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Volumn 5, Issue 1, 2014, Pages

Validation of high throughput sequencing and microbial forensics applications

(16)  Budowle, Bruce a,b   Connell, Nancy D c   Bielecka Oder, Anna d   Colwell, Rita R e,f,g,h   Corbett, Cindi R i,j   Fletcher, Jacqueline k   Forsman, Mats l   Kadavy, Dana R m   Markotic, Alemka n   Morse, Stephen A o   Murch, Randall S p   Sajantila, Antti a,q   Schmedes, Sarah E a   Ternus, Krista L c   Turner, Stephen D r   Minot, Samuel m  


Author keywords

Bioinformatics; High throughput sequencing; Library preparation; Microbial forensics; Sample preparation; Validation

Indexed keywords

BIOCHEMISTRY; BIOINFORMATICS; FALSE NEGATIVE RESULT; FALSE POSITIVE RESULT; FORENSIC SCIENCE; HIGH THROUGHPUT SEQUENCING; HUMAN; LIMIT OF DETECTION; MEASUREMENT ACCURACY; MEASUREMENT PRECISION; MEASUREMENT REPEATABILITY; MICROBIAL FORENSICS; NONHUMAN; PRIORITY JOURNAL; REFERENCE DATABASE; REPRODUCIBILITY; REVIEW; SENSITIVITY AND SPECIFICITY; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL ANALYSIS; VALIDATION PROCESS; COMMUNITY STRUCTURE; COMPUTER PROGRAM; DATA ANALYSIS; GENE SEQUENCE; INFORMATION PROCESSING; MICROBIAL FORENSIC; MICROBIAL GENOME; MICROBIOLOGY; NUCLEIC ACID ANALYSIS; POLYMERASE CHAIN REACTION; POPULATION ABUNDANCE; SAMPLING; TAXONOMY;

EID: 84904841142     PISSN: None     EISSN: 20412223     Source Type: Journal    
DOI: 10.1186/2041-2223-5-9     Document Type: Review
Times cited : (66)

References (139)
  • 1
    • 0035969492 scopus 로고    scopus 로고
    • Index case of fatal inhalational anthrax due to bioterrorism in the United States
    • Bush LM, Abrams BH, Beall A, Johnson CC. Index case of fatal inhalational anthrax due to bioterrorism in the United States. N Engl J Med 2001, 345:1607-1610.
    • (2001) N Engl J Med , vol.345 , pp. 1607-1610
    • Bush, L.M.1    Abrams, B.H.2    Beall, A.3    Johnson, C.C.4
  • 6
    • 2142705302 scopus 로고    scopus 로고
    • Microbial forensics: building a national capacity to investigate bioterrorism
    • Murch RS. Microbial forensics: building a national capacity to investigate bioterrorism. Biosecur Bioterror 2003, 1:117-122.
    • (2003) Biosecur Bioterror , vol.1 , pp. 117-122
    • Murch, R.S.1
  • 8
    • 33744527832 scopus 로고    scopus 로고
    • Microbial forensics: application to bioterrorism preparedness and response
    • Morse SA, Budowle B. Microbial forensics: application to bioterrorism preparedness and response. Infect Dis Clin North Am 2006, 20:455-473.
    • (2006) Infect Dis Clin North Am , vol.20 , pp. 455-473
    • Morse, S.A.1    Budowle, B.2
  • 9
    • 0036314263 scopus 로고    scopus 로고
    • Bioterrorism preparedness. II: the community and emergency medical services systems
    • Flowers LK, Mothershead JL, Blackwell TH. Bioterrorism preparedness. II: the community and emergency medical services systems. Emerg Med Clin North Am 2002, 20:457-476.
