Tag gene_network [43 articles] Export

Recent papers classified by the tag gene_network.

	Reconstruct modular phenotype-specific gene networks by knowledge-driven matrix factorization. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 17. (1 September 2009), pp. 2236-2243. by Xuerui Yang, Yang Zhou, Rong Jin, Christina Chan posted to network_topology matrix_factorization gene_network gene_expression_data correlation_matrix by enelkinsan on 2009-12-04 06:47:20 as along with 3 people ekotelnikova ptrobajo guhjy
	Minimal Gene Regulatory Circuits that Can Count like Bacteriophage Lambda [My Copy] Journal of Molecular Biology, Vol. 394, No. 4. (11 December 2009), pp. 681-693. by M. Avlund, Ian B. Dodd, K. Sneppen, S. Krishna posted to phage gene_network feedback bistability by jjray on 2009-11-23 17:32:41 as
	Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles [My Copy] PLoS Biol, Vol. 5, No. 1. (9 January 2007), e8. by Jeremiah J. Faith, Boris Hayete, Joshua T. Thaden, et al.Ilaria Mogno, Jamey Wierzbowski, Guillaume Cottarel, Simon Kasif, James J. Collins, Timothy S. Gardner posted to reverse_engineering_gene_networks mutual_information gene_network e-coli compendium clr by frohike on 2009-11-13 12:48:15 as along with 8 people and 2 groups icases jfr teuder nickluscombe aswin heliopais austin roys EBI-regulation TNT
	Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function [My Copy] Genome Biology, Vol. 10, No. 9. (2009), R97. by James Costello, Mehmet Dalkilic, Scott Beason, et al.Jeff Gehlhausen, Rupali Patwardhan, Sumit Middha, Brian Eads, Justen Andrews posted to protein_protein_interaction ppi gene_network function_prediction expression drosophila_melanogaster 13-nov-09 by bdessailly to the group Orengo Group Journal Picks on 2009-11-13 10:13:07 as along with 8 people and 1 group meanerelk abc623 Borelli carlk sotacam kiekyon druvus daveGerrard BergmanLab
	Functional Partitioning of Yeast Co-Expression Networks after Genome Duplication [My Copy] PLoS Biol, Vol. 4, No. 4. (4 April 2006), e109. by Gavin C. Conant, Kenneth H. Wolfe posted to yeast redundancy network_evolution module_rewiring modularity genome_duplication gene_network gene_duplication gene_coexpression by biomcgary on 2009-11-12 19:13:00 as along with 3 people and 1 group dpollard nirfriedman bpcusack EisenLab
	GeNGe: systematic generation of gene regulatory networks. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 9. (1 May 2009), pp. 1205-1207. by Hendrik Hache, Christoph Wierling, Hans Lehrach, Ralf Herwig posted to pathways networks network_topology gene_regulatory_networks gene_network by ekotelnikova on 2009-11-10 22:31:25 as along with 7 people ptrobajo sotacam reyez tonamswish TRHvidsten rdiaz guhjy
	A logical analysis of the Drosophila gap-gene system. [My Copy] J Theor Biol, Vol. 211, No. 2. (21 July 2001), pp. 115-141. by L. Sánchez, D. Thieffry posted to regulatory_circuits logical_formalization gene_network dynamic_behaviormodelisation by Antoine_Decrulle on 2009-11-01 18:20:36 as along with 4 people and 2 groups bshkspr bayesian dpollard adepace EisenLab UH - Computational Biology
	A gene network regulating lysosomal biogenesis and function. [My Copy] Science (New York, N.Y.), Vol. 325, No. 5939. (24 July 2009), pp. 473-477. by Marco Sardiello, Michela Palmieri, Alberto di Ronza, et al.Diego Luis L. Medina, Marta Valenza, Vincenzo Alessandro A. Gennarino, Chiara Di Malta, Francesca Donaudy, Valerio Embrione, Roman S. Polishchuk, Sandro Banfi, Giancarlo Parenti, Elena Cattaneo, Andrea Ballabio posted to lysosomal_biogenesis gene_network cbjc by josephjose on 2009-10-31 08:20:39 as along with 1 person jbhiatt
	Regulative recovery in the sea urchin embryo and the stabilizing role of fail-safe gene network wiring [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 43. (27 October 2009), pp. 18291-18296. by Joel Smith, Eric H. Davidson posted to gene_network by gbloeb on 2009-10-27 20:46:14 as
