-
1
-
-
0025183708
-
Basic local alignment search tool
-
Altschul S.F., et al. (1990). Basic local alignment search tool. J. Mol. Biol., 215, 403-410
-
(1990)
J. Mol. Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
-
2
-
-
75549090056
-
Gen bank
-
Benson D.A., et al. (2010). GenBank. Nucleic Acids Res., 38, D46-D51
-
(2010)
Nucleic Acids Res
, vol.38
, pp. D46-D51
-
-
Benson, D.A.1
-
3
-
-
0030297089
-
The indigenous gastrointestinal microflora
-
Berg R.D. (1996). The indigenous gastrointestinal microflora. Trends Microbiol., 4, 430-435
-
(1996)
Trends Microbiol
, vol.4
, pp. 430-435
-
-
Berg, R.D.1
-
4
-
-
43149086380
-
Allpaths: De novo assembly of whole-genome shotgun microreads
-
Butler J., et al. (2008). ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res., 18, 810-820
-
(2008)
Genome Res
, vol.18
, pp. 810-820
-
-
Butler, J.1
-
5
-
-
66249131497
-
Global sequencing: A review of current molecular data and new methods available to assess microbial diversity
-
Christen R. (2008). Global sequencing: a review of current molecular data and new methods available to assess microbial diversity. Microbes Environ. JSME, 23, 253-268
-
(2008)
Microbes Environ. JSME
, vol.23
, pp. 253-268
-
-
Christen, R.1
-
6
-
-
58149194632
-
Petabyte-scale innovations at the European nucleotide archive
-
Cochrane G., et al. (2009). Petabyte-scale innovations at the European nucleotide archive. Nucleic Acids Res., 37, D19-D25
-
(2009)
Nucleic Acids Res
, vol.37
, pp. D19-D25
-
-
Cochrane, G.1
-
7
-
-
13444304367
-
The ribosomal database project (rdp-ii): Sequences and tools for high-throughput rrna analysis
-
Cole J.R., et al. (2005). The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res., 33 (Suppl. 1) , D294-D296
-
(2005)
Nucleic Acids Res
, vol.33
, pp. D294-D296
-
-
Cole, J.R.1
-
9
-
-
84863004113
-
Reconstruction of ribosomal RNA genes from metagenomic data
-
Fan L., et al. (2012). Reconstruction of ribosomal RNA genes from metagenomic data. PloS One, 7, e39948
-
(2012)
Plos One
, vol.7
, pp. e39948
-
-
Fan, L.1
-
10
-
-
84860523681
-
Readjoiner: A fast and memory efficient string graph-based sequence assembler
-
Gonnella G. and Kurtz S. (2012). Readjoiner: a fast and memory efficient string graph-based sequence assembler. BMC Bioinformatics, 13, 82
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 82
-
-
Gonnella, G.1
Kurtz, S.2
-
11
-
-
67650021209
-
Microbial community profiling for human microbiome projects: Tools, techniques, and challenges
-
Hamady M. and Knight R. (2009). Microbial community profiling for human microbiome projects: tools, techniques, and challenges. Genome Res., 19, 1141-1152
-
(2009)
Genome Res
, vol.19
, pp. 1141-1152
-
-
Hamady, M.1
Knight, R.2
-
12
-
-
80052960863
-
Next-generation transcriptome assembly
-
Jeffrey A.M. and Zhong W. (2011). Next-generation transcriptome assembly. Nat. Rev. Genet., 12, 671-682
-
(2011)
Nat. Rev. Genet
, vol.12
, pp. 671-682
-
-
Jeffrey, A.M.1
Zhong, W.2
-
13
-
-
65549118801
-
Local RNA structure alignment with incomplete sequence
-
Kolbe D.L. and Eddy S.R. (2009). Local RNA structure alignment with incomplete sequence. Bioinformatics, 25, 1236-1243
-
(2009)
Bioinformatics
, vol.25
, pp. 1236-1243
-
-
Kolbe, D.L.1
Eddy, S.R.2
-
14
-
-
0036426322
-
The cell membrane plays a crucial role in survival of bacteria and archaea in extreme environments
-
Konings W.N., et al. (2002). The cell membrane plays a crucial role in survival of bacteria and archaea in extreme environments. Antonie Van Leeuwenhoek, 81, 61-72