    • (2002) Emerg Med Clin North Am , vol.20 , pp. 457-476
    • Flowers, L.K.1    Mothershead, J.L.2    Blackwell, T.H.3
  • 11
    • 84882874868 scopus 로고    scopus 로고
    • The need for forensic tools in a balanced national agricultural security program
    • Springer Science + Business Media B.V, Gullino M, Fletcher J, Gamliel A, Stacks J
    • Fletcher J. The need for forensic tools in a balanced national agricultural security program. Crop Biosecurity: Assuring Our Global Food Supply 2008, 93-101. Springer Science + Business Media B.V, Gullino M, Fletcher J, Gamliel A, Stacks J.
    • (2008) Crop Biosecurity: Assuring Our Global Food Supply , pp. 93-101
    • Fletcher, J.1
  • 12
  • 14
    • 52649154721 scopus 로고    scopus 로고
    • Admissibility standards for scientific evidence
    • Academic Press, Budowle B, Schutzer SE, Breeze RG
    • Harmon R. Admissibility standards for scientific evidence. Microbial Forensics 2005, 382-392. Academic Press, Budowle B, Schutzer SE, Breeze RG.
    • (2005) Microbial Forensics , pp. 382-392
    • Harmon, R.1
  • 20
    • 82355173436 scopus 로고    scopus 로고
    • Genome sequence analyses of two isolates from the recent Escherichia coli outbreak in Germany reveal the emergence of a new pathotype: Entero-Aggregative-Haemorrhagic Escherichia coli (EAHEC)
    • Brzuszkiewicz E, Thürmer A, Schuldes J, Leimbach A, Liesegang H, Meyer FD, Boelter J, Petersen H, Gottschalk G, Daniel R. Genome sequence analyses of two isolates from the recent Escherichia coli outbreak in Germany reveal the emergence of a new pathotype: Entero-Aggregative-Haemorrhagic Escherichia coli (EAHEC). Arch Microbiol 2011, 193:883-891.
    • (2011) Arch Microbiol , vol.193 , pp. 883-891
    • Brzuszkiewicz, E.1    Thürmer, A.2    Schuldes, J.3    Leimbach, A.4    Liesegang, H.5    Meyer, F.D.6    Boelter, J.7    Petersen, H.8    Gottschalk, G.9    Daniel, R.10
  • 24
    • 33947221422 scopus 로고    scopus 로고
    • Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes
    • Eisen JA. Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes. PLoS Biol 2007, 5:e82.
    • (2007) PLoS Biol , vol.5
    • Eisen, J.A.1
  • 31
    • 63249121217 scopus 로고    scopus 로고
    • Application of " next-generation" sequencing technologies to microbial genetics
    • MacLean D, Jones JD, Studholme DJ. Application of " next-generation" sequencing technologies to microbial genetics. Nat Rev Microbiol 2009, 7:287-296.
    • (2009) Nat Rev Microbiol , vol.7 , pp. 287-296
    • MacLean, D.1    Jones, J.D.2    Studholme, D.J.3
  • 42
    • 84905830420 scopus 로고    scopus 로고
    • Screening metagenomic data for viruses using the e-probe diagnostic nucleic acid assay (EDNA)
    • in press
    • Stobbe AH, Schneider W, Hoyt P, Melcher U. Screening metagenomic data for viruses using the e-probe diagnostic nucleic acid assay (EDNA). Phytopathology in press.
    • Phytopathology
    • Stobbe, A.H.1    Schneider, W.2    Hoyt, P.3    Melcher, U.4
  • 45
    • 84905822388 scopus 로고    scopus 로고
    • The microbial forensics pathway for use of massively-parallel sequencing technologies
    • Washington DC: The National Academies Press
    • Budowle B, Schmedes S, Murch RS. The microbial forensics pathway for use of massively-parallel sequencing technologies. The Science and Applications of Microbial Genomics 2013, 117-133. Washington DC: The National Academies Press.
    • (2013) The Science and Applications of Microbial Genomics , pp. 117-133
    • Budowle, B.1    Schmedes, S.2    Murch, R.S.3
  • 50
    • 84870495569 scopus 로고    scopus 로고
    • Progress in ion torrent semiconductor chip based sequencing
    • Merriman B, Rothberg JM. Progress in ion torrent semiconductor chip based sequencing. Electrophoresis 2012, 33:3397-3417.
