Christos Ouzounis, Ph.D. - Publications


165 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2015 Promponas VJ, Iliopoulos I, Ouzounis CA. Annotation inconsistencies beyond sequence similarity-based function prediction - phylogeny and genome structure. Standards in Genomic Sciences. 10: 108. PMID 26594309 DOI: 10.1186/s40793-015-0101-2  0.6
2015 Baichoo S, Botha G, Jaufeerally-Fakim Y, Mungloo-Dilmohamud Z, Lundin D, Mulder N, Promponas VJ, Ouzounis CA. H3ABioNet computational metagenomics workshop in Mauritius: Training to analyse microbial diversity for Africa Standards in Genomic Sciences. DOI: 10.1186/s40793-015-0111-0  0.6
2015 Vitsios DM, Psomopoulos FE, Mitkas PA, Ouzounis CA. Inference of pathway decomposition across multiple species through gene clustering International Journal On Artificial Intelligence Tools. 24. DOI: 10.1142/S0218213015400035  0.6
2014 Salta E, Kanata E, Ouzounis CA, Gilch S, Schätzl H, Sklaviadis T. Assessing proteinase K resistance of fish prion proteins in a scrapie-infected mouse neuroblastoma cell line. Viruses. 6: 4398-421. PMID 25402173 DOI: 10.3390/v6114398  0.6
2014 Papanikolaou N, Pavlopoulos GA, Pafilis E, Theodosiou T, Schneider R, Satagopam VP, Ouzounis CA, Eliopoulos AG, Promponas VJ, Iliopoulos I. BioTextQuest(+): a knowledge integration platform for literature mining and concept discovery. Bioinformatics (Oxford, England). 30: 3249-56. PMID 25100685 DOI: 10.1093/Bioinformatics/Btu524  0.6
2014 Kyrpides NC, Hugenholtz P, Eisen JA, Woyke T, Göker M, Parker CT, Amann R, Beck BJ, Chain PS, Chun J, Colwell RR, Danchin A, Dawyndt P, Dedeurwaerdere T, DeLong EF, ... ... Ouzounis CA, et al. Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. Plos Biology. 12: e1001920. PMID 25093819 DOI: 10.1371/Journal.Pbio.1001920  0.6
2014 Pavlopoulos GA, Promponas VJ, Ouzounis CA, Iliopoulos I. Biological information extraction and co-occurrence analysis. Methods in Molecular Biology (Clifton, N.J.). 1159: 77-92. PMID 24788262 DOI: 10.1007/978-1-4939-0709-0_5  0.6
2014 Katsani KR, Irimia M, Karapiperis C, Scouras ZG, Blencowe BJ, Promponas VJ, Ouzounis CA. Functional genomics evidence unearths new moonlighting roles of outer ring coat nucleoporins. Scientific Reports. 4: 4655. PMID 24722254 DOI: 10.1038/srep04655  0.6
2014 Promponas VJ, Ouzounis CA, Iliopoulos I. Experimental evidence validating the computational inference of functional associations from gene fusion events: a critical survey. Briefings in Bioinformatics. 15: 443-54. PMID 23220349 DOI: 10.1093/bib/bbs072  0.6
2013 Hamodrakas SJ, Iliopoulos I, Ouzounis CA, Bagos PG, Promponas VJ. Meeting report: the seventh conference of the hellenic society for computational biology and bioinformatics. Computational and Structural Biotechnology Journal. 6: e201303006. PMID 24688714 DOI: 10.5936/csbj.201303006  0.6
2013 Drozdov I, Didangelos A, Yin X, Zampetaki A, Abonnenc M, Murdoch C, Zhang M, Ouzounis CA, Mayr M, Tsoka S, Shah AM. Gene network and proteomic analyses of cardiac responses to pathological and physiological stress. Circulation. Cardiovascular Genetics. 6: 588-97. PMID 24214729 DOI: 10.1161/CIRCGENETICS.113.000063  0.6
2013 Ganopoulos I, Aravanopoulos F, Madesis P, Pasentsis K, Bosmali I, Ouzounis C, Tsaftaris A. Taxonomic identification of mediterranean pines and their hybrids based on the high resolution melting (HRM) and trnL approaches: from cytoplasmic inheritance to timber tracing. Plos One. 8: e60945. PMID 23577179 DOI: 10.1371/Journal.Pone.0060945  0.6
2013 Belda E, Sekowska A, Le Fèvre F, Morgat A, Mornico D, Ouzounis C, Vallenet D, Médigue C, Danchin A. An updated metabolic view of the Bacillus subtilis 168 genome. Microbiology (Reading, England). 159: 757-70. PMID 23429746 DOI: 10.1099/Mic.0.064691-0  0.6
2013 Psomopoulos FE, Mitkas PA, Ouzounis CA. Detection of genomic idiosyncrasies using fuzzy phylogenetic profiles. Plos One. 8: e52854. PMID 23341912 DOI: 10.1371/Journal.Pone.0052854  0.6
2012 Psomopoulos FE, Siarkou VI, Papanikolaou N, Iliopoulos I, Tsaftaris AS, Promponas VJ, Ouzounis CA. The chlamydiales pangenome revisited: structural stability and functional coherence. Genes. 3: 291-319. PMID 24704919 DOI: 10.3390/genes3020291  0.6
2012 Ainali C, Valeyev N, Perera G, Williams A, Gudjonsson JE, Ouzounis CA, Nestle FO, Tsoka S. Transcriptome classification reveals molecular subtypes in psoriasis. Bmc Genomics. 13: 472. PMID 22971201 DOI: 10.1186/1471-2164-13-472  0.6
2012 Ouzounis CA. Rise and demise of bioinformatics? Promise and progress. Plos Computational Biology. 8: e1002487. PMID 22570600 DOI: 10.1371/journal.pcbi.1002487  0.6
