Gordon, Paul M. K., Schütz, Ekkehard, Beck, Julia, Urnovitz, Howard B., Graham, Catherine, Clark, Renee, ...
To gain insight into the disease progression of transmissible spongiform encephalopathies (TSE), we searched for disease-specific patterns in circulating nucleic acids (CNA) in elk and cattle. In a...
Soh, Jung, Gordon, Paul MK, Taschuk, Morgan L, Dong, Anguo, Ah-Seng, Andrew C, Turinsky, Andrei L, ...
Abstract Background The Bluejay genome browser has been developed over several years to address the challenges posed by the ever increasing number of data types as well as the increasing volume of...
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...
Bioinformatics Programmers, Quang Trinh, Christoph W. Sensen
Summary: Several semantic Web Services clients for Bioinformatics have been released, but to date no support systems for service providers have been described. We have created a framework...
A Pilot Study into the Usability of a Scientific Workflow Construction Tool (2008)
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...
Visual Comparison of Multiple Gene Expression Datasets in a Genomic Context (2008)
Borowski, Krzysztof, Soh, Jung, Sensen, Christoph W.
The need for novel methods of visualizing microarray data is growing. New perspectives are beneficial to finding patterns in expression data. The Bluejay genome browser provides an integrative way of...
Bmc Bioinformatics, Jung Soh, Paul Mk Gordon, Morgan L Taschuk, Anguo Dong, ...
Software Bluejay 1.0: genome browsing and comparison with rich customization provision and dynamic resource linking
Corresponding Editor: B. Golding. (2007)
Robert L. Charlebois, Rama K. Singh, Ghislaine Allard, Cynthia Chow, Fabrice Confalonieri, ...
Gene content and organization of a 281-kbp
MAGPIE: A Responsive System for Data Collection and Analysis (2007)
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...
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...
Semantic Web Service provision: a realistic framework for Bioinformatics programmers (2007)
Gordon, Paul M.K., Trinh, Quang, Sensen, Christoph W.
Summary: Several semantic Web Services clients for Bioinformatics have been released, but to date no support systems for service providers have been described. We have created a framework...
Seahawk: Moving Beyond HTML in Web-based Bioinformatics Analysis (2007)
Paul Mk Gordon, Christoph W Sensen
Software
04281 Abstracts Collection -- Integrative Bioinformatics - Aspects of the Virtual Cell (2006)
Collado-Vides, Julio, Hofestädt, Ralf, Sensen, Christoph W.
From 04.07.04 to 09.07.04, the Dagstuhl Seminar 04281 ``Integrative Bioinformatics - Aspects of the Virtual Cell'' was held in the International Conference and Research Center (IBFI), Schloss...
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...
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...
Phylogenetic Analysis of the ING Family of PHD Finger Proteins (2005)
He, Gordon H.Y., Helbing, Caren C., Wagner, Mary J., Sensen, Christoph W., Riabowol, Karl
Since the discovery of ING1 class II tumor suppressors in 1996, five different ING genes (ING1 to ING5) encoding proteins with highly conserved plant homeodomain (PHD) motifs and several splicing...
Phylogenetic Analysis of the ING Family of PHD Finger Proteins (2004)
He, Gordon H.Y., Helbing, Caren C., Wagner, Mary J., Sensen, Christoph W., Riabowol, Karl
Since the discovery of ING1 class II tumour suppressors in 1996, five different ING genes (ING1-5) encoding proteins with highly conserved plant homeodomain (PHD) motifs, and several splicing...
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...
Phylogenetic Analysis of the ING Family of PHD Finger Proteins (2004)
He, Gordon H.Y., Helbing, Caren C., Wagner, Mary J., Sensen, Christoph W., Riabowol, Karl
Since the discovery of ING1 class II tumour suppressors in 1996, five different ING genes (ING1-5) encoding proteins with highly conserved plant homeodomain (PHD) motifs, and several splicing...
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...
Hannaert, Véronique, Brinkmann, Henner, Nowitzki, Ulrich, Lee, Jennifer A., Albert, Marie-Astrid, Sensen, Christoph W., ...
Genomic or cDNA clones for the glycolytic enzyme enolase were isolated from the amitochondriate pelobiont Mastigamoeba balamuthi, from the kinetoplastid Trypanosoma brucei, and from the euglenid...
MAGPIE/EGRET Annotation of the 2.9-Mb Drosophila melanogaster Adh Region (2000)
Gaasterland, Terry, Sczyrba, Alexander, Thomas, Elizabeth, Aytekin-Kurban, Gulriz, Gordon, Paul, Sensen, Christoph W.
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...
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...
Terry Gaasterland, Christoph W. Sensen
A wealth of sequence analysis and interpretation tools enables interested researchers to inspect, query and, ultimately, interpret DNA sequence data. In the context of sequencing an entire genome,...
Sensen, Christoph W., Heimann, Kirsten, Melkonian, Michael
Unialgal cultures of the flagellate algae Cyanophora paradoxa, Haematococcus lacustris, Monomastix sp., Scherffelia dubia and Spermatozopsis similis which contained bacteria were sorted by flow...
Sensen, Christoph W., Heimann, Kirsten, Melkonian, Michael
Unialgal cultures of the flagellate algae Cyanophora paradoxa, Haematococcus lacustris, Monomastix sp., Scherffelia dubia and Spermatozopsis similis which contained bacteria were sorted by flow...
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....
Interspecies data mining to predict novel ING-protein interactions in human
Gordon, Paul MK, Soliman, Mohamed A, Bose, Pinaki, Trinh, Quang, Sensen, Christoph W, Riabowol, Karl
Soh, Jung, Gordon, Paul MK, Taschuk, Morgan L, Dong, Anguo, Ah-Seng, Andrew C, Turinsky, Andrei L, ...
Gordon, Paul M. K., Schütz, Ekkehard, Beck, Julia, Urnovitz, Howard B., Graham, Catherine, Clark, Renee, ...
To gain insight into the disease progression of transmissible spongiform encephalopathies (TSE), we searched for disease-specific patterns in circulating nucleic acids (CNA) in elk and cattle. In a...
Soh, Jung, Turinsky, Andrei L, Trinh, Quang M, Chang, Jasmine, Sabhaney, Ajay, Dong, Xiaoli, ...
We have developed a computational framework for spatiotemporal integration of molecular and anatomical datasets in a virtual reality environment. Using two case studies involving gene expression data...
Soh, Jung, Turinsky, Andrei L, Trinh, Quang M, Chang, Jasmine, Sabhaney, Ajay, Dong, Xiaoli, ...
We have developed a computational framework for spatiotemporal integration of molecular and anatomical datasets in a virtual reality environment. Using two case studies involving gene expression data...