Partitioning Biological Data with Transitivity Clustering

Wittkop T, Emig D, Lange SJ, Rahmann S, Albrecht M, Morris JH, Böcker S, Stoye J, Baumbach J (2010)
Nature Methods 7(6): 419-420.

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DOI
Autor*in
Wittkop, Tobias; Emig, Dorothea; Lange, Sita J.; Rahmann, Sven; Albrecht, Mario; Morris, John H.; Böcker, Sebastian; Stoye, JensUniBi ; Baumbach, Jan
Einrichtung
Technische Fakultät > AG Genominformatik
Centrum für Biotechnologie > Arbeitsgruppe J. Stoye
Center of Excellence - Cognitive Interaction Technology CITEC
Centrum für Biotechnologie > Institut für Bioinformatik
Erscheinungsjahr
2010
Zeitschriftentitel
Nature Methods
Band
7
Ausgabe
6
Seite(n)
419-420
ISSN
1548-7091
eISSN
1548-7105
Page URI
https://pub.uni-bielefeld.de/record/1795670

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Wittkop T, Emig D, Lange SJ, et al. Partitioning Biological Data with Transitivity Clustering. Nature Methods. 2010;7(6):419-420.
Wittkop, T., Emig, D., Lange, S. J., Rahmann, S., Albrecht, M., Morris, J. H., Böcker, S., et al. (2010). Partitioning Biological Data with Transitivity Clustering. Nature Methods, 7(6), 419-420. https://doi.org/10.1038/nmeth0610-419
Wittkop, Tobias, Emig, Dorothea, Lange, Sita J., Rahmann, Sven, Albrecht, Mario, Morris, John H., Böcker, Sebastian, Stoye, Jens, and Baumbach, Jan. 2010. “Partitioning Biological Data with Transitivity Clustering”. Nature Methods 7 (6): 419-420.
Wittkop, T., Emig, D., Lange, S. J., Rahmann, S., Albrecht, M., Morris, J. H., Böcker, S., Stoye, J., and Baumbach, J. (2010). Partitioning Biological Data with Transitivity Clustering. Nature Methods 7, 419-420.
Wittkop, T., et al., 2010. Partitioning Biological Data with Transitivity Clustering. Nature Methods, 7(6), p 419-420.
T. Wittkop, et al., “Partitioning Biological Data with Transitivity Clustering”, Nature Methods, vol. 7, 2010, pp. 419-420.
Wittkop, T., Emig, D., Lange, S.J., Rahmann, S., Albrecht, M., Morris, J.H., Böcker, S., Stoye, J., Baumbach, J.: Partitioning Biological Data with Transitivity Clustering. Nature Methods. 7, 419-420 (2010).
Wittkop, Tobias, Emig, Dorothea, Lange, Sita J., Rahmann, Sven, Albrecht, Mario, Morris, John H., Böcker, Sebastian, Stoye, Jens, and Baumbach, Jan. “Partitioning Biological Data with Transitivity Clustering”. Nature Methods 7.6 (2010): 419-420.

