Interspecies data mining to predict novel ING-protein interactions in human (2008)
Gordon, Paul MK, Soliman, Mohamed A, Bose, Pinaki, Trinh, Quang, Sensen, Christoph W, Riabowol, Karl
Abstract Background The IN hibitor of G rowth (ING) family of type II tumor suppressors (ING1–ING5) is involved in many cellular processes such as cell aging, apoptosis, DNA repair and...
A Pilot Study into the Usability of a Scientific Workflow Construction Tool (2007)
Gordon, Paul M. K., Sensen, Christoph W.
We describe a recent pilot study into the usability of the scientific workflow creation and enactment tool called Taverna. Both programmers and non-programmers were used as subjects for a defined...
A Pilot Study into the Usability of a Scientific Workflow Construction Tool (2007)
Gordon, Paul M. K., Sensen, Christoph W.
We describe a recent pilot study into the usability of the scientific workflow creation and enactment tool called Taverna. Both programmers and non-programmers were used as subjects for a defined...
Seahawk: moving beyond HTML in Web-based bioinformatics analysis (2007)
Gordon, Paul MK, Sensen, Christoph W
Abstract Background Traditional HTML interfaces for input to and output from Bioinformatics analysis on the Web are highly variable in style, content and data formats. Combining multiple analyses can...
Maintenance of ancestral complexity and non-metazoan genes in two basal cnidarians (2005)
Technau, Ulrich, Rudd, Stephen, Maxwell, Peter, Gordon, Paul M.K., Saina, Michael, Grasso, Lauretta C., ...
Cnidarians are among the simplest extant animals; however EST analyses reveal that they have a remarkably high level of genetic complexity. In this article, we show that the full diversity of...
Maintenance of ancestral complexity and non-metazoan genes in two basal cnidarians (2005)
Technau, Ulrich, Rudd, Stephen, Maxwell, Peter, Gordon, Paul M.K., Saina, Michael, Grasso, Lauretta C., ...
Cnidarians are among the simplest extant animals; however EST analyses reveal that they have a remarkably high level of genetic complexity. In this article, we show that the full diversity of...
Maintenance of ancestral complexity and non-metazoan genes in two basal cnidarians (2005)
Technau, Ulrich, Rudd, Stephen, Maxwell, Peter, Gordon, Paul M. K., Saina, Michael, Grasso, Lauretta C., ...
Cnidarians are among the simplest extant animals; however EST analyses reveal that they have a remarkably high level of genetic complexity. In this article, we show that the full diversity of...
Maintenance of ancestral complexity and non-metazoan genes in two basal cnidarians (2005)
Technau, Ulrich, Rudd, Stephen, Maxwell, Peter, Gordon, Paul M. K., Saina, Michael, Grasso, Lauretta C., ...
Cnidarians are among the simplest extant animals; however EST analyses reveal that they have a remarkably high level of genetic complexity. In this article, we show that the full diversity of...
NOBUKO ARISUE, TETSUO HASHIMOTO, JENNIFER A. LEE, DOROTHY V. MOORE, PAUL GORDON, CHRISTOPH W. SENSEN, ...
The taxonomic position and phylogenetic relationships of the Pelobionta, an amitochondriate amoeboflagellate group, are not yet completely settled. To provide more information, we obtained sequences...
Gene Content and Organization of a 281-Kbp (2000)
Robert L. Charlebois, Rama K. Singh, Ghislaine Allard, Cynthia Chow, Fabrice Confalonieri, ...
The sequence of a 281-kbp contig from the crenarchaeote Sulfolobus solfataricus P2 was determined and analysed. Notable features in this region include 29 ribosomal protein genes, 12 tRNA genes (four...
Christoph W. Sensen, Robert L. Charlebois, Cynthia Chow, Ib Groth, Clausen Bruce Curtis, W. Ford, ...
The Sulfolobus solfataricus P2 genome collaborators are poised to sequence the entire 3-Mbp genome of this crenarchaeote archaeon. About 80% of the genome has been sequenced to date, with the rest of...
Bluejay: A Browser For Linear Units In Java (1999)
Paul Gordon, Christoph W. Sensen
Abstract: The World Wide Web illustrates the power of using a common, simple markup language (HTML) to describe distributed documents. To expand this power to other types of data, a system for the...
Albers, Sonja-V., Elferink, Marieke G.L., Charlebois, Robert L., Sensen, Christoph W., Driessen, Arnold J.M., Konings, Wil N.
The archaeon Sulfolobus solfataricus grows optimally at 80°C and pH 2.5 to 3.5 on carbon sources such as yeast extracts, tryptone, and various sugars. Cells rapidly accumulate glucose. This...
Terry Gaasterland, Christoph W. Sensen
rom the fact that during the lifetime of a genome sequencing project, the sequence is growing and changing; the public sequence databases are also growing and changing; new and improved software...
