-
1
-
-
10344227692
-
Metagenomics: Application of genomics to uncultured microorganisms
-
DOI 10.1128/MMBR.68.4.669-685.2004
-
J. Handelsman, "Metagenomics: Application of Genomics to Uncultured Microorganisms," Microbiology and Molecular Biology Reviews, Vol. 68, No.4, pp. 669-685, 2004 (Pubitemid 39628532)
-
(2004)
Microbiology and Molecular Biology Reviews
, vol.68
, Issue.4
, pp. 669-685
-
-
Handelsman, J.1
-
2
-
-
10944226351
-
Metagenomics: Genomic analysis of microbial communities
-
DOI 10.1146/annurev.genet.38.072902.091216
-
C.S. Riesenfeld, P.D. Schloss, and J. Handelsman, "Metagenomics: genomic analysis of microbial communities," Annu. Rev. Genet, 38, 525-552, 2004. (Pubitemid 40013737)
-
(2004)
Annual Review of Genetics
, vol.38
, pp. 525-552
-
-
Riesenfeld, C.S.1
Schloss, P.D.2
Handelsman, J.3
-
3
-
-
11144354360
-
Environmental Genome Shotgun Sequencing of the Sargasso Sea
-
DOI 10.1126/science.1093857
-
J.C. Venter, K. Remington, J.F. Heidelberg, A.L. Halpern, D. Rusch, J.A. Eisen, D. Wu, I. Paulsen, K.E. Nelson, W. Nelson, D.E. Fouts, S. Levy, A.H. Knap, M.W. Lomas, K. Nealson, O. White, J. Peterson, J. Hoffman, R. Parsons, H.B. Tillson, C. Pfannkoch, Y.H. Rogers, H.O. Smith, "Environmental genome shotgun sequencing of the Sargasso Sea," Science, 304, 66-74, 2004. (Pubitemid 38451457)
-
(2004)
Science
, vol.304
, Issue.5667
, 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
Fouts, D.E.11
Levy, S.12
Knap, A.H.13
Lomas, M.W.14
Nealson, K.15
White, O.16
Peterson, J.17
Hoffman, J.18
Parsons, R.19
Baden-Tillson, H.20
Pfannkoch, C.21
Rogers, Y.-H.22
Smith, H.O.23
more..
-
4
-
-
1542377296
-
Community structure and metabolism through reconstruction of microbial genomes from the environment
-
DOI 10.1038/nature02340
-
G.W. Tyson, J. Chapman, P. Hugenholtz, E.E. Allen, R.J. Ram, P.M. Richardson, V.V. Solovyev, E.M. Rubin, D.S. Rokhsar and J.F. Banfield, "Community structure and metabolism through reconstruction of microbial genomes from the environment," Nature, 428: 37-43, 2004. (Pubitemid 38332350)
-
(2004)
Nature
, vol.428
, Issue.6978
, pp. 37-43
-
-
Tyson, G.W.1
Chapman, J.2
Hugenholtz, P.3
Allen, E.E.4
Ram, R.J.5
Richardson, P.M.6
Solovyev, V.V.7
Rubin, E.M.8
Rokhsar, D.S.9
Banfield, J.F.10
-
5
-
-
33947221422
-
Environmental shotgun sequencing: Its potential and challenges for studying the hidden world of microbes
-
DOI 10.1371/journal.pbio.0050082
-
J.A. Eisen, "Environmental Shotgun Sequencing: Its Potential and Challenges for Studying the Hidden World of Microbes," PLoS Biol, Vol. 5, No. 3, 2007. (Pubitemid 46422961)
-
(2007)
PLoS Biology
, vol.5
, Issue.3
, pp. 0384-0388
-
-
Eisen, J.A.1
-
6
-
-
67650388617
-
A novel binning approach and its application to a metagenome from a multiple extreme environment
-
North Bethesda, Md, USA
-
N. Maltsev, M. Syed, A. Rodriguez, B. Gopalan and F. Brockman, "A novel binning approach and its application to a metagenome from a multiple extreme environment," in Proceedings of the Joint Genomics: GTL Awardee Workshop V and 10 Journal of Biomedicine and Biotechnology Metabolic Engineering and USDA-DOE Plant Feedstock Genomics for Bioenergy Awardee Workshop, North Bethesda, Md, USA, 2007.
