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タグ: gene-networks [75 articles]

Recent papers classified by the tag gene-networks.
  • Homeostasis and differentiation in random genetic control networks.
    Nature, Vol. 224, No. 5215. (11 October 1969), pp. 177-178.
    by S Kauffman
    posted to boolean gene-networks modelling simulation by pmendes on 2008-04-26 15:13:41 as **
  • Artificial gene networks for objective comparison of analysis algorithms.
    Bioinformatics, Vol. 19 Suppl 2 (October 2003)
    by P Mendes, W Sha, K Ye
    posted to gene-networks mendes modelling reverse-engineering simulation transcriptomics by pmendes on 2008-02-29 17:21:30 as read along with 4 people and 2 groups camster tmmurali dragonrez lfriedl dbk-lab kdl
  • Metabolic stability and epigenesis in randomly constructed genetic nets.
    J Theor Biol, Vol. 22, No. 3. (March 1969), pp. 437-467.
    by SA Kauffman
    posted to boolean gene-networks modelling simulation by pmendes on 2008-04-26 15:07:34 as ** along with 2 people hito gurkanbebek
  • Quantifying gene networks with regulatory strengths.
    Mol Biol Rep, Vol. 29, No. 1-2. (2002), pp. 73-77.
    by A de la Fuente, P Mendes
    posted to gene-networks mendes reverse-engineering systems-biology transcriptomics by pmendes on 2008-02-29 17:27:21 as read
  • Modeling gene expression with differential equations.
    Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, Vol. 4 (1999), pp. 29-40.
    by T Chen, HL He, GM Church
    posted to gene-networks modelling by pmendes on 2008-04-26 15:57:59 as read
  • The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks.
    J Mol Biol, Vol. 334, No. 2. (21 November 2003), pp. 197-204.
    by S Mangan, A Zaslaver, U Alon
    posted to gene-networks modelling theory by pmendes on 2008-04-26 17:48:51 as ** along with 2 people jstajic karfunkel
  • A connectionist model of development.
    Journal of theoretical biology, Vol. 152, No. 4. (21 October 1991), pp. 429-453.
    by E Mjolsness, DH Sharp, J Reinitz
    posted to gene-networks modelling theory by pmendes on 2008-04-26 17:04:57 as **
  • Cytoscape: a software environment for integrated models of biomolecular interaction networks.
    Genome Res, Vol. 13, No. 11. (November 2003), pp. 2498-2504.
    by P Shannon, A Markiel, O Ozier, NS Baliga, JT Wang, D Ramage, N Amin, B Schwikowski, T Ideker
    posted to gene-networks software systems-biology visualization by pmendes on 2008-02-29 17:24:33 as * along with 12 people and 3 groups dragonrez balajis tvdbulck frohike carmaus dagmar natstreet jlh64 Evangelia yggdrasil carlk Borelli dIEMoSIRIS MoSi-Rostock compneur
  • A computational algebra approach to the reverse engineering of gene regulatory networks.
    Journal of theoretical biology, Vol. 229, No. 4. (21 August 2004), pp. 523-537.
    by R Laubenbacher, B Stigler
    posted to discrete gene-networks modelling reverse-engineering systems-biology by pmendes on 2008-04-26 15:30:50 as read
  • Gene regulation networks: a theory for their global structure and behaviors.
    Curr Top Dev Biol, Vol. 6, No. 6. (1971), pp. 145-182.
    by S Kauffman
    posted to boolean gene-networks modelling review simulation by pmendes on 2008-04-26 15:12:25 as **
  • A mathematical framework for describing and analysing gene regulatory networks.
    Journal of theoretical biology, Vol. 176, No. 2. (21 September 1995), pp. 291-300.
    by T Mestl, E Plahte, SW Omholt
    posted to gene-networks modelling theory by pmendes on 2008-04-26 16:37:30 as **
  • The large scale structure and dynamics of gene control circuits: an ensemble approach.
    Journal of theoretical biology, Vol. 44, No. 1. (March 1974), pp. 167-190.
    by S Kauffman
    posted to boolean gene-networks modelling simulation by pmendes on 2008-04-26 15:10:30 as **
  • Gene networks: how to put the function in genomics.
    Trends Biotechnol, Vol. 20, No. 11. (November 2002), pp. 467-472.
    by P Brazhnik, A de la Fuente, P Mendes
    posted to gene-networks mendes review systems-biology transcriptomics by pmendes on 2008-02-29 17:26:27 as read along with 1 person frohike
  • Linking the genes: inferring quantitative gene networks from microarray data.
