ynaito's library 78 articles Export

	In silico modeling and metabolome analysis of long-stored erythrocytes to improve blood storage methods. [My Copy] Journal of biotechnology (18 August 2009) by Taiko Nishino, Ayako Yachie-Kinoshita, Akiyoshi Hirayama, Tomoyoshi Soga, Makoto Suematsu, Masaru Tomita posted to mt-rg erythrocyte e-cell computer-simulation by ynaito on 2009-09-24 02:07:04 as
	Multiple high-throughput analyses monitor the response of E. coli to perturbations. [My Copy] Science (New York, N.Y.), Vol. 316, No. 5824. (27 April 2007), pp. 593-597. by Nobuyoshi Ishii, Kenji Nakahigashi, Tomoya Baba, et al.Martin Robert, Tomoyoshi Soga, Akio Kanai, Takashi Hirasawa, Miki Naba, Kenta Hirai, Aminul Hoque, Pei Yee Y. Ho, Yuji Kakazu, Kaori Sugawara, Saori Igarashi, Satoshi Harada, Takeshi Masuda, Naoyuki Sugiyama, Takashi Togashi, Miki Hasegawa, Yuki Takai, Katsuyuki Yugi, Kazuharu Arakawa, Nayuta Iwata, Yoshihiro Toya, Yoichi Nakayama, Takaaki Nishioka, Kazuyuki Shimizu, Hirotada Mori, Masaru Tomita posted to systems-biology e-cell computer-simulation by ynaito on 2009-09-23 07:20:06 as along with 8 people and 1 group JeremyZucker cgaugain thomaskelder jjray raiyar dylan77 ytoya IgorG steinmetzlab
	Computational biology in the study of cardiac ion channels and cell electrophysiology [My Copy] Quarterly Reviews of Biophysics, Vol. 39, No. 01. (19 July 2006), pp. 57-116. by Yoram Rudy, Jonathan R. Silva posted to computer-simulation myocardium by ynaito on 2009-06-13 02:05:51 as along with 2 people and 1 group Dangerfc brocktice TulaneCEP
	Directed transdifferentiation of mouse mesoderm to heart tissue by defined factors [My Copy] Nature (26 April 2009) by Jun K. Takeuchi, Benoit G. Bruneau posted to development myocardium by ynaito on 2009-06-13 01:48:02 as along with 3 people and 1 group joseph_x_zhou fenghezi leliavski bioNetwork_sysBio
	Developmental biology: The early heart remodelled [My Copy] Nature, Vol. 459, No. 7247. (4 June 2009), pp. 654-655. by Fu-Sen Liang, Gerald R. Crabtree posted to development myocardium review by ynaito on 2009-06-13 01:32:49 as along with 1 person fenghezi
	Genesis and regulation of the heart automaticity. [My Copy] Physiological reviews, Vol. 88, No. 3. (July 2008), pp. 919-982. by M. E. Mangoni, J. Nargeot posted to automaticity myocardium by ynaito on 2009-05-11 03:30:59 as
	Ascaris haemoglobin is a nitric oxide-activated 'deoxygenase'. [My Copy] Nature, Vol. 401, No. 6752. (30 September 1999), pp. 497-502. by D. M. Minning, A. J. Gow, J. Bonaventura, et al.R. Braun, M. Dewhirst, D. E. Goldberg, J. S. Stamler posted to hemoglobin by ynaito on 2009-04-13 09:36:45 as
	An enzymatic globin from a marine worm. [My Copy] Nature, Vol. 401, No. 6752. (30 September 1999) by L. Lebioda, M. W. LaCount, E. Zhang, et al.Y. P. Chen, K. Han, M. M. Whitton, D. E. Lincoln, S. A. Woodin posted to hemoglobin by ynaito on 2009-04-13 09:35:36 as
	The haemoglobin enzyme. [My Copy] Nature, Vol. 401, No. 6752. (30 September 1999) by K. Imai posted to hemoglobin by ynaito on 2009-04-13 09:34:43 as
	ATP-induced reverse temperature effect in isohemoglobins from the endothermic porbeagle shark (Lamna nasus). [My Copy] The Journal of biological chemistry, Vol. 278, No. 33. (15 August 2003), pp. 30741-30747. by C. Larsen, H. Malte, R. E. Weber posted to hemoglobin by ynaito on 2009-04-13 09:33:00 as
