메뉴 건너뛰기




Volumn 18, Issue 1, 2017, Pages

Correction to: Comprehensive benchmarking and ensemble approaches for metagenomic classifiers (Genome Biology (2017) 18 (182) DOI: 10.1186/s13059-017-1299-7);Comprehensive benchmarking and ensemble approaches for metagenomic classifiers

(20)  McIntyre, Alexa B R a,b,c   Ounit, Rachid d   Afshinnekoo, Ebrahim b,c,e   Prill, Robert J f   Hénaff, Elizabeth b,c   Alexander, Noah b,c   Minot, Samuel S g   Danko, David a,b,c   Foox, Jonathan b,c   Ahsanuddin, Sofia b,c   Tighe, Scott h   Hasan, Nur A i,j   Subramanian, Poorani i   Moffat, Kelly i   Levy, Shawn k   Lonardi, Stefano d   Greenfield, Nick g   Colwell, Rita R i,l   Rosen, Gail L m   Mason, Christopher E b,c,n  


Author keywords

Classification; Comparison; Ensemble methods; Meta classification; Metagenomics; Pathogen detection; Shotgun sequencing; Taxonomy

Indexed keywords

BENCHMARKING; CLASSIFIER; CONTROLLED STUDY; EXPERIMENTAL DESIGN; FALSE POSITIVE RESULT; FILTRATION; GENUS; METAGENOMICS; MICROORGANISM DETECTION; RECALL; SIMULATION; CONTIG MAPPING; DNA BARCODING; DNA SEQUENCE; HUMAN; METAGENOME; MICROFLORA; PHYLOGENY; PROCEDURES; SOFTWARE; STANDARDS;

EID: 85029756134     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/s13059-019-1687-2     Document Type: Erratum
Times cited : (232)