2012 Vitsios DM, Psomopoulos FE, Mitkas PA, Ouzounis CA. Multi-genome core pathway identification through gene clustering Ifip Advances in Information and Communication Technology. 382: 545-555. DOI: 10.1007/978-3-642-33412-2_56  0.6
2012 Ouzounis CA, Promponas VJ, Iliopoulos I. The quest for an upper limit in systems biology Journal of Biological Research (Greece). 18: 353-358.  0.6
2011 Drozdov I, Ouzounis CA, Shah AM, Tsoka S. Functional Genomics Assistant (FUGA): a toolbox for the analysis of complex biological networks. Bmc Research Notes. 4: 462. PMID 22035155 DOI: 10.1186/1756-0500-4-462  0.6
2011 Papanikolaou N, Pafilis E, Nikolaou S, Ouzounis CA, Iliopoulos I, Promponas VJ. BioTextQuest: a web-based biomedical text mining suite for concept discovery. Bioinformatics (Oxford, England). 27: 3327-8. PMID 21994227 DOI: 10.1093/Bioinformatics/Btr564  0.6
2011 Stokes A, Drozdov I, Guerra E, Ouzounis CA, Warnakulasuriya S, Gleeson MJ, McGurk M, Tavassoli M, Odell EW. Copy number and loss of heterozygosity detected by SNP array of formalin-fixed tissues using whole-genome amplification. Plos One. 6: e24503. PMID 21966361 DOI: 10.1371/journal.pone.0024503  0.6
2011 Ainali C, Simon M, Freilich S, Espinosa O, Hazelwood L, Tsoka S, Ouzounis CA, Hancock JM. Protein coalitions in a core mammalian biochemical network linked by rapidly evolving proteins. Bmc Evolutionary Biology. 11: 142. PMID 21612628 DOI: 10.1186/1471-2148-11-142  0.6
2010 Valeyev NV, Hundhausen C, Umezawa Y, Kotov NV, Williams G, Clop A, Ainali C, Ouzounis C, Tsoka S, Nestle FO. A systems model for immune cell interactions unravels the mechanism of inflammation in human skin. Plos Computational Biology. 6: e1001024. PMID 21152006 DOI: 10.1371/journal.pcbi.1001024  0.6
2010 Drozdov I, Tsoka S, Ouzounis CA, Shah AM. Genome-wide expression patterns in physiological cardiac hypertrophy. Bmc Genomics. 11: 557. PMID 20937113 DOI: 10.1186/1471-2164-11-557  0.6
2010 Pantzartzi C, Drosopoulou E, Yiangou M, Drozdov I, Tsoka S, Ouzounis CA, Scouras ZG. Promoter complexity and tissue-specific expression of stress response components in Mytilus galloprovincialis, a sessile marine invertebrate species. Plos Computational Biology. 6: e1000847. PMID 20628614 DOI: 10.1371/journal.pcbi.1000847  0.6
2010 Maffettone C, Chen G, Drozdov I, Ouzounis C, Pantopoulos K. Tumorigenic properties of iron regulatory protein 2 (IRP2) mediated by its specific 73-amino acids insert. Plos One. 5: e10163. PMID 20405006 DOI: 10.1371/Journal.Pone.0010163  0.6
2009 Freilich S, Goldovsky L, Gottlieb A, Blanc E, Tsoka S, Ouzounis CA. Stratification of co-evolving genomic groups using ranked phylogenetic profiles. Bmc Bioinformatics. 10: 355. PMID 19860884 DOI: 10.1186/1471-2105-10-355  0.6
2009 Juncker AS, Jensen LJ, Pierleoni A, Bernsel A, Tress ML, Bork P, von Heijne G, Valencia A, Ouzounis CA, Casadio R, Brunak S. Sequence-based feature prediction and annotation of proteins. Genome Biology. 10: 206. PMID 19226438 DOI: 10.1186/Gb-2009-10-2-206  0.6
2009 Huminiecki L, Goldovsky L, Freilich S, Moustakas A, Ouzounis C, Heldin CH. Emergence, development and diversification of the TGF-beta signalling pathway within the animal kingdom. Bmc Evolutionary Biology. 9: 28. PMID 19192293 DOI: 10.1186/1471-2148-9-28  0.6
2008 Freilich S, Goldovsky L, Ouzounis CA, Thornton JM. Metabolic innovations towards the human lineage. Bmc Evolutionary Biology. 8: 247. PMID 18782449 DOI: 10.1186/1471-2148-8-247  0.6
2008 Theodosiou T, Darzentas N, Angelis L, Ouzounis CA. PuReD-MCL: a graph-based PubMed document clustering methodology. Bioinformatics (Oxford, England). 24: 1935-41. PMID 18593717 DOI: 10.1093/bioinformatics/btn318  0.6
2008 Murray F, Darzentas N, Hadzidimitriou A, Tobin G, Boudjogra M, Scielzo C, Laoutaris N, Karlsson K, Baran-Marzsak F, Tsaftaris A, Moreno C, Anagnostopoulos A, Caligaris-Cappio F, Vaur D, Ouzounis C, et al. Stereotyped patterns of somatic hypermutation in subsets of patients with chronic lymphocytic leukemia: implications for the role of antigen selection in leukemogenesis. Blood. 111: 1524-33. PMID 17959859 DOI: 10.1182/Blood-2007-07-099564  0.6
2008 Bourguignon PY, Van Helden J, Ouzounis C, Schächter V. Computational analysis of metabolic networks Modern Genome Annotation: the Biosapiens Network. 329-351. DOI: 10.1007/978-3-211-75123-7_16  0.6
2007 Peregrín-Alvarez JM, Ouzounis CA. The comparative genomics of protein interactions. Genome Informatics. International Conference On Genome Informatics. 19: 131-41. PMID 18546511  0.6
2007 Kamburov A, Goldovsky L, Freilich S, Kapazoglou A, Kunin V, Enright AJ, Tsaftaris A, Ouzounis CA. Denoising inferred functional association networks obtained by gene fusion analysis. Bmc Genomics. 8: 460. PMID 18081932 DOI: 10.1186/1471-2164-8-460  0.6