    • (2012) Electrophoresis , vol.33 , pp. 3397-3417
    • Merriman, B.1    Rothberg, J.M.2
  • 51
    • 72849144434 scopus 로고    scopus 로고
    • Sequencing technologies - the next generation
    • Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet 2010, 11:31-46.
    • (2010) Nat Rev Genet , vol.11 , pp. 31-46
    • Metzker, M.L.1
  • 53
    • 53649106195 scopus 로고    scopus 로고
    • Next-generation DNA sequencing
    • Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol 2008, 26:1135-1145.
    • (2008) Nat Biotechnol , vol.26 , pp. 1135-1145
    • Shendure, J.1    Ji, H.2
  • 56
    • 84859643160 scopus 로고    scopus 로고
    • Oxford Nanopore announcement sets sequencing sector abuzz
    • Eisenstein M. Oxford Nanopore announcement sets sequencing sector abuzz. Nat Biotechnol 2012, 30:295-296.
    • (2012) Nat Biotechnol , vol.30 , pp. 295-296
    • Eisenstein, M.1
  • 57
  • 59
    • 84883897500 scopus 로고    scopus 로고
    • Working Group of the American College of Medical Genetics and Genomics Laboratory Quality Assurance Committee: ACMG clinical laboratory standards for next-generation sequencing
    • Rehm HL, Bale SJ, Bayrak-Toydemir P, Berg JS, Brown KK, Deignan JL, Friez MJ, Funke BH, Hegde MR, Lyon E. Working Group of the American College of Medical Genetics and Genomics Laboratory Quality Assurance Committee: ACMG clinical laboratory standards for next-generation sequencing. Genet Med 2013, 15:733-747.
    • (2013) Genet Med , vol.15 , pp. 733-747
    • Rehm, H.L.1    Bale, S.J.2    Bayrak-Toydemir, P.3    Berg, J.S.4    Brown, K.K.5    Deignan, J.L.6    Friez, M.J.7    Funke, B.H.8    Hegde, M.R.9    Lyon, E.10
  • 62
    • 85014940645 scopus 로고    scopus 로고
    • Validation guidelines for DNA analysis methods
    • Available at: , SWGDAM
    • SWGDAM Validation guidelines for DNA analysis methods. 2012, Available at: http://swgdam.org/SWGDAM_Validation_Guidelines_APPROVED_Dec_2012.pdf, SWGDAM.
    • (2012)
  • 65
    • 19144366982 scopus 로고    scopus 로고
    • The metagenomics of soil
    • Daniel R. The metagenomics of soil. Nat Rev Microbiol 2005, 3:470-478.
    • (2005) Nat Rev Microbiol , vol.3 , pp. 470-478
    • Daniel, R.1
  • 66
    • 19144362371 scopus 로고    scopus 로고
    • Microbial community genomics in the ocean
    • DeLong EF. Microbial community genomics in the ocean. Nat Rev Microbiol 2005, 3:459-469.
    • (2005) Nat Rev Microbiol , vol.3 , pp. 459-469
    • DeLong, E.F.1
  • 69
    • 84862276328 scopus 로고    scopus 로고
    • Structure, function and diversity of the healthy human microbiome
    • Human Microbiome Project Consortium
    • Human Microbiome Project Consortium Structure, function and diversity of the healthy human microbiome. Nature 2012, 486:207-214. Human Microbiome Project Consortium.
    • (2012) Nature , vol.486 , pp. 207-214
  • 70
    • 84862286169 scopus 로고    scopus 로고
    • A framework for human microbiome research
    • Human Microbiome Project Consortium
    • Human Microbiome Project Consortium A framework for human microbiome research. Nature 2012, 486:215-221. Human Microbiome Project Consortium.
    • (2012) Nature , vol.486 , pp. 215-221
  • 71
    • 84862989346 scopus 로고    scopus 로고
    • Metagenomics - a guide from sampling to data analysis
    • Thomas T, Gilbert J, Meyer F. Metagenomics - a guide from sampling to data analysis. Microb Inform Exp 2012, 2:3.