References (72)
  • 1
    • 84866549438 scopus 로고    scopus 로고
    • Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment
    • Morgan XC, Tickle TL, Sokol H, Gevers D, Devaney KL, Ward DV, et al. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol. 2012;13:R79.
    • (2012) Genome Biol , vol.13 , pp. R79
    • Morgan, X.C.1    Tickle, T.L.2    Sokol, H.3    Gevers, D.4    Devaney, K.L.5    Ward, D.V.6
  • 2
    • 85018271203 scopus 로고    scopus 로고
    • Genomic methods and microbiological technologies for profiling novel and extreme environments for the Extreme Microbiome Project (XMP)
    • Tighe S, Afshinnekoo A, Rock TM, McGrath K, Alexander N. Genomic methods and microbiological technologies for profiling novel and extreme environments for the Extreme Microbiome Project (XMP). J Biomol Tech. 2017;28(2):93.
    • (2017) J Biomol Tech , vol.28 , Issue.2 , pp. 93
    • Tighe, S.1    Afshinnekoo, A.2    Rock, T.M.3    McGrath, K.4    Alexander, N.5
  • 3
    • 0035000085 scopus 로고    scopus 로고
    • Climate variability and change in the United States: potential impacts on water-and foodborne diseases caused by microbiologic agents
    • Rose JB, Epstein PR, Lipp EK, Sherman BH, Bernard SM, Patz JA. Climate variability and change in the United States: potential impacts on water-and foodborne diseases caused by microbiologic agents. Environ Health Perspect. 2001;109:211.
    • (2001) Environ Health Perspect , vol.109 , pp. 211
    • Rose, J.B.1    Epstein, P.R.2    Lipp, E.K.3    Sherman, B.H.4    Bernard, S.M.5    Patz, J.A.6
  • 5
    • 77953050946 scopus 로고    scopus 로고
    • A catalog of reference genomes from the human microbiome
    • The Human Microbiome Jumpstart Reference Strains Consortium, Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, et al. A catalog of reference genomes from the human microbiome. Science. 2010;328:994-9.
    • (2010) Science , vol.328 , pp. 994-999
    • Nelson, K.E.1    Weinstock, G.M.2    Highlander, S.K.3    Worley, K.C.4    Creasy, H.H.5
  • 6
    • 84906829581 scopus 로고    scopus 로고
    • The Earth Microbiome project: successes and aspirations
    • Gilbert JA, Jansson JK, Knight R. The Earth Microbiome project: successes and aspirations. BMC Biol. 2014;12:1.
    • (2014) BMC Biol , vol.12 , pp. 1
    • Gilbert, J.A.1    Jansson, J.K.2    Knight, R.3
  • 8
    • 84936070895 scopus 로고    scopus 로고
    • The distribution, diversity, and importance of 16S rRNA gene introns in the order Thermoproteales
    • Jay ZJ, Inskeep WP. The distribution, diversity, and importance of 16S rRNA gene introns in the order Thermoproteales. Biolgy Direct. 2015;10:35.
    • (2015) Biolgy Direct , vol.10 , pp. 35
    • Jay, Z.J.1    Inskeep, W.P.2
  • 9
    • 85029763463 scopus 로고    scopus 로고
    • Unexplored archaeal diversity in the great ape gut microbiome
    • Raymann K, Moeller AH, Goodman AL, Ochman H. Unexplored archaeal diversity in the great ape gut microbiome. mSphere. 2017;2:e00026-17.
    • (2017) mSphere , vol.2
    • Raymann, K.1    Moeller, A.H.2    Goodman, A.L.3    Ochman, H.4
  • 10
  • 11
    • 84995814400 scopus 로고    scopus 로고
    • Marker genes that are less conserved in their sequences are useful for predicting genome-wide similarity levels between closely related prokaryotic strains
    • Lan Y, Rosen G, Hershberg R. Marker genes that are less conserved in their sequences are useful for predicting genome-wide similarity levels between closely related prokaryotic strains. Microbiome. 2016;4:1-13.
    • (2016) Microbiome , vol.4 , pp. 1-13
    • Lan, Y.1    Rosen, G.2    Hershberg, R.3
  • 12
    • 85026644382 scopus 로고    scopus 로고
    • Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing
    • Tessler T, Neumann JS, Afshinnekoo E, Pineda M, Hersch R, Velho LF, et al. Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing. Sci Rep. 2017;7:6589.
    • (2017) Sci Rep , vol.7 , pp. 6589
    • Tessler, T.1    Neumann, J.S.2    Afshinnekoo, E.3    Pineda, M.4    Hersch, R.5    Velho, L.F.6
  • 13
    • 84954556725 scopus 로고    scopus 로고
    • An evaluation of the accuracy and speed of metagenome analysis tools
    • Lindgreen S, Adair KL, Gardner PP. An evaluation of the accuracy and speed of metagenome analysis tools. Sci Rep. 2016;6:19233.
    • (2016) Sci Rep , vol.6 , pp. 19233
    • Lindgreen, S.1    Adair, K.L.2    Gardner, P.P.3
  • 14
    • 84929174408 scopus 로고    scopus 로고
    • CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers
    • Ounit R, Wanamaker S, Close TJ, Lonardi S. CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers. BMC Genomics. 2015;16:236.
