-
1
-
-
10344227692
-
Metagenomics: Application of genomics to uncultured microorganisms
-
Handelsman, J. (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol. Mol. Biol. Rev., 68, 669-685.
-
(2004)
Microbiol. Mol. Biol. Rev
, vol.68
, pp. 669-685
-
-
Handelsman, J.1
-
2
-
-
84855896297
-
From bacterial to microbial ecosystems (metagenomics)
-
Williamson, S.J. and Yooseph, S. (2012) From bacterial to microbial ecosystems (metagenomics). Methods Mol. Biol., 804, 35-55.
-
(2012)
Methods Mol. Biol
, vol.804
, pp. 35-55
-
-
Williamson, S.J.1
Yooseph, S.2
-
3
-
-
24044455869
-
Genome sequencing in microfabricated high-density picolitre reactors
-
Margulies, M., Egholm, M., Altman, W.E., Attiya, S., Bader, J.S., Bemben, L.A., Berka, J., Braverman, M.S., Chen, Y.J., Chen, Z. et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437, 376-380.
-
(2005)
Nature
, vol.437
, pp. 376-380
-
-
Margulies, M.1
Egholm, M.2
Altman, W.E.3
Attiya, S.4
Bader, J.S.5
Bemben, L.A.6
Berka, J.7
Braverman, M.S.8
Chen, Y.J.9
Chen, Z.10
-
4
-
-
33750953227
-
Whole-genome re-sequencing
-
Bentley, D.R. (2006) Whole-genome re-sequencing. Curr. Opin. Genet. Dev., 16, 545-552.
-
(2006)
Curr. Opin. Genet. Dev
, vol.16
, pp. 545-552
-
-
Bentley, D.R.1
-
5
-
-
46449103738
-
A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning
-
Valouev, A., Ichikawa, J., Tonthat, T., Stuart, J., Ranade, S., Peckham, H., Zeng, K., Malek, J.A., Costa, G., McKernan, K. et al. (2008) A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res., 18, 1051-1063.
-
(2008)
Genome Res
, vol.18
, pp. 1051-1063
-
-
Valouev, A.1
Ichikawa, J.2
Tonthat, T.3
Stuart, J.4
Ranade, S.5
Peckham, H.6
Zeng, K.7
Malek, J.A.8
Costa, G.9
McKernan, K.10
-
6
-
-
33947238287
-
The sorcerer II global ocean sampling expedition: Northwest Atlantic through Eastern Tropical Pacific
-
Rusch, D.B., Halpern, A.L., Sutton, G., Heidelberg, K.B., Williamson, S., Yooseph, S., Wu, D., Eisen, J.A., Hoffman, J.M., Remington, K. et al. (2007) The sorcerer II global ocean sampling expedition: Northwest Atlantic through Eastern Tropical Pacific. PLoS Biol., 5, e77.
-
(2007)
PLoS Biol
, vol.5
-
-
Rusch, D.B.1
Halpern, A.L.2
Sutton, G.3
Heidelberg, K.B.4
Williamson, S.5
Yooseph, S.6
Wu, D.7
Eisen, J.A.8
Hoffman, J.M.9
Remington, K.10
-
7
-
-
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
-
8
-
-
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
-
-
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
-
10
-
-
84858992875
-
MetaVelvet: An extension of Velvet assembler to de novo metagenome assembly from short sequence reads
-
ACM, Chicago, Illinois
-
Namiki, T., Hachiya, T., Tanaka, H. and Sakakibara, Y. (2011) MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads. In: Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM, Chicago, Illinois, pp. 116-124.
-
(2011)
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
, pp. 116-124
-
-
Namiki, T.1
Hachiya, T.2
Tanaka, H.3
Sakakibara, Y.4
-
11
-
-
84861760530
-
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.
-
(2012)
Bioinformatics
, vol.28
, pp. 1420-1428
-
-
Peng, Y.1
Leung, H.C.2
Yiu, S.M.3
Chin, F.Y.4
-
12
-
-
33745067721
-
Ten years of bacterial genome sequencing: Comparativegenomics-based discoveries
-
Binnewies, T.T., Motro, Y., Hallin, P.F., Lund, O., Dunn, D., La, T., Hampson, D.J., Bellgard, M., Wassenaar, T.M. and Ussery, D.W. (2006) Ten years of bacterial genome sequencing: comparativegenomics-based discoveries. Funct. Integr. Genomics, 6, 165-185.