    • (2012) Microb Inform Exp , vol.2 , pp. 3
    • Thomas, T.1    Gilbert, J.2    Meyer, F.3
  • 73
    • 0036774995 scopus 로고    scopus 로고
    • Molecular subtyping of Bacillus anthracis and the 2001 bioterrorism-associated anthrax outbreak, United States
    • Hoffmaster AR, Fitzgerald CC, Ribot E, Mayer LW, Popovic T. Molecular subtyping of Bacillus anthracis and the 2001 bioterrorism-associated anthrax outbreak, United States. Emerg Infect Dis 2002, 8:1111-1116.
    • (2002) Emerg Infect Dis , vol.8 , pp. 1111-1116
    • Hoffmaster, A.R.1    Fitzgerald, C.C.2    Ribot, E.3    Mayer, L.W.4    Popovic, T.5
  • 74
    • 77954678952 scopus 로고    scopus 로고
    • Use of forensic methods under exigent circumstances without full validation
    • Schutzer SE, Keim P, Czerwinski K, Budowle B. Use of forensic methods under exigent circumstances without full validation. Sci Transl Med 2009, 1:8cm7.
    • (2009) Sci Transl Med , vol.1 , pp. 7-8
    • Schutzer, S.E.1    Keim, P.2    Czerwinski, K.3    Budowle, B.4
  • 76
    • 84905830413 scopus 로고    scopus 로고
    • Practice Guidelines for Targeted Next Generation Sequencing Analysis and Interpretation. Clinical Molecular GeneticsSociety: Taylor GR, Available at:
    • Ellard S, Charlton R, Lindsay H, Camm N, Watson C, Abb S. Mattocks C 2012, Practice Guidelines for Targeted Next Generation Sequencing Analysis and Interpretation. Clinical Molecular GeneticsSociety: Taylor GR, Available at: http://cmgsweb.shared.hosting.zen.co.uk/BPGs/BPG%20for%20targeted%20next%20generation%20sequencing%20final.pdf.
    • (2012) Mattocks C
    • Ellard, S.1    Charlton, R.2    Lindsay, H.3    Camm, N.4    Watson, C.5    Abb, S.6
  • 77
    • 84905830414 scopus 로고    scopus 로고
    • PCR-free sample preparation kits for whole genome DNA sequencing
    • Available at:
    • Illumina PCR-free sample preparation kits for whole genome DNA sequencing. 2013, Available at: http://www.illumina.com/products/truseq-dna-pcr-free-sample-prep-kits.ilmn, Illumina.
    • (2013)
  • 78
    • 84905830415 scopus 로고    scopus 로고
    • HaloPlex target enrichment system-ILM
    • Available at: Agilent
    • Agilent HaloPlex target enrichment system-ILM. 2013, Available at: http://www.chem.agilent.com/Library/usermanuals/Public/G9900-90001.pdf, Agilent.
    • (2013)
  • 79
    • 84905830411 scopus 로고    scopus 로고
    • Nextera XT DNA sample preparation kit
    • Available at: , Illumina
    • Illumina Nextera XT DNA sample preparation kit. 2013, Available at: http://www.illumina.com/products/nextera_xt_dna_sample_prep_kit.ilmn, Illumina.
    • (2013)
  • 82
    • 0026736251 scopus 로고
    • Degenerate oligonucleotide-primed PCR: general amplification of target DNA by a single degenerate primer
    • Telenius H, Carter NP, Bebb CE, Nordenskjöld M, Ponder BA, Tunnacliffe A. Degenerate oligonucleotide-primed PCR: general amplification of target DNA by a single degenerate primer. Genomics 1992, 13:718-725.
