Works matching AU Akiyama, Yutaka

Results: 54

Myopericytoma in urinary bladder: a case report.

Published in:

2017

By:

Takahiro Nagai;
Toshio Kamimura;
Kaoru Itou;
Masato Fujii;
Hiromasa Tsukino;
Shoichiro Mukai;
Toshiyuki Kamoto;
Yutaka Akiyama;
Hiroaki Kataoka;
Nagai, Takahiro;
Kamimura, Toshio;
Itou, Kaoru;
Fujii, Masato;
Tsukino, Hiromasa;
Mukai, Shoichiro;
Akiyama, Yutaka;
Kataoka, Hiroaki;
Kamoto, Toshiyuki

Publication type:

journal article

Spresso: an ultrafast compound pre-screening method based on compound decomposition.

Published in:

Bioinformatics, 2017, v. 33, n. 23, p. 3836, doi. 10.1093/bioinformatics/btx178

By:

Keisuke Yanagisawa;
Shunta Komine;
Suzuki, Shogo D.;
Masahito Ohue;
Takashi Ishida;
Yutaka Akiyama

Publication type:

Article

Faster sequence homology searches by clustering subsequences.

Published in:

Bioinformatics, 2015, v. 31, n. 8, p. 1183, doi. 10.1093/bioinformatics/btu780

By:

Shuji Suzuki;
Masanori Kakuta;
Takashi Ishida;
Yutaka Akiyama

Publication type:

Article

Faster sequence homology searches by clustering subsequences.

Published in:

Bioinformatics, 2015, v. 31, n. 7, p. 1183, doi. 10.1093/bioinformatics/btu780

By:

Shuji Suzuki;
Masanori Kakuta;
Takashi Ishida;
Yutaka Akiyama

Publication type:

Article

MEGADOCK 4.0: an ultra–high-performance protein–protein docking software for heterogeneous supercomputers.

Published in:

Bioinformatics, 2014, v. 30, n. 22, p. 3281

By:

Matsuzaki, Yuri;
Ishida, Takashi;
Ohue, Masahito;
Shimoda, Takehiro;
Akiyama, Yutaka;
Suzuki, Shuji

Publication type:

Article

Multiple hepatic peribiliary cysts with cirrhosis.

Published in:

Journal of Gastroenterology, 2004, v. 39, n. 4, p. 384, doi. 10.1007/s00535-003-1307-4

By:

Seguchi, Tomoko;
Akiyama, Yutaka;
Itoh, Hiroshi;
Tanaka, Hiroyuki;
Naganuma, Seiji;
Nagaike, Koki;
Uchiyama, Shuichiro;
Kataoka, Hiroaki

Publication type:

Article

Improved Large-Scale Homology Search by Two-Step Seed Search Using Multiple Reduced Amino Acid Alphabets.

Published in:

Genes, 2021, v. 12, n. 9, p. 1455, doi. 10.3390/genes12091455

By:

Takabatake, Kazuki;
Izawa, Kazuki;
Akikawa, Motohiro;
Yanagisawa, Keisuke;
Ohue, Masahito;
Akiyama, Yutaka

Publication type:

Article

A rare association between true thymic hyperplasia and thyroid follicular tumor: a case report.

Published in:

2020

By:

Kiwaki, Takumi;
Tanaka, Hiroyuki;
Akiyama, Yutaka;
Akaki, Mayumi;
Tomita, Masaki;
Kataoka, Hiroaki

Publication type:

Case Study

Primary cutaneous Langerhans cell histiocytosis showing malignant phenotype in an elderly woman: report of a fatal case.

Published in:

Journal of Cutaneous Pathology, 2001, v. 28, n. 7, p. 371, doi. 10.1034/j.1600-0560.2001.280707.x

By:

Itoh, Hiroshi;
Miyaguni, Hitoshi;
Kataoka, Hiroaki;
Akiyama, Yutaka;
Tateyama, Sunao;
Marutsuka, Kousuke;
Asada, Yujiro;
Ogata, Katsumi;
Koono, Masashi

Publication type:

Article

Optimizing substitution matrices by separating score distributions.

Published in:

Bioinformatics, 2004, v. 20, n. 6, p. 863, doi. 10.1093/bioinformatics/btg494

By:

Yuichiro Hourai;
Tatsuya Akutsu;
Yutaka Akiyama

Publication type:

Article

FORTE: a profileprofile comparison tool for protein fold recognition.

