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Items: 1 to 50 of 62

1.

Adaptation of Patterns of Motile Filaments under Dynamic Boundary Conditions.

Inoue D, Gutmann G, Nitta T, Kabir AMR, Konagaya A, Tokuraku K, Sada K, Hess H, Kakugo A.

ACS Nano. 2019 Oct 17. doi: 10.1021/acsnano.9b01450. [Epub ahead of print]

PMID:
31585030
2.

Significance of Data Selection in Deep Learning for Reliable Binding Mode Prediction of Ligands in the Active Site of CYP3A4.

Sato A, Tanimura N, Honma T, Konagaya A.

Chem Pharm Bull (Tokyo). 2019 Nov 1;67(11):1183-1190. doi: 10.1248/cpb.c19-00443. Epub 2019 Aug 17.

3.

Stabilization of microtubules by cevipabulin.

Nasrin SR, Rashedul Kabir AM, Konagaya A, Ishihara T, Sada K, Kakugo A.

Biochem Biophys Res Commun. 2019 Aug 27;516(3):760-764. doi: 10.1016/j.bbrc.2019.06.095. Epub 2019 Jun 26.

PMID:
31253401
4.

Artificial Smooth Muscle Model Composed of Hierarchically Ordered Microtubule Asters Mediated by DNA Origami Nanostructures.

Matsuda K, Kabir AMR, Akamatsu N, Saito A, Ishikawa S, Matsuyama T, Ditzer O, Islam MS, Ohya Y, Sada K, Konagaya A, Kuzuya A, Kakugo A.

Nano Lett. 2019 Jun 12;19(6):3933-3938. doi: 10.1021/acs.nanolett.9b01201. Epub 2019 May 3.

PMID:
31037942
6.

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.

Nanoscale. 2018 Apr 5;10(14):6323-6332. doi: 10.1039/C7NR05099B.

PMID:
29557448
8.

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.

Nat Commun. 2016 Oct 3;7:12557. doi: 10.1038/ncomms12557.

9.

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.

Nanoscale. 2015 Nov 21;7(43):18054-61. doi: 10.1039/c5nr02213d.

10.

Implementing a modeling software for animated protein-complex interactions using a physics simulation library.

Ueno Y, Ito S, Konagaya A.

J Bioinform Comput Biol. 2014 Dec;12(6):1442003. doi: 10.1142/S0219720014420037.

PMID:
25385079
11.

Molecular robots with sensors and intelligence.

Hagiya M, Konagaya A, Kobayashi S, Saito H, Murata S.

Acc Chem Res. 2014 Jun 17;47(6):1681-90. doi: 10.1021/ar400318d. Epub 2014 Jun 6.

PMID:
24905779
12.
13.

On experiences of i2b2 (Informatics for integrating biology and the bedside) database with Japanese clinical patients' data.

Takai-Igarashi T, Akasaka R, Suzuki K, Furukawa T, Yoshida M, Inoue K, Maruyama T, Maejima T, Bando M, Takasaki M, Sakota M, Eguchi M, Konagaya A, Matsuura H, Suzumura T, Tanaka H.

Bioinformation. 2011 Mar 26;6(2):86-90.

14.

The phenotype and genotype experiment object model (PaGE-OM): a robust data structure for information related to DNA variation.

Brookes AJ, Lehvaslaiho H, Muilu J, Shigemoto Y, Oroguchi T, Tomiki T, Mukaiyama A, Konagaya A, Kojima T, Inoue I, Kuroda M, Mizushima H, Thorisson GA, Dash D, Rajeevan H, Darlison MW, Woon M, Fredman D, Smith AV, Senger M, Naito K, Sugawara H.

Hum Mutat. 2009 Jun;30(6):968-77. doi: 10.1002/humu.20973.

PMID:
19479963
15.

Coincidence between transcriptome analyses on different microarray platforms using a parametric framework.

Konishi T, Konishi F, Takasaki S, Inoue K, Nakayama K, Konagaya A.

PLoS One. 2008;3(10):e3555. doi: 10.1371/journal.pone.0003555. Epub 2008 Oct 29.

16.

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.

BMC Bioinformatics. 2008 May 28;9 Suppl 6:S11. doi: 10.1186/1471-2105-9-S6-S11.

17.

Microchromosomal deletions involving SCN1A and adjacent genes in severe myoclonic epilepsy in infancy.

Wang JW, Kurahashi H, Ishii A, Kojima T, Ohfu M, Inoue T, Ogawa A, Yasumoto S, Oguni H, Kure S, Fujii T, Ito M, Okuno T, Shirasaka Y, Natsume J, Hasegawa A, Konagaya A, Kaneko S, Hirose S.

Epilepsia. 2008 Sep;49(9):1528-34. doi: 10.1111/j.1528-1167.2008.01609.x. Epub 2008 Apr 21.

18.

Introduction to the special section on BioGrid: biomedical computations on the grid.

Huang CH, Konagaya A, Lanza V, Sloot PM.

