메뉴 건너뛰기




Volumn 7, Issue JUN, 2016, Pages

Identification, recovery, and refinement of hitherto undescribed population-level genomes from the human gastrointestinal tract

Author keywords

Binning; Genome recovery; Metagenome; Reference genomes; Refinement

Indexed keywords

ALPHAPROTEOBACTERIA; CANOPY; CLOSTRIDIALES; GASTROINTESTINAL TRACT; HUMAN; METAGENOME; METAGENOMICS; MICROBIAL COMMUNITY; MOLLICUTES;

EID: 84979978324     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2016.00884     Document Type: Article
Times cited : (8)

References (65)
  • 1
    • 84879678051 scopus 로고    scopus 로고
    • Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes
    • Albertsen, M., Hugenholtz, P., Skarshewski, A., Nielsen, K. R. L., Tyson, G. W., and Nielsen, P. H. (2013). Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat. Biotechnol. 31, 533-538. doi: 10.1038/nbt.2579
    • (2013) Nat. Biotechnol , vol.31 , pp. 533-538
    • Albertsen, M.1    Hugenholtz, P.2    Skarshewski, A.3    Nielsen, K.R.L.4    Tyson, G.W.5    Nielsen, P.H.6
  • 3
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • Altschul, S., Madden, T., Schaffer, A., Zhang, J., Zhang, Z., Miller, W., et al. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402. doi: 10.1093/nar/25.17.3389
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.1    Madden, T.2    Schaffer, A.3    Zhang, J.4    Zhang, Z.5    Miller, W.6
  • 5
    • 33745256005 scopus 로고    scopus 로고
    • Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative
    • Anisimova, M., and Gascuel, O. (2006). Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative. Syst. Biol. 55, 539-552. doi: 10.1080/10635150600755453
    • (2006) Syst. Biol , vol.55 , pp. 539-552
    • Anisimova, M.1    Gascuel, O.2
  • 6
    • 0141476314 scopus 로고    scopus 로고
    • Elevation of Mycobacterium tuberculosis subsp. caprae Aranaz et al. 1999 to species rank as Mycobacterium caprae comb. nov., sp. nov
    • Aranaz, A., Cousins, D., Mateos, A., and Dominguez, L. (2003). Elevation of Mycobacterium tuberculosis subsp. caprae Aranaz et al. 1999 to species rank as Mycobacterium caprae comb. nov., sp. nov. Int. J. Syst. Evol. Microbiol. 53, 1785-1789. doi: 10.1099/ijs.0.02532-0
    • (2003) Int. J. Syst. Evol. Microbiol , vol.53 , pp. 1785-1789
    • Aranaz, A.1    Cousins, D.2    Mateos, A.3    Dominguez, L.4
  • 7
    • 40549120596 scopus 로고    scopus 로고
    • The RAST Server: rapid annotations using subsystems technology
    • Aziz, R. K., Bartels, D., Best, A. A., DeJongh, M., Disz, T., Edwards, R. A., et al. (2008). The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:75. doi: 10.1186/1471-2164-9-75
    • (2008) BMC Genomics , vol.9 , pp. 75
    • Aziz, R.K.1    Bartels, D.2    Best, A.A.3    DeJongh, M.4    Disz, T.5    Edwards, R.A.6
  • 8
    • 4444240785 scopus 로고    scopus 로고
    • Silent nucleotide polymorphisms and a phylogeny for Mycobacterium tuberculosis
    • Baker, L., Brown, T., Maiden, M. C., and Drobniewski, F. (2004). Silent nucleotide polymorphisms and a phylogeny for Mycobacterium tuberculosis. Emerg. Infect. Dis. 10, 1568-1577. doi: 10.3201/eid1009.040046
    • (2004) Emerg. Infect. Dis , vol.10 , pp. 1568-1577
    • Baker, L.1    Brown, T.2    Maiden, M.C.3    Drobniewski, F.4
  • 9
    • 84860771820 scopus 로고    scopus 로고
    • SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing
    • Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., et al. (2012). SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455-477. doi: 10.1089/cmb.2012.0021
    • (2012) J. Comput. Biol , vol.19 , pp. 455-477
    • Bankevich, A.1    Nurk, S.2    Antipov, D.3    Gurevich, A.A.4    Dvorkin, M.5    Kulikov, A.S.6
  • 10
    • 84890559057 scopus 로고    scopus 로고
    • rpoB gene as a novel molecular marker to infer phylogeny in Planctomycetales
    • Bondoso, J., Harder, J., and Lage, O. M. (2013). rpoB gene as a novel molecular marker to infer phylogeny in Planctomycetales. Antonie Van Leeuwenhoek 104, 477-488. doi: 10.1007/s10482-013-9980-7
    • (2013) Antonie Van Leeuwenhoek , vol.104 , pp. 477-488
    • Bondoso, J.1    Harder, J.2    Lage, O.M.3
  • 12
    • 0034043778 scopus 로고    scopus 로고
    • Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
    • Castresana, J. (2000). Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17, 540-552. doi: 10.1093/oxfordjournals.molbev.a026334
    • (2000) Mol. Biol. Evol , vol.17 , pp. 540-552
    • Castresana, J.1
  • 13
    • 74349123303 scopus 로고    scopus 로고
    • Three new RelE-homologous mRNA interferases of Escherichia coli differentially induced by environmental stresses
    • Christensen-Dalsgaard, M., Jørgensen, M. G., and Gerdes, K. (2010). Three new RelE-homologous mRNA interferases of Escherichia coli differentially induced by environmental stresses. Mol. Microbiol. 75, 333-348. doi: 10.1111/j.1365-2958.2009.06969.x
    • (2010) Mol. Microbiol , vol.75 , pp. 333-348
    • Christensen-Dalsgaard, M.1    Jørgensen, M.G.2    Gerdes, K.3
  • 14
    • 48249102000 scopus 로고    scopus 로고
    • Phylogeny.fr: robust phylogenetic analysis for the non-specialist
    • Dereeper, A., Guignon, V., Blanc, G., Audic, S., Buffet, S., Chevenet, F., et al. (2008). Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res. 36, W465-W469. doi: 10.1093/nar/gkn180
    • (2008) Nucleic Acids Res , vol.36 , pp. W465-W469
    • Dereeper, A.1    Guignon, V.2    Blanc, G.3    Audic, S.4    Buffet, S.5    Chevenet, F.6
  • 15
    • 1542510099 scopus 로고    scopus 로고
    • Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting
    • Desper, R., and Gascuel, O. (2004). Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting. Mol. Biol. Evol. 21, 587-598. doi: 10.1093/molbev/msh049
    • (2004) Mol. Biol. Evol , vol.21 , pp. 587-598
    • Desper, R.1    Gascuel, O.2
  • 16
    • 84885143535 scopus 로고    scopus 로고
    • The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria
    • Di Rienzi, S. C., Sharon, I., Wrighton, K. C., Koren, O., Hug, L. A., Thomas, B. C., et al. (2013). The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria. Elife 2:e01102. doi: 10.7554/eLife.01102
    • (2013) Elife , vol.2
    • Di Rienzi, S.C.1    Sharon, I.2    Wrighton, K.C.3    Koren, O.4    Hug, L.A.5    Thomas, B.C.6
  • 18
    • 84861342496 scopus 로고    scopus 로고
    • Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage
    • Dupont, C. L., Rusch, D. B., Yooseph, S., Lombardo, M.-J., Richter, R. A., Valas, R., et al. (2012). Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. ISME J. 6, 1186-1199. doi: 10.1038/ismej.2011.189
    • (2012) ISME J , vol.6 , pp. 1186-1199
    • Dupont, C.L.1    Rusch, D.B.2    Yooseph, S.3    Lombardo, M.-J.4    Richter, R.A.5    Valas, R.6
  • 20
