agonzale's modeling [55 articles] Export

Recent papers added to agonzale's library classified by the tag modeling. You can also see everyone's modeling.

	cPath: open source software for collecting, storing, and querying biological pathways [My Copy] BMC Bioinformatics, Vol. 7, No. 1. (13 November 2006), 497. by Ethan Cerami, Gary Bader, Benjamin Gross, Chris Sander posted to modeling by agonzale on 2009-10-26 05:25:57 as along with 10 people and 2 groups irenas fgibson shikin jfr dquest carmaus bootsy cerami AlexanderPico srp33 dIEMoSIRIS MoSi-Rostock
	Executing multicellular differentiation: quantitative predictive modelling of C.elegans vulval development [My Copy] Bioinformatics, Vol. 25, No. 19. (1 October 2009), 2624. by Nicola Bonzanni, Elzbieta Krepska, K. Anton Feenstra, et al.Wan Fokkink, Thilo Kielmann, Henri Bal, Jaap Heringa posted to network multicellular modeling by agonzale on 2009-09-28 02:07:44 as along with 1 person laurabertens
	Fgf8 morphogen gradient forms by a source-sink mechanism with freely diffusing molecules [My Copy] Nature, Vol. 461, No. 7263. (09 September 2009), pp. 533-536. by Shuizi R. Yu, Markus Burkhardt, Matthias Nowak, et al.Jonas Ries, Zdenek Petrasek, Steffen Scholpp, Petra Schwille, Michael Brand posted to parameter modeling diffusion by agonzale on 2009-09-24 08:39:38 as along with 3 people chigle davidcsterratt paulschlesinger
	A Method for determining the dobustness of bio-molecular oscillator models [My Copy] BMC Systems Biology, Vol. 3, No. 1. (2009), 95. by Reza Ghaemi, Jing Sun, Pablo Iglesias, Domitilla Del Vecchio posted to robustness_analysis oscillations modeling by agonzale on 2009-09-23 09:27:35 as along with 1 person abhishek_tiwari
	Modelling and analysis of gene regulatory networks [My Copy] Nat Rev Mol Cell Biol, Vol. 9, No. 10. (October 2008), pp. 770-780. by Guy Karlebach, Ron Shamir posted to review network modeling by agonzale on 2009-09-03 07:28:30 as along with 14 people antonkratz cannin tklee aviad_work kaarsinogen thomaskelder fgibson druvus balicea brianb nedwards dakelley guhjy tmmurali
	Scaling of the BMP activation gradient in Xenopus embryos [My Copy] Nature, Vol. 453, No. 7199. (26 June 2008), pp. 1205-1211. by Danny Ben-Zvi, Ben-Zion Shilo, Abraham Fainsod, Naama Barkai posted to modeling gradient by agonzale on 2009-09-03 04:39:10 as along with 1 person alhufton
	Probing the Limits to Positional Information [My Copy] Vol. 130, No. 1. (13 July 2007), pp. 153-164. by Thomas Gregor, David W. Tank, Eric F. Wieschaus, William Bialek posted to modeling drosophila by agonzale on 2009-09-01 06:06:43 as
	Stable, Precise, and Reproducible Patterning of Bicoid and Hunchback Molecules in the Early Drosophila Embryo [My Copy] PLoS Comput Biol, Vol. 5, No. 8. (28 August 2009), e1000486. by Yurie Okabe-Oho, Hiroki Murakami, Suguru Oho, Masaki Sasai posted to modeling drosophila by agonzale on 2009-08-31 03:31:24 as along with 1 person keigoi
	A mass action model of a Fibroblast Growth Factor signaling pathway and its simplification. [My Copy] Bulletin of mathematical biology, Vol. 70, No. 8. (1 November 2008), pp. 2229-2263. by E. A. Gaffney, J. K. Heath, M. Z. Kwiatkowska posted to ode modeling fgf by agonzale on 2009-08-24 10:46:07 as
	Comparing different ODE modelling approaches for gene regulatory networks [My Copy] Journal of Theoretical Biology, Vol. 261, No. 4. (21 December 2009), pp. 511-530. by A. Polynikis, S. J. Hogan, M. di Bernardo posted to review ode modeling by agonzale on 2009-08-14 06:06:47 as along with 1 person joseph_x_zhou
	Uncovering operational interactions in genetic networks using asynchronous Boolean dynamics [My Copy] Journal of Theoretical Biology (12 June 2009) by L. Tournier, M. Chavesa posted to boolean modeling network by agonzale on 2009-06-18 03:03:53 as
	Computational Models of the Notch Network Elucidate Mechanisms of Context-dependent Signaling [My Copy] PLoS Comput Biol, Vol. 5, No. 5. (22 May 2009), e1000390. by Smita Agrawal, Colin Archer, David V. Schaffer posted to modeling notch by agonzale on 2009-05-25 03:40:44 as along with 2 people trfield cassj
