Research article  

Phylogenetically informed logic relationships improve detection of biological network organization

Jike Cui, Todd F DeLuca, Jae-Yoon Jung, Dennis P Wall BMC Bioinformatics 2011, 12:476 (15 December 2011)

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Software  

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 (9 November 2011)

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Research article  

Selection of organisms for the co-evolution-based study of protein interactions

Dorota Herman, David Ochoa, David Juan, Daniel Lopez, Alfonso Valencia, Florencio Pazos BMC Bioinformatics 2011, 12:363 (12 September 2011)

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Research article  

Prioritizing orphan proteins for further study using phylogenomics and gene expression profiles in Streptomyces coelicolor

Mohammad Alam, Eriko Takano, Rainer Breitling BMC Research Notes 2011, 4:325 (7 September 2011)

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Research article  

Comparison of eukaryotic phylogenetic profiling approaches using species tree aware methods

Valentín Ruano-Rubio, Olivier Poch, Julie D Thompson BMC Bioinformatics 2009, 10:383 (24 November 2009)

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Research  

Co-evolutionary networks of genes and cellular processes across fungal species

Tamir Tuller, Martin Kupiec, Eytan Ruppin Genome Biology 2009, 10:R48 (5 May 2009)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

Research article  

In silico prioritisation of candidate genes for prokaryotic gene function discovery: an application of phylogenetic profiles

Frank PY Lin, Enrico Coiera, Ruiting Lan, Vitali Sintchenko BMC Bioinformatics 2009, 10:86 (17 March 2009)

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Research article  

Predicting protein linkages in bacteria: Which method is best depends on task

Anis Karimpour-Fard, Sonia M Leach, Ryan T Gill, Lawrence E Hunter BMC Bioinformatics 2008, 9:397 (24 September 2008)

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Research article  

The topology of the bacterial co-conserved protein network and its implications for predicting protein function

Anis Karimpour-Fard, Sonia M Leach, Lawrence E Hunter, Ryan T Gill BMC Genomics 2008, 9:313 (30 June 2008)

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Research article  

Limited functional conservation of a global regulator among related bacterial genera: Lrp in Escherichia, Proteus and Vibrio

Robert E Lintner, Pankaj K Mishra, Poonam Srivastava, Betsy M Martinez-Vaz, Arkady B Khodursky, Robert M Blumenthal BMC Microbiology 2008, 8:60 (11 April 2008)

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Research article  

Denoising inferred functional association networks obtained by gene fusion analysis

Atanas Kamburov, Leon Goldovsky, Shiri Freilich, Aliki Kapazoglou, Victor Kunin, Anton J Enright, Athanasios Tsaftaris, Christos A Ouzounis BMC Genomics 2007, 8:460 (14 December 2007)

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Research article  

Investigation of factors affecting prediction of protein-protein interaction networks by phylogenetic profiling

Anis Karimpour-Fard, Lawrence Hunter, Ryan T Gill BMC Genomics 2007, 8:393 (29 October 2007)

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Methodology article  

InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes

Jingchun Sun, Yan Sun, Guohui Ding, Qi Liu, Chuan Wang, Youyu He, Tieliu Shi, Yixue Li, Zhongming Zhao BMC Bioinformatics 2007, 8:414 (26 October 2007)

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