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At least 1,171 records · Page 65Linked to original sources
PubMed2003

Genome-wide loss of heterozygosity analysis from laser capture microdissected prostate cancer using single nucleotide polymorphic allele (SNP) arrays and a novel bioinformatics platform dChipSNP.

Oligonucleotide arrays that detect single nucleotide polymorphisms were used to generate genome-wide loss of heterozygosity (LOH) maps from laser capture microdissected paraffin-embedded samples using as little as 5 ng of DNA. The allele detection rate from such samples was comparable with that obtained with standard amounts of DNA prepared from frozen tissues. A novel informatics platform, dChipSNP, was used to automate the definition of statistically valid regions of LOH, assign LOH genotypes to prostate cancer samples, and organize by hierarchical clustering prostate cancers based on the pattern of LOH. This organizational strategy revealed apparently distinct genetic subsets of prostate cancer.

Alleles↗
PubMed2003

Bioinformatic strategies for better understanding of immune function.

Novartis Foundation sponsored a Symposium which brought together a group of experimental immunologists, theoretical immunologists, and bioinformaticians to discuss the new field of immunoinformatics. The discussion focused on immunological databases, antigen processing and presentation, immunogenomics, host-pathogen interactions, and mathematical modelling of the immune system. A main conclusion of the meeting is the critical role played by immunoinformatics in current immunology research. In particular, immunoinformatics provides a foundation for the emerging fields of systems immunology and immunogenomics.

Allergy and Immunology↗
PubMed2003

[Bioinformatic analysis of dengue virus cDNAs and design of oligonucleotide probes for microarray detection of the virus].

OBJECTIVE: To design oligonucleotide probes for microarray detection of dengue virus. METHODS: By analyzing the cDNAs of dengue viruses of 4 different serotypes with BLAST program, a group of specific sequences for the candidate probes was acquired. Oligo6.0 software was applied to analyze the candidates to select the probes with high specificity, identical length and similar melting temperature (Tm). RESULT: Altogether 48 oligonucleotide probes were designed, and deposited on oligonucleotide chips as the microarray for dengue virus detection. CONCLUSION: BLAST program and Oligo6.0 software are simple and effective means for designing the oligonucleotide probes.

Base Sequence↗
PubMed2003

A new addition to the structural bioinformatics toolbox: 3D models of short bioactive peptides from multiple sequences using feedback restrained molecular dynamics (FRMD).

Modem molecular biology techniques allow the use of new approaches for the 3D mapping of 1D information. Molecular biology techniques are capable of producing large amounts of 1D information (sequences) from a number of different sources (phage displays, ESTs, etc.). In this work, we present a technique that takes advantage of large sets of 1D information and increasingly available computer power to create 3D models. For the purpose of validation the technique is first applied to the modeling of an erythropoietin analog of known 3D structure from 1D information only. The technique is then used to model the immunoreactive region of echinococcus granulosus AgB based on phage raised mimotopes for which there is no previous structural information. The technique here presented is of general application to similar problems where 1D information is available and structure activity relationships (SAR) is needed.

Animals↗
PubMed2003

Viral bioinformatics: computational views of host and pathogen.

Wherever cellular life occurs, viruses are also found. As a result, complex organism and cellular antiviral responses co-evolve with virally encoded countermeasures. Since viruses co-opt or interfere with specific cellular pathways during their replication, knowledge of viral genome sequences has helped fundamental understanding of host biology. During viral infection, shifts in the balance between host and viral biological processes result in acute or chronic viral disease pathology accompanied with either active viral replication, viral containment/persistence or viral clearance. Studying host-virus interactions at the level of single gene effects, however, fails to produce a global systems-level understanding. This should now be achievable in the context of complete host and pathogen genome sequences. New experimental methods and computational approaches are rapidly developing, allowing global views of dynamic viral and cellular molecular mechanisms. Systems level virology using DNA microarrays and specific viral data resources will reveal the detailed cellular context in which viruses replicate, highlighting common and distinct antiviral mechanisms, the effect of different host cell gene expression programs, and the response of cells to similar or diverse virus types. Ultimately, microbiology and immunology will tend towards a systems-level view of how host and pathogen interact.

Amino Acid Motifs↗
PubMed2003

Bioinformatics for medical diagnostics: assessment of microarray data in the context of clinical databases.

MOTIVATION: To identify genes suitable for medical diagnostics microarray data is assessed in the context of clinical databases, which store complex information about the patient phenotype. The wealth of data and lacking standards make it difficult to analyse this kind of data. RESULTS: We present a workflow for exploratory analysis of microarray data together with clinical data consisting of four steps: definition of clinically meaningful research questions in a masterfile, generation of analysis files, selection and characterization of differentially expressed genes, and estimation of classification accuracy. We applied this workflow to large data sets from the field of cardiology and oncology (n~500 patients). Systematic data management of microarray data and clinical data helps to make results more transparent and comparable.

Cardiology↗
PubMed2003

The NCI/CIT microArray database (mAdb) system - bioinformatics for the management and analysis of Affymetrix and spotted gene expression microarrays.

A scalable, modular, enterprise-level system for both microarray databasing and analysis over the Internet has been developed over the past four years by the National Cancer Institute's Center for Cancer Research in collaboration with NIH's Center for Information Technology. This completely Web-based system, called mAdb (for microArray database), is currently supporting over 810 registered users and collaborators at NIH and contains over 22,000 microarray experiments, making it one of the largest collections of microarray data in existence. In addition, the mAdb system has been ported for the Netherlands Cancer Institute, the Genome Institute of Singapore, and the CDC. This system has been used for a wide variety of scientific experiments spanning the range from cancer to studies of early development, and for human, mouse, rat, yeast, and numerous microbial organisms.

Animals↗