Research Topics
| C A OuzounisSummaryAffiliation: Wellcome Trust Genome Campus Country: UK Publications
| Collaborators
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Detail Information
Publications
Beyond 100 genomesPaul Janssen
Genome Biol 4:402. 2003..An overview of these genomes reveals certain interesting trends and provides valuable insights into possible future developments...- Genome sequences and great expectationsI Iliopoulos
Computational Genomics Group, Research Programme, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge, CB10 1SD, UK
Genome Biol 2:INTERACTIONS0001. 2001..Despite progress in computational biology, there will always be a great need for large-scale experimental determination of protein function... - Functional associations of proteins in entire genomes by means of exhaustive detection of gene fusionsA J Enright
Computational Genomics Group, European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
Genome Biol 2:RESEARCH0034. 2001..CONCLUSIONS: These results provide an exhaustive set of functionally associated genes and also delineate the power of fusion analysis for the prediction of protein interactions... - The past, present and future of genome-wide re-annotationChristos A Ouzounis
Bioinformatics Research Group, AI Center, SRI International, Menlo Park, CA 94025, USA
Genome Biol 3:COMMENT2001. 2002..We define the process of annotating a previously annotated genome sequence as 're-annotation', and examine the strengths and weaknesses of current manual and automatic genome-wide re-annotation approaches... - Myriads of protein families, and still countingVictor Kunin
Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge, UK
Genome Biol 4:401. 2003..From the historical record of genome sequencing, we show that the rate of discovery of new families has remained constant over time, indicating that our knowledge of sequence space is far from complete... - Structural and functional properties of genes involved in human cancerSimon J Furney
Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
BMC Genomics 7:3. 2006..One of the main goals of cancer genetics is to identify the causative elements at the molecular level leading to cancer... - Probabilistic annotation of protein sequences based on functional classificationsEmmanuel D Levy
Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
BMC Bioinformatics 6:302. 2005..Most automatic approaches developed to date rely on the identification of clusters of homologous proteins and the mapping of new proteins onto these clusters, which are expected to share functional characteristics... - Clustering the annotation space of proteinsVictor Kunin
Computational Genomics Group, EMBL EBI, Cambridge, CB10 1SO, UK
BMC Bioinformatics 6:24. 2005..Current protein clustering methods rely on either sequence or functional similarities between proteins, thereby limiting inferences to one of these areas... 
Ancestral state reconstructions for genomesChristos A Ouzounis
Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
Curr Opin Genet Dev 15:595-600. 2005....- Classification schemes for protein structure and functionChristos A Ouzounis
Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
Nat Rev Genet 4:508-19. 2003.... - Maps, books and other metaphors for systems biologyChristos Ouzounis
Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
Biosystems 85:6-10. 2006..Finally, we propose a metaphor for systems biology that provides an illuminating perspective for the ambitious goals of this field and delimits its current agenda... - Early bioinformatics: the birth of a discipline--a personal viewChristos A Ouzounis
Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
Bioinformatics 19:2176-90. 2003.... - Global properties of the metabolic map of Escherichia coliC A Ouzounis
Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge, CB10 1SD, UK
Genome Res 10:568-76. 2000..The dimensions chosen for this analysis can be employed for comparative functional analysis of complete genomes... - The balance of driving forces during genome evolution in prokaryotesVictor Kunin
Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
Genome Res 13:1589-94. 2003..This approach indicates that it is possible to trace genome content history and quantify the factors that shape contemporary prokaryotic genomes... - Strain-specific genes of Helicobacter pylori: distribution, function and dynamicsP J Janssen
Computational Genomics Group, Research Programme, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
Nucleic Acids Res 29:4395-404. 2001..If these are taken into account, a common pattern for the genome dynamics of the two Helicobacter strains emerges, suggestive of certain spatial constraints that may act as control mechanisms of gene flux... - CoGenT++: an extensive and extensible data environment for computational genomicsLeon Goldovsky
Computational Genomics Group, The European Bioinformatics Institute EMBL, Cambridge Outstation, Cambridge CB10 1SD, UK