Terry Gaasterland, Christoph W. Sensen
es from the fact that during the lifetime of a genome sequencing project, the sequence is growing and changing; the public sequence databases are also growing and changing; new and improved software...
MAGPIE: A Responsive System for Data Collection and Analysis (1998)
Terry Gaasterland, Christoph W. Sensen
The MAGPIE system has been designed and implemented to address the data management and analysis problems that arise during the interpretation of whole microbial genomes. The system consists of a...
The complete genome of the crenarchaeon Sulfolobus solfataricus P2
She, Qunxin, Singh, Rama K., Confalonieri, Fabrice, Zivanovic, Yvan, Allard, Ghislaine, Awayez, Mariana J., ...
The genome of the crenarchaeon Sulfolobus solfataricus P2 contains 2,992,245 bp on a single chromosome and encodes 2,977 proteins and many RNAs. One-third of the encoded proteins have no detectable...
Napoli, Alessandra, Van Der Oost, John, Sensen, Christoph W., Charlebois, Robert L., Rossi, Mosé, Ciaramella, Maria
Regulation of gene expression in the domain Archaea, and specifically hyperthermophiles, has been poorly investigated so far. Biochemical experiments and genome sequencing have shown that, despite...
Albers, Sonja-V., Elferink, Marieke G. L., Charlebois, Robert L., Sensen, Christoph W., Driessen, Arnold J. M., Konings, Wil N.
The archaeon Sulfolobus solfataricus grows optimally at 80°C and pH 2.5 to 3.5 on carbon sources such as yeast extracts, tryptone, and various sugars. Cells rapidly accumulate glucose. This...
Müller, Miklós, Lee, Jennifer A., Gordon, Paul, Gaasterland, Terry, Sensen, Christoph W.
Inorganic pyrophosphate-dependent phosphofructokinase (PPi-PFK) of the amitochondriate eukaryote Mastigamoeba balamuthi was sequenced and showed about 60% identity to PPi-PFKs from two eubacteria,...
Martusewitsch, Erika, Sensen, Christoph W., Schleper, Christa
We have isolated uracil-auxotrophic mutants of the hyperthermophilic archaeon Sulfolobus solfataricus in order to explore the genomic stability and mutational frequencies of this organism and to...
Bapteste, Eric, Brinkmann, Henner, Lee, Jennifer A., Moore, Dorothy V., Sensen, Christoph W., Gordon, Paul, ...
The phylogenetic relationships of amoebae are poorly resolved. To address this difficult question, we have sequenced 1,280 expressed sequence tags from Mastigamoeba balamuthi and assembled a large...
Transcription Profiling of Candida albicans Cells Undergoing the Yeast-to-Hyphal TransitionD⃞
Nantel, André, Dignard, Daniel, Bachewich, Catherine, Harcus, Doreen, Marcil, Anne, Bouin, Anne-Pascale, ...
The ability of the pathogenic fungus Candida albicans to switch from a yeast to a hyphal morphology in response to external signals is implicated in its pathogenicity. We used glass DNA microarrays...
MAGPIE/EGRET Annotation of the 2.9-Mb Drosophila melanogaster Adh Region
Gaasterland, Terry, Sczyrba, Alexander, Thomas, Elizabeth, Aytekin-Kurban, Gulriz, Gordon, Paul, Sensen, Christoph W.
Our challenge in annotating the 2.91-Mb Adh region of the Drosophila melanogaster genome was to identify genetic and genomic features automatically, completely, and precisely within a 6-week period....
Siebers, Bettina, Tjaden, Britta, Michalke, Klaus, Dörr, Christine, Ahmed, Hatim, Zaparty, Melanie, ...
The hyperthermophilic, facultatively heterotrophic crenarchaeum Thermoproteus tenax was analyzed using a low-coverage shotgun-sequencing approach. A total of 1.81 Mbp (representing 98.5% of the total...
Gordon, Paul M. K., Sensen, Christoph W.
We have developed a software package called Osprey for the calculation of optimal oligonucleotides for DNA sequencing and the creation of microarrays based on either PCR-products or directly spotted...
The complete genome of the crenarchaeon Sulfolobus solfataricus P2
She, Qunxin, Singh, Rama K., Confalonieri, Fabrice, Zivanovic, Yvan, Allard, Ghislaine, Awayez, Mariana J., ...
The genome of the crenarchaeon Sulfolobus solfataricus P2 contains 2,992,245 bp on a single chromosome and encodes 2,977 proteins and many RNAs. One-third of the encoded proteins have no detectable...
Napoli, Alessandra, Van Der Oost, John, Sensen, Christoph W., Charlebois, Robert L., Rossi, Mosé, Ciaramella, Maria
Regulation of gene expression in the domain Archaea, and specifically hyperthermophiles, has been poorly investigated so far. Biochemical experiments and genome sequencing have shown that, despite...