IEEE Trans Inf Technol Biomed. 2008 Mar;12(2):133-7. No abstract available.

PMID:
18416025
19.

Integrative genome-wide expression analysis bears evidence of estrogen receptor-independent transcription in heregulin-stimulated MCF-7 cells.

Nagashima T, Suzuki T, Kondo S, Kuroki Y, Takahashi K, Ide K, Yumoto N, Hasegawa A, Toyoda T, Kojima T, Konagaya A, Suzuki H, Hayashizaki Y, Sakaki Y, Hatakeyama M.

PLoS One. 2008 Mar 19;3(3):e1803. doi: 10.1371/journal.pone.0001803.

20.

The chloroplast genome from a lycophyte (microphyllophyte), Selaginella uncinata, has a unique inversion, transpositions and many gene losses.

Tsuji S, Ueda K, Nishiyama T, Hasebe M, Yoshikawa S, Konagaya A, Nishiuchi T, Yamaguchi K.

J Plant Res. 2007 Mar;120(2):281-90. Epub 2007 Feb 13.

PMID:
17297557
21.

Novel peroxisomal protease Tysnd1 processes PTS1- and PTS2-containing enzymes involved in beta-oxidation of fatty acids.

Kurochkin IV, Mizuno Y, Konagaya A, Sakaki Y, Schönbach C, Okazaki Y.

EMBO J. 2007 Feb 7;26(3):835-45. Epub 2007 Jan 25.

22.

Selecting effective siRNA sequences by using radial basis function network and decision tree learning.

Takasaki S, Kawamura Y, Konagaya A.

BMC Bioinformatics. 2006 Dec 18;7 Suppl 5:S22.

23.

Trends in life science grid: from computing grid to knowledge grid.

Konagaya A.

BMC Bioinformatics. 2006 Dec 18;7 Suppl 5:S10. Review.

24.

Particle simulation approach for subcellular dynamics and interactions of biological molecules.

Azuma R, Kitagawa T, Kobayashi H, Konagaya A.

BMC Bioinformatics. 2006 Dec 12;7 Suppl 4:S20.

25.

Selecting effective siRNA target sequences for mammalian genes.

Takasaki S, Kotani S, Konagaya A.

RNA Biol. 2005 Jan;2(1):21-7. Epub 2005 Jan 5.

PMID:
17132936
26.

RARTF: database and tools for complete sets of Arabidopsis transcription factors.

Iida K, Seki M, Sakurai T, Satou M, Akiyama K, Toyoda T, Konagaya A, Shinozaki K.

DNA Res. 2005;12(4):247-56.

PMID:
16769687
27.

Selecting effective siRNA sequences based on the self-organizing map and statistical techniques.

Takasaki S, Kawamura Y, Konagaya A.

Comput Biol Chem. 2006 Jun;30(3):169-78. Epub 2006 Apr 5.

PMID:
16600687
28.

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.

Biochem Biophys Res Commun. 2006 Apr 28;343(1):90-8. Epub 2006 Mar 2.

PMID:
16529717
29.

A flexible representation of omic knowledge for thorough analysis of microarray data.

Hasegawa Y, Seki M, Mochizuki Y, Heida N, Hirosawa K, Okamoto N, Sakurai T, Satou M, Akiyama K, Iida K, Lee K, Kanaya S, Demura T, Shinozaki K, Konagaya A, Toyoda T.

Plant Methods. 2006 Mar 2;2:5.

30.

Bead-like passage of chloride ions through ClC chloride channels.

Suenaga A, Yeh JZ, Taiji M, Toyama A, Takeuchi H, Son M, Takayama K, Iwamoto M, Sato I, Narahashi T, Konagaya A, Goto K.

Biophys Chem. 2006 Mar 1;120(1):36-43. Epub 2005 Nov 9.

PMID:
16288955
31.

Compensation effect of the MAPK cascade on formation of phospho-protein gradients.

Naka T, Hatakeyama M, Sakamoto N, Konagaya A.

Biosystems. 2006 Feb-Mar;83(2-3):167-77. Epub 2005 Oct 19.

PMID:
16236425
32.

Sequence-based discovery of the human and rodent peroxisomal proteome.

Kurochkin IV, Nagashima T, Konagaya A, Schönbach C.

Appl Bioinformatics. 2005;4(2):93-104.

PMID:
16128611
33.

Three-dimensional definition of leaf morphological traits of Arabidopsis in silico phenotypic analysis.

Kaminuma E, Heida N, Tsumoto Y, Nakazawa M, Goto N, Konagaya A, Matsui M, Toyoda T.

J Bioinform Comput Biol. 2005 Apr;3(2):401-14.

PMID:
15852512
34.

RARGE: a large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome.

Sakurai T, Satou M, Akiyama K, Iida K, Seki M, Kuromori T, Ito T, Konagaya A, Toyoda T, Shinozaki K.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D647-50.

35.

Textmining in support of knowledge discovery for vaccine development.

