Hyperbolic SOM-based clustering of DNA fragment features for taxonomic visualization and classification
Martin C, Diaz NN, Ontrup J, Nattkemper TW (2008)
Bioinformatics 24(14): 1568-1574.
Zeitschriftenaufsatz
| Veröffentlicht | Englisch
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
Autor*in
Einrichtung
Stichworte
Genomics;
HSOM;
hyperbolic SOM;
information visualization;
Metagenomics;
Meta genomics;
SOM;
Self-Organizing Map;
classification;
Bioinformatics;
taxonomic classification
Erscheinungsjahr
2008
Zeitschriftentitel
Bioinformatics
Band
24
Ausgabe
14
Seite(n)
1568-1574
ISSN
1367-4803
eISSN
1460-2059
Page URI
https://pub.uni-bielefeld.de/record/1587052
Zitieren
Martin C, Diaz NN, Ontrup J, Nattkemper TW. Hyperbolic SOM-based clustering of DNA fragment features for taxonomic visualization and classification. Bioinformatics. 2008;24(14):1568-1574.
Martin, C., Diaz, N. N., Ontrup, J., & Nattkemper, T. W. (2008). Hyperbolic SOM-based clustering of DNA fragment features for taxonomic visualization and classification. Bioinformatics, 24(14), 1568-1574. https://doi.org/10.1093/bioinformatics/btn257
Martin, Christian, Diaz, Naryttza N., Ontrup, Jörg, and Nattkemper, Tim Wilhelm. 2008. “Hyperbolic SOM-based clustering of DNA fragment features for taxonomic visualization and classification”. Bioinformatics 24 (14): 1568-1574.
Martin, C., Diaz, N. N., Ontrup, J., and Nattkemper, T. W. (2008). Hyperbolic SOM-based clustering of DNA fragment features for taxonomic visualization and classification. Bioinformatics 24, 1568-1574.
Martin, C., et al., 2008. Hyperbolic SOM-based clustering of DNA fragment features for taxonomic visualization and classification. Bioinformatics, 24(14), p 1568-1574.
C. Martin, et al., “Hyperbolic SOM-based clustering of DNA fragment features for taxonomic visualization and classification”, Bioinformatics, vol. 24, 2008, pp. 1568-1574.
Martin, C., Diaz, N.N., Ontrup, J., Nattkemper, T.W.: Hyperbolic SOM-based clustering of DNA fragment features for taxonomic visualization and classification. Bioinformatics. 24, 1568-1574 (2008).
Martin, Christian, Diaz, Naryttza N., Ontrup, Jörg, and Nattkemper, Tim Wilhelm. “Hyperbolic SOM-based clustering of DNA fragment features for taxonomic visualization and classification”. Bioinformatics 24.14 (2008): 1568-1574.
Daten bereitgestellt von European Bioinformatics Institute (EBI)
9 Zitationen in Europe PMC
Daten bereitgestellt von Europe PubMed Central.
Viral population analysis of the taiga tick, Ixodes persulcatus, by using Batch Learning Self-Organizing Maps and BLAST search.
Qiu Y, Abe T, Nakao R, Satoh K, Sugimoto C., J Vet Med Sci 81(3), 2019
PMID: 30674747
Qiu Y, Abe T, Nakao R, Satoh K, Sugimoto C., J Vet Med Sci 81(3), 2019
PMID: 30674747
Comparison of Acceleration Techniques for Selected Low-Level Bioinformatics Operations.
Langenkämper D, Jakobi T, Feld D, Jelonek L, Goesmann A, Nattkemper TW., Front Genet 7(), 2016
PMID: 26904094
Langenkämper D, Jakobi T, Feld D, Jelonek L, Goesmann A, Nattkemper TW., Front Genet 7(), 2016
PMID: 26904094
Development of self-compressing BLSOM for comprehensive analysis of big sequence data.
Kikuchi A, Ikemura T, Abe T., Biomed Res Int 2015(), 2015
PMID: 26495297
Kikuchi A, Ikemura T, Abe T., Biomed Res Int 2015(), 2015
PMID: 26495297
AKE - the Accelerated k-mer Exploration web-tool for rapid taxonomic classification and visualization.
