-
1
-
-
85006986456
-
Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard—a report from a May 23–24, 2016 workshop (Gothenburg, Sweden)
-
Abarenkov K, Adams RI, Laszlo I et al. (2016) Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard—a report from a May 23–24, 2016 workshop (Gothenburg, Sweden). MycoKeys, 16, 1.
-
(2016)
MycoKeys
, vol.16
, pp. 1
-
-
Abarenkov, K.1
Adams, R.I.2
Laszlo, I.3
-
2
-
-
84860672197
-
A comparative evaluation of sequence classification programs
-
Bazinet AL, Cummings MP (2012) A comparative evaluation of sequence classification programs. BMC Bioinformatics, 13, 1–13.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 1-13
-
-
Bazinet, A.L.1
Cummings, M.P.2
-
3
-
-
84986562973
-
Pollen DNA barcoding: current applications and future prospects
-
Bell KL, Brosi BJ, de Vere N et al. (2016) Pollen DNA barcoding: current applications and future prospects. Genome, 59, 1–12.
-
(2016)
Genome
, vol.59
, pp. 1-12
-
-
Bell, K.L.1
Brosi, B.J.2
de Vere, N.3
-
4
-
-
84943580979
-
Metaxa2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data
-
Bengtsson-Palme J, Hartmann M, Eriksson KM et al. (2015) Metaxa2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data. Molecular Ecology Resources, 15, 1403–1414.
-
(2015)
Molecular Ecology Resources
, vol.15
, pp. 1403-1414
-
-
Bengtsson-Palme, J.1
Hartmann, M.2
Eriksson, K.M.3
-
5
-
-
13444304389
-
GenBank
-
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL (2005) GenBank. Nucleic Acids Research, 33, D34–D38.
-
(2005)
Nucleic Acids Research
, vol.33
, pp. D34-D38
-
-
Benson, D.A.1
Karsch-Mizrachi, I.2
Lipman, D.J.3
Ostell, J.4
Wheeler, D.L.5
-
6
-
-
84955199272
-
Obitools: a unix-inspired software package for DNA metabarcoding
-
Boyer F, Mercier C, Bonin A, Le Bras Y, Taberlet P, Coissac E (2016) Obitools: a unix-inspired software package for DNA metabarcoding. Molecular Ecology Resources, 16, 176–182.
-
(2016)
Molecular Ecology Resources
, vol.16
, pp. 176-182
-
-
Boyer, F.1
Mercier, C.2
Bonin, A.3
Le Bras, Y.4
Taberlet, P.5
Coissac, E.6
-
7
-
-
69549135124
-
Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models
-
Brady A, Salzberg SL (2009) Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Nature Methods, 6, 673–676.
-
(2009)
Nature Methods
, vol.6
, pp. 673-676
-
-
Brady, A.1
Salzberg, S.L.2
-
8
-
-
84956958206
-
Taxonomic characterization of honey bee (Apis mellifera) pollen foraging based on non-overlapping paired-end sequencing of nuclear ribosomal loci
-
Cornman RS, Otto CRV, Iwanowicz D, Pettis JS (2015) Taxonomic characterization of honey bee (Apis mellifera) pollen foraging based on non-overlapping paired-end sequencing of nuclear ribosomal loci. PLoS One, 10, e0145365.
-
(2015)
PLoS One
, vol.10
-
-
Cornman, R.S.1
Otto, C.R.V.2
Iwanowicz, D.3
Pettis, J.S.4
-
9
-
-
84947092950
-
Climatic warming and the future of bison as grazers
-
Craine JM, Towne EG, Miller M, Fierer N (2015) Climatic warming and the future of bison as grazers. Scientific Reports, 5, 16738.
-
(2015)
Scientific Reports
, vol.5
, pp. 16738
-
-
Craine, J.M.1
Towne, E.G.2
Miller, M.3
Fierer, N.4
-
10
-
-
77957244650
-
Search and clustering orders of magnitude faster than BLAST
-
Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26, 2460–2461.