Schönbach C, Nagashima T, Konagaya A.

Methods. 2004 Dec;34(4):488-95. Review.

PMID:
15542375
36.

Use of morphological analysis in protein name recognition.

Yamamoto K, Kudo T, Konagaya A, Matsumoto Y.

J Biomed Inform. 2004 Dec;37(6):471-82.

37.

Novel mechanism of interaction of p85 subunit of phosphatidylinositol 3-kinase and ErbB3 receptor-derived phosphotyrosyl peptides.

Suenaga A, Takada N, Hatakeyama M, Ichikawa M, Yu X, Tomii K, Okimoto N, Futatsugi N, Narumi T, Shirouzu M, Yokoyama S, Konagaya A, Taiji M.

J Biol Chem. 2005 Jan 14;280(2):1321-6. Epub 2004 Nov 1.

38.

Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm.

Kimura S, Ide K, Kashihara A, Kano M, Hatakeyama M, Masui R, Nakagawa N, Yokoyama S, Kuramitsu S, Konagaya A.

Bioinformatics. 2005 Apr 1;21(7):1154-63. Epub 2004 Oct 28.

PMID:
15514004
39.

Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences.

Iida K, Seki M, Sakurai T, Satou M, Akiyama K, Toyoda T, Konagaya A, Shinozaki K.

Nucleic Acids Res. 2004 Sep 27;32(17):5096-103. Print 2004.

40.

Drug interaction ontology (DIO) for inferences of possible drug-drug interactions.

Yoshikawa S, Satou K, Konagaya A.

Stud Health Technol Inform. 2004;107(Pt 1):454-8.

PMID:
15360854
41.

TraitMap: an XML-based genetic-map database combining multigenic loci and biomolecular networks.

Heida N, Hasegawa Y, Mochizuki Y, Hirosawa K, Konagaya A, Toyoda T.

Bioinformatics. 2004 Aug 4;20 Suppl 1:i152-60.

PMID:
15262794
42.

An effective method for selecting siRNA target sequences in mammalian cells.

Takasaki S, Kotani S, Konagaya A.

Cell Cycle. 2004 Jun;3(6):790-5. Epub 2004 Jun 1.

PMID:
15118413
43.

Automatic quantification of morphological traits via three-dimensional measurement of Arabidopsis.

Kaminuma E, Heida N, Tsumoto Y, Yamamoto N, Goto N, Okamoto N, Konagaya A, Matsui M, Toyoda T.

Plant J. 2004 Apr;38(2):358-65.

44.

Transformation potency of ErbB heterodimer signaling is determined by B-Raf kinase.

Hatakeyama M, Yumoto N, Yu X, Shirouzu M, Yokoyama S, Konagaya A.

Oncogene. 2004 Jun 24;23(29):5023-31.

PMID:
15064721
45.

OBIYagns: a grid-based biochemical simulator with a parameter estimator.

Kimura S, Kawasaki T, Hatakeyama M, Naka T, Konishi F, Konagaya A.

Bioinformatics. 2004 Jul 10;20(10):1646-8. Epub 2004 Feb 12.

PMID:
14962919
46.

Efficient filtering methods for clustering cDNAs with spliced sequence alignment.

Shibuya T, Kashima H, Konagaya A.

Bioinformatics. 2004 Jan 1;20(1):29-39.

PMID:
14693805
47.

FREP: a database of functional repeats in mouse cDNAs.

Nagashima T, Matsuda H, Silva DG, Petrovsky N, Konagaya A, Schönbach C, Kasukawa T, Arakawa T, Carninci P, Kawai J, Hayashizaki Y; RIKEN GER Group; Genome Science Laoratory Members.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D471-5.

48.

Increased rigidity of domain structures enhances the stability of a mutant enzyme created by directed evolution.

Hoseki J, Okamoto A, Takada N, Suenaga A, Futatsugi N, Konagaya A, Taiji M, Yano T, Kuramitsu S, Kagamiyama H.

Biochemistry. 2003 Dec 16;42(49):14469-75.

PMID:
14661958
49.

Tyr-317 phosphorylation increases Shc structural rigidity and reduces coupling of domain motions remote from the phosphorylation site as revealed by molecular dynamics simulations.

Suenaga A, Kiyatkin AB, Hatakeyama M, Futatsugi N, Okimoto N, Hirano Y, Narumi T, Kawai A, Susukita R, Koishi T, Furusawa H, Yasuoka K, Takada N, Ohno Y, Taiji M, Ebisuzaki T, Hoek JB, Konagaya A, Kholodenko BN.

J Biol Chem. 2004 Feb 6;279(6):4657-62. Epub 2003 Nov 12.

50.

Inferring higher functional information for RIKEN mouse full-length cDNA clones with FACTS.

Nagashima T, Silva DG, Petrovsky N, Socha LA, Suzuki H, Saito R, Kasukawa T, Kurochkin IV, Konagaya A, Schönbach C.

Genome Res. 2003 Jun;13(6B):1520-33.

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