinION for the detection of antimicrobial resistance genes. J Antimicrob Chemother 2015; doi:10.1093/jac/dkv206
-
(2015)
J Antimicrob Chemother
-
-
Judge, K.1
Harris, S.R.2
Reuter, S.3
-
15
-
-
84938851187
-
MinION nanopore sequencing of an influenza genome
-
Wang J, Moore NE, Deng Y-M et al. 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
-
16
-
-
84938850442
-
Bacterial and viral identification and differentiation by amplicon sequencing on the MinION nanopore sequencer
-
Kilianski A, Haas JL, Corriveau EJ 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
Corriveau, E.J.3
-
17
-
-
84942518081
-
Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis
-
Greninger AL, Naccache SN, Federman S et al. Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis. Genom Med 2015;7:99
-
(2015)
Genom Med
, vol.7
, pp. 99
-
-
Greninger, A.L.1
Naccache, S.N.2
Federman, S.3
-
18
-
-
85011408917
-
Extreme metagenomics using nanopore DNA sequencing: a field report from Svalbard, 78 N
-
Edwards A, Debbonaire AR, Sattler B et al. Extreme metagenomics using nanopore DNA sequencing: a field report from Svalbard, 78 N. bioRxiv 2016; doi: http://dx.doi.org/10.1101/073965
-
(2016)
bioRxiv
-
-
Edwards, A.1
Debbonaire, A.R.2
Sattler, B.3
-
19
-
-
85023197237
-
Supporting data for "MinION nanopore sequencing of environmental metagenomes: a synthetic approach"
-
(28 October 2016)
-
Brown BL, Watson M, Minot SS et al. Supporting data for "MinION nanopore sequencing of environmental metagenomes: a synthetic approach" GigaScience Database. 2017 http://dx.doi.org/10.5524/100278 (28 October 2016)
-
(2017)
GigaScience Database
-
-
Brown, B.L.1
Watson, M.2
Minot, S.S.3
-
20
-
-
84922368174
-
poRe: an R package for the visualization and analysis of nanopore sequencing data
-
Watson M, Thomson M, Risse J 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
-
21
-
-
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
-
22
-
-
84959879117
-
NanoOK: Multireference alignment analysis of nanopore sequencing data, quality, and error profiles
-
Leggett RM, Heavens D, Caccamo M et al. NanoOK: Multireference alignment analysis of nanopore sequencing data, quality, and error profiles. Bioinformatics 2015;32:142-4
-
(2015)
Bioinformatics
, vol.32
, pp. 142-144
-
-
Leggett, R.M.1
Heavens, D.2
Caccamo, M.3
-
23
-
-
53549118607
-
The metagenomics RAST server-a public resource for the automatic phylogenetic and functional analysis of metagenomes
-
Meyer F, Paarmann D, D'Souza M et al. The metagenomics RAST server-a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinfo 2008;9:386
-
(2008)
BMC Bioinfo
, vol.9
, pp. 386
-
-
Meyer, F.1
Paarmann, D.2
D'Souza, M.3
-
25
-
-
84899090573
-
Kraken: ultrafast metagenomic sequence classification using exact alignments
-
Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol 2014;15:R46
-
(2014)
Genome Biol
, vol.15
, pp. R46
-
-
Wood, D.E.1
Salzberg, S.L.2
-
26
-
-
84978499039
-
One Codex: a sensitive and accurate data platform for genomic microbial identification
-
Minot SS, Krumm N, Greenfield NB. One Codex: a sensitive and accurate data platform for genomic microbial identification. bioRxiv 2015; doi: http://dx.doi.org/10.1101/027607
-
(2015)
bioRxiv
-
-
Minot, S.S.1
Krumm, N.2
Greenfield, N.B.3
-
27
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
Altschul SF, Madden TL, Schaffer AA et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Acids Res 1997;25:3389
