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Molecular robots with sensors and intelligence.
Hagiya M, Konagaya A, Kobayashi S, Saito H, Murata S. Hagiya M, et al. Among authors: konagaya a. Acc Chem Res. 2014 Jun 17;47(6):1681-90. doi: 10.1021/ar400318d. Epub 2014 Jun 6. Acc Chem Res. 2014. PMID: 24905779
Depletion force induced collective motion of microtubules driven by kinesin.
Inoue D, Mahmot B, Kabir AM, Farhana TI, Tokuraku K, Sada K, Konagaya A, Kakugo A. Inoue D, et al. Among authors: konagaya a. Nanoscale. 2015 Nov 21;7(43):18054-61. doi: 10.1039/c5nr02213d. Nanoscale. 2015. PMID: 26260025 Free article.
Construction of artificial cilia from microtubules and kinesins through a well-designed bottom-up approach.
Sasaki R, Kabir AMR, Inoue D, Anan S, Kimura AP, Konagaya A, Sada K, Kakugo A. Sasaki R, et al. Among authors: konagaya a. Nanoscale. 2018 Apr 5;10(14):6323-6332. doi: 10.1039/C7NR05099B. Nanoscale. 2018. PMID: 29557448
Sensing surface mechanical deformation using active probes driven by motor proteins.
Inoue D, Nitta T, Kabir AMR, Sada K, Gong JP, Konagaya A, Kakugo A. Inoue D, et al. Among authors: konagaya a. Nat Commun. 2016 Oct 3;7:12557. doi: 10.1038/ncomms12557. Nat Commun. 2016. PMID: 27694937 Free PMC article.
Stabilization of microtubules by cevipabulin.
Nasrin SR, Rashedul Kabir AM, Konagaya A, Ishihara T, Sada K, Kakugo A. Nasrin SR, et al. Among authors: konagaya a. Biochem Biophys Res Commun. 2019 Aug 27;516(3):760-764. doi: 10.1016/j.bbrc.2019.06.095. Epub 2019 Jun 26. Biochem Biophys Res Commun. 2019. PMID: 31253401
Drug interaction prediction using ontology-driven hypothetical assertion framework for pathway generation followed by numerical simulation.
Arikuma T, Yoshikawa S, Azuma R, Watanabe K, Matsumura K, Konagaya A. Arikuma T, et al. Among authors: konagaya a. BMC Bioinformatics. 2008 May 28;9 Suppl 6(Suppl 6):S11. doi: 10.1186/1471-2105-9-S6-S11. BMC Bioinformatics. 2008. PMID: 18541046 Free PMC article.
Structure and dynamics of RNA polymerase II elongation complex.
Suenaga A, Okimoto N, Futatsugi N, Hirano Y, Narumi T, Ohno Y, Yanai R, Hirokawa T, Ebisuzaki T, Konagaya A, Taiji M. Suenaga A, et al. Among authors: konagaya a. Biochem Biophys Res Commun. 2006 Apr 28;343(1):90-8. doi: 10.1016/j.bbrc.2006.02.124. Epub 2006 Mar 2. Biochem Biophys Res Commun. 2006. PMID: 16529717
Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.
Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H, Yamanaka I, Kiyosawa H, Yagi K, Tomaru Y, Hasegawa Y, Nogami A, Schönbach C, Gojobori T, Baldarelli R, Hill DP, Bult C, Hume DA, Quackenbush J, Schriml LM, Kanapin A, Matsuda H, Batalov S, Beisel KW, Blake JA, Bradt D, Brusic V, Chothia C, Corbani LE, Cousins S, Dalla E, Dragani TA, Fletcher CF, Forrest A, Frazer KS, Gaasterland T, Gariboldi M, Gissi C, Godzik A, Gough J, Grimmond S, Gustincich S, Hirokawa N, Jackson IJ, Jarvis ED, Kanai A, Kawaji H, Kawasawa Y, Kedzierski RM, King BL, Konagaya A, Kurochkin IV, Lee Y, Lenhard B, Lyons PA, Maglott DR, Maltais L, Marchionni L, McKenzie L, Miki H, Nagashima T, Numata K, Okido T, Pavan WJ, Pertea G, Pesole G, Petrovsky N, Pillai R, Pontius JU, Qi D, Ramachandran S, Ravasi T, Reed JC, Reed DJ, Reid J, Ring BZ, Ringwald M, Sandelin A, Schneider C, Semple CA, Setou M, Shimada K, Sultana R, Takenaka Y, Taylor MS, Teasdale RD, Tomita M, Verardo R, Wagner L, Wahlestedt C, Wang Y, Watanabe Y, Wells C, Wilming LG, Wynshaw-Boris A, Yanagisawa M, Yang I, Yang L, Yuan Z, Zavolan M, Zhu Y, Zimmer A, Carninci P, Hayatsu N, Hirozane-Kishikawa T, Konno H, Nakamura M, Sakazume N, Sato K, Shiraki T, Waki K, Kawai J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Imotani K, Ishii Y, Itoh M, Kagawa I, Miyazaki A, Sakai K, Sasaki D, Shibata K, Shinagawa A, Yasunishi A, Yoshino M, Waterston R, Lander ES, Rogers J, Birney E, Hayashizaki Y; FANTOM Consortium; RIKEN Genome Exploration Research Group Phase I & II Team. Okazaki Y, et al. Among authors: konagaya a. Nature. 2002 Dec 5;420(6915):563-73. doi: 10.1038/nature01266. Nature. 2002. PMID: 12466851
Accurate Estimation of In Vivo Inhibition Constants of Inhibitors and Fraction Metabolized of Substrates with Physiologically Based Pharmacokinetic Drug-Drug Interaction Models Incorporating Parent Drugs and Metabolites of Substrates with Cluster Newton Method.
Yoshida K, Maeda K, Konagaya A, Kusuhara H. Yoshida K, et al. Among authors: konagaya a. Drug Metab Dispos. 2018 Nov;46(11):1805-1816. doi: 10.1124/dmd.118.081828. Epub 2018 Aug 22. Drug Metab Dispos. 2018. PMID: 30135241
Constraint-based perturbation analysis with cluster Newton method: a case study of personalized parameter estimations with irinotecan whole-body physiologically based pharmacokinetic model.
Asami S, Kiga D, Konagaya A. Asami S, et al. Among authors: konagaya a. BMC Syst Biol. 2017 Dec 21;11(Suppl 7):129. doi: 10.1186/s12918-017-0513-2. BMC Syst Biol. 2017. PMID: 29322928 Free PMC article.
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