    Trends Genet, Vol. 18, No. 8. (August 2002), pp. 395-398.
    by A de la Fuente, P Brazhnik, P Mendes
    posted to gene-networks mendes reverse-engineering systems-biology transcriptomics by pmendes on 2008-02-29 17:31:10 as read along with 2 people and 3 groups beapen heliopais Atopic_and_Seborrhoeic_Dermatitis Skin_Deep Applied_Bimatics
  • Sexual reproduction selects for robustness and negative epistasis in artificial gene networks
    Nature, Vol. 440, No. 7080. (2006), pp. 87-90.
    by Ricardo BR Azevedo, Rolf Lohaus, Suraj Srinivasan, Kristen K Dang, Christina L Burch
    posted to epistasis evolution gene-networks grn robustness sex by mjoach on 2008-07-04 12:17:00 as read along with 2 people and 1 group eldan cmm FAB-lab
  • Graph Theory and Networks in Biology
    (6 Apr 2006)
    by Oliver Mason, Mark Verwoerd
    posted to algorithms gene-networks gene-regulation graph grn modularity survey theory by mjoach on 2008-06-06 16:21:09 as read along with 12 people imouthesmp BarrosH onyx lshaw karfunkel ptpases carlk saket Borelli ilkert ansobol dpf
  • Spontaneous emergence of modularity in cellular networks
    Journal of The Royal Society Interface, Vol. 5, No. 18. (6 January 2008), pp. 129-133.
    by Ricard V Solé, Sergi Valverde
    posted to emergence evolution grn modularity self-organization gene-networks gene-regulation by mjoach on 2008-06-02 15:07:02 as **** along with 3 people and 2 groups mattjb smgomez stefanoallesina ComplexAdaptiveSystems DSTO-CAS
  • Subnets of scale-free networks are not scale-free: sampling properties of networks.
    Proc Natl Acad Sci U S A, Vol. 102, No. 12. (22 March 2005), pp. 4221-4224.
    by MP Stumpf, C Wiuf, RM May
    posted to gene-networks network sampling scale-free subsets by mjoach on 2008-07-18 14:30:14 as ** along with 8 people kentsis bpb griota lshaw somasanyal iris_2001 Pao-Yang ilkert
  • Graph theory and networks in Biology
    Systems Biology, IET, Vol. 1, No. 2. (2007), pp. 89-119.
    by O Mason, M Verwoerd
    posted to algorithms gene-networks gene-regulation graph grn modularity survey theory by mjoach on 2008-07-15 13:40:00 as read along with 2 people AbnerCYH pedagand
  • Bio-logic: gene expression and the laws of combinatorial logic.
    Artificial life, Vol. 14, No. 1. (2008), pp. 121-133.
    by MJ Schilstra, CL Nehaniv
    posted to alife gene-networks gene-regulation grn logic by mjoach on 2008-07-24 16:59:15 as **
  • Evidence against the selfish operon theory
    Trends in Genetics, Vol. 20, No. 6. (1 June 2004), pp. 232-234.
    by Csaba Pal, Laurence D Hurst
    posted to evolution grn hgt modularity operons selfish gene-networks gene-regulation by mjoach on 2008-06-02 13:18:42 as **** along with 1 person rabu
  • Regulatory gene networks and the properties of the developmental process.
    Proc Natl Acad Sci U S A, Vol. 100, No. 4. (18 February 2003), pp. 1475-1480.
    by EH Davidson, DR McClay, L Hood
    posted to development embryogenesis evo-devo evolution evolution-of-shape gene-networks gene-regulation grn by mjoach on 2008-06-06 16:19:08 as **** along with 3 people nsamways margaritis shikin
  • Evolving Dynamics in an Artificial Regulatory Network Model
    Parallel Problem Solving from Nature - PPSN VIII, Vol. 3242 (2004), pp. 571-580.
    by Dwight P Kuo, André Leier, Wolfgang Banzhaf
    posted to alife evolution grn modelling gene-networks gene-regulation by mjoach on 2008-05-19 15:45:58 as read
  • notes Modelling the evolution of genetic regulatory networks
    Journal of Theoretical Biology, Vol. 238, No. 4. (21 February 2006), pp. 737-753.
    by AP Quayle, S Bullock
    posted to alife evolution grn gene-networks gene-regulation by mjoach on 2008-05-14 09:26:17 as **** along with 1 person ramakris
  • The Origins of Order: Self-Organization and Selection in Evolution
    (01 May 1993)
    by Stuart A Kauffman
    posted to boolean gene-networks gene-regulation grn modelling network self-organization by mjoach on 2008-07-18 15:26:27 as ** along with 13 people and 2 groups sjung eldan bayesian balicea pchiusano voiklis daveh echinotrix spirit_of_numenor kray avo MarkVanHeeswijk santi515 ComplexAdaptiveSystems ColDyn
  • Exploring regenerative mechanisms found in flatworms by artificial evolutionary techniques using genetic regulatory networks
    Evolutionary Computation, 2003. CEC '03. The 2003 Congress on, Vol. 3 (2003), pp. 2026-2033.
    by Peter Eggenberger-Hotz
    posted to alife embryogenesis evolution evolution-of-shape grn gene-networks gene-regulation by mjoach on 2008-05-19 15:33:53 as read
  • notes Evolving complete agents using artificial ontogeny
    (2003), pp. 237-258.
    by J Bongard, R Pfeifer
    posted to alife ann embryogenesis evolution evolution-of-shape grn locomotion gene-networks gene-regulation by mjoach on 2008-05-14 09:19:32 as read along with 1 person and 1 group dlobo GEB
  • Design of genetic networks with specified functions by evolution in silico.
