Research interests:

* Theory and applications of biological sequence comparison
* Data and knowledge representation for genomics
* Molecular diversity, evolution of protein function
* Evolution of genetic information-processing systems
* Biologically-inspired hardware and software engineering
* Unsupervised machine learning in very large datasets

http://www.ebi.ac.uk/~ouzounis/

Application of compression-based distance measures to protein sequence classification: a methodological study. Kocsor A, Kertész-Farkas A, Kaján L, Pongor S Bioinformatics 2006 Feb 15 22(4):407-12 [abstract on PubMed] [related articles] [FREE full text] Selected by | Christos Ouzounis Evaluated 2 Apr 2007 Comparative metagenomics of microbial communities. Tringe SG, von Mering C, …, Hugenholtz P, Rubin EM Science 2005 Apr 22 308(5721):554-7 [abstract on PubMed] [related articles] [FREE full text] Selected by | Daniel Vaulot / Jeffrey Lawrence / John Jaenike / Robert Jackson / Gerard Muyzer / Christos Ouzounis Evaluated 1 Aug 2005 Use of logic relationships to decipher protein network organization. Bowers PM, Cokus SJ, Eisenberg D, Yeates TO Science 2004 Dec 24 306(5705):2246-9 [abstract on PubMed] [related articles] [FREE full text] Selected by | Christos Ouzounis Evaluated 29 Jul 2005 On the number of protein-protein interactions in the yeast proteome. Grigoriev A Nucleic Acids Res 2003 Jul 15 31(14):4157-61 [abstract on PubMed] [related articles] [FREE full text] Selected by | Christos Ouzounis Evaluated 29 Nov 2004 Trends between gene content and genome size in prokaryotic species with larger genomes. Konstantinidis KT, Tiedje JM Proc Natl Acad Sci U S A 2004 Mar 2 101(9):3160-5 [abstract on PubMed] [related articles] [FREE full text] Selected by | Peter Williams / Jonathan A. Eisen / Christos Ouzounis Evaluated 29 Nov 2004 Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements. Wu M, Sun LV, …, O'Neill SL, Eisen JA PLoS Biol 2004 Mar 2(3):E69 [abstract on PubMed] [related articles] [FREE full text] Selected by | Julian Parkhill / Christos Ouzounis Evaluated 29 Nov 2004 A map of the interactome network of the metazoan C. elegans. Li S, Armstrong CM, …, Hill DE, Vidal M Science 2004 Jan 23 303(5657):540-3 [abstract on PubMed] [related articles] [FREE full text] Selected by | Ulf Pettersson / Christos Ouzounis Evaluated 29 Nov 2004 Domains, motifs and clusters in the protein universe. Liu J, Rost B Curr Opin Chem Biol 2003 Feb 7(1):5-11 [abstract on PubMed] [related articles] [order article] Selected by | Christos Ouzounis Evaluated 25 Nov 2004 A protein interaction map of Drosophila melanogaster. Giot L, Bader JS, …, Chant J, Rothberg JM Science 2003 Dec 5 302(5651):1727-36 [abstract on PubMed] [related articles] [FREE full text] Selected by | Rob Russell / Michael Meisterernst / Jeffrey Lawrence / Christos Ouzounis Evaluated 25 Nov 2004 A cross-genomic approach for systematic mapping of phenotypic traits to genes. Jim K, Parmar K, Singh M, Tavazoie S Genome Res 2004 Jan 14(1):109-15 [abstract on PubMed] [related articles] [FREE full text] Selected by | Christos Ouzounis Evaluated 25 Nov 2004 Identification of functional links between genes using phylogenetic profiles. Wu J, Kasif S, DeLisi C Bioinformatics 2003 Aug 12 19(12):1524-30 [abstract on PubMed] [related articles] [FREE full text] Selected by | Christos Ouzounis Evaluated 24 Nov 2004 Metagenes and molecular pattern discovery using matrix factorization. Brunet JP, Tamayo P, Golub TR, Mesirov JP Proc Natl Acad Sci U S A 2004 Mar 23 101(12):4164-9 [abstract on PubMed] [related articles] [FREE full text] Selected by | Christos Ouzounis Evaluated 24 Nov 2004 Network analysis of metabolic enzyme evolution in Escherichia coli. Light S, Kraulis P BMC Bioinformatics 2004 Feb 18 5:15 [abstract on PubMed] [related articles] [FREE full text] Selected by | Christos Ouzounis Evaluated 24 Nov 2004 The archaeal feast/famine regulatory protein: potential roles of its assembly forms for regulating transcription. Koike H, Ishijima SA, Clowney L, Suzuki M Proc Natl Acad Sci U S A 2004 Mar 2 101(9):2840-5 [abstract on PubMed] [related articles] [FREE full text] Selected by | Christos Ouzounis Evaluated 24 Nov 2004 Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision. Graur D, Martin W Trends Genet 2004 Feb 20(2):80-6 [abstract on PubMed] [related articles] [order article] Selected by | Nicolas Galtier / Christos Ouzounis Evaluated 23 Nov 2004 Extending the upper temperature limit for life. Kashefi K, Lovley DR Science 2003 Aug 15 301(5635):934 [abstract on PubMed] [related articles] [FREE full text] Selected by | Edward Stiefel / Ian M. Head / Terrance Beveridge / Christos Ouzounis Evaluated 12 Nov 2004 The genome reduction hypothesis and the phylogeny of eukaryotes. Bapteste E, Gribaldo S Trends Genet 2003 Dec 19(12):696-700 [abstract on PubMed] [related articles] [order article] Selected by | William Martin / Christos Ouzounis Evaluated 12 Nov 2004 Life cycles of successful genes. Hoffmann R, Valencia A Trends Genet 2003 Feb 19(2):79-81 [abstract on PubMed] [related articles] [order article] Selected by | Susan Barker / Christos Ouzounis Evaluated 12 Nov 2004 The metabolic world of Escherichia coli is not small. Arita M Proc Natl Acad Sci U S A 2004 Feb 10 101(6):1543-7 [abstract on PubMed] [related articles] [FREE full text] Selected by | Christos Ouzounis Evaluated 12 Nov 2004 Global organization of metabolic fluxes in the bacterium Escherichia coli. Almaas E, Kovács B, …, Oltvai ZN, Barabási AL Nature 2004 Feb 26 427(6977):839-43 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Christos Ouzounis Evaluated 12 Nov 2004 Identifying functional links between genes using conserved chromosomal proximity. Yanai I, Mellor JC, DeLisi C Trends Genet 2002 Apr 18(4):176-9 [abstract on PubMed] [related articles] [order article] Selected by | Christos Ouzounis Evaluated 26 Feb 2003 Combinatorial synthesis of genetic networks. Guet CC, Elowitz MB, Hsing W, Leibler S Science 2002 May 24 296(5572):1466-70 [abstract on PubMed] [related articles] [FREE full text] Selected by | Greg Gibson / Christos Ouzounis / Alfonso Martinez Arias Evaluated 26 Feb 2003 Specificity and stability in topology of protein networks. Maslov S, Sneppen K Science 2002 May 3 296(5569):910-3 [abstract on PubMed] [related articles] [FREE full text] Selected by | Christos Ouzounis Evaluated 24 Feb 2003 Analyzing yeast protein-protein interaction data obtained from different sources. Bader GD, Hogue CW Nat Biotechnol 2002 Oct 20(10):991-7 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Marilyn Parsons / Christos Ouzounis / Golan Yona Evaluated 24 Feb 2003 Evolution of amino acid frequencies in proteins over deep time: inferred order of introduction of amino acids into the genetic code. Brooks DJ, Fresco JR, Lesk AM, Singh M Mol Biol Evol 2002 Oct 19(10):1645-55 [abstract on PubMed] [related articles] [FREE full text] Selected by | Christos Ouzounis Evaluated 24 Feb 2003 In silico two-hybrid system for the selection of physically interacting protein pairs. Pazos F, Valencia A Proteins 2002 May 1 47(2):219-27 [abstract on PubMed] [related articles] [order article] Selected by | Christos Ouzounis Evaluated 24 Feb 2003 The global phylogeny of glycolytic enzymes. Canback B, Andersson SG, Kurland CG Proc Natl Acad Sci U S A 2002 Apr 30 99(9):6097-102 [abstract on PubMed] [related articles] [FREE full text] Selected by | Christos Ouzounis Evaluated 24 Feb 2003 Network motifs in the transcriptional regulation network of Escherichia coli. Shen-Orr SS, Milo R, Mangan S, Alon U Nat Genet 2002 May 31(1):64-8 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Philip Benfey / Golan Yona / Christos Ouzounis Evaluated 24 Feb 2003 Amino acid composition of genomes, lifestyles of organisms, and evolutionary trends: a global picture with correspondence analysis. Tekaia F, Yeramian E, Dujon B Gene 2002 Sep 4 297(1-2):51-60 [abstract on PubMed] [related articles] [order article] Selected by | Christos Ouzounis Evaluated 24 Feb 2003 Molecular evolution of the lysine biosynthetic pathways. Velasco AM, Leguina JI, Lazcano A J Mol Evol 2002 Oct 55(4):445-59 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Christos Ouzounis Evaluated 24 Feb 2003 Genomes in flux: the evolution of archaeal and proteobacterial gene content. Snel B, Bork P, Huynen MA Genome Res 2002 Jan 12(1):17-25 [abstract on PubMed] [related articles] [FREE full text] Selected by | Arcady Mushegian / Christos Ouzounis / Eugene Koonin Evaluated 25 Mar 2002 A literature network of human genes for high-throughput analysis of gene expression. Jenssen TK, Laegreid A, Komorowski J, Hovig E Nat Genet 2001 May 28(1):21-8 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Christos Ouzounis Evaluated 25 Mar 2002 Evolution of gene order conservation in prokaryotes. Tamames J Genome Biol 2001 2(6):RESEARCH0020 [abstract on PubMed] [related articles] [FREE full text] Selected by | Christos Ouzounis Evaluated 25 Mar 2002 Universal trees based on large combined protein sequence data sets. Brown JR, Douady CJ, …, Marshall WE, Stanhope MJ Nat Genet 2001 Jul 28(3):281-5 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Christos Ouzounis Evaluated 10 Dec 2001 Genes linked by fusion events are generally of the same functional category: a systematic analysis of 30 microbial genomes. Yanai I, Derti A, DeLisi C Proc Natl Acad Sci U S A 2001 Jul 3 98(14):7940-5 [abstract on PubMed] [related articles] [FREE full text] Selected by | Christos Ouzounis Evaluated 3 Dec 2001 Pathway databases: a case study in computational symbolic theories. Karp PD Science 2001 Sep 14 293(5537):2040-4 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Christos Ouzounis Evaluated 29 Nov 2001

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