	Fish hemoglobins. [My Copy] Brazilian journal of medical and biological research = Revista brasileira de pesquisas médicas e biológicas / Sociedade Brasileira de Biofísica ... [et al.], Vol. 40, No. 6. (June 2007), pp. 769-778. by P. C. de Souza, G. O. Bonilla-Rodriguez posted to hemoglobin by ynaito on 2009-04-13 09:31:48 as
	The origin of protein interactions and allostery in colocalization. [My Copy] Nature, Vol. 450, No. 7172. (13 December 2007), pp. 983-990. by John Kuriyan, David Eisenberg posted to facilitated-variation hemoglobin by ynaito on 2009-04-13 09:29:54 as along with 6 people and 1 group yanjiang cjeans sobolevnrm mingzhi phoenixzxl higueruelo baker-group
	Evolutionarily conserved networks of residues mediate allosteric communication in proteins [My Copy] Nature Structural & Molecular Biology, Vol. 10, No. 1. (16 December 2002), pp. 59-69. by Gurol M. Suel, Steve W. Lockless, Mark A. Wall, Rama Ranganathan posted to facilitated-variation hemoglobin by ynaito on 2009-04-13 09:28:05 as along with 20 people and 3 groups mgomes qluo arjun_citeulike RebeccaHamer lna dimka marcius eckart_bindewald gbart analogAI nirfriedman dgront caporaso choonpeng efge carlescorbi mingzhi yalexeev weisblum ca3295 biomedical-nlp BioinfoCIPF SGU-CIPF
	Evolution of allosteric models for hemoglobin. [My Copy] IUBMB Life, Vol. 59, No. 8-9. (p 2007), pp. 586-599. by W. A. Eaton, E. R. Henry, J. Hofrichter, S. Bettati, C. Viappiani, A. Mozzarelli posted to facilitated-variation hemoglobin by ynaito on 2009-04-13 09:11:33 as along with 1 person kjell
	A quantum-chemical picture of hemoglobin affinity [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 47. (20 November 2007), pp. 18451-18455. by R. E. Alcantara, C. Xu, T. G. Spiro, V. Guallar posted to facilitated-variation hemoglobin by ynaito on 2009-04-13 09:07:08 as along with 1 person and 1 group sobolevnrm baker-group
	Cooperativity and allostery in haemoglobin function. [My Copy] IUBMB life, Vol. 60, No. 2. (February 2008), pp. 112-123. by C. Ciaccio, A. Coletta, G. De Sanctis, S. Marini, M. Coletta posted to facilitated-variation hemoglobin by ynaito on 2009-04-13 09:03:12 as
	The evolution of hierarchical gene regulatory networks [My Copy] Nat Rev Genet, Vol. 10, No. 2. (February 2009), pp. 141-148. by Douglas H. Erwin, Eric H. Davidson posted to gene-expression review systems-biology by ynaito on 2009-04-10 05:14:56 as along with 10 people PabloMarin Scis0000002 erel10 dakelley wangbo natstreet druvus balicea Borelli balabu
	Philosophical Basis and Some Historical Aspects of Systems Biology: From Hegel to Noble - Applications for Bioenergetic Research [My Copy] INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, Vol. 10, No. 3. (March 2009), pp. 1161-1192. by V. Saks, C. Monge, R. Guzun posted to computer-simulation electrophysiology kyoto-model systems-biology by ynaito on 2009-04-10 04:55:30 as
	Facilitated Variation: How Evolution Learns from Past Environments To Generalize to New Environments [My Copy] PLoS Comput Biol, Vol. 4, No. 11. (7 November 2008), e1000206. by Merav Parter, Nadav Kashtan, Uri Alon posted to facilitated-variation by ynaito on 2009-04-08 05:50:30 as along with 10 people and 1 group cambray rouault ocs djkt balicea shoshin rebeccamancy cabbagesofdoom dlobo kentsis GEB
	Analysis of heterogeneity and epistasis in physiological mixed populations by combined structural equation modelling and latent class analysis. [My Copy] BMC Genetics, Vol. 9 (08 July 2008), 43. by Mogens Fenger, Allan Linneberg, Thomas Werge, Torben Jorgensen posted to evolution evolvability by ynaito on 2009-03-25 13:30:28 as along with 2 people tomhebbron guhjy
	Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation. [My Copy] Nature reviews. Genetics (1 July 2008) by Luis López-Maury, Samuel Marguerat, Jürg Bähler posted to evolution evolvability gene-expression by ynaito on 2009-03-25 13:25:56 as along with 14 people and 2 groups gridqueenundercover lingxuan Zephyrus rouault lp2 vertikalist Ema jmjimenez bootsy jjray klo cambray bpcusack guhjy R.E.A.D BTS-PT-AS-CS
	Historical and contingent factors affect re-evolution of a complex feature lost during mass extinction in communities of digital organisms [My Copy] Journal of Evolutionary Biology, Vol. 21, No. 5. (September 2008), pp. 1335-1357. by G. Yedid, C. A. Ofria, R. E. Lenski posted to evolution by ynaito on 2009-03-25 13:22:57 as along with 1 person druvus
	Biological theory: Postmodern evolution? [My Copy] Nature, Vol. 455, No. 7211. (18 September 2008), pp. 281-284. by J. Whitfield posted to evolution by ynaito on 2009-03-25 13:20:18 as
	cDNA sequences for transcription factors and signaling proteins of the hemichordate Saccoglossus kowalevskii: efficacy of the expressed sequence tag (EST) approach for evolutionary and developmental studies of a new organism. [My Copy] The Biological bulletin, Vol. 214, No. 3. (June 2008), pp. 284-302. by R. M. Freeman, M. Wu, M. M. Cordonnier-Pratt, et al.L. H. Pratt, C. E. Gruber, M. Smith, E. S. Lander, N. Stange-Thomann, C. J. Lowe, J. Gerhart, M. Kirschner posted to evolution systems-biology by ynaito on 2009-03-25 12:48:59 as
	Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida [My Copy] Nature (18 October 2006) by Sarah J. Bourlat, Thorhildur Juliusdottir, Christopher J. Lowe, et al.Robert Freeman, Jochanan Aronowicz, Mark Kirschner, Eric S. Lander, Michael Thorndyke, Hiroaki Nakano, Andrea B. Kohn, Andreas Heyland, Leonid L. Moroz, Richard R. Copley, Maximilian J. Telford posted to evolution systems-biology by ynaito on 2009-03-25 12:46:41 as along with 3 people Auger maximilianh cmzmasek
	The theory of facilitated variation. [My Copy] Proc Natl Acad Sci U S A (9 May 2007) by John Gerhart, Marc Kirschner posted to evolution systems-biology by ynaito on 2009-03-25 12:43:42 as along with 4 people and 3 groups balicea cambray mattjb biomcgary ComplexAdaptiveSystems DSTO-CAS Marcotte_Lab
	Hemichordates and the origin of chordates. [My Copy] Current opinion in genetics & development, Vol. 15, No. 4. (August 2005), pp. 461-467. by J. Gerhart, C. Lowe, M. Kirschner posted to evolution systems-biology by ynaito on 2009-03-25 12:34:51 as
	Evolvability. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 95, No. 15. (21 July 1998), pp. 8420-8427. by M. Kirschner, J. Gerhart posted to evolution evolvability systems-biology by ynaito on 2009-03-25 12:08:14 as along with 12 people and 1 group chica Scis0000002 rklancer betainverse sccook eldan ryang balicea larios timflutre qwermish mahmoodr Centre de Recherches Interdisciplinaires
	The relationship between evolutionary and physiological variation in hemoglobin. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 43. (23 October 2007), pp. 16998-17003. by R. Milo, J. H. Hou, M. Springer, M. P. Brenner, M. W. Kirschner posted to evolution systems-biology by ynaito on 2009-03-25 12:04:59 as
	The Meaning of Systems Biology [My Copy] Cell, Vol. 121, No. 4. (20 May 2005), pp. 503-504. by M. Kirschner posted to systems-biology by ynaito on 2009-03-25 11:50:42 as along with 5 people bertelsen LeightonP wnpx biosv lpfernandes