Langenkämper D, Goesmann A, Nattkemper TW., BMC Bioinformatics 15(), 2014
PMID: 25495116
Langenkämper D, Goesmann A, Nattkemper TW., BMC Bioinformatics 15(), 2014
PMID: 25495116
A novel approach, based on BLSOMs (Batch Learning Self-Organizing Maps), to the microbiome analysis of ticks.
Nakao R, Abe T, Nijhof AM, Yamamoto S, Jongejan F, Ikemura T, Sugimoto C., ISME J 7(5), 2013
PMID: 23303373
Nakao R, Abe T, Nijhof AM, Yamamoto S, Jongejan F, Ikemura T, Sugimoto C., ISME J 7(5), 2013
PMID: 23303373
Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective.
Teeling H, Glöckner FO., Brief Bioinform 13(6), 2012
PMID: 22966151
Teeling H, Glöckner FO., Brief Bioinform 13(6), 2012
PMID: 22966151
Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics.
Weber M, Teeling H, Huang S, Waldmann J, Kassabgy M, Fuchs BM, Klindworth A, Klockow C, Wichels A, Gerdts G, Amann R, Glöckner FO., ISME J 5(5), 2011
PMID: 21160538
Weber M, Teeling H, Huang S, Waldmann J, Kassabgy M, Fuchs BM, Klindworth A, Klockow C, Wichels A, Gerdts G, Amann R, Glöckner FO., ISME J 5(5), 2011
PMID: 21160538
Distinguishing microbial genome fragments based on their composition: evolutionary and comparative genomic perspectives.
Perry SC, Beiko RG., Genome Biol Evol 2(), 2010
PMID: 20333228
Perry SC, Beiko RG., Genome Biol Evol 2(), 2010
PMID: 20333228
Community-wide analysis of microbial genome sequence signatures.
Dick GJ, Andersson AF, Baker BJ, Simmons SL, Thomas BC, Yelton AP, Banfield JF., Genome Biol 10(8), 2009
PMID: 19698104
Dick GJ, Andersson AF, Baker BJ, Simmons SL, Thomas BC, Yelton AP, Banfield JF., Genome Biol 10(8), 2009
PMID: 19698104
27 References
Daten bereitgestellt von Europe PubMed Central.
A novel bioinformatic strategy for unveiling hidden genome signatures of eukaryotes: self-organizing map of oligonucleotide frequency.
Abe T, Kanaya S, Kinouchi M, Ichiba Y, Kozuki T, Ikemura T., Genome Inform 13(), 2002
PMID: 14571370
Abe T, Kanaya S, Kinouchi M, Ichiba Y, Kozuki T, Ikemura T., Genome Inform 13(), 2002
PMID: 14571370
Novel phylogenetic studies of genomic sequence fragments derived from uncultured microbe mixtures in environmental and clinical samples.
Abe T, Sugawara H, Kinouchi M, Kanaya S, Ikemura T., DNA Res. 12(5), 2005
PMID: 16769690
Abe T, Sugawara H, Kinouchi M, Kanaya S, Ikemura T., DNA Res. 12(5), 2005
PMID: 16769690
A novel bioinformatics tool for phylogenetic classification of genomic sequence fragments derived from mixed genomes of uncultured environmental microbes
Abe, Polar Biosci 20(), 2006
Abe, Polar Biosci 20(), 2006
AUTHOR UNKNOWN, 0
Exploration of phylogenetic data using a global sequence analysis method.
Chapus C, Dufraigne C, Edwards S, Giron A, Fertil B, Deschavanne P., BMC Evol. Biol. 5(), 2005
PMID: 16280081
Chapus C, Dufraigne C, Edwards S, Giron A, Fertil B, Deschavanne P., BMC Evol. Biol. 5(), 2005
PMID: 16280081
Genomic signature: characterization and classification of species assessed by chaos game representation of sequences.
Deschavanne PJ, Giron A, Vilain J, Fagot G, Fertil B., Mol. Biol. Evol. 16(10), 1999
PMID: 10563018
Deschavanne PJ, Giron A, Vilain J, Fagot G, Fertil B., Mol. Biol. Evol. 16(10), 1999
PMID: 10563018
Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes.
Gupta RS., Microbiol. Mol. Biol. Rev. 62(4), 1998
PMID: 9841678
Gupta RS., Microbiol. Mol. Biol. Rev. 62(4), 1998
PMID: 9841678
Handelsmann, 2007
Hastie, 2001
Dinucleotide relative abundance extremes: a genomic signature.