Bioinformatics 21:3806-10. 2005..Conclusion: CoGenT++ provides a comprehensive environment for computational genomics, accessible primarily for large-scale analyses as well as manual browsing... - GeneTRACE-reconstruction of gene content of ancestral speciesVictor Kunin
Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
Bioinformatics 19:1412-6. 2003.... - The net of life: reconstructing the microbial phylogenetic networkVictor Kunin
Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, United Kingdom
Genome Res 15:954-9. 2005..We propose that genes might propagate extremely rapidly across microbial species through the HGT network, using certain organisms as hubs... - Protein interaction maps for complete genomes based on gene fusion eventsA J Enright
Computational Genomics Group, Research Programme, The European Bioinformatics Institute, EMBL Cambridge Outstation, UK
Nature 402:86-90. 1999..The approach is general, and can be applied even to genes of unknown function... - Functional versatility and molecular diversity of the metabolic map of Escherichia coliS Tsoka
Computational Genomics Group, Research Programme, The European Bioinformatics Institute, European Molecular Biology Laboratory, Cambridge Outstation, Cambridge CB10 1SD, UK
Genome Res 11:1503-10. 2001..Finally, the distribution of enzyme family members across different pathways provides support for the "recruitment" hypothesis of biochemical pathway evolution... - MagicMatch--cross-referencing sequence identifiers across databasesMike Smith
Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
Bioinformatics 21:3429-30. 2005..The program, called MagicMatch, is able to cross-link any of the major sequence databases within a few seconds on a modest desktop computer... - Protein families and TRIBES in genome sequence spaceAnton J Enright
Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
Nucleic Acids Res 31:4632-8. 2003..Finally, we analyse the functional diversity of protein families in entire genome sequences. The TRIBES protein family resource is accessible at http://www.ebi.ac.uk/research/cgg/tribes/... - Evaluation of annotation strategies using an entire genome sequenceIoannis Iliopoulos
Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
Bioinformatics 19:717-26. 2003..The most surprising result of this comparative study is that automatic systems might perform as well as the teams of experts annotating genome sequences... - Genome-wide detection and family clustering of ion channelsRachel Harte
Computational Genomics Group, Research Programme, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
FEBS Lett 514:129-34. 2002..A total of 299 putative ion channel protein sequences were detected, with significant variations across species. The clustering of these sequences reveals complex relationships between the different ion channel families... - Transcription-associated protein families are primarily taxon-specificR M Coulson
Computational Genomics Group, Research Programme, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
Bioinformatics 17:95-7. 2001..Our results for the primary phylogenetic domains (Archaea, Bacteria and Eukaryota) show that TAP families are mostly taxon-specific and very few transcriptional regulators are common across these domains... - Modeling the percolation of annotation errors in a database of protein sequencesWalter R Gilks
Medical Research Council Biostatistics Unit, Cambridge, UK
Bioinformatics 18:1641-9. 2002..By exploring the consequences of the model for annotation quality it is evident that this iterative approach leads to a systematic deterioration of database quality... - Identification of thermophilic species by the amino acid compositions deduced from their genomesD P Kreil
University of Cambridge and European Bioinformatics Institute, Computational Genomics Group, Research Programme, The European Bioinformatics Institute, EMBL Outstation, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
Nucleic Acids Res 29:1608-15. 2001..We expect this simple yet novel approach to be a useful additional tool for the study of phylogeny at the genome level... - BioLayout(Java): versatile network visualisation of structural and functional relationshipsLeon Goldovsky
Computational Genomics Group, European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge, UK
Appl Bioinformatics 4:71-4. 2005..BioLayout(Java) provides broader functionality, various analysis techniques, extensions for better visualisation and a new user interface. Examples of analysis of biological networks using BioLayout(Java) are presented... - The properties of protein family space depend on experimental designVictor Kunin
Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
Bioinformatics 21:2618-22. 2005..We conclude that these properties are complementary rather than contradictory, while describing the protein universe from different perspectives... - Measuring genome conservation across taxa: divided strains and united kingdomsVictor Kunin
Computational Genomics Group, The European Bioinformatics Institute EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