-
(1997)
Nucl Acids Res
, vol.25
, pp. 3389
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
-
28
-
-
84964927929
-
-
Vienna: R Foundation for Statistical Computing (22 June 2016)
-
R Core Team. R: A Language and Environment for Statistical Computing. Vienna: R Foundation for Statistical Computing, 2015 https://www. R-project.org/(22 June 2016)
-
(2015)
R: A Language and Environment for Statistical Computing
-
-
-
29
-
-
0034896940
-
Degradation of the cyanobacterial hepatotoxin microcystin by a new bacterium isolated from a hypertrophic lake
-
Park H-D, Sasaki Y, Maruyama T et al. Degradation of the cyanobacterial hepatotoxin microcystin by a new bacterium isolated from a hypertrophic lake. Environ Toxicol 2001;16:337-43
-
(2001)
Environ Toxicol
, vol.16
, pp. 337-343
-
-
Park, H.-D.1
Sasaki, Y.2
Maruyama, T.3
-
30
-
-
84946781151
-
Library preparation methodology can influence genomic and functional predictions in human microbiome research
-
Jones MB, Highlander SK, Anderson EL et al. Library preparation methodology can influence genomic and functional predictions in human microbiome research. Proc Nat Acad Sci 2015;45:14024-9
-
(2015)
Proc Nat Acad Sci
, vol.45
-
-
Jones, M.B.1
Highlander, S.K.2
Anderson, E.L.3
-
32
-
-
84941756052
-
Metagenomic analysis of planktonic microbial consortia from a non-tidal urban-impacted segment of James River
-
Brown BL, LePrell RV, Franklin RB et al. Metagenomic analysis of planktonic microbial consortia from a non-tidal urban-impacted segment of James River. Stand Genomic Sci 2015;10:65
-
(2015)
Stand Genomic Sci
, vol.10
, pp. 65
-
-
Brown, B.L.1
LePrell, R.V.2
Franklin, R.B.3
-
33
-
-
84929143068
-
Pooled assembly of marine metagenomic datasets: enriching annotation through chimerism
-
Magasin JD, GerloffDL. Pooled assembly of marine metagenomic datasets: enriching annotation through chimerism. Bioinformatics 2015;31:311-7
-
(2015)
Bioinformatics
, vol.31
, pp. 311-317
-
-
Magasin, J.D.1
Gerloff, D.L.2
-
34
-
-
84931267206
-
Accurate readbased metagenome characterization using a hierarchical suite of unique signatures
-
Freitas TAK, Li P-E, Scholz MB et al. Accurate readbased metagenome characterization using a hierarchical suite of unique signatures. Nucl Acids Res 2015; doi: 10.1093/nar/gkv180
-
(2015)
Nucl Acids Res
-
-
Freitas, T.A.K.1
Li, P.-E.2
Scholz, M.B.3
-
35
-
-
84857521888
-
Artificial functional difference between microbial communities caused by length difference of sequencing reads
-
Zhang Q, Ye Y, Doak TG. Artificial functional difference between microbial communities caused by length difference of sequencing reads. Biocomputing 2012;259-70
-
(2012)
Biocomputing
, pp. 259-270
-
-
Zhang, Q.1
Ye, Y.2
Doak, T.G.3
-
36
-
-
84969172659
-
Improved metagenome assemblies and taxonomic binning using longread circular consensus sequence data
-
Frank JA, Pan Y, Tooming-Klunderud A et al. Improved metagenome assemblies and taxonomic binning using longread circular consensus sequence data. Sci Rep 2016:6:25373
-
(2016)
Sci Rep
, vol.6
-
-
Frank, J.A.1
Pan, Y.2
Tooming-Klunderud, A.3
-
37
-
-
84964528782
-
Fast and sensitive mapping of nanopore sequencing reads with GraphMap
-
Sovíc I, Šikíc M, Wilm A et al. Fast and sensitive mapping of nanopore sequencing reads with GraphMap. Nat Comm 2016;11307
-
(2016)
Nat Comm
-
-
Sovíc, I.1
Šikíc, M.2
Wilm, A.3
-
38
-
-
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 Bioinfo 2012;13:238
