Atsushi Ogiwara

Research Field

Sequence (biology)

10.11234/gi1990.8.320

Cite

Citations (1)

Nested Case Control Study of Proteomic Biomarkers for Interstitial Lung Disease in Japanese Patients With Non-Small Cell Lung Cancer Treated With Erlotinib

Annals of Oncology (2012)

Nobuyuki Katakami Shinji Atagi Hiroshige Yoshioka M. Fukuoka Atsushi Ogiwara

10.1016/s0923-7534(20)32800-3

Cite

Citations (0)

Quantitative Proteomic Analysis System: i-OPAL

Journal of Computer Chemistry Japan (2010)

Mitsuhiro Kanazawa Hisae Anyoji Hsiao-kun Tu Umpei NAGASHIMI Atsushi Ogiwara

Recently, significant improvements have been shown in proteomics, an analytical technology recognized as a method to discover biomarkers. Several methods for proteome differential display have been developed to discover biomarkers, and these are based on labeling methods such as ICAT™ reagent. These labeling methods are not easily able to detect biomarkers in complex biological samples, and they have several issues such as the limitation of the modification site and the production of artificial errors. We therefore developed a computational quantitative proteomic analysis system i-OPAL (internal standard guided Optimal Profile ALignment) based on LC-MS measurements for biomarker discovery. This system can provide extensive quantitative analysis because it does not involve any artificial labels that might cause sampling bias and limitation of quantifiable proteins.

Proteome

Biomarker Discovery

10.2477/jccj.h2117

Cite

Citations (0)

Automatic Procedure to Extract Signature Pentapeptides from the Protein Sequence Database

Ikuo Uchiyama Atsushi Ogiwara Zenmei Ohkubo Minoru Kanehisa

Signature (topology)

Sequence (biology)

10.11234/gi1990.4.255

Cite

Citations (1)

A WWW Database of Bacillus Subtilis ORFs determined by the International Project of Sequencing B. Subtilis Genome

Proceedings Genome Informatics Workshop/Genome informatics (1995)

Atsushi Ogiwara Toshiyuki Takagi Naotaka Ogasawara

ORFS

10.11234/gi1990.6.162

Cite

Citations (2)

Multiple Alignment by Parallel Simulated Annealing

Masato Ishikawa Tomoyuki Toya Masaki Hoshida Katsumi Nitta Atsushi Ogiwara

10.11234/gi1990.2.112

Cite

Citations (2)

Sequence Motif Analysis and Retrieval Tool

Atsushi Ogiwara Ikuo Uchiyama Minoru Kanehisa

Motif (music)

Sequence motif

Sequence (biology)

10.11234/gi1990.4.402

Cite

Citations (2)

MRMPROBS suite for metabolomics using large-scale MRM assays

Bioinformatics (2014)

Hiroshi Tsugawa Mitsuhiro Kanazawa Atsushi Ogiwara Masanori Arita

Summary: We developed new software environment for the metabolome analysis of large-scale multiple reaction monitoring (MRM) assays. It supports the data format of four major mass spectrometer vendors and mzML common data format. This program provides a process pipeline from the raw-format import to high-dimensional statistical analyses. The novel aspect is graphical user interface-based visualization to perform peak quantification, to interpolate missing values and to normalize peaks interactively based on quality control samples. Together with the software platform, the MRM standard library of 301 metabolites with 775 transitions is also available, which contributes to the reliable peak identification by using retention time and ion abundances. Availability and implementation: MRMPROBS is available for Windows OS under the creative-commons by-attribution license at http://prime.psc.riken.jp. Contact: hiroshi.tsugawa@riken.jp Supplementary information: Supplementary Data are available at Bioinformatics online.

Software suite

Graphical user interface

Identification

MIT License

10.1093/bioinformatics/btu203

Cite

Citations (90)

Automatic construction of a dictionary of sequence motifs that characterize groups of similar proteins

Proceedings Genome Informatics Workshop/Genome informatics (1991)

Atsushi Ogiwara Ikuo Uchiyama Minoru Kanehisa

Sequence (biology)

Sequence motif