Reverse engineering of genetic networks generally requires establishing correlative behavior within and between a very large number of genes. This becomes a difficult analytical problem for even a few hundred genes an...
详细信息
ISBN:
(纸本)0769521940
Reverse engineering of genetic networks generally requires establishing correlative behavior within and between a very large number of genes. This becomes a difficult analytical problem for even a few hundred genes and the difficulty tends to grow exponentially as more genes are examined Using a hybrid data analysis method known as Fractal Genomics Modeling (FGM), this problem is reduced to examining correlative behavior within small gene groups that can then be compared and integrated to produce a picture of larger networks using a type of shotgun approach. We have applied FGM toward examining genetic networks involved in HIV infection in the brain. These networks have relevance both to processes related to HIV infection and neurodegenerative disorders. Our preliminary findings have produced conjectures of related pathways and networks as well new candidates for genetic markers in HIV brain infection. Evidence has also been produced which appears to show the presence of a hierarchical network structure within the genes studied We will discuss the background and methodology of FGM as well as our recent findings.
World-wide structural genomics initiatives are rapidly accumulating structures for which limited functional information is available. Additionally, state-of-the art structural prediction programs are now capable of ge...
详细信息
ISBN:
(纸本)0769521940
World-wide structural genomics initiatives are rapidly accumulating structures for which limited functional information is available. Additionally, state-of-the art structural prediction programs are now capable of generating at least low resolution structural models of target proteins. Accurate detection and classification of functional sites within both solved and modelled protein structures therefore represents an important challenge. We present a fully automatic site detection method, FuncSite, that uses neural network classifiers to predict the location and type of functionally important sites in protein structures. The method is designed primarily to require only backbone residue positions without the need for specific side-chain atoms to be present. In order to highlight effective site detection in low resolution structural models FuncSite was used to screen model proteins generated using mGenTHREADER on a set of newly released structures. We found effective metal site detection even for moderate quality protein models illustrating the robustness of the method.
作者：
Karp, PSRI Int
Bioinformat Res Grp Menlo Pk CA 94025 USA
Pathway bioinformatics is a subfield of bioinformatics that is concerned with pathway algorithms, ontologies, visualizations, and databases [4]. This talk will provide an overview of the pathway databases and software...
详细信息
The paper introduces the knowledge engineering (KE) approach for the modeling and the discovery of new knowledge in bioinformatics. This approach extends the machine learning approach with various rule extraction and ...
详细信息
ISBN:
(纸本)0780382781
The paper introduces the knowledge engineering (KE) approach for the modeling and the discovery of new knowledge in bioinformatics. This approach extends the machine learning approach with various rule extraction and other knowledge representation procedures. Examples of the KE approach, and especially of one of the recently developed techniques - evolving connectionist systems (ECOS), to challenging problems in bioinformatics are given, that include: DNA sequence analysis, microarray gene expression profiling, protein structure prediction, finding gene regulatory networks, medical prognostic systems, computational neurogenetic modeling.
A phylogenetic tree represents the evolutionary history of a group of organisms. In this work, we introduce a novel interactive tool for constructing phylogenetic trees, Phylogenetic Tree Construction package. The pac...
详细信息
ISBN:
(纸本)0769520006
A phylogenetic tree represents the evolutionary history of a group of organisms. In this work, we introduce a novel interactive tool for constructing phylogenetic trees, Phylogenetic Tree Construction package. The package supports four well-known algorithms, Unweighted Pair Group Method using Arithmetic average, Neighbor Joining, Fitch Margoliash, and Maximum Parsimony.
Cutting-edge biological and bioinformatics research seeks a systems perspective through the analysis of multiple types of high-throughput and other experimental data for the same sample. systems-level analysis require...
详细信息
ISBN:
(纸本)0769523447
Cutting-edge biological and bioinformatics research seeks a systems perspective through the analysis of multiple types of high-throughput and other experimental data for the same sample. systems-level analysis requires the integration and fusion of such data, typically through advanced statistics and mathematics. Visualization is a complementary computational approach that supports integration and analysis of complex data or its derivatives. We present a bioinformatics visualization prototype, Juxter, which depicts categorical information derived from or assigned to these diverse data for the purpose of comparing patterns across categorizations. The visualization allows users to easily, discern correlated and anomalous patterns in the data. These patterns, which might not be detected automatically by, algorithms, may, reveal valuable information leading to insight and discovery. We describe the visualization and interaction capabilities and demonstrate its utility in a new field, metagenomics, which combines molecular biology and genetics to identify and characterize genetic material from multi-species microbial samples.
This project represents an interdisciplinary approach to integrating computational methods into the knowledge-discovery process associated with understanding biological systems impacted by the loss or destruction of s...
详细信息
ISBN:
(纸本)0769520006
This project represents an interdisciplinary approach to integrating computational methods into the knowledge-discovery process associated with understanding biological systems impacted by the loss or destruction of sensitive habitats. We specifically developed bioinformatics tools for the study of (1) beach mouse communities and (2) marginal fish habitats. Data mining was used in these projects to intelligently query databases and to elucidate broad patterns that facilitate overall data interpretation. Visualization techniques that were developed present mined data in ways where context, perceptual cues, and spatial reasoning skills can be applied to uncover significant trends in behavioral patterns, habitat use, species diversity, and community composition.
作者：
D. PuiuCSBC
Virginia Commonwealth University USA
SUPERCONTIGS is a genome-finishing tool that orders, orients and groups contigs based on clone pair information and an alignment with a related genome. The program can be used in the genome finishing and gap closing p...
详细信息
SUPERCONTIGS is a genome-finishing tool that orders, orients and groups contigs based on clone pair information and an alignment with a related genome. The program can be used in the genome finishing and gap closing process. SUPERCONTIGS is a Perl script that runs on Unix-like systems. It is available at http://***/csbc/bccl/*** as a copy-left public domain program.
暂无评论