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Items: 1 to 20 of 206

1.

SCPS: a fast implementation of a spectral method for detecting protein families on a genome-wide scale.

Nepusz T, Sasidharan R, Paccanaro A.

BMC Bioinformatics. 2010 Mar 9;11:120. doi: 10.1186/1471-2105-11-120.

2.

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. 2007 Oct 17;8:396.

3.

Spectral clustering of protein sequences.

Paccanaro A, Casbon JA, Saqi MA.

Nucleic Acids Res. 2006 Mar 17;34(5):1571-80. Print 2006.

4.

ProClust: improved clustering of protein sequences with an extended graph-based approach.

Pipenbacher P, Schliep A, Schneckener S, Schönhuth A, Schomburg D, Schrader R.

Bioinformatics. 2002;18 Suppl 2:S182-91.

PMID:
12386002
5.

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. 2011 Nov 9;12:436. doi: 10.1186/1471-2105-12-436.

6.

Evaluation and improvements of clustering algorithms for detecting remote homologous protein families.

Bernardes JS, Vieira FR, Costa LM, Zaverucha G.

BMC Bioinformatics. 2015 Feb 5;16:34. doi: 10.1186/s12859-014-0445-4.

7.

Using affinity propagation combined post-processing to cluster protein sequences.

Yang F, Zhu Q, Tang D, Zhao M.

Protein Pept Lett. 2010 Jun;17(6):681-9.

PMID:
19594428
8.

Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space.

Loewenstein Y, Portugaly E, Fromer M, Linial M.

Bioinformatics. 2008 Jul 1;24(13):i41-9. doi: 10.1093/bioinformatics/btn174.

9.

SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition.

Melvin I, Ie E, Kuang R, Weston J, Stafford WN, Leslie C.

BMC Bioinformatics. 2007 May 22;8 Suppl 4:S2.

10.
11.

Evaluation of BLAST-based edge-weighting metrics used for homology inference with the Markov Clustering algorithm.

Gibbons TR, Mount SM, Cooper ED, Delwiche CF.

BMC Bioinformatics. 2015 Jul 10;16:218. doi: 10.1186/s12859-015-0625-x. Erratum in: BMC Bioinformatics. 2015;16:274.

12.

Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms.

Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D311-4.

13.

Cross-over between discrete and continuous protein structure space: insights into automatic classification and networks of protein structures.

Pascual-García A, Abia D, Ortiz AR, Bastolla U.

PLoS Comput Biol. 2009 Mar;5(3):e1000331. doi: 10.1371/journal.pcbi.1000331. Epub 2009 Mar 27.

14.

Searching remote homology with spectral clustering with symmetry in neighborhood cluster kernels.

Maulik U, Sarkar A.

PLoS One. 2013;8(2):e46468. doi: 10.1371/journal.pone.0046468. Epub 2013 Feb 15.

15.

Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution.

Apeltsin L, Morris JH, Babbitt PC, Ferrin TE.

Bioinformatics. 2011 Feb 1;27(3):326-33. doi: 10.1093/bioinformatics/btq655. Epub 2010 Nov 29.

16.

Detecting clusters of different geometrical shapes in microarray gene expression data.

Kim DW, Lee KH, Lee D.

Bioinformatics. 2005 May 1;21(9):1927-34. Epub 2005 Jan 12.

PMID:
15647300
17.

Towards an automatic classification of protein structural domains based on structural similarity.

Sam V, Tai CH, Garnier J, Gibrat JF, Lee B, Munson PJ.

BMC Bioinformatics. 2008 Jan 31;9:74. doi: 10.1186/1471-2105-9-74.

18.

On the quality of tree-based protein classification.

Lazareva-Ulitsky B, Diemer K, Thomas PD.

Bioinformatics. 2005 May 1;21(9):1876-90. Epub 2005 Jan 12.

PMID:
15647305
19.

Revealing remote protein homology with sequence similarity and a modularity-based approach.

Mei J, Yang X, Zhou W.

Theor Biol Forum. 2011;104(1):57-68.

PMID:
22220355
20.

Large scale hierarchical clustering of protein sequences.

Krause A, Stoye J, Vingron M.

BMC Bioinformatics. 2005 Jan 22;6:15.

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