Group: baker-group - with tag systems_biology [166 articles] Export

Recent papers posted by members of the baker-group group with tag systems_biology

	GNU MCSim: Bayesian statistical inference for SBML-coded systems biology models [My Copy] Bioinformatics, Vol. 25, No. 11. (1 June 2009), pp. 1453-1454. by Frederic Y. Bois posted to software statistics systems_biology by sobolevnrm to the group baker-group on 2009-05-15 12:47:10 as along with 1 person guhjy
	SBML2L(A)T(E)X: conversion of SBML files into human-readable reports. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 11. (1 June 2009), pp. 1455-1456. by Andreas Dräger, Hannes Planatscher, Dieudonné Motsou Wouamba, et al.Adrian Schröder, Michael Hucka, Lukas Endler, Martin Golebiewski, Wolfgang Müller, Andreas Zell posted to software systems_biology by sobolevnrm to the group baker-group on 2009-05-15 12:47:01 as along with 6 people jfr tonamswish dullhunk guhjy nuin renatomilani
	Modeling dynamics from only output data [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 79, No. 5. (2009), 056208. by Evan Monroig, Kazuyuki Aihara, Yozo Fujino posted to clustering kinetics misc molecular_dynamics systems_biology by sobolevnrm to the group baker-group on 2009-05-11 12:27:10 as
	Internal coarse-graining of molecular systems [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 16. (21 April 2009), pp. 6453-6458. by Jérôme Feret, Vincent Danos, Jean Krivine, Russ Harmer, Walter Fontana posted to graph_theory multiscale systems_biology by sobolevnrm to the group baker-group on 2009-04-23 12:31:17 as along with 9 people jvb leemond31 superpyrin Scis0000002 reyez trfield paulschlesinger jjray kshundyak
	Extracting the multiscale backbone of complex weighted networks [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 16. (21 April 2009), pp. 6483-6488. by M. Ãngeles Serrano, MariÃ¡n BoguÃ±Ã¡, Alessandro Vespignani posted to allostery graph_theory multiscale systems_biology by sobolevnrm to the group baker-group on 2009-04-23 12:30:54 as along with 9 people rdiaz tomt21 edws rsantana trfield pinney deanmalmgren kevinchannon kshundyak
	A stochastic spectral analysis of transcriptional regulatory cascades [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 16. (21 April 2009), pp. 6529-6534. by Aleksandra M. Walczak, Andrew Mugler, Chris H. Wiggins posted to graph_theory mathematics systems_biology by sobolevnrm to the group baker-group on 2009-04-23 12:30:42 as along with 5 people roys erel10 kshundyak jjray bais
	Phenotypes and tolerances in the design space of biochemical systems [My Copy] Proceedings of the National Academy of Sciences (11 March 2009) by Michael A. Savageau, Pedro M. Coelho, Rick A. Fasani, Dean A. Tolla, Armindo Salvador posted to review systems_biology by sobolevnrm to the group baker-group on 2009-04-23 12:30:32 as along with 2 people vvoorr jjray
	Extreme Pathway Analysis of Human Red Blood Cell Metabolism [My Copy] Vol. 83, No. 2. (1 August 2002), pp. 808-818. by Sharon J. Wiback, Bernhard O. Palsson posted to systems_biology by sobolevnrm to the group baker-group on 2009-04-20 12:35:03 as
	Information flow analysis of interactome networks. [My Copy] PLoS computational biology, Vol. 5, No. 4. (10 April 2009), e1000350. by Patrycja Vasilyev V. Missiuro, Kesheng Liu, Lihua Zou, et al.Brian C. Ross, Guoyan Zhao, Jun S. Liu, Hui Ge posted to bioinformatics graph_theory systems_biology by sobolevnrm to the group baker-group on 2009-04-16 12:36:01 as along with 18 people jfr freesci flbarroso peteruetz phoenixzxl robfsouza reyez VGreiff colmryan hryk shikin dswan fgibson coela ddahlem mstumpf zwang friendpine