44 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Time-Resolved Systems Medicine Reveals Viral Infection-Modulating Host Targets.
Wiwie C, Kuznetsova I, Mostafa A, Rauch A, Haakonsson A, Barrio-Hernandez I, Blagoev B, Mandrup S, Schmidt HHHW, Pleschka S, Röttger R, Baumbach J., Syst Med (New Rochelle) 2(1), 2019
PMID: 31119214
A comprehensive evaluation of module detection methods for gene expression data.
Saelens W, Cannoodt R, Saeys Y., Nat Commun 9(1), 2018
PMID: 29545622
MOCASSIN-prot: a multi-objective clustering approach for protein similarity networks.
Keel BN, Deng B, Moriyama EN., Bioinformatics 34(8), 2018
PMID: 29186344
Bipartite graphs in systems biology and medicine: a survey of methods and applications.
Pavlopoulos GA, Kontou PI, Pavlopoulou A, Bouyioukos C, Markou E, Bagos PG., Gigascience 7(4), 2018
PMID: 29648623
Detecting complexes from edge-weighted PPI networks via genes expression analysis.
Zhang Z, Song J, Tang J, Xu X, Guo F., BMC Syst Biol 12(suppl 4), 2018
PMID: 29745859
fMLC: fast multi-level clustering and visualization of large molecular datasets.
Vu D, Georgievska S, Szoke S, Kuzniar A, Robert V., Bioinformatics 34(9), 2018
PMID: 29253070
Guiding biomedical clustering with ClustEval.
Wiwie C, Baumbach J, Röttger R., Nat Protoc 13(6), 2018
PMID: 29844526
A novel methodology on distributed representations of proteins using their interacting ligands.
Öztürk H, Ozkirimli E, Özgür A., Bioinformatics 34(13), 2018
PMID: 29949957
Software updates in the Illumina HiSeq platform affect whole-genome bisulfite sequencing.
Toh H, Shirane K, Miura F, Kubo N, Ichiyanagi K, Hayashi K, Saitou M, Suyama M, Ito T, Sasaki H., BMC Genomics 18(1), 2017
PMID: 28056787
Empirical Comparison of Visualization Tools for Larger-Scale Network Analysis.
Pavlopoulos GA, Paez-Espino D, Kyrpides NC, Iliopoulos I., Adv Bioinformatics 2017(), 2017
PMID: 28804499
De novo pathway-based biomarker identification.
Alcaraz N, List M, Batra R, Vandin F, Ditzel HJ, Baumbach J., Nucleic Acids Res 45(16), 2017
PMID: 28934488
An uncertain model-based approach for identifying dynamic protein complexes in uncertain protein-protein interaction networks.
Zhang Y, Lin H, Yang Z, Wang J, Liu Y., BMC Genomics 18(suppl 7), 2017
PMID: 29513194
RiceAntherNet: a gene co-expression network for identifying anther and pollen development genes.
Lin H, Yu J, Pearce SP, Zhang D, Wilson ZA., Plant J 92(6), 2017
PMID: 29031031
Improving Gene Regulatory Network Inference by Incorporating Rates of Transcriptional Changes.
Desai JS, Sartor RC, Lawas LM, Jagadish SVK, Doherty CJ., Sci Rep 7(1), 2017
PMID: 29222512
CLUSTOM-CLOUD: In-Memory Data Grid-Based Software for Clustering 16S rRNA Sequence Data in the Cloud Environment.
Oh J, Choi CH, Park MK, Kim BK, Hwang K, Lee SH, Hong SG, Nasir A, Cho WS, Kim KM., PLoS One 11(3), 2016
PMID: 26954507
Venus flytrap carnivorous lifestyle builds on herbivore defense strategies.
Bemm F, Becker D, Larisch C, Kreuzer I, Escalante-Perez M, Schulze WX, Ankenbrand M, Van de Weyer AL, Krol E, Al-Rasheid KA, Mithöfer A, Weber AP, Schultz J, Hedrich R., Genome Res 26(6), 2016
PMID: 27197216
Finding approximate gene clusters with Gecko 3.
Winter S, Jahn K, Wehner S, Kuchenbecker L, Marz M, Stoye J, Böcker S., Nucleic Acids Res 44(20), 2016
PMID: 27679480
Evaluation and improvements of clustering algorithms for detecting remote homologous protein families.
Bernardes JS, Vieira FR, Costa LM, Zaverucha G., BMC Bioinformatics 16(), 2015
PMID: 25651949
FlowerNet: a gene expression correlation network for anther and pollen development.
Pearce S, Ferguson A, King J, Wilson ZA., Plant Physiol 167(4), 2015
PMID: 25667314
Carotta: Revealing Hidden Confounder Markers in Metabolic Breath Profiles.
Hauschild AC, Frisch T, Baumbach JI, Baumbach J., Metabolites 5(2), 2015
PMID: 26065494
CMRegNet-An interspecies reference database for corynebacterial and mycobacterial regulatory networks.
Abreu VA, Almeida S, Tiwari S, Hassan SS, Mariano D, Silva A, Baumbach J, Azevedo V, Röttger R., BMC Genomics 16(), 2015
PMID: 26062809
Comparison of topological clustering within protein networks using edge metrics that evaluate full sequence, full structure, and active site microenvironment similarity.
Leuthaeuser JB, Knutson ST, Kumar K, Babbitt PC, Fetrow JS., Protein Sci 24(9), 2015
PMID: 26073648
Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels.
Sayavedra L, Kleiner M, Ponnudurai R, Wetzel S, Pelletier E, Barbe V, Satoh N, Shoguchi E, Fink D, Breusing C, Reusch TB, Rosenstiel P, Schilhabel MB, Becher D, Schweder T, Markert S, Dubilier N, Petersen JM., Elife 4(), 2015
PMID: 26371554
Comparing the performance of biomedical clustering methods.