Karlin S, Burge C., Trends Genet. 11(7), 1995
PMID: 7482779
Karlin S, Burge C., Trends Genet. 11(7), 1995
PMID: 7482779
The self-organizing map
Kohonen, Proc. IEEE 78(), 1990
Kohonen, Proc. IEEE 78(), 1990
A focus + context technique based on hyperbolic geometry for visualizing large hierarchies
Lamping, 1995
Lamping, 1995
Li, 1997
Genome sequencing in microfabricated high-density picolitre reactors.
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM., Nature 437(7057), 2005
PMID: 16056220
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM., Nature 437(7057), 2005
PMID: 16056220
Genome feature exploration using hyperbolic self-organising maps
Martin, 2007
Martin, 2007
Accurate phylogenetic classification of variable-length DNA fragments.
McHardy AC, Martin HG, Tsirigos A, Hugenholtz P, Rigoutsos I., Nat. Methods 4(1), 2006
PMID: 17179938
McHardy AC, Martin HG, Tsirigos A, Hugenholtz P, Rigoutsos I., Nat. Methods 4(1), 2006
PMID: 17179938
Hyperbolic self-organizing maps for semantic navigation
Ontrup, 2001
Ontrup, 2001
Large-scale data exploration with the hierarchically growing hyperbolic SOM.
Ontrup J, Ritter H., Neural Netw 19(6-7), 2006
PMID: 16806818
Ontrup J, Ritter H., Neural Netw 19(6-7), 2006
PMID: 16806818
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes.
Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crecy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Ruckert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V., Nucleic Acids Res. 33(17), 2005
PMID: 16214803
Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crecy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Ruckert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V., Nucleic Acids Res. 33(17), 2005
PMID: 16214803
Whole proteome prokaryote phylogeny without sequence alignment: a K-string composition approach.
Qi J, Wang B, Hao BI., J. Mol. Evol. 58(1), 2004
PMID: 14743310
Qi J, Wang B, Hao BI., J. Mol. Evol. 58(1), 2004
PMID: 14743310
Self-organizing maps in non-euclidian spaces
Ritter, 1999
Ritter, 1999
A vector space model for automatic indexing
Salton, Inf. Retr 18(), 1975
Salton, Inf. Retr 18(), 1975
DNA sequencing with chain-terminating inhibitors.
Sanger F, Nicklen S, Coulson AR., Proc. Natl. Acad. Sci. U.S.A. 74(12), 1977
PMID: 271968
Sanger F, Nicklen S, Coulson AR., Proc. Natl. Acad. Sci. U.S.A. 74(12), 1977
PMID: 271968
A comprehensive vertebrate phylogeny using vector representations of protein sequences from whole genomes.
Stuart GW, Moffett K, Leader JJ., Mol. Biol. Evol. 19(4), 2002
PMID: 11919297
Stuart GW, Moffett K, Leader JJ., Mol. Biol. Evol. 19(4), 2002
PMID: 11919297
TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences.
Teeling H, Waldmann J, Lombardot T, Bauer M, Glockner FO., BMC Bioinformatics 5(), 2004
PMID: 15507136
Teeling H, Waldmann J, Lombardot T, Bauer M, Glockner FO., BMC Bioinformatics 5(), 2004
PMID: 15507136
Self-organizing neural networks for visualization and classification
Ultsch, 1993
Ultsch, 1993
Database resources of the National Center for Biotechnology Information: 2002 update.
Wheeler DL, Church DM, Lash AE, Leipe DD, Madden TL, Pontius JU, Schuler GD, Schriml LM, Tatusova TA, Wagner L, Rapp BA., Nucleic Acids Res. 30(1), 2002
PMID: 11752242
Wheeler DL, Church DM, Lash AE, Leipe DD, Madden TL, Pontius JU, Schuler GD, Schriml LM, Tatusova TA, Wagner L, Rapp BA., Nucleic Acids Res. 30(1), 2002
PMID: 11752242
Export
Markieren/ Markierung löschen
Markierte Publikationen
Web of Science
Dieser Datensatz im Web of Science®Quellen
PMID: 18535082
PubMed | Europe PMC
Suchen in
Google Scholar