Biomedical subjects

Tetsuo Shibuya

Publications and source records attributed to Tetsuo Shibuya.

3 recordsLinked to original sources

PubMed2003

The web server of IBM's Bioinformatics and Pattern Discovery group.

We herein present and discuss the services and content which are available on the web server of IBM's Bioinformatics and Pattern Discovery group. The server is operational around the clock and provides access to a variety of methods that have been published by the group's members and collaborators. The available tools correspond to applications ranging from the discovery of patterns in streams of events and the computation of multiple sequence alignments, to the discovery of genes in nucleic acid sequences and the interactive annotation of amino acid sequences. Additionally, annotations for more than 70 archaeal, bacterial, eukaryotic and viral genomes are available on-line and can be searched interactively. The tools and code bundles can be accessed beginning at http://cbcsrv.watson.ibm.com/Tspd.html whereas the genomics annotations are available at http://cbcsrv.watson.ibm.com/Annotations/.

Computational Biology↗

PubMed2002

Dictionary-driven prokaryotic gene finding.

Gene identification, also known as gene finding or gene recognition, is among the important problems of molecular biology that have been receiving increasing attention with the advent of large scale sequencing projects. Previous strategies for solving this problem can be categorized into essentially two schools of thought: one school employs sequence composition statistics, whereas the other relies on database similarity searches. In this paper, we propose a new gene identification scheme that combines the best characteristics from each of these two schools. In particular, our method determines gene candidates among the ORFs that can be identified in a given DNA strand through the use of the Bio-Dictionary, a database of patterns that covers essentially all of the currently available sample of the natural protein sequence space. Our approach relies entirely on the use of redundant patterns as the agents on which the presence or absence of genes is predicated and does not employ any additional evidence, e.g. ribosome-binding site signals. The Bio-Dictionary Gene Finder (BDGF), the algorithm's implementation, is a single computational engine able to handle the gene identification task across distinct archaeal and bacterial genomes. The engine exhibits performance that is characterized by simultaneous very high values of sensitivity and specificity, and a high percentage of correctly predicted start sites. Using a collection of patterns derived from an old (June 2000) release of the Swiss-Prot/TrEMBL database that contained 451 602 proteins and fragments, we demonstrate our method's generality and capabilities through an extensive analysis of 17 complete archaeal and bacterial genomes. Examples of previously unreported genes are also shown and discussed in detail.

Algorithms↗

PubMed2002

Metachronous adenocarcinoma occurring at a colostomy site after abdominoperineal resection for rectal carcinoma.

Carcinomas rarely occur at the site of a colostomy. A 73-year-old man underwent abdominoperineal resection (Miles' surgical procedure) for rectal carcinoma in September 1988. He did not return to the hospital until September 1995, when he was admitted with stricture of the stoma. Neither tumor nor ulcer was detected at the stoma. The tip of the doctor's little finger was able to pass through the stoma, and manual expanding alleviated the stricture. The patient did not return to the hospital again until August 1996, at age 81 years, when he visited the hospital because of complete stricture of the stoma. A biopsy revealed an adenomatous carcinoma, but the results of various examinations suggested no metastasis. A portion of the intestine, including the stoma and surrounding skin, was resected, and a new stoma was created in the descending colon. We report this rare carcinoma occurring at the site of a colostomy, and we review the literature.

Adenocarcinoma↗