-
(2010)
Bioinformatics
, vol.26
, pp. 2460-2461
-
-
Edgar, R.C.1
-
12
-
-
85020608174
-
-
(accessed 6 January 2016)
-
Edgar RC (2015b) Validating taxonomy classifiers. Available at: www.drive5.com/usearch/manual/taxonomy_validation.html (accessed 6 January 2016).
-
(2015)
Validating taxonomy classifiers
-
-
Edgar, R.C.1
-
13
-
-
85020608177
-
-
(accessed 6 January 2016)
-
Edgar RC (2015c) UTAX algorithm. Available at: http://www.drive5.com/usearch/manual/utax_algo.html (accessed 6 January 2016).
-
(2015)
UTAX algorithm
-
-
Edgar, R.C.1
-
15
-
-
84947252666
-
Deep-sea, deep-sequencing: metabarcoding extracellular DNA from sediments of marine canyons
-
Guardiola M, Uriz MJ, Taberlet P, Coissac E, Wangensteen OW, Turon X (2015) Deep-sea, deep-sequencing: metabarcoding extracellular DNA from sediments of marine canyons. PLoS One, 10, e0139633.
-
(2015)
PLoS One
, vol.10
-
-
Guardiola, M.1
Uriz, M.J.2
Taberlet, P.3
Coissac, E.4
Wangensteen, O.W.5
Turon, X.6
-
16
-
-
84943229982
-
Using DNA metabarcoding to identify the floral composition of honey: a new tool for investigating honey bee foraging preferences
-
Hawkins J, de Vere N, Griffith A et al. (2015) Using DNA metabarcoding to identify the floral composition of honey: a new tool for investigating honey bee foraging preferences. PLoS One, 10, e0134735.
-
(2015)
PLoS One
, vol.10
-
-
Hawkins, J.1
de Vere, N.2
Griffith, A.3
-
17
-
-
0037423543
-
Biological identifications through DNA barcodes
-
Hebert PDN, Cywinska A, Ball SL, deWaard JR (2003) Biological identifications through DNA barcodes. Proceedings of the Royal Society of London. Series B, Biological Sciences, 270, 313–321.
-
(2003)
Proceedings of the Royal Society of London. Series B, Biological Sciences
, vol.270
, pp. 313-321
-
-
Hebert, P.D.N.1
Cywinska, A.2
Ball, S.L.3
deWaard, J.R.4
-
18
-
-
6944255373
-
Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator
-
Hebert PDN, Penton EH, Burns JM, Janzen DH, Hallwachs W (2004) Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proceedings of the National Academy of Sciences, 101, 14812–14817.
-
(2004)
Proceedings of the National Academy of Sciences
, vol.101
, pp. 14812-14817
-
-
Hebert, P.D.N.1
Penton, E.H.2
Burns, J.M.3
Janzen, D.H.4
Hallwachs, W.5
-
19
-
-
80052549504
-
Integrative analysis of environmental sequences using MEGAN 4
-
Huson DH, Mitra S, Ruscheweyh H-J, Weber N, Schuster SC (2011) Integrative analysis of environmental sequences using MEGAN 4. Genome Research, 21, 1552–1560.
-
(2011)
Genome Research
, vol.21
, pp. 1552-1560
-
-
Huson, D.H.1
Mitra, S.2
Ruscheweyh, H.-J.3
Weber, N.4
Schuster, S.C.5
-
20
-
-
84924247676
-
Evaluating multiplexed next generation sequencing as a method in palynology for mixed pollen samples
-
Keller A, Danner N, Grimmer G et al. (2015) Evaluating multiplexed next generation sequencing as a method in palynology for mixed pollen samples. Plant Biology, 17, 558–566.
-
(2015)
Plant Biology
, vol.17
, pp. 558-566
-
-
Keller, A.1
Danner, N.2
Grimmer, G.3
-
21
-
-
84923096062
-
Efficient and sensitive identification and quantification of airborne pollen using next generation DNA sequencing
-
Kraaijeveld K, De Weger LA, Garcia MV et al. (2015) Efficient and sensitive identification and quantification of airborne pollen using next generation DNA sequencing. Molecular Ecology Resources, 15, 8–16.
