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joseph_x_zhou's library [106 articles]

Recent papers added to joseph_x_zhou's library.
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  • Minireview: Transcriptional Regulation in Pancreatic Development
    Endocrinology, Vol. 146, No. 3. (1 March 2005), pp. 1025-1034.
    by Joel F Habener, Daniel M Kemp, Melissa K Thomas
    posted to review pancrea_dev journal by joseph_x_zhou on 2009-01-05 19:40:23 as **
  • Tweaking biological switches through a better understanding of bistability behavior
    Current Opinion in Biotechnology, Vol. 19, No. 5. (October 2008), pp. 475-481.
    by A Chatterjee, Y Kaznessis, W Hu
    posted to journal gene_switch gene_network_dyn gene_netwok by joseph_x_zhou on 2008-12-30 21:12:13 as ** along with 1 person and 1 group balicea bioNetwork_sysBio
  • Neutrality and Robustness in Evo-Devo: Emergence of Lateral Inhibition
    PLoS Comput Biol, Vol. 4, No. 11. (21 November 2008), e1000226.
    by Andreea Munteanu, Ricard V Solé
    posted to journal gene_network_dyn gene_netwok by joseph_x_zhou on 2008-12-30 21:02:19 as ***** along with 3 people and 3 groups bayesian dlobo bpcusack Evolutionary Dynamics Math Bio bioNetwork_sysBio GEB
  • Robustness and state-space structure of Boolean gene regulatory models
    Journal of Theoretical Biology, Vol. 249, No. 4. (21 December 2007), pp. 749-765.
    by K Willadsen, J Wiles
    posted to robustness journal gene_network_dyn gene_netwok by joseph_x_zhou on 2008-12-30 20:56:42 as *****
  • Bifurcation dynamics in lineage-commitment in bipotent progenitor cells
    Developmental Biology, Vol. 305, No. 2. (15 May 2007), pp. 695-713.
    by S Huang, Y Guo, G May, T Enver
    posted to journal cell_reprogram by joseph_x_zhou on 2008-12-30 20:49:12 as *****
  • Gene networks: how to put the function in genomics
    Trends in Biotechnology, Vol. 20, No. 11. (01 November 2002), pp. 467-472.
    by P Brazhnik, A Delafuente, P Mendes
    posted to sys_bio review journal gene_regulation_network by joseph_x_zhou on 2008-12-24 19:27:10 as ***** along with 1 group bioNetwork_sysBio
  • Gene regulatory factors in pancreatic development
    Developmental Dynamics, Vol. 229, No. 1. (2004), pp. 176-200.
    by Jan Jensen
    posted to pancrea_dev journal genetic gene_regulation_network by joseph_x_zhou on 2008-12-23 20:00:09 as *****
  • Remodeling the exocrine pancreas at metamorphosis in Xenopus laevis
    Proceedings of the National Academy of Sciences, Vol. 105, No. 26. (1 July 2008), pp. 8962-8967.
    by Sandeep Mukhi, Jinzhe Mao, Donald D Brown
    posted to pancrea_dev journal gene_regulation_network by joseph_x_zhou on 2008-12-19 16:18:31 as ***
  • Generation and Regeneration of Cells of the Liver and Pancreas
    Science, Vol. 322, No. 5907. (5 December 2008), pp. 1490-1494.
    by Kenneth S Zaret, Markus Grompe
    posted to pancrea_dev journal gene_regulation_network by joseph_x_zhou on 2008-12-15 14:59:17 as ***** along with 1 person and 1 group Zephyrus BCDC Lab Notebook
  • A Multipotent Progenitor Domain Guides Pancreatic Organogenesis
    Developmental Cell, Vol. 13, No. 1. (03 July 2007), pp. 103-114.
    by Q Zhou, A Law, J Rajagopal, W Anderson, P Gray, D Melton
    posted to journal gene_regulation_network cell_reprogram by joseph_x_zhou on 2008-12-09 19:47:04 as **
  • Boolean network model predicts cell cycle sequence of fission yeast.