2007 Darzentas N, Goldovsky L, Ouzounis CA, Karapiperis K, Karapiperis C. Science communication media for scientists and the public. Embo Reports. 8: 886-7. PMID 17906664 DOI: 10.1038/sj.embor.7401074  0.6
2007 Audit B, Levy ED, Gilks WR, Goldovsky L, Ouzounis CA. CORRIE: enzyme sequence annotation with confidence estimates. Bmc Bioinformatics. 8: S3. PMID 17570146 DOI: 10.1186/1471-2105-8-S4-S3  0.6
2007 Coulson RM, Touboul N, Ouzounis CA. Lineage-specific partitions in archaeal transcription. Archaea (Vancouver, B.C.). 2: 117-25. PMID 17350932  0.6
2006 Tiffin N, Adie E, Turner F, Brunner HG, van Driel MA, Oti M, Lopez-Bigas N, Ouzounis C, Perez-Iratxeta C, Andrade-Navarro MA, Adeyemo A, Patti ME, Semple CA, Hide W. Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes. Nucleic Acids Research. 34: 3067-81. PMID 16757574 DOI: 10.1093/Nar/Gkl381  0.6
2006 Ouzounis C, Mazière P. Maps, books and other metaphors for systems biology. Bio Systems. 85: 6-10. PMID 16757097 DOI: 10.1016/J.Biosystems.2006.02.007  0.6
2006 Ouzounis CA, Kunin V, Darzentas N, Goldovsky L. A minimal estimate for the gene content of the last universal common ancestor--exobiology from a terrestrial perspective. Research in Microbiology. 157: 57-68. PMID 16431085 DOI: 10.1016/j.resmic.2005.06.015  0.6
2006 Furney SJ, Higgins DG, Ouzounis CA, López-Bigas N. Structural and functional properties of genes involved in human cancer. Bmc Genomics. 7: 3. PMID 16405732 DOI: 10.1186/1471-2164-7-3  0.6
2006 López-Bigas N, Blencowe BJ, Ouzounis CA. Highly consistent patterns for inherited human diseases at the molecular level. Bioinformatics (Oxford, England). 22: 269-77. PMID 16287936 DOI: 10.1093/bioinformatics/bti781  0.6
2005 Levy ED, Ouzounis CA, Gilks WR, Audit B. Probabilistic annotation of protein sequences based on functional classifications. Bmc Bioinformatics. 6: 302. PMID 16354297 DOI: 10.1186/1471-2105-6-302  0.6
2005 Karp PD, Ouzounis CA, Moore-Kochlacs C, Goldovsky L, Kaipa P, Ahrén D, Tsoka S, Darzentas N, Kunin V, López-Bigas N. Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Research. 33: 6083-9. PMID 16246909 DOI: 10.1093/nar/gki892  0.6
2005 Darzentas N, Rigoutsos I, Ouzounis CA. Sensitive detection of sequence similarity using combinatorial pattern discovery: a challenging study of two distantly related protein families. Proteins. 61: 926-37. PMID 16224785 DOI: 10.1002/prot.20608  0.6
2005 Goldovsky L, Janssen P, Ahrén D, Audit B, Cases I, Darzentas N, Enright AJ, López-Bigas N, Peregrin-Alvarez JM, Smith M, Tsoka S, Kunin V, Ouzounis CA. CoGenT++: an extensive and extensible data environment for computational genomics. Bioinformatics (Oxford, England). 21: 3806-10. PMID 16216832 DOI: 10.1093/Bioinformatics/Bti579  0.6
2005 Ouzounis CA. Ancestral state reconstructions for genomes. Current Opinion in Genetics & Development. 15: 595-600. PMID 16216489 DOI: 10.1016/j.gde.2005.09.011  0.6
2005 Goldovsky L, Cases I, Enright AJ, Ouzounis CA. BioLayout(Java): versatile network visualisation of structural and functional relationships. Applied Bioinformatics. 4: 71-4. PMID 16000016 DOI: 10.2165/00822942-200504010-00009  0.6
2005 Kunin V, Goldovsky L, Darzentas N, Ouzounis CA. The net of life: reconstructing the microbial phylogenetic network. Genome Research. 15: 954-9. PMID 15965028 DOI: 10.1101/gr.3666505  0.6
2005 Smith M, Kunin V, Goldovsky L, Enright AJ, Ouzounis CA. MagicMatch--cross-referencing sequence identifiers across databases. Bioinformatics (Oxford, England). 21: 3429-30. PMID 15961438 DOI: 10.1093/bioinformatics/bti548  0.6
2005 Janssen P, Goldovsky L, Kunin V, Darzentas N, Ouzounis CA. Genome coverage, literally speaking. The challenge of annotating 200 genomes with 4 million publications. Embo Reports. 6: 397-9. PMID 15864286 DOI: 10.1038/Sj.Embor.7400412  0.6
2005 López-Bigas N, Audit B, Ouzounis C, Parra G, Guigó R. Are splicing mutations the most frequent cause of hereditary disease? Febs Letters. 579: 1900-3. PMID 15792793 DOI: 10.1016/J.Febslet.2005.02.047  0.6
2005 Kunin V, Teichmann SA, Huynen MA, Ouzounis CA. The properties of protein family space depend on experimental design. Bioinformatics (Oxford, England). 21: 2618-22. PMID 15769834 DOI: 10.1093/Bioinformatics/Bti386  0.6
2005 Gilks WR, Audit B, de Angelis D, Tsoka S, Ouzounis CA. Percolation of annotation errors through hierarchically structured protein sequence databases. Mathematical Biosciences. 193: 223-34. PMID 15748731 DOI: 10.1016/j.mbs.2004.08.001  0.6
2005 Kunin V, Ouzounis CA. Clustering the annotation space of proteins. Bmc Bioinformatics. 6: 24. PMID 15703069 DOI: 10.1186/1471-2105-6-24  0.6