Albers, Sonja-V., Elferink, Marieke G. L., Charlebois, Robert L., Sensen, Christoph W., Driessen, Arnold J. M., Konings, Wil N.
The archaeon Sulfolobus solfataricus grows optimally at 80°C and pH 2.5 to 3.5 on carbon sources such as yeast extracts, tryptone, and various sugars. Cells rapidly accumulate glucose. This...
Müller, Miklós, Lee, Jennifer A., Gordon, Paul, Gaasterland, Terry, Sensen, Christoph W.
Inorganic pyrophosphate-dependent phosphofructokinase (PPi-PFK) of the amitochondriate eukaryote Mastigamoeba balamuthi was sequenced and showed about 60% identity to PPi-PFKs from two eubacteria,...
Martusewitsch, Erika, Sensen, Christoph W., Schleper, Christa
We have isolated uracil-auxotrophic mutants of the hyperthermophilic archaeon Sulfolobus solfataricus in order to explore the genomic stability and mutational frequencies of this organism and to...
Bapteste, Eric, Brinkmann, Henner, Lee, Jennifer A., Moore, Dorothy V., Sensen, Christoph W., Gordon, Paul, ...
The phylogenetic relationships of amoebae are poorly resolved. To address this difficult question, we have sequenced 1,280 expressed sequence tags from Mastigamoeba balamuthi and assembled a large...
Transcription Profiling of Candida albicans Cells Undergoing the Yeast-to-Hyphal TransitionD⃞
Nantel, André, Dignard, Daniel, Bachewich, Catherine, Harcus, Doreen, Marcil, Anne, Bouin, Anne-Pascale, ...
The ability of the pathogenic fungus Candida albicans to switch from a yeast to a hyphal morphology in response to external signals is implicated in its pathogenicity. We used glass DNA microarrays...
MAGPIE/EGRET Annotation of the 2.9-Mb Drosophila melanogaster Adh Region
Gaasterland, Terry, Sczyrba, Alexander, Thomas, Elizabeth, Aytekin-Kurban, Gulriz, Gordon, Paul, Sensen, Christoph W.
Our challenge in annotating the 2.91-Mb Adh region of the Drosophila melanogaster genome was to identify genetic and genomic features automatically, completely, and precisely within a 6-week period....
Siebers, Bettina, Tjaden, Britta, Michalke, Klaus, Dörr, Christine, Ahmed, Hatim, Zaparty, Melanie, ...
The hyperthermophilic, facultatively heterotrophic crenarchaeum Thermoproteus tenax was analyzed using a low-coverage shotgun-sequencing approach. A total of 1.81 Mbp (representing 98.5% of the total...
Gordon, Paul M. K., Sensen, Christoph W.
We have developed a software package called Osprey for the calculation of optimal oligonucleotides for DNA sequencing and the creation of microarrays based on either PCR-products or directly spotted...
Reconstructing the Mosaic Glycolytic Pathway of the Anaerobic Eukaryote Monocercomonoides▿ †
Liapounova, Natalia A., Hampl, Vladimir, Gordon, Paul M. K., Sensen, Christoph W., Gedamu, Lashitew, Dacks, Joel B.
All eukaryotes carry out glycolysis, interestingly, not all using the same enzymes. Anaerobic eukaryotes face the challenge of fewer molecules of ATP extracted per molecule of glucose due to their...
Tracking Host Sources of Cryptosporidium spp. in Raw Water for Improved Health Risk Assessment▿
Ruecker, Norma J., Braithwaite, Shannon L., Topp, Edward, Edge, Thomas, Lapen, David R., Wilkes, Graham, ...
Recent molecular evidence suggests that different species and/or genotypes of Cryptosporidium display strong host specificity, altering our perceptions regarding the zoonotic potential of this...
Response of the Hyperthermophilic Archaeon Sulfolobus solfataricus to UV Damage▿ †
Fröls, Sabrina, Gordon, Paul M. K., Panlilio, Mayi Arcellana, Duggin, Iain G., Bell, Stephen D., Sensen, Christoph W., ...
In order to characterize the genome-wide transcriptional response of the hyperthermophilic, aerobic crenarchaeote Sulfolobus solfataricus to UV damage, we used high-density DNA microarrays which...
Turinsky, Andrei L, Sensen, Christoph W
Genetic diseases and developmental patterns should be studied on several levels: from macroscale (organs and tissues) to nanoscale (cells, genes, proteins). Due to the overwhelming complexity of the...
Caffrey, Sean M., Park, Hyung Soo, Been, Jenny, Gordon, Paul, Sensen, Christoph W., Voordouw, Gerrit
The genome sequence of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough was reanalyzed to design unique 70-mer oligonucleotide probes against 2,824 probable protein-coding regions....