	Sending signals dynamically. [My Copy] Science (New York, N.Y.), Vol. 324, No. 5924. (10 April 2009), pp. 198-203. by Robert G. Smock, Lila M. Gierasch posted to protein-protein_interactions review systems_biology by sobolevnrm to the group baker-group on 2009-04-16 12:35:49 as along with 7 people guhjy kjell chica pablocarb biomcgary renatomilani hsekiguc
	A multi-time-scale analysis of chemical reaction networks: I. Deterministic systems [My Copy] Journal of Mathematical Biology by Chang Lee, Hans Othmer posted to kinetics mathematics multiscale systems_biology by sobolevnrm to the group baker-group on 2009-04-15 12:11:57 as
	Systems Biology Metabolic Modeling Assistant (SBMM): An on-tology-based tool for the integration of metabolic data in kinetic modeling. [My Copy] Bioinformatics (Oxford, England) (2 February 2009) by Armando Reyes-Palomares, Raul Montañez, Alejando Del Real-Chicharro, et al.Othmane Chniber, Amine Kerzazi, Ismael Navas-Delgado, Miguel Ángel A. Medina, José Aldana A. Montes, Francisca Sánchez-Jiménez posted to bioinformatics ontology systems_biology by sobolevnrm to the group baker-group on 2009-03-26 11:34:12 as along with 6 people mdstobbe agomez imina dagmar allysonlister dullhunk
	How to deal with large models[quest] [My Copy] Mol Syst Biol, Vol. 5 (20 January 2009) by William S. Hlavacek posted to systems_biology by sobolevnrm to the group baker-group on 2009-03-18 11:27:39 as along with 3 people lptolik agonzale brianb
	Sensitivity and Robustness in Chemical Reaction Networks [My Copy] SIAM Journal on Applied Mathematics, Vol. 69, No. 4. (2009), pp. 977-998. by Guy Shinar, Uri Alon, Martin Feinberg posted to kinetics mathematics systems_biology by sobolevnrm to the group baker-group on 2009-03-16 11:57:44 as
	Quantifying the global cellular thiolâdisulfide status [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 2. (13 January 2009), pp. 422-427. by Rosa E. Hansen, Doris Roth, Jakob R. Winther posted to nitric_oxide systems_biology by sobolevnrm to the group baker-group on 2009-03-13 11:25:41 as along with 1 person NiamhShanahan
	Photosynthetic apparatus of purple bacteria [My Copy] Quarterly Reviews of Biophysics, Vol. 35, No. 01. (2002), pp. 1-62. by Xiche Hu, Thorsten Ritz, Ana Damjanovic, Felix Autenrieth, Klaus Schulten posted to diffusion review systems_biology by sobolevnrm to the group baker-group on 2009-03-13 11:20:36 as
	Virtual Cell modelling and simulation software environment [My Copy] IET Systems Biology, Vol. 2, No. 5. (2008), pp. 352-362. by I. I. Moraru, J. C. Schaff, B. M. Slepchenko, et al.M. L. Blinov, F. Morgan, A. Lakshminarayana, F. Gao, Y. Li, L. M. Loew posted to software systems_biology by sobolevnrm to the group baker-group on 2009-02-10 12:58:23 as
	Computational Insights on the Competing Effects of Nitric Oxide in Regulating Apoptosis [My Copy] PLoS ONE, Vol. 3, No. 5. (28 May 2008), e2249. by Elife Z. Bagci, Yoram Vodovotz, Timothy R. Billiar, Bard Ermentrout, Ivet Bahar posted to nitric_oxide systems_biology by sobolevnrm to the group baker-group on 2008-07-23 12:11:10 as
	The principle of flux minimization and its application to estimate stationary fluxes in metabolic networks. [My Copy] Eur J Biochem, Vol. 271, No. 14. (July 2004), pp. 2905-2922. by H. G. Holzhütter posted to nitric_oxide systems_biology by sobolevnrm to the group baker-group on 2008-06-18 22:36:56 as along with 4 people schwartzjmc alexg pmendes JeremyZucker
	Controlling the rates of biochemical reactions and signaling networks by shape and volume changes [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 11. (18 March 2008), pp. 4099-4104. by L. Lizana, B. Bauer, O. Orwar posted to diffusion systems_biology by sobolevnrm to the group baker-group on 2008-05-19 11:22:52 as along with 1 person rmorenoe
