Works by Niida, Atsushi

Results: 38

Sensitivity analysis of agent-based simulation utilizing massively parallel computation and interactive data visualization.

Published in:

PLoS ONE, 2019, v. 14, n. 3, p. 1, doi. 10.1371/journal.pone.0210678

By:

Niida, Atsushi;
Hasegawa, Takanori;
Miyano, Satoru

Publication type:

Article

Mutational landscape and clonal architecture in grade II and III gliomas.

Published in:

Nature Genetics, 2015, v. 47, n. 5, p. 458, doi. 10.1038/ng.3273

By:

Suzuki, Hiromichi;
Aoki, Kosuke;
Abe, Tatsuya;
Muragaki, Yoshihiro;
Watanabe, Reiko;
Ito, Ichiro;
Chiba, Kenichi;
Shiraishi, Yuichi;
Niida, Atsushi;
Tanaka, Hiroko;
Miyano, Satoru;
Sato, Yusuke;
Shiozawa, Yusuke;
Yoshizato, Tetsuichi;
Kataoka, Keisuke;
Yoshida, Kenichi;
Nagata, Yasunobu;
Sato-Otsubo, Aiko;
Sanada, Masashi;
Ogawa, Seishi

Publication type:

Article

Integrated molecular analysis of clear-cell renal cell carcinoma.

Published in:

Nature Genetics, 2013, v. 45, n. 8, p. 860, doi. 10.1038/ng.2699

By:

Sato, Yusuke;
Yoshizato, Tetsuichi;
Shiraishi, Yuichi;
Maekawa, Shigekatsu;
Okuno, Yusuke;
Kamura, Takumi;
Shimamura, Teppei;
Sato-Otsubo, Aiko;
Nagae, Genta;
Suzuki, Hiromichi;
Nagata, Yasunobu;
Yoshida, Kenichi;
Kon, Ayana;
Suzuki, Yutaka;
Chiba, Kenichi;
Tanaka, Hiroko;
Niida, Atsushi;
Fujimoto, Akihiro;
Tsunoda, Tatsuhiko;
Morikawa, Teppei

Publication type:

Article

Multiregion Genomic Analysis of Serially Transplanted Patient-derived Xenograft Tumors.

Published in:

Cancer Genomics & Proteomics (1109-6535), 2019, v. 16, n. 1, p. 21, doi. 10.21873/cgp.20109

By:

KUNIAKI SATO;
ATSUSHI NIIDA;
TAKAAKI MASUDA;
DAI SHIMIZU;
TARO TOBO;
YOUSUKE KURODA;
HIDETOSHI EGUCHI;
TAKASHI NAKAGAWA;
YUTAKA SUZUKI;
KOSHI MIMORI

Publication type:

Article

Overexpression of Cohesion Establishment Factor DSCC1 through E2F in Colorectal Cancer.

Published in:

PLoS ONE, 2014, v. 9, n. 1, p. 1, doi. 10.1371/journal.pone.0085750

By:

Yamaguchi, Kiyoshi;
Yamaguchi, Rui;
Takahashi, Norihiko;
Ikenoue, Tsuneo;
Fujii, Tomoaki;
Shinozaki, Masaru;
Tsurita, Giichiro;
Hata, Keisuke;
Niida, Atsushi;
Imoto, Seiya;
Miyano, Satoru;
Nakamura, Yusuke;
Furukawa, Yoichi

Publication type:

Article

The Tumor-Suppressive <i>miR-497-195</i> Cluster Targets Multiple Cell-Cycle Regulators in Hepatocellular Carcinoma.

Published in:

PLoS ONE, 2013, v. 8, n. 3, p. 1, doi. 10.1371/journal.pone.0060155

By:

Furuta, Mayuko;
Kozaki, Ken-ichi;
Tanimoto, Kousuke;
Tanaka, Shinji;
Arii, Shigeki;
Shimamura, Teppei;
Niida, Atsushi;
Miyano, Satoru;
Inazawa, Johji

Publication type:

Article

A Novel Network Profiling Analysis Reveals System Changes in Epithelial-Mesenchymal Transition.