    PLoS ONE, Vol. 3, No. 2. (2008)
    by MI Davidich, S Bornholdt
    posted to journal gene_regulation_network boolean_network by joseph_x_zhou on 2008-12-09 19:41:37 as ***** along with 2 people lflorez larsjuhljensen
  • The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster
    Journal of Theoretical Biology, Vol. 223, No. 1. (07 July 2003), pp. 1-18.
    by R Albert
    posted to journal gene_regulation_network drosophila by joseph_x_zhou on 2008-12-09 19:37:58 as read
  • Mathematical Modeling of Gene Networks
    Neuron, Vol. 26, No. 3. (June 2000), pp. 567-580.
    by P Smolen
    posted to math_model journal gene_netwok by joseph_x_zhou on 2008-12-03 09:20:19 as ***** along with 1 group bioNetwork_sysBio
  • Systems biology: a brief overview.
    Science, Vol. 295, No. 5560. (1 March 2002), pp. 1662-1664.
    by H Kitano
    posted to systems_biology review journal by joseph_x_zhou on 2008-12-03 09:17:01 as ** along with 24 people and 6 groups rsantana reyez softsimu irenas Yanno Borelli wnpx biosv shivakumar3_14 dgront kehan cconboy mmt margaritis grahamc roland_ewald carmaus jdiezperezj maburkitt mertnuhoglu edvin lenov soramame_0518 nsamways dbk-lab biodiversity_conservation Bioinformatics GrassBase dIEMoSIRIS MoSi-Rostock
  • Mathematical model of the morphogenesis checkpoint in budding yeast -- Ciliberto et al. 163 (6): 1243 -- The Journal of Cell Biology
    The Journal of Cell Biology, Vol. 163, No. 6. (December 2003), pp. 1243-1254.
    by Andrea Ciliberto, Bela Novak, John J Tyson1
    posted to math_model journal gene_regulation_network by joseph_x_zhou on 2008-11-28 17:01:42 as **
  • A fast, robust and tunable synthetic gene oscillator.
    Nature (29 October 2008)
    by Jesse Stricker, Scott Cookson, Matthew R R Bennett, William H H Mather, Lev S S Tsimring, Jeff Hasty
    posted to synthesis_bio oscillation journal gene_regulation_network by joseph_x_zhou on 2008-11-28 16:53:05 as ***** along with 7 people and 2 groups stasaki stringertheory allysonlister yxue jbhiatt grahamc dbikard bioNetwork_sysBio SynBioSys
  • SIRT1 Redistribution on Chromatin Promotes Genomic Stability but Alters Gene Expression during Aging
    Cell, Vol. 135, No. 5. (28 November 2008), pp. 907-918.
    by P Oberdoerffer, S Michan, M Mcvay, R Mostoslavsky, J Vann, S Park, A Hartlerode, J Stegmuller, A Hafner, P Loerch
    posted to journal gene_regulation_network aging by joseph_x_zhou on 2008-11-28 16:47:02 as ** along with 2 people zhlei renatomilani
  • Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis
    Genome Biology, Vol. 8 (11 January 2007), R7.
    by Rodrigo A Gutierrez, Laurence Lejay, Alexis Dean, Francesca Chiaromonte, Dennis E Shasha, Gloria M Coruzzi
    posted to qualitative_network journal gene_netwok by joseph_x_zhou on 2008-11-20 20:26:31 as ** along with 2 people and 1 group xwbcn natstreet bioNetwork_sysBio
  • Using a quantitative blueprint to reprogram the dynamics of the flagella gene network.
    Cell, Vol. 117, No. 6. (11 June 2004), pp. 713-720.
    by S Kalir, U Alon
    posted to journal gene_netwok cell_reprogram by joseph_x_zhou on 2008-11-20 19:33:29 as ** along with 3 people and 2 groups dbikard comb adria bioNetwork_sysBio TNT
  • Metabolic gene regulation in a dynamically changing environment
    Nature (30 July 2008)
    by Matthew R Bennett, Wyming L Pang, Natalie A Ostroff, Bridget L Baumgartner, Sujata Nayak, Lev S Tsimring, Jeff Hasty
    posted to metabolic journal gene_regulation_network by joseph_x_zhou on 2008-11-18 20:34:39 as ** along with 7 people and 1 group guhjy emptyhb erel10 caseybrown bayesian klo margaritis bioNetwork_sysBio
  • Statistical Prediction and Molecular Dynamics Simulation
    Biophys. J. (1 August 2008), biophysj.108.131623.
    by Ben Cooke, Scott Schmidler
    posted to statistical_prediction protein_dynamics journal by joseph_x_zhou on 2008-11-16 21:08:25 as ** along with 3 people Diego_Prada agrossfield paulschlesinger
  • Modelling the Establishment of PAR Protein Polarity in the One-Cell C. elegans Embryo.