-
(2006)
Funct. Integr. Genomics
, vol.6
, pp. 165-185
-
-
Binnewies, T.T.1
Motro, Y.2
Hallin, P.F.3
Lund, O.4
Dunn La D, T.5
Hampson, D.J.6
Bellgard, M.7
Wassenaar, T.M.8
Ussery, D.W.9
-
13
-
-
0026458378
-
Amino acid substitution matrices from protein blocks
-
Henikoff, S. and Henikoff, J.G. (1992) Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. USA, 89, 10915-10919.
-
(1992)
Proc. Natl Acad. Sci. USA
, vol.89
, pp. 10915-10919
-
-
Henikoff, S.1
Henikoff, J.G.2
-
14
-
-
0000228203
-
-
3rd edn. National Biomedical Research Foundation, Washington DC
-
Dayhoff, M.O., Schwartz, R.M. and Orcutt, B.C. (eds), (1978) A Model of Evolutionary Change in Proteins, 3rd edn. National Biomedical Research Foundation, Washington DC.
-
(1978)
A Model of Evolutionary Change in Proteins
-
-
Dayhoff, M.O.1
Schwartz, R.M.2
Orcutt, B.C.3
-
15
-
-
59149090570
-
MetaGeneAnnotator: Detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes
-
Noguchi, H., Taniguchi, T. and Itoh, T. (2008) MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes. DNA Res., 15, 387-396.
-
(2008)
DNA Res
, vol.15
, pp. 387-396
-
-
Noguchi, H.1
Taniguchi, T.2
Itoh, T.3
-
16
-
-
78651326786
-
FragGeneScan: Predicting genes in short and error-prone reads
-
Rho, M., Tang, H. and Ye, Y. (2010) FragGeneScan: predicting genes in short and error-prone reads. Nucleic Acids Res., 38, e191.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Rho, M.1
Tang, H.2
Ye, Y.3
-
17
-
-
67849095415
-
Orphelia: Predicting genes in metagenomic sequencing reads
-
Hoff, K.J., Lingner, T., Meinicke, P. and Tech, M. (2009) Orphelia: predicting genes in metagenomic sequencing reads. Nucleic Acids Res., 37, W101-W105.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Hoff, K.J.1
Lingner, T.2
Meinicke, P.3
Tech, M.4
-
18
-
-
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
-
19
-
-
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
-
20
-
-
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
-
21
-
-
80755159050
-
How to apply de Bruijn graphs to genome assembly
-
Compeau, P.E., Pevzner, P.A. and Tesler, G. (2011) How to apply de Bruijn graphs to genome assembly. Nat. Biotechnol., 29, 987-991.
-
(2011)
Nat. Biotechnol
, vol.29
, pp. 987-991
-
-
Compeau, P.E.1
Pevzner, P.A.2
Tesler, G.3
-
22
-
-
0035072551
-
Clustering of highly homologous sequences to reduce the size of large protein databases
-
Li, W., Jaroszewski, L. and Godzik, A. (2001) Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics, 17, 282-283.
-
(2001)
Bioinformatics
, vol.17
, pp. 282-283
-
-
Li, W.1
Jaroszewski, L.2
Godzik, A.3
-
23
-
-
33745634395
-
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.
-
(2006)
Bioinformatics
, vol.22
, pp. 1658-1659
-
-
Li, W.1
Godzik, A.2
-
24
-
-
54949137701
-
MetaSim: A sequencing simulator for genomics and metagenomics
-
Richter, D.C., Ott, F., Auch, A.F., Schmid, R. and Huson, D.H. (2008) MetaSim: a sequencing simulator for genomics and metagenomics. PLoS One, 3, e3373.
-
(2008)
PLoS One
, vol.3
-
-
Richter, D.C.1
Ott, F.2
Auch, A.F.3
Schmid, R.4
Huson, D.H.5
-
26
-
-
68549104404
-
The sequence alignment/map format and SAMtools
-
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G. and Durbin, R. (2009) The sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078-2079.
