Heger, Andreas, Ponting, Chris P., Holmes, Ian
XRATE implements algorithms for comparative annotation, ancestral reconstruction, evolutionary rate estimation, and simulation. Its modeling repertoire includes phylogenetic stochastic context–free...
Barragán, Isabel, O'Driscoll, Ciara A., Goodstadt, Leo, Prigmore, Elena, Borrego, Salud, ...
3 pages, 2 figures, 1 table.-- PMID: 18836446 [PubMed].-- Supporting information (Suppl. Methods, Suppl. Note, Suppl. Figs 1–4, Suppl. Table 1) available at:...
BIOINFORMATICS DISCOVERY NOTE Sequence analysis (2008)
Meisetz and the birth of the KRAB motif
Laukaitis, Christina M, Heger, Andreas, Blakley, Tyler D, Munclinger, Pavel, Ponting, Chris P, Karn, Robert C
Abstract Background The draft mouse ( Mus musculus ) genome sequence revealed an unexpected proliferation of gene duplicates encoding a family of secretoglobin proteins including the androgen-binding...
Genome analysis of the platypus reveals unique signatures of evolution (2008)
Warren, Wesley C., Hillier, LaDeana W., Marshall Graves, Jennifer A., Birney, Ewan, Ponting, Chris P., Grützner, Frank, ...
We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a...
Sexual Selection and the Adaptive Evolution of Mammalian Ejaculate Proteins (2008)
Ramm, Steven A., Oliver, Peter L., Ponting, Chris P., Stockley, Paula, Emes, Richard D.
An elevated rate of substitution characterizes the molecular evolution of reproductive proteins from a wide range of taxa. Although the selective pressures explaining this rapid evolution are yet to...
OPTIC: orthologous and paralogous transcripts in clades (2008)
Heger, Andreas, Ponting, Chris P.
The genome sequences of a large number of metazoan species are now known. As multiple closely related genomes are sequenced, comparative studies that previously focussed on only pairs of genomes can...
Nguyen, Duc-Quang, Webber, Caleb, Hehir-Kwa, Jayne, Pfundt, Rolph, Veltman, Joris, Ponting, Chris P.
Copy number variation is a dominant contributor to genomic variation and may frequently underlie an individual’s variable susceptibilities to disease. Here we question our previous proposition that...
Goodstadt, Leo, Heger, Andreas, Webber, Caleb, Ponting, Chris P.
The newly sequenced genome of Monodelphis domestica not only provides the out-group necessary to better understand our own eutherian lineage, but it enables insights into the innovative biology of...
Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs (2007)
Ponjavic, Jasmina, Ponting, Chris P., Lunter, Gerton
Long transcripts that do not encode protein have only rarely been the subject of experimental scrutiny. Presumably, this is owing to the current lack of evidence of their functionality, thereby...
OPTIC: orthologous and paralogous transcripts in clades (2007)
Andreas Heger, Chris P. Ponting
The genome sequences of a large number of metazoan species are now known. As multiple closely related genomes are sequenced, comparative studies that previously focussed on only pairs of genomes can...
Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes (2007)
Heger, Andreas, Ponting, Chris P.
The newly sequenced genome sequences of 11 Drosophila species provide the first opportunity to investigate variations in evolutionary rates across a clade of closely related species. Protein-coding...
Phylogenetic Reconstruction of Orthology, Paralogy, and Conserved Synteny for Dog and Human (2006)
Leo Goodstadt, Chris P. Ponting
Accurate predictions of orthology and paralogy relationships are necessary to infer human molecular function from experiments in model organisms. Previous genome-scale approaches to predicting these...
Bias of Selection on Human Copy-Number Variants (2006)
Duc-Quang Nguyen, Caleb Webber, Chris P. Ponting
Although large-scale copy-number variation is an important contributor to conspecific genomic diversity, whether these variants frequently contribute to human phenotype differences remains unknown....
Bias Of Selection On Human Copy Number Variants (2006)
Duc-Quang Nguyen, Caleb Webber, Chris P. Ponting
Although large-scale copy number variation is an important contributor to conspecific genomic diversity, whether these variants frequently contribute to human phenotype differences remains unknown....
Genome-Wide Identification of Human Functional DNA Using a Neutral Indel Model (2006)
Gerton Lunter, Chris P. Ponting, Jotun Hein
It has become clear that a large proportion of functional DNA in the human genome does not code for protein. Identification of this non-coding functional sequence using comparative approaches is...
Running Title: Novel Domains in Microcephaly and Ciliary Proteins (2006)
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for...