    Biophys J (2008)
    by F Tostevin, M Howard
    posted to journal cell_polarity cell_biology by joseph_x_zhou on 2008-11-16 21:04:39 as ** along with 2 people and 1 group Doug tharris C. elegans / WormBase
  • New Proposed Mechanism of Actin-Polymerization-Driven Motility
    Biophys. J., Vol. 95, No. 10. (15 November 2008), pp. 4529-4539.
    by Kun-Chun Lee, Andrea J Liu
    posted to journal cell_motility by joseph_x_zhou on 2008-11-16 21:01:31 as **
  • The Rough Guide to In Silico Function Prediction, or How To Use Sequence and Structure Information To Predict Protein Function
    PLoS Comput Biol, Vol. 4, No. 10. (31 October 2008), e1000160.
    by Marco Punta, Yanay Ofran
    posted to review protein_strut_func journal by joseph_x_zhou on 2008-11-16 20:21:33 as ** along with 16 people and 1 group niallhaslam daforerog Zalanszabo bpcusack Katje taguchi sjcockell markchen ptrobajo chad_davis druvus mdstobbe giovenko nilanjanroy reyez GeeSharpMinor microbiology_nijmegen
  • Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web
    PLoS Comput Biol, Vol. 4, No. 10. (31 October 2008), e1000204.
    by Duncan Hull, Steve R Pettifer, Douglas B Kell
    posted to research_tools journal digital_lib by joseph_x_zhou on 2008-11-16 20:17:57 as ** along with 80 people and 8 groups OriginalLurch sototozo akraemer thegoose kharke niallhaslam rdmagnuson JuanGiarrizzo pkonings jennialp lgibson rmasur GJNauta puchu rrbarb amarois mneeley dr_lee_xray IRTADOC zilvlan curthh mount_misery narroyo rdiaz treangen hpaces bumatic BerndBerndsen esterhasz phreeza dbk rempeljl teachingaging cs02 continea Rosetta fletchad Betelgeuse60 tomroper 1971biblio timrwatkins rschulz cisevol ryan smithrise silberbauer natstreet pick600 xjlibod ukppdadsr robertlischke bookwormzz NIlz junwang4 taguchi tag barry kristgy caseybrown Gaetan bcondon lynnefox marekrud nuin sdgsilvana ckai1 guhjy neils carlfulp norris jago druvus alhoori emayorga GeeSharpMinor fgibson chad_davis Zephyrus leonardo dullhunk MEHTRadiology Département Hypermédia - Master NET JacksonLab BergmanLab McCammon kpa-resources structural_bioinformatics Roswell Cancer Crosstalk
  • An End to Endless Forms: Epistasis, Phenotype Distribution Bias, and Nonuniform Evolution
    PLoS Comput Biol, Vol. 4, No. 10. (24 October 2008), e1000202.
    by Elhanan Borenstein, David C Krakauer
    posted to limited_phenotype journal gene_regulation_network by joseph_x_zhou on 2008-11-16 20:10:28 as ** along with 12 people and 2 groups bpcusack qwermish bayesian biomcgary davfre jago Zephyrus mjoach grahamc alhufton dlobo djkt R.E.A.D GEB
  • Nonidentifiability of the Source of Intrinsic Noise in Gene Expression from Single-Burst Data
    PLoS Comput Biol, Vol. 4, No. 10. (10 October 2008), e1000192.
    by Piers J Ingram, Michael P Stumpf, Jaroslav Stark
    posted to noise journal gene_regulation_network gene_netwok by joseph_x_zhou on 2008-11-16 20:05:44 as ** along with 2 people jjray balabu
  • Analysis of gene regulatory networks in the Mammalian circadian rhythm.
    PLoS computational biology, Vol. 4, No. 10. (October 2008)
    by J Yan, H Wang, Y Liu, C Shao
    posted to journal gene_regulation_network circadian bio_network by joseph_x_zhou on 2008-11-16 20:02:36 as ** along with 1 person talponer
  • Biophysical Basis for Three Distinct Dynamical Mechanisms of Action Potential Initiation
    PLoS Comput Biol, Vol. 4, No. 10. (10 October 2008), e1000198.
    by Steven A Prescott, Yves De Koninck, Terrence J Sejnowski
    posted to neuron_coding neuron journal by joseph_x_zhou on 2008-11-16 19:53:46 as ** along with 1 person bayesian
  • Discarding Functional Residues from the Substitution Table Improves Predictions of Active Sites within Three-Dimensional Structures
    PLoS Comput Biol, Vol. 4, No. 10. (3 October 2008), e1000179.
