01.04.2011 | Götz, Stefan; Arnold, Roland; Sebastián-León, Patricia; Martín-Rodríguez, Samuel; Tischler, Patrick; Jehl, Marc-Andr ..., Bioinformatics, 2011

Motivation: Functional genomics research has expanded enormously in the last decade thanks to the cost reduction in high-throughput technologies and the development of computational tools that generate, standardize and share information on gene and protein function such as the Gene Ontology ...

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01.04.2011 | Shieh, Grace S.; Zheng, Shurong; Johnson, Richard A.; Chang, Yi-Feng; Shimizu, Kunio; Wang, Chia-Chang; Tang, Sen-Lin, Bioinformatics, 2011

Motivation: Most prokaryotic genomes are circular with a single chromosome (called circular genomes), which consist of bacteria and archaea. Orthologous genes (abbreviated as orthologs) are genes directly evolved from an ancestor gene, and can be traced through different species in ...

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01.04.2011 | Linke, Burkhard; Giegerich, Robert; Goesmann, Alexander, Bioinformatics, 2011

Motivation: The rapidly increasing amounts of data available from new high-throughput methods have made data processing without automated pipelines infeasible. As was pointed out in several publications, integration of data and analytic resources into workflow systems provides a solution to ...

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01.04.2011 | Luck, Katja; Travé, Gilles, Bioinformatics, 2011

Motivation: The phage display peptide selection approach is widely used for defining binding specificities of globular domains. PDZ domains recognize partner proteins via C-terminal motifs and are often used as a model for interaction predictions. Here, we investigated to which extent phage ...

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01.04.2011 | Siddle, K. J.; Goodship, J. A.; Keavney, B.; Santibanez-Koref, M. F., Bioinformatics, 2011

Mononucleotide repeats (MNRs) are abundant in eukaryotic genomes and exhibit a high degree of length variability due to insertion and deletion events. However, the relationship between these repeats and mutation rates in surrounding sequences has not been systematically investigated. We have ...

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15.03.2011 | Tong, Mark Y.; Cassa, Christopher A.; Kohane, Isaac S., Bioinformatics, 2011

Summary: Accurate annotations of genomic variants are necessary to achieve full-genome clinical interpretations that are scientifically sound and medically relevant. Many disease associations, especially those reported before the completion of the HGP, are limited in applicability because of ...

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15.03.2011 | Down, Thomas A.; Piipari, Matias; Hubbard, Tim J. P., Bioinformatics, 2011

Summary: Dalliance is a new genome viewer which offers a high level of interactivity while running within a web browser. All data is fetched using the established distributed annotation system (DAS) protocol, making it easy to customize the browser and add extra data. Availability and ...

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15.03.2011 | Louhimo, Riku; Hautaniemi, Sampsa, Bioinformatics, 2011

Summary: Gene copy number and DNA methylation alterations are key regulators of gene expression in cancer. Accordingly, genes that show simultaneous methylation, copy number and expression alterations are likely to have a key role in tumor progression. We have implemented a novel software ...

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15.03.2011 | Chignola, Francesca; Mari, Silvia; Stevens, Tim J.; Fogh, Rasmus H.; Mannella, Valeria; Boucher, Wayne; Musco, Giovanna, Bioinformatics, 2011

Summary: We present here the freely available Metabolomics Project resource specifically designed to work under the CcpNmr Analysis program produced by CCPN (Collaborative Computing Project for NMR) (Vranken et al., 2005, The CCPN data model for NMR spectroscopy: development of a software ...

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15.03.2011 | Hao, Yanqi; Merkoulovitch, Anna; Vlasblom, James; Pu, Shuye; Turinsky, Andrei L.; Roudeva, Denitza; Turner, Brian; G ..., Bioinformatics, 2011

Motivation: Protein interaction networks contain a wealth of biological information, but their large size often hinders cross-organism comparisons. We present OrthoNets, a Cytoscape plugin that displays protein–protein interaction (PPI) networks from two organisms simultaneously, ...

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