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...
Mapping and identification of essential gene functions on the X chromosome of Drosophila (2002)
Peter, Annette, Schoettler, Petra, Werner, Meike, Beinert, Nicole, Dowe, Gordon, Burkert, Peter, ...
The Drosophila melanogaster genome consists of four chromosomes that contain 165 Mb of DNA, 120 Mb of which are euchromatic. The two Drosophila Genome Projects, in collaboration with Celera Genomics...
Benos, Panayiotis V., Gatt, Melanie K., Murphy, Lee, Harris, David, Barrell, Bart, Ferraz, Concepcion, ...
We present the sequence of a contiguous 2.63 Mb of DNA extending from the tip of the X chromosome of Drosophila melanogaster. Within this sequence, we predict 277 protein coding genes, of which 94...
Additivity in protein–DNA interactions: how good an approximation is it?
Benos, Panayiotis V., Bulyk, Martha L., Stormo, Gary D.
Man and Stormo and Bulyk et al. recently presented their results on the study of the DNA binding affinity of proteins. In both of these studies the main conclusion is that the additivity assumption,...
Benos, Panayiotis V., Gatt, Melanie K., Murphy, Lee, Harris, David, Barrell, Bart, Ferraz, Concepcion, ...
We present the sequence of a contiguous 2.63 Mb of DNA extending from the tip of the X chromosome of Drosophila melanogaster. Within this sequence, we predict 277 protein coding genes, of which 94...
Mapping and identification of essential gene functions on the X chromosome of Drosophila
Peter, Annette, Schöttler, Petra, Werner, Meike, Beinert, Nicole, Dowe, Gordon, Burkert, Peter, ...
The Drosophila melanogaster genome consists of four chromosomes that contain 165 Mb of DNA, 120 Mb of which are euchromatic. The two Drosophila Genome Projects, in collaboration with Celera Genomics...
Corcoran, David L., Feingold, Eleanor, Dominick, Jessica, Wright, Marietta, Harnaha, Jo, Trucco, Massimo, ...
The search for mammalian DNA regulatory regions poses a challenging problem in computational biology. The short length of the DNA patterns compared with the size of the promoter regions and the...
FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting
Corcoran, David L., Feingold, Eleanor, Benos, Panayiotis V.
FOOTER is a newly developed algorithm that analyzes homologous mammalian promoter sequences in order to identify transcriptional DNA regulatory ‘signals’. FOOTER uses prior knowledge about the...
enoLOGOS: a versatile web tool for energy normalized sequence logos
Workman, Christopher T., Yin, Yutong, Corcoran, David L., Ideker, Trey, Stormo, Gary D., Benos, Panayiotis V.
enoLOGOS is a web-based tool that generates sequence logos from various input sources. Sequence logos have become a popular way to graphically represent DNA and amino acid sequence patterns from a...
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...
Deregulation of common genes by c-Myc and its direct target, MT-MC1
Rogulski, Kenneth R., Cohen, Debra E., Corcoran, David L., Benos, Panayiotis V., Prochownik, Edward V.
In addition to its role in cancer, the c-Myc oncoprotein controls many normal cellular processes as a consequence of its function as a basic helix–loop–helix leucine zipper transcription factor....
Additivity in protein–DNA interactions: how good an approximation is it?
Benos, Panayiotis V., Bulyk, Martha L., Stormo, Gary D.
Man and Stormo and Bulyk et al. recently presented their results on the study of the DNA binding affinity of proteins. In both of these studies the main conclusion is that the additivity assumption,...
Benos, Panayiotis V., Gatt, Melanie K., Murphy, Lee, Harris, David, Barrell, Bart, Ferraz, Concepcion, ...
We present the sequence of a contiguous 2.63 Mb of DNA extending from the tip of the X chromosome of Drosophila melanogaster. Within this sequence, we predict 277 protein coding genes, of which 94...
Mapping and identification of essential gene functions on the X chromosome of Drosophila
Peter, Annette, Schöttler, Petra, Werner, Meike, Beinert, Nicole, Dowe, Gordon, Burkert, Peter, ...
The Drosophila melanogaster genome consists of four chromosomes that contain 165 Mb of DNA, 120 Mb of which are euchromatic. The two Drosophila Genome Projects, in collaboration with Celera Genomics...
Corcoran, David L., Feingold, Eleanor, Dominick, Jessica, Wright, Marietta, Harnaha, Jo, Trucco, Massimo, ...
The search for mammalian DNA regulatory regions poses a challenging problem in computational biology. The short length of the DNA patterns compared with the size of the promoter regions and the...
FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting
Corcoran, David L., Feingold, Eleanor, Benos, Panayiotis V.
FOOTER is a newly developed algorithm that analyzes homologous mammalian promoter sequences in order to identify transcriptional DNA regulatory ‘signals’. FOOTER uses prior knowledge about the...
enoLOGOS: a versatile web tool for energy normalized sequence logos
Workman, Christopher T., Yin, Yutong, Corcoran, David L., Ideker, Trey, Stormo, Gary D., Benos, Panayiotis V.
enoLOGOS is a web-based tool that generates sequence logos from various input sources. Sequence logos have become a popular way to graphically represent DNA and amino acid sequence patterns from a...
Deregulation of common genes by c-Myc and its direct target, MT-MC1
Rogulski, Kenneth R., Cohen, Debra E., Corcoran, David L., Benos, Panayiotis V., Prochownik, Edward V.
In addition to its role in cancer, the c-Myc oncoprotein controls many normal cellular processes as a consequence of its function as a basic helix–loop–helix leucine zipper transcription factor....
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...
Feng, Huichen, Taylor, Jennifer L., Benos, Panayiotis V., Newton, Robert, Waddell, Keith, Lucas, Sebastien B., ...
Digital transcript subtraction (DTS) was developed to subtract in silico known human sequences from expression library data sets, leaving candidate nonhuman sequences for further analysis. This...
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.