-
(2015)
Molecular Ecology Resources
, vol.15
, pp. 8-16
-
-
Kraaijeveld, K.1
De Weger, L.A.2
Garcia, M.V.3
-
22
-
-
42449162998
-
Phylogenetic classification of short environmental DNA fragments
-
Krause L, Diaz NN, Goesmann A et al. (2008) Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Research, 36, 2230–2239.
-
(2008)
Nucleic Acids Research
, vol.36
, pp. 2230-2239
-
-
Krause, L.1
Diaz, N.N.2
Goesmann, A.3
-
23
-
-
84949908582
-
Statistical approaches to account for false-positive errors in environmental DNA samples
-
Lahoz-Monfort JJ, Guillera-Arroita G, Tingley R (2016) Statistical approaches to account for false-positive errors in environmental DNA samples. Molecular Ecology Resources, 16, 673–685.
-
(2016)
Molecular Ecology Resources
, vol.16
, pp. 673-685
-
-
Lahoz-Monfort, J.J.1
Guillera-Arroita, G.2
Tingley, R.3
-
24
-
-
84869030635
-
CREST—classification resources for environmental sequence tags
-
Lanzén A, Jørgensen SL, Huson DH et al. (2012) CREST—classification resources for environmental sequence tags. PLoS One, 7, e49334.
-
(2012)
PLoS One
, vol.7
-
-
Lanzén, A.1
Jørgensen, S.L.2
Huson, D.H.3
-
25
-
-
84963701152
-
Characterization of pollen and bacterial community composition in brood provisions of a small carpenter bee
-
McFrederick QS, Rehan SM (2016) Characterization of pollen and bacterial community composition in brood provisions of a small carpenter bee. Molecular Ecology, 25, 2302–2311.
-
(2016)
Molecular Ecology
, vol.25
, pp. 2302-2311
-
-
McFrederick, Q.S.1
Rehan, S.M.2
-
26
-
-
53849133826
-
Statistical assignment of DNA sequences using Bayesian phylogenetics
-
Munch K, Boomsma W, Huelsenbeck JP, Willerslev E, Nielsen R (2008) Statistical assignment of DNA sequences using Bayesian phylogenetics. Systematic Biology, 57, 750–757.
-
(2008)
Systematic Biology
, vol.57
, pp. 750-757
-
-
Munch, K.1
Boomsma, W.2
Huelsenbeck, J.P.3
Willerslev, E.4
Nielsen, R.5
-
27
-
-
84916234886
-
Improving ITS sequence data for identification of plant pathogenic fungi
-
Nilsson RH, Hyde KD, Pawłowska J et al. (2014) Improving ITS sequence data for identification of plant pathogenic fungi. Fungal Diversity, 67, 11–19.
-
(2014)
Fungal Diversity
, vol.67
, pp. 11-19
-
-
Nilsson, R.H.1
Hyde, K.D.2
Pawłowska, J.3
-
28
-
-
85020572525
-
-
Columbus, Ohio, USA
-
Ohio Supercomputer Center (1987) Citation. Columbus, Ohio, USA. Available at: http://osc.edu/ark:/19495/f5s1ph73.
-
(1987)
Citation
-
-
-
29
-
-
84946412300
-
Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities
-
Peabody MA, Van Rossum T, Lo R, Brinkman FSL (2015) Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities. BMC Bioinformatics, 16, 363.
-
(2015)
BMC Bioinformatics
, vol.16
, pp. 363
-
-
Peabody, M.A.1
Van Rossum, T.2
Lo, R.3
Brinkman, F.S.L.4
-
30
-
-
84860470994
-
Factors that affect large subunit ribosomal DNA amplicon sequencing studies of fungal communities: classification method, primer choice, and error
-
Porter TM, Golding GB (2012) Factors that affect large subunit ribosomal DNA amplicon sequencing studies of fungal communities: classification method, primer choice, and error. PLoS One, 7, e35749.
