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Ключевое слово gene_regulation [183 articles]

Recent papers classified by the tag gene_regulation.
  • Two strategies for gene regulation by promoter nucleosomes
    Genome Res. (30 April 2008), gr.076059.108.
    by Itay Tirosh, Naama Barkai
    posted to nucleosome gene_regulation gene_expression by roys on 2008-05-19 03:37:09 as ** along with 9 people siebert inesdesantiago dchughes aalibes djkt fpattyn vega emptyhb nklee
  • Inference of combinatorial regulation in yeast transcriptional networks: A case study of sporulation
    PNAS, Vol. 102, No. 6. (8 February 2005), pp. 1998-2003.
    by Wei Wang, Michael J Cherry, Yigal Nochomovitz, Emmitt Jolly, David Botstein, Hao Li
    posted to gene_regulation networks yeast by nicg on 2006-09-15 04:07:31 as *** along with 1 person vega
  • Data-based model and parameter evaluation in dynamic transcriptional regulatory networks
    Proteins: Structure, Function, and Bioinformatics, Vol. 55, No. 2. (2004), pp. 339-350.
    by German Cavelier, Dimitris Anastassiou
    posted to gene_regulation models by nicg on 2006-09-15 04:06:38 as **
  • The complexity of simplicity.
    Genome Biol, Vol. 2, No. 2. (2001)
    by SN Peterson, CM Fraser
    posted to complexity gene_regulation minimal_genome by nicg on 2006-09-28 03:49:06 as ** along with 3 people and 1 group operon madhadron livingthingdan livingthing
  • Expression profiling in primates reveals a rapid evolution of human transcription factors
    Nature, Vol. 440, No. 7081. (March 2006), pp. 242-245.
    by Yoav Gilad, Alicia Oshlack, Gordon K Smyth, Terence P Speed, Kevin P White
    posted to evolution gene_regulation primates by nicg on 2006-09-27 01:11:38 as ** along with 15 people and 4 groups stevanspringer ccots eckart_bindewald dchughes tabu nirfriedman nickluscombe ranb johncumbers djkt mikaelhuss JeffR100 candypmcg emarker emptyhb FAB-lab G4ID EBI-regulation Genetics-of-Gambling
  • MOLECULAR BIOLOGY: A New RNA Dimension to Genome Control.
    Science, Vol. 313, No. 5785. (21 July 2006), pp. 305-306.
    by RW Carthew
    posted to gene_regulation noncoding_rna by nicg on 2006-09-27 00:31:27 as *** along with 7 people and 4 groups dayjm marcius eckart_bindewald tardigrade dchughes mtagaya jackjackjjj G4ID BioinfoCIPF SGU-CIPF Genetics-of-Gambling
  • Epistasis correlates to genomic complexity
    PNAS, Vol. 103, No. 39. (26 September 2006), pp. 14402-14405.
    by Rafael Sanjuan, Santiago F Elena
    posted to complexity gene_regulation by nicg on 2006-09-26 23:56:13 as **** along with 2 people and 1 group mjoach cmm FAB-lab
  • Tandem riboswitch architectures exhibit complex gene control functions.
    Science, Vol. 314, No. 5797. (13 October 2006), pp. 300-304.
    by N Sudarsan, MC Hammond, KF Block, R Welz, JE Barrick, A Roth, RR Breaker
    posted to gene_regulation riboswitch by namtonthat on 2006-10-19 00:29:14 as read along with 1 person aswin
  • A biochemical logic gate using an enzyme and its inhibitor. Part II: The logic gate.
    Biosystems, Vol. 70, No. 1. (June 2003), pp. 21-33.
    by S Sivan, S Tuchman, N Lotan
    posted to circuit computation control gene_networks gene_regulation logic_gate by monod on 2005-08-01 18:28:00 as *** along with 1 person rklancer
  • Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations.
    Biophys J, Vol. 81, No. 6. (December 2001), pp. 3116-3136.
    by TB Kepler, TC Elston
    posted to gene_regulation noise robustness by monod on 2005-12-03 00:05:59 as ** along with 2 people jjray margaritis
  • Creating small-molecule-dependent switches to modulate biological functions.