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: multiple sequence alignment with high accuracy and high throughput
    • Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797. doi: 10.1093/nar/gkh340
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 21
    • 84870431038 scopus 로고    scopus 로고
    • CD-HIT: accelerated for clustering the next-generation sequencing data
    • Fu, L., Niu, B., Zhu, Z., Wu, S., and Li, W. (2012). CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28, 3150-3152. doi: 10.1093/bioinformatics/bts565
    • (2012) Bioinformatics , vol.28 , pp. 3150-3152
    • Fu, L.1    Niu, B.2    Zhu, Z.3    Wu, S.4    Li, W.5
  • 23
    • 77950806408 scopus 로고    scopus 로고
    • New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0
    • Guindon, S., Dufayard, J. F., Lefort, V., Anisimova, M., Hordijk, W., and Gascuel, O. (2010). New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 307-321. doi: 10.1093/sysbio/syq010
    • (2010) Syst. Biol , vol.59 , pp. 307-321
    • Guindon, S.1    Dufayard, J.F.2    Lefort, V.3    Anisimova, M.4    Hordijk, W.5    Gascuel, O.6
  • 24
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    • Guindon, S., and Gascuel, O. (2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52, 696-704. doi: 10.1080/10635150390235520
    • (2003) Syst. Biol , vol.52 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 25
    • 33847702910 scopus 로고    scopus 로고
    • MEGAN analysis of metagenomic data
    • Huson, D. H., Auch, A. F., Qi, J., and Schuster, S. C. (2007). MEGAN analysis of metagenomic data. Genome Res. 17, 377-386. doi: 10.1101/gr.5969107
    • (2007) Genome Res , vol.17 , pp. 377-386
    • Huson, D.H.1    Auch, A.F.2    Qi, J.3    Schuster, S.C.4
  • 26
    • 84862276328 scopus 로고    scopus 로고
    • Structure, function and diversity of the healthy human microbiome
    • Huttenhower, C., Gevers, D., Knight, R., Abubucker, S., Badger, J. H., Chinwalla, A. T., et al. (2012). Structure, function and diversity of the healthy human microbiome. Nature 486, 207-214. doi: 10.1038/nature11234
    • (2012) Nature , vol.486 , pp. 207-214
    • Huttenhower, C.1    Gevers, D.2    Knight, R.3    Abubucker, S.4    Badger, J.H.5    Chinwalla, A.T.6
  • 27
    • 84865561269 scopus 로고    scopus 로고
    • Gene and translation initiation site prediction in metagenomic sequences
    • Hyatt, D., LoCascio, P. F., Hauser, L. J., and Uberbacher, E. C. (2012). Gene and translation initiation site prediction in metagenomic sequences. Bioinformatics 28, 2223-2230. doi: 10.1093/bioinformatics/bts429
    • (2012) Bioinformatics , vol.28 , pp. 2223-2230
    • Hyatt, D.1    LoCascio, P.F.2    Hauser, L.J.3    Uberbacher, E.C.4
  • 30
    • 84940387197 scopus 로고    scopus 로고
    • MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
    • Kang, D. D., Froula, J., Egan, R., and Wang, Z. (2015). MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ 3:e1165. doi: 10.7717/peerj.1165
    • (2015) PeerJ , vol.3
    • Kang, D.D.1    Froula, J.2    Egan, R.3    Wang, Z.4
  • 31
    • 0033986599 scopus 로고    scopus 로고
    • Differentiation of phylogenetically related slowly growing mycobacteria by their gyrB sequences
    • Kasai, H., Ezaki, T., and Harayama, S. (2000). Differentiation of phylogenetically related slowly growing mycobacteria by their gyrB sequences. J. Clin. Microbiol. 38, 301-308.
