Metabolic innovations towards the human lineage (2008)
Freilich, Shiri, Goldovsky, Leon, Ouzounis, Christos A, Thornton, Janet M
Abstract Background We describe a function-driven approach to the analysis of metabolism which takes into account the phylogenetic origin of biochemical reactions to reveal subtle lineage-specific...
Denoising inferred functional association networks obtained by gene fusion analysis (2007)
Kamburov, Atanas, Goldovsky, Leon, Freilich, Shiri, Kapazoglou, Aliki, Kunin, Victor, Enright, Anton J, ...
Abstract Background Gene fusion detection – also known as the 'Rosetta Stone' method – involves the identification of fused composite genes in a set of reference genomes, which indicates...
Probabilistic annotation of protein sequences based on functional classifications. (2007)
Levy, Emmanuel D, Ouzounis, Christos A, Gilks, Walter R, Audit, Benjamin
BACKGROUND: One of the most evident achievements of bioinformatics is the development of methods that transfer biological knowledge from characterised proteins to uncharacterised sequences. This mode...
Probabilistic annotation of protein sequences based on functional classifications (2007)
Levy, Emmanuel D., Ouzounis, Christos A., Gilks, Walter R., Audit, Benjamin
BACKGROUND: One of the most evident achievements of bioinformatics is the development of methods that transfer biological knowledge from characterised proteins to uncharacterised sequences. This mode...
Probabilistic annotation of protein sequences based on functional classifications. (2007)
Levy, Emmanuel D, Ouzounis, Christos A, Gilks, Walter R, Audit, Benjamin
BACKGROUND: One of the most evident achievements of bioinformatics is the development of methods that transfer biological knowledge from characterised proteins to uncharacterised sequences. This mode...
CORRIE: enzyme sequence annotation with confidence estimates (2007)
Audit, Benjamin, Levy, Emmanuel D, Gilks, Wally R, Goldovsky, Leon, Ouzounis, Christos A
Abstract Using a previously developed automated method for enzyme annotation, we report the re-annotation of the ENZYME database and the analysis of local error rates per class. In control...
Denoising inferred functional association networks obtained by gene fusion analysis (2007)
Kamburov, Atanas, Goldovsky, Leon, Freilich, Shiri, Kapazoglou, Aliki, Kunin, Victor, Enright, Anton J., ...
Background Gene fusion detection – also known as the 'Rosetta Stone' method – involves the identification of fused composite genes in a set of reference genomes, which indicates potential...
Structural and functional properties of genes involved in human cancer (2006)
Furney, Simon J, Higgins, Desmond G, Ouzounis, Christos A, López-Bigas, Núria
Abstract Background One of the main goals of cancer genetics is to identify the causative elements at the molecular level leading to cancer. Results We have conducted an analysis of a set of genes...
Ioannis Iliopoulos, Anton J. Enright, Patrick Poullet, Christos A. Ouzounis
We have previously shown that the detection of gene fusion events can contribute towards the elucidation of functional associations of proteins within entire genomes. Here we have analysed the entire...
Probabilistic annotation of protein sequences based on functional classifications (2005)
Levy, Emmanuel D, Ouzounis, Christos A, Gilks, Walter R, Audit, Benjamin
Abstract Background One of the most evident achievements of bioinformatics is the development of methods that transfer biological knowledge from characterised proteins to uncharacterised sequences....
Clustering the annotation space of proteins (2005)
Kunin, Victor, Ouzounis, Christos A
Abstract Background Current protein clustering methods rely on either sequence or functional similarities between proteins, thereby limiting inferences to one of these areas. Results Here we report a...
Janssen, Paul, Audit, Benjamin, Cases, Ildefonso, Darzentas, Nikos, Goldovsky, Leon, Kunin, Victor, ...
No abstract available.
Myriads of protein families, and still counting (2003)
Kunin, Victor, Cases, Ildefonso, Enright, Anton J, De Lorenzo, Victor, Ouzounis, Christos A
Abstract 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...
Myriads of protein families, and still counting (2003)
Kunin, Victor, Cases, Ildefonso, Enright, Anton J., Lorenzo, Víctor De, Ouzounis, Christos A.
The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2003/4/2/401
The past, present and future of genome-wide re-annotation (2002)
Ouzounis, Christos A, Karp, Peter D
Abstract Annotation, the process by which structural or functional information is inferred for genes or proteins, is crucial for obtaining value from genome sequences. We define the process of...
Enright, Anton J, Ouzounis, Christos A
Abstract Background It has recently been shown that the detection of gene fusion events across genomes can be used for predicting functional associations of proteins, including physical interaction...
Genome sequences and great expectations (2000)
Iliopoulos, Ioannis, Tsoka, Sophia, Andrade, Miguel A, Janssen, Paul, Audit, Benjamin, Tramontano, Anna, ...