    Chem Biol, Vol. 12, No. 2. (February 2005), pp. 151-161.
    by AR Buskirk, DR Liu
    posted to gene_networks gene_regulation synthetic_biology by monod on 2005-08-20 16:12:27 as read along with 4 people grahamc rklancer mdimmic lna
  • Limitations of quantitative gene regulation models: a case study.
    Genome Res, Vol. 13, No. 11. (November 2003), pp. 2391-2395.
    by PM Kim, B Tidor
    posted to gene_regulation by monod on 2005-09-27 07:09:47 as ** along with 4 people rklancer wnpx mmt lambda
  • The regulation of bacterial transcription initiation.
    Nat Rev Microbiol, Vol. 2, No. 1. (January 2004), pp. 57-65.
    by DF Browning, SJ Busby
    posted to gene_regulation microbiology by monod on 2005-06-07 16:55:45 as *** along with 3 people and 1 group dquest jstajic nickluscombe EBI-regulation
  • Efficiency, Robustness and Stochasticity of Gene Regulatory Networks in Systems Biology: lambda Switch as a Working Example
    (2 Dec 2005)
    by X Zhu, L Yin, L Hood, D Galas, P Ao
    posted to biological_networks gene_regulation modelling networks robustness synthetic_biology by mmt on 2006-05-30 00:35:31 as ** along with 2 people monod entropy
  • A vision for the future of genomics research
    Nature, Vol. 422, No. 6934. (24 April 2003), pp. 835-847.
    by Francis S Collins, Eric D Green, Alan E Guttmacher, Mark S Guyer
    posted to gene_regulation genome signaling_pathways transcription_factor by kaarsinogen on 2006-06-28 22:44:51 as ** along with 2 people massivemayhem jasonbobe
  • Matrix Formalism to Describe Functional States of Transcriptional Regulatory Systems
    PLoS Computational Biology, Vol. 2, No. 8. (1 August 2006), e101.
    by Erwin P Gianchandani, Jason A Papin, Nathan D Price, Andrew R Joyce, Bernhard O Palsson
    posted to 2005_2006_dnabp gene_regulation protein-dna_interaction signaling_pathways transcription_factor by kaarsinogen on 2006-09-20 18:40:00 as *** along with 2 people and 1 group jfr indigoviolet EisenLab
  • Sequencing and comparison of yeast species to identify genes and regulatory elements
    Nature, Vol. 423, No. 6937. (15 May 2003), pp. 241-254.
    by Manolis Kellis, Nick Patterson, Matthew Endrizzi, Bruce Birren, Eric S Lander
    posted to gene_regulation genome protein-dna_interaction transcription_factor by kaarsinogen on 2006-07-11 20:47:55 as ** along with 3 people kmdaily lyongu nklee
  • Whole-Genome Discovery of Transcription Factor Binding Sites by Network-Level Conservation
    Genome Res., Vol. 14, No. 1. (1 January 2004), pp. 99-108.
    by Moshe Pritsker, Yir-Chung Liu, Michael A Beer, Saeed Tavazoie
    posted to dna_binding e_coli gene_regulation genome protein-dna_interaction transcription_factor by kaarsinogen on 2006-07-17 22:47:37 as ** along with 2 people xili03 koller
  • A motif co-occurrence approach for genome-wide prediction of transcription-factor-binding sites in Escherichia coli.
    Genome Res, Vol. 14, No. 2. (February 2004), pp. 201-208.
    by ML Bulyk, AM McGuire, N Masuda, GM Church
    posted to dna_binding e_coli gene_regulation genome protein-dna_interaction transcription_factor by kaarsinogen on 2006-07-17 22:24:10 as ** along with 2 people sconlan LeightonP
  • Deciphering gene expression regulatory networks.
    Curr Opin Genet Dev, Vol. 12, No. 2. (April 2002), pp. 130-136.
    by JJ Wyrick, RA Young
    posted to gene_regulation protein-dna_interaction by kaarsinogen on 2006-09-07 22:01:22 as **
  • Evolution of transcription factors and the gene regulatory network in Escherichia coli.
    Nucleic Acids Res, Vol. 31, No. 4. (15 February 2003), pp. 1234-1244.
    by M Madan Babu, SA Teichmann
    posted to evolution gene_regulation transcription transcription_factor by kaarsinogen on 2005-11-18 22:28:53 as *** along with 3 people LeightonP hununu discreteonyxorb
  • Promoter Crosstalk Effects on Gene Expression
    Journal of Molecular Biology, Vol. 365, No. 4. (26 January 2007), pp. 911-920.
    by Mathias Hampf, Manfred Gossen
    posted to crosstalk gene_regulation noise promoter systems_approach transcription by jjray on 2007-01-04 16:57:06 as *** along with 1 person margaritis
  • Requirement for multiple activation signals by anti-inflammatory feedback in macrophages.