    • (2015) BMC Genomics , vol.16 , pp. 236
    • Ounit, R.1    Wanamaker, S.2    Close, T.J.3    Lonardi, S.4
  • 15
  • 17
  • 21
    • 84946412300 scopus 로고    scopus 로고
    • Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities
    • Peabody MA, Van Rossum T, Lo R, Brinkman FS. Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities. BMC Bioinformatics. 2015;16:1.
    • (2015) BMC Bioinformatics , vol.16 , pp. 1
    • Peabody, M.A.1    Rossum, T.2    Lo, R.3    Brinkman, F.S.4
  • 23
    • 84952009484 scopus 로고    scopus 로고
    • Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis
    • Bradley P, Gordon NC, Walker TM, Dunn L, Heys S, Huang B, et al. Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis. Nat Commun. 2015;6:10063.
    • (2015) Nat Commun , vol.6 , pp. 10063
    • Bradley, P.1    Gordon, N.C.2    Walker, T.M.3    Dunn, L.4    Heys, S.5    Huang, B.6
  • 24
    • 84949675208 scopus 로고    scopus 로고
    • The microbiome quality control project: baseline study design and future directions
    • Sinha R, Abnet CC, White O, Knight R, Huttenhower C. The microbiome quality control project: baseline study design and future directions. Genome Biol. 2015;16:1.
    • (2015) Genome Biol , vol.16 , pp. 1
    • Sinha, R.1    Abnet, C.C.2    White, O.3    Knight, R.4    Huttenhower, C.5
  • 25
    • 85029770214 scopus 로고    scopus 로고
    • accessed 17 Jan 2017.
    • IMMSA. Mission Statement NIST. 2016. https://www.nist.gov/mml/bbd/immsa-mission-statement , accessed 17 Jan 2017.
    • (2016)
  • 26
    • 84995783733 scopus 로고    scopus 로고
    • The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report
    • MetaSUB International Consortium. The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report. Microbiome. 2016;4:1-14.
    • (2016) Microbiome , vol.4 , pp. 1-14
  • 27
    • 85029757769 scopus 로고    scopus 로고
    • accessed 10 Feb 2016
    • CAMI - Critical Assessment of Metagenomic Interpretation. http://www.cami-challenge.org (accessed 10 Feb 2016].
  • 28
    • 85018548144 scopus 로고    scopus 로고
    • Critical Assessment of Metagenome Interpretation - a benchmark of computational metagenomics software.
    • bioRxiv.
    • Sczyrba A, Hofmann P, Belmann P, Koslicki D, Janssen S, Droege J, et al. Critical Assessment of Metagenome Interpretation - a benchmark of computational metagenomics software. bioRxiv. 2017;99127.
    • (2017) , pp. 99127
    • Sczyrba, A.1    Hofmann, P.2    Belmann, P.3    Koslicki, D.4    Janssen, S.5    Droege, J.6
  • 29
    • 85005983418 scopus 로고    scopus 로고
    • Evaluating and optimizing the performance of software commonly used for the taxonomic classification of DNA metabarcoding sequence data
    • Richardson RT, Bengtsson-Palme J, Johnson RM. Evaluating and optimizing the performance of software commonly used for the taxonomic classification of DNA metabarcoding sequence data. Mol Ecol Resour. 2017;17:760-9.
    • (2017) Mol Ecol Resour , vol.17 , pp. 760-769
    • Richardson, R.T.1    Bengtsson-Palme, J.2    Johnson, R.M.3
  • 30
    • 84860672197 scopus 로고    scopus 로고
    • A comparative evaluation of sequence classification programs
    • Bazinet AL, Cummings MP. A comparative evaluation of sequence classification programs. BMC Bioinformatics. 2012;13:1.
    • (2012) BMC Bioinformatics , vol.13 , pp. 1
    • Bazinet, A.L.1    Cummings, M.P.2
  • 32
    • 85029748410 scopus 로고    scopus 로고
    • Détermination de sondes oligonucléotidiques pour l'exploration à haut débit de la diversité taxonomique et fonctionnelle d'environnements complexes.
    • Parisot N. Détermination de sondes oligonucléotidiques pour l'exploration à haut débit de la diversité taxonomique et fonctionnelle d'environnements complexes. 2014. https://tel.archives-ouvertes.fr/tel-01086970/.
    • (2014)
    • Parisot, N.1
  • 34
    • 84931267206 scopus 로고    scopus 로고
    • Accurate read-based metagenome characterization using a hierarchical suite of unique signatures
    • Freitas TAK, Li P-E, Scholz MB, Chain PS. Accurate read-based metagenome characterization using a hierarchical suite of unique signatures. Nucleic Acids Res. 2015;43(10):e69.
    • (2015) Nucleic Acids Res , vol.43 , Issue.10
    • Freitas, T.A.K.1    Li, P.-E.2    Scholz, M.B.3    Chain, P.S.4
  • 37
    • 84994123816 scopus 로고    scopus 로고
    • Higher classification sensitivity of short metagenomic reads with CLARK-S
    • Ounit R, Lonardi S. Higher classification sensitivity of short metagenomic reads with CLARK-S. Bioinformatics. 2016;32:3823-5.
    • (2016) Bioinformatics , vol.32 , pp. 3823-3825