    • (2000) J. Clin. Microbiol , vol.38 , pp. 301-308
    • Kasai, H.1    Ezaki, T.2    Harayama, S.3
  • 32
    • 84867634981 scopus 로고    scopus 로고
    • MOCAT: a metagenomics assembly and gene prediction toolkit
    • Kultima, J. R., Sunagawa, S., Li, J., Chen, W., Chen, H., Mende, D. R., et al. (2012). MOCAT: a metagenomics assembly and gene prediction toolkit. PLoS ONE 7:e47656. doi: 10.1371/journal.pone.0047656
    • (2012) PLoS ONE , vol.7
    • Kultima, J.R.1    Sunagawa, S.2    Li, J.3    Chen, W.4    Chen, H.5    Mende, D.R.6
  • 34
    • 84897374590 scopus 로고    scopus 로고
    • Alignment-free visualization of metagenomic data by nonlinear dimension reduction
    • Laczny, C. C., Pinel, N., Vlassis, N., and Wilmes, P. (2014). Alignment-free visualization of metagenomic data by nonlinear dimension reduction. Sci. Rep. 4, 4516. doi: 10.1038/srep04516
    • (2014) Sci. Rep , vol.4 , pp. 4516
    • Laczny, C.C.1    Pinel, N.2    Vlassis, N.3    Wilmes, P.4
  • 35
    • 84938483160 scopus 로고    scopus 로고
    • VizBin-an application for reference-independent visualization and human-augmented binning of metagenomic data
    • Laczny, C. C., Sternal, T., Plugaru, V., Gawron, P., Atashpendar, A., Margossian, H. H., et al. (2015). VizBin-an application for reference-independent visualization and human-augmented binning of metagenomic data. Microbiome 3, 1. doi: 10.1186/s40168-014-0066-1
    • (2015) Microbiome , vol.3 , pp. 1
    • Laczny, C.C.1    Sternal, T.2    Plugaru, V.3    Gawron, P.4    Atashpendar, A.5    Margossian, H.H.6
  • 36
    • 84869113067 scopus 로고    scopus 로고
    • Microbial culturomics: paradigm shift in the human gut microbiome study
    • Lagier, J. C., Armougom, F., Million, M., Hugon, P., Pagnier, I., Robert, C., et al. (2012). Microbial culturomics: paradigm shift in the human gut microbiome study. Clin. Microbiol. Infect. 18, 1185-1193. doi: 10.1111/1469-0691.12023
    • (2012) Clin. Microbiol. Infect , vol.18 , pp. 1185-1193
    • Lagier, J.C.1    Armougom, F.2    Million, M.3    Hugon, P.4    Pagnier, I.5    Robert, C.6
  • 38
    • 68549104404 scopus 로고    scopus 로고
    • The Sequence Alignment/Map format and SAMtools
    • Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., et al. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079. doi: 10.1093/bioinformatics/btp352
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1    Handsaker, B.2    Wysoker, A.3    Fennell, T.4    Ruan, J.5    Homer, N.6
  • 39
    • 67650711615 scopus 로고    scopus 로고
    • SOAP2: an improved ultrafast tool for short read alignment
    • Li, R., Yu, C., Li, Y., Lam, T. W., Yiu, S. M., Kristiansen, K., et al. (2009). SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25, 1966-1967. doi: 10.1093/bioinformatics/btp336
    • (2009) Bioinformatics , vol.25 , pp. 1966-1967
    • Li, R.1    Yu, C.2    Li, Y.3    Lam, T.W.4    Yiu, S.M.5    Kristiansen, K.6
  • 40
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
    • Li, W., and Godzik, A. (2006). Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658-1659. doi: 10.1093/bioinformatics/btl158
    • (2006) Bioinformatics , vol.22 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 42
    • 84902986307 scopus 로고    scopus 로고
    • A phylogenomic view of ecological specialization in the lachnospiraceae, a family of digestive tract-associated bacteria
    • Meehan, C. J., and Beiko, R. G. (2014). A phylogenomic view of ecological specialization in the lachnospiraceae, a family of digestive tract-associated bacteria. Genome Biol. Evol. 6, 703-713. doi: 10.1093/gbe/evu050
    • (2014) Genome Biol. Evol , vol.6 , pp. 703-713
    • Meehan, C.J.1    Beiko, R.G.2
  • 43
    • 84961251149 scopus 로고    scopus 로고
    • The GyrA encoded gene: a pertinent marker for the phylogenetic revision of Helicobacter genus