Published in:

Bioinformatics, 2004, v. 20, n. 4, p. 594, doi. 10.1093/bioinformatics/btg474

By:

Kentaro Tomii;
Yutaka Akiyama

Publication type:

Article

Quick selection of representative protein chain sets based on customizable requirements.

Published in:

Bioinformatics, 2000, v. 16, n. 6, p. 520, doi. 10.1093/bioinformatics/16.6.520

By:

Noguchi, Tamotsu;
Onizuka, Kentaro;
Ando, Makoto;
Matsuda, Hideo;
Akiyama, Yutaka

Publication type:

Article

A case of carcinoma ex pleomorphic adenoma arising from multinodular pleomorphic adenoma of the buccal region.

Published in:

Clinical Case Reports, 2019, v. 7, n. 10, p. 1994, doi. 10.1002/ccr3.2417

By:

Yamamoto, Koji;
Sato, Yuichiro;
Kondo, Yuudai;
Tanaka, Hiroyuki;
Akiyama, Yutaka;
Yamashita, Yoshihiro;
Kataoka, Hiroaki

Publication type:

Article

GHOSTX: An Improved Sequence Homology Search Algorithm Using a Query Suffix Array and a Database Suffix Array.

Published in:

PLoS ONE, 2014, v. 9, n. 8, p. 1, doi. 10.1371/journal.pone.0103833

By:

Suzuki, Shuji;
Kakuta, Masanori;
Ishida, Takashi;
Akiyama, Yutaka

Publication type:

Article

Re-Docking Scheme for Generating Near-Native Protein Complexes by Assembling Residue Interaction Fingerprints.

Published in:

PLoS ONE, 2013, v. 8, n. 7, p. 1, doi. 10.1371/journal.pone.0069365

By:

Uchikoga, Nobuyuki;
Matsuzaki, Yuri;
Ohue, Masahito;
Hirokawa, Takatsugu;
Akiyama, Yutaka

Publication type:

Article

GHOSTM: A GPU-Accelerated Homology Search Tool for Metagenomics.

Published in:

PLoS ONE, 2012, v. 7, n. 5, p. 1, doi. 10.1371/journal.pone.0036060

By:

Suzuki, Shuji;
Ishida, Takashi;
Kurokawa, Ken;
Akiyama, Yutaka

Publication type:

Article

Amide-to-ester substitution as a stable alternative to N-methylation for increasing membrane permeability in cyclic peptides.

Published in:

Nature Communications, 2023, v. 14, p. 1, doi. 10.1038/s41467-023-36978-z

By:

Hosono, Yuki;
Uchida, Satoshi;
Shinkai, Moe;
Townsend, Chad E.;
Kelly, Colin N.;
Naylor, Matthew R.;
Lee, Hsiau-Wei;
Kanamitsu, Kayoko;
Ishii, Mayumi;
Ueki, Ryosuke;
Ueda, Takumi;
Takeuchi, Koh;
Sugita, Masatake;
Akiyama, Yutaka;
Lokey, Scott R.;
Morimoto, Jumpei;
Sando, Shinsuke

Publication type:

Article

Clinical relevance of hepsin and hepatocyte growth factor activator inhibitor type 2 expression in renal cell carcinoma.

Published in:

Cancer Science, 2007, v. 98, n. 4, p. 491, doi. 10.1111/j.1349-7006.2007.00412.x

By:

Betsunoh, Hironori;
Mukai, Shoichiro;
Akiyama, Yutaka;
Fukushima, Tsuyoshi;
Minamiguchi, Naoki;
Hasui, Yoshihiro;
Osada, Yukio;
Kataoka, Hiroaki

Publication type:

Article

MEGADOCK 3.0: a high-performance protein-protein interaction prediction software using hybrid parallel computing for petascale supercomputing environments.

Published in:

Source Code for Biology & Medicine, 2013, v. 8, n. 1, p. 1, doi. 10.1186/1751-0473-8-18

By:

Yuri Matsuzaki;
Nobuyuki Uchikoga;
Masahito Ohue;
Takehiro Shimoda;
Toshiyuki Sato;
Takashi Ishida;
Yutaka Akiyama

Publication type:

Article

Protein-protein docking on hardware accelerators: comparison of GPU and MIC architectures.

