Pan-vertebrate conserved non-coding sequences associated with developmental regulation (2009)
Whilst coding sequences are readily recognised in vertebrate genomes using computational approaches, the identification of non-coding regulatory sequences has traditionally been much more difficult,...
Tim J. Carver, Tanya Vavouri, Martin Frith, Martin J. Bishop, Greg Elgar
Theatre is a web-based computing system designed for the comparative analysis of genomic sequences, especially with respect to motifs likely to be involved in the regulation of gene expression....
Resource Fugu ESTs: New Resources for Transcription Analysis and Genome Annotation (2008)
Melody S. Clark, Dan Peterson, Ra W. Clifton, A J. Thompson, Masahide Sasaki, ...
The draft Fugu rubripes genome was released in 2002, at which time relatively few cDNAs were available to aid in the annotation of genes. The data presented here describe the sequencing and analysis...
Persistence of duplicated PAC1receptors in the teleost, Sparus auratus (2007)
Cardoso, João CR, De Vet, Edwin CJM, Louro, Bruno, Elgar, Greg, Clark, Melody S, Power, Deborah M
Abstract Background: Duplicated genes are common in vertebrate genomes. Their persistence is assumed to be either a consequence of gain of novel function (neofunctionalisation) or partitioning of the...
CONDOR: a database resource of developmentally associated conserved non-coding elements (2007)
Woolfe, Adam, Goode, Debbie K, Cooke, Julie, Callaway, Heather, Smith, Sarah, Snell, Phil, ...
Abstract Background Comparative genomics is currently one of the most popular approaches to study the regulatory architecture of vertebrate genomes. Fish-mammal genomic comparisons have proved...
Comparative genomics using Fugureveals insights into regulatory subfunctionalization (2007)
Abstract Background A major mechanism for the preservation of gene duplicates in the genome is thought to be mediated via loss or modification of cis -regulatory subfunctions between paralogs...
Vavouri, Tanya, Walter, Klaudia, Gilks, Walter R, Lehner, Ben, Elgar, Greg
Abstract Background The human genome contains thousands of non-coding sequences that are often more conserved between vertebrate species than protein-coding exons. These highly conserved non-coding...
Environment and plasticity of myogenesis in teleost fish (2007)
Matthew G. Mackenzie, Greg Elgar, Yuzuru Suzuki, Shugo Watabe, James R. Kinghorn, ...
doi:10.1152/physiolgenomics.00087.2005 You might find this additional information useful... Supplemental material for this article can be found at:
2007 Woolfe Volume and 8, Issue Elgar4, Article R53 Open Access (2007)
Comparative genomics using Fugu reveals insights into regulatory subfunctionalization
McEwen, Gayle K., Woolfe, Adam, Goode, Debbie, Vavouri, Tanya, Callaway, Heather, Elgar, Greg
Fish–mammal genomic comparisons have proved powerful in identifying conserved noncoding elements likely to be cis-regulatory in nature, and the majority of those tested in vivo have been shown to...
McEwen, Gayle K., Woolfe, Adam, Goode, Debbie, Vavouri, Tanya, Callaway, Heather, Elgar, Greg
Fish–mammal genomic comparisons have proved powerful in identifying conserved noncoding elements likely to be cis-regulatory in nature, and the majority of those tested in vivo have been shown to...
Highly Conserved Non-Coding Sequences Are Associated with Vertebrate Development (2005)
Adam Woolfe, Martin Goodson, Debbie K. Goode, Phil Snell, Gayle K. McEwen, Tanya Vavouri, ...
Highly conserved non-coding sequences in vertebrate genomes are frequently located around genes involved in development and can direct tissue-specific gene expression in functional assays.
Highly Conserved Non-Coding Sequences Are Associated with Vertebrate Development (2005)
Adam Woolfe, Martin Goodson, Debbie K. Goode, Phil Snell, Gayle K. McEwen, Tanya Vavouri, ...
In addition to protein coding sequence, the human genome contains a significant amount of regulatory DNA, the identification of which is proving somewhat recalcitrant to both in silico and functional...
Amanda Cottage, Lisa Mullan, Elizabeth Hellen, Tim Carver, Sunil Patel, ...
Abstract: The activities of vertebrate lysosomes are critical to many essential cellular processes. The yeast vacuole is analogous to the mammalian lysosome and is used as a tool to gain insights...
Plenty more fish in the sea: Comparative and functional genomics using teleost models (2004)
Biology has collaborated with evolution to create an enormous repertoire of animal variation. This in turn has provided experimental biologists with models that can be used in the lab to simulate...
