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Tag qualifier [174 articles]

Recent papers classified by the tag qualifier.
  • An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences
    Proteins: Structure, Function, and Genetics, Vol. 7, No. 1. (1990), pp. 41-51.
    by Charles E Lawrence, Andrew A Reilly
    posted to chemical_kinetics qualifier by RamuAnandakrishnan on 2008-01-30 19:06:02 as ** along with 1 person wenhan
  • Efficient step size selection for the tau-leaping simulation method
    The Journal of Chemical Physics, Vol. 124, No. 4. (2006)
    by Yang Cao, Daniel T Gillespie, Linda R Petzold
    posted to chemical_kinetics qualifier by RamuAnandakrishnan on 2008-01-24 22:16:07 as ** along with 1 person jporternj
  • Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons
    Bioinformatics, Vol. 21, No. 10. (15 May 2005), pp. 2347-2355.
    by Richard J Morris, Rafael J Najmanovich, Abdullah Kahraman, Janet M Thornton
    posted to ligand qualifier by RamuAnandakrishnan on 2007-10-15 23:52:48 as ** along with 1 person kallberg
  • Integrative analysis of cell cycle control in budding yeast.
    Mol Biol Cell, Vol. 15, No. 8. (August 2004), pp. 3841-3862.
    by KC Chen, L Calzone, A Csikasz-Nagy, FR Cross, B Novak, JJ Tyson
    posted to chemical_kinetics qualifier by RamuAnandakrishnan on 2008-01-20 01:37:15 as ** along with 2 people monod jbchang
  • Automated prediction of ligand-binding sites in proteins
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Rodney Harris, Arthur J Olson, David S Goodsell
    posted to binding_site ligand qualifier by RamuAnandakrishnan on 2007-10-25 01:05:21 as ** along with 2 people tjimenez carlescorbi
  • Stochastically driven genetic circuits
    Chaos: An Interdisciplinary Journal of Nonlinear Science, Vol. 16, No. 2. (2006)
    by LS Tsimring, D Volfson, J Hasty
    posted to qualifier by RamuAnandakrishnan on 2008-01-03 22:54:52 as **
  • Noise Propagation and Signaling Sensitivity in Biological Networks: A Role for Positive Feedback
    PLoS Computational Biology, Vol. 4, No. 1. (1 January 2008), e8.
    by Gil Hornung, Naama Barkai
    posted to qualifier by RamuAnandakrishnan on 2008-01-04 15:13:32 as ** along with 1 person fpattyn
  • Time scale and dimension analyses of a budding yeast cell cycle model
    BMC Bioinformatics, Vol. 7 (09 November 2006), 494.
    by Anna Lovrics, Attila Csikasz-Nagy, Istvan GY Zsely, Judit Zador, Tamas Turanyi, Bela Novak
    posted to chemical_kinetics qualifier by RamuAnandakrishnan on 2008-01-20 01:33:16 as **
  • Preservation of Duplicate Genes by Complementary, Degenerative Mutations
    Genetics, Vol. 151, No. 4. (1 April 1999), pp. 1531-1545.
    by Allan Force, Michael Lynch, Bryan F Pickett, Angel Amores, Yi-Lin Yan, John Postlethwait
    posted to evolution qualifier by RamuAnandakrishnan on 2007-10-13 14:50:12 as read along with 3 people gurkanbebek BioNica skumagai
  • Hybrid method for the chemical master equation
    J. Comput. Phys., Vol. 227, No. 1. (November 2007), pp. 100-122.
    by Andreas Hellander, Per Lötstedt
    posted to qualifier by RamuAnandakrishnan on 2008-01-03 14:12:19 as ** along with 1 person hugo_yas
  • Topological complexity, contact order, and protein folding rates
    The Journal of Chemical Physics, Vol. 117, No. 18. (2002), pp. 8587-8591.
    by PFN Faisca, RC Ball
    posted to folding qualifier by RamuAnandakrishnan on 2008-01-11 00:32:19 as **
  • Efficient large-scale sequence comparison by locality-sensitive hashing
    Bioinformatics, Vol. 17, No. 5. (1 May 2001), pp. 419-428.