	Classification and biomarker identification using gene network modules and support vector machines [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (15 October 2009), 337. by Malik Yousef, Mohamed Ketany, Larry Manevitz, Louise Showe, Michael Showe posted to svm gene_network classification biomarker by frohike on 2009-10-16 13:56:13 as along with 6 people and 1 group brianb nuin sillitoe ptrobajo ashishanand manduca Orengo Group Journal Picks
	Optimizing information flow in small genetic networks [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 80, No. 3. (2009), 031920. by Gašper Tkačik, Aleksandra M. Walczak, William Bialek posted to optimization noise information gene_network gene_expression by jjray on 2009-09-30 22:00:57 as
	Evolvability and hierarchy in rewired bacterial gene networks [My Copy] Nature, Vol. 452, No. 7189. (17 April 2008), pp. 840-845. by Mark Isalan, Caroline Lemerle, Konstantinos Michalodimitrakis, et al.Carsten Horn, Pedro Beltrao, Emanuele Raineri, Mireia Garriga-Canut, Luis Serrano posted to transcription_factor_binding_site transcription_factor rewiring network_evolution heirarchy gene_network gene_duplication evolvability by biomcgary on 2009-09-08 21:48:26 as along with 26 people and 4 groups Asclepius yyfwuhan megraw chica jimineep balabu kaarsinogen aalibes tmmurali dullhunk neils cmzmasek AbnerCYH josedavid biehl caseybrown Garamonfok austin hryk dbikard cactus margaritis chad_davis michaelbarton aheilbut zwang GEB Centre de Recherches Interdisciplinaires SynBioSys BergmanLab
	Predicting Functional Gene Links from Phylogenetic-Statistical Analyses of Whole Genomes [My Copy] PLoS Comput Biol, Vol. 1, No. 1. (24 June 2005), e3. by Daniel Barker, Mark Pagel posted to phylogenomics maximum_likelihood gene_network gene_loss functional_network correlated_evolution contingent_evolution by biomcgary on 2009-09-02 23:32:37 as along with 10 people and 1 group jperkins skembel Robinder rw294 balajis maryee arunyan bartleby pradiptaray rvosa iSEEM
	Incorporating Existing Network Information into Gene Network Inference [My Copy] PLoS ONE, Vol. 4, No. 8. (27 August 2009), e6799. by Scott Christley, Qing Nie, Xiaohui Xie posted to differential-equation regulatory_network priors ode gene_network chip_chip by frohike on 2009-08-27 09:18:03 as along with 5 people rdiaz coffeerv tmmurali TRHvidsten installe
	Global Prediction of Tissue-Specific Gene Expression and Context-Dependent Gene Networks in <italic>Caenorhabditis elegans</italic> [My Copy] PLoS Comput Biol, Vol. 5, No. 6. (19 June 2009), e1000417. by Maria D. Chikina, Curtis Huttenhower, Coleen T. Murphy, Olga G. Troyanskaya posted to functional_network gene_expression gene_network predictive_biology tissue_specific by biomcgary on 2009-07-15 19:14:25 as along with 4 people grahamc phoenixzxl roys oelemento
	Inferring Gene Regulatory Networks From Expression Data by Discovering Fuzzy Dependency Relationships [My Copy] Fuzzy Systems, IEEE Transactions on In Fuzzy Systems, IEEE Transactions on, Vol. 16, No. 2. (2008), pp. 455-465. by P. C. H. Ma, K. C. C. Chan posted to fuzzy_logic gene_network by qluo on 2009-07-08 16:17:52 as
	Bayesian network classification using spline-approximated kernel density estimation [My Copy] Pattern Recognition Letters, Vol. 26, No. 11. (August 2005), pp. 1761-1771. by Y. Gurwicz, B. Lerner posted to bayesian gene_network by qluo on 2009-07-08 11:36:57 as
	A Bayesian network classification methodology for gene expression data. [My Copy] Journal of computational biology : a journal of computational molecular cell biology, Vol. 11, No. 4. (2004), pp. 581-615. by P. Helman, R. Veroff, S. R. Atlas, C. Willman posted to bayesian gene_network by qluo on 2009-07-08 11:32:10 as