2005 Kunin V, Ahren D, Goldovsky L, Janssen P, Ouzounis CA. Measuring genome conservation across taxa: divided strains and united kingdoms. Nucleic Acids Research. 33: 616-21. PMID 15681613 DOI: 10.1093/Nar/Gki181  0.6
2005 Pereira-Leal JB, Audit B, Peregrin-Alvarez JM, Ouzounis CA. An exponential core in the heart of the yeast protein interaction network. Molecular Biology and Evolution. 22: 421-5. PMID 15496552 DOI: 10.1093/Molbev/Msi024  0.6
2004 Tsoka S, Simon D, Ouzounis CA. Automated metabolic reconstruction for Methanococcus jannaschii. Archaea (Vancouver, B.C.). 1: 223-9. PMID 15810431 DOI: 10.1155/2004/324925  0.6
2004 Ahren DG, Ouzounis CA. Robustness of metabolic map reconstruction. Journal of Bioinformatics and Computational Biology. 2: 589-93. PMID 15359428 DOI: 10.1142/S021972000400079X  0.6
2004 Coulson RM, Hall N, Ouzounis CA. Comparative genomics of transcriptional control in the human malaria parasite Plasmodium falciparum. Genome Research. 14: 1548-54. PMID 15256513 DOI: 10.1101/gr.2218604  0.6
2004 López-Bigas N, Ouzounis CA. Genome-wide identification of genes likely to be involved in human genetic disease. Nucleic Acids Research. 32: 3108-14. PMID 15181176 DOI: 10.1093/nar/gkh605  0.6
2004 Kunin V, Pereira-Leal JB, Ouzounis CA. Functional evolution of the yeast protein interaction network. Molecular Biology and Evolution. 21: 1171-6. PMID 15071090 DOI: 10.1093/Molbev/Msh085  0.6
2004 Pereira-Leal JB, Enright AJ, Ouzounis CA. Detection of functional modules from protein interaction networks. Proteins. 54: 49-57. PMID 14705023 DOI: 10.1002/Prot.10505  0.6
2003 Iliopoulos I, Enright AJ, Poullet P, Ouzounis CA. Mapping functional associations in the entire genome of Drosophila melanogaster using fusion analysis. Comparative and Functional Genomics. 4: 337-41. PMID 18629289 DOI: 10.1002/cfg.287  0.6
2003 Tsoka S, Ouzounis CA. Metabolic database systems for the analysis of genome-wide function. Biotechnology and Bioengineering. 84: 750-5. PMID 14708115 DOI: 10.1002/bit.10881  0.6
2003 von Mering C, Zdobnov EM, Tsoka S, Ciccarelli FD, Pereira-Leal JB, Ouzounis CA, Bork P. Genome evolution reveals biochemical networks and functional modules. Proceedings of the National Academy of Sciences of the United States of America. 100: 15428-33. PMID 14673105 DOI: 10.1073/Pnas.2136809100  0.6
2003 Ouzounis CA, Valencia A. Early bioinformatics: the birth of a discipline--a personal view. Bioinformatics (Oxford, England). 19: 2176-90. PMID 14630646 DOI: 10.1093/Bioinformatics/Btg309  0.6
2003 Kreil DP, Ouzounis CA. Comparison of sequence masking algorithms and the detection of biased protein sequence regions. Bioinformatics (Oxford, England). 19: 1672-81. PMID 12967964 DOI: 10.1093/bioinformatics/btg212  0.6
2003 Audit B, Ouzounis CA. From genes to genomes: universal scale-invariant properties of microbial chromosome organisation. Journal of Molecular Biology. 332: 617-33. PMID 12963371 DOI: 10.1016/S0022-2836(03)00811-8  0.6
2003 Weinel C, Ermolaeva MD, Ouzounis C. PseuRECA: genome annotation and gene context analysis for Pseudomonas aeruginosa PAO1. Bioinformatics (Oxford, England). 19: 1457-60. PMID 12912824 DOI: 10.1093/bioinformatics/btg184  0.6
2003 Enright AJ, Kunin V, Ouzounis CA. Protein families and TRIBES in genome sequence space. Nucleic Acids Research. 31: 4632-8. PMID 12888524 DOI: 10.1093/nar/gkg495  0.6
2003 Janssen P, Enright AJ, Audit B, Cases I, Goldovsky L, Harte N, Kunin V, Ouzounis CA. COmplete GENome Tracking (COGENT): a flexible data environment for computational genomics. Bioinformatics (Oxford, England). 19: 1451-2. PMID 12874064 DOI: 10.1093/Bioinformatics/Btg161  0.6
2003 Kunin V, Ouzounis CA. GeneTRACE-reconstruction of gene content of ancestral species. Bioinformatics (Oxford, England). 19: 1412-6. PMID 12874054 DOI: 10.1093/bioinformatics/btg174  0.6
2003 Kunin V, Ouzounis CA. The balance of driving forces during genome evolution in prokaryotes. Genome Research. 13: 1589-94. PMID 12840037 DOI: 10.1101/gr.1092603  0.6
2003 Ouzounis CA, Coulson RM, Enright AJ, Kunin V, Pereira-Leal JB. Classification schemes for protein structure and function. Nature Reviews. Genetics. 4: 508-19. PMID 12838343 DOI: 10.1038/Nrg1113  0.6
2003 Cases I, de Lorenzo V, Ouzounis CA. Transcription regulation and environmental adaptation in bacteria. Trends in Microbiology. 11: 248-53. PMID 12823939 DOI: 10.1016/S0966-842X(03)00103-3  0.6
2003 Janssen P, Audit B, Cases I, Darzentas N, Goldovsky L, Kunin V, Lopez-Bigas N, Peregrin-Alvarez JM, Pereira-Leal JB, Tsoka S, Ouzounis CA. Beyond 100 genomes. Genome Biology. 4: 402. PMID 12734008 DOI: 10.1186/Gb-2003-4-5-402  0.6