	Bayesian ranking of biochemical system models [My Copy] Bioinformatics, Vol. 24, No. 6. (5 December 2008), pp. 833-839. by Vladislav Vyshemirsky, Mark A. Girolami posted to bioinformatics statistics systems_biology by sobolevnrm to the group baker-group on 2008-04-24 11:32:12 as along with 6 people bertelsen ggallone guhjy bootsy lenov keithvass
	Modularization of biochemical networks based on classification of Petri net t-invariants [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008) by Eva G. Belau, Falk Schreiber, Monika Heiner, et al.Andrea Sackmann, Bjorn Junker, Stefanie Grunwald, Astrid Speer, Katja Winder, Ina Koch posted to graph_theory systems_biology by sobolevnrm to the group baker-group on 2008-02-08 12:20:33 as along with 5 people reyez guhjy bootsy maralena roys
	Variable-free exploration of stochastic models: a gene regulatory network example [My Copy] (6 Nov 2006) by Radek Erban, Thomas A. Frewen, Xiao Wang, et al.Timothy C. Elston, Ronald Coifman, Boaz Nadler, Ioannis G. Kevrekidis posted to kinetics multiscale systems_biology by sobolevnrm to the group baker-group on 2008-02-01 21:23:37 as along with 1 person j_vinals
	Getting Started in Probabilistic Graphical Models [My Copy] PLoS Computational Biology, Vol. 3, No. 12. (1 December 2007), e252. by Edoardo M. Airoldi posted to bioinformatics systems_biology by sobolevnrm to the group baker-group on 2008-02-01 12:54:37 as along with 14 people buyske mhamada guhjy balicea AbnerCYH stajich cjeans GustavoLacerda GeeSharpMinor cabbagezs nklee biehl softsimu jfr
	A mathematical tool for exploring the dynamics of biological networks [My Copy] Proceedings of the National Academy of Sciences (21 November 2007), 0709955104. by Paolo E. Barbano, Marina Spivak, Marc Flajolet, Angus C. Nairn, Paul Greengard, Leslie Greengard posted to mathematics systems_biology by sobolevnrm to the group baker-group on 2008-01-10 12:32:48 as along with 11 people Scis0000002 agomez tmmurali cjeans zwang cactus forgoston lenov sdbneuro mdramirez phoenixzxl
	On anti-portfolio effects in science and technology with application to reaction kinetics, chemical synthesis, and molecular biology [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 47. (20 November 2007), pp. 18398-18403. by Marcel O. Vlad, Alexandru D. Corlan, Vlad T. Popa, John Ross posted to mathematics systems_biology by sobolevnrm to the group baker-group on 2007-12-21 12:32:30 as along with 1 person RamuAnandakrishnan
	Robustness and modular design of the Drosophila segment polarity network [My Copy] Mol Syst Biol, Vol. 2 (12 December 2006) by Wenzhe Ma, Luhua Lai, Qi Ouyang, Chao Tang posted to systems_biology by sobolevnrm to the group baker-group on 2007-12-20 12:21:09 as along with 3 people fastjoe23 faisalm Heute
	Universally Sloppy Parameter Sensitivities in Systems Biology Models [My Copy] PLoS Comput Biol, Vol. 3, No. 10. (5 October 2007), e189. by Ryan N. Gutenkunst, Joshua J. Waterfall, Fergal P. Casey, Kevin S. Brown, Christopher R. Myers, James P. Sethna posted to systems_biology by sobolevnrm to the group baker-group on 2007-11-09 12:12:44 as along with 12 people and 1 group dadiamah jjray arne mhasoba Borelli cjryan biomcgary faisalm fishtank cjeans afenley entropy Savage Lab, UCLA
	Toward realistic modeling of dynamic processes in cell signaling: Quantification of macromolecular crowding effects [My Copy] The Journal of Chemical Physics, Vol. 127, No. 15. (2007) by Jian Sun, Harel Weinstein posted to diffusion kinetics systems_biology by sobolevnrm to the group baker-group on 2007-11-06 12:40:05 as along with 4 people choonpeng jonesn ARobson cactus
	From Pathways Databases to Network Models of Switching Behavior [My Copy] PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e152. by Baltazar D. Aguda, Andrew B. Goryachev posted to bioinformatics systems_biology by sobolevnrm to the group baker-group on 2007-10-04 12:52:53 as along with 6 people thegoose2 balicea cjeans GustavoLacerda thomaskelder tharris