Nucleic Acids Res 33:616-21. 2005..All phylogenetic reconstructions are available at the genome phylogeny server: <http://maine.ebi.ac.uk:8000/cgi-bin/gps/GPS.pl>... - COmplete GENome Tracking (COGENT): a flexible data environment for computational genomicsPaul Janssen
Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Welcome Trust Genome Campus, Cambridge CB10 1SD, UK
Bioinformatics 19:1451-2. 2003..For its design we have implemented an extremely simple yet powerful schema to allow linking of genome sequence data to other resources. AVAILABILITY: http://maine.ebi.ac.uk:8000/services/cogent/.. - Detection of functional modules from protein interaction networksJose B Pereira-Leal
Computational Genomics Group, The European Bioinformatics Institute, Cambridge, United Kingdom
Proteins 54:49-57. 2004..We use an extensive statistical validation procedure to establish the biological significance of the detected modules and explore this complex, hierarchical network of modular interactions from which pathways can be inferred... - Metabolic database systems for the analysis of genome-wide functionSophia Tsoka
Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB1O 1SD, UK
Biotechnol Bioeng 84:750-5. 2003..We illustrate the design features of metabolic databases and discuss the challenges facing metabolic as well as databases of other functional type... - Transcription regulation and environmental adaptation in bacteriaIldefonso Cases
Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK
Trends Microbiol 11:248-53. 2003..This suggests that under complex conditions, gene expression regulation and signal integration have been strongly selected for to enable rapid adaptation to environmental conditions... - The phylogenetic diversity of eukaryotic transcriptionRichard M R Coulson
Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
Nucleic Acids Res 31:653-60. 2003..This contrasts with transcriptional regulator families, that are primarily taxon-specific, indicating proteins controlling gene activation exhibit considerable sequence diversity across the eukaryotic domain... - A minimal estimate for the gene content of the last universal common ancestor--exobiology from a terrestrial perspectiveChristos A Ouzounis
Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
Res Microbiol 157:57-68. 2006.... - Lineage-specific partitions in archaeal transcriptionRichard M R Coulson
Microarray Group, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Archaea 2:117-25. 2007..Strikingly, the hidden Markov model profile searches revealed that archaeal chromatin and histone-modifying enzymes also display extensive taxon-restrictedness, both across and within the two phyla... - Denoising inferred functional association networks obtained by gene fusion analysisAtanas Kamburov
Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
BMC Genomics 8:460. 2007..The precision of this method typically improves with an ever-increasing number of reference genomes... - The comparative genomics of protein interactionsJose M Peregrin-Alvarez
Sick Kids Research Institute, TMDT MARS Building, 101 College St, 15th Floor, East Tower, M5G 1L7 Toronto, ON, Canada
Genome Inform 19:131-41. 2007.... - From genes to genomes: universal scale-invariant properties of microbial chromosome organisationBenjamin Audit
Wellcome Trust Genome Campus, Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge, CB10 1SD, UK
J Mol Biol 332:617-33. 2003.... - Automated metabolic reconstruction for Methanococcus jannaschiiSophia Tsoka
Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
Archaea 1:223-9. 2004..Our results, in the form of enzymatic assignments and metabolic pathway predictions, form a database (MJCyc) that is accessible over the World Wide Web for further dissemination among members of the scientific community... - Metabolic innovations towards the human lineageShiri Freilich
The European Bioinformatics Institute, EMBL Cambridge Outstation, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
BMC Evol Biol 8:247. 2008.... - Robustness of metabolic map reconstructionDag G Ahren
Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
J Bioinform Comput Biol 2:589-93. 2004..We also discuss the implications of the results on reference genome projects as well as other large-scale sequencing data... - Genome-wide identification of genes likely to be involved in human genetic diseaseNuria Lopez-Bigas
Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
Nucleic Acids Res 32:3108-14. 2004..The probability score assignments for the human genome are accessible at http://maine.ebi. ac.uk:8000/services/dgp... - Functional evolution of the yeast protein interaction networkVictor Kunin
Computational Genomics Group, The European Bioinformatics Institute EMBL Cambridge Outstation, Cambridge, UK
Mol Biol Evol 21:1171-6. 2004..We propose that the understanding of the mechanisms that generate the scale-free protein interaction network, and possibly other biological networks, requires consideration of protein function... - Comparison of sequence masking algorithms and the detection of biased protein sequence regionsDavid P Kreil
Department of Genetics Inference Group Cavendish Laboratory, University of Cambridge, Cambridge, UK