2003 Iliopoulos I, Tsoka S, Andrade MA, Enright AJ, Carroll M, Poullet P, Promponas V, Liakopoulos T, Palaios G, Pasquier C, Hamodrakas S, Tamames J, Yagnik AT, Tramontano A, Devos D, ... ... Ouzounis CA, et al. Evaluation of annotation strategies using an entire genome sequence. Bioinformatics (Oxford, England). 19: 717-26. PMID 12691983 DOI: 10.1093/Bioinformatics/Btg077  0.6
2003 Kunin V, Cases I, Enright AJ, de Lorenzo V, Ouzounis CA. Myriads of protein families, and still counting. Genome Biology. 4: 401. PMID 12620116 DOI: 10.1186/gb-2003-4-2-401  0.6
2003 Peregrin-Alvarez JM, Tsoka S, Ouzounis CA. The phylogenetic extent of metabolic enzymes and pathways. Genome Research. 13: 422-7. PMID 12618373 DOI: 10.1101/gr.246903  0.6
2003 Coulson RM, Ouzounis CA. The phylogenetic diversity of eukaryotic transcription. Nucleic Acids Research. 31: 653-60. PMID 12527774 DOI: 10.1093/nar/gkg156  0.6
2003 Hatzimanikatis V, Ouzounis C, Quackenbush J. Systems Approaches to Biotechnology: Systems Biotechnology in the Making. Editorial Biotechnology and Bioengineering. 84: i.  0.6
2002 Gilks WR, Audit B, De Angelis D, Tsoka S, Ouzounis CA. Modeling the percolation of annotation errors in a database of protein sequences. Bioinformatics (Oxford, England). 18: 1641-9. PMID 12490449 DOI: 10.1093/bioinformatics/18.12.1641  0.6
2002 Garcia-Vallvé S, Janssen PJ, Ouzounis CA. Genetic variation between Helicobacter pylori strains: gene acquisition or loss? Trends in Microbiology. 10: 445-7. PMID 12377549 DOI: 10.1016/S0966-842X(02)02446-0  0.6
2002 Harte R, Ouzounis CA. Genome-wide detection and family clustering of ion channels. Febs Letters. 514: 129-34. PMID 11943138 DOI: 10.1016/S0014-5793(01)03254-9  0.6
2002 Ouzounis C. Bioinformatics and the theoretical foundations of molecular biology. Bioinformatics (Oxford, England). 18: 377-8. PMID 11934735  0.6
2002 Enright AJ, Van Dongen S, Ouzounis CA. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Research. 30: 1575-84. PMID 11917018 DOI: 10.1093/NAR/30.7.1575  0.6
2002 Ouzounis CA, Karp PD. The past, present and future of genome-wide re-annotation. Genome Biology. 3: COMMENT2001. PMID 11864365  0.6
2001 Enright AJ, Ouzounis CA. Functional associations of proteins in entire genomes by means of exhaustive detection of gene fusions. Genome Biology. 2: RESEARCH0034. PMID 11820254 DOI: 10.1186/gb-2001-2-9-research0034  0.6
2001 Boucher L, Ouzounis CA, Enright AJ, Blencowe BJ. A genome-wide survey of RS domain proteins. Rna (New York, N.Y.). 7: 1693-701. PMID 11780626  0.6
2001 Janssen PJ, Audit B, Ouzounis CA. Strain-specific genes of Helicobacter pylori: distribution, function and dynamics. Nucleic Acids Research. 29: 4395-404. PMID 11691927  0.6
2001 Enright AJ, Ouzounis CA. BioLayout--an automatic graph layout algorithm for similarity visualization. Bioinformatics (Oxford, England). 17: 853-4. PMID 11590107 DOI: 10.1093/bioinformatics/17.9.853  0.6
2001 Tsoka S, Ouzounis CA. Functional versatility and molecular diversity of the metabolic map of Escherichia coli. Genome Research. 11: 1503-10. PMID 11544193 DOI: 10.1101/gr.187501  0.6
2001 Kreil DP, Ouzounis CA. Identification of thermophilic species by the amino acid compositions deduced from their genomes. Nucleic Acids Research. 29: 1608-15. PMID 11266564  0.6
2001 Iliopoulos I, Enright AJ, Ouzounis CA. Textquest: document clustering of Medline abstracts for concept discovery in molecular biology. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 384-95. PMID 11262957 DOI: 10.1142/9789814447362_0038  0.6
2001 Coulson RM, Enright AJ, Ouzounis CA. Transcription-associated protein families are primarily taxon-specific. Bioinformatics (Oxford, England). 17: 95-7. PMID 11222266 DOI: 10.1093/bioinformatics/17.1.95  0.6
2001 Iliopoulos I, Tsoka S, Andrade MA, Janssen P, Audit B, Tramontano A, Valencia A, Leroy C, Sander C, Ouzounis CA. Genome sequences and great expectations. Genome Biology. 2: INTERACTIONS0001. PMID 11178275 DOI: 10.1186/Gb-2000-2-1-Interactions0001  0.6
2000 Promponas VJ, Enright AJ, Tsoka S, Kreil DP, Leroy C, Hamodrakas S, Sander C, Ouzounis CA. CAST: an iterative algorithm for the complexity analysis of sequence tracts. Complexity analysis of sequence tracts. Bioinformatics (Oxford, England). 16: 915-22. PMID 11120681 DOI: 10.1093/Bioinformatics/16.10.915  0.6
2000 Kyrpides NC, Ouzounis CA, Iliopoulos I, Vonstein V, Overbeek R. Analysis of the Thermotoga maritima genome combining a variety of sequence similarity and genome context tools. Nucleic Acids Research. 28: 4573-6. PMID 11071948  0.6