Published in:

BMC Systems Biology, 2015, v. 9, p. 1, doi. 10.1186/1752-0509-9-S1-S6

By:

Takehiro Shimoda;
Shuji Suzuki;
Masahito Ohue;
Takashi Ishida;
Yutaka Akiyama

Publication type:

Article

Systematic comparison of catalytic mechanisms of hydrolysis and transfer reactions classified in the EzCatDB database.

Published in:

Proteins, 2007, v. 66, n. 1, p. 147, doi. 10.1002/prot.21193

By:

Nagano, Nozomi;
Noguchi, Tamotsu;
Akiyama, Yutaka

Publication type:

Article

CycPeptMP: enhancing membrane permeability prediction of cyclic peptides with multi-level molecular features and data augmentation.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae417

By:

Li, Jianan;
Yanagisawa, Keisuke;
Akiyama, Yutaka

Publication type:

Article

Malignant mesothelioma with squamous differentiation.

Published in:

2018

By:

Tanaka, Hiroyuki;
Akiyama, Yutaka;
Kitamura, Akiko;
Matsumoto, Nobuhiro;
Tomita, Masaki;
Kataoka, Hiroaki

Publication type:

Case Study

Expression of hepatocyte growth factor activator inhibitor type 1 in endothelial cells.

Published in:

Human Cell, 2006, v. 19, n. 3, p. 91, doi. 10.1111/j.1749-0774.2006.00015.x

By:

Akiyama, Yutaka;
Nagai, Miyuki;
Komaki, Wataru;
Marutsuka, Kousuke;
Asada, Yujiro;
Kataoka, Hiroaki

Publication type:

Article

Clinical characteristics of adult T-cell leukemia/lymphoma infiltration in the gastrointestinal tract.

Published in:

2020

By:

Miike, Tadashi;
Kawakami, Hiroshi;
Kameda, Takuro;
Yamamoto, Shojiro;
Tahara, Yoshihiro;
Hidaka, Tomonori;
Kubuki, Yoko;
Yorita, Kenji;
Akiyama, Yutaka;
Arimura, Yasuji;
Kubota, Yoshimasa;
Kataoka, Hiroaki;
Shimoda, Kazuya

Publication type:

journal article

MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions.

Published in:

2018

By:

Hayashi, Takanori;
Matsuzaki, Yuri;
Yanagisawa, Keisuke;
Ohue, Masahito;
Akiyama, Yutaka

Publication type:

Abstract

Multidomain protein structure prediction using information about residues interacting on multimeric protein interfaces.

Published in:

Biophysics & Physicobiology, 2020, v. 17, n. 1, p. 2, doi. 10.2142/biophysico.BSJ-2019050

By:

Shumpei Matsuno;
Masahito Ohue;
Yutaka Akiyama

Publication type:

Article

Synthetic aporphine alkaloids are potential therapeutics for Leigh syndrome.

Published in:

Scientific Reports, 2024, v. 11, n. 1, p. 1, doi. 10.1038/s41598-024-62445-w

By:

Kobayashi, Mizuki;
Miyauchi, Akihiko;
Jimbo, Eriko F.;
Oishi, Natsumi;
Aoki, Shiho;
Watanabe, Miyuki;
Yoshikawa, Yasushi;
Akiyama, Yutaka;
Yamagata, Takanori;
Osaka, Hitoshi

Publication type:

Article

In Silico Prediction of Major Clearance Pathways of Drugs among 9 Routes with Two-Step Support Vector Machines.

Published in:

Pharmaceutical Research, 2018, v. 35, n. 10, p. 1, doi. 10.1007/s11095-018-2479-1

By:

Wakayama, Naomi;
Toshimoto, Kota;
Maeda, Kazuya;
Hotta, Shun;
Ishida, Takashi;
Akiyama, Yutaka;
Sugiyama, Yuichi

Publication type:

Article

Comprehensive Fungal Community Analysis of House Dust Using Next-Generation Sequencing.