Halling-Brown, Mark, Sansom, Clare, Moss, David S., Elgar, Greg, Edwards, Yvonne J. K.
A web server has been developed to access annotation and graphical reports of synteny and gene order between the Fugu genome and human genes. In this system, the assembled Fugu genomic sequences...
Heaney, Simon J H, Purdie, Lorna A, Li, Li, Oostra, Ben A, ...
Unequivocal identification of the full composition of a gene is made difficult by the cryptic nature of regulatory elements. Regulatory elements are notoriously difficult to locate and may reside at...
Edwards, Yvonne J. K., Carver, Tim J., Vavouri, Tanya, Frith, Martin, Bishop, Martin J., Elgar, Greg
Theatre is a web-based computing system designed for the comparative analysis of genomic sequences, especially with respect to motifs likely to be involved in the regulation of gene expression....
Fugu ESTs: New Resources for Transcription Analysis and Genome Annotation (2003)
Clark, Melody S., Edwards, Yvonne J.K., Peterson, Dan, Clifton, Sandra W., Thompson, Amanda J., Sasaki, Masahide, ...
The draft Fugu rubripes genome was released in 2002, at which time relatively few cDNAs were available to aid in the annotation of genes. The data presented here describe the sequencing and analysis...
Miles, Colin G., Rankin, Lesley, Smith, Shirley I., Niksic, Martina, Elgar, Greg, Hastie, Nicholas D.
The teleost fish are widely used as model organisms in vertebrate biology. The compact genome of the pufferfish, Fugu rubripes, has proven a valuable tool in comparative genome analyses, aiding the...
Pozzoli, Uberto, Elgar, Greg, Cagliani, Rachele, Riva, Laura, Comi, Giacomo P., Bresolin, Nereo, ...
The human DMD gene is the largest known to date, spanning > 2000 kb on the X chromosome. The gene size is mainly accounted for by huge intronic regions. We sequenced 190 kb of Fugu rubripes...
Fugu ESTs: New Resources for Transcription Analysis and Genome Annotation (2003)
Clark, Melody S., Edwards, Yvonne J.K., Peterson, Dan, Clifton, Sandra W., Thompson, Amanda J., Sasaki, Masahide, ...
The draft Fugu rubripes genome was released in 2002, at which time relatively few cDNAs were available to aid in the annotation of genes. The data presented here describe the sequencing and analysis...
Lettice, Laura A., Heaney, Simon J.H., Purdie, Lorna A., Li, Li, De Beer, Philippe, Oostra, Ben A., ...
Unequivocal identification of the full composition of a gene is made difficult by the cryptic nature of regulatory elements. Regulatory elements are notoriously difficult to locate and may reside at...
Xena, a Full-Length Basal Retroelement from Tetraodontid Fish (2002)
Dalle Nogare, Damian E., Clark, Melody S., Elgar, Greg, Frame, Ian G., Poulter, Russell T. M.
Mobile genetic elements are ubiquitous throughout the eukaryote superkingdom. We have sequenced a highly unusual full-length retroelement from the Fugu fish, Takifugu rubripes. This element, which we...
Smith, Sarah F., Snell, Philip, Gruetzner, Frank, Bench, Anthony J., Haaf, Thomas, Metcalfe, Judith A., ...
Smith, Sarah F., Snell, Philip, Gruetzner, Frank, Bench, Anthony J., Haaf, Thomas, Metcalfe, Judith A., ...
SAND, a New Protein Family: From Nucleic Acid to Protein Structure and Function Prediction (2001)
As a result of genome, EST and cDNA sequencing projects, there are huge numbers of predicted and/or partially characterised protein sequences compared with a relatively small number of proteins with...
SAND, a New Protein Family: From Nucleic Acid to Protein Structure and Function Prediction (2001)
As a result of genome, EST and cDNA sequencing projects, there are huge numbers of predicted and/or partially characterised protein sequences compared with a relatively small number of proteins with...
Elgar, Greg, Clark, Melody S., Meek, Stephen, Smith, Sarah, Warner, Sarah, Edwards, Yvonne J.K., ...
RspX I: a new restriction endonuclease with a recognition sequence of 5'T/CATGA3' (1988)
Tsui, Wing-Cheong, Elgar, Greg, Merrill, Colin, Maunders, Martin
Miles, Colin, Elgar, Greg, Coles, Edward, Kleinjan, Dirk-Jan, Van Heyningen, Veronica, Hastie, Nicholas
The pufferfish Fugu rubripes has a genome ≈7.5 times smaller than that of mammals but with a similar number of genes. Although conserved synteny has been demonstrated between pufferfish and mammals...