    Proc Natl Acad Sci U S A, Vol. 101, No. 2. (13 January 2004), pp. 580-585.
    by P François, V Hakim
    posted to evolution grn model modularity gene-networks gene-regulation by mjoach on 2008-05-29 11:55:54 as read along with 5 people rklancer eldan monod dbikard discreteonyxorb
  • Epistasis correlates to genomic complexity
    PNAS, Vol. 103, No. 39. (26 September 2006), pp. 14402-14405.
    by Rafael Sanjuán, Santiago F Elena
    posted to alife epistasis gene-networks gene-regulation grn by mjoach on 2008-07-25 10:16:02 as **** along with 2 people and 1 group cmm nicg FAB-lab
  • Genome-physics interaction as a new concept to reduce the number of genetic parameters in artificial evolution
    Evolutionary Computation, 2003. CEC '03. The 2003 Congress on, Vol. 1 (2003), pp. 191-198.
    by Peter Eggenberger-Hotz
    posted to alife embryogenesis evolution-of-shape grn gene-networks gene-regulation by mjoach on 2008-05-19 15:24:17 as read
  • Toward A Biologically Defensible Model Of Development
    (1995)
    by Frank Dellaert
    posted to alife embryogenesis evolution evolution-of-shape gene-networks gene-regulation grn morphogen by mjoach on 2008-06-24 13:39:08 as **
  • Evolving morphologies of simulated 3D organisms based on differential gene expression
    (1997), pp. 205-213.
    by Peter Eggenberger-Hotz
    posted to alife embryogenesis evolution-of-shape grn gene-networks gene-regulation by mjoach on 2008-05-19 15:17:27 as read
  • notes On the Dynamics of an Artificial Regulatory Network
    Advances in Artificial Life, Vol. 2801 (2003), pp. 217-227.
    by Wolfgang Banzhaf
    posted to alife grn gene-networks gene-regulation by mjoach on 2008-05-14 09:10:25 as read
  • Evolving Fractal Proteins
    Evolvable Systems: From Biology to Hardware, Vol. 2606 (2003), pp. 81-92.
    by Peter Bentley
    posted to alife cis-regulation grn gene-networks gene-regulation by mjoach on 2008-05-16 01:11:49 as read
  • Estimating the size of the human interactome
    Proceedings of the National Academy of Sciences (12 May 2008), 0708078105.
    by Michael P Stumpf, Thomas Thorne, Eric de Silva, Ronald Stewart, Hyeong J An, Michael Lappe, Carsten Wiuf
    posted to complexity evolution grn interactome measure gene-networks gene-regulation by mjoach on 2008-05-19 20:53:12 as **** along with 21 people and 1 group tharris zwang chrissp100 sanchezbuelna jyuh phoenixzxl tmmurali neils paolomarcatili xingxu Ema cabbagesofdoom balicea marck friendpine brianb roys Evangelia dragonrez chad_davis bpcusack C. elegans / WormBase
  • Stochastic gene expression in a single cell.
    Science, Vol. 297, No. 5584. (16 August 2002), pp. 1183-1186.
    by MB Elowitz, AJ Levine, ED Siggia, PS Swain
    posted to ecoli gene-networks gene-regulation grn model modelling noise by mjoach on 2008-07-18 14:54:54 as ** along with 16 people and 3 groups wilvc madhadron cottrell mmt litam mhucka timflutre margaritis roland_ewald ptupper tvdbulck jiny balicea dylanwalker jjray austin UWNICU dIEMoSIRIS MoSi-Rostock
  • Harnessing Morphogenesis
    (1995), pp. 29-41.
    by N Jakobi
    posted to alife ann cis-regulation grn modelling gene-networks gene-regulation by mjoach on 2008-05-16 00:39:27 as read along with 1 person and 1 group dlobo GEB
  • Selfish Operons: Horizontal Transfer May Drive the Evolution of Gene Clusters
    Genetics, Vol. 143, No. 4. (1 August 1996), pp. 1843-1860.
    by JG Lawrence, JR Roth
    posted to evolution grn hgt modularity operons selfish gene-networks gene-regulation by mjoach on 2008-06-02 13:09:15 as **** along with 1 person AaronDarling
  • The use of neutral genotype-phenotype mappings for improved evolutionary search
    BT Technology Journal, Vol. 18, No. 4. (2000), pp. 103-111.
    by Rob Shipman, Mark Shackleton, Inman Harvey
    posted to boolean evolution gene-networks gene-regulation grn mutations network neutrality robustness by mjoach on 2008-06-27 15:04:53 as read
  • Noise in eukaryotic gene expression.