Published in:

International Journal of Environmental Research & Public Health, 2020, v. 17, n. 16, p. 5842, doi. 10.3390/ijerph17165842

By:

Izawa, Kazuki;
Kubosaki, Atsutaka;
Kobayashi, Naoki;
Akiyama, Yutaka;
Yamazaki, Akiko;
Hashimoto, Kazuhiro;
Konuma, Rumi;
Kamata, Yoichi;
Hara-Kudo, Yukiko;
Hasegawa, Kenichi;
Ikaga, Toshiharu;
Watanabe, Maiko

Publication type:

Article

QUBO Problem Formulation of Fragment-Based Protein–Ligand Flexible Docking.

Published in:

Entropy, 2024, v. 26, n. 5, p. 397, doi. 10.3390/e26050397

By:

Yanagisawa, Keisuke;
Fujie, Takuya;
Takabatake, Kazuki;
Akiyama, Yutaka

Publication type:

Article

Solving Generalized Polyomino Puzzles Using the Ising Model.

Published in:

Entropy, 2022, v. 24, n. 3, p. 354, doi. 10.3390/e24030354

By:

Takabatake, Kazuki;
Yanagisawa, Keisuke;
Akiyama, Yutaka

Publication type:

Article

Highly precise protein-protein interaction prediction based on consensus between template-based and de novo docking methods.

Published in:

2013

By:

Masahito Ohue;
Yuri Matsuzaki;
Takehiro Shimoda;
Takashi Ishida;
Yutaka Akiyama

Publication type:

Conference Paper/Materials

GPU-Acceleration of Sequence Homology Searches with Database Subsequence Clustering.

Published in:

PLoS ONE, 2016, v. 11, n. 8, p. 1, doi. 10.1371/journal.pone.0157338

By:

Suzuki, Shuji;
Kakuta, Masanori;
Ishida, Takashi;
Akiyama, Yutaka

Publication type:

Article

Adenoid glioblastoma arising in a patient with neurofibromatosis type-1.

Published in:

Pathology International, 2005, v. 55, n. 6, p. 348, doi. 10.1111/j.1440-1827.2005.01835.x

By:

Miyata, Shiro;
Sugimoto, Tetsuaki;
Kodama, Takao;
Akiyama, Yutaka;
Nakano, Shinichi;
Wakisaka, Shinichiro;
Itoh, Hiroshi;
Kataoka, Hiroaki

Publication type:

Article

Case Report Ovarian teratoma showing a predominant hemangiomatous element with stromal luteinization: Report of a case and review of the literature.

Published in:

Pathology International, 2004, v. 54, n. 4, p. 279, doi. 10.1111/j.1440-1827.2004.01621.x

By:

Itoh, Hiroshi;
Wada, Toshiro;
Michikata, Kaori;
Sato, Yuichiro;
Seguchi, Tomoko;
Akiyama, Yutaka;
Kataoka, Hiroaki

Publication type:

Article

Case Report Ovarian pregnancy: Report of four cases and review of the literature.

Published in:

Pathology International, 2003, v. 53, n. 11, p. 806, doi. 10.1046/j.1440-1827.2003.01554.x

By:

Itoh, Hiroshi;
Ishihara, Akira;
Koita, Hiroyuki;
Hatakeyama, Kinta;
Seguchi, Tomoko;
Akiyama, Yutaka;
Kataoka, Hiroaki

Publication type:

Article

Tubal ectopic pregnancy associated with an adenomatoid tumor.

Published in:

Pathology International, 2001, v. 51, n. 3, p. 211, doi. 10.1046/j.1440-1827.2001.01183.x

By:

Koono, Masashi;
Inoue, Teruhiko;
Nabeshima, Kazuki;
Shimao, Yoshiya;
Akiyama, Yutaka;
Ohtsuka, Teruo

Publication type:

Article

Solitary fibrous tumor of the spinal nerve rootlet: Case report and literature survey.

Published in:

Pathology International, 1999, v. 49, n. 9, p. 826, doi. 10.1046/j.1440-1827.1999.00946.x

By:

Koono, Masashi;
Kataoka, Hiroaki;
Akiyama, Yutaka;
Kubo, Shinichiro;
Itoh, Hiroshi;
Hamasuna, Ryouichi;
Tajima, Naoya

Publication type:

Article

Retroperitoneal bronchogenic cyst: Report of a case and literature review.