    by Jeremy Buhler
    posted to homology qualifier by RamuAnandakrishnan on 2007-10-15 23:55:55 as ** along with 1 person nedwards
  • Stochastic Approach to Chemical Kinetics
    Journal of Applied Probability, Vol. 4, No. 3. (1967), pp. 413-478.
    by Donald A Mcquarrie
    posted to qualifier by RamuAnandakrishnan on 2008-01-03 16:18:27 as **
  • Contact order, transition state placement and the refolding rates of single domain proteins
    Journal of Molecular Biology, Vol. 277, No. 4. (10 April 1998), pp. 985-994.
    by Kevin W Plaxco, Kim T Simons, David Baker
    posted to contact folding qualifier by RamuAnandakrishnan on 2007-10-04 22:17:40 as *****
  • A Hidden Markov Model for Transcriptional Regulation in Single Cells
    IEEE/ACM Trans. Comput. Biol. Bioinformatics, Vol. 3, No. 1. (January 2006)
    by John Goutsias
    posted to qualifier by RamuAnandakrishnan on 2008-01-04 00:18:58 as **
  • Contact order and ab initio protein structure prediction.
    Protein Sci, Vol. 11, No. 8. (August 2002), pp. 1937-1944.
    by R Bonneau, I Ruczinski, J Tsai, D Baker
    posted to contact folding qualifier by RamuAnandakrishnan on 2008-01-20 00:24:01 as ** along with 1 person jwm
  • Finding motifs using random projections
    (2001), pp. 69-76.
    by Jeremy Buhler, Martin Tompa
    posted to homology qualifier by RamuAnandakrishnan on 2007-10-16 00:00:20 as ** along with 2 people nedwards lptolik
  • Predicting Gene Regulatory Elements in Silico on a Genomic Scale
    Genome Res., Vol. 8, No. 11. (1 November 1998), pp. 1202-1215.
    by Alvis Brazma, Inge Jonassen, Jaak Vilo, Esko Ukkonen
    posted to qualifier by RamuAnandakrishnan on 2008-01-07 20:56:51 as **
  • Diffusive searches in high-dimensional spaces and apparent ‘two-state’ behaviour in protein folding
    Journal of Physics: Condensed Matter, Vol. 18, No. 6. (2006), pp. 1861-1868.
    by TCB Mcleish
    posted to contact folding qualifier by RamuAnandakrishnan on 2008-01-30 16:08:20 as **
  • Transition State Contact Orders Correlate with Protein Folding Rates
    Journal of Molecular Biology, Vol. 352, No. 3. (23 September 2005), pp. 495-500.
    by Emanuele Paci, Kresten Lindorff-Larsen, Christopher M Dobson, Martin Karplus, Michele Vendruscolo
    posted to folding qualifier by RamuAnandakrishnan on 2008-01-11 00:35:44 as ** along with 2 people and 2 groups ana allmensch structural_bioinformatics Bioinformatics
  • Protein folding: Matching speed and locality
    Nature, Vol. 392, No. 6678. (23 April 1998), pp. 761-763.
    by Hue S Chan
    posted to folding qualifier by RamuAnandakrishnan on 2008-01-11 02:57:58 as **
  • Ohno's dilemma: Evolution of new genes under continuous selection
    Proceedings of the National Academy of Sciences, Vol. 104, No. 43. (23 October 2007), pp. 17004-17009.
    by Ulfar Bergthorsson, Dan I Andersson, John R Roth
    posted to evolution qualifier by RamuAnandakrishnan on 2007-10-25 00:46:38 as *** along with 3 people dchughes bpowell9180 bpcusack
  • Contact order revisited: influence of protein size on the folding rate.
