Search Results - "Gotoh, Osamu"

Cooperation of Spaln and Prrn5 for Construction of Gene-Structure-Aware Multiple Sequence Alignment by Gotoh, Osamu

“…Gene-structure-aware multiple sequence alignment (GSA-MSA) is conventionally used as a tool for analyzing evolutionary changes in gene structure, i.e., gain…”
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space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence by Gotoh, Osamu

“…The mapping and alignment of transcripts (cDNA, expressed sequence tag or amino acid sequences) onto a genomic sequence is a fundamental step for genome…”
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Direct mapping and alignment of protein sequences onto genomic sequence by Gotoh, Osamu

“…Motivation: Finding protein-coding genes in a newly determined genomic sequence is the first step toward understanding the content written in the genome…”
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Evolution of Cytochrome P450 Genes from the Viewpoint of Genome Informatics by Gotoh, Osamu

“…Cytochrome P450 (CYP) constitutes a large gene superfamily descended from a single common ancestor. CYP genes are widely distributed in all domains of life…”
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Evolutionary origin of mitochondrial cytochrome P450 by Omura, Tsuneo, Gotoh, Osamu

“…Different molecular species of cytochrome P450 (P450) are distributed between endoplasmic reticulum (microsomes) and mitochondria in animal cells. Plants and…”
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Clinically relevant molecular subtypes and genomic alteration-independent differentiation in gynecologic carcinosarcoma by Gotoh, Osamu, Sugiyama, Yuko, Takazawa, Yutaka, Kato, Kazuyoshi, Tanaka, Norio, Omatsu, Kohei, Takeshima, Nobuhiro, Nomura, Hidetaka, Hasegawa, Kosei, Fujiwara, Keiichi, Taki, Mana, Matsumura, Noriomi, Noda, Tetsuo, Mori, Seiichi

“…Carcinosarcoma (CS) of the uterus or ovary is a rare, aggressive and biphasic neoplasm composed of carcinoma and sarcoma elements. Previous genomic studies…”
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Genomic alterations in gynecological malignancies: histotype-associated driver mutations, molecular subtyping schemes, and tumorigenic mechanisms by Mori, Seiichi, Gotoh, Osamu, Kiyotani, Kazuma, Low, Siew Kee

“…There are numerous histological subtypes (histotypes) of gynecological malignancies, with each histotype considered to largely reflect a feature of the "cell…”
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T-cell complexity and density are associated with sensitivity to neoadjuvant chemoradiotherapy in patients with rectal cancer by Akiyoshi, Takashi, Gotoh, Osamu, Tanaka, Norio, Kiyotani, Kazuma, Yamamoto, Noriko, Ueno, Masashi, Fukunaga, Yosuke, Mori, Seiichi

“…Emerging evidence suggests that an increased density of pre-treatment CD8 + tumor-infiltrating lymphocytes (TILs) is associated with good response to…”
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Sequencing artifacts derived from a library preparation method using enzymatic fragmentation by Tanaka, Norio, Takahara, Akihisa, Hagio, Taichi, Nishiko, Rika, Kanayama, Junko, Gotoh, Osamu, Mori, Seiichi

“…DNA fragmentation is a fundamental step during library preparation in hybridization capture-based, short-read sequencing. Ultra-sonication has been used thus…”
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Two Distinct Tumorigenic Processes in Endometrial Endometrioid Adenocarcinoma by Sugiyama, Yuko, Gotoh, Osamu, Fukui, Nobuyuki, Tanaka, Norio, Hasumi, Katsuhiko, Takazawa, Yutaka, Noda, Tetsuo, Mori, Seiichi

“…Endometrial endometrioid adenocarcinoma (EEA) is conventionally considered to be a single pathologic entity that develops through a hyperplasia-carcinoma…”
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Comparative analysis of information contents relevant to recognition of introns in many species by Iwata, Hiroaki, Gotoh, Osamu