Published in:

Pathology International, 1999, v. 49, n. 2, p. 152, doi. 10.1046/j.1440-1827.1999.00837.x

By:

Itoh, Hiroshi;
Shitamura, Takahiro;
Kataoka, Hiroaki;
Ide, Hisamitsu;
Akiyama, Yutaka;
Hamasuna, Ryoichi;
Hasui, Yoshihiro;
Osada, Yukio;
Koono, Masashi

Publication type:

Article

PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003.

Published in:

Nucleic Acids Research, 2003, v. 31, n. 1, p. 492, doi. 10.1093/nar/gkg022

By:

Noguchi, Tamotsu;
Akiyama, Yutaka

Publication type:

Article

PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB).

Published in:

Nucleic Acids Research, 2001, v. 29, n. 1, p. 219, doi. 10.1093/nar/29.1.219

By:

Noguchi, Tamotsu;
Matsuda, Hideo;
Akiyama, Yutaka

Publication type:

Article

Taxonomic and Gene Category Analyses of Subgingival Plaques from a Group of Japanese Individuals with and without Periodontitis.

Published in:

International Journal of Molecular Sciences, 2021, v. 22, n. 10, p. 5298, doi. 10.3390/ijms22105298

By:

Izawa, Kazuki;
Okamoto-Shibayama, Kazuko;
Kita, Daichi;
Tomita, Sachiyo;
Saito, Atsushi;
Ishida, Takashi;
Ohue, Masahito;
Akiyama, Yutaka;
Ishihara, Kazuyuki;
Yoneda, Masahiro;
Grenier, Daniel;
Suzuki, Nao;
Yoshinaga, Yasunori

Publication type:

Article

A Massively Parallel Sequence Similarity Search for Metagenomic Sequencing Data.

Published in:

International Journal of Molecular Sciences, 2017, v. 18, n. 10, p. 2124, doi. 10.3390/ijms18102124

By:

Masanori Kakuta;
Shuji Suzuki;
Kazuki Izawa;
Takashi Ishida;
Yutaka Akiyama

Publication type:

Article

CLAST: CUDA implemented large-scale alignment search tool.

Published in:

BMC Bioinformatics, 2014, v. 15, n. 1, p. 564, doi. 10.1186/s12859-014-0406-y

By:

Masahiro Yano;
Hiroshi Mori;
Yutaka Akiyama;
Takuji Yamada;
Ken Kurokawa

Publication type:

Article

Acceleration of sequence clustering using longest common subsequence filtering.

Published in:

BMC Bioinformatics, 2013, v. 14, n. Suppl 8, p. 1, doi. 10.1186/1471-2105-14-S8-S7

By:

Namiki, Youhei;
Ishida, Takashi;
Akiyama, Yutaka

Publication type:

Article

Plasma protein binding prediction focusing on residue-level features and circularity of cyclic peptides by deep learning.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 1110, doi. 10.1093/bioinformatics/btab726

By:

Li, Jianan;
Yanagisawa, Keisuke;
Yoshikawa, Yasushi;
Ohue, Masahito;
Akiyama, Yutaka

Publication type:

Article

Professor Yasuhiko Torii: An Obituary.

Published in:

2020

By:

Akiyama, Yutaka;
Hill, Hal;
Ichimura, Shin‐ichi;
Kohsaka, Akira;
Urata, Shujiro

Publication type:

Obituary

Identification of type I and type II inhibitors of c-Yes kinase using <italic>in silico</italic> and experimental techniques.

Published in:

Journal of Biomolecular Structure & Dynamics, 2018, v. 36, n. 6, p. 1566, doi. 10.1080/07391102.2017.1329098

By:

Ramakrishnan, Chandrasekaran;
Mary Thangakani, Anthony;
Velmurugan, Devadasan;
Anantha Krishnan, Dhanabalan;
Sekijima, Masakazu;
Akiyama, Yutaka;
Gromiha, M. Michael

Publication type:

Article

Computational prediction of plasma protein binding of cyclic peptides from small molecule experimental data using sparse modeling techniques.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 19, p. 157, doi. 10.1186/s12859-018-2529-z

By:

Tajimi, Takashi;
Wakui, Naoki;
Yanagisawa, Keisuke;
Yoshikawa, Yasushi;
Ohue, Masahito;
Akiyama, Yutaka

Publication type:

Article