Meisetz and the birth of the KRAB motif (2006)
The largest family of transcription factors in mammals is of Cys2His 2 zinc finger-proteins, each with an NH 2-terminal KRAB motif. Extensive expansions of this family have occurred in separate...
Meisetz and the birth of the KRAB motif (2006)
Birtle, Zoë, Ponting, Chris P.
The largest family of transcription factors in mammals is of Cys2His2 zinc finger-proteins, each with an NH2-terminal KRAB motif. Extensive expansions of this family have occurred in separate...
Signatures of adaptive evolution within human non-coding sequence (2006)
Ponting, Chris P., Lunter, Gerton
The human genome is often portrayed as consisting of three sequence types, each distinguished by their mode of evolution. Purifying selection is estimated to act on 2.5–5.0% of the genome, whereas...
A novel domain suggests a ciliary function for ASPM, a brain size determining gene (2006)
The N-terminal domain of abnormal spindle-like microcephaly-associated protein (ASPM) is identified as a member of a novel family of ASH (ASPM, SPD-2, Hydin) domains. These domains are present in...
Genome-wide identification of human functional DNA using a neutral indel model (2005)
Gerton Lunter, Chris P Ponting, Jotun Hein
It has recently become clear that a large proportion of functional DNA in the human genome does not code for protein. Identification of this non-coding functional sequence using comparative...
Winter, Eitan E, Ponting, Chris P
Abstract Background The identification of sequence innovations in the genomes of mammals facilitates understanding of human gene function, as well as sheds light on the molecular mechanisms which...
Laukaitis, Christina M, Dlouhy, Stephen R, Emes, Richard D, Ponting, Chris P, Karn, Robert C
Abstract Background The genes for salivary androgen-binding protein (ABP) subunits have been evolving rapidly in ancestors of the house mouse Mus musculus , as evidenced both by recent and extensive...
InterPro, progress and status in 2005 (2005)
Nicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam,...
InterPro, progress and status in 2005 (2005)
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam,...
Hotspots of mutation and breakage in dog and human chromosomes (2005)
Webber, Caleb, Ponting, Chris P.
Sequencing of the dog genome allows an investigation of the location-dependent evolutionary processes that occurred since the common ancestor of primates and carnivores, ∼95 million years ago. We...
A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms (2004)
Liu, Bin, Wang, Jun, Zhang, Yong, Yang, Xu, Zhang, Zengjin, ...
We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms (SNPs). This map is based on a comparison of the sequences of three domestic chicken...
Huang, Hui, Winter, Eitan E, Wang, Huajun, Weinstock, Keith G, Xing, Heming, Goodstadt, Leo, ...
Abstract Background Model organisms have contributed substantially to our understanding of the etiology of human disease as well as having assisted with the development of new treatment modalities....
Evolution and Comparative Genomics of Odorant- and Pheromone-Associated Genes in Rodents (2004)
Richard D. Emes, Scott A. Beatson, Chris P. Ponting, Leo Goodstadt
This paper was prepared during our analysis of the Brown Norway Rat Genome sequence (published in Nature, Apr 2004). I identified codons of rodent pheromones and their receptors that were likely to...
SMART 4.0: towards genomic data integration (2004)
Letunic, Ivica, Copley, Richard R., Schmidt, Steffen, Ciccarelli, Francesca D., Doerks, Tobias, Schultz, Jörg, ...
SMART (Simple Modular Architecture Research Tool) is a web tool (http://smart.embl.de/) for the identification and annotation of protein domains, and provides a platform for the comparative study of...
Evolution and Comparative Genomics of Odorant- and Pheromone-Associated Genes in Rodents (2004)
Richard D. Emes, Scott A. Beatson, Chris P. Ponting, Leo Goodstadt
This paper was prepared during our analysis of the Brown Norway Rat Genome sequence (published in Nature, Apr 2004). I identified codons of rodent pheromones and their receptors that were likely to...
Beatson, Scott, Ponting, Chris P.
We describe GIFT [for GldG, intraflagellar transport (IFT)] domains in the flavobacterial gliding protein GldG and eukaryotic IFT-52. In eukaryotes, domain homologues are also found in the eukaryotic...
Evolution and comparative genomics of odorant-and pheromone-associated genes in rodents (2004)
Emes, Richard D., Beatson, Scott A., Ponting, Chris P., Goodstadt, Leo
Chemical cues influence a range of behavioral responses in rodents. The involvement of protein odorants and odorant receptors in mediating reproductive behavior, foraging, and predator avoidance...
Beatson, Scott, Ponting, Chris P.