2000 Tsoka S, Ouzounis CA. Prediction of protein interactions: metabolic enzymes are frequently involved in gene fusion. Nature Genetics. 26: 141-2. PMID 11017064 DOI: 10.1038/79847  0.6
2000 Tsoka S, Ouzounis CA. Recent developments and future directions in computational genomics. Febs Letters. 480: 42-8. PMID 10967327 DOI: 10.1016/S0014-5793(00)01776-2  0.6
2000 Thomas J, Milward D, Ouzounis C, Pulman S, Carroll M. Automatic extraction of protein interactions from scientific abstracts. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 541-52. PMID 10902201  0.6
2000 Enright AJ, Ouzounis CA. GeneRAGE: a robust algorithm for sequence clustering and domain detection. Bioinformatics (Oxford, England). 16: 451-7. PMID 10871267 DOI: 10.1093/bioinformatics/16.5.451  0.6
2000 Ouzounis C. Two or three myths about bioinformatics. Bioinformatics (Oxford, England). 16: 187-9. PMID 10869011  0.6
2000 Ouzounis CA, Karp PD. Global properties of the metabolic map of Escherichia coli. Genome Research. 10: 568-76. PMID 10779499 DOI: 10.1101/gr.10.4.568  0.6
1999 Blaschke C, Andrade MA, Ouzounis C, Valencia A. Automatic extraction of biological information from scientific text: protein-protein interactions. Proceedings / ... International Conference On Intelligent Systems For Molecular Biology ; Ismb. International Conference On Intelligent Systems For Molecular Biology. 60-7. PMID 10786287  0.6
1999 Rigoutsos I, Floratos A, Ouzounis C, Gao Y, Parida L. Dictionary building via unsupervised hierarchical motif discovery in the sequence space of natural proteins. Proteins. 37: 264-77. PMID 10584071 DOI: 10.1002/(Sici)1097-0134(19991101)37:2<264::Aid-Prot11>3.0.Co;2-C  0.6
1999 Enright AJ, Iliopoulos I, Kyrpides NC, Ouzounis CA. Protein interaction maps for complete genomes based on gene fusion events. Nature. 402: 86-90. PMID 10573422 DOI: 10.1038/47056  0.6
1999 Andrade MA, Ouzounis C, Sander C, Tamames J, Valencia A. Functional classes in the three domains of life Journal of Molecular Evolution. 49: 551-557. PMID 10552036 DOI: 10.1007/Pl00006576  0.6
1999 Raghavan S, Ouzounis CA. Novel coding regions in four complete archaeal genomes Nucleic Acids Research. 27: 4405-4408. PMID 10536149 DOI: 10.1093/nar/27.22.4405  0.6
1999 Ouzounis C. Orthology: Another terminology muddle Trends in Genetics. 15: 445. PMID 10529805 DOI: 10.1016/S0168-9525(99)01845-4  0.6
1999 Kyrpides N, Overbeek R, Ouzounis C. Universal protein families and the functional content of the last universal common ancestor Journal of Molecular Evolution. 49: 413-423. PMID 10485999 DOI: 10.1007/Pl00006564  0.6
1999 Kyrpides NC, Ouzounis CA. Transcription in Archaea Proceedings of the National Academy of Sciences of the United States of America. 96: 8545-8550. PMID 10411912 DOI: 10.1073/pnas.96.15.8545  0.6
1999 Tsoka S, Promponas V, Ouzounis CA. Reproducibility in genome sequence annotation: The Plasmodium falciparum chromosome 2 case Febs Letters. 451: 354-355. PMID 10371220 DOI: 10.1016/S0014-5793(99)00599-2  0.6
1999 Andrade MA, Brown NP, Leroy C, Hoersch S, De Daruvar A, Reich C, Franchini A, Tamames J, Valencia A, Ouzounis C, Sander C. Automated genome sequence analysis and annotation Bioinformatics. 15: 391-412. PMID 10366660 DOI: 10.1093/Bioinformatics/15.5.391  0.6
1999 Kyrpides NC, Ouzounis CA. Whole-genome sequence annotation: Going wrong with confidence [3] Molecular Microbiology. 32: 886-887. PMID 10361291 DOI: 10.1046/j.1365-2958.1999.01380.x  0.6
1999 Blencowe BJ, Ouzounis CA. The PWI motif: a new protein domain in splicing factors. Trends in Biochemical Sciences. 24: 179-80. PMID 10322432 DOI: 10.1016/S0968-0004(99)01387-0  0.6
1998 Ouzounis C, Pérez-Irratxeta C, Sander C, Valencia A. Are binding residues conserved? Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 401-412. PMID 9697199  0.6
1998 Tamames J, Ouzounis C, Casari G, Sander C, Valencia A. EUCLID : Automatic classification of proteins in functional classes by their database annotations Bioinformatics. 14: 542-543. PMID 9694995 DOI: 10.1093/Bioinformatics/14.6.542  0.6
1998 Rodriguez-Monge L, Ouzounis CA, Kyrpides NC. A ferredoxin-like domain in RNA polymerase 30/40-kDa subunits Trends in Biochemical Sciences. 23: 169-170. PMID 9612079 DOI: 10.1016/S0968-0004(98)01203-1  0.6
1998 Papadopoulos GK, Ouzounis C, Eliopoulos E. RGD sequences in several receptor proteins: Novel cell adhesion function of receptors? International Journal of Biological Macromolecules. 22: 51-57. PMID 9513816 DOI: 10.1016/S0141-8130(97)00087-1  0.6
1997 Ouzounis CA, Kyrpides NC. ThidD-TenA: A gene pair fusion in eukaryotes Journal of Molecular Evolution. 45: 708-711. PMID 9419250 DOI: 10.1007/PL00013145  0.6