	Roles of Hemoglobin Allostery in Hypoxia-induced Metabolic Alterations in Erythrocytes: SIMULATION AND ITS VERIFICATION BY METABOLOME ANALYSIS [My Copy] J. Biol. Chem., Vol. 282, No. 14. (6 April 2007), pp. 10731-10741. by Ayako Kinoshita, Kosuke Tsukada, Tomoyoshi Soga, et al.Takako Hishiki, Yuki Ueno, Yoichi Nakayama, Masaru Tomita, Makoto Suematsu posted to computer-simulation e-cell mt-rg by ynaito on 2009-03-25 05:11:03 as along with 1 person and 1 group sobolevnrm baker-group
	A mathematical model for the Kai-protein-based chemical oscillator and clock gene expression rhythms in cyanobacteria. [My Copy] Journal of biological rhythms, Vol. 22, No. 1. (February 2007), pp. 69-80. by F. Miyoshi, Y. Nakayama, K. Kaizu, H. Iwasaki, M. Tomita posted to computer-simulation e-cell mt-rg by ynaito on 2009-03-25 05:08:42 as
	Over-representation of Chi sequences caused by di-codon increase in Escherichia coli K-12. [My Copy] Gene, Vol. 380, No. 1. (15 September 2006), pp. 30-37. by R. Uno, Y. Nakayama, M. Tomita posted to mt-rg by ynaito on 2009-03-25 05:08:21 as
	A simplified method for power-law modelling of metabolic pathways from time-course data and steady-state flux profiles [My Copy] Theoretical Biology and Medical Modelling, Vol. 3, No. 1. (17 July 2006), 24. by Tomoya Kitayama, Ayako Kinoshita, Masahiro Sugimoto, Yoichi Nakayama, Masaru Tomita posted to computer-simulation mt-rg by ynaito on 2009-03-25 05:06:26 as along with 1 person bertelsen
	A microarray data-based semi-kinetic method for predicting quantitative dynamics of genetic networks. [My Copy] BMC Bioinformatics, Vol. 6 (2005) by K. Yugi, Y. Nakayama, S. Kojima, T. Kitayama, M. Tomita posted to computer-simulation e-cell mt-rg by ynaito on 2009-03-25 05:04:27 as along with 2 people gespim bertelsen
	Hybrid dynamic/static method for large-scale simulation of metabolism [My Copy] Theoretical Biology and Medical Modelling, Vol. 2, No. 1. (2005), 42. by Katsuyuki Yugi, Yoichi Nakayama, Ayako Kinoshita, Masaru Tomita posted to computer-simulation e-cell mt-rg by ynaito on 2009-03-25 05:02:09 as along with 1 person abhishek_tiwari
	Dynamic simulation of red blood cell metabolism and its application to the analysis of a pathological condition [My Copy] Theoretical Biology and Medical Modelling, Vol. 2, No. 1. (2005) by Yoichi Nakayama, Ayako Kinoshita, Masaru Tomita posted to computer-simulation e-cell mt-rg by ynaito on 2009-03-25 05:01:48 as along with 2 people fishtank csanford
	Toward large-scale modeling of the microbial cell for computer simulation. [My Copy] J Biotechnol, Vol. 113, No. 1-3. (30 September 2004), pp. 281-294. by N. Ishii, M. Robert, Y. Nakayama, A. Kanai, M. Tomita posted to computer-simulation e-cell mt-rg by ynaito on 2009-03-25 05:01:24 as along with 9 people and 3 groups csanford eldan wnpx Doug cottrell livingthingdan josepe fishtank roland_ewald livingthing dIEMoSIRIS MoSi-Rostock
	On dynamics of overlapping genes in bacterial genomes. [My Copy] Gene, Vol. 323 (24 December 2003), pp. 181-187. by Y. Fukuda, Y. Nakayama, M. Tomita posted to mt-rg by ynaito on 2009-03-25 05:00:18 as along with 1 person druvus
	[Computer models of plant metabolism] [My Copy] Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme, Vol. 48, No. 15 Suppl. (November 2003), pp. 2205-2210. by N. Ishii, Y. Nakayama, M. Tomita posted to computer-simulation e-cell japanese mt-rg by ynaito on 2009-03-25 04:59:45 as
	[E-Cell simulation system and its application to the modeling of circadian rhythm] [My Copy] Seikagaku. The Journal of Japanese Biochemical Society, Vol. 75, No. 1. (January 2003), pp. 5-16. by F. Miyoshi, Y. Nakayama, M. Tomita posted to computer-simulation e-cell japanese mt-rg by ynaito on 2009-03-25 04:59:13 as