“…The basic process of RNA splicing is conserved among eukaryotic species. Three signals (5' and 3' splice sites and branch site) are commonly used to directly…”
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Genomic determinants impacting the clinical outcome of mogamulizumab treatment for adult T-cell leukemia/lymphoma by Tanaka, Norio, Mori, Seiichi, Kiyotani, Kazuma, Ota, Yuki, Gotoh, Osamu, Kusumoto, Shigeru, Nakano, Nobuaki, Suehiro, Youko, Ito, Asahi, Choi, Ilseung, Ohtsuka, Eiichi, Hidaka, Michihiro, Nosaka, Kisato, Yoshimitsu, Makoto, Imaizumi, Yoshitaka, Iida, Shinsuke, Utsunomiya, Atae, Noda, Tetsuo, Nishikawa, Hiroyoshi, Ueda, Ryuzo, Ishida, Takashi

“…To identify genomic biomarkers for the outcome of mogamulizumabcontaining treatment, an integrated molecular analysis of adult T-cell leukemia/lymphoma (ATL)…”
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Genomic features of Helicobacter pylori‐naïve diffuse‐type gastric cancer by Namikawa, Ken, Tanaka, Norio, Ota, Yuki, Takamatsu, Manabu, Kosugi, Mayuko, Tokai, Yoshitaka, Yoshimizu, Shoichi, Horiuchi, Yusuke, Ishiyama, Akiyoshi, Yoshio, Toshiyuki, Hirasawa, Toshiaki, Amino, Sayuri, Furuya, Rie, Gotoh, Osamu, Kaneyasu, Tomoko, Nakayama, Izuma, Imamura, Yu, Noda, Tetsuo, Fujisaki, Junko, Mori, Seiichi

“…Helicobacter pylori (HP) is a major etiologic driver of diffuse‐type gastric cancer (DGC). However, improvements in hygiene have led to an increase in the…”
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Pathogenicity assessment of variants for breast cancer susceptibility genes based on BRCAness of tumor sample by Yoshida, Reiko, Hagio, Taichi, Kaneyasu, Tomoko, Gotoh, Osamu, Osako, Tomo, Tanaka, Norio, Amino, Sayuri, Yaguchi, Noriko, Nakashima, Eri, Kitagawa, Dai, Ueno, Takayuki, Ohno, Shinji, Nakajima, Takeshi, Nakamura, Seigo, Miki, Yoshio, Hirota, Toru, Takahashi, Shunji, Matsuura, Masaaki, Noda, Tetsuo, Mori, Seiichi

“…Genes involved in the homologous recombination repair pathway—as exemplified by BRCA1, BRCA2, PALB2, ATM, and CHEK2—are frequently associated with hereditary…”
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A multiplex RNA quantification method to determine the absolute amounts of mRNA without reverse transcription by Yokomori, Maasa, Gotoh, Osamu, Murakami, Yasufumi, Fujimoto, Kenzo, Suyama, Akira

“…We have developed a highly sensitive microarray-based method that determines the absolute amounts of mRNA in a total RNA sample in a multiplex manner without…”
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Accurate molecular classification of cancer using simple rules by Wang, Xiaosheng, Gotoh, Osamu

“…One intractable problem with using microarray data analysis for cancer classification is how to reduce the extremely high-dimensionality gene feature data to…”
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Significant Improvement in Accuracy of Multiple Protein Sequence Alignments by Iterative Refinement as Assessed by Reference to Structural Alignments by Gotoh, Osamu

“…The relative performances of four strategies for aligning a large number of protein sequences were assessed by referring to corresponding structural alignments…”
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A method of sample-wise region-set enrichment analysis for DNA methylomics by Minegishi, Ryu, Gotoh, Osamu, Tanaka, Norio, Maruyama, Reo, Chang, Jeffrey T, Mori, Seiichi

“…Gene set analysis has commonly been used to interpret DNA methylome data. However, summarizing the DNA methylation level of a gene is challenging due to…”
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Characterization of moss ent-kaurene oxidase (CYP701B1) using a highly purified preparation by Noguchi, Chisato, Miyazaki, Sho, Kawaide, Hiroshi, Gotoh, Osamu, Yoshida, Yuzo, Aoyama, Yuri

“…CYP701B1 of the moss, Physcomitrella patents, might be a unique cytochrome P450 having the ent-kaurene oxidase (KO) activity occurring in nonvascular plant…”
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Cgaln: fast and space-efficient whole-genome alignment by Nakato, Ryuichiro, Gotoh, Osamu

“…Whole-genome sequence alignment is an essential process for extracting valuable information about the functions, evolution, and peculiarities of genomes under…”
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