Combined analysis reveals a core set of cycling genes (2007)
Lu, Yong, Mahony, Shaun, Benos, Panayiotis V, Rosenfeld, Roni, Simon, Itamar, Breeden, Linda L, ...
Abstract Background Global transcript levels throughout the cell cycle have been characterized using microarrays in several species. Early analysis of these experiments focused on individual species....
Mahony, Shaun, Corcoran, David L, Feingold, Eleanor, Benos, Panayiotis V
Abstract Background Being the first noneutherian mammal sequenced, Monodelphis domestica (opossum) offers great potential for enhancing our understanding of the evolutionary processes that take place...
Shaun Mahony, Philip E. Auron, Panayiotis V. Benos
Transcription factor (TF) proteins recognize a small number of DNA sequences with high specificity and control the expression of neighbouring genes. The evolution of TF binding preference has been...
Shaun Mahony, Philip Auron, Panayiotis (Takis) V. Benos
Transcription factor (TF) proteins recognize a small number of DNA sequences with high specificity and control the expression of neighbouring genes. The evolution of TF binding preference has been...
Katherine Belov, Janine E. Deakin, Anthony T. Papenfuss, Michelle L. Baker, Sandra D. Melman, Hannah V. Siddle, ...
Opossum genomic sequence data permit researchers to fill gaps in our knowledge of how the Major Histocompatibility Complex evolved within the mammalian lineage.
Katherine Belov, Janine E. Deakin, Anthony T. Papenfuss, Michelle L. Baker, Sandra D. Melman, Hannah V. Siddle, ...
The first sequenced marsupial genome promises to reveal unparalleled insights into mammalian evolution. We have used the Monodelphis domestica (gray short-tailed opossum) sequence to construct the...
Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models (2004)
Mahony, Shaun, McInerney, James O, Smith, Terry J, Golden, Aaron
Abstract Background Many current gene prediction methods use only one model to represent protein-coding regions in a genome, and so are less likely to predict the location of genes that have an...
Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models (2004)
Mahony, Shaun, McInerney, James O, Smith, Terry J, Golden, Aaron
Background: Many current gene prediction methods use only one model to represent proteincoding regions in a genome, and so are less likely to predict the location of genes that have an atypical...
Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models
Mahony, Shaun, McInerney, James O, Smith, Terry J, Golden, Aaron
Belov, Katherine, Deakin, Janine E, Papenfuss, Anthony T, Baker, Michelle L, Melman, Sandra D, Siddle, Hannah V, ...
The first sequenced marsupial genome promises to reveal unparalleled insights into mammalian evolution. We have used theMonodelphis domestica (gray short-tailed opossum) sequence to construct the...
Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models
Mahony, Shaun, McInerney, James O, Smith, Terry J, Golden, Aaron
Belov, Katherine, Deakin, Janine E, Papenfuss, Anthony T, Baker, Michelle L, Melman, Sandra D, Siddle, Hannah V, ...
The first sequenced marsupial genome promises to reveal unparalleled insights into mammalian evolution. We have used theMonodelphis domestica (gray short-tailed opossum) sequence to construct the...
Mahony, Shaun, Auron, Philip E, Benos, Panayiotis V
Transcription factor (TF) proteins recognize a small number of DNA sequences with high specificity and control the expression of neighbouring genes. The evolution of TF binding preference has been...
Mahony, Shaun, Corcoran, David L, Feingold, Eleanor, Benos, Panayiotis V
A study of conservation of non-coding sequences, cis-regulatory elements and biological functions of regulated genes in opossum and other vertebrates enables better estimation of promoter...
STAMP: a web tool for exploring DNA-binding motif similarities
Mahony, Shaun, Benos, Panayiotis V.
STAMP is a newly developed web server that is designed to support the study of DNA-binding motifs. STAMP may be used to query motifs against databases of known motifs; the software aligns input...
ORegAnno: an open-access community-driven resource for regulatory annotation
Griffith, Obi L., Montgomery, Stephen B., Bernier, Bridget, Chu, Bryan, Kasaian, Katayoon, Aerts, Stein, ...
ORegAnno is an open-source, open-access database and literature curation system for community-based annotation of experimentally identified DNA regulatory regions, transcription factor binding sites...
Combined analysis reveals a core set of cycling genes
Lu, Yong, Mahony, Shaun, Benos, Panayiotis V, Rosenfeld, Roni, Simon, Itamar, Breeden, Linda L, ...
The simultaneous analysis of expression data from multiple species reveals a core set of conserved cycling genes that is much larger than previously thought.