Published in:

PLoS ONE, 2011, v. 6, n. 6, p. 1, doi. 10.1371/journal.pone.0020804

By:

Shimamura, Teppei;
Imoto, Seiya;
Shimada, Yukako;
Hosono, Yasuyuki;
Niida, Atsushi;
Nagasaki, Masao;
Yamaguchi, Rui;
Takahashi, Takashi;
Miyano, Satoru

Publication type:

Article

Gene Set-Based Module Discovery Decodes cis- Regulatory Codes Governing Diverse Gene Expression across Human Multiple Tissues.

Published in:

PLoS ONE, 2010, v. 5, n. 6, p. 1, doi. 10.1371/journal.pone.0010910

By:

Niida, Atsushi;
Imoto, Seiya;
Yamaguchi, Rui;
Nagasaki, Masao;
Miyano, Satoru

Publication type:

Article

Impaired tumor immune response in metastatic tumors is a selective pressure for neutral evolution in CRC cases.

Published in:

PLoS Genetics, 2021, v. 17, n. 1, p. 1, doi. 10.1371/journal.pgen.1009113

By:

Sakimura, Shotaro;
Nagayama, Satoshi;
Fukunaga, Mitsuko;
Hu, Qingjiang;
Kitagawa, Akihiro;
Kobayashi, Yuta;
Hasegawa, Takanori;
Noda, Miwa;
Kouyama, Yuta;
Shimizu, Dai;
Saito, Tomoko;
Niida, Atsushi;
Tsuruda, Yusuke;
Otsu, Hajime;
Matsumoto, Yoshihiro;
Uchida, Hiroki;
Masuda, Takaaki;
Sugimachi, Keishi;
Sasaki, Shin;
Yamada, Kazutaka

Publication type:

Article

A clinical trial of somatic and germline analyses for healthy longevity in a postoperative cancer patient.

Published in:

Surgery Today, 2019, v. 49, n. 9, p. 738, doi. 10.1007/s00595-019-01789-7

By:

Hayashi, Naoki;
Kuroda, Yosuke;
Saito, Tomoko;
Tsuruda, Yusuke;
Niida, Atsushi;
Otsu, Hajime;
Eguchi, Hidetoshi;
Masuda, Takaaki;
Suzuki, Yutaka;
Natsugoe, Shoji;
Mimori, Koshi

Publication type:

Article

Implementable assay for monitoring minimum residual disease after radical treatment for colorectal cancer.

Published in:

Cancer Science, 2024, v. 115, n. 6, p. 1989, doi. 10.1111/cas.16149

By:

Nakano, Takafumi;
Takao, Seiichiro;
Dairaku, Katsushi;
Uno, Naoki;
Low, Siew‐Kee;
Hashimoto, Masahiro;
Tsuda, Yasuo;
Hisamatsu, Yuichi;
Toshima, Takeo;
Yonemura, Yusuke;
Masuda, Takaaki;
Eto, Ken;
Ikegami, Toru;
Fukunaga, Yosuke;
Niida, Atsushi;
Nagayama, Satoshi;
Mimori, Koshi

Publication type:

Article

Genetic landscape of external auditory canal squamous cell carcinoma.

Published in:

Cancer Science, 2020, v. 111, n. 8, p. 3010, doi. 10.1111/cas.14515

By:

Sato, Kuniaki;
Komune, Noritaka;
Hongo, Takahiro;
Koike, Kensuke;
Niida, Atsushi;
Uchi, Ryutaro;
Noda, Teppei;
Kogo, Ryunosuke;
Matsumoto, Nozomu;
Yamamoto, Hidetaka;
Masuda, Muneyuki;
Oda, Yoshinao;
Mimori, Koshi;
Nakagawa, Takashi

Publication type:

Article

Understanding intratumor heterogeneity by combining genome analysis and mathematical modeling.

Published in:

Cancer Science, 2018, v. 109, n. 4, p. 884, doi. 10.1111/cas.13510

By:

Niida, Atsushi;
Nagayama, Satoshi;
Miyano, Satoru;
Mimori, Koshi

Publication type:

Article

Japanese genome-wide association study identifies a significant colorectal cancer susceptibility locus at chromosome 10p14.