	Proteomic and network analysis characterize stage-specific metabolism in Trypanosoma cruzi [My Copy] BMC Systems Biology, Vol. 3, No. 1. (2009), 52. by Seth Roberts, Jennifer Robichaux, Arvind Chavali, et al.Patricio Manque, Vladimir Lee, Ana Lara, Jason Papin, Gregory Buck posted to metabolic modeling network by agonzale on 2009-05-17 02:36:11 as
	Delayed coupling theory of vertebrate segmentation [My Copy] HFSP Journal, Vol. 3, No. 1. (2009), pp. 55-66. by Luis G. Morelli, Saúl Ares, Leah Herrgen, Christian Schröter, Frank Jülicher, Andrew C. Oates posted to kuramoto modeling segmentation by agonzale on 2009-03-18 05:52:42 as
	Dissecting the dynamics of the Hes1 genetic oscillator. [My Copy] Journal of theoretical biology, Vol. 254, No. 4. (21 October 2008), pp. 784-798. by H. Momiji, N. A. Monk posted to modeling segmentation by agonzale on 2009-02-20 23:16:18 as
	Input-output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data [My Copy] Mol Syst Biol, Vol. 5 (20 January 2009) by William W. Chen, Birgit Schoeberl, Paul J. Jasper, et al.Mario Niepel, Ulrik B. Nielsen, Douglas A. Lauffenburger, Peter K. Sorger posted to modeling parameter_estimation by agonzale on 2009-02-20 02:24:29 as along with 5 people mhellmann agomez cjryan stringertheory brianb
	A Self-Regulatory System of Interlinked Signaling Feedback Loops Controls Mouse Limb Patterning [My Copy] Science, Vol. 323, No. 5917. (20 February 2009), pp. 1050-1053. by Jean-Denis Benazet, Mirko Bischofberger, Eva Tiecke, et al.Alexandre Goncalves, James F. Martin, Aimee Zuniga, Felix Naef, Rolf Zeller posted to development modeling by agonzale on 2009-02-20 02:11:03 as along with 2 people provero renatomilani
	Delay-Induced Degrade-and-Fire Oscillations in Small Genetic Circuits [My Copy] Physical Review Letters, Vol. 102, No. 6. (2009) by William Mather, Matthew R. Bennett, Jeff Hasty, Lev S. Tsimring posted to dde modeling self-repressed-gene by agonzale on 2009-02-18 07:37:24 as
	Oscillations in the Expression of a Self-Repressed Gene Induced by a Slow Transcriptional Dynamics [My Copy] Physical Review Letters, Vol. 102, No. 6. (2009) by Pierre E. Morant, Quentin Thommen, Fran\ccois Lemaire, Constant Vandermoëre, Benjamin Parent, Marc Lefranc posted to dde modeling self-repressed segmentation by agonzale on 2009-02-18 07:33:54 as along with 1 person boko4ikameto
	Pulmonary effects of inhaled limonene ozone reaction products in elderly rats. [My Copy] Toxicology and applied pharmacology, Vol. 222, No. 2. (15 July 2007), pp. 211-220. by V. R. Sunil, R. J. Laumbach, K. J. Patel, et al.B. J. Turpin, H. J. Lim, H. M. Kipen, J. D. Laskin, D. L. Laskin posted to mapk modeling by agonzale on 2009-02-14 08:39:17 as
	Effect of the MAPK cascade structure, nuclear translocation and regulation of transcription factors on gene expression. [My Copy] Bio Systems, Vol. 85, No. 2. (August 2006), pp. 144-157. by V. K. Mutalik, K. V. Venkatesh posted to mapk modeling by agonzale on 2009-02-14 08:38:16 as
	Systems analysis of MAPK signal transduction. [My Copy] Essays in biochemistry, Vol. 45 (2008), pp. 95-107. by N. Blüthgen, S. Legewie posted to mapk modeling by agonzale on 2009-02-14 08:37:52 as
	When kinases meet mathematics: the systems biology of MAPK signalling. [My Copy] FEBS letters, Vol. 579, No. 8. (21 March 2005), pp. 1891-1895. by Walter Kolch, Muffy Calder, David Gilbert posted to mapk modeling by agonzale on 2009-02-14 08:37:18 as along with 2 people guhjy arne
	Robust, Tunable Biological Oscillations from Interlinked Positive and Negative Feedback Loops [My Copy] Science, Vol. 321, No. 5885. (4 July 2008), pp. 126-129. by Tony Y. Tsai, Yoon S. Choi, Wenzhe Ma, Joseph R. Pomerening, Chao Tang, James E. Ferrell posted to modeling oscillations by agonzale on 2009-02-05 11:34:52 as along with 11 people and 3 groups balabu jjray jasonpark1 t_richardson margaritis madhadron Borelli kentsis caseybrown stringertheory dbikard Synthetic Biology BP205 SynBioSys
