-
1
-
-
11144354360
-
Environmental genome shotgun sequencing of the Sargasso Sea
-
Venter, J.C., Remington, K., Heidelberg, J.F., Halpern, A.L., Rusch, D., Eisen, J.A., Wu, D., Paulsen, I., Nelson, K.E., Nelson, W. et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science, 304, 66-74.
-
(2004)
Science
, vol.304
, pp. 66-74
-
-
Venter, J.C.1
Remington, K.2
Heidelberg, J.F.3
Halpern, A.L.4
Rusch, D.5
Eisen, J.A.6
Wu, D.7
Paulsen, I.8
Nelson, K.E.9
Nelson, W.10
-
2
-
-
38449088143
-
Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes
-
Kurokawa, K., Itoh, T., Kuwahara, T., Oshima, K., Toh, H., Toyoda, A., Takami, H., Morita, H., Sharma, V.K., Srivastava, T.P. et al. (2007) Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res., 14, 169-181.
-
(2007)
DNA Res.
, vol.14
, pp. 169-181
-
-
Kurokawa, K.1
Itoh, T.2
Kuwahara, T.3
Oshima, K.4
Toh, H.5
Toyoda, A.6
Takami, H.7
Morita, H.8
Sharma, V.K.9
Srivastava, T.P.10
-
3
-
-
77950251400
-
A human gut microbial gene catalogue established by metagenomic sequencing
-
Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K.S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., Yamada, T. et al. (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature, 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
Nielsen, T.7
Pons, N.8
Levenez, F.9
Yamada, T.10
-
4
-
-
77449144323
-
Parallel, tag-directed assembly of locally derived short sequence reads
-
Hiatt, J.B., Patwardhan, R.P., Turner, E.H., Lee, C. and and Shendure, J. (2010) Parallel, tag-directed assembly of locally derived short sequence reads. Nat. Methods, 7, 119-122.
-
(2010)
Nat. Methods
, vol.7
, pp. 119-122
-
-
Hiatt, J.B.1
Patwardhan, R.P.2
Turner, E.H.3
Lee, C.4
Shendure, J.5
-
5
-
-
55449131166
-
Bioinformatics for whole-genome shotgun sequencing of microbial communities
-
Chen, K. and Pachter, L. (2005) Bioinformatics for whole-genome shotgun sequencing of microbial communities. PLoS Comput. Biol., 1, 106-112.
-
(2005)
PLoS Comput. Biol.
, vol.1
, pp. 106-112
-
-
Chen, K.1
Pachter, L.2
-
6
-
-
79959422558
-
Meta-IDBA: A de novo assembler for metagenomic data
-
Peng, Y., Leung, H.C., Yiu, S.M. and Chin, F.Y. (2011) Meta-IDBA: a de novo assembler for metagenomic data. Bioinformatics, 27, i94-i101.
-
(2011)
Bioinformatics
, vol.27
-
-
Peng, Y.1
Leung, H.C.2
Yiu, S.M.3
Chin, F.Y.4
-
7
-
-
79952374428
-
Genovo: De novo assembly for metagenomes
-
Laserson, J., Jojic, V. and Koller, D. (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
Jojic, V.2
Koller, D.3
-
9
-
-
67149088568
-
An ORFome assembly approach to metagenomics sequences analysis
-
Ye, Y. and Tang, H. (2009) An ORFome assembly approach to metagenomics sequences analysis. J. Bioinform. Comput. Biol., 7, 455-471.
-
(2009)
J. Bioinform. Comput. Biol.
, vol.7
, pp. 455-471
-
-
Ye, Y.1
Tang, H.2
-
10
-
-
71549119487
-
The oligonucleotide frequency derived error gradient and its application to the binning of metagenome fragments
-
Saeed, I. and Halgamuge, S.K. (2009) The oligonucleotide frequency derived error gradient and its application to the binning of metagenome fragments. BMC Genomics, 10(Suppl. 3), S10.
-
(2009)
BMC Genomics
, vol.10
, Issue.SUPPL. 3
-
-
Saeed, I.1
Halgamuge, S.K.2
-
11
-
-
77952894198
-
Unsupervised binning of environmental genomic fragments based on an error robust selection of l-mers
-
Yang, B., Peng, Y., Leung, H.C., Yiu, S.M., Chen, J.C. and Chin, F.Y. (2010) Unsupervised binning of environmental genomic fragments based on an error robust selection of l-mers. BMC Bioinformatics, 11(Suppl. 2), S5.
-
(2010)
BMC Bioinformatics
, vol.11
, Issue.SUPPL. 2
-
-
Yang, B.1
Peng, Y.2
Leung, H.C.3
Yiu, S.M.4
Chen, J.C.5
Chin, F.Y.6
-
12
-
-
79952425617
-
A novel abundance-based algorithm for binning metagenomic sequences using l-tuples
-
Wu, Y.W. and Ye, Y. (2011) A novel abundance-based algorithm for binning metagenomic sequences using l-tuples. J. Comput. Biol., 18, 523-534.
-
(2011)
J. Comput. Biol.
, vol.18
, pp. 523-534
-
-
Wu, Y.W.1
Ye, Y.2
-
13
-
-
57349141505
-
A bioinformatician's guide to metagenomics
-
Kunin, V., Copeland, A., Lapidus, A., Mavromatis, K. and Hugenholtz, P. (2008) A bioinformatician's guide to metagenomics. Microbiol. Mol. Biol. Rev., 72, 557-578.