    J Theor Biol, Vol. 241, No. 2. (21 July 2006), pp. 276-294.
    by JC Ray, DE Kirschner
    posted to biochemical_systems_theory evolution feedback gene_regulation ifn-gamma immune_activation inos iron lps mathematical_model mathematically_controlled_comparison murine_macrophage network network_motifs nf-kappab nitric_oxide piecewise_power-law power_law response_time robustness sensitivity_analysis signaling stat1 synergistic_signals systems_approach by jjray on 2006-09-28 21:24:15 as read
  • Chemokines and tuberculosis
    Cytokine & Growth Factor Reviews, Vol. 14, No. 6. (December 2003), pp. 467-477.
    by Holly M Algood, John Chan, Joanne L Flynn
    posted to chemokine cytokine gene_regulation granuloma host-pathogen_interaction ifn-gamma immune_activation immune_cell_kinetics lung mycobacterium_tuberculosis pattern_formation review temporal_response by jjray on 2006-10-10 19:38:23 as read
  • Modularity and Dynamics of Cellular Networks
    PLoS Computational Biology, Vol. 2, No. 12. (1 December 2006), e174.
    by Yuan Qi, Hui Ge
    posted to systems_approach saccharomyces_cerevisiae robustness review network_motifs network gene_regulation feedforward feedback dense_overlapping_regulon by jjray on 2007-01-10 16:18:25 as *** along with 3 people and 1 group teuder dolhuis mikaelhuss SNE
  • The TorR high-affinity binding site plays a key role in both torR autoregulation and torCAD operon expression in Escherichia coli.
    J Bacteriol, Vol. 182, No. 4. (February 2000), pp. 961-966.
    by M Ansaldi, G Simon, M Lepelletier, V Méjean
    posted to e_coli gene_regulation tor two-component_system by jjray on 2008-03-27 21:03:43 as read
  • Binding of the TorR regulator to cis-acting direct repeats activates tor operon expression.
    Mol Microbiol, Vol. 17, No. 5. (September 1995), pp. 971-980.
    by G Simon, C Jourlin, M Ansaldi, MC Pascal, M Chippaux, V Méjean
    posted to e_coli gene_regulation tor two-component_system by jjray on 2008-03-27 21:03:28 as **
  • Anticipating an alkaline stress through the Tor phosphorelay system in Escherichia coli.
    Mol Microbiol, Vol. 48, No. 1. (April 2003), pp. 211-223.
    by C Bordi, L Théraulaz, V Méjean, C Jourlin-Castelli
    posted to e_coli gene_regulation tor two-component_system by jjray on 2008-03-27 20:53:18 as **
  • An unsuspected autoregulatory pathway involving apocytochrome TorC and sensor TorS in Escherichia coli.
    Proc Natl Acad Sci U S A, Vol. 98, No. 20. (25 September 2001), pp. 11615-11620.
    by S Gon, C Jourlin-Castelli, L Théraulaz, V Méjean
    posted to e_coli gene_regulation tor two-component_system by jjray on 2008-03-27 20:53:06 as **
  • Rapid Dephosphorylation of the TorR Response Regulator by the TorS Unorthodox Sensor in Escherichia coli
    J. Bacteriol., Vol. 183, No. 8. (15 April 2001), pp. 2691-2695.
    by Mireille Ansaldi, Cecile Jourlin-Castelli, Michele Lepelletier, Laurence Théraulaz, Vincent Méjean
    posted to e_coli gene_regulation tor two-component_system by jjray on 2008-03-27 20:52:42 as **
  • Genetic Properties Influencing the Evolvability of Gene Expression.
