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Detection of evolutionarily stable fragments of cellular pathways by hierarchical clustering of phyletic patterns
Galina V Glazko, Arcady R Mushegian
Genome Biol. 2004; 5(5): R32. Published online 2004 April 27.
PMCID:
PMC416468
Abstract Full Text PDF–609K Supplementary Material
 Is Cited by the Following 16 Articles in this Archive:
ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process
Malay K Basu, Jeremy D Selengut, Daniel H Haft
BMC Bioinformatics. 2011; 12: 434. Published online 2011 November 9. doi: 10.1186/1471-2105-12-434
PMCID:
PMC3226654
Abstract Full Text PDF–443K Supplementary Material
Toward an Efficient Method of Identifying Core Genes for Evolutionary and Functional Microbial Phylogenies
Nicola Segata, Curtis Huttenhower
PLoS One. 2011; 6(9): e24704. Published online 2011 September 12. doi: 10.1371/journal.pone.0024704
PMCID:
PMC3171473
Abstract Full Text PDF–1.7M Supplementary Material
Proteins with Complex Architecture as Potential Targets for Drug Design: A Case Study of Mycobacterium tuberculosis
Bálint Mészáros, Judit Tóth, Beáta G. Vértessy, Zsuzsanna Dosztányi, István Simon
PLoS Comput Biol. 2011 July; 7(7): e1002118. Published online 2011 July 21. doi: 10.1371/journal.pcbi.1002118
PMCID:
PMC3140968
Abstract Full Text PDF–507K Supplementary Material
Evolutionary plasticity determination by orthologous groups distribution
Rodrigo JS Dalmolin, Mauro AA Castro, José L Rybarczyk Filho, Luis HT Souza, Rita MC de Almeida, José CF Moreira
Biol Direct. 2011; 6: 22. Published online 2011 May 17. doi: 10.1186/1745-6150-6-22
PMCID:
PMC3117832
Abstract Full Text PDF–1.0M Supplementary Material
Comparison of eukaryotic phylogenetic profiling approaches using species tree aware methods
Valentín Ruano-Rubio, Olivier Poch, Julie D Thompson
BMC Bioinformatics. 2009; 10: 383. Published online 2009 November 24. doi: 10.1186/1471-2105-10-383
PMCID:
PMC2787529
Abstract Full Text PDF–1.9M
Detection of Biochemical Pathways by Probabilistic Matching of Phyletic Vectors
Hua Li, David M. Kristensen, Michael K. Coleman, Arcady Mushegian
PLoS ONE. 2009; 4(4): e5326. Published online 2009 April 24. doi: 10.1371/journal.pone.0005326
PMCID:
PMC2670198
Abstract Full Text PDF–192K Supplementary Material
Cohesive versus Flexible Evolution of Functional Modules in Eukaryotes
Like Fokkens, Berend Snel
PLoS Comput Biol. 2009 January; 5(1): e1000276. Published online 2009 January 30. doi: 10.1371/journal.pcbi.1000276
PMCID:
PMC2615111
Abstract Full Text PDF–594K Supplementary Material
Protein Complex Evolution Does Not Involve Extensive Network Rewiring
Teunis J. P. van Dam, Berend Snel
PLoS Comput Biol. 2008 July; 4(7): e1000132. Published online 2008 July 25. doi: 10.1371/journal.pcbi.1000132
PMCID:
PMC2517612
Abstract Full Text PDF–278K Supplementary Material
Inferring modules of functionally interacting proteins using the Bond Energy Algorithm
Ryosuke LA Watanabe, Enrique Morett, Edgar E Vallejo
BMC Bioinformatics. 2008; 9: 285. Published online 2008 June 17. doi: 10.1186/1471-2105-9-285
PMCID:
PMC2474619
Abstract Full Text PDF–418K Supplementary Material
Coevolution of gene families in prokaryotes
Otto X. Cordero, Berend Snel, Paulien Hogeweg
Genome Res. 2008 March; 18(3): 462–468. doi: 10.1101/gr.6815508
PMCID:
PMC2259110
Abstract Full Text PDF–802K
Automatic generation of 3D motifs for classification of protein binding sites
Jean-Christophe Nebel, Pawel Herzyk, David R Gilbert
BMC Bioinformatics. 2007; 8: 321. Published online 2007 August 30. doi: 10.1186/1471-2105-8-321
PMCID:
PMC1995225
Abstract Full Text PDF–435K Supplementary Material
Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution
Philip R. Kensche, Vera van Noort, Bas E. Dutilh, Martijn A. Huynen
J R Soc Interface. 2008 February 6; 5(19): 151–170. Published online 2007 May 30. doi: 10.1098/rsif.2007.1047
PMCID:
PMC2405902
Abstract Full Text PDF–859K Supplementary Material
Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment
Raja Jothi, Teresa M Przytycka, L Aravind
BMC Bioinformatics. 2007; 8: 173. Published online 2007 May 23. doi: 10.1186/1471-2105-8-173
PMCID:
PMC1904249
Abstract Full Text PDF–2.9M Supplementary Material
The 90S Preribosome Is a Multimodular Structure That Is Assembled through a Hierarchical Mechanism
Jorge Pérez-Fernández, Ángel Román, Javier De Las Rivas, Xosé R. Bustelo, Mercedes Dosil
Mol Cell Biol. 2007 August; 27(15): 5414–5429. Published online 2007 May 21. doi: 10.1128/MCB.00380-07
PMCID:
PMC1952102
Abstract Full Text PDF–1.2M Supplementary Material
Similarity searches in genome-wide numerical data sets
Galina Glazko, Michael Coleman, Arcady Mushegian
Biol Direct. 2006; 1: 13. Published online 2006 May 30. doi: 10.1186/1745-6150-1-13
PMCID:
PMC1489924
Abstract Full Text PDF–651K Supplementary Material
A metabolic network in the evolutionary context: Multiscale structure and modularity
Victor Spirin, Mikhail S. Gelfand, Andrey A. Mironov, Leonid A. Mirny
Proc Natl Acad Sci U S A. 2006 June 6; 103(23): 8774–8779. Published online 2006 May 26. doi: 10.1073/pnas.0510258103
PMCID:
PMC1482654
Abstract Full Text PDF–712K Supplementary Material
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