Published in:

Cancer Science, 2017, v. 108, n. 11, p. 2239, doi. 10.1111/cas.13391

By:

Takahashi, Yusuke;
Sugimachi, Keishi;
Yamamoto, Ken;
Niida, Atsushi;
Shimamura, Teppei;
Sato, Tetsuya;
Watanabe, Masahiko;
Tanaka, Junichi;
Kudo, Shinei;
Sugihara, Kenichi;
Hase, Kazuo;
Kusunoki, Masato;
Yamada, Kazutaka;
Shimada, Yasuhiro;
Moriya, Yoshihiro;
Suzuki, Yutaka;
Miyano, Satoru;
Mori, Masaki;
Mimori, Koshi

Publication type:

Article

Human homolog of NOTUM, overexpressed in hepatocellular carcinoma, is regulated transcriptionally by β-catenin/TCF.

Published in:

Cancer Science, 2008, v. 99, n. 6, p. 1139, doi. 10.1111/j.1349-7006.2008.00814.x

By:

Torisu, Yuichi;
Watanabe, Akira;
Nonaka, Aya;
Midorikawa, Yutaka;
Makuuchi, Masatoshi;
Shimamura, Takahiro;
Sugimura, Haruhiko;
Niida, Atsushi;
Akiyama, Tetsu;
Iwanari, Hiroko;
Kodama, Tatsuhiko;
Zeniya, Mikio;
Aburatani, Hiroyuki

Publication type:

Article

Integrated Multiregional Analysis Proposing a New Model of Colorectal Cancer Evolution.

Published in:

PLoS Genetics, 2016, v. 12, n. 2, p. 1, doi. 10.1371/journal.pgen.1005778

By:

Uchi, Ryutaro;
Takahashi, Yusuke;
Niida, Atsushi;
Shimamura, Teppei;
Hirata, Hidenari;
Sugimachi, Keishi;
Sawada, Genta;
Iwaya, Takeshi;
Kurashige, Junji;
Shinden, Yoshiaki;
Iguchi, Tomohiro;
Eguchi, Hidetoshi;
Chiba, Kenichi;
Shiraishi, Yuichi;
Nagae, Genta;
Yoshida, Kenichi;
Nagata, Yasunobu;
Haeno, Hiroshi;
Yamamoto, Hirofumi;
Ishii, Hideshi

Publication type:

Article

Cell cycle-dependent gene networks for cell proliferation activated by nuclear CK2α complexes.

Published in:

Life Science Alliance, 2024, v. 7, n. 1, p. 1, doi. 10.26508/lsa.202302077

By:

Miwako Kato Homma;
Ryuichiro Nakato;
Atsushi Niida;
Masashige Bando;
Katsunori Fujiki;
Naoko Yokota;
So Yamamoto;
Takeshi Shibata;
Motoki Takagi;
Junko Yamaki;
Hiroko Kozuka-Hata;
Masaaki Oyama;
Katsuhiko Shirahige;
Yoshimi Homma

Publication type:

Article

Palindromic amplification of the ERBB2 oncogene in primary HER2-positive breast tumors.

Published in:

Scientific Reports, 2017, p. 41921, doi. 10.1038/srep41921

By:

Marotta, Michael;
Onodera, Taku;
Johnson, Jeffrey;
Budd, G. Thomas;
Watanabe, Takaaki;
Cui, Xiaojiang;
Giuliano, Armando E.;
Niida, Atsushi;
Tanaka, Hisashi

Publication type:

Article

Integrated Molecular Profiling of Human Gastric Cancer Identifies DDR2 as a Potential Regulator of Peritoneal Dissemination.

Published in:

Scientific Reports, 2016, p. 22371, doi. 10.1038/srep22371

By:

Kurashige, Junji;
Hasegawa, Takanori;
Niida, Atsushi;
Sugimachi, Keishi;
Deng, Niantao;
Mima, Kosuke;
Uchi, Ryutaro;
Sawada, Genta;
Takahashi, Yusuke;
Eguchi, Hidetoshi;
Inomata, Masashi;
Kitano, Seigo;
Fukagawa, Takeo;
Sasako, Mitsuru;
Sasaki, Hiroki;
Sasaki, Shin;
Mori, Masaki;
Yanagihara, Kazuyoshi;
Baba, Hideo;
Miyano, Satoru

Publication type:

Article

A temporal shift of the evolutionary principle shaping intratumor heterogeneity in colorectal cancer.