Abstract To assess how automatic function assignment will contribute to genome annotation in the next five years, we have performed an analysis of 31 available genome sequences. An emerging pattern...
Global Properties of the Metabolic Map of Escherichia coli (2000)
Christos A. Ouzounis, Peter D. Karp
This paper characterizes qualitative aspects of the E. coli metabolic network rather than quantitative aspects. We are interested in the connectivity relationships of the network; its partitioning...
Kyrpides, Nikos C., Ouzounis, Christos A.
Using the sequences of all the known transcription-associated proteins from Bacteria and Eucarya (a total of 4,147), we have identified their homologous counterparts in the four complete archaeal...
Identification of thermophilic species by the amino acid compositions deduced from their genomes
Kreil, David P., Ouzounis, Christos A.
The global amino acid compositions as deduced from the complete genomic sequences of six thermophilic archaea, two thermophilic bacteria, 17 mesophilic bacteria and two eukaryotic species were...
Strain-specific genes of Helicobacter pylori: distribution, function and dynamics
Janssen, Paul J., Audit, Benjamin, Ouzounis, Christos A.
Whole-genome clustering of the two available genome sequences of Helicobacter pylori strains 26695 and J99 allows the detection of 110 and 52 strain-specific genes, respectively. This set of...
Kyrpides, Nikos C., Ouzounis, Christos A., Iliopoulos, Ioannis, Vonstein, Veronika, Overbeek, Ross
The proliferation of genome sequence data has led to the development of a number of tools and strategies that facilitate computational analysis. These methods include the identification of motif...
The past, present and future of genome-wide re-annotation
Ouzounis, Christos A, Karp, Peter D
Annotation, the process by which structural or functional information is inferred for genes or proteins, is crucial for obtaining value from genome sequences. We define the process of annotating a...
The phylogenetic diversity of eukaryotic transcription
Coulson, Richard M. R., Ouzounis, Christos A.
Eukaryotic transcription is a highly regulated process involving interactions between large numbers of proteins. To analyse the phylogenetic distribution of the components of this process, six crown...
Genome sequences and great expectations
Iliopoulos, Ioannis, Tsoka, Sophia, Andrade, Miguel A, Janssen, Paul, Audit, Benjamin, Tramontano, Anna, ...
To assess how automatic function assignment will contribute to genome annotation in the next five years, we have performed an analysis of 31 available genome sequences. An emerging pattern is that...
Myriads of protein families, and still counting
Kunin, Victor, Cases, Ildefonso, Enright, Anton J, De Lorenzo, Victor, Ouzounis, Christos A
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...
Janssen, Paul, Audit, Benjamin, Cases, Ildefonso, Darzentas, Nikos, Goldovsky, Leon, Kunin, Victor, ...
By the end of 2002, we witnessed the landmark submission of the 100th complete genome sequence in the databases. An overview of these genomes reveals certain interesting trends and provides valuable...
Protein families and Tribes in genome sequence space
Enright, Anton J., Kunin, Victor, Ouzounis, Christos A.
Accurate detection of protein families allows assignment of protein function and the analysis of functional diversity in complete genomes. Recently, we presented a novel algorithm called TribeMCL for...
Genome evolution reveals biochemical networks and functional modules
Von Mering, Christian, Zdobnov, Evgeny M., Tsoka, Sophia, Ciccarelli, Francesca D., Pereira-Leal, Jose B., Ouzounis, Christos A., ...
The analysis of completely sequenced genomes uncovers an astonishing variability between species in terms of gene content and order. During genome history, the genes are frequently rear-ranged,...
Global Properties of the Metabolic Map of Escherichia coli
Ouzounis, Christos A., Karp, Peter D.
The EcoCyc database characterizes the known network of Escherichia coli small-molecule metabolism. Here we present a computational analysis of the global properties of that network, which consists of...
Functional Versatility and Molecular Diversity of the Metabolic Map of Escherichia coli
Tsoka, Sophia, Ouzounis, Christos A.
We have analyzed the known metabolic enzymes of Escherichia coli in relation to their biochemical reaction properties and their involvement in biochemical pathways. All enzymes involved in...
The Balance of Driving Forces During Genome Evolution in Prokaryotes
Kunin, Victor, Ouzounis, Christos A.
Genomes are shaped by evolutionary processes such as gene genesis, horizontal gene transfer (HGT), and gene loss. To quantify the relative contributions of these processes, we analyze the...
The Phylogenetic Extent of Metabolic Enzymes and Pathways
Peregrin-Alvarez, José Manuel, Tsoka, Sophia, Ouzounis, Christos A.
The evolution of metabolic enzymes and pathways has been a subject of intense study for more than half a century. Yet, so far, previous studies have focused on a small number of enzyme families or...