	Algorithms and Software for Stochastic Simulation of Biochemical Reacting Systems [My Copy] Biotechnol. Prog. (26 September 2007) by H. Li, Y. Cao, L. R. Petzold, D. T. Gillespie posted to kinetics mathematics systems_biology by sobolevnrm to the group baker-group on 2007-10-02 12:42:54 as along with 1 person and 1 group dagmar compneur
	Towards a theory of biological robustness [My Copy] Mol Syst Biol, Vol. 3 (18 September 2007) by Hiroaki Kitano posted to systems_biology by sobolevnrm to the group baker-group on 2007-09-25 12:30:28 as along with 12 people abhishek_tiwari xxavx VGreiff sjayanthi jjray dullhunk margaritis massivemayhem fishtank bootsy Ema jf76
	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 systems_biology nitric_oxide by sobolevnrm to the group baker-group on 2007-09-18 14:18:57 as along with 1 person ynaito
	Computer Modeling of Mitochondrial Tricarboxylic Acid Cycle, Oxidative Phosphorylation, Metabolite Transport, and Electrophysiology [My Copy] J. Biol. Chem., Vol. 282, No. 34. (24 August 2007), pp. 24525-24537. by Fan Wu, Feng Yang, Kalyan C. Vinnakota, Daniel A. Beard posted to systems_biology by sobolevnrm to the group baker-group on 2007-08-22 12:25:15 as along with 1 person paulschlesinger
	Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity [My Copy] Proceedings of the National Academy of Sciences of the United States of America (in press) by Q. K. Beg, A. Vazquez, J. Ernst, et al.M. A. de Menezes, Bar Z. Joseph, A. L. Barabási, Z. N. Oltvai posted to systems_biology by sobolevnrm to the group baker-group on 2007-07-25 13:01:34 as
	Metabolic Engineering [My Copy] Annual Review of Biomedical Engineering, Vol. 1 (1999), pp. 535-57. by M. Koffas, C. Roberge, K. Lee, G. Stephanopoulos posted to systems_biology by sobolevnrm to the group baker-group on 2007-07-11 13:28:13 as
	Automated reverse engineering of nonlinear dynamical systems [My Copy] Proceedings of the National Academy of Sciences of the United States of America (in press) by J. Bongard, H. Lipson posted to teaching systems_biology mathematics by sobolevnrm to the group baker-group on 2007-06-18 13:08:48 as along with 1 person trichner
	$My PDF le ma\itre_07_multiresolutionanalysis.pdf$ Multi-Resolution-Analysis Scheme for Uncertainty Quantification in Chemical Systems [My Copy] SIAM Journal on Scientific Computing, Vol. 29, No. 2. (2007), pp. 864-89. by O. P. Le Ma\itre, H. N. Najm, P. P. Pébay, R. G. Ghanem, O. M. Knio posted to systems_biology mathematics by sobolevnrm to the group baker-group on 2007-05-25 14:38:05 as
	Regularizing capacity of metabolic networks [My Copy] Physical Review E, Vol. 75 (2007) by C. Marr, Müller M. Linow, M. T. Hütt posted to systems_biology by sobolevnrm to the group baker-group on 2007-05-25 14:38:05 as
	Self-organization of actin filament orientation in the dendritic-nucleation/array-treadmilling model [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 17. (2007), pp. 7086-91. by T. E. Schaus, E. W. Taylor, G. G. Borisy posted to systems_biology cytoskeleton biomembranes by sobolevnrm to the group baker-group on 2007-05-25 14:37:08 as
	Deterministic characterization of stochastic genetic circuits [My Copy] Proceedings of the National Academy of Sciences of the United States of America (in press) by M. Scott, T. Hwa, B. Ingalls posted to systems_biology kinetics by sobolevnrm to the group baker-group on 2007-05-25 14:37:08 as
	Numerical Matrices Method for Nonlinear System Identification and Description of Dynamics of Biochemical Reaction Networks [My Copy] Biophysical Journal, Vol. 92, No. 10. (2007), pp. 3459-73. by A. V. Karnaukhov, E. V. Karnaukhova, J. R. Williamson posted to systems_biology by sobolevnrm to the group baker-group on 2007-05-25 14:37:07 as