	How to deal with large models[quest] [My Copy] Mol Syst Biol, Vol. 5 (20 January 2009) by William S. Hlavacek posted to modeling by agonzale on 2009-02-05 06:30:26 as along with 3 people and 1 group sobolevnrm lptolik brianb baker-group
	Cell-signalling dynamics in time and space [My Copy] Nat Rev Mol Cell Biol, Vol. 7, No. 3. (15 March 2006), pp. 165-176. by Boris N. Kholodenko posted to mapk modeling by agonzale on 2009-02-04 07:22:24 as along with 8 people and 1 group cmetzner fierykylin mhellmann aviad_work julius balabu rmk karfunkel SysbioMPI-TCells
	Signaling gradients in cascades of two-state reaction-diffusion systems [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 4. (27 January 2009), pp. 1087-1092. by Alexander M. Berezhkovskii, Mathieu Coppey, Stanislav Y. Shvartsman posted to mapk modeling pde by agonzale on 2009-02-04 07:19:59 as
	Dynamical behaviour of biological regulatory networks--I. Biological role of feedback loops and practical use of the concept of the loop-characteristic state. [My Copy] Bull Math Biol, Vol. 57, No. 2. (Mar 1995), pp. 247-276. by R. Thomas, D. Thieffry, M. Kaufman posted to logical modeling by agonzale on 2009-02-03 23:24:44 as
	Dynamical behaviour of biological regulatory networks--II. Immunity control in bacteriophage lambda. [My Copy] Bull Math Biol, Vol. 57, No. 2. (Mar 1995), pp. 277-297. by D. Thieffry, R. Thomas posted to logical modeling by agonzale on 2009-02-03 23:24:44 as
	Alternative epigenetic states understood in terms of specific regulatory structures. [My Copy] Ann N Y Acad Sci, Vol. 981 (Dec 2002), pp. 135-153. by Denis Thieffry, Lucas Sanchez posted to logical modeling by agonzale on 2009-02-03 23:24:44 as
	Dynamical modelling of pattern formation during embryonic development. [My Copy] Curr Opin Genet Dev, Vol. 13, No. 4. (Aug 2003), pp. 326-330. by Denis Thieffry, Lucas Sanchez posted to logical modeling by agonzale on 2009-02-03 23:24:44 as
	Dynamical roles of biological regulatory circuits. [My Copy] Brief Bioinform, Vol. 8, No. 4. (Jul 2007), pp. 220-225. by Denis Thieffry posted to logical modeling by agonzale on 2009-02-03 23:24:44 as
	A logical analysis of the Drosophila gap-gene system. [My Copy] J Theor Biol, Vol. 211, No. 2. (Jul 2001), pp. 115-141. by L. Sánchez, D. Thieffry posted to logical modeling by agonzale on 2009-02-03 23:24:44 as
	Segmenting the fly embryo: a logical analysis of the pair-rule cross-regulatory module. [My Copy] J Theor Biol, Vol. 224, No. 4. (Oct 2003), pp. 517-537. by Lucas Sánchez, Denis Thieffry posted to logical modeling by agonzale on 2009-02-03 23:24:44 as
	Segmenting the fly embryo: logical analysis of the role of the Segment Polarity cross-regulatory module. [My Copy] Int J Dev Biol, Vol. 52, No. 8. (2008), pp. 1059-1075. by Lucas Sanchez, Claudine Chaouiya, Denis Thieffry posted to logical modeling by agonzale on 2009-02-03 23:24:43 as
	Establishement of the dorso-ventral pattern during embryonic development of drosophila melanogasater: a logical analysis [My Copy] J Theor Biol, Vol. 189, No. 4. (Dec 1997), pp. 377-389. by Sanchez, J. van Helden, Thieffry posted to logical modeling by agonzale on 2009-02-03 23:24:43 as
	Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance. [My Copy] BMC Syst Biol, Vol. 3, No. 1. (Jan 2009) by Ozgur Sahin, Holger Frohlich, Christian Lobke, et al.Ulrike Korf, Sara Burmester, Meher Majety, Jens Mattern, Ingo Schupp, Claudine Chaouiya, Denis Thieffry, Annemarie Poustka, Stefan Wiemann, Tim Beissbarth, Dorit Arlt posted to logical modeling by agonzale on 2009-02-03 23:24:43 as
	Dynamical analysis of the regulatory network defining the dorsal-ventral boundary of the Drosophila wing imaginal disc. [My Copy] Genetics, Vol. 174, No. 3. (Nov 2006), pp. 1625-1634. by Aitor González, Claudine Chaouiya, Denis Thieffry posted to logical modeling by agonzale on 2009-02-03 23:24:43 as