Genome-wide identification of genes likely to be involved in human genetic disease
López-Bigas, Núria, Ouzounis, Christos A.
Sequence analysis of the group of proteins known to be associated with hereditary diseases allows the detection of key distinctive features shared within this group. The disease proteins are...
Comparative Genomics of Transcriptional Control in the Human Malaria Parasite Plasmodium falciparum
Coulson, Richard M.R., Hall, Neil, Ouzounis, Christos A.
The life cycle of the parasite Plasmodium falciparum, responsible for the most deadly form of human malaria, requires specialized protein expression for survival in the mammalian host and insect...
Measuring genome conservation across taxa: divided strains and united kingdoms
Kunin, Victor, Ahren, Dag, Goldovsky, Leon, Janssen, Paul, Ouzounis, Christos A.
Species evolutionary relationships have traditionally been defined by sequence similarities of phylogenetic marker molecules, recently followed by whole-genome phylogenies based on gene order,...
The net of life: Reconstructing the microbial phylogenetic network
Kunin, Victor, Goldovsky, Leon, Darzentas, Nikos, Ouzounis, Christos A.
It has previously been suggested that the phylogeny of microbial species might be better described as a network containing vertical and horizontal gene transfer (HGT) events. Yet, all phylogenetic...
Expansion of the BioCyc collection of pathway/genome databases to 160 genomes
Karp, Peter D., Ouzounis, Christos A., Moore-Kochlacs, Caroline, Goldovsky, Leon, Kaipa, Pallavi, Ahrén, Dag, ...
The BioCyc database collection is a set of 160 pathway/genome databases (PGDBs) for most eukaryotic and prokaryotic species whose genomes have been completely sequenced to date. Each PGDB in the...
Probabilistic annotation of protein sequences based on functional classifications
Levy, Emmanuel D, Ouzounis, Christos A, Gilks, Walter R, Audit, Benjamin
Structural and functional properties of genes involved in human cancer
Furney, Simon J, Higgins, Desmond G, Ouzounis, Christos A, López-Bigas, Núria
Genome coverage, literally speaking
Janssen, Paul, Goldovsky, Leon, Kunin, Victor, Darzentas, Nikos, Ouzounis, Christos A.
The challenge of annotating 200 genomes with 4 million publications
Kyrpides, Nikos C., Ouzounis, Christos A.
Using the sequences of all the known transcription-associated proteins from Bacteria and Eucarya (a total of 4,147), we have identified their homologous counterparts in the four complete archaeal...
Identification of thermophilic species by the amino acid compositions deduced from their genomes
Kreil, David P., Ouzounis, Christos A.
The global amino acid compositions as deduced from the complete genomic sequences of six thermophilic archaea, two thermophilic bacteria, 17 mesophilic bacteria and two eukaryotic species were...
Strain-specific genes of Helicobacter pylori: distribution, function and dynamics
Janssen, Paul J., Audit, Benjamin, Ouzounis, Christos A.
Whole-genome clustering of the two available genome sequences of Helicobacter pylori strains 26695 and J99 allows the detection of 110 and 52 strain-specific genes, respectively. This set of...
Kyrpides, Nikos C., Ouzounis, Christos A., Iliopoulos, Ioannis, Vonstein, Veronika, Overbeek, Ross
The proliferation of genome sequence data has led to the development of a number of tools and strategies that facilitate computational analysis. These methods include the identification of motif...
The past, present and future of genome-wide re-annotation
Ouzounis, Christos A, Karp, Peter D
Annotation, the process by which structural or functional information is inferred for genes or proteins, is crucial for obtaining value from genome sequences. We define the process of annotating a...
The phylogenetic diversity of eukaryotic transcription
Coulson, Richard M. R., Ouzounis, Christos A.
Eukaryotic transcription is a highly regulated process involving interactions between large numbers of proteins. To analyse the phylogenetic distribution of the components of this process, six crown...
Genome sequences and great expectations
Iliopoulos, Ioannis, Tsoka, Sophia, Andrade, Miguel A, Janssen, Paul, Audit, Benjamin, Tramontano, Anna, ...
To assess how automatic function assignment will contribute to genome annotation in the next five years, we have performed an analysis of 31 available genome sequences. An emerging pattern is that...
Myriads of protein families, and still counting
Kunin, Victor, Cases, Ildefonso, Enright, Anton J, De Lorenzo, Victor, Ouzounis, Christos A
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...
Janssen, Paul, Audit, Benjamin, Cases, Ildefonso, Darzentas, Nikos, Goldovsky, Leon, Kunin, Victor, ...
By the end of 2002, we witnessed the landmark submission of the 100th complete genome sequence in the databases. An overview of these genomes reveals certain interesting trends and provides valuable...
Protein families and Tribes in genome sequence space
Enright, Anton J., Kunin, Victor, Ouzounis, Christos A.
