Year |
Citation |
Score |
2023 |
Pavlopoulos GA, Baltoumas FA, Liu S, Selvitopi O, Camargo AP, Nayfach S, Azad A, Roux S, Call L, Ivanova NN, Chen IM, Paez-Espino D, Karatzas E, Iliopoulos I, Konstantinidis K, ... ... Ouzounis CA, et al. Unraveling the functional dark matter through global metagenomics. Nature. 622: 594-602. PMID 37821698 DOI: 10.1038/s41586-023-06583-7 |
0.415 |
|
2023 |
Kouros CE, Makri V, Ouzounis CA, Chasapi A. Disease association and comparative genomics of compositional bias in human proteins. F1000research. 12: 198. PMID 37082000 DOI: 10.12688/f1000research.129929.2 |
0.315 |
|
2021 |
Neches RY, Kyrpides NC, Ouzounis CA. Atypical Divergence of SARS-CoV-2 Orf8 from Orf7a within the Coronavirus Lineage Suggests Potential Stealthy Viral Strategies in Immune Evasion. Mbio. 12. PMID 33468697 DOI: 10.1128/mBio.03014-20 |
0.31 |
|
2020 |
Psomopoulos FE, van Helden J, Médigue C, Chasapi A, Ouzounis CA. Ancestral state reconstruction of metabolic pathways across pangenome ensembles. Microbial Genomics. PMID 32924924 DOI: 10.1099/mgen.0.000429 |
0.322 |
|
2018 |
Danchin A, Ouzounis C, Tokuyasu T, Zucker JD. No wisdom in the crowd: genome annotation in the era of big data - current status and future prospects. Microbial Biotechnology. PMID 29806194 DOI: 10.1111/1751-7915.13284 |
0.409 |
|
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 |
0.394 |
|
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 |
0.414 |
|
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 |
0.413 |
|
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 |
0.317 |
|
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 |
0.372 |
|
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 |
0.302 |
|
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 |
0.304 |
|
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 |
0.372 |
|
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 |
0.303 |
|
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 |
0.314 |
|
2007 |
Peregrín-Alvarez JM, Ouzounis CA. The comparative genomics of protein interactions. Genome Informatics. International Conference On Genome Informatics. 19: 131-41. PMID 18546511 |
0.387 |
|
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 |
0.382 |
|
2007 |
Coulson RM, Touboul N, Ouzounis CA. Lineage-specific partitions in archaeal transcription. Archaea (Vancouver, B.C.). 2: 117-25. PMID 17350932 |
0.375 |
|
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 |
0.325 |
|
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 |
0.35 |
|
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 |
0.311 |
|
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 |
0.385 |
|
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 |
0.31 |
|
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 |
0.341 |
|
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 |
0.479 |
|
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 |
0.356 |
|
2005 |
Kunin V, Ouzounis CA. Clustering the annotation space of proteins. Bmc Bioinformatics. 6: 24. PMID 15703069 DOI: 10.1186/1471-2105-6-24 |
0.319 |
|
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 |
0.34 |
|
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 |
0.621 |
|
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 |
0.343 |
|
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 |
0.324 |
|
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 |
0.635 |
|
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 |
0.606 |
|
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 |
0.388 |
|
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 |
0.657 |
|
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 |
0.352 |
|
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 |
0.309 |
|
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 |
0.585 |
|
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 |
0.612 |
|
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 |
0.324 |
|
2003 |
Coulson RM, Ouzounis CA. The phylogenetic diversity of eukaryotic transcription. Nucleic Acids Research. 31: 653-60. PMID 12527774 DOI: 10.1093/nar/gkg156 |
0.338 |
|
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 |
0.368 |
|
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 |
0.369 |
|
2002 |
Ouzounis CA, Karp PD. The past, present and future of genome-wide re-annotation. Genome Biology. 3: COMMENT2001. PMID 11864365 |
0.365 |
|
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 |
0.397 |
|
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 |
0.377 |
|
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 |
0.382 |
|
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 |
0.45 |
|
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 |
0.411 |
|
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 |
0.381 |
|
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 |
0.319 |
|
1999 |
Ouzounis C. Orthology: Another terminology muddle Trends in Genetics. 15: 445. PMID 10529805 DOI: 10.1016/S0168-9525(99)01845-4 |
0.401 |
|
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 |
0.453 |
|
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 |
0.442 |
|
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 |
0.406 |
|
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 |
0.305 |
|
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 |
0.442 |
|
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 |
0.422 |
|
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 |
0.379 |
|
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 |
0.449 |
|
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 |
0.489 |
|
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 |
0.421 |
|
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 |
0.481 |
|
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 |
0.429 |
|
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 |
0.357 |
|
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 |
0.481 |
|
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 |
0.353 |
|
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 |
0.398 |
|
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 |
0.35 |
|
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 |
0.395 |
|
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 |
0.465 |
|
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 |
0.383 |
|
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