1997 Kyrpides NC, Ouzounis CA. Bacterial σ70 transcription factor DNA-binding domains in the archaeon methanococcus jannaschii Journal of Molecular Evolution. 45: 706-707. PMID 9419249  0.6
1997 Perrakis A, Ouzounis C, Wilson KS. Evolution of immunoglobulin-like modules in chitinases: Their structural flexibility and functional implications Folding and Design. 2: 291-294. PMID 9377712 DOI: 10.1016/S1359-0278(97)00040-0  0.6
1997 des Jardins M, Karp PD, Krummenacker M, Lee TJ, Ouzounis CA. Prediction of enzyme classification from protein sequence without the use of sequence similarity Proceedings / ... International Conference On Intelligent Systems For Molecular Biology ; Ismb. International Conference On Intelligent Systems For Molecular Biology. 5: 92-99. PMID 9322021  0.6
1997 Andrade M, Casari G, de Daruvar A, Sander C, Schneider R, Tamames J, Valencia A, Ouzounis C. Sequence analysis of the Methanococcus jannaschii genome and the prediction of protein function. Computer Applications in the Biosciences : Cabios. 13: 481-3. PMID 9283767 DOI: 10.1093/Bioinformatics/13.4.481  0.6
1997 Tamames J, Casari G, Ouzounis C, Valencia A. Conserved clusters of functionally related genes in two bacterial genomes Journal of Molecular Evolution. 44: 66-73. PMID 9010137 DOI: 10.1007/Pl00006122  0.6
1996 Ouzounis CA, Kyrpides NC. The core histone fold: limits to functional versatility Journal of Molecular Evolution. 43: 541-542. PMID 8995050  0.6
1996 Ouzounis C, Casari G, Sander C, Tamames J, Valencia A. Computational comparisons of model genomes Trends in Biotechnology. 14: 280-285. PMID 8987458 DOI: 10.1016/0167-7799(96)10043-3  0.6
1996 Kyrpides NC, Woese CR, Ouzounis CA. KOW: a novel motif linking a bacterial transcription factor with ribosomal proteins. Trends in Biochemical Sciences. 21: 425-6. PMID 8987397 DOI: 10.1016/S0968-0004(96)30036-4  0.6
1996 Paliakasis K, Routsias J, Petratos K, Ouzounis C, Kokkinidis M, Papadopoulos GK. Novel structural features of the human histocompatibility molecules HLA-DQ as revealed by modeling based on the published structure of the related molecule HLA-DR1 Journal of Structural Biology. 117: 145-163. PMID 8931340 DOI: 10.1006/Jsbi.1996.0079  0.6
1996 Ouzounis CA, Kyrpides NC. Parallel origins of the nucleosome core and eukaryotic transcription from archaea Journal of Molecular Evolution. 42: 234-239. PMID 8919875 DOI: 10.1007/BF02198849  0.6
1996 Karp PD, Ouzounis C, Paley S. HinCyc: a knowledge base of the complete genome and metabolic pathways of H. influenzae Proceedings / ... International Conference On Intelligent Systems For Molecular Biology ; Ismb. International Conference On Intelligent Systems For Molecular Biology. 4: 116-124. PMID 8877511  0.6
1996 Ouzounis C, Casari G, Valencia A, Sander C. Novelties from the complete genome of Mycoplasma genitalium [3] Molecular Microbiology. 20: 898-900. PMID 8793887 DOI: 10.1111/J.1365-2958.1996.Tb02529.X  0.6
1996 Ouzounis C, Kyrpides N. The emergence of major cellular processes in evolution Febs Letters. 390: 119-123. PMID 8706840 DOI: 10.1016/0014-5793(96)00631-X  0.6
1996 Tamames J, Ouzounis C, Sander C, Valencia A. Genomes with distinct function composition Febs Letters. 389: 96-101. PMID 8682215 DOI: 10.1016/0014-5793(96)00527-3  0.6
1995 Ouzounis C, Bork P, Casari G, Sander C. New protein functions in yeast chromosome VIII. Protein Science : a Publication of the Protein Society. 4: 2424-8. PMID 8563640 DOI: 10.1002/Pro.5560041121  0.6
1995 Ouzounis C, Kyrpides N, Sander C. Novel protein families in archaean genomes Nucleic Acids Research. 23: 565-570. PMID 7899076 DOI: 10.1093/Nar/23.4.565  0.6
1995 Kyrpides NC, Ouzounis CA. The eubacterial transcriptional activator Lrp is present in the Archaeon Pyrococcus furiosus Trends in Biochemical Sciences. 20: 140-141. PMID 7770911 DOI: 10.1016/S0968-0004(00)88988-4  0.6
1995 Bork P, Ouzounis C, McEntyre J. Ready for a motif submission? A proposed checklist. Trends in Biochemical Sciences. 20: 104. PMID 7709426 DOI: 10.1016/S0968-0004(00)88974-4  0.6
1995 Casari G, Andrade MA, Bork P, Boyle J, Daruvar A, Ouzounis C, Schneider R, Tamames J, Valencia A, Sander C. Challenging times for bioinformatics. Nature. 376: 647-8. PMID 7651513 DOI: 10.1038/376647A0  0.6
1995 Konstantopoulou I, Ouzounis CA, Drosopoulou E, Yiangou M, Sideras P, Sander C, Scouras ZG. A Drosophila hsp70 gene contains long, antiparallel, coupled open reading frames (LAC ORFs) conserved in homologous loci Journal of Molecular Evolution. 41: 414-420. PMID 7563128 DOI: 10.1007/Bf00160312  0.6
1995 Kyrpides NC, Ouzounis CA. Nucleic acid-binding metabolic enzymes: Living fossils of stereochemical interactions? Journal of Molecular Evolution. 40: 564-569. PMID 7543949 DOI: 10.1007/BF00160502  0.6