    • Menard, A., Buissonniere, A., Prouzet-Mauleon, V., Sifre, E., and Megraud, F. (2016). The GyrA encoded gene: a pertinent marker for the phylogenetic revision of Helicobacter genus. Syst. Appl. Microbiol. 39, 77-87. doi: 10.1016/j.syapm.2015.09.008
    • (2016) Syst. Appl. Microbiol , vol.39 , pp. 77-87
    • Menard, A.1    Buissonniere, A.2    Prouzet-Mauleon, V.3    Sifre, E.4    Megraud, F.5
  • 45
    • 84923224630 scopus 로고    scopus 로고
    • Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage
    • Muller, E. E. L., Pinel, N., Laczny, C. C., Hoopmann, M. R., Narayanasamy, S., Lebrun, L. A., et al. (2014). Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage. Nat. Commun. 5, 5603. doi: 10.1038/ncomms6603
    • (2014) Nat. Commun , vol.5 , pp. 5603
    • Muller, E.E.L.1    Pinel, N.2    Laczny, C.C.3    Hoopmann, M.R.4    Narayanasamy, S.5    Lebrun, L.A.6
  • 46
    • 84905730761 scopus 로고    scopus 로고
    • Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
    • Nielsen, H. B., Almeida, M., Juncker, A. S., Rasmussen, S., Li, J., Sunagawa, S., et al. (2014). Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nat. Biotechnol. 32, 822-828. doi: 10.1038/nbt.2939
    • (2014) Nat. Biotechnol , vol.32 , pp. 822-828
    • Nielsen, H.B.1    Almeida, M.2    Juncker, A.S.3    Rasmussen, S.4    Li, J.5    Sunagawa, S.6
  • 47
    • 84891804612 scopus 로고    scopus 로고
    • The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
    • Overbeek, R., Olson, R., Pusch, G. D., Olsen, G. J., Davis, J. J., Disz, T., et al. (2014). The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 42, D206-D214. doi: 10.1093/nar/gkt1226
    • (2014) Nucleic Acids Res , vol.42 , pp. D206-D214
    • Overbeek, R.1    Olson, R.2    Pusch, G.D.3    Olsen, G.J.4    Davis, J.J.5    Disz, T.6
  • 48
    • 84861760530 scopus 로고    scopus 로고
    • IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
    • Peng, Y., Leung, H. C., Yiu, S. M., and Chin, F. Y. (2012). IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28, 1420-1428. doi: 10.1093/bioinformatics/bts174
    • (2012) Bioinformatics , vol.28 , pp. 1420-1428
    • Peng, Y.1    Leung, H.C.2    Yiu, S.M.3    Chin, F.Y.4
  • 49
    • 77950251400 scopus 로고    scopus 로고
    • A human gut microbial gene catalogue established by metagenomic sequencing
    • Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., et al. (2010). A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59-65. doi: 10.1038/nature08821
    • (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
  • 50
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: a flexible suite of utilities for comparing genomic features
    • Quinlan, A. R., and Hall, I. M. (2010). BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842. doi: 10.1093/bioinformatics/btq033
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 51
    • 84927692256 scopus 로고    scopus 로고
    • The first 1000 cultured species of the human gastrointestinal microbiota
    • Rajilic-Stojanovic, M., and de Vos, W. M. (2014). The first 1000 cultured species of the human gastrointestinal microbiota. FEMS Microbiol. Rev. 38, 996-1047. doi: 10.1111/1574-6976.12075
    • (2014) FEMS Microbiol. Rev , vol.38 , pp. 996-1047
    • Rajilic-Stojanovic, M.1    de Vos, W.M.2
  • 52
    • 84884539107 scopus 로고    scopus 로고
    • Sequential isolation of metabolites, RNA, DNA, and proteins from the same unique sample
    • Roume, H., Heintz-Buschart, A., Muller, E. E. L., and Wilmes, P. (2013). Sequential isolation of metabolites, RNA, DNA, and proteins from the same unique sample. Methods Enzymol. 531, 219-236. doi: 10.1016/B978-0-12-407863-5.00011-3
    • (2013) Methods Enzymol , vol.531 , pp. 219-236
    • Roume, H.1    Heintz-Buschart, A.2    Muller, E.E.L.3    Wilmes, P.4
  • 53
    • 0023375195 scopus 로고
    • The neighbor-joining method: a new method for reconstructing phylogenetic trees