    • Ounit, R.1    Lonardi, S.2
  • 38
    • 84925021592 scopus 로고    scopus 로고
    • Fast and sensitive protein alignment using DIAMOND
    • Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12:59-60.
    • (2015) Nat Methods , vol.12 , pp. 59-60
    • Buchfink, B.1    Xie, C.2    Huson, D.H.3
  • 39
    • 84899090573 scopus 로고    scopus 로고
    • 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
  • 43
    • 78650549608 scopus 로고    scopus 로고
    • NBC: the Naive Bayes Classification tool webserver for taxonomic classification of metagenomic reads
    • Rosen GL, Reichenberger ER, Rosenfeld AM. NBC: the Naive Bayes Classification tool webserver for taxonomic classification of metagenomic reads. Bioinformatics. 2011;27:127-9.
    • (2011) Bioinformatics , vol.27 , pp. 127-129
    • Rosen, G.L.1    Reichenberger, E.R.2    Rosenfeld, A.M.3
  • 45
  • 46
    • 84920644670 scopus 로고    scopus 로고
    • Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
    • Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO, Moffatt MF, et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 2014;12:87.
    • (2014) BMC Biol , vol.12 , pp. 87
    • Salter, S.J.1    Cox, M.J.2    Turek, E.M.3    Calus, S.T.4    Cookson, W.O.5    Moffatt, M.F.6
  • 48
    • 84882651790 scopus 로고    scopus 로고
    • Quikr: a method for rapid reconstruction of bacterial communities via compressive sensing
    • Koslicki D, Foucart S, Rosen G. Quikr: a method for rapid reconstruction of bacterial communities via compressive sensing. Bioinformatics. 2013;29:2096-102.
    • (2013) Bioinformatics , vol.29 , pp. 2096-2102
    • Koslicki, D.1    Foucart, S.2    Rosen, G.3
  • 49
    • 84946819260 scopus 로고    scopus 로고
    • Comparative metagenomics reveals impact of contaminants on groundwater microbiomes
    • Hemme CL, Tu Q, Qin Y, Gao W, Deng Y, Nostrand JDV, et al. Comparative metagenomics reveals impact of contaminants on groundwater microbiomes. Front Microbiol. 2015;6:1205.
    • (2015) Front Microbiol , vol.6 , pp. 1205
    • Hemme, C.L.1    Tu, Q.2    Qin, Y.3    Gao, W.4    Deng, Y.5    Nostrand, J.D.V.6
  • 50
    • 84924046414 scopus 로고    scopus 로고
    • Comparative metagenomics of biogas-producing microbial communities from production-scale biogas plants operating under wet or dry fermentation conditions
    • Stolze Y, Zakrzewski M, Maus I, Eikmeyer F, Jaenicke S, Rottmann N, et al. Comparative metagenomics of biogas-producing microbial communities from production-scale biogas plants operating under wet or dry fermentation conditions. Biotechnol Biofuels. 2015;8:14.
    • (2015) Biotechnol Biofuels , vol.8 , pp. 14
    • Stolze, Y.1    Zakrzewski, M.2    Maus, I.3    Eikmeyer, F.4    Jaenicke, S.5    Rottmann, N.6
  • 52
    • 84919870992 scopus 로고    scopus 로고
    • Viral metagenomics reveal blooms of anelloviruses in the respiratory tract of lung transplant recipients
    • Young JC, Chehoud C, Bittinger K, Bailey A, Diamond JM, Cantu E, et al. Viral metagenomics reveal blooms of anelloviruses in the respiratory tract of lung transplant recipients. Am J Transplant. 2015;15:200-9.
    • (2015) Am J Transplant , vol.15 , pp. 200-209
    • Young, J.C.1    Chehoud, C.2    Bittinger, K.3    Bailey, A.4    Diamond, J.M.5    Cantu, E.6
  • 53
    • 85010902656 scopus 로고    scopus 로고
    • Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery
    • Chu DM, Ma J, Prince AL, Antony KM, Seferovic MD, Aagaard KM. Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery. Nat Med. 2017;23:314-26.
    • (2017) Nat Med , vol.23 , pp. 314-326
    • Chu, D.M.1    Ma, J.2    Prince, A.L.3    Antony, K.M.4    Seferovic, M.D.5    Aagaard, K.M.6
  • 54
    • 0034069482 scopus 로고    scopus 로고
    • Strain, clone and species: comments on three basic concepts of bacteriology
    • Dijkshoorn L, Ursing B, Ursing J. Strain, clone and species: comments on three basic concepts of bacteriology. J Med Microbiol. 2000;49:397-401.
    • (2000) J Med Microbiol , vol.49 , pp. 397-401
    • Dijkshoorn, L.1    Ursing, B.2    Ursing, J.3
  • 55
    • 84961392884 scopus 로고    scopus 로고
    • Strain-level microbial epidemiology and population genomics from shotgun metagenomics
    • Scholz M, Ward DV, Pasolli E, Tolio T, Zolfo M, Asnicar F, et al. Strain-level microbial epidemiology and population genomics from shotgun metagenomics. Nat Methods. 2016;13:435-8.
    • (2016) Nat Methods , vol.13 , pp. 435-438
    • Scholz, M.1    Ward, D.V.2    Pasolli, E.3    Tolio, T.4    Zolfo, M.5    Asnicar, F.6
  • 57
    • 84969749326 scopus 로고    scopus 로고