	Evolution of genetic networks underlying the emergence of thymopoiesis in vertebrates. [My Copy] Cell, Vol. 138, No. 1. (10 July 2009), pp. 186-197. by Baubak Bajoghli, Narges Aghaallaei, Isabell Hess, et al.Immanuel Rode, Nikolai Netuschil, Boon-Hui H. Tay, Byrappa Venkatesh, Jr-Kai K. Yu, Stacy L. Kaltenbach, Nicholas D. Holland, Dagmar Diekhoff, Christiane Happe, Michael Schorpp, Thomas Boehm posted to agnathan evo-devo evolution gene_network immune_system lamprey lymphocyte network_evolution thymus vertebrate by biomcgary on 2009-07-03 21:26:40 as along with 2 people yyfwuhan leliavski
	Modeling and Simulation of Genetic Regulatory Systems: A Literature Review [My Copy] Journal of Computational Biology, Vol. 9, No. 1. (January 2002), pp. 67-103. by Hidde de Jong posted to gene_network by qluo on 2009-07-02 15:55:25 as along with 27 people and 6 groups mjoach Borelli antonkratz reyez tlse65 wangbo dlobo jago behindtherabbit cswinburne ggallone softsimu eldan tmmurali bayesian balicea Happybene wnpx kengg noano sstoma josepe dagmar jo_davies roys maburkitt phoenixzxl smac GEB Jarman Lab VirtualPlants Plantandetc compneur
	The human disease network [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 21. (22 May 2007), pp. 8685-8690. by Kwang-Il Goh, Michael E. Cusick, David Valle, Barton Childs, Marc Vidal, Albert-LÃ¡szlÃ³ BarabÃ¡si posted to gene_network by qluo on 2009-07-02 14:03:13 as along with 39 people and 9 groups robfsouza bertelsen smichan biomcgary pawelsobko CurAbility Scis0000002 cbforrest daforerog nedwards Dulcinea saket kaarsinogen roys Yanno guhjy aalibes cannin kuhn jfr yas balicea neveaire bundschu raiyar grahamc joepickrell leSyl henning dejori xingxu winterschlaefer naegele shoshin shikin nolodie mingzhi carlk yaredo Network Analysis of Genes Regulated in Renal Diseases Biostatistics Computational-Genomics Bioinformatics Neuroscience steinmetzlab ic4 generif_paper GomezLab
	Synthetic Gene Networks That Count [My Copy] Science, Vol. 324, No. 5931. (29 May 2009), pp. 1199-1202. by Ari E. Friedland, Timothy K. Lu, Xiao Wang, David Shi, George Church, James J. Collins posted to bacteria e_coli gene_network mathematical_model synthetic_biology by jjray on 2009-05-29 16:01:17 as along with 15 people dbikard pyjamashark abhishek_tiwari mjoach myzhang reyez austin alexknight twatanab kshundyak phoenixzxl sen_cheng leliavski jbhiatt dswan
	Optimizing genetic circuits by global sensitivity analysis. [My Copy] Biophys J, Vol. 87, No. 4. (October 2004), pp. 2195-2202. by X. J. Feng, S. Hooshangi, D. Chen, G. Li, R. Weiss, H. Rabitz posted to gene_network optimization sensitivity_analysis by jjray on 2009-04-30 20:37:44 as along with 3 people ClaireFB rklancer dbikard
	Summing up the noise in gene networks. [My Copy] Nature, Vol. 427, No. 6973. (29 January 2004), pp. 415-418. by J. Paulsson posted to feedback fluctuation-dissipation gene_network gene_regulation mathematical_model network noise review stochastic by jjray on 2009-04-08 20:36:09 as along with 10 people ddcttrl pkm bayesian balabu jiyu mhucka timflutre margaritis marcio dylanwalker
	Critical behavior of a model for catalyzed autoamplification [My Copy] The Journal of Chemical Physics, Vol. 130, No. 13. (2009), 134906. by Martin Tchernookov, Aryeh Warmflash, Aaron R. Dinner posted to biophysics criticality dynamical_system feedback gene_network mathematical_model network by jjray on 2009-04-07 22:55:03 as
	Optimizing information flow in small genetic networks. I [My Copy] (26 Mar 2009) by Gasper Tkacik, Aleksandra M. Walczak, William Bialek posted to gene_network information mathematical_model optimization by jjray on 2009-03-27 22:20:44 as
	Bayesian Network Analysis of Signaling Networks: A Primer [My Copy] Sci. STKE, Vol. 2005, No. 281. (26 April 2005), pl4. by Dana Pe'er posted to bayesian-network gene_network primer regulatory reverse_engineering_gene_networks by frohike on 2009-02-09 16:18:47 as along with 8 people abhishek_tiwari ptrobajo saman_vp tmmurali Borelli ryang wnpx jhatrimatri