    • (1992) Genomics , vol.13 , pp. 718-725
    • Telenius, H.1    Carter, N.P.2    Bebb, C.E.3    Nordenskjöld, M.4    Ponder, B.A.5    Tunnacliffe, A.6
  • 83
    • 0029966845 scopus 로고    scopus 로고
    • Whole genome amplification using a degenerate oligonucleotide primer allows hundreds of genotypes to be performed on less than one nanogram of genomic DNA
    • Cheung VG, Nelson SF. Whole genome amplification using a degenerate oligonucleotide primer allows hundreds of genotypes to be performed on less than one nanogram of genomic DNA. Proc Natl Acad Sci U S A 1996, 93:14676-14679.
    • (1996) Proc Natl Acad Sci U S A , vol.93 , pp. 14676-14679
    • Cheung, V.G.1    Nelson, S.F.2
  • 85
    • 79961051856 scopus 로고    scopus 로고
    • Next-generation sequencing library preparation: simultaneous fragmentation and tagging using in vitro transposition
    • Available at:
    • Syed F, Gruenwald H, Caruccio N. Next-generation sequencing library preparation: simultaneous fragmentation and tagging using in vitro transposition. Nat Methods 2009, Available at: http://www.nature.com/nmeth/journal/v6/n11/full/nmeth.f.272.html.
    • (2009) Nat Methods
    • Syed, F.1    Gruenwald, H.2    Caruccio, N.3
  • 86
    • 84856305295 scopus 로고    scopus 로고
    • Generating barcoded libraries for multiplex high-throughput sequencing
    • Knapp M, Stiller M, Meyer M. Generating barcoded libraries for multiplex high-throughput sequencing. Methods Mol Biol 2012, 840:155-170.
    • (2012) Methods Mol Biol , vol.840 , pp. 155-170
    • Knapp, M.1    Stiller, M.2    Meyer, M.3
  • 87
    • 40149103278 scopus 로고    scopus 로고
    • Error-correcting barcoded primers allow hundreds of samples to be pyrosequenced in multiplex
    • Hamady M, Walker JJ, Harris JK, Gold NJ, Knight R. Error-correcting barcoded primers allow hundreds of samples to be pyrosequenced in multiplex. Nat Methods 2012, 5:235-237.
    • (2012) Nat Methods , vol.5 , pp. 235-237
    • Hamady, M.1    Walker, J.J.2    Harris, J.K.3    Gold, N.J.4    Knight, R.5
  • 89
    • 84862182131 scopus 로고    scopus 로고
    • Next-generation sequencing technologies and applications for human genetic history and forensics
    • Berglund EC, Kiialainen A, Syvänen AC. Next-generation sequencing technologies and applications for human genetic history and forensics. Investig Genet 2011, 2:23.
    • (2011) Investig Genet , vol.2 , pp. 23
    • Berglund, E.C.1    Kiialainen, A.2    Syvänen, A.C.3
  • 95
    • 0031978181 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred
    • Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 1998, 8:186-194.
    • (1998) II. Error probabilities. Genome Res , vol.8 , pp. 186-194
    • Ewing, B.1    Green, P.2
  • 99
    • 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
    • Wood, D.E.1    Salzberg, S.L.2
  • 101
    • 84882729023 scopus 로고    scopus 로고
    • Harnessing virtual machines to simplify next-generation DNA sequencing analysis
    • Nocq J, Celton M, Gendron P, Lemieux S, Wilhelm BT. Harnessing virtual machines to simplify next-generation DNA sequencing analysis. Bioinformatics 2013, 29:2075-2083.
    • (2013) Bioinformatics , vol.29 , pp. 2075-2083
    • Nocq, J.1    Celton, M.2    Gendron, P.3    Lemieux, S.4    Wilhelm, B.T.5
  • 102
    • 0003726721 scopus 로고
    • IEEE Standard 610.12 Glossary of software engineering terminology
    • Available at: , Board IS
    • Board IS IEEE Standard 610.12 Glossary of software engineering terminology. 1990, Available at: http://ieeexplore.ieee.org/xpl/mostRecentIssue.jsp?reload=true&punumber=2238, Board IS.
    • (1990)
  • 104
    • 79952580139 scopus 로고    scopus 로고
    • Compression of DNA sequence reads in FASTQ format
    • Deorowicz S, Grabowski S. Compression of DNA sequence reads in FASTQ format. Bioinformatics 2011, 27:860-862.