	Logical modelling of the role of the Hh pathway in the patterning of the Drosophila wing disc. [My Copy] Bioinformatics, Vol. 24, No. 16. (Aug 2008), pp. i234-i240. by Aitor González, Claudine Chaouiya, Denis Thieffry posted to logical modeling by agonzale on 2009-02-03 23:24:43 as
	GINsim: a software suite for the qualitative modelling, simulation and analysis of regulatory networks. [My Copy] Biosystems, Vol. 84, No. 2. (May 2006), pp. 91-100. by Gonzalez A. Gonzalez, A. Naldi, L. Sánchez, D. Thieffry, C. Chaouiya posted to logical modeling by agonzale on 2009-02-03 23:24:43 as
	Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle. [My Copy] Bioinformatics, Vol. 22, No. 14. (Jul 2006), pp. e124-e131. by Adrien Fauré, Aurélien Naldi, Claudine Chaouiya, Denis Thieffry posted to logical modeling by agonzale on 2009-02-03 23:24:42 as
	Dynamical modeling of biological regulatory networks. [My Copy] Biosystems, Vol. 84, No. 2. (May 2006), pp. 77-80. by Claudine Chaouiya, Hidde de Jong, Denis Thieffry posted to logical modeling by agonzale on 2009-02-03 23:24:42 as
	Traveling wave formation in vertebrate segmentation. [My Copy] Journal of theoretical biology (9 January 2009) by Koichiro Uriu, Yoshihiro Morishita, Yoh Iwasa posted to modeling segmentation by agonzale on 2009-02-03 09:39:22 as
	Negative Autoregulation by FAS Mediates Robust Fetal Erythropoiesis [My Copy] PLoS Biology, Vol. 5 (xx 2007) posted to modeling experimental by agonzale on 2009-02-03 07:12:42 as
	Model of the reception of hedgehog morphogen concentration gradient: comparison with an extended range of experimental data. [My Copy] Journal of bioinformatics and computational biology, Vol. 5 (Apr 2007), pp. 491-506. by Konstantin Gunbin, Leonid Omelyanchuk, Vladislav Kogai, Stanislav Fadeev, Nikolay Kolchanov posted to hedgehog modeling by agonzale on 2009-02-03 07:12:41 as
	A Self-Organized Vortex Array of Hydrodynamically Entrained Sperm Cells [My Copy] Science, Vol. 309 (xx 2005) posted to modeling experimental by agonzale on 2009-02-03 07:12:41 as
	Synchrony Dynamics During Initiation, Failure, and Rescue of the Segmentation Clock [My Copy] Science, Vol. 317 (xx 2007) posted to modeling experimental by agonzale on 2009-02-03 07:12:41 as
	Complex Regulation of cyp26a1 Creates a Robust Retinoic Acid Gradient in the Zebrafish Embryo [My Copy] PLoS Biology, Vol. 5 (xx 2007) posted to modeling experimental by agonzale on 2009-02-03 07:12:40 as
	7 Coordinated Action of N-CAM, N-cadherin, EphA4, and ephrinB2 Translates Genetic Prepatterns into Structure during Somitogenesis in Chick. [My Copy] Current topics in developmental biology, Vol. 81 (xx 2007), pp. 205-247. by James A. Glazier, Ying Zhang, Maciej Swat, Benjamin Zaitlen, Santiago Schnell posted to modeling by agonzale on 2009-02-03 07:12:40 as
	Noise-resistant and synchronized oscillation of the segmentation clock [My Copy] Nature, Vol. 441 (Jun 2006), pp. 719-723. by Kazuki Horikawa, Kana Ishimatsu, Eiichi Yoshimoto, Shigeru Kondo, Hiroyuki Takeda posted to modeling experimental by agonzale on 2009-02-03 07:12:40 as

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segmentation	252
drosophila	249
ap_boundary	178
mouse	158
experimental	156
dv_boundary	70
tfbs	63
thermodynamic_model	59
modeling	55
network	26
parameter_estimation	21
dde	21
logical	16
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mapk	13
human	12
zebrafish	11
fgf	10
inference	9
plde	8
reviews	8
hedgehog	8
xenopus	8
synchronization	8
chick	8
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gene	7
review	6
values	6
wing_disc	6
retinoic	6
notch	5
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ode	5
mackey-glass	5
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erk	3
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kuramoto	3
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wing	3
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dynamics	2
boolean	2
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multicellular	1
topology	1
fuzzy_logic	1
logic	1
gradient	1
fluorescence	1
logical_models	1

agonzale's modeling [55 articles] Export

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