-
(2007)
Proceedings of the Joint Genomics: GTL Awardee Workshop V and 10 Journal of Biomedicine and Biotechnology Metabolic Engineering and USDA-DOE Plant Feedstock Genomics for Bioenergy Awardee Workshop
-
-
Maltsev, N.1
Syed, M.2
Rodriguez, A.3
Gopalan, B.4
Brockman, F.5
-
7
-
-
38649143159
-
Using growing self-organising maps to improve the binning process in environmental whole-genome shotgun sequencing
-
DOI 10.1155/2008/513701, PII S1110724308513701
-
C.KK. Chan, A.L. Hsu, S.L. Tang and S.K. Halgamuge, "Using Growing Self-Organising Maps to Improve the Binning Process in Environmental Whole-Genome Shotgun Sequencing," Journal of Biomedicine and Biotechnology, Article ID 513701, doi: 10.1155/2008/513701Volume 2008. (Pubitemid 351171854)
-
(2008)
Journal of Biomedicine and Biotechnology
, vol.2008
, Issue.1
, pp. 513701
-
-
Chan, C.-K.K.1
Hsu, A.L.2
Tang, S.-L.3
Halgamuge, S.K.4
-
8
-
-
34249794257
-
Use of simulated data sets to evaluate the fidelity of metagenomic processing methods
-
DOI 10.1038/nmeth1043, PII NMETH1043
-
K. Mavromatis, N. Ivanova, K. Barry, H. Shapiro, E. Goltsman, A.C. McHardy, I. Rigoutsos, A. Salamov, F. Korzeniewski, M. Land, A. Lapidus, I. Grigoriev, P. Richardson, P. Hugenholtz and N.C. Kyrpides, "Use of simulated data sets to evaluate the fidelity of metagenomic processing methods," Nature Methods, 4, (6), 495-500, 2007. (Pubitemid 46852075)
-
(2007)
Nature Methods
, vol.4
, Issue.6
, pp. 495-500
-
-
Mavromatis, K.1
Ivanova, N.2
Barry, K.3
Shapiro, H.4
Goltsman, E.5
McHardy, A.C.6
Rigoutsos, I.7
Salamov, A.8
Korzeniewski, F.9
Land, M.10
Lapidus, A.11
Grigoriev, I.12
Richardson, P.13
Hugenholtz, P.14
Kyrpides, N.C.15
-
9
-
-
33749858537
-
Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities
-
DOI 10.1038/nbt1247, PII NBT1247
-
H.G. Martln, N. Ivanova, V. Kunin, F. Warnecke, K.W. Barry, A.C. McHardy, C. Yeates, S. He, A.A. Salamov, E. Szeto, E. Dalin, N.H. Putnam, H.J. Shapiro, J.L. Pangilinan, I. Rigoutsos, N.C. Kyrpides, L.L. Blackall, K.D. McMahon, P. Hugenholtz, "Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities," Nat. Biotechnol, 24, 1263-1269 2006. (Pubitemid 44564773)
-
(2006)
Nature Biotechnology
, vol.24
, Issue.10
, pp. 1263-1269
-
-
Martin, H.G.1
Ivanova, N.2
Kunin, V.3
Warnecke, F.4
Barry, K.W.5
McHardy, A.C.6
Yeates, C.7
He, S.8
Salamov, A.A.9
Szeto, E.10
Dalin, E.11
Putnam, N.H.12
Shapiro, H.J.13
Pangilinan, J.L.14
Rigoutsos, I.15
Kyrpides, N.C.16
Blackall, L.L.17
McMahon, K.D.18
Hugenholtz, P.19
-
10
-
-
67650385757
-
-
Edited by Xu, Y. and Gogarten, J.P., Imperial College Press
-
Arima, K. and Wooley, J., "Metagenomics," in Computational Methods for Understanding Archaeal and Bacterial Genomes, Edited by Xu, Y. and Gogarten, J.P., Imperial College Press, 2008.
-
(2008)
Metagenomics in Computational Methods for Understanding Archaeal and Bacterial Genomes
-
-
Arima, K.1
Wooley, J.2
-
11
-
-
13244253777
-
TETRA: A web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences
-
DOI 10.1186/1471-2105-5-163
-
H. Teeling, J. Waldmann, T. Lombardot, M. Bauer and F.O. Glockner, "TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences," BMC Bioinformatics, 5, 163, 2004. (Pubitemid 40195345)
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 163
-
-
Teeling, H.1
Waldmann, J.2
Lombardot, T.3
Bauer, M.4
Glockner, F.O.5
-
12
-
-
33845957530
-
Accurate phylogenetic classification of variable-length DNA fragments
-
DOI 10.1038/nmeth976, PII NMETH976
-
A.C. McHardy, H.G. Martln, A. Tsirigos, P. Hugenholtz and I. Rigoutsos, "Accurate phylogenetic classification of variable-length DNA fragments," Nautre Methods, 4, (1), 63-72, 2007. (Pubitemid 46029478)
-
(2007)
Nature Methods
, vol.4
, Issue.1
, pp. 63-72
-
-
McHardy, A.C.1
Martin, H.G.2
Tsirigos, A.3
Hugenholtz, P.4
Rigoutsos, I.5
-
13
-
-
0032823783
-
Genomic signature: Characterization and classification of species assessed by chaos game representation of sequences