    Science (24 May 2007)
    by Christian R R Landry, Bernardo Lemos, Scott A A Rifkin, W J J Dickinson, Daniel L L Hartl
    posted to evolution evolvability gene_expression gene_regulation stochastic by jjray on 2007-07-18 21:04:29 as *** along with 10 people and 3 groups klo brant balicea sebastien_vigneau grahamc emarker heliopais cisevol caseybrown emptyhb EisenLab ParkinsonLab_at_MaRS cis-regulatory-evolution
  • Expression profiling of host pathogen interactions: how Mycobacterium tuberculosis and the macrophage adapt to one another
    Microbes and Infection, Vol. 8, No. 4. (April 2006), pp. 1132-1140.
    by Dirk Schnappinger, Gary K Schoolnik, Sabine Ehrt
    posted to gene_regulation host-pathogen_interaction ider immune_activation inos intracellular lam mrna murine_macrophage mycobacterium_tuberculosis reciprocal_adaptation transcriptional_reprogramming by jjray on 2006-09-19 16:46:48 as read
  • Deterministic characterization of stochastic genetic circuits
    PNAS, Vol. 104, No. 18. (1 May 2007), pp. 7402-7407.
    by Matthew Scott, Terence Hwa, Brian Ingalls
    posted to gene_regulation mathematical_model noise stochastic by jjray on 2007-05-01 19:40:41 as *** along with 2 people balabu margaritis
  • Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells
    Cell, Vol. 133, No. 6. (13 June 2008), pp. 1106-1117.
    by Xi Chen, Han Xu, Ping Yuan, Fang Fang, Mikael Huss, Vinsensius B Vega, Eleanor Wong, Yuriy L Orlov, Weiwei Zhang, Jianming Jiang, Yuin-Han Loh, Hock C Yeo, Zhen X Yeo, Vipin Narang, Kunde R Govindarajan, Bernard Leong, Atif Shahab, Yijun Ruan, Guillaume Bourque, Wing-Kin Sung, Neil D Clarke, Chia-Lin Wei, Huck-Hui Ng
    posted to transcriptional_regulation network gene_regulation es_cell by jjray on 2008-06-13 19:29:49 as ** along with 4 people gdb inesdesantiago kengg caseybrown
  • Co-regulation of metabolic genes is better explained by flux coupling than by network distance.
    PLoS Comput Biol, Vol. 4, No. 1. (January 2008)
    by RA Notebaart, B Teusink, RJ Siezen, B Papp
    posted to saccharomyces_cerevisiae network metabolism gene_regulation gene_order e_coli by jjray on 2008-04-29 23:25:04 as ** along with 1 person maralena
  • A Systems Approach to Measuring the Binding Energy Landscapes of Transcription Factors
    Science, Vol. 315, No. 5809. (12 January 2007), pp. 233-237.
    by Sebastian J Maerkl, Stephen R Quake
    posted to transcription systems_approach microfluidics gene_regulation biophysics by jjray on 2007-01-12 19:57:23 as *** along with 8 people and 2 groups brant dpollard emilyhare adepace aswin skoch3 blobbybirdman emptyhb EisenLab Koch_Lab
  • Expression of Many Immunologically Important Genes in Mycobacterium tuberculosis-Infected Macrophages Is Independent of Both TLR2 and TLR4 but Dependent on IFN-alphabeta Receptor and STAT1
    J Immunol, Vol. 175, No. 5. (1 September 2005), pp. 3318-3328.
    by Shuangping Shi, Antje Blumenthal, Christopher M Hickey, Sheetal Gandotra, David Levy, Sabine Ehrt
    posted to cytokine gene_regulation ifn-gamma immune_activation murine_macrophage mycobacterium_tuberculosis myd88 toll-like_receptor by jjray on 2006-09-19 16:26:36 as read
  • Diffusion of transcription factors can drastically enhance the noise in gene expression.
    Biophys J, Vol. 91, No. 12. (15 December 2006), pp. 4350-4367.
    by JS van Zon, MJ Morelli, S Tănase-Nicola, PR ten Wolde
    posted to gene_regulation gillespie_algorithm mathematical_model noise stochastic transcription by jjray on 2007-05-30 19:23:39 as *** along with 3 people ddcttrl balabu margaritis
  • Computational analysis of the synergy among multiple interacting genes
    Mol Syst Biol, Vol. 3 (13 February 2007)
    by Dimitris Anastassiou
    posted to gene_regulation synergistic_signals systems_approach theory by jjray on 2007-02-28 00:35:14 as read along with 1 person frohike
  • Global regulatory logic for specification of an embryonic cell lineage
    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 brant Minty
  • Autoamplification of a two-component regulatory system results in "learning" behavior.