We describe GIFT [for GldG, intraflagellar transport (IFT)] domains in the flavobacterial gliding protein GldG and eukaryotic IFT-52. In eukaryotes, domain homologues are also found in the eukaryotic...
Evolution and comparative genomics of odorant-and pheromone-associated genes in rodents (2004)
Emes, Richard D., Beatson, Scott A., Ponting, Chris P., Goodstadt, Leo
Chemical cues influence a range of behavioral responses in rodents. The involvement of protein odorants and odorant receptors in mediating reproductive behavior, foraging, and predator avoidance...
Smart 4.0: towards genomic data integration (2004)
Ivica Letunic, Richard R. Copley, Steffen Schmidt, Francesca D. Ciccarelli, Tobias Doerks, Joè Rg Schultz, ...
SMART (Simple Modular Architecture Research Tool) is a web tool
Comparative Evolutionary Genomics of Androgen-Binding Protein Genes (2004)
Emes, Richard D., Riley, Matthew C., Laukaitis, Christina M., Goodstadt, Leo, Karn, Robert C., Ponting, Chris P.
Allelic variation within the mouse androgen-binding protein (ABP) α subunit gene (Abpa) has been suggested to promote assortative mating and thus prezygotic isolation. This is consistent with the...
Elevated Rates of Protein Secretion, Evolution, and Disease Among Tissue-Specific Genes (2004)
Winter, Eitan E., Goodstadt, Leo, Ponting, Chris P.
Variation in gene expression has been held responsible for the functional and morphological specialization of tissues. The tissue specificity of genes is known to correlate positively with gene...
Occurrence and Consequences of Coding Sequence Insertions and Deletions in Mammalian Genomes (2004)
Taylor, Martin S., Ponting, Chris P., Copley, Richard R.
Nucleotide insertion and deletion (indel) events, together with substitutions, represent the major mutational processes of gene evolution. Through the alignment of 8148 orthologous genes from human,...
Evolution and Comparative Genomics of Odorant- and Pheromone-Associated Genes in Rodents (2004)
Emes, Richard D., Beatson, Scott A., Ponting, Chris P., Goodstadt, Leo
Chemical cues influence a range of behavioral responses in rodents. The involvement of protein odorants and odorant receptors in mediating reproductive behavior, foraging, and predator avoidance...
SMART 4.0: towards genomic data integration (2004)
Letunic, Ivica, Copley, Richard R., Schmidt, Steffen, Ciccarelli, Francesca D., Doerks, Tobias, Schultz, Jörg, ...
SMART (Simple Modular Architecture Research Tool) is a web tool (http://smart.embl.de/) for the identification and annotation of protein domains, and provides a platform for the comparative study of...
Comparative Evolutionary Genomics of Androgen-Binding Protein Genes (2004)
Emes, Richard D., Riley, Matthew C., Laukaitis, Christina M., Goodstadt, Leo, Karn, Robert C., Ponting, Chris P.
Allelic variation within the mouse androgen-binding protein (ABP) α subunit gene (Abpa) has been suggested to promote assortative mating and thus prezygotic isolation. This is consistent with the...
THoR: a tool for domain discovery and curation of multiple alignments (2003)
Dickens, Nicholas J, Ponting, Chris P
Abstract We describe a tool, THoR, that automatically creates and curates multiple sequence alignments representing protein domains. This exploits both PSI-BLAST and HMMER algorithms and provides an...
Comparison of the genomes of human and mouse lays the foundation of genome zoology (2003)
Emes, Richard D., Goodstadt, Leo, Winter, Eitan E., Ponting, Chris P.
The extensive similarities between the genomes of human and model organisms are the foundation of much of modern biology, with model organism experimentation permitting valuable insights into...
The InterPro Database, 2003 brings increased coverage and new features (2003)
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Barrell, Daniel, Bateman, Alex, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created in 1999 as a means of amalgamating the major protein signature databases into one...
The InterPro Database, 2003 brings increased coverage and new features (2003)
Nicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Daniel Barrell, Alex Bateman, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created in 1999 as a means of amalgamating the major protein signature databases into one...
The InterPro Database, 2003 brings increased coverage and new features (2003)
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Barrell, Daniel, Bateman, Alex, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created in 1999 as a means of amalgamating the major protein signature databases into one...
Comparison of the genomes of human and mouse lays the foundation of genome zoology (2003)
Emes, Richard D., Goodstadt, Leo, Winter, Eitan E., Ponting, Chris P.
The extensive similarities between the genomes of human and model organisms are the foundation of much of modern biology, with model organism experimentation permitting valuable insights into...