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-05226-0

By:

Saito, Tomoko;
Niida, Atsushi;
Uchi, Ryutaro;
Hirata, Hidenari;
Komatsu, Hisateru;
Sakimura, Shotaro;
Hayashi, Shuto;
Nambara, Sho;
Kuroda, Yosuke;
Ito, Shuhei;
Eguchi, Hidetoshi;
Masuda, Takaaki;
Sugimachi, Keishi;
Tobo, Taro;
Nishida, Haruto;
Daa, Tsutomu;
Chiba, Kenichi;
Shiraishi, Yuichi;
Yoshizato, Tetsuichi;
Kodama, Masaaki

Publication type:

Article

The impact of surgery resident training on the duration of tibial plateau leveling osteotomy surgery.

Published in:

Veterinary Surgery, 2024, v. 53, n. 5, p. 808, doi. 10.1111/vsu.14113

By:

Niida, Atsushi;
Chou, Po‐Yen;
Filliquist, Barbro;
Marcellin‐Little, Denis J.;
Kapatkin, Amy S.;
Kass, Philip H.

Publication type:

Article

A unified simulation model for understanding the diversity of cancer evolution.

Published in:

PeerJ, 2020, p. 1, doi. 10.7717/peerj.8842

By:

Atsushi Niida;
Takanori Hasegawa;
Hideki Innan;
Tatsuhiro Shibata;
Koshi Mimori;
Satoru Miyano

Publication type:

Article

Possible Role of Cytochrome P450 1B1 in the Mechanism of Gemcitabine Resistance in Pancreatic Cancer.

Published in:

Biomedicines, 2021, v. 9, n. 10, p. 1396, doi. 10.3390/biomedicines9101396

By:

Yada, Erica;
Kasajima, Rika;
Niida, Atsushi;
Imoto, Seiya;
Miyano, Satoru;
Miyagi, Yohei;
Sasada, Tetsuro;
Wada, Satoshi

Publication type:

Article

Variant analysis of prostate cancer in Japanese patients and a new attempt to predict related biological pathways.

Published in:

Oncology Reports, 2020, v. 43, n. 3, p. 943, doi. 10.3892/or.2020.7481

By:

Kasajima, Rika;
Yamaguchi, Rui;
Shimizu, Eigo;
Tamada, Yoshinori;
Niida, Atsushi;
Tremmel, George;
Kishida, Takeshi;
Aoki, Ichiro;
Imoto, Seiya;
Miyano, Satoru;
Uemura, Hiroji;
Miyagi, Yohei

Publication type:

Article

Correction: Integrated Multiregional Analysis Proposing a New Model of Colorectal Cancer Evolution.

Published in:

2017

By:

Uchi, Ryutaro;
Takahashi, Yusuke;
Niida, Atsushi;
Shimamura, Teppei;
Hirata, Hidenari;
Sugimachi, Keishi;
Sawada, Genta;
Iwaya, Takeshi;
Kurashige, Junji;
Shinden, Yoshiaki;
Iguchi, Tomohiro;
Eguchi, Hidetoshi;
Chiba, Kenichi;
Shiraishi, Yuichi;
Nagae, Genta;
Yoshida, Kenichi;
Nagata, Yasunobu;
Haeno, Hiroshi;
Yamamoto, Hirofumi;
Ishii, Hideshi

Publication type:

Correction Notice

DKK1, a negative regulator of Wnt signaling, is a target of theß-catenin/TCF pathway.

Published in:

Oncogene, 2004, v. 23, n. 52, p. 8520, doi. 10.1038/sj.onc.1207892

By:

Niida, Atsushi;
Hiroko, Takatoshi;
Kasai, Mana;
Furukawa, Yoichi;
Nakamura, Yusuke;
Suzuki, Yutaka;
Sugano, Sumio;
Akiyama, Tetsu

Publication type:

Article

An Integrative Analysis to Identify Driver Genes in Esophageal Squamous Cell Carcinoma.