-
(2002)
Antonie Van Leeuwenhoek
, vol.81
, pp. 61-72
-
-
Konings, W.N.1
-
15
-
-
79952374428
-
Genovo: De novo assembly for metagenomes
-
Laserson J., et al. (2011). Genovo: de novo assembly for metagenomes. J. Comput. Biol., 18, 429-443
-
(2011)
J. Comput. Biol
, vol.18
, pp. 429-443
-
-
Laserson, J.1
-
17
-
-
75649124547
-
De novo assembly of human genomes with massively parallel short read sequencing
-
Li R., et al. (2010). De novo assembly of human genomes with massively parallel short read sequencing. Genome Res., 20, 265-272
-
(2010)
Genome Res
, vol.20
, pp. 265-272
-
-
Li, R.1
-
18
-
-
0035955371
-
Biodiversity and ecosystem functioning: Current knowledge and future challenges
-
Loreau M., et al. (2001). Biodiversity and ecosystem functioning: current knowledge and future challenges. Science, 294, 804-808
-
(2001)
Science
, vol.294
, pp. 804-808
-
-
Loreau, M.1
-
19
-
-
84858863014
-
Individual genome assembly from complex community short-read metagenomic datasets
-
Luo C., et al. (2012). Individual genome assembly from complex community short-read metagenomic datasets. ISME J., 6, 898-901
-
(2012)
ISME J.
, vol.6
, pp. 898-901
-
-
Luo, C.1
-
20
-
-
79956041561
-
Emirge: Reconstruction of full-length ribosomal genes from microbial community short read sequencing data
-
Miller C.S., et al. (2011). EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data. Genome Biol., 12, R44
-
(2011)
Genome Biol
, vol.12
, pp. R44
-
-
Miller, C.S.1
-
21
-
-
84867397631
-
Metavelvet: An extension of velvet assembler to de novo metagenome assembly from short sequence reads
-
Namiki T., et al. (2012). MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads. Nucleic Acids Res., 40, e155-e155
-
(2012)
Nucleic Acids Res
, vol.40
, pp. e155-e155
-
-
Namiki, T.1
-
22
-
-
65549111754
-
Infernal 1.0: Inference of RNA alignments
-
Nawrocki E.P., et al. (2009). Infernal 1.0: inference of RNA alignments. Bioinformatics, 25, 1335-1337
-
(2009)
Bioinformatics
, vol.25
, pp. 1335-1337
-
-
Nawrocki, E.P.1
-
23
-
-
79959422558
-
Meta-IDBA: A de novo assembler for metagenomic data
-
Peng Y., et al. (2011). Meta-IDBA: a de novo assembler for metagenomic data. Bioinformatics, 27, i94-i101
-
(2011)
Bioinformatics
, vol.27
, pp. i94-i101
-
-
Peng, Y.1
-
24
-
-
84861760530
-
Idba-ud: A de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
-
Peng Y., et al. (2012). IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics, 28, 1420-1428
-
(2012)
Bioinformatics
, vol.28
, pp. 1420-1428
-
-
Peng, Y.1
-
25
-
-
0035931866
-
Life in extreme environments
-
Rothschild L.J. and Mancinelli R.L. (2001). Life in extreme environments. Nature, 409, 1092-1101
-
(2001)
Nature
, vol.409
, pp. 1092-1101
-
-
Rothschild, L.J.1
Mancinelli, R.L.2
-
26
-
-
52949083195
-
Gene-boosted assembly of a novel bacterial genome from very short reads
-
Salzberg S.L., et al. (2008). Gene-boosted assembly of a novel bacterial genome from very short reads. PLOS Comput. Biol., 4, e1000186
-
(2008)
Plos Comput. Biol
, vol.4
, pp. e1000186
-
-
Salzberg, S.L.1
-
27
-
-
0017341656
-
Microbial ecology of the gastrointestinal tract
-
Savage D.C. (1977). Microbial ecology of the gastrointestinal tract. Annu. Rev. Microbiol., 31, 107-133
-
(1977)
Annu. Rev. Microbiol
, vol.31
, pp. 107-133
-
-
Savage, D.C.1
-
28
-
-
84878647680
-
Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities
-