	A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas [My Copy] Mol Syst Biol, Vol. 4 (12 February 2008) by Kartik M. Mani, Celine Lefebvre, Kai Wang, et al.Wei K. Lim, Katia Basso, Riccardo Dalla-Favera, Andrea Califano posted to gene_network lymphoma network network_disease reverse_engineering_gene_networks by frohike on 2009-02-09 15:01:52 as along with 8 people ipark-kaist ihpark jfr tmmurali ealloza shikin dap5087 dragonrez
	A Gene Regulatory Network Subcircuit Drives a Dynamic Pattern of Gene Expression [My Copy] Science, Vol. 318, No. 5851. (2 November 2007), pp. 794-797. by Joel Smith, Christina Theodoris, Eric H. Davidson posted to development feedback gene_network gene_regulation by jjray on 2009-01-14 18:53:41 as along with 8 people and 2 groups leemond31 joseph_x_zhou cwbrown lshaw shigepong zwang heliopais hpaces bioNetwork_sysBio EisenLab
	Sexual reproduction selects for robustness and negative epistasis in artificial gene networks [My Copy] Nature, Vol. 440, No. 7080. (2006), pp. 87-90. by Ricardo B. R. Azevedo, Rolf Lohaus, Suraj Srinivasan, Kristen K. Dang, Christina L. Burch posted to evolution gene_network robustness by jjray on 2009-01-08 20:17:27 as along with 4 people and 2 groups adamnellis eldan cmm mjoach GEB FAB-lab
	Extinction and resurrection in gene networks [My Copy] Proceedings of the National Academy of Sciences (25 November 2008) by Daniel Schultz, Aleksandra M. Walczak, José N. Onuchic, Peter G. Wolynes posted to biophysics dynamical_system gene_network mathematical_model stochastic by jjray on 2008-11-26 17:39:15 as along with 3 people akraemer kshundyak stk
	A transdimensional Bayesian model for pattern recognition in DNA sequences [My Copy] Biostat, Vol. 9, No. 4. (1 October 2008), pp. 668-685. by Sierra M. Li, Jon Wakefield, Steve Self posted to gene_network gene_regulatory_networks module_networks by orzenil on 2008-09-29 23:54:14 as along with 1 person maximilianh
	Gene network inference via structural equation modeling in genetical genomics experiments. [My Copy] Genetics, Vol. 178, No. 3. (3 March 2008), pp. 1763-1776. by B. Liu, A. de la Fuente, I. Hoeschele posted to gene_network genetic_genomics module_networks by orzenil on 2008-09-29 18:50:36 as along with 8 people and 1 group roys Scis0000002 dpollard raiyar xingxu caseybrown smgomez guhjy EisenLab
	Constructing disease-specific gene networks using pair-wise relevance metric: application to colon cancer identifies interleukin 8, desmin and enolase 1 as the central elements [My Copy] BMC Systems Biology, Vol. 2, No. 1. (2008) by Wei Jiang, Xia Li, Shaoqi Rao, et al.Lihong Wang, Lei Du, Chuanxing Li, Chao Wu, Hongzhi Wang, Yadong Wang, Baofeng Yang posted to colon_cancer disease gene_network by frohike on 2008-09-09 14:37:49 as along with 1 person jfr
	Transcriptional Control in the Segmentation Gene Network of Drosophila [My Copy] PLoS Biol, Vol. 2, No. 9. (31 August 2004), e271. by Mark D. Schroeder, Michael Pearce, John Fak, et al.HongQing Fan, Ulrich Unnerstall, Eldon Emberly, Nikolaus Rajewsky, Eric D. Siggia, Ulrike Gaul posted to drosophila gene_network motif network regulation by pradiptaray on 2008-08-07 16:19:52 as along with 8 people and 5 groups daveGerrard indigoviolet dpollard adepace wrowell emptyhb dlmace balicea BergmanLab TranscriptionalRegulationWithThermodynamicModels EisenLab Cline_lab UH - Computational Biology
	An Improved, Bias-Reduced Probabilistic Functional Gene Network of Baker's Yeast, Saccharomyces cerevisiae [My Copy] PLoS ONE, Vol. 2, No. 10. (3 October 2007), e988. by Insuk Lee, Zhihua Li, Edward M. Marcotte posted to bioinformatics gene_network saccharomyces by stajich to the group Mycology on 2008-07-21 05:00:25 as along with 3 people karthikraman aelef jiny
	Noise in genetic and neural networks. [My Copy] Chaos, Vol. 16, No. 2. (June 2006) by P. S. Swain, A. Longtin posted to gene_network mathematical_model neural_network noise by jjray on 2008-07-01 18:09:49 as along with 3 people and 2 groups bayesian cudmore suizan APprecision 8_01
