P083 - GCB 2006 - German Conference on Bioinformatics 2006
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- KonferenzbeitragGenomic variation and incipient speciation in Arabidopsis thaliana(German Conference on Bioinformatics, 2006) Weigel, Detlef
- KonferenzbeitragMPI-ClustDB: A fast string matching strategy utilizing parallel computing(German Conference on Bioinformatics, 2006) Hamborg, Thomas; Kleffe, JürgenClustDB is a tool for the identification of perfect matches in large sets of sequences. It is faster and can handle at least 8 times more data than VMATCH, the most memory efficient exact program currently available. Still ClustDB needs about four hours to compare all Human ESTs. We therefore present a distributed and parallel implementation of ClustDB to reduce the execution time. It uses a message-passing library called MPI and runs on distributed workstation clusters with significant runtime savings. MPI-ClustDB is written in ANSI C and freely available on request from the authors.
- KonferenzbeitragFunctional evaluation of domain-domain interactions and human protein interaction networks(German Conference on Bioinformatics, 2006) Schlicker, Andreas; Huthmacher, Carola; Ramírez, Fidel; Lengauer, Thomas; Albrecht, MarioLarge amounts of protein and domain interaction data are being produced by experimental high-throughput techniques and computational approaches. To gain insight into the value of the provided data, we used our new similarity measure based on the Gene Ontology to evaluate the molecular functions and biological processes of interacting proteins or domains. The applied measure particularly addresses the frequent annotation of proteins or domains with multiple Gene Ontology terms. Using our similarity measure, we compare predicted domain-domain and human protein-protein interactions with experimentally derived interactions. The results show that our similarity measure is of significant benefit in quality assessment and confidence ranking of domain and protein networks. We also derive useful confidence score thresholds for dividing domain interaction predictions into subsets of low and high confidence.
- KonferenzbeitragComparison of human protein-protein interaction maps(German Conference on Bioinformatics, 2006) Futschik, Matthias E.; Chaurasia, Gautam; Wanker, Erich; Herzel, HanspeterLarge-scale mappings of protein-protein interactions have started to give us new views of the complex molecular mechanisms inside a cell. After initial projects to systematically map protein interactions in model organisms such as yeast, worm and fly, researchers have begun to focus on the mapping of the human interactome. To tackle this enormous challenge, different approaches have been proposed and pursued. While several large-scale human protein interaction maps have recently been published, their quality remains to be critically assessed. We present here a first comparative analysis of eight currently available large-scale maps with a total of over 10000 unique proteins and 57000 interactions included. They are based either on literature search, orthology or by yeast-two-hybrid assays. Comparison reveals only a small, but statistically significant overlap. More importantly, our analysis gives clear indications that all interaction maps suffer under selection and detection biases. These results have to be taken into account for future assembly of the human interactome.
- KonferenzbeitragAnnotation-based distance measures for patient subgroup discovery in clinical microarray studies(German Conference on Bioinformatics, 2006) Lottaz, Claudio; Toedling, Joern; Spang, RainerBackground: Clustering algorithms are widely used in the analysis of microarray data. In clinical studies, they are often applied to find groups of co-regulated genes. Clustering, however, can also stratify patients by similarity of their gene expression profiles, thereby defining novel disease entities based on molecular characteristics. Several distance-based cluster algorithms have been suggested, but little attention has been given to the choice of the distance measure between patients. Even with the Euclidean metric, including and excluding genes from the analysis leads to different distances between the same objects, and consequently different clustering results. Methodology: We describe a novel clustering algorithm, in which gene selection is used to derive biologically meaningful clusterings of samples. Our method combines expression data and functional annotation data. According to gene annotations, candidate gene sets with specific functional characterizations are generated. Each set defines a different distance measure between patients, and consequently different clusterings. These clusterings are filtered using a novel resampling based significance measure. Significant clusterings are reported together with the underlying gene sets and their functional definition. Conclusions: Our method reports clusterings defined by biologically focused sets of genes. In annotation driven clusterings, we have recovered clinically relevant patient subgroups through biologically plausible sets of genes, as well as novel subgroupings. We conjecture that our method has the potential to reveal so far unknown, clinically relevant classes of patients in an unsupervised manner.
- KonferenzbeitragDocking protein domains using a contact map representation(German Conference on Bioinformatics, 2006) Lise, Stefano; Jones, David
- KonferenzbeitragMicroarray layout as quadratic assignment problem(German Conference on Bioinformatics, 2006) Carvalho Jr., Sérgio A. de; Rahmann, SvenThe production of commercial DNA microarrays is based on a light-directed chemical synthesis driven by a set of masks or micromirror arrays. Because of the natural properties of light and the ever shrinking feature sizes, the arrangement of the probes on the chip and the order in which their nucleotides are synthesized play an important role on the quality of the final product. We propose a new model called conflict index for evaluating microarray layouts, and we show that the probe placement problem is an instance of the quadratic assignment problem (QAP), which opens up the way for using QAP heuristics. We use an existing heuristic called GRASP to design the layout of small artificial chips with promising results. We compare this approach with the best known algorithm and describe how it can be combined with other existing algorithms to design the latest million-probe microarrays.
- KonferenzbeitragComparative analysis of cyclic sequences: Viroids and other small circular RNAs(German Conference on Bioinformatics, 2006) Mosig, Axel; Hofacker, Ivo L.; Stadler, Peter F.The analysis of small circular sequences requires specialized tools. While the differences between linear and circular sequences can be neglected in the case of long molecules such as bacterial genomes since in practice all analysis is performed in sequence windows, this is not true for viroids and related sequences which are usually only a few hundred basepairs long. In this contribution we present basic algorithms and corresponding software for circular RNAs. In particular, we discuss the problem of pairwise and multiple cyclic sequence alignments with affine gap costs, and an extension of a recent approach to circular RNA folding to the computation of consensus structures.
- KonferenzbeitragA novel, comprehensive method to detect and predict protein-protein interactions applied to the study of vesicular trafficking(German Conference on Bioinformatics, 2006) Winter, Christof; Baust, Thorsten; Hoflack, Bernard; Schroeder, MichaelMotivation. Computational methods to predict protein-protein interactions are of great need. They can help to formulate hypotheses, guide experimental research and serve as additional measures to assess the quality of data obtained in high-throughput interaction experiments. Here, we describe a fully automated threestep procedure to predict and confirm protein-protein interactions. By maximising the information from text mining of the biomedical literature, data from interaction databases, and from available protein structures, we aim at generating a comprehensive picture of known and novel potential interactions between a given set of proteins. Results. A recent proteomics assay to identify the protein machinery involved in vesicular trafficking between the biosynthetic and the endosomal compartments revealed 35 proteins that were found as part of membrane coats on liposomes. When applying our method to this data set, we are able to reconstruct most of the interactions known to the molecular biologist. In addition, we predict novel interactions, among these potential linkers of the AP-1 and the Arp2/3 complex to membrane-bound proteins as well as a potential GTPase-GTPase effector interaction. Conclusions. Our method allows for a comprehensive network reconstruction that can assist the molecular biologist. Predicted interactions are backed up by structural or experimental evidence and can be inferred at varying levels of confidence. Our method pinpoints existing key interactions and can facilitate the generation of hypotheses.
- KonferenzbeitragImaging-based systems biology(German Conference on Bioinformatics, 2006) Myers, Gene