Wiwie C, Baumbach J, Röttger R., Nat Methods 12(11), 2015
PMID: 26389570
Bi-Force: large-scale bicluster editing and its application to gene expression data biclustering.
Sun P, Speicher NK, Röttger R, Guo J, Baumbach J., Nucleic Acids Res 42(9), 2014
PMID: 24682815
On the limits of computational functional genomics for bacterial lifestyle prediction.
Barbosa E, Röttger R, Hauschild AC, Azevedo V, Baumbach J., Brief Funct Genomics 13(5), 2014
PMID: 24855068
NRfamPred: a proteome-scale two level method for prediction of nuclear receptor proteins and their sub-families.
Kumar R, Kumari B, Srivastava A, Kumar M., Sci Rep 4(), 2014
PMID: 25351274
Massive fungal biodiversity data re-annotation with multi-level clustering.
Vu D, Szöke S, Wiwie C, Baumbach J, Cardinali G, Röttger R, Robert V., Sci Rep 4(), 2014
PMID: 25355642
Density parameter estimation for finding clusters of homologous proteins--tracing actinobacterial pathogenicity lifestyles.
Röttger R, Kalaghatgi P, Sun P, Soares Sde C, Azevedo V, Wittkop T, Baumbach J., Bioinformatics 29(2), 2013
PMID: 23142964
Ecogenomic perspectives on domains of unknown function: correlation-based exploration of marine metagenomes.
Buttigieg PL, Hankeln W, Kostadinov I, Kottmann R, Yilmaz P, Duhaime MB, Glöckner FO., PLoS One 8(3), 2013
PMID: 23516388
CLUSTOM: a novel method for clustering 16S rRNA next generation sequences by overlap minimization.
Hwang K, Oh J, Kim TK, Kim BK, Yu DS, Hou BK, Caetano-Anollés G, Hong SG, Kim KM., PLoS One 8(5), 2013
PMID: 23650520
BiCluE - Exact and heuristic algorithms for weighted bi-cluster editing of biomedical data.
Sun P, Guo J, Baumbach J., BMC Proc 7(suppl 7), 2013
PMID: 24565035
Partitioning the genetic diversity of a virus family: approach and evaluation through a case study of picornaviruses.
Lauber C, Gorbalenya AE., J Virol 86(7), 2012
PMID: 22278230
On the trail of EHEC/EAEC--unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria.
Pauling J, Röttger R, Neuner A, Salgado H, Collado-Vides J, Kalaghatgi P, Azevedo V, Tauch A, Pühler A, Baumbach J., Integr Biol (Camb) 4(7), 2012
PMID: 22318347
A laboratory information management system for DNA barcoding workflows.
Vu TD, Eberhardt U, Szöke S, Groenewald M, Robert V., Integr Biol (Camb) 4(7), 2012
PMID: 22344310
Efficient key pathway mining: combining networks and OMICS data.
Alcaraz N, Friedrich T, Kötzing T, Krohmer A, Müller J, Pauling J, Baumbach J., Integr Biol (Camb) 4(7), 2012
PMID: 22353882
High-quality sequence clustering guided by network topology and multiple alignment likelihood.
Miele V, Penel S, Daubin V, Picard F, Kahn D, Duret L., Bioinformatics 28(8), 2012
PMID: 22368255
DEFOG: discrete enrichment of functionally organized genes.
Wittkop T, Berman AE, Fleisch KM, Mooney SD., Integr Biol (Camb) 4(7), 2012
PMID: 22706384
Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution.
Apeltsin L, Morris JH, Babbitt PC, Ferrin TE., Bioinformatics 27(3), 2011
PMID: 21118823
A combined approach for comparative exoproteome analysis of Corynebacterium pseudotuberculosis.
Pacheco LG, Slade SE, Seyffert N, Santos AR, Castro TL, Silva WM, Santos AV, Santos SG, Farias LM, Carvalho MA, Pimenta AM, Meyer R, Silva A, Scrivens JH, Oliveira SC, Miyoshi A, Dowson CG, Azevedo V., BMC Microbiol 11(1), 2011
PMID: 21241507
Comprehensive cluster analysis with Transitivity Clustering.
Wittkop T, Emig D, Truss A, Albrecht M, Böcker S, Baumbach J., Nat Protoc 6(3), 2011
PMID: 21372810
Deep sequencing of organ- and stage-specific microRNAs in the evolutionarily basal insect Blattella germanica (L.) (Dictyoptera, Blattellidae).
Cristino AS, Tanaka ED, Rubio M, Piulachs MD, Belles X., PLoS One 6(4), 2011
PMID: 21552535
clusterMaker: a multi-algorithm clustering plugin for Cytoscape.
Morris JH, Apeltsin L, Newman AM, Baumbach J, Wittkop T, Su G, Bader GD, Ferrin TE., BMC Bioinformatics 12(), 2011
PMID: 22070249
On the power and limits of evolutionary conservation--unraveling bacterial gene regulatory networks.
Baumbach J., Nucleic Acids Res 38(22), 2010
PMID: 20699275

3 References

Daten bereitgestellt von Europe PubMed Central.

Integration of biological networks and gene expression data using Cytoscape.
Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD., Nat Protoc 2(10), 2007
PMID: 17947979
An efficient algorithm for large-scale detection of protein families.
Enright AJ, Van Dongen S, Ouzounis CA., Nucleic Acids Res. 30(7), 2002
PMID: 11917018
Large scale clustering of protein sequences with FORCE -A layout based heuristic for weighted cluster editing.
Wittkop T, Baumbach J, Lobo FP, Rahmann S., BMC Bioinformatics 8(), 2007
PMID: 17941985
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