	A quantitative measure of error minimization in the genetic code. [My Copy] Journal of molecular evolution, Vol. 33, No. 5. (November 1991), pp. 412-417. by D. Haig, L. D. Hurst posted to evolution genetic-code by ynaito on 2009-03-24 14:23:56 as
	Eye evolution: the blurry beginning. [My Copy] Current biology : CB, Vol. 18, No. 23. (9 December 2008) by D. E. Nilsson, D. Arendt posted to evolution eye by ynaito on 2009-03-24 14:22:22 as
	E-CELL: Software Environment for Whole Cell Simulation. [My Copy] Genome informatics. Workshop on Genome Informatics, Vol. 8 (1997), pp. 147-155. by M. Tomita, K. Hashimoto, K. Takahashi, et al.T. Shimizu, Y. Matsuzaki, F. Miyoshi, K. Saito, S. Tanida, K. Yugi, J. C. Venter, C. A. Hutchison posted to computer-simulation e-cell mt-rg by ynaito on 2009-03-24 14:19:51 as
	E-CELL: software environment for whole-cell simulation [My Copy] Bioinformatics, Vol. 15, No. 1. (1 January 1999), pp. 72-84. by M. Tomita, K. Hashimoto, K. Takahashi, et al.T. S. Shimizu, Y. Matsuzaki, F. Miyoshi, K. Saito, S. Tanida, K. Yugi, J. C. Venter, Ca Hutchison posted to computer-simulation e-cell mt-rg by ynaito on 2009-03-24 14:19:35 as along with 3 people antonkratz chrn johnpeterwalsh
	Simulation analysis of intracellular Na+ and Cl- homeostasis during beta 1-adrenergic stimulation of cardiac myocyte. [My Copy] Progress in biophysics and molecular biology, Vol. 96, No. 1-3. (r 2008), pp. 171-186. by M. Kuzumoto, A. Takeuchi, H. Nakai, C. Oka, A. Noma, S. Matsuoka posted to computer-simulation kyoto-model myocardium by ynaito on 2009-03-24 14:17:47 as
	Ionic mechanisms underlying the positive chronotropy induced by beta1-adrenergic stimulation in guinea pig sinoatrial node cells: a simulation study. [My Copy] The journal of physiological sciences : JPS, Vol. 58, No. 1. (February 2008), pp. 53-65. by Y. Himeno, N. Sarai, S. Matsuoka, A. Noma posted to computer-simulation kyoto-model myocardium by ynaito on 2009-03-24 14:16:43 as
	A simulation study to rescue the Na+/Ca2+ exchanger knockout mice. [My Copy] The journal of physiological sciences : JPS, Vol. 56, No. 3. (June 2006), pp. 211-217. by N. Sarai, T. Kobayashi, S. Matsuoka, A. Noma posted to computer-simulation kyoto-model myocardium by ynaito on 2009-03-24 14:16:21 as
	Modelling Cl- homeostasis and volume regulation of the cardiac cell. [My Copy] Philosophical transactions. Series A, Mathematical, physical, and engineering sciences, Vol. 364, No. 1842. (15 May 2006), pp. 1245-1265. by K. Terashima, A. Takeuchi, N. Sarai, et al.S. Matsuoka, E. B. Shim, C. H. Leem, A. Noma posted to computer-simulation kyoto-model myocardium by ynaito on 2009-03-24 14:15:51 as
	simBio: a Java package for the development of detailed cell models. [My Copy] Progress in biophysics and molecular biology, Vol. 90, No. 1-3. (r 2006), pp. 360-377. by N. Sarai, S. Matsuoka, A. Noma posted to computer-simulation kyoto-model myocardium by ynaito on 2009-03-24 14:15:28 as

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computer-simulation	28
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hemoglobin	10
systems-biology	10
facilitated-variation	6
gene-expression	4
liver	4
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eye	2
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genetic-code	1
gluconeogenesis	1
metabolic-heterogeneity	1
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