Miles, Colin G., Rankin, Lesley, Smith, Shirley I., Niksic, Martina, Elgar, Greg, Hastie, Nicholas D.
The teleost fish are widely used as model organisms in vertebrate biology. The compact genome of the pufferfish, Fugu rubripes, has proven a valuable tool in comparative genome analyses, aiding the...
Theatre: a software tool for detailed comparative analysis and visualization of genomic sequence
Edwards, Yvonne J. K., Carver, Tim J., Vavouri, Tanya, Frith, Martin, Bishop, Martin J., Elgar, Greg
Theatre is a web-based computing system designed for the comparative analysis of genomic sequences, especially with respect to motifs likely to be involved in the regulation of gene expression....
Smith, Sarah F., Snell, Philip, Gruetzner, Frank, Bench, Anthony J., Haaf, Thomas, Metcalfe, Judith A., ...
Cosmid and BAC contig maps have been constructed across two Fugu genomic regions containing the orthologs of human genes mapping to human chromosome 20q. Contig gene contents have been assessed by...
Elgar, Greg, Clark, Melody S., Meek, Stephen, Smith, Sarah, Warner, Sarah, Edwards, Yvonne J.K., ...
We have generated and analyzed >50,000 shotgun clones from 1059 Fugu cosmid clones. All sequences have been minimally edited and searched against protein and DNA databases. These data are all...
Fugu ESTs: New Resources for Transcription Analysis and Genome Annotation
Clark, Melody S., Edwards, Yvonne J.K., Peterson, Dan, Clifton, Sandra W., Thompson, Amanda J., Sasaki, Masahide, ...
The draft Fugu rubripes genome was released in 2002, at which time relatively few cDNAs were available to aid in the annotation of genes. The data presented here describe the sequencing and analysis...
Halling-Brown, Mark, Sansom, Clare, Moss, David S., Elgar, Greg, Edwards, Yvonne J. K.
A web server has been developed to access annotation and graphical reports of synteny and gene order between the Fugu genome and human genes. In this system, the assembled Fugu genomic sequences...
Comparative Analysis of Vertebrate Dystrophin Loci Indicate Intron Gigantism as a Common Feature
Pozzoli, Uberto, Elgar, Greg, Cagliani, Rachele, Riva, Laura, Comi, Giacomo P., Bresolin, Nereo, ...
The human DMD gene is the largest known to date, spanning > 2000 kb on the X chromosome. The gene size is mainly accounted for by huge intronic regions. We sequenced 190 kb of Fugu rubripes...
Highly Conserved Non-Coding Sequences Are Associated with Vertebrate Development
Woolfe, Adam, Goodson, Martin, Goode, Debbie K, Snell, Phil, McEwen, Gayle K, Vavouri, Tanya, ...
In addition to protein coding sequence, the human genome contains a significant amount of regulatory DNA, the identification of which is proving somewhat recalcitrant to both in silico and functional...
Ancient duplicated conserved noncoding elements in vertebrates: A genomic and functional analysis
McEwen, Gayle K., Woolfe, Adam, Goode, Debbie, Vavouri, Tanya, Callaway, Heather, Elgar, Greg
Fish–mammal genomic comparisons have proved powerful in identifying conserved noncoding elements likely to be cis-regulatory in nature, and the majority of those tested in vivo have been shown to...
Miles, Colin, Elgar, Greg, Coles, Edward, Kleinjan, Dirk-Jan, Van Heyningen, Veronica, Hastie, Nicholas
The pufferfish Fugu rubripes has a genome ≈7.5 times smaller than that of mammals but with a similar number of genes. Although conserved synteny has been demonstrated between pufferfish and mammals...
Miles, Colin G., Rankin, Lesley, Smith, Shirley I., Niksic, Martina, Elgar, Greg, Hastie, Nicholas D.
The teleost fish are widely used as model organisms in vertebrate biology. The compact genome of the pufferfish, Fugu rubripes, has proven a valuable tool in comparative genome analyses, aiding the...
Theatre: a software tool for detailed comparative analysis and visualization of genomic sequence
Edwards, Yvonne J. K., Carver, Tim J., Vavouri, Tanya, Frith, Martin, Bishop, Martin J., Elgar, Greg
Theatre is a web-based computing system designed for the comparative analysis of genomic sequences, especially with respect to motifs likely to be involved in the regulation of gene expression....