Published in:

PLoS ONE, 2015, v. 10, n. 10, p. 1, doi. 10.1371/journal.pone.0139808

By:

Sawada, Genta;
Niida, Atsushi;
Hirata, Hidenari;
Komatsu, Hisateru;
Uchi, Ryutaro;
Shimamura, Teppei;
Takahashi, Yusuke;
Kurashige, Junji;
Matsumura, Tae;
Ueo, Hiroki;
Takano, Yuki;
Ueda, Masami;
Sakimura, Shotaro;
Shinden, Yoshiaki;
Eguchi, Hidetoshi;
Sudo, Tomoya;
Sugimachi, Keishi;
Yamasaki, Makoto;
Tanaka, Fumiaki;
Tachimori, Yuji

Publication type:

Article

Subclonal accumulation of immune escape mechanisms in microsatellite instability-high colorectal cancers.

Published in:

British Journal of Cancer, 2023, v. 129, n. 7, p. 1105, doi. 10.1038/s41416-023-02395-8

By:

Kobayashi, Yuta;
Niida, Atsushi;
Nagayama, Satoshi;
Saeki, Koichi;
Haeno, Hiroshi;
Takahashi, Kazuki K.;
Hayashi, Shuto;
Ozato, Yuki;
Saito, Hideyuki;
Hasegawa, Takanori;
Nakamura, Hiromi;
Tobo, Taro;
Kitagawa, Akihiro;
Sato, Kuniaki;
Shimizu, Dai;
Hirata, Hidenari;
Hisamatsu, Yuichi;
Toshima, Takeo;
Yonemura, Yusuke;
Masuda, Takaaki

Publication type:

Article

Serial mutational tracking in surgically resected locally advanced colorectal cancer with neoadjuvant chemotherapy.

Published in:

2018

By:

Sugimachi, Keishi;
Sakimura, Shotaro;
Kuramitsu, Shotaro;
Hirata, Hidenari;
Niida, Atsushi;
Iguchi, Tomohiro;
Eguchi, Hidetoshi;
Masuda, Takaaki;
Morita, Masaru;
Toh, Yasushi;
Maehara, Yoshihiko;
Suzuki, Yutaka;
Mimori, Koshi

Publication type:

journal article

Gene set-based module discovery in the breast cancer transcriptome.

Published in:

BMC Bioinformatics, 2009, v. 10, p. 1, doi. 10.1186/1471-2105-10-71

By:

Niida, Atsushi;
Smith, Andrew D.;
Imoto, Seiya;
Aburatani, Hiroyuki;
Zhang, Michael Q.;
Akiyama, Tetsu

Publication type:

Article

Neoantimon: a multifunctional R package for identification of tumor-specific neoantigens.

Published in:

Bioinformatics, 2020, v. 36, n. 18, p. 4813, doi. 10.1093/bioinformatics/btaa616

By:

Hasegawa, Takanori;
Hayashi, Shuto;
Shimizu, Eigo;
Mizuno, Shinichi;
Niida, Atsushi;
Yamaguchi, Rui;
Miyano, Satoru;
Nakagawa, Hidewaki;
Imoto, Seiya

Publication type:

Article

8q24 Polymorphisms and Diabetes Mellitus Regulate Apolipoprotein A-IV in Colorectal Carcinogenesis.

Published in:

Annals of Surgical Oncology: An Oncology Journal for Surgeons, 2016, v. 23, p. 546, doi. 10.1245/s10434-016-5374-1

By:

Sugimachi, Keishi;
Yamaguchi, Rui;
Eguchi, Hidetoshi;
Ueda, Masami;
Niida, Atsushi;
Sakimura, Shotaro;
Hirata, Hidenari;
Uchi, Ryutaro;
Shinden, Yoshiaki;
Iguchi, Tomohiro;
Morita, Kazutoyo;
Yamamoto, Ken;
Miyano, Satoru;
Mori, Masaki;
Maehara, Yoshihiko;
Mimori, Koshi

Publication type:

Article

Allelic Imbalance at an 8q24 Oncogenic SNP is Involved in Activating MYC in Human Colorectal Cancer.