Bioinformatics 19:1672-81. 2003..This is not the case for sequence bias, which hence seems to be a genuinely biological phenomenon in contrast to patches of low complexity... - An efficient algorithm for large-scale detection of protein familiesA J Enright
Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
Nucleic Acids Res 30:1575-84. 2002..The method has been used to detect and categorise protein families within the draft human genome and the resulting families have been used to annotate a large proportion of human proteins... - BioLayout--an automatic graph layout algorithm for similarity visualizationA J Enright
Computational Genomics Group, Research Programme, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
Bioinformatics 17:853-4. 2001..AVAILABILITY: BioLayout is available for most UNIX platforms at the following web-site: http://www.ebi.ac.uk/research/cgg/services/layout... - The phylogenetic extent of metabolic enzymes and pathwaysJosé Manuel PeregrÃn-Alvarez
Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
Genome Res 13:422-7. 2003..In addition, our analysis suggests that despite the sequence conservation and the extensive phylogenetic distribution of metabolic enzymes, their groupings into biochemical pathways are much more variable than previously thought... - Comparative genomics of transcriptional control in the human malaria parasite Plasmodium falciparumRichard M R Coulson
Computational Genomics Group, The European Bioinformatics Institute, European Molecular Biology Laboratory Cambridge Outstation, Cambridge CB10 1SD, United Kingdom
Genome Res 14:1548-54. 2004..falciparum genome. This observation, together with the paucity of malarial transcriptional regulators identified, suggests Plasmodium protein levels are primarily determined by posttranscriptional mechanisms... - An exponential core in the heart of the yeast protein interaction networkJose B Pereira-Leal
Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Wellcome Trust Genome Campus, Cambridge, UK
Mol Biol Evol 22:421-5. 2005..Finally, we propose that this core exponential network may represent a generic scaffold around which organism-specific and taxon-specific proteins and interactions coalesce... - Sensitive detection of sequence similarity using combinatorial pattern discovery: a challenging study of two distantly related protein familiesNikos Darzentas
Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge, UK
Proteins 61:926-37. 2005..Our analysis suggests that pattern discovery methods can be substantially more sensitive in detecting remote protein relationships while at the same time guaranteeing high specificity... - CORRIE: enzyme sequence annotation with confidence estimatesBenjamin Audit
Laboratoire Joliot Curie and Laboratoire de Physique, CNRS UMR5672, Ecole Normale Superieure, Lyon Cedex 07, France
BMC Bioinformatics 8:S3. 2007..The CORRIE server is available at: http://www.genomes.org/services/corrie/... - Genetic variation between Helicobacter pylori strains: gene acquisition or loss?Santiago Garcia-Vallve
Departament de Bioquimica i Biotecnologia, Universitat Rovira i Virgili, Pl Imperial Tarraco 1, Tarragona, Spain
Trends Microbiol 10:445-7. 2002.... - Highly consistent patterns for inherited human diseases at the molecular levelNuria Lopez-Bigas
Genome Bioinformatics Laboratory, Center for Genomic Regulation, Universitat Pompeu Fabra, Pg Maritim de la Barceloneta 37 49, E 08003, Barcelona, Spain
Bioinformatics 22:269-77. 2006..The results further indicate that a comparative genomics approach for the analysis of genes linked to human genetic diseases will facilitate the elucidation of the underlying molecular and cellular mechanisms... - Expansion of the BioCyc collection of pathway/genome databases to 160 genomesPeter D Karp
Bioinformatics Research Group, SRI International EK207, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA
Nucleic Acids Res 33:6083-9. 2005..Only by harnessing the expertise of many scientists we can hope to produce biological databases, which accurately reflect the depth and breadth of knowledge that the biomedical research community is producing... - Genome coverage, literally speaking. The challenge of annotating 200 genomes with 4 million publicationsPaul Janssen
Belgian Nuclear Research Centre, Belgium
EMBO Rep 6:397-9. 2005 - Genome evolution reveals biochemical networks and functional modulesChristian von Mering
European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
Proc Natl Acad Sci U S A 100:15428-33. 2003..The results indicate that modularity in protein networks is intrinsically encoded in present-day genomes... - Percolation of annotation errors through hierarchically structured protein sequence databasesWalter R Gilks
Medical Research Council Biostatistics Unit, Institute of Public Health, University of Forvive Site, Robinson Way, Cambridge CB2 2SR, UK
Math Biosci 193:223-34. 2005..Here we apply the theory to hierarchically structured protein sequence databases, and draw conclusions about database quality at different levels of the hierarchy...