Smith, Sarah F., Snell, Philip, Gruetzner, Frank, Bench, Anthony J., Haaf, Thomas, Metcalfe, Judith A., ...
Cosmid and BAC contig maps have been constructed across two Fugu genomic regions containing the orthologs of human genes mapping to human chromosome 20q. Contig gene contents have been assessed by...
Elgar, Greg, Clark, Melody S., Meek, Stephen, Smith, Sarah, Warner, Sarah, Edwards, Yvonne J.K., ...
We have generated and analyzed >50,000 shotgun clones from 1059 Fugu cosmid clones. All sequences have been minimally edited and searched against protein and DNA databases. These data are all...
Fugu ESTs: New Resources for Transcription Analysis and Genome Annotation
Clark, Melody S., Edwards, Yvonne J.K., Peterson, Dan, Clifton, Sandra W., Thompson, Amanda J., Sasaki, Masahide, ...
The draft Fugu rubripes genome was released in 2002, at which time relatively few cDNAs were available to aid in the annotation of genes. The data presented here describe the sequencing and analysis...
Halling-Brown, Mark, Sansom, Clare, Moss, David S., Elgar, Greg, Edwards, Yvonne J. K.
A web server has been developed to access annotation and graphical reports of synteny and gene order between the Fugu genome and human genes. In this system, the assembled Fugu genomic sequences...
Comparative Analysis of Vertebrate Dystrophin Loci Indicate Intron Gigantism as a Common Feature
Pozzoli, Uberto, Elgar, Greg, Cagliani, Rachele, Riva, Laura, Comi, Giacomo P., Bresolin, Nereo, ...
The human DMD gene is the largest known to date, spanning > 2000 kb on the X chromosome. The gene size is mainly accounted for by huge intronic regions. We sequenced 190 kb of Fugu rubripes...
Highly Conserved Non-Coding Sequences Are Associated with Vertebrate Development
Woolfe, Adam, Goodson, Martin, Goode, Debbie K, Snell, Phil, McEwen, Gayle K, Vavouri, Tanya, ...
In addition to protein coding sequence, the human genome contains a significant amount of regulatory DNA, the identification of which is proving somewhat recalcitrant to both in silico and functional...
Ancient duplicated conserved noncoding elements in vertebrates: A genomic and functional analysis
McEwen, Gayle K., Woolfe, Adam, Goode, Debbie, Vavouri, Tanya, Callaway, Heather, Elgar, Greg
Fish–mammal genomic comparisons have proved powerful in identifying conserved noncoding elements likely to be cis-regulatory in nature, and the majority of those tested in vivo have been shown to...
Human GLI3 Intragenic Conserved Non-Coding Sequences Are Tissue-Specific Enhancers
Abbasi, Amir Ali, Paparidis, Zissis, Malik, Sajid, Goode, Debbie K., Callaway, Heather, Elgar, Greg, ...
The zinc-finger transcription factor GLI3 is a key regulator of development, acting as a primary transducer of Sonic hedgehog (SHH) signaling in a combinatorial context dependent fashion controlling...
Vavouri, Tanya, Walter, Klaudia, Gilks, Walter R, Lehner, Ben, Elgar, Greg
Invertebrate conserved noncoding elements (CNEs) are associated with the same core set of genes as vertebrate CNEs, and may reflect the parallel evolution of enhancers in the gene regulatory networks...
Comparative genomics using Fugu reveals insights into regulatory subfunctionalization
Fish-mammal genomic alignments were used to compare over 800 conserved non-coding elements that associate with genes that have undergone fish-specific duplication and retention, revealing a pattern...
CONDOR: a database resource of developmentally associated conserved non-coding elements
Woolfe, Adam, Goode, Debbie K, Cooke, Julie, Callaway, Heather, Smith, Sarah, Snell, Phil, ...
Persistence of duplicated PAC1 receptors in the teleost, Sparus auratus
Cardoso, João CR, De Vet, Edwin CJM, Louro, Bruno, Elgar, Greg, Clark, Melody S, Power, Deborah M
SAND, a New Protein Family: From Nucleic Acid to Protein Structure and Function Prediction
Cottage, Amanda, Edwards, Yvonne J. K., Elgar, Greg
As a result of genome, EST and cDNA sequencing projects, there are huge numbers of predicted and/or partially characterised protein sequences compared with a relatively small number of proteins with...