-
(2012)
BMC Bioinfo
, vol.13
, pp. 238
-
-
Chaisson, M.J.1
Tesler, G.2
-
39
-
-
0019418722
-
Note: Pseudomonas maltophilia sp. nov., nom. rev
-
Hugh R. Note: Pseudomonas maltophilia sp. nov., nom. rev. Int J System Evol Microbiol 1981;31:195
-
(1981)
Int J System Evol Microbiol
, vol.31
, pp. 195
-
-
Hugh, R.1
-
40
-
-
40249095175
-
Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology
-
Binga EK, Lasken RS, Neufeld JD. Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology. ISME J 2008;2: 233-41
-
(2008)
ISME J
, vol.2
, pp. 233-241
-
-
Binga, E.K.1
Lasken, R.S.2
Neufeld, J.D.3
-
41
-
-
34247489656
-
Mechanism of chimera formation during the multiple displacement amplification reaction
-
Lasken RS, Stockwell TB. Mechanism of chimera formation during the multiple displacement amplification reaction. BMC Biotechnol 2007;7:19
-
(2007)
BMC Biotechnol
, vol.7
, pp. 19
-
-
Lasken, R.S.1
Stockwell, T.B.2
-
42
-
-
85007313404
-
INC-Seq: accurate single molecule reads using nanopore sequencing
-
Li C, Chng KR, Boey EJH et al. INC-Seq: accurate single molecule reads using nanopore sequencing. GigaScience 2016;5:34
-
(2016)
GigaScience
, vol.5
, pp. 34
-
-
Li, C.1
Chng, K.R.2
Boey, E.J.H.3
-
43
-
-
85006184217
-
Species-level resolution of 16S rRNA gene amplicons sequenced through the MinIONTM portable nanopore sequencer
-
Benítez-Paez A, Portune KJ, Sanz Y. Species-level resolution of 16S rRNA gene amplicons sequenced through the MinIONTM portable nanopore sequencer. GigaScience 2016;5:4
-
(2016)
GigaScience
, vol.5
, pp. 4
-
-
Benítez-Paez, A.1
Portune, K.J.2
Sanz, Y.3
-
44
-
-
84946557268
-
Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome
-
Goodwin S, Gurtowski J, Ethe-Sayers S et al. Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome. Genome Res 2015b;25:1750-6
-
(2015)
Genome Res
, vol.25
, pp. 1750-1756
-
-
Goodwin, S.1
Gurtowski, J.2
Ethe-Sayers, S.3
-
45
-
-
84936764311
-
Scaffolding of a bacterial genome using MinION nanopore sequencing
-
Karlsson E, Lärkeryd A, Sj ödin A et al. Scaffolding of a bacterial genome using MinION nanopore sequencing. Scientif Rep 2015;5:11996
-
(2015)
Scientif Rep
, vol.5
-
-
Karlsson, E.1
Lärkeryd, A.2
Sjödin, A.3
-
47
-
-
0026794640
-
The bacteriophage phi 29 DNA polymerase, a proofreading enzyme
-
Garmendia C, Bernad A, Esteban JA et al. The bacteriophage phi 29 DNA polymerase, a proofreading enzyme. J Biol Chem 1992;267:2594-9
-
(1992)
J Biol Chem
, vol.267
, pp. 2594-2599
-
-
Garmendia, C.1
Bernad, A.2
Esteban, J.A.3
-
48
-
-
84970952281
-
MinION Analysis and Reference Consortium: Phase 1 data release and analysis
-
Ip CLC, Loose M, Tyson JR et al. MinION Analysis and Reference Consortium: Phase 1 data release and analysis. F1000Research 2015;4:1075
-
(2015)
F1000Research
, vol.4
, pp. 1075
-
-
Ip, C.L.C.1
Loose, M.2
Tyson, J.R.3
-
49
-
-
0036226603
-
BLAT-the BLAST-like alignment tool
-
Kent WJ. BLAT-the BLAST-like alignment tool. Genome Res 2002;12:656-64
-
(2002)
Genome Res
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
-
50
-
-
79958265126
-
Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end Illumina reads
-
Bartram AK, Lynch MD, Stearns JC et al. Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end Illumina reads. Appl Environ Micro 2011;77:3846-52
-
(2011)
Appl Environ Micro
, vol.77
, pp. 3846-3852
-
-
Bartram, A.K.1
Lynch, M.D.2
Stearns, J.C.3
|