	Parameter estimation in ordinary differential equations for biochemical processes using the method of multiple shooting [My Copy] IET Systems Biology, Vol. 1, No. 2. (2007), pp. 78-88. by M. Peifer, J. Timmer posted to systems_biology by sobolevnrm to the group baker-group on 2007-05-25 14:37:07 as
	Efficient algorithms for ordinary differential equation model identification of biological systems [My Copy] IET Systems Biology, Vol. 1, No. 2. (2007), pp. 120-9. by P. Gennemark, D. Wedelin posted to systems_biology by sobolevnrm to the group baker-group on 2007-05-25 14:37:07 as
	Modeling Networks of Coupled Enzymatic Reactions Using the Total Quasi-Steady State Approximation [My Copy] PLoS Computational Biology, Vol. 3, No. 3. (2007) by A. Ciliberto, F. Capuani, J. J. Tyson posted to systems_biology by sobolevnrm to the group baker-group on 2007-05-25 14:37:06 as
	Bridging from molecular simulation to biochemical networks [My Copy] Current Opinion in Structural Biology (in press) by M. Stein, R. R. Gabdoulline, R. C. Wade posted to systems_biology multiscale kinetics diffusion by sobolevnrm to the group baker-group on 2007-05-25 14:37:06 as
	Simplicity in biology [My Copy] Nature, Vol. 446, No. 7135. (2007) by U. Alon posted to systems_biology by sobolevnrm to the group baker-group on 2007-05-25 14:36:49 as
	Classical versus Stochastic Kinetics Modeling of Biochemical Reaction Systems [My Copy] Biophysical Journal, Vol. 92, No. 7. (2007), pp. 2350-65. by J. Goutsias posted to systems_biology kinetics by sobolevnrm to the group baker-group on 2007-05-25 14:36:49 as
	Discrimination of dynamical system models for biological and chemical processes [My Copy] Journal of Computational Chemistry (in press) by S. Lorenz, E. Diederichs, R. Telgmann, C. Schã¼tte posted to systems_biology kinetics by sobolevnrm to the group baker-group on 2007-05-25 14:36:48 as
	Multinomial tau-leaping method for stochastic kinetic simulations [My Copy] Journal of Chemical Physics, Vol. 126 (2007) by M. F. Pettigrew, H. Resat posted to systems_biology kinetics by sobolevnrm to the group baker-group on 2007-05-25 14:36:29 as

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network	101
review	70
cancer	52
bioinformatics	49
genomics	42
evolution	30
gene_expression	26
genego	26
networks	23
metabolism	22
software	21
synthetic_biology	21
microarray	18
yeast	17
robustness	16
in_thesis	15
nature_sysbio_08	15
ppi	14
biology	13
kinetics	13
mathematics	13
pathway	13
regulatory_network	13
noise	12
expression	11
modularity	11
multiscale	11
cdp_center	10
disease	10
graph_theory	10
modelling	10
pathway-analysis	10
phenotype	10
regulation	10
topology	10
ideker	9
interactions	9
systems	9
visualization	9
complexity	8
drug_discovery	8
gene_networks	8
integration	8
metabolomics	8
nitric_oxide	8
ontology	8
statistics	8
xml	8
complex_systems	7
composition	7
data_integration	7
database	7
machine_learning	7
methodology	7
modeling	7
omics	7
proteomics	7
structure-based	7
text_mining	7
breast_cancer	6
diffusion	6
model	6
pathways	6
semantic_web	6
stem_cells	6
theory	6
tool	6
toxicology	6
bacteria	5
bayesian_network	5
cell_cycle	5
diabetes	5
diagnostics	5
emergence	5
gene	5
genetic_network	5
graphical_models	5
hood	5
method	5
methods	5
perturbation	5
protein	5
protein-protein	5
simulation	5
structure_learning	5
books	4
breast	4
data	4
development	4
functional_analysis	4
gene_regulation	4
human	4
kinetics_modeling	4
pollution	4
qualitative_modeling	4
redox	4
rna	4
sbml	4
signalling	4
variation	4

Group: baker-group - with tag systems_biology [166 articles] Export

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