    Protein Sci, Vol. 12, No. 9. (September 2003), pp. 2057-2062.
    by DN Ivankov, SO Garbuzynskiy, E Alm, KW Plaxco, D Baker, AV Finkelstein
    posted to contact folding qualifier by RamuAnandakrishnan on 2008-01-30 14:57:23 as ** along with 3 people and 2 groups kentsis ana choonpeng structural_bioinformatics Bioinformatics
  • Characterization of local geometry of protein surfaces with the visibility criterion
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Bin Li, Srinivasan Turuvekere, Manish Agrawal, David La, Karthik Ramani, Daisuke Kihara
    posted to binding_site qualifier by RamuAnandakrishnan on 2007-11-03 20:36:13 as **
  • Search for a correlation length in a simulation of the glass transition
    Physical Review B, Vol. 43, No. 10. (1 April 1991), 8070.
    by Richard M Ernst, Sidney R Nagel, Gary S Grest
    posted to glass qualifier structure by kedmond on 2007-07-30 16:27:35 as ** along with 2 people weeks dchen
  • A colloidal model system with an interaction tunable from hard sphere to soft and dipolar
    Nature, Vol. 421, No. 6922. (30 January 2003), pp. 513-517.
    by Anand Yethiraj, Alfons van Blaaderen
    posted to colloidal qualifier salt by kedmond on 2007-04-10 04:47:33 as **** along with 1 person dchen
  • notes Relation between Rotational and Translational Dynamic Heterogeneities in Water
    Physical Review Letters, Vol. 96, No. 5. (2006)
    by Marco G Mazza, Nicolas Giovambattista, Francis W Starr, Eugene H Stanley
    posted to fluid qualifier rotation simulation structure by kedmond on 2007-06-26 01:40:23 as read along with 1 person weeks
  • Observation of a glass transition in suspensions of spherical colloidal particles
    Physical Review Letters, Vol. 59, No. 18. (2 November 1987), 2083.
    by PN Pusey, W van Megen
    posted to colloidal glass qualifier structure supercooled by kedmond on 2007-06-12 15:55:03 as **** along with 1 person dchen
  • notes Dynamics of the rotational degrees of freedom in a supercooled liquid of diatomic molecules
    Physical Review E, Vol. 56 (November 1997), 5450.
    by Stefan Kämmerer, Walter Kob, Rolf Schilling
    posted to qualifier rotation simulation supercooled theory by kedmond on 2007-06-26 14:24:15 as **
  • Bifurcation of translational and rotational non-Gaussian behaviors in two-dimensional liquid
    Physics Letters A, Vol. 293, No. 3-4. (28 January 2002), pp. 156-160.
    by Genzou Matsui, Seiji Kojima
    posted to qualifier rotation simulation supercooled theory by kedmond on 2007-08-09 18:16:43 as ** along with 1 person and 1 group rodney Kopelman_Group
  • notes Viscous Liquids and the Glass Transition: A Potential Energy Barrier Picture
    The Journal of Chemical Physics, Vol. 51, No. 9. (1969), pp. 3728-3739.
    by Martin Goldstein
    posted to glass qualifier structure supercooled theory by kedmond on 2007-05-28 16:16:00 as **** along with 2 people dchen weeks
  • notes Preparation of monodisperse PMMA microspheres in nonpolar solvents by dispersion polymerization with a macromonomeric stabilizer
    Colloid & Polymer Science, Vol. 282, No. 1. (1 December 2003), pp. 7-13.
    by Sascham Klein, Vinothann Manoharan, Davidj Pine, Fredf Lange
    posted to clusters colloidal monodisperse qualifier synthesis by kedmond on 2007-05-27 22:15:17 as *** along with 2 people dchen weeks
  • notes Supercooled Liquids and Glasses
    J. Phys. Chem., Vol. 100, No. 31. (1 August 1996), pp. 13200-13212.
    by MD Ediger, CA Angell, SR Nagel
    posted to glass qualifier review supercooled by kedmond on 2007-05-31 20:56:10 as **** along with 4 people cgguido erdomi dchen weeks
  • Phase behaviour of concentrated suspensions of nearly hard colloidal spheres
    Nature, Vol. 320, No. 6060. (27 March 1986