-
(2012)
PLoS One
, vol.7
-
-
Porter, T.M.1
Golding, G.B.2
-
31
-
-
68149089830
-
Community analysis of chronic wound bacteria using 16S rRNA gene-based pyrosequencing: impact of diabetes and antibiotics on chronic wound microbiota
-
Price LB, Liu CM, Melendez JH et al. (2009) Community analysis of chronic wound bacteria using 16S rRNA gene-based pyrosequencing: impact of diabetes and antibiotics on chronic wound microbiota. PLoS One, 4, e6462.
-
(2009)
PLoS One
, vol.4
-
-
Price, L.B.1
Liu, C.M.2
Melendez, J.H.3
-
32
-
-
84875104888
-
A DNA metabarcoding study of a primate dietary diversity and plasticity across its entire fragmented range
-
Quéméré E, Hibert F, Miquel C et al. (2013) A DNA metabarcoding study of a primate dietary diversity and plasticity across its entire fragmented range. PLoS One, 8, e58971.
-
(2013)
PLoS One
, vol.8
-
-
Quéméré, E.1
Hibert, F.2
Miquel, C.3
-
34
-
-
34248149943
-
Bold: the barcode of life data system
-
Ratnasingham S, Hebert PDN (2007) Bold: the barcode of life data system (http://www.barcodinglife.org). Molecular Ecology Notes, 7, 355–364.
-
(2007)
Molecular Ecology Notes
, vol.7
, pp. 355-364
-
-
Ratnasingham, S.1
Hebert, P.D.N.2
-
35
-
-
84946600688
-
Rank-based characterization of pollen assemblages collected by honey bees using a multi-locus metabarcoding approach
-
Richardson RT, Lin C-H, Quijia JQ, Riusech NS, Goodell K, Johnson RM (2015a) Rank-based characterization of pollen assemblages collected by honey bees using a multi-locus metabarcoding approach. Applications in Plant Sciences, 3, 1500043.
-
(2015)
Applications in Plant Sciences
, vol.3
, pp. 1500043
-
-
Richardson, R.T.1
Lin, C.-H.2
Quijia, J.Q.3
Riusech, N.S.4
Goodell, K.5
Johnson, R.M.6
-
36
-
-
84937735841
-
Application of ITS2 metabarcoding to determine the provenance of pollen collected by honey bees in a field-crop dominated agroecosystem
-
Richardson RT, Lin C-H, Quijia JQ, Sponsler BD, Goodell K, Johnson RM (2015b) Application of ITS2 metabarcoding to determine the provenance of pollen collected by honey bees in a field-crop dominated agroecosystem. Applications in Plant Sciences, 3, 1400066.
-
(2015)
Applications in Plant Sciences
, vol.3
, pp. 1400066
-
-
Richardson, R.T.1
Lin, C.-H.2
Quijia, J.Q.3
Sponsler, B.D.4
Goodell, K.5
Johnson, R.M.6
-
37
-
-
84955172656
-
Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes
-
Salazar G, Cornejo-Castillo FM, Borrull E et al. (2015) Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes. Molecular Ecology, 24, 5692–5706.
-
(2015)
Molecular Ecology
, vol.24
, pp. 5692-5706
-
-
Salazar, G.1
Cornejo-Castillo, F.M.2
Borrull, E.3
-
38
-
-
84876532610
-
Database resources of the National Center for Biotechnology Information
-
Sayers EW, Barrett T, Benson DA et al. (2013) Database resources of the National Center for Biotechnology Information. Nucleic Acids Research, 41, D8–D20.
-
(2013)
Nucleic Acids Research
, vol.41
, pp. D8-D20
-
-
Sayers, E.W.1
Barrett, T.2
Benson, D.A.3
-
39
-
-
84860241679
-
Screening mammal biodiversity using DNA from Leeches
-
Schnell IB, Thomsen PF, Wilkinson N et al. (2012) Screening mammal biodiversity using DNA from Leeches. Current Biology, 22, 262–263.