Accurate detection of protein families allows assignment of protein function and the analysis of functional diversity in complete genomes. Recently, we presented a novel algorithm called TribeMCL for...
Genome evolution reveals biochemical networks and functional modules
Von Mering, Christian, Zdobnov, Evgeny M., Tsoka, Sophia, Ciccarelli, Francesca D., Pereira-Leal, Jose B., Ouzounis, Christos A., ...
The analysis of completely sequenced genomes uncovers an astonishing variability between species in terms of gene content and order. During genome history, the genes are frequently rear-ranged,...
Global Properties of the Metabolic Map of Escherichia coli
Ouzounis, Christos A., Karp, Peter D.
The EcoCyc database characterizes the known network of Escherichia coli small-molecule metabolism. Here we present a computational analysis of the global properties of that network, which consists of...
Functional Versatility and Molecular Diversity of the Metabolic Map of Escherichia coli
Tsoka, Sophia, Ouzounis, Christos A.
We have analyzed the known metabolic enzymes of Escherichia coli in relation to their biochemical reaction properties and their involvement in biochemical pathways. All enzymes involved in...
The Balance of Driving Forces During Genome Evolution in Prokaryotes
Kunin, Victor, Ouzounis, Christos A.
Genomes are shaped by evolutionary processes such as gene genesis, horizontal gene transfer (HGT), and gene loss. To quantify the relative contributions of these processes, we analyze the...
The Phylogenetic Extent of Metabolic Enzymes and Pathways
Peregrin-Alvarez, José Manuel, Tsoka, Sophia, Ouzounis, Christos A.
The evolution of metabolic enzymes and pathways has been a subject of intense study for more than half a century. Yet, so far, previous studies have focused on a small number of enzyme families or...
Genome-wide identification of genes likely to be involved in human genetic disease
López-Bigas, Núria, Ouzounis, Christos A.
Sequence analysis of the group of proteins known to be associated with hereditary diseases allows the detection of key distinctive features shared within this group. The disease proteins are...
Comparative Genomics of Transcriptional Control in the Human Malaria Parasite Plasmodium falciparum
Coulson, Richard M.R., Hall, Neil, Ouzounis, Christos A.
The life cycle of the parasite Plasmodium falciparum, responsible for the most deadly form of human malaria, requires specialized protein expression for survival in the mammalian host and insect...
Measuring genome conservation across taxa: divided strains and united kingdoms
Kunin, Victor, Ahren, Dag, Goldovsky, Leon, Janssen, Paul, Ouzounis, Christos A.
Species evolutionary relationships have traditionally been defined by sequence similarities of phylogenetic marker molecules, recently followed by whole-genome phylogenies based on gene order,...
The net of life: Reconstructing the microbial phylogenetic network
Kunin, Victor, Goldovsky, Leon, Darzentas, Nikos, Ouzounis, Christos A.
It has previously been suggested that the phylogeny of microbial species might be better described as a network containing vertical and horizontal gene transfer (HGT) events. Yet, all phylogenetic...
Expansion of the BioCyc collection of pathway/genome databases to 160 genomes
Karp, Peter D., Ouzounis, Christos A., Moore-Kochlacs, Caroline, Goldovsky, Leon, Kaipa, Pallavi, Ahrén, Dag, ...
The BioCyc database collection is a set of 160 pathway/genome databases (PGDBs) for most eukaryotic and prokaryotic species whose genomes have been completely sequenced to date. Each PGDB in the...
Genome coverage, literally speaking
Janssen, Paul, Goldovsky, Leon, Kunin, Victor, Darzentas, Nikos, Ouzounis, Christos A.
The challenge of annotating 200 genomes with 4 million publications
Probabilistic annotation of protein sequences based on functional classifications
Levy, Emmanuel D, Ouzounis, Christos A, Gilks, Walter R, Audit, Benjamin
Structural and functional properties of genes involved in human cancer
Furney, Simon J, Higgins, Desmond G, Ouzounis, Christos A, López-Bigas, Núria
CORRIE: enzyme sequence annotation with confidence estimates
Audit, Benjamin, Levy, Emmanuel D, Gilks, Wally R, Goldovsky, Leon, Ouzounis, Christos A
Using a previously developed automated method for enzyme annotation, we report the re-annotation of the ENZYME database and the analysis of local error rates per class. In control experiments, we...
Denoising inferred functional association networks obtained by gene fusion analysis
Kamburov, Atanas, Goldovsky, Leon, Freilich, Shiri, Kapazoglou, Aliki, Kunin, Victor, Enright, Anton J, ...
Iliopoulos, Ioannis, Enright, Anton J., Poullet, Patrick, Ouzounis, Christos A.
We have previously shown that the detection of gene fusion events can contribute towards the elucidation of functional associations of proteins within entire genomes. Here we have analysed the entire...