Published in:

Annals of Surgical Oncology: An Oncology Journal for Surgeons, 2014, v. 21, p. 515, doi. 10.1245/s10434-013-3468-6

By:

Sugimachi, Keishi;
Niida, Atsushi;
Yamamoto, Ken;
Shimamura, Teppei;
Imoto, Seiya;
Iinuma, Hisae;
Shinden, Yoshiaki;
Eguchi, Hidetoshi;
Sudo, Tomoya;
Watanabe, Masahiko;
Tanaka, Junichi;
Kudo, Shinei;
Hase, Kazuo;
Kusunoki, Masato;
Yamada, Kazutaka;
Shimada, Yasuhiro;
Sugihara, Kenichi;
Maehara, Yoshihiko;
Miyano, Satoru;
Mori, Masaki

Publication type:

Article

Loss of CDCP1 Expression Promotes Invasiveness and Poor Prognosis in Esophageal Squamous Cell Carcinoma.

Published in:

Annals of Surgical Oncology: An Oncology Journal for Surgeons, 2014, v. 21, p. 640, doi. 10.1245/s10434-014-3740-4

By:

Sawada, Genta;
Takahashi, Yusuke;
Niida, Atsushi;
Shimamura, Teppei;
Kurashige, Junji;
Matsumura, Tae;
Ueo, Hiroki;
Uchi, Ryutaro;
Takano, Yuki;
Ueda, Masami;
Hirata, Hidenari;
Sakimura, Shotaro;
Shinden, Yoshiaki;
Eguchi, Hidetoshi;
Sudo, Tomoya;
Sugimachi, Keishi;
Miyano, Satoru;
Doki, Yuichiro;
Mori, Masaki;
Mimori, Koshi

Publication type:

Article

The rs6983267 SNP Is Associated with MYC Transcription Efficiency, Which Promotes Progression and Worsens Prognosis of Colorectal Cancer.

Published in:

Annals of Surgical Oncology: An Oncology Journal for Surgeons, 2013, v. 20, n. 4, p. 1395, doi. 10.1245/s10434-012-2657-z

By:

Takatsuno, Yasushi;
Mimori, Koshi;
Yamamoto, Ken;
Sato, Tetsuya;
Niida, Atsushi;
Inoue, Hiroshi;
Imoto, Seiya;
Kawano, Shuhei;
Yamaguchi, Rui;
Toh, Hiroyuki;
Iinuma, Hisae;
Ishimaru, Shinya;
Ishii, Hideshi;
Suzuki, Sadao;
Tokudome, Shinkan;
Watanabe, Masahiko;
Tanaka, Jun-ichi;
Kudo, Shin-ei;
Mochizuki, Hidetaka;
Kusunoki, Masato

Publication type:

Article

Gene expression signatures as candidate biomarkers of response to PD-1 blockade in non-small cell lung cancers.

Published in:

PLoS ONE, 2021, v. 16, n. 11, p. 1, doi. 10.1371/journal.pone.0260500

By:

Aiba, Tomoiki;
Hattori, Chieko;
Sugisaka, Jun;
Shimizu, Hisashi;
Ono, Hirotaka;
Domeki, Yutaka;
Saito, Ryohei;
Kawana, Sachiko;
Kawashima, Yosuke;
Terayama, Keisuke;
Toi, Yukihiro;
Nakamura, Atsushi;
Yamanda, Shinsuke;
Kimura, Yuichiro;
Suzuki, Yutaka;
Niida, Atsushi;
Sugawara, Shunichi

Publication type:

Article

Neutral Theory in Cancer Cell Population Genetics.

Published in:

Molecular Biology & Evolution, 2018, v. 35, n. 6, p. 1316, doi. 10.1093/molbev/msy091

By:

Niida, Atsushi;
Iwasaki, Watal M;
Innan, Hideki

Publication type:

Article

phyC: Clustering cancer evolutionary trees.

Published in:

PLoS Computational Biology, 2017, v. 13, n. 5, p. 1, doi. 10.1371/journal.pcbi.1005509

By:

Matsui, Yusuke;
Niida, Atsushi;
Uchi, Ryutaro;
Mimori, Koshi;
Miyano, Satoru;
Shimamura, Teppei

Publication type:

Article