Shakya M., et al. (2013). Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities. Environ. Microbiol., 15, 1882-1899
-
(2013)
Environ. Microbiol
, vol.15
, pp. 1882-1899
-
-
Shakya, M.1
-
29
-
-
84857838310
-
Efficient de novo assembly of large genomes using compressed data structures
-
Simpson J.T. and Durbin R. (2012). Efficient de novo assembly of large genomes using compressed data structures. Genome Res., 22, 549-556
-
(2012)
Genome Res
, vol.22
, pp. 549-556
-
-
Simpson, J.T.1
Durbin, R.2
-
30
-
-
66449136667
-
Abyss: A parallel assembler for short read sequence data
-
Simpson J.T., et al. (2009). ABySS: a parallel assembler for short read sequence data. Genome Res., 19, 1117-1123
-
(2009)
Genome Res
, vol.19
, pp. 1117-1123
-
-
Simpson, J.T.1
-
31
-
-
0036081078
-
DNA Data Bank of Japan (DDBJ) for genome scale research in life science
-
Tateno Y., et al. (2002). DNA Data Bank of Japan (DDBJ) for genome scale research in life science. Nucleic Acids Res., 30, 27-30
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 27-30
-
-
Tateno, Y.1
-
32
-
-
84872152255
-
Metamos: A modular and open source metagenomic assembly and analysis pipeline
-
Treangen T., et al. (2013). MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. Genome Biol., 14, R2
-
(2013)
Genome Biol
, vol.14
, pp. R2
-
-
Treangen, T.1
-
33
-
-
20244376755
-
Comparative metagenomics of microbial communities
-
Tringe S.G., et al. (2005). Comparative metagenomics of microbial communities. Science, 308, 554-557
-
(2005)
Science
, vol.308
, pp. 554-557
-
-
Tringe, S.G.1
-
34
-
-
34548293679
-
Nave Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
-
Wang Q., et al. (2007). Nave Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol., 73, 5261-5267
-
(2007)
Appl. Environ. Microbiol
, vol.73
, pp. 5261-5267
-
-
Wang, Q.1
-
35
-
-
0001271789
-
Phylogenetic structure of the prokaryotic domain: The primary kingdoms
-
Woese C.R. and Fox G.E. (1977). Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl. Acad. Sci., 74, 5088-5090
-
(1977)
Proc. Natl. Acad. Sci
, vol.74
, pp. 5088-5090
-
-
Woese, C.R.1
Fox, G.E.2
-
36
-
-
0025300402
-
Towards a natural system of organisms: Proposal for the domains Archaea
-
Woese C.R., et al. (1990). Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. U.S.A, 87, 4576-4579
-
(1990)
Bacteria, and Eucarya. Proc. Natl. Acad. Sci. U.S.A
, vol.87
, pp. 4576-4579
-
-
Woese, C.R.1
-
37
-
-
84866468781
-
Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics
-
Wu Y., et al. (2012). Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics. Bioinformatics, 28, i363-i369
-
(2012)
Bioinformatics
, vol.28
, pp. i363-i369
-
-
Wu, Y.1
-
38
-
-
84886422310
-
Rna-code: A noncoding rna classification tool for short reads in ngs data lacking reference genomes
-
Yuan C. and Sun Y. (2013). RNA-CODE: A noncoding RNA classification tool for short reads in NGS data lacking reference genomes. PLoS One, 8, e77596
-
(2013)
Plos One
, vol.8
, pp. e77596
-
-
Yuan, C.1
Sun, Y.2
-
39
-
-
43149115851
-
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
-
(2008)
Genome Res
, vol.18
, pp. 821-829
-
-
Zerbino, D.R.1
Birney, E.2
-
40
-
-
84921297659
-
A scalable and accurate targeted gene assembly tool (sat-assembler) for next-generation sequencing data
-
Zhang Y., et al. (2014). A scalable and accurate targeted gene assembly tool (SAT-assembler) for next-generation sequencing data. PLoS Comput. Biol., 10, e1003737
-
(2014)
Plos Comput. Biol
, vol.10
, pp. e1003737
-
-
Zhang, Y.1
|