過去の発表論文

2016年の発表論文

Multidisciplinary insight into clonal expansion of HTLV-1-infected cells in adult T-cell leukemia via modeling by deterministic finite automata coupled with high-throughput sequencing.

*Amir Farmanbar, Sanaz Firouzi, Sung-Joon Park, Kenta Nakai, Kaoru Uchimaru, and Toshiki Watanabe
BMC Medical Genomics
(2016/12/22)

博士課程2年 Amir Farmanbar    機能解析イン・シリコ分野(中井謙太研究室)
本論文では、成人T細胞白血病において、HTLV-1感染細胞がそのクローン数を拡大していく様子を、ハイ・スループットシークエンシングによるクローン数測定データを数学的モデル(具体的には決定性有限オートマトン)の言葉で直感的に表現・可視化する試みについて述べている。

Selective control of up-regulated and down-regulated genes by temporal patterns and doses of insulin

*Takanori Sano, Kentaro Kawata, Satoshi Ohno, Katsuyuki Yugi, Hiroaki Kakuda, Hiroyuki Kubota, Shinsuke Uda, Masashi Fujii, Katsuyuki Kunida, Daisuke Hoshino, Atsushi Hatano, Yuki Ito, Miharu Sato, Yutaka Suzuki, Shinya Kuroda
Sci. Signal. 9, ra112 (2016)  doi: 10.1126/scisignal.aaf3739
http://stke.sciencemag.org/content/9/455/ra112

A new genotype of bovine leukemia virus in South America identified by NGS‑based

*Meripet Polat, Shin‑nosuke Takeshima, Kazuyoshi Hosomichi, Jiyun Kim, Taku Miyasaka, Kazunori Yamada, Mariluz Arainga, Tomoyuki Murakami, Yuki Matsumoto, Veronica de la Barra Diaz, Carlos Javier Pane, Ester Teresa González, Misao Kanemaki, Misao Onuma, Guillermo Giovambattista, Yoko Aida (2016)
Retrovirology 13:4  DOI: 10.1186/s12977-016-0239-z
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4709907/

Protein ligand-binding site comparison by a reduced vector representation derived from multidimensional scaling of generalized description of binding sites

*Tsukasa Nakamura and Kentaro Tomii
Methods 93, 35-40 (2016)  doi: 10.1016/j.ymeth.2015.08.007
http://www.sciencedirect.com/science/article/pii/S1046202315300451

Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment

Marc F. Lensink, Sameer Velankar, Andriy Kryshtafovych, Dina Schneidman, Andrej Sali, Joan Segura, Narcis Fernandez-Fuentes, Shruthi Viswanath, Ron Elber, Sergei Grudinin, Petr Popov, Emilie Neveu, Hasup Lee, Minkyung Baek, Sangwoo Park, Lim Heo, Gyu Rie Lee, Chaok Seok, Sanbo Qin, Huan-Xiang Zhou, David W. Ritchie, Bernard Maigret, Marie-Dominique Devignes, Anisah Ghoorah, Mieczyslaw Torchala, Raphael A.G. Chaleil, Paul A. Bates, Efrat Ben-Zeev, Miriam Eisenstein, Surendra S. Negi, Zhiping Weng, Thom Vreven, Brian G. Pierce, Tyler M. Borrman, Jinchao Yu, Francoise Ochsenbein, Raphael Guerois, Anna Vangone, Joao P.G.L.M. Rodrigues, Gydo van Zundert, Mehdi Nellen, Li Xue, Ezgi Karaca, Adrien S.J. Melquiond, Koen Visscher, Panagiotis L. Kastritis, Alexandre M.J.J. Bonvin, Xianjin Xu, Liming Qiu, Chengfei Yan, Jilong Li, Zhiwei Ma, Jianlin Cheng, Xiaoqin Zou, Yang Shen, Lenna X. Peterson, Hyung-Rae Kim, Amit Roy, Xusi Han, Juan Esquivel-Rodriguez, Daisuke Kihara, Xiaofeng Yu, Neil J. Bruce, Jonathan C. Fuller, Rebecca C. Wade, Ivan Anishchenko, Petras J. Kundrotas, Ilya A. Vakser, Kenichiro Imai, Kazunori Yamada, Toshiyuki Oda, *Tsukasa Nakamura, Kentaro Tomii, Chiara Pallara, Miguel Romero-Durana, Brian Jimenez-Garcia, Iain H. Moal, Juan Fernandez-Recio, Jong Young Joung, Jong Yun Kim, Keehyoung Joo, Jooyoung Lee, Sandor Vajda, Scott Mottarella, David R. Hall, Dmitri Beglov, Artem Mamonov, Bing Xia, Tanggis Bohnuud, Carlos A. Del Carpio, Eichiro Ichiishi, Jeff Gray, Edrisse Chermak, Luigi Cavallo, Romina Oliva, Shoshana J. Wodak
Proteins: Structure, Function, and Bioinformatics  doi: 10.1002/prot.25007.
http://www.ncbi.nlm.nih.gov/pubmed/27122118




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