    Journal of bacteriology, Vol. 183, No. 16. (August 2001), pp. 4914-4917.
    by SM Hoffer, HV Westerhoff, KJ Hellingwerf, PW Postma, J Tommassen
    posted to two-component_system gene_regulation feedback bacteria by jjray on 2008-07-13 19:31:16 as read
  • Making informed decisions: regulatory interactions between two-component systems.
    Trends in microbiology, Vol. 11, No. 8. (August 2003), pp. 359-366.
    by JJ Bijlsma, EA Groisman
    posted to two-component_system gene_regulation bacteria by jjray on 2008-07-13 19:30:06 as read
  • An excitable gene regulatory circuit induces transient cellular differentiation
    Nature, Vol. 440, No. 7083., pp. 545-550.
    by Gã¼rol M Sã¼el, Jordi Garcia-Ojalvo, Louisa M Liberman, Michael B Elowitz
    posted to bacillus_subtilis competence gene_regulation noise stochastic by jjray on 2008-01-15 20:14:01 as read along with 10 people and 1 group rklancer alexg madhadron balabu nickluscombe comb dbikard mhucka margaritis paurue EBI-regulation
  • Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters.
    J Mol Biol, Vol. 193, No. 4. (20 February 1987), pp. 723-750.
    by OG Berg, PH von Hippel
    posted to dna_binding gene_regulation statistical_mechanics by jjray on 2008-01-24 16:06:24 as ** along with 7 people and 2 groups zambujo brant indigoviolet lusk discreteonyxorb cisevol Ema EisenLab cis-regulatory-evolution
  • Bacillus subtilis sporulation and stationary phase gene expression
    Cellular and Molecular Life Sciences (CMLS), Vol. 59, No. 3. (6 March 2002), pp. 392-402.
    by ZEV Phillips, MA Strauch
    posted to bacillus_subtilis gene_expression gene_regulation review spooa by jjray on 2008-01-02 21:43:46 as **
  • On the specificity of DNA-protein interactions.
    Proc Natl Acad Sci U S A, Vol. 83, No. 6. (March 1986), pp. 1608-1612.
    by PH von Hippel, OG Berg
    posted to dna_binding gene_regulation thermodynamics by jjray on 2008-04-01 20:34:15 as ** along with 3 people and 1 group stsaft cisevol lambda cis-regulatory-evolution
  • Estimation of the Source-by-Source Effect of Autorepression on Genetic Noise
    Biophys. J., Vol. 95, No. 3. (1 August 2008), pp. 1063-1074.
    by Hiroyuki Okano, Tetsuya J Kobayashi, Hirokazu Tozaki, Hidenori Kimura
    posted to noise gene_regulation feedback extrinsic_noise by jjray on 2008-07-21 22:57:14 as **
  • Identification of a novel regulatory protein (CsrD) that targets the global regulatory RNAs CsrB and CsrC for degradation by RNase E.
    Genes Dev, Vol. 20, No. 18. (15 September 2006), pp. 2605-2617.
    by K Suzuki, P Babitzke, SR Kushner, T Romeo
    posted to csra gene_order gene_regulation metabolism two-component_system by jjray on 2008-02-08 17:08:03 as ** along with 2 people dbikard martainn
  • Gata2, Fli1, and Scl form a recursively wired gene-regulatory circuit during early hematopoietic development.
    Proc Natl Acad Sci U S A (25 October 2007)
    by John E E Pimanda, Katrin Ottersbach, Kathy Knezevic, Sarah Kinston, Wan Y I Y Chan, Nicola K K Wilson, Josette-Renée R Landry, Andrew D D Wood, Anja Kolb-Kokocinski, Anthony R R Green, David Tannahill, Georges Lacaud, Valerie Kouskoff, Berthold Göttgens
    posted to development gene_regulation stem_cell transcription triad by jjray on 2008-01-16 16:57:07 as read along with 2 people maximilianh idonaldson
  • Comparative analyses of bidirectional promoters in vertebrates.
    BMC bioinformatics, Vol. 9 Suppl 6 (2008)
    by MQ Yang, J Taylor, L Elnitski
    posted to promoter phylogeny gene_regulation evolution chromosome_organization by jjray on 2008-06-30 23:20:37 as ** along with 1 person bootsy
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