    • Scaling laws predict global microbial diversity
    • Locey KJ, Lennon JT. Scaling laws predict global microbial diversity. Proc Natl Acad Sci. 2016;113:5970-5.
    • (2016) Proc Natl Acad Sci , vol.113 , pp. 5970-5975
    • Locey, K.J.1    Lennon, J.T.2
  • 60
    • 84988548188 scopus 로고    scopus 로고
    • Urban transit system microbial communities differ by surface type and interaction with humans and the environment
    • Hsu T, Joice R, Vallarino J, Abu-Ali G, Hartmann EM, Shafquat A, et al. Urban transit system microbial communities differ by surface type and interaction with humans and the environment. mSystems. 2016;1:e00018-16.
    • (2016) mSystems , vol.1
    • Hsu, T.1    Joice, R.2    Vallarino, J.3    Abu-Ali, G.4    Hartmann, E.M.5    Shafquat, A.6
  • 61
    • 77950251400 scopus 로고    scopus 로고
    • A human gut microbial gene catalogue established by metagenomic sequencing
    • Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464:59-65.
    • (2010) Nature , vol.464 , pp. 59-65
    • Qin, J.1    Li, R.2    Raes, J.3    Arumugam, M.4    Burgdorf, K.S.5    Manichanh, C.6
  • 63
    • 84942879480 scopus 로고    scopus 로고
    • A vision for ubiquitous sequencing
    • Erlich Y. A vision for ubiquitous sequencing. Genome Res. 2015;25:1411-6.
    • (2015) Genome Res , vol.25 , pp. 1411-1416
    • Erlich, Y.1
  • 64
    • 84968860982 scopus 로고    scopus 로고
    • Using mobile sequencers in an academic classroom
    • Zaaijer S, Erlich Y. Using mobile sequencers in an academic classroom. Elife. 2016;5:e14258.
    • (2016) Elife , vol.5
    • Zaaijer, S.1    Erlich, Y.2
  • 65
    • 84991702475 scopus 로고    scopus 로고
    • WEVOTE: weighted voting taxonomic identification method of microbial sequences
    • Metwally A, Dai Y, Finn P, Perkins D. WEVOTE: weighted voting taxonomic identification method of microbial sequences. PLoS One. 2016;11:e0163527.
    • (2016) PLoS One , vol.11
    • Metwally, A.1    Dai, Y.2    Finn, P.3    Perkins, D.4
  • 66
    • 84857145150 scopus 로고    scopus 로고
    • ART: a next-generation sequencing read simulator
    • Huang W, Li L, Myers JR, Marth GT. ART: a next-generation sequencing read simulator. Bioinformatics. 2012;28:593-4.
    • (2012) Bioinformatics , vol.28 , pp. 593-594
    • Huang, W.1    Li, L.2    Myers, J.R.3    Marth, G.T.4
  • 67
    • 84947788619 scopus 로고    scopus 로고
    • Higher classification accuracy of short metagenomic reads by discriminative spaced k-mers.
    • In: Pop M, Touzet H, editors. Berlin, Heidelberg: Springer
    • Ounit R, Lonardi S. Higher classification accuracy of short metagenomic reads by discriminative spaced k-mers. In: Pop M, Touzet H, editors. Algorithms in bioinformatics. WABI 2015. Lecture notes in computer science, vol. 9289. Berlin, Heidelberg: Springer; 2015. p. 286-95.
    • (2015) Algorithms in bioinformatics. WABI 2015. Lecture notes in computer science , vol.9289 , pp. 286-295
    • Ounit, R.1    Lonardi, S.2
  • 68
    • 84856363643 scopus 로고    scopus 로고
    • NBC update: The addition of viral and fungal databases to the Naïve Bayes classification tool
    • Rosen GL, Lim TY. NBC update: The addition of viral and fungal databases to the Naïve Bayes classification tool. BMC Res Notes. 2012;5:1.
    • (2012) BMC Res Notes , vol.5 , pp. 1
    • Rosen, G.L.1    Lim, T.Y.2
  • 69
    • 84886486483 scopus 로고    scopus 로고
    • Area under the precision-recall curve: point estimates and confidence intervals.
    • In: Blockeel H, Kersting K, Nijssen S, Železný F, editors. Berlin, Heidelberg: Springer
    • Boyd K, Eng KH, Page CD. Area under the precision-recall curve: point estimates and confidence intervals. In: Blockeel H, Kersting K, Nijssen S, Železný F, editors. Machine learning and knowledge discovery in databases. ECML PKDD 2013. Lecture notes in computer science, vol. 8190. Berlin, Heidelberg: Springer; 2013. p. 451-66.
    • (2013) Machine learning and knowledge discovery in databases. ECML PKDD 2013. Lecture notes in computer science , vol.8190 , pp. 451-466
    • Boyd, K.1    Eng, K.H.2    Page, C.D.3
  • 72
    • 85017132229 scopus 로고    scopus 로고
    • Microbial community patterns associated with automated teller machine keypads in New York City
    • Bik HM, Maritz JM, Luong A, Shin H, Dominguez-Bello MG, Carlton JM. Microbial community patterns associated with automated teller machine keypads in New York City. mSphere. 2016;1:e00226-16.
    • (2016) mSphere , vol.1
    • Bik, H.M.1    Maritz, J.M.2    Luong, A.3    Shin, H.4    Dominguez-Bello, M.G.5    Carlton, J.M.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.