-
P.J. Deschavanne, A. Giron, J. Vilain, G. Fagot and B. Fertil, "Genomic signature: characterization and classification of species assessed by chaos game representation of sequences," Mol Biol Evol, 16, (10), 1391- 1399, 1999. (Pubitemid 29473232)
-
(1999)
Molecular Biology and Evolution
, vol.16
, Issue.10
, pp. 1391-1399
-
-
Deschavanne, P.J.1
Giron, A.2
Vilain, J.3
Fagot, G.4
Fertit, B.5
-
14
-
-
0033529862
-
Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA
-
DOI 10.1073/pnas.96.16.9184
-
A. Campbell, J. Mrazek and S. Karlin, "Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA," Proc. Natl Acad. Sci., USA 96, 9184-9189, 1999. (Pubitemid 29374729)
-
(1999)
Proceedings of the National Academy of Sciences of the United States of America
, vol.96
, Issue.16
, pp. 9184-9189
-
-
Campbell, A.1
Mrazek, J.2
Karlin, S.3
-
15
-
-
0034887748
-
Capturing whole-genome characteristics in short sequences using a naive Bayesian classifier
-
DOI 10.1101/gr.186401
-
R. Sandberg, G. Winberg, C.-I. Branden, A. Kaske, I. Ernberg and J. Coster, "Capturing Whole-Genome Characteristics in Short Sequences Using a Naive Bayesian Classifier," Genome Res, 11, 8, 1404-1409, 2001. (Pubitemid 32771547)
-
(2001)
Genome Research
, vol.11
, Issue.8
, pp. 1404-1409
-
-
Sandberg, R.1
Winberg, G.2
Branden, C.-I.3
Kaske, A.4
Ernberg, I.5
Coster, J.6
-
19
-
-
0032518163
-
Microbial gene identification using interpolated Markov models
-
DOI 10.1093/nar/26.2.544
-
S.L. Salzberg, A.L. Delcher., S. Kasif and O. White, "Microbial gene identification using interpolated Markov models," Nucleic Acids Res, 26, (2), pp. 544-548, 1998. (Pubitemid 28291582)
-
(1998)
Nucleic Acids Research
, vol.26
, Issue.2
, pp. 544-548
-
-
Salzberg, S.L.1
Deicher, A.L.2
Kasif, S.3
White, O.4
-
20
-
-
33751436704
-
PathogenMIPer: A tool for the design of molecular inversion probes to detect multiple pathogens
-
DOI 10.1186/1471-2105-7-500
-
S. Thiyagarajan, M. Karhanek, M. Akhras, R.W. Davis and N. Pourmand, "PathogenMIPer: a tool for the design of molecular inversion probes to detect multiple pathogens," BMC Bioinformatics, 7: 500, 2006. (Pubitemid 44816700)
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 500
-
-
Thiyagarajan, S.1
Karhanek, M.2
Akhras, M.3
Davis, R.W.4
Pourmand, N.5
-
21
-
-
0346061723
-
High-dimensional data analysis: The curses and blessings of dimensionality
-
August 6-11
-
D.L. Donoho, "High-dimensional data analysis: The curses and blessings of dimensionality," Proc. AMS Conf. Math. Challenges of the 21st Century, August 6-11, 2000.
-
(2000)
Proc. AMS Conf. Math. Challenges of the 21st Century
-
-
Donoho, D.L.1
-
23
-
-
67650354446
-
-
"http://en.wikipedia.org/wiki/Linearclassifier".
-
-
-
-
25
-
-
44649090674
-
Gene prediction in metagenomic fragments: A large scale machine learning approach
-
DOI 10.1186/1471-2105-9-217
-
K.J. Hoff, M. Tech, T. Lingner, R. Daniel, B. Morgenstern and P. Meinicke, "Gene prediction in metagenomic fragments: A large scale machine learning approach," BMC Bioinformatics, 9:217, 2008. (Pubitemid 351785135)
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 217
-
-
Hoff, K.J.1
Tech, M.2
Lingner, T.3
Daniel, R.4
Morgenstern, B.5
Meinicke, P.6
-
26
-
-
85164392958
-
A study of cross-validation and bootstrap for accuracy estimation and model selection
-
C.S. Mellish, (Ed.) Morgan Kaufmann
-
R. Kohavi, "A study of cross-validation and bootstrap for accuracy estimation and model selection". In C.S. Mellish, (Ed.), Proceedings IJCAI-95, Morgan Kaufmann, 1137-1143, 1995.
-
(1995)
Proceedings IJCAI-95
, pp. 1137-1143
-
-
Kohavi, R.1
-
27
-
-
0018079655
-
Basic principles of ROC analysis
-
C.E. Metz, "Basic principles of ROC analysis", Semin Nucl Med, 8, (4), pp: 283-198, 1978 (Pubitemid 9075026)
-
(1978)
Seminars in Nuclear Medicine
, vol.8
, Issue.4
, pp. 283-298
-
-
Metz, C.E.1
|