1995 Bork P, Ouzounis C, Casari G, Schneider R, Sander C, Dolan M, Gilbert W, Gillevet PM. Exploring the Mycoplasma capricolum genome: a minimal cell reveals its physiology. Molecular Microbiology. 16: 955-67. PMID 7476192 DOI: 10.1111/J.1365-2958.1995.Tb02321.X  0.6
1995 Ouzounis C, Valencia A, Tamames J, Bork P, Sander C. The functional composition of living machines as a design principle for artificial organisms Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 929: 843-851. DOI: 10.1007/3-540-59496-5_347  0.6
1994 Simos G, Panagiotidis CA, Skoumbas A, Choli D, Ouzounis C, Georgatsos JG. Barley β-glucosidase: Expression during seed germination and maturation and partial amino acids sequences Bba - General Subjects. 1199: 52-58. PMID 8280753 DOI: 10.1016/0304-4165(94)90095-7  0.6
1994 Ouzounis CA, Kyrpides NC. Reverse interpretation: A hypothetical selection mechanism for adaptive mutagenesis based on autoregulated mRNA stability Journal of Theoretical Biology. 167: 373-380. PMID 8207952 DOI: 10.1006/jtbi.1994.1076  0.6
1994 Ouzounis CA, Kyrpides NC. On the evolution of arginases and related enzymes Journal of Molecular Evolution. 39: 101-104. PMID 8064866 DOI: 10.1007/BF00178255  0.6
1994 Ouzounis C, Bork P, Sander C. The modular structure of NifU proteins. Trends in Biochemical Sciences. 19: 199-200. PMID 8048161 DOI: 10.1016/0968-0004(94)90021-3  0.6
1994 Scharf M, Schneider R, Casari G, Bork P, Valencia A, Ouzounis C, Sander C. GeneQuiz: a workbench for sequence analysis. Proceedings / ... International Conference On Intelligent Systems For Molecular Biology ; Ismb. International Conference On Intelligent Systems For Molecular Biology. 2: 348-53. PMID 7584411  0.6
1994 Bork P, Ouzounis C, Sander C. From genome sequences to protein function Current Opinion in Structural Biology. 4: 393-403. DOI: 10.1016/S0959-440X(94)90109-0  0.6
1993 Gounari F, Merdes A, Quinlan R, Hess J, FitzGerald PG, Ouzounis CA, Georgatos SD. Bovine filensin possesses primary and secondary structure similarity to intermediate filament proteins. The Journal of Cell Biology. 121: 847-53. PMID 8491777 DOI: 10.1083/Jcb.121.4.847  0.6
1993 Ouzounis C, Sander C. Homology of the NifS family of proteins to a new class of pyridoxal phosphate-dependent enzymes Febs Letters. 322: 159-164. PMID 8482384 DOI: 10.1016/0014-5793(93)81559-I  0.6
1993 Ouzounis C, Sander C, Scharf M, Schneider R. Prediction of protein structure by evaluation of sequence-structure fitness. Aligning sequences to contact profiles derived from three-dimensional structures. Journal of Molecular Biology. 232: 805-25. PMID 8355272 DOI: 10.1006/Jmbi.1993.1433  0.6
1993 Kyrpides NC, Ouzounis CA. Mechanisms of specificity in mRNA degradation: Autoregulation and cognate interactions Journal of Theoretical Biology. 163: 373-392. PMID 8246508 DOI: 10.1006/jtbi.1993.1126  0.6
1993 Ouzounis C, Sander C. Commentary response Febs Letters. 330: 242.  0.6
1992 Bork P, Ouzounis C, Sander C, Scharf M, Schneider R, Sonnhammer E. What's in a genome? Nature. 358: 287. PMID 1641000 DOI: 10.1038/358287A0  0.6
1992 Ouzounis C, Sander C. TFIIB, an evolutionary link between the transcription machineries of archaebacteria and eukaryotes Cell. 71: 189-190. PMID 1423586 DOI: 10.1016/0092-8674(92)90347-F  0.6
1992 Holm L, Ouzounis C, Sander C, Tuparev G, Vriend G. A database of protein structure families with common folding motifs Protein Science. 1: 1691-1698. PMID 1304898 DOI: 10.1002/Pro.5560011217  0.6
1992 Bork P, Ouzounis C, Sander C, Scharf M, Schneider R, Sonnhammer E. Comprehensive sequence analysis of the 182 predicted open reading frames of yeast chromosome III. Protein Science : a Publication of the Protein Society. 1: 1677-90. PMID 1304897 DOI: 10.1002/Pro.5560011216  0.6
1991 Ouzounis CA, Melvin WT. Primary and secondary structural patterns in eukaryotic cytochrome P-450 families correspond to structures of the helix-rich domain of Pseudomonas putida cytochrome P-450(cam). Indications for a similar overall topology European Journal of Biochemistry. 198: 307-315. PMID 2040297  0.6
1991 Ouzounis C, Sander C. A structure-derived sequence pattern for the detection of type I copper binding domains in distantly related proteins Febs Letters. 279: 73-78. PMID 1995346 DOI: 10.1016/0014-5793(91)80254-Z  0.6
1991 Ouzounis CA, Blencowe BJ. Bacterial DNA replication initiation factor priA is related to proteins belonging to the 'DEAD-box' family. Nucleic Acids Research. 19: 6953. PMID 1662369 DOI: 10.1093/nar/19.24.6953  0.6
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