    • Saitou, N., and Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
    • (1987) Mol. Biol. Evol , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 54
    • 84901417347 scopus 로고    scopus 로고
    • Prokka: rapid prokaryotic genome annotation
    • Seemann, T. (2014). Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068-2069. doi: 10.1093/bioinformatics/btu153
    • (2014) Bioinformatics , vol.30 , pp. 2068-2069
    • Seemann, T.1
  • 55
    • 84883116930 scopus 로고    scopus 로고
    • PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes
    • Segata, N., Börnigen, D., Morgan, X. C., and Huttenhower, C. (2013). PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nat. Commun. 4, 2304. doi: 10.1038/ncomms3304
    • (2013) Nat. Commun , vol.4 , pp. 2304
    • Segata, N.1    Börnigen, D.2    Morgan, X.C.3    Huttenhower, C.4
  • 56
    • 84871956840 scopus 로고    scopus 로고
    • Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization
    • Sharon, I., Morowitz, M. J., Thomas, B. C., Costello, E. K., Relman, D. A., and Banfield, J. F. (2013). Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization. Genome Res. 23, 111-120. doi: 10.1101/gr.142315.112
    • (2013) Genome Res , vol.23 , pp. 111-120
    • Sharon, I.1    Morowitz, M.J.2    Thomas, B.C.3    Costello, E.K.4    Relman, D.A.5    Banfield, J.F.6
  • 58
    • 80051972336 scopus 로고    scopus 로고
    • "Next generation sequence assembly with AMOS, "
    • 33rd Edn (Hoboken, NJ: John Wiley & Sons, Inc.)
    • Treangen, T. J., Sommer, D. D., Angly, F. E., Koren, S., and Pop, M. (2011). "Next generation sequence assembly with AMOS, "in Current Protocols in Bioinformatics, 33rd Edn (Hoboken, NJ: John Wiley & Sons, Inc.). doi: 10.1002/0471250953.bi1108s33
    • (2011) Current Protocols in Bioinformatics
    • Treangen, T.J.1    Sommer, D.D.2    Angly, F.E.3    Koren, S.4    Pop, M.5
  • 61
    • 84859242353 scopus 로고    scopus 로고
    • Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2
    • Wu, M., and Scott, A. J. (2012). Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 28, 1033-1034. doi: 10.1093/bioinformatics/bts079
    • (2012) Bioinformatics , vol.28 , pp. 1033-1034
    • Wu, M.1    Scott, A.J.2
  • 62
    • 84925636192 scopus 로고    scopus 로고
    • MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm
    • Wu, Y.-W., Tang, Y.-H., Tringe, S. G., Simmons, B. A., and Singer, S. W. (2014). MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm. Microbiome 2, 26. doi: 10.1186/2049-2618-2-26
    • (2014) Microbiome , vol.2 , pp. 26
    • Wu, Y.-W.1    Tang, Y.-H.2    Tringe, S.G.3    Simmons, B.A.4    Singer, S.W.5
  • 63
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: algorithms for de novo short read assembly using de Bruijn graphs
    • Zerbino, D. R., and Birney, E. (2008). Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821-829. doi: 10.1101/gr.074492107
    • (2008) Genome Res , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 64
    • 84864462812 scopus 로고    scopus 로고
    • EvolView, an online tool for visualizing, annotating and managing phylogenetic trees
    • Zhang, H., Gao, S., Lercher, M. J., Hu, S., and Chen, W. H. (2012). EvolView, an online tool for visualizing, annotating and managing phylogenetic trees. Nucleic Acids Res. 40, 569-572. doi: 10.1093/nar/gks576
    • (2012) Nucleic Acids Res , vol.40 , pp. 569-572
    • Zhang, H.1    Gao, S.2    Lercher, M.J.3    Hu, S.4    Chen, W.H.5
  • 65
    • 0034053725 scopus 로고    scopus 로고
    • A greedy algorithm for aligning DNAsequences
    • Zhang, Z., Schwartz, S., Wagner, L., and Miller, W. (2000). A greedy algorithm for aligning DNAsequences. J. Comput. Biol. 7, 203-214. doi: 10.1089/10665270050081478
    • (2000) J. Comput. Biol , vol.7 , pp. 203-214
    • Zhang, Z.1    Schwartz, S.2    Wagner, L.3    Miller, W.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.