    • (2011) Bioinformatics , vol.27 , pp. 860-862
    • Deorowicz, S.1    Grabowski, S.2
  • 105
    • 84875363204 scopus 로고    scopus 로고
    • Compression of FASTQ and SAM format sequencing data
    • Bonfield J, Mahoney M. Compression of FASTQ and SAM format sequencing data. PLoS One 2013, 8:e59190.
    • (2013) PLoS One , vol.8
    • Bonfield, J.1    Mahoney, M.2
  • 106
    • 84886206473 scopus 로고    scopus 로고
    • Washington DC: American Academy of Microbiology, Available at:
    • Buckley M, Roberts RJ. Reconciling Microbial Systematics and Genomics 2007, Washington DC: American Academy of Microbiology, Available at: http://academy.asm.org/index.php/genetics-genomics-molecular-microbiology/454-reconciling-microbial-systematics-and-genomics.
    • (2007) Reconciling Microbial Systematics and Genomics
    • Buckley, M.1    Roberts, R.J.2
  • 107
    • 84880673210 scopus 로고    scopus 로고
    • Molecular evolution in court analysis of a large hepatitis C virus outbreak from an evolving source
    • Gonzalez-Candelas F, Bracho M, Wrobel B, Moya A. Molecular evolution in court analysis of a large hepatitis C virus outbreak from an evolving source. BMC Biol 2013, 11:76.
    • (2013) BMC Biol , vol.11 , pp. 76
    • Gonzalez-Candelas, F.1    Bracho, M.2    Wrobel, B.3    Moya, A.4
  • 109
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: algorithms for de novo short read assembly using de Bruijn graphs
    • Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008, 18:821-829.
    • (2008) Genome Res , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 110
    • 79955724657 scopus 로고    scopus 로고
    • Comparing de novo genome assembly: the long and short of it
    • Narzisi G, Mishra B. Comparing de novo genome assembly: the long and short of it. PLoS One 2011, 6:e19175.
    • (2011) PLoS One , vol.6
    • Narzisi, G.1    Mishra, B.2
  • 111
    • 43149085041 scopus 로고    scopus 로고
    • De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer
    • Hernandez D, François P, Farinelli L, Osterås M, Schrenzel J. De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Genome Res 2008, 18:802-809.
    • (2008) Genome Res , vol.18 , pp. 802-809
    • Hernandez, D.1    François, P.2    Farinelli, L.3    Osterås, M.4    Schrenzel, J.5
  • 112
    • 39049156065 scopus 로고    scopus 로고
    • Short read fragment assembly of bacterial genomes
    • Chaisson MJ, Pevzner PA. Short read fragment assembly of bacterial genomes. Genome Res 2008, 18:324-330.
    • (2008) Genome Res , vol.18 , pp. 324-330
    • Chaisson, M.J.1    Pevzner, P.A.2
  • 114
  • 116
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012, 9:357-359.
    • (2012) Nat Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 119
    • 84862697946 scopus 로고    scopus 로고
    • The PhyloPythiaS web server for taxonomic assignment of metagenome sequences
    • Patil KR, Roune L, McHardy AC. The PhyloPythiaS web server for taxonomic assignment of metagenome sequences. PLoS One 2012, 7:e38581.
    • (2012) PLoS One , vol.7
    • Patil, K.R.1    Roune, L.2    McHardy, A.C.3
  • 120
    • 69549135124 scopus 로고    scopus 로고
    • Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models
    • Brady A, Salzberg SL. Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Nat Methods 2009, 6:673-676.
    • (2009) Nat Methods , vol.6 , pp. 673-676
    • Brady, A.1    Salzberg, S.L.2
  • 121
    • 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, 27:127-129.
    • (2011) Bioinformatics , vol.27 , pp. 127-129
    • Rosen, G.L.1    Reichenberger, E.R.2    Rosenfeld, A.M.3
  • 125
    • 84859358278 scopus 로고    scopus 로고
    • Fast and accurate taxonomic assignments of metagenomic sequences using MetaBin
    • Sharma VK, Kumar N, Prakash T, Taylor TD. Fast and accurate taxonomic assignments of metagenomic sequences using MetaBin. PLoS One 2012, 7:e34030.