    Nature, Vol. 422, No. 6932. (10 April 2003), pp. 633-637.
    by WJ Blake, M KAErn, CR Cantor, JJ Collins
    posted to expression grn noise transcription translation gene-networks gene-regulation by mjoach on 2008-05-29 10:59:01 as ** along with 6 people rklancer cottrell dbikard margaritis jiny klo
  • Operons in eukaryotes.
    Briefings in Functional Genomics and Proteomics, Vol. 3, No. 3. (November 2004), pp. 199-211.
    by T Blumenthal
    posted to grn operons gene-networks gene-regulation by mjoach on 2008-05-14 09:35:20 as ** along with 2 people imouthesmp Eonwe
  • A Network Model for the Correlation between Epistasis and Genomic Complexity
    PLoS ONE, Vol. 3, No. 7. (16 July 2008), e2663.
    by Rafael Sanjuán, Miguel R Nebot
    posted to alife epistasis gene-networks gene-regulation grn robustness by mjoach on 2008-07-25 10:18:01 as ***** along with 1 person tomhebbron
  • Modeling genetic networks and their evolution: a complex dynamical systems perspective.
    Biological chemistry, Vol. 382, No. 9. (September 2001), pp. 1289-1299.
    by S Bornholdt
    posted to alife grn modelling gene-networks gene-regulation by mjoach on 2008-05-14 09:15:38 as ****
  • Coevolution of robustness, epistasis, and recombination favors asexual reproduction.
    Proc Natl Acad Sci U S A (23 July 2007)
    by Thomas Maccarthy, Aviv Bergman
    posted to alife epistasis evolution grn recombination robustness sex gene-networks gene-regulation evolution-of-sex by mjoach on 2008-05-14 09:46:00 as read along with 1 person sebastien_vigneau
  • Evolving modular genetic regulatory networks
    Evolutionary Computation, 2002. CEC '02. Proceedings of the 2002 Congress on, Vol. 2 (2002), pp. 1872-1877.
    by J Bongard
    posted to alife evolution gene-networks gene-regulation grn modularity by mjoach on 2008-07-18 22:01:14 as read along with 1 person and 1 group dlobo GEB
  • The evolution of modularity in bacterial metabolic networks
    Proceedings of the National Academy of Sciences (6 May 2008), 0712149105.
    by Anat Kreimer, Elhanan Borenstein, Uri Gophna, Eytan Ruppin
    posted to evolution grn modularity network gene-networks gene-regulation by mjoach on 2008-05-19 20:51:54 as read along with 11 people hryk qwermish deanmalmgren carlk jjray skato_toyaku tmmurali phoenixzxl roys pinney saket
  • Computational representation of developmental genetic regulatory networks.
    Dev Biol, Vol. 283, No. 1. (1 July 2005), pp. 1-16.
    by WJ Longabaugh, EH Davidson, H Bolouri
    posted to gene-networks gene-regulation network-motifs by margaritis on 2007-06-25 12:10:50 as **
  • Genetic regulatory networks programming hematopoietic stem cells and erythroid lineage specification
    Developmental Biology, Vol. 294, No. 2. (15 June 2006), pp. 525-540.
    by Gemma Swiers, Roger Patient, Matthew Loose
    posted to gene-networks gene-regulation network-motifs by margaritis on 2007-06-25 11:45:42 as **
  • Gene regulatory networks and the evolution of animal body plans.
    Science, Vol. 311, No. 5762. (10 February 2006), pp. 796-800.
    by EH Davidson, DH Erwin
    posted to gene-expression gene-networks network-motifs review by margaritis on 2007-06-25 12:07:29 as ** along with 14 people and 4 groups eldan bayesian dpollard xico dchughes brixtonmc Liusha josepe cjeans sujaikumar Garamonfok jtomasch Ema natstreet EisenLab WetBiology G4ID Genetics-of-Gambling
  • Gene regulatory networks for development.
    Proc Natl Acad Sci U S A, Vol. 102, No. 14. (5 April 2005), pp. 4936-4942.
    by M Levine, EH Davidson
    posted to gene-networks gene-regulation network-motifs by margaritis on 2007-06-25 11:53:53 as ** along with 3 people Happybene Liusha jtomasch
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