    by Sungsam Gong, Tom L Blundell
    posted to protein_strut_func protein journal by joseph_x_zhou on 2008-11-16 19:48:19 as ** along with 4 people zwang bicko massivemayhem reyez
  • EXPLORING THE SUITABILITY OF COARSE-GRAINED TECHNIQUES FOR THE REPRESENTATION OF PROTEIN DYNAMICS
    Biophys. J. (16 May 2008), biophysj.107.119115.
    by Agusti Emperador, Oliver Carrillo, Manuel Rueda, Modesto Orozco
    posted to protein_dynamics journal coarse_grained_model by joseph_x_zhou on 2008-10-15 16:34:48 as **** along with 1 person and 1 group paulschlesinger protein_Dyn
  • Four-body contact potentials derived from two protein datasets to discriminate native structures from decoys
    Proteins: Structure, Function, and Bioinformatics, Vol. 68, No. 1. (2007), pp. 57-66.
    by Yaping Feng, Andrzej Kloczkowski, Robert L Jernigan
    posted to protein_structure journal decoy by joseph_x_zhou on 2008-10-01 15:29:16 as *** along with 1 group protein_Dyn
  • Adaptive inhibitors of the HIV-1 protease
    Progress in Biophysics and Molecular Biology, Vol. 88, No. 2. (June 2005), pp. 193-208.
    by Hiroyasu Ohtaka, Ernesto Freire
    posted to journal hiv drug_resistance adaptive_dr by joseph_x_zhou on 2008-09-18 15:13:57 as **** along with 1 group HIV_DR
  • notes Structural and kinetic analysis of drug resistant mutants of HIV-1 protease
    European Journal of Biochemistry, Vol. 263, No. 1. (1999), pp. 238-244.
    by Bhuvaneshwari Mahalingam, John M Louis, Charles C Reed, Jill M Adomat, Jennifer Krouse, Yuan-Fang Wang, Robert W Harrison, Irene T Weber
    posted to journal hiv drug_resistance by joseph_x_zhou on 2008-09-18 14:33:49 as ** along with 1 group HIV_DR
  • notes Structural implications of drug-resistant mutants of HIV-1 protease: High-resolution crystal structures of the mutant protease/substrate analogue complexes
    Proteins: Structure, Function, and Genetics, Vol. 43, No. 4. (2001), pp. 455-464.
    by Bhuvaneshwari Mahalingam, John M Louis, Jason Hung, Robert W Harrison, Irene T Weber
    posted to journal hiv drug_resistance by joseph_x_zhou on 2008-09-18 14:12:48 as ** along with 1 group HIV_DR
  • notes Crystal Structures of a Multidrug-Resistant Human Immunodeficiency Virus Type 1 Protease Reveal an Expanded Active-Site Cavity
    J. Virol., Vol. 78, No. 6. (15 March 2004), pp. 3123-3132.
    by Bradley C Logsdon, John F Vickrey, Philip Martin, Gheorghe Proteasa, Jay I Koepke, Stanley R Terlecky, Zdzislaw Wawrzak, Mark A Winters, Thomas C Merigan, Ladislau C Kovari
    posted to multidrug journal hiv drug_resistance by joseph_x_zhou on 2008-09-17 16:43:22 as **** along with 1 person and 1 group miorel HIV_DR
  • Viracept (Nelfinavir Mesylate, AG1343): A Potent, Orally Bioavailable Inhibitor of HIV-1 Protease
    J. Med. Chem., Vol. 40, No. 24. (21 November 1997), pp. 3979-3985.
    by SW Kaldor, VJ Kalish, JF Davies, BV Shetty, JE Fritz, K Appelt, JA Burgess, KM Campanale, NY Chirgadze, DK Clawson, BA Dressman, SD Hatch, DA Khalil, MB Kosa, PP Lubbehusen, MA Muesing, AK Patick, SH Reich, KS Su, JH Tatlock
    posted to protein_structure journal hiv_pr by joseph_x_zhou on 2008-09-17 16:24:38 as ** along with 1 group HIV_DR
  • Atomic resolution crystal structures of HIV-1 protease and mutants V82A and I84V with saquinavir
    Proteins: Structure, Function, and Bioinformatics, Vol. 67, No. 1. (2007), pp. 232-242.