    • (2012) PLoS One , vol.7
    • Sharma, V.K.1    Kumar, N.2    Prakash, T.3    Taylor, T.D.4
  • 126
    • 79960869431 scopus 로고    scopus 로고
    • Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences
    • Liu B, Gibbons T, Ghodsi M, Treangen T, Pop M. Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences. BMC Genomics 2011, 12(Suppl 2):S4.
    • (2011) BMC Genomics , vol.12 , Issue.SUPPL. 2
    • Liu, B.1    Gibbons, T.2    Ghodsi, M.3    Treangen, T.4    Pop, M.5
  • 128
    • 84864446502 scopus 로고    scopus 로고
    • High-speed microbial community profiling
    • Haft DH, Tovchigrechko A. High-speed microbial community profiling. Nat Methods 2012, 9:793-794.
    • (2012) Nat Methods , vol.9 , pp. 793-794
    • Haft, D.H.1    Tovchigrechko, A.2
  • 130
    • 74049132798 scopus 로고    scopus 로고
    • WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads
    • Gerlach W, Jünemann S, Tille F, Goesmann A, Stoye J. WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads. BMC Bioinformatics 2009, 10:430.
    • (2009) BMC Bioinformatics , vol.10 , pp. 430
    • Gerlach, W.1    Jünemann, S.2    Tille, F.3    Goesmann, A.4    Stoye, J.5
  • 133
    • 84863049441 scopus 로고    scopus 로고
    • MetaCluster 4.0: a novel binning algorithm for NGS reads and huge number of species
    • Wang Y, Leung HC, Yiu SM, Chin FY. MetaCluster 4.0: a novel binning algorithm for NGS reads and huge number of species. J Comput Biol 2012, 19:241-249.
    • (2012) J Comput Biol , vol.19 , pp. 241-249
    • Wang, Y.1    Leung, H.C.2    Yiu, S.M.3    Chin, F.Y.4
  • 134
    • 84864945803 scopus 로고    scopus 로고
    • Rapid identification of high-confidence taxonomic assignments for metagenomic data
    • MacDonald NJ, Parks DH, Beiko RG. Rapid identification of high-confidence taxonomic assignments for metagenomic data. Nucleic Acids Res 2012, 40:e111.
    • (2012) Nucleic Acids Res , vol.40
    • MacDonald, N.J.1    Parks, D.H.2    Beiko, R.G.3
  • 135
    • 79955611184 scopus 로고    scopus 로고
    • PhymmBL expanded: confidence scores, custom databases, parallelization and more
    • Brady A, Salzberg S. PhymmBL expanded: confidence scores, custom databases, parallelization and more. Nat Methods 2011, 8:367.
    • (2011) Nat Methods , vol.8 , pp. 367
    • Brady, A.1    Salzberg, S.2
  • 136
    • 84860672197 scopus 로고    scopus 로고
    • A comparative evaluation of sequence classification programs
    • Bazinet A, Cummings M. A comparative evaluation of sequence classification programs. BMC Bioinformatics 2012, 13:1-13.
    • (2012) BMC Bioinformatics , vol.13 , pp. 1-13
    • Bazinet, A.1    Cummings, M.2
  • 138
    • 0000594195 scopus 로고
    • Evolution and measurement of species diversity
    • Whittaker RH. Evolution and measurement of species diversity. Taxon 1972, 21:213-251.
    • (1972) Taxon , vol.21 , pp. 213-251
    • Whittaker, R.H.1
  • 139
    • 84890558766 scopus 로고    scopus 로고
    • Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions
    • Fricke WF, Rasko DA. Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions. Nat Rev Genet 2013, 15:49-55.
    • (2013) Nat Rev Genet , vol.15 , pp. 49-55
    • Fricke, W.F.1    Rasko, D.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.