-
(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
Marth, G.7
Abecasis, G.8
Durbin, R.9
-
27
-
-
78149272458
-
Genomic and functional adaptation in surface ocean planktonic prokaryotes
-
Yooseph, S., Nealson, K.H., Rusch, D.B., McCrow, J.P., Dupont, C.L., Kim, M., Johnson, J., Montgomery, R., Ferriera, S., Beeson, K. et al. (2010) Genomic and functional adaptation in surface ocean planktonic prokaryotes. Nature, 468, 60-66.
-
(2010)
Nature
, vol.468
, pp. 60-66
-
-
Yooseph, S.1
Nealson, K.H.2
Rusch, D.B.3
McCrow, J.P.4
Dupont, C.L.5
Kim, M.6
Johnson, J.7
Montgomery, R.8
Ferriera, S.9
Beeson, K.10
-
28
-
-
70449713952
-
The NIH human microbiome project
-
Peterson, J., Garges, S., Giovanni, M., McInnes, P., Wang, L., Schloss, J.A., Bonazzi, V., McEwen, J.E., Wetterstrand, K.A., Deal, C. et al. (2009) The NIH human microbiome project. Genome Res., 19, 2317-2323.
-
(2009)
Genome Res
, vol.19
, pp. 2317-2323
-
-
Peterson, J.1
Garges, S.2
Giovanni, M.3
McInnes, P.4
Wang, L.5
Schloss, J.A.6
Bonazzi, V.7
McEwen, J.E.8
Wetterstrand, K.A.9
Deal, C.10
-
29
-
-
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
-
30
-
-
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
-
31
-
-
77957357555
-
The human oral microbiome
-
Dewhirst, F.E., Chen, T., Izard, J., Paster, B.J., Tanner, A.C., Yu, W.H., Lakshmanan, A. and Wade, W.G. (2010) The human oral microbiome. J. Bacteriol., 192, 5002-5017.
-
(2010)
J. Bacteriol
, vol.192
, pp. 5002-5017
-
-
Dewhirst, F.E.1
Chen, T.2
Izard, J.3
Paster, B.J.4
Tanner, A.C.5
Yu, W.H.6
Lakshmanan, A.7
Wade, W.G.8
-
32
-
-
84862286169
-
A framework for human microbiome research
-
Methe, B.A., Nelson, K.E., Pop, M., Creasy, H.H., Giglio, M.G., Huttenhower, C., Gevers, D., Petrosino, J.F., Abubucker, S., Badger, J.H. et al. (2012) A framework for human microbiome research. Nature, 486, 215-221.
-
(2012)
Nature
, vol.486
, pp. 215-221
-
-
Methe, B.A.1
Nelson, K.E.2
Pop, M.3
Creasy, H.H.4
Giglio, M.G.5
Huttenhower, C.6
Gevers, D.7
Petrosino, J.F.8
Abubucker, S.9
Badger, J.H.10
-
33
-
-
33846062023
-
Database resources of the National Center for Biotechnology Information
-
Wheeler, D.L., Barrett, T., Benson, D.A., Bryant, S.H., Canese, K., Chetvernin, V., Church, D.M., DiCuccio, M., Edgar, R., Federhen, S. et al. (2007) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 35, D5-D12.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Wheeler, D.L.1
Barrett, T.2
Benson, D.A.3
Bryant, S.H.4
Canese, K.5
Chetvernin, V.6
Church, D.M.7
Dicuccio, M.8
Edgar, R.9
Federhen, S.10
-
34
-
-
67650311860
-
A statistical framework for the functional analysis of metagenomes
-
Springer Tucson Arizona
-
Sharon, I., Pati, A., Markowitz, V.M. and Pinter, R.Y. (2009) A Statistical Framework for the Functional Analysis of Metagenomes. In: Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology. Springer, Tucson, Arizona, pp. 496-511.
-
(2009)
Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology
, pp. 496-511
-
-
Sharon, I.1
Pati, A.2
Markowitz, V.M.3
Pinter, R.Y.4
|