	Rate constants rather than biochemical mechanism determine behaviour of genetic clocks [My Copy] Journal of The Royal Society Interface, Vol. 5, No. Suppl 1. (6 August 2008), pp. S9-S15. by Emery Conrad, Avraham E. Mayo, Alexander J. Ninfa, Daniel B. Forger posted to feedback gene_network gene_regulation kinetics mathematical_model oscillation parameter by jjray on 2008-06-23 20:00:00 as along with 1 person abhishek_tiwari
	Nuclear Receptor-Enhanced Transcription Requires Motor- and LSD1-Dependent Gene Networking in Interchromatin Granules [My Copy] Cell, Vol. 132, No. 6. (21 March 2008), pp. 996-1010. by Esperanza Nunez, Young-Soo Kwon, Kasey R. Hutt, et al.Qidong Hu, Maria D. Cardamone, Kenneth A. Ohgi, Ivan Garcia-Bassets, David W. Rose, Christopher K. Glass, Michael G. Rosenfeld, Xiang-Dong Fu posted to chromatin gene_expression gene_network nucleus transcription transcriptional_reprogramming by jjray on 2008-04-23 23:35:16 as along with 1 person dquest
	Global regulatory logic for specification of an embryonic cell lineage [My Copy] Proceedings of the National Academy of Sciences (14 April 2008), 0711220105. by Paola Oliveri, Qiang Tu, Eric H. Davidson posted to gene_network gene_regulation stem_cell by jjray on 2008-04-15 18:25:49 as along with 2 people Minty brant
	Evolutionary cores of domain co-occurrence networks. [My Copy] BMC Evol Biol, Vol. 5, No. 1. (2005) by S. Wuchty, E. Almaas posted to gene_network multicellular network by stajich on 2006-12-08 19:48:47 as along with 5 people davidecellai agustinarce tny neils phoenixzxl
	[Applications of puromycin for evolutionary molecular engineering of proteins and analysis of gene networks] [My Copy] Tanpakushitsu Kakusan Koso, Vol. 46, No. 2. (February 2001), pp. 138-147. by E. Miyamoto-Sato, H. Yanagawa posted to gene_network by numata on 2005-06-06 20:39:36 as along with 1 person satsumakenji
	Expression of a cascading genetic network within liposomes. [My Copy] FEBS Lett, Vol. 576, No. 3. (22 October 2004), pp. 387-390. by K. Ishikawa, K. Sato, Y. Shima, I. Urabe, T. Yomo posted to gene_network synthetic_biology by satsumakenji on 2005-05-22 14:50:00 as along with 1 person rklancer

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mathematical_model	7
feedback	5
network	5
gene_regulation	4
gene_expression	3
network_evolution	3
noise	3
optimization	3
reverse_engineering_gene_networks	3
13-nov-09	2
bacteria	2
bayesian	2
bioinformatics	2
biophysics	2
classification	2
drosophila_melanogaster	2
dynamical_system	2
evolution	2
evolvability	2
expression	2
function_prediction	2
functional_network	2
gene_duplication	2
gene_regulatory_networks	2
information	2
module_networks	2
network_topology	2
ppi	2
protein_protein_interaction	2
saccharomyces	2
stochastic	2
synthetic_biology	2
agnathan	1
bayesian-network	1
biomarker	1
bistability	1
cbjc	1
chip_chip	1
chromatin	1
clr	1
colon_cancer	1
compendium	1
contingent_evolution	1
correlation_matrix	1
criticality	1
development	1
differential-equation	1
disease	1
drosophila	1
dynamic_behaviormodelisation	1
e-coli	1
e_coli	1
evo-devo	1
fluctuation-dissipation	1
fuzzy_logic	1
gene_coexpression	1
gene_expression_data	1
genetic_genomics	1
genome_duplication	1
heirarchy	1
hydra	1
immune_system	1
kinetics	1
lamprey	1
logical_formalization	1
lymphocyte	1
lymphoma	1
matrix_factorization	1
microarray_data_analysis	1
modularity	1
module_rewiring	1
morphological_novelty	1
motif	1
multicellular	1
neural_network	1
ode	1
ontogeny	1
oscillation	1
parameter	1
pathways	1
phage	1
phenotype	1
primer	1
priors	1
redundancy	1
regulation	1
regulatory	1
regulatory_circuits	1
regulatory_network	1
review	1
rewiring	1
sensitivity_analysis	1
stem_cell	1
svm	1
thymus	1
tissue_specific	1
transcription	1
transcription_factor_binding_site	1
transcriptional_reprogramming	1
yeast	1

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