    by Yunfeng Tie, Andrey Y Kovalevsky, Peter Boross, Yuan-Fang Wang, Arun K Ghosh, Jozsef Tozser, Robert W Harrison, Irene T Weber
    posted to protein_structure journal hiv by joseph_x_zhou on 2008-09-17 15:40:18 as **
  • Gaussian Dynamics of Folded Proteins
    Physical Review Letters, Vol. 79, No. 16. (20 October 1997), 3090.
    by Turkan Haliloglu, Ivet Bahar, Burak Erman
    posted to protein_dynamics journal by joseph_x_zhou on 2008-09-15 20:59:24 as ** along with 1 person and 1 group aqeel protein_Dyn
  • Abstract fluctuation theorem
    Ergodic Theory and Dynamical Systems, Vol. Forthcoming, No. -1. (2008), pp. 1-7.
    by Maciej P Wojtkowski
    posted to statmech non_eq by joseph_x_zhou on 2008-09-13 09:35:28 as *** along with 1 group NonEquilibrium
  • Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models
    Bioinformatics, Vol. 23, No. 13. (1 July 2007), pp. i175-184.
    by Eran Eyal, Chakra Chennubhotla, Lee-Wei Yang, Ivet Bahar
    posted to protein_dynamics journal enm aa_specific by joseph_x_zhou on 2008-09-10 16:42:46 as ** along with 3 people and 1 group simone aqeel jlh64 protein_Dyn
  • Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
    Folding and Design, Vol. 2, No. 3. (June 1997), pp. 173-181.
    by Ivet Bahar, Ali R Atilgan, Burak Erman
    posted to protein_dynamics gnm by joseph_x_zhou on 2008-09-09 20:12:54 as read along with 1 group protein_Dyn
  • Vibrational dynamics of transfer RNAs: comparison of the free and synthetase-bound forms.
    J Mol Biol, Vol. 281, No. 5. (4 September 1998), pp. 871-884.
    by I Bahar, RL Jernigan
    posted to soft_mode protein_dynamics by joseph_x_zhou on 2008-09-09 15:54:01 as ** along with 2 people and 1 group aqeel simone protein_Dyn
  • Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis
    Physical Review Letters, Vol. 77, No. 9. (1996), 1905.
    by Monique M Tirion
    posted to protein_dynamics by joseph_x_zhou on 2008-09-09 15:47:30 as ** along with 2 people and 1 group aqeel Diego_Prada protein_Dyn
  • An Introduction to Systems Biology: Design Principles of Biological Circuits (Chapman & Hall/Crc Mathematical and Computational Biology Series)
    (07 July 2006)
    by Uri Alon
    posted to textbook systems_biology books by joseph_x_zhou on 2008-09-08 16:12:41 as ** along with 10 people and 2 groups flyme dullhunk aalibes balajis balicea mattjb fishtank akastrin jjray azazello ComplexAdaptiveSystems DSTO-CAS
  • Systems Biology: Definitions and Perspectives (Topics in Current Genetics)
    (16 November 2007)
    posted to textbook systems_biology books by joseph_x_zhou on 2008-09-08 16:11:32 as **
  • Systems Biology: Philosophical Foundations
    (20 April 2007)
    posted to systems_biology philosophy books by joseph_x_zhou on 2008-09-08 16:02:23 as **
  • Systems Biology: International Research and Development
    (05 March 2007)
    by Marvin Cassman, Adam Arkin, Frank Doyle, Fumiaki Katagiri, Douglas Lauffenburger, Cynthia Stokes
    posted to systems_biology review books by joseph_x_zhou on 2008-09-08 15:59:50 as **
  • Cooperative Molecular Motors
    Physical Review Letters, Vol. 75, No. 13. (1995), 2618.
    by Frank Jülicher, Jacques Prost
    posted to molecular_machine molecular_motor by joseph_x_zhou on 2008-08-28 21:50:03 as **** along with 2 people and 4 groups dherkova rodney biophysics NonEquilibrium protein_Dyn Soft Matter
  • Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins.
    Proc Natl Acad Sci U S A, Vol. 100, No. 22. (28 October 2003), pp. 12570-12575.
    by O Miyashita, JN Onuchic, PG Wolynes
    posted to protein_dynamics by joseph_x_zhou on 2008-08-28 21:47:49 as ** along with 1 person and 2 groups aqeel biophysics protein_Dyn
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