Recent improvements to the SMART domain-based sequence annotation resource (2002)
Letunic, Ivica, Goodstadt, Leo, Dickens, Nicholas J., Doerks, Tobias, Schultz, Joerg, Mott, Richard, ...
SMART (Simple Modular Architecture Research Tool, http://smart.embl-heidelberg.de) is a web-based resource used for the annotation of protein domains and the analysis of domain architectures, with...
Novel domains and orthologues of eukaryotic transcription elongation factors (2002)
The passage of RNA polymerase II across eukaryotic genes is impeded by the nucleosome, an octamer of histones H2A, H2B, H3 and H4 dimers. More than a dozen factors in the yeast Saccharomyces...
Mulder, Nicola J., Apweiler, Rolf, Attwood, Terri K., Bairoch, Amos, Bateman, Alex, ...
The exponential increase in the submission of nucleotide sequences to the nucleotide sequence database by genome sequencing centres has resulted in a need for rapid, automatic methods for...
Recent improvements to the SMART domain-based sequence annotation resource (2002)
Letunic, Ivica, Goodstadt, Leo, Dickens, Nicholas J., Doerks, Tobias, Schultz, Joerg, Mott, Richard, ...
SMART (Simple Modular Architecture Research Tool, http://smart.embl-heidelberg.de) is a web-based resource used for the annotation of protein domains and the analysis of domain architectures,...
Identification of a novel family of presenilin homologues (2002)
Ponting, Chris P., Hutton, Mike, Nyborg, Andrew, Baker, Matthew, Jansen, Karen, Golde, Todd E.
Presenilin 1 and presenilin 2 are polytopic membrane proteins, whose genes are mutated in some individuals with Alzheimer's disease. Presenilins have been shown to influence limited proteolysis of...
Systematic Identification of Novel Protein Domain Families Associated with Nuclear Functions (2002)
Doerks, Tobias, Copley, Richard R., Schultz, Jörg, Ponting, Chris P., Bork, Peer
Novel domains and orthologues of eukaryotic transcription elongation factors (2002)
The passage of RNA polymerase II across eukaryotic genes is impeded by the nucleosome, an octamer of histones H2A, H2B, H3 and H4 dimers. More than a dozen factors in the yeast Saccharomyces...
Genome cartography through domain annotation (2001)
Ponting, Chris P, Dickens, Nicholas J
Abstract The evolutionary history of eukaryotic proteins involves rapid sequence divergence, addition and deletion of domains, and fusion and fission of genes. Although the protein repertoires of...
CHROMA: consensus-based colouring of multiple alignments for publication (2001)
Goodstadt, Leo, Ponting, Chris P.
CHROMA annotates multiple protein sequence alignments by consensus to produce formatted and coloured text suitable for incorporation into other documents for publication. The package is designed to...
Blanco, Gonzalo, Coulton, GaryR., Biggin, Andrew, Grainge, Christopher, Moss, Jill, Barrett, Michael, ...
The ky mouse mutant exhibits a primary degenerative myopathy preceding chronic thoraco-lumbar kyphoscoliosis. The histopathology of the ky mutant suggests that Ky protein activity is crucial for...
Sequence variation and disease in the wake of the draft human genome (2001)
Goodstadt, Leo, Ponting, Chris P.
The sequencing phase of the human genome project will soon be over. In its wake, repertoires of sequence polymorphisms among the human population are being sampled and a battery of functional...
Blanco, Gonzalo, Coulton, Gary R., Biggin, Andrew, Grainge, Christopher, Moss, Jill, Barrett, Michael, ...
The ky mouse mutant exhibits a primary degenerative myopathy preceding chronic thoraco-lumbar kyphoscoliosis. The histopathology of the ky mutant suggests that Ky protein activity is crucial for...
One of the defining characteristics of neurodegenerative diseases, including Parkinson’s, Alzheimer’s and Huntington’s diseases, is abnormal accumulations of iron, specifically in affected...
Emes, Richard D., Ponting, Chris P.
A previously unidentified sequence motif has been identified in the products of genes mutated in Miller-Dieker lissencephaly, Treacher Collins, oral–facial–digital type 1 and contiguous syndrome...
Issues in predicting protein function from sequence (2001)
Identifying homologues, defined as genes that arose from a common evolutionary ancestor, is often a relatively straightforward task, thanks to recent advances made in estimating the statistical...
CHROMA: consensus-based colouring of multiple alignments for publication (2001)
Goodstadt, Leo, Ponting, Chris P.
