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At least 901 records · Page 50Linked to original sources
PubMed2000

A brief history of genome research and bioinformatics in France.

The development of in silico genomics has progressed slowly in France for a number of political reasons. Two administrative organizations, the Groupement de Recherche sur les Génomes (GREG) and the Groupement de Recherche 1029 (GDR 1029) of the Centre National de la Recherche Scientifique (CNRS) have been established. These organizations have created the dynamics that hopefully will place France (which coordinated consortia that completed several of the first large microbial genomes) among the developed nations that support Large-Scale Biology.

Computational Biology↗
PubMed2000

PIR: a new resource for bioinformatics.

UNLABELLED: The Protein Information Resource (PIR) has greatly expanded its Web site and developed a set of interactive search and analysis tools to facilitate the analysis, annotation, and functional identification of proteins. New search engines have been implemented to combine sequence similarity search results with database annotation information. The new PIR search systems have proved very useful in providing enriched functional annotation of protein sequences, determining protein superfamily-domain relationships, and detecting annotation errors in genomic database archives. AVAILABILITY: http://pir.georgetown.edu/. CONTACT: mcgarvey@nbrf.georgetown.edu

Animals↗
PubMed2001

ISYS: a decentralized, component-based approach to the integration of heterogeneous bioinformatics resources.

MOTIVATION: Heterogeneity of databases and software resources continues to hamper the integration of biological information. Top-down solutions are not feasible for the full-scale problem of integration across biological species and data types. Bottom-up solutions so far have not integrated, in a maximally flexible way, dynamic and interactive graphical-user-interface components with data repositories and analysis tools. RESULTS: We present a component-based approach that relies on a generalized platform for component integration. The platform enables independently-developed components to synchronize their behavior and exchange services, without direct knowledge of one another. An interface-based data model allows the exchange of information with minimal component interdependency. From these interactions an integrated system results, which we call ISYSf1.gif" BORDER="0">. By allowing services to be discovered dynamically based on selected objects, ISYS encourages a kind of exploratory navigation that we believe to be well-suited for applications in genomic research.

Arabidopsis↗
PubMed2002

A bioinformatics tool to select sequences for microarray studies of mouse models of oncogenesis.

UNLABELLED: One of the challenges to the effective utilization of cDNA microarray analysis in mouse models of oncogenesis is the choice of a critical set of probes that are informative for human disease. Given the thousands of genes with a potential role in human oncogenesis and the hundreds of thousands of mouse sequences available for use as probes, selection of an informative set of mouse probes can be an overwhelming task. We have developed a web based sequence mining tool using DataBase Independent (DBI) Perl to annotate publicly available sequences. The Mouse Oncochip Design Tool uses the Mouse Genome Database (MGD) developed and maintained by the Jackson Laboratories for mouse DNA sequences. There are over 380 000 sequences in their database. The output list has been ordered to present the genes more likely to be informative in a mouse model of human cancer using a candidate set of oncogenes to order the list. Mouse sequences that represent genes that are homologous with a member of a human oncogene set are listed first. In addition it provides a set of links for information on clone source gene function. CONTACT: http://nciarray.nci.nih.gov/cgi-bin/me/mouse_design.cgi

Animals↗
PubMed2002

A bioinformatic strategy to rapidly characterize cDNA libraries.

MOTIVATION: Complementary DNA libraries can define the genetic constituents of specific cells and/or tissues. Their sequencing will illuminate the transcriptome but it is a monumental task requiring considerable resources. RESULTS: We have employed a computational search in conjunction with a microarray-based strategy to alleviate the impediments of deriving a consensus of records that describe testis gene expression. This strategy identified 5681 unique testes-expressed genes of which 3265 were previously portrayed in the UniGene database. Interestingly, a total of 2416 novel testes-expressed genes were identified. This clearly demonstrates that microarrays can be used to rapidly discover a large number of new transcripts.

Adolescent↗
PubMed2003

Wavelets in bioinformatics and computational biology: state of art and perspectives.

MOTIVATION: At a recent meeting, the wavelet transform was depicted as a small child kicking back at its father, the Fourier transform. Wavelets are more efficient and faster than Fourier methods in capturing the essence of data. Nowadays there is a growing interest in using wavelets in the analysis of biological sequences and molecular biology-related signals. RESULTS: This review is intended to summarize the potential of state of the art wavelets, and in particular wavelet statistical methodology, in different areas of molecular biology: genome sequence, protein structure and microarray data analysis. I conclude by discussing the use of wavelets in modeling biological structures.

Algorithms↗