-
(2008)
Microbiol. Mol. Biol. Rev.
, vol.72
, pp. 557-578
-
-
Kunin, V.1
Copeland, A.2
Lapidus, A.3
Mavromatis, K.4
Hugenholtz, P.5
-
14
-
-
77950797411
-
Whole genome assembly of a natto production strain Bacillus subtilis natto from very short read data
-
Nishito, Y., Osana, Y., Hachiya, T., Popendorf, K., Toyoda, A., Fujiyama, A., Itaya, M. and Sakakibara, Y. (2010) Whole genome assembly of a natto production strain Bacillus subtilis natto from very short read data. BMC Genomics, 11, 243.
-
(2010)
BMC Genomics
, vol.11
, pp. 243
-
-
Nishito, Y.1
Osana, Y.2
Hachiya, T.3
Popendorf, K.4
Toyoda, A.5
Fujiyama, A.6
Itaya, M.7
Sakakibara, Y.8
-
15
-
-
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
-
16
-
-
77949511368
-
Pebble and rock band: Heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler
-
Zerbino, D.R., McEwen, G.K., Margulies, E.H. and Birney, E. (2009) Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler. PLoS One, 4, e8407.
-
(2009)
PLoS One
, vol.4
-
-
Zerbino, D.R.1
McEwen, G.K.2
Margulies, E.H.3
Birney, E.4
-
17
-
-
0029312687
-
A new algorithm for DNA sequence assembly
-
Idury, R.M. and Waterman, M.S. (1995) A new algorithm for DNA sequence assembly. J. Comput. Biol., 2, 291-306.
-
(1995)
J. Comput. Biol.
, vol.2
, pp. 291-306
-
-
Idury, R.M.1
Waterman, M.S.2
-
18
-
-
0035859921
-
An Eulerian path approach to DNA fragment assembly
-
Pevzner, P.A., Tang, H. and Waterman, M.S. (2001) An Eulerian path approach to DNA fragment assembly. Proc. Natl Acad. Sci. USA, 98, 9748-9753.
-
(2001)
Proc. Natl Acad. Sci. USA
, vol.98
, pp. 9748-9753
-
-
Pevzner, P.A.1
Tang, H.2
Waterman, M.S.3
-
19
-
-
75349109607
-
ALLPATHS 2: Small genomes assembled accurately and with high continuity from short paired reads
-
Maccallum, I., Przybylski, D., Gnerre, S., Burton, J., Shlyakhter, I., Gnirke, A., Malek, J., McKernan, K. et al. (2009) ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads. Genome Biol., 10, R103.
-
(2009)
Genome Biol.
, vol.10
-
-
MacCallum, I.1
Przybylski, D.2
Gnerre, S.3
Burton, J.4
Shlyakhter, I.5
Gnirke, A.6
Malek, J.7
McKernan, K.8
-
20
-
-
66449136667
-
ABySS: A parallel assembler for short read sequence data
-
Simpson, J.T., Wong, K., Jackman, S.D., Schein, J.E., Jones, S.J. and Birol, I. (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
Wong, K.2
Jackman, S.D.3
Schein, J.E.4
Jones, S.J.5
Birol, I.6
-
21
-
-
0023988195
-
Genomic mapping by fingerprinting random clones: A mathematical analysis
-
Lander, E.S. and Waterman, M.S. (1988) Genomic mapping by fingerprinting random clones: a mathematical analysis. Genomics, 2, 231-239.
-
(1988)
Genomics
, vol.2
, pp. 231-239
-
-
Lander, E.S.1
Waterman, M.S.2
-
22
-
-
75649124547
-
De novo assembly of human genomes with massively parallel short read sequencing
-
Li, R., Zhu, H., Ruan, J., Qian, W., Fang, X., Shi, Z., Li, Y., Li, S., Shan, G., Kristiansen, K. 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
Zhu, H.2
Ruan, J.3
Qian, W.4
Fang, X.5
Shi, Z.6
Li, Y.7
Li, S.8
Shan, G.9
Kristiansen, K.10
-
23
-
-
33750976398
-
MetaGene: Prokaryotic gene finding from environmental genome shotgun sequences
-
Noguchi, H., Park, J. and Takagi, T. (2006) MetaGene: prokaryotic gene finding from environmental genome shotgun sequences. Nucleic Acids Res., 34, 5623-5630.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 5623-5630
-
-
Noguchi, H.1
Park, J.2
Takagi, T.3
-
24
-
-
78651322088
-
Species abundance distributions and richness estimations in fungal metagenomics - Lessons learned from community ecology
-
Unterseher, M., Jumpponen, A., Opik, M., Tedersoo, L., Moora, M., Dormann, C.F. and Schnittler, M. (2011) Species abundance distributions and richness estimations in fungal metagenomics - lessons learned from community ecology. Mol. Ecol., 20, 275-285.
-
(2011)
Mol. Ecol.
, vol.20
, pp. 275-285
-
-
Unterseher, M.1
Jumpponen, A.2
Opik, M.3
Tedersoo, L.4
Moora, M.5
Dormann, C.F.6
Schnittler, M.7
|