-
(2012)
Current Biology
, vol.22
, pp. 262-263
-
-
Schnell, I.B.1
Thomsen, P.F.2
Wilkinson, N.3
-
40
-
-
84937239051
-
Increased efficiency in identifying mixed pollen samples by meta-barcoding with a dual-indexing approach
-
Sickel W, Ankenbrand MJ, Grimmer G et al. (2015) Increased efficiency in identifying mixed pollen samples by meta-barcoding with a dual-indexing approach. BMC Ecology, 15, 1–9.
-
(2015)
BMC Ecology
, vol.15
, pp. 1-9
-
-
Sickel, W.1
Ankenbrand, M.J.2
Grimmer, G.3
-
41
-
-
84862631902
-
Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences
-
Soergel D, Neelendu Dey AW, Knight R, Brenner SE (2012) Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences. The ISME Journal, 6, 1440–1444.
-
(2012)
The ISME Journal
, vol.6
, pp. 1440-1444
-
-
Soergel, D.1
Neelendu Dey, A.W.2
Knight, R.3
Brenner, S.E.4
-
42
-
-
84859598363
-
Towards next-generation biodiversity assessment using DNA metabarcoding
-
Taberlet P, Coissac E, Pompanon F, Brochmann C, Willerslev E (2012) Towards next-generation biodiversity assessment using DNA metabarcoding. Molecular Ecology, 21, 2045–2050.
-
(2012)
Molecular Ecology
, vol.21
, pp. 2045-2050
-
-
Taberlet, P.1
Coissac, E.2
Pompanon, F.3
Brochmann, C.4
Willerslev, E.5
-
43
-
-
84941808021
-
High-throughput monitoring of wild bee diversity and abundance via mitogenomics
-
Tang M, Hardman CJ, Ji Y et al. (2015) High-throughput monitoring of wild bee diversity and abundance via mitogenomics. Methods in Ecology and Evolution, 6, 1034–1043.
-
(2015)
Methods in Ecology and Evolution
, vol.6
, pp. 1034-1043
-
-
Tang, M.1
Hardman, C.J.2
Ji, Y.3
-
44
-
-
84865580050
-
Detection of a diverse marine fish fauna using environmental DNA from seawater samples
-
Thomsen PF, Kielgast J, Iversen LL, Møller PR, Morten Rasmussen M, Willerslev E (2012) Detection of a diverse marine fish fauna using environmental DNA from seawater samples. PLoS One, 7, e41732.
-
(2012)
PLoS One
, vol.7
-
-
Thomsen, P.F.1
Kielgast, J.2
Iversen, L.L.3
Møller, P.R.4
Morten Rasmussen, M.5
Willerslev, E.6
-
45
-
-
84958280498
-
Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding
-
Valentini A, Taberlet P, Miaud C et al. (2016) Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Molecular Ecology, 25, 929–942.
-
(2016)
Molecular Ecology
, vol.25
, pp. 929-942
-
-
Valentini, A.1
Taberlet, P.2
Miaud, C.3
-
46
-
-
84960888359
-
What you need is what you eat? Prey selection by the bat Myotis daubentonii
-
Vesterinen EJ, Ruokolainen L, Wahlberg N et al. (2016) What you need is what you eat? Prey selection by the bat Myotis daubentonii. Molecular Ecology, 25, 1581–1594.
-
(2016)
Molecular Ecology
, vol.25
, pp. 1581-1594
-
-
Vesterinen, E.J.1
Ruokolainen, L.2
Wahlberg, N.3
-
47
-
-
34548293679
-
Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
-
Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology, 73, 5261–5267.
-
(2007)
Applied and Environmental Microbiology
, vol.73
, pp. 5261-5267
-
-
Wang, Q.1
Garrity, G.M.2
Tiedje, J.M.3
Cole, J.R.4
|