CHROMA annotates multiple protein sequence alignments by consensus to produce formatted and coloured text suitable for incorporation into other documents for publication. The package is designed to...
Sialidase-like Asp-boxes: Sequence-similar structures within different protein folds (2001)
Copley, Richard R., Russell, Robert B., Ponting, Chris P.
Sequence similarity is the most common measure currently used to infer homology between proteins. Typically, homologous protein domains show sequence similarity over their entire lengths. Here we...
SMART: a web-based tool for the study of genetically mobile domains (2000)
Schultz, Jörg, Copley, Richard R., Doerks, Tobias, Ponting, Chris P., Bork, Peer
SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures (http://SMART.embl-heidelberg.de )....
SMART: a web-based tool for the study of genetically mobile domains (2000)
Schultz, Jörg, Copley, Richard R., Doerks, Tobias, Ponting, Chris P., Bork, Peer
SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures...
Ponting, Chris P., Schultz, Jörg, Milpetz, Frank, Bork, Peer
SMART is a simple modular architecture research tool and database that provides domain identification and annotation on the WWW (http://coot.embl-heidelberg.de/SMART ). The tool compares query...
SMART, a simple modular architecture research tool: Identification of signaling domains
Schultz, Jörg, Milpetz, Frank, Bork, Peer, Ponting, Chris P.
Accurate multiple alignments of 86 domains that occur in signaling proteins have been constructed and used to provide a Web-based tool (SMART: simple modular architecture research tool) that allows...
Recent improvements to the SMART domain-based sequence annotation resource
Letunic, Ivica, Goodstadt, Leo, Dickens, Nicholas J., Doerks, Tobias, Schultz, Joerg, Mott, Richard, ...
SMART (Simple Modular Architecture Research Tool, http://smart.embl-heidelberg.de) is a web-based resource used for the annotation of protein domains and the analysis of domain architectures, with...
SMART: a web-based tool for the study of genetically mobile domains
Schultz, Jörg, Copley, Richard R., Doerks, Tobias, Ponting, Chris P., Bork, Peer
SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures (http://SMART.embl-heidelberg.de )....
SURVEY AND SUMMARY: Novel domains and orthologues of eukaryotic transcription elongation factors
The passage of RNA polymerase II across eukaryotic genes is impeded by the nucleosome, an octamer of histones H2A, H2B, H3 and H4 dimers. More than a dozen factors in the yeast Saccharomyces...
Genome cartography through domain annotation
Ponting, Chris P, Dickens, Nicholas J
The evolutionary history of eukaryotic proteins involves rapid sequence divergence, addition and deletion of domains, and fusion and fission of genes. Although the protein repertoires of distantly...
The InterPro Database, 2003 brings increased coverage and new features
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Barrell, Daniel, Bateman, Alex, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created in 1999 as a means of amalgamating the major protein signature databases into one...
Predicting Protein Cellular Localization Using a Domain Projection Method
Mott, Richard, Schultz, Jörg, Bork, Peer, Ponting, Chris P.
We investigate the co-occurrence of domain families in eukaryotic proteins to predict protein cellular localization. Approximately half (300) of SMART domains form a “small-world network”, linked...
THoR: a tool for domain discovery and curation of multiple alignments
Dickens, Nicholas J, Ponting, Chris P
A tool, THoR, has been described that automatically creates and curates multiple sequence alignments representing protein domains. This exploits both PSI-BLAST and HMMER algorithms and provides an...
Guigó, Roderic, Dermitzakis, Emmanouil T., Agarwal, Pankaj, Ponting, Chris P., Parra, Genís, Reymond, Alexandre, ...
A primary motivation for sequencing the mouse genome was to accelerate the discovery of mammalian genes by using sequence conservation between mouse and human to identify coding exons. Achieving this...
SMART 4.0: towards genomic data integration
Letunic, Ivica, Copley, Richard R., Schmidt, Steffen, Ciccarelli, Francesca D., Doerks, Tobias, Schultz, Jörg, ...
SMART (Simple Modular Architecture Research Tool) is a web tool (http://smart.embl.de/) for the identification and annotation of protein domains, and provides a platform for the comparative study of...
Elevated Rates of Protein Secretion, Evolution, and Disease Among Tissue-Specific Genes
Winter, Eitan E., Goodstadt, Leo, Ponting, Chris P.
Variation in gene expression has been held responsible for the functional and morphological specialization of tissues. The tissue specificity of genes is known to correlate positively with gene...
Occurrence and Consequences of Coding Sequence Insertions and Deletions in Mammalian Genomes
Taylor, Martin S., Ponting, Chris P., Copley, Richard R.
Nucleotide insertion and deletion (indel) events, together with substitutions, represent the major mutational processes of gene evolution. Through the alignment of 8148 orthologous genes from human,...
Evolution and Comparative Genomics of Odorant- and Pheromone-Associated Genes in Rodents
Emes, Richard D., Beatson, Scott A., Ponting, Chris P., Goodstadt, Leo
Chemical cues influence a range of behavioral responses in rodents. The involvement of protein odorants and odorant receptors in mediating reproductive behavior, foraging, and predator avoidance...
Evolutionary conservation and selection of human disease gene orthologs in the rat and mouse genomes
Huang, Hui, Winter, Eitan E, Wang, Huajun, Weinstock, Keith G, Xing, Heming, Goodstadt, Leo, ...
Human disease genes differ significantly from their rodent orthologs with respect to their overall levels of conservation and their rates of evolutionary change. Rodent orthologs of human...
Comparative Evolutionary Genomics of Androgen-Binding Protein Genes
Emes, Richard D., Riley, Matthew C., Laukaitis, Christina M., Goodstadt, Leo, Karn, Robert C., Ponting, Chris P.
Allelic variation within the mouse androgen-binding protein (ABP) α subunit gene (Abpa) has been suggested to promote assortative mating and thus prezygotic isolation. This is consistent with the...
InterPro, progress and status in 2005
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam,...
Brockington, Martin, Blake, Derek J., Prandini, Paola, Brown, Susan C., Torelli, Silvia, Benson, Matthew A., ...
The congenital muscular dystrophies (CMD) are a heterogeneous group of autosomal recessive disorders presenting in infancy with muscle weakness, contractures, and dystrophic changes on...
Genome-Wide Identification of Human Functional DNA Using a Neutral Indel Model
Lunter, Gerton, Ponting, Chris P, Hein, Jotun
It has become clear that a large proportion of functional DNA in the human genome does not code for protein. Identification of this non-coding functional sequence using comparative approaches is...
Bias of Selection on Human Copy-Number Variants
Nguyen, Duc-Quang, Webber, Caleb, Ponting, Chris P
Although large-scale copy-number variation is an important contributor to conspecific genomic diversity, whether these variants frequently contribute to human phenotype differences remains unknown....
Systematic Identification of Novel Protein Domain Families Associated with Nuclear Functions
Doerks, Tobias, Copley, Richard R., Schultz, Jörg, Ponting, Chris P., Bork, Peer
A systematic computational analysis of protein sequences containing known nuclear domains led to the identification of 28 novel domain families. This represents a 26% increase in the starting set of...
Hotspots of mutation and breakage in dog and human chromosomes
Webber, Caleb, Ponting, Chris P.
Sequencing of the dog genome allows an investigation of the location-dependent evolutionary processes that occurred since the common ancestor of primates and carnivores, ∼95 million years ago. We...
Phylogenetic Reconstruction of Orthology, Paralogy, and Conserved Synteny for Dog and Human
Goodstadt, Leo, Ponting, Chris P
Accurate predictions of orthology and paralogy relationships are necessary to infer human molecular function from experiments in model organisms. Previous genome-scale approaches to predicting these...
SMART, a simple modular architecture research tool: Identification of signaling domains
Schultz, Jörg, Milpetz, Frank, Bork, Peer, Ponting, Chris P.
Accurate multiple alignments of 86 domains that occur in signaling proteins have been constructed and used to provide a Web-based tool (SMART: simple modular architecture research tool) that allows...
Recent improvements to the SMART domain-based sequence annotation resource
Letunic, Ivica, Goodstadt, Leo, Dickens, Nicholas J., Doerks, Tobias, Schultz, Joerg, Mott, Richard, ...
SMART (Simple Modular Architecture Research Tool, http://smart.embl-heidelberg.de) is a web-based resource used for the annotation of protein domains and the analysis of domain architectures, with...
SMART: a web-based tool for the study of genetically mobile domains
Schultz, Jörg, Copley, Richard R., Doerks, Tobias, Ponting, Chris P., Bork, Peer
SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures (http://SMART.embl-heidelberg.de )....
SURVEY AND SUMMARY: Novel domains and orthologues of eukaryotic transcription elongation factors
The passage of RNA polymerase II across eukaryotic genes is impeded by the nucleosome, an octamer of histones H2A, H2B, H3 and H4 dimers. More than a dozen factors in the yeast Saccharomyces...
Genome cartography through domain annotation
Ponting, Chris P, Dickens, Nicholas J
The evolutionary history of eukaryotic proteins involves rapid sequence divergence, addition and deletion of domains, and fusion and fission of genes. Although the protein repertoires of distantly...
Systematic Identification of Novel Protein Domain Families Associated with Nuclear Functions
Doerks, Tobias, Copley, Richard R., Schultz, Jörg, Ponting, Chris P., Bork, Peer
A systematic computational analysis of protein sequences containing known nuclear domains led to the identification of 28 novel domain families. This represents a 26% increase in the starting set of...
The InterPro Database, 2003 brings increased coverage and new features
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Barrell, Daniel, Bateman, Alex, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created in 1999 as a means of amalgamating the major protein signature databases into one...
Predicting Protein Cellular Localization Using a Domain Projection Method
Mott, Richard, Schultz, Jörg, Bork, Peer, Ponting, Chris P.
We investigate the co-occurrence of domain families in eukaryotic proteins to predict protein cellular localization. Approximately half (300) of SMART domains form a “small-world network”, linked...
THoR: a tool for domain discovery and curation of multiple alignments
Dickens, Nicholas J, Ponting, Chris P
A tool, THoR, has been described that automatically creates and curates multiple sequence alignments representing protein domains. This exploits both PSI-BLAST and HMMER algorithms and provides an...
Guigó, Roderic, Dermitzakis, Emmanouil T., Agarwal, Pankaj, Ponting, Chris P., Parra, Genís, Reymond, Alexandre, ...
A primary motivation for sequencing the mouse genome was to accelerate the discovery of mammalian genes by using sequence conservation between mouse and human to identify coding exons. Achieving this...
SMART 4.0: towards genomic data integration
Letunic, Ivica, Copley, Richard R., Schmidt, Steffen, Ciccarelli, Francesca D., Doerks, Tobias, Schultz, Jörg, ...
SMART (Simple Modular Architecture Research Tool) is a web tool (http://smart.embl.de/) for the identification and annotation of protein domains, and provides a platform for the comparative study of...
Elevated Rates of Protein Secretion, Evolution, and Disease Among Tissue-Specific Genes
Winter, Eitan E., Goodstadt, Leo, Ponting, Chris P.
Variation in gene expression has been held responsible for the functional and morphological specialization of tissues. The tissue specificity of genes is known to correlate positively with gene...
Occurrence and Consequences of Coding Sequence Insertions and Deletions in Mammalian Genomes
Taylor, Martin S., Ponting, Chris P., Copley, Richard R.
Nucleotide insertion and deletion (indel) events, together with substitutions, represent the major mutational processes of gene evolution. Through the alignment of 8148 orthologous genes from human,...
Evolution and Comparative Genomics of Odorant- and Pheromone-Associated Genes in Rodents
Emes, Richard D., Beatson, Scott A., Ponting, Chris P., Goodstadt, Leo
Chemical cues influence a range of behavioral responses in rodents. The involvement of protein odorants and odorant receptors in mediating reproductive behavior, foraging, and predator avoidance...
Evolutionary conservation and selection of human disease gene orthologs in the rat and mouse genomes
Huang, Hui, Winter, Eitan E, Wang, Huajun, Weinstock, Keith G, Xing, Heming, Goodstadt, Leo, ...
Human disease genes differ significantly from their rodent orthologs with respect to their overall levels of conservation and their rates of evolutionary change. Rodent orthologs of human...
Comparative Evolutionary Genomics of Androgen-Binding Protein Genes
Emes, Richard D., Riley, Matthew C., Laukaitis, Christina M., Goodstadt, Leo, Karn, Robert C., Ponting, Chris P.
Allelic variation within the mouse androgen-binding protein (ABP) α subunit gene (Abpa) has been suggested to promote assortative mating and thus prezygotic isolation. This is consistent with the...
InterPro, progress and status in 2005
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam,...
Brockington, Martin, Blake, Derek J., Prandini, Paola, Brown, Susan C., Torelli, Silvia, Benson, Matthew A., ...
The congenital muscular dystrophies (CMD) are a heterogeneous group of autosomal recessive disorders presenting in infancy with muscle weakness, contractures, and dystrophic changes on...
Genome-Wide Identification of Human Functional DNA Using a Neutral Indel Model
Lunter, Gerton, Ponting, Chris P, Hein, Jotun
It has become clear that a large proportion of functional DNA in the human genome does not code for protein. Identification of this non-coding functional sequence using comparative approaches is...
Hotspots of mutation and breakage in dog and human chromosomes
Webber, Caleb, Ponting, Chris P.
Sequencing of the dog genome allows an investigation of the location-dependent evolutionary processes that occurred since the common ancestor of primates and carnivores, ∼95 million years ago. We...
Bias of Selection on Human Copy-Number Variants
Nguyen, Duc-Quang, Webber, Caleb, Ponting, Chris P
Although large-scale copy-number variation is an important contributor to conspecific genomic diversity, whether these variants frequently contribute to human phenotype differences remains unknown....
Phylogenetic Reconstruction of Orthology, Paralogy, and Conserved Synteny for Dog and Human
Goodstadt, Leo, Ponting, Chris P
Accurate predictions of orthology and paralogy relationships are necessary to infer human molecular function from experiments in model organisms. Previous genome-scale approaches to predicting these...
Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs
Ponjavic, Jasmina, Ponting, Chris P., Lunter, Gerton
Long transcripts that do not encode protein have only rarely been the subject of experimental scrutiny. Presumably, this is owing to the current lack of evidence of their functionality, thereby...
Goodstadt, Leo, Heger, Andreas, Webber, Caleb, Ponting, Chris P.
The newly sequenced genome of Monodelphis domestica not only provides the out-group necessary to better understand our own eutherian lineage, but it enables insights into the innovative biology of...
Variable Strength of Translational Selection Among 12 Drosophila Species
Heger, Andreas, Ponting, Chris P.
Codon usage bias in Drosophila melanogaster genes has been attributed to negative selection of those codons whose cellular tRNA abundance restricts rates of mRNA translation. Previous studies, which...
OPTIC: orthologous and paralogous transcripts in clades
Heger, Andreas, Ponting, Chris P.
The genome sequences of a large number of metazoan species are now known. As multiple closely related genomes are sequenced, comparative studies that previously focussed on only pairs of genomes can...
Laukaitis, Christina M, Heger, Andreas, Blakley, Tyler D, Munclinger, Pavel, Ponting, Chris P, Karn, Robert C
Sialidase-like Asp-boxes: Sequence-similar structures within different protein folds
Copley, Richard R., Russell, Robert B., Ponting, Chris P.
Sequence similarity is the most common measure currently used to infer homology between proteins. Typically, homologous protein domains show sequence similarity over their entire lengths. Here we...
Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes
Heger, Andreas, Ponting, Chris P.
The newly sequenced genome sequences of 11 Drosophila species provide the first opportunity to investigate variations in evolutionary rates across a clade of closely related species. Protein-coding...
Defensins and the convergent evolution of platypus and reptile venom genes
Whittington, Camilla M., Papenfuss, Anthony T., Bansal, Paramjit, Torres, Allan M., Wong, Emily S.W., Deakin, Janine E., ...
When the platypus (Ornithorhynchus anatinus) was first discovered, it was thought to be a taxidermist’s hoax, as it has a blend of mammalian and reptilian features. It is a most remarkable mammal,...
Bakrania, Preeti, Efthymiou, Maria, Klein, Johannes C., Salt, Alison, Bunyan, David J., Wyatt, Alex, ...
Developmental ocular malformations, including anophthalmia-microphthalmia (AM), are heterogeneous disorders with frequent sporadic or non-Mendelian inheritance. Recurrent interstitial deletions of...
Reduced purifying selection prevails over positive selection in human copy number variant evolution
Nguyen, Duc-Quang, Webber, Caleb, Hehir-Kwa, Jayne, Pfundt, Rolph, Veltman, Joris, Ponting, Chris P.
Copy number variation is a dominant contributor to genomic variation and may frequently underlie an individual’s variable susceptibilities to disease. Here we question our previous proposition that...
Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse
Church, Deanna M., Goodstadt, Leo, Hillier, LaDeana W., Zody, Michael C., Goldstein, Steve, She, Xinwe, ...
A finished clone-based assembly of the mouse genome reveals extensive recent sequence duplication during recent evolution and rodent-specific expansion of certain gene families. Newly assembled...
Forging Links between Human Mental Retardation–Associated CNVs and Mouse Gene Knockout Models
Webber, Caleb, Hehir-Kwa, Jayne Y., Nguyen, Duc-Quang, Veltman, Joris A., Ponting, Chris P.
Rare copy number variants (CNVs) are frequently associated with common neurological disorders such as mental retardation (MR; learning disability), autism, and schizophrenia. CNV screening in...
Ponjavic, Jasmina, Oliver, Peter L., Lunter, Gerton, Ponting, Chris P.
Besides protein-coding mRNAs, eukaryotic transcriptomes include many long non-protein-coding RNAs (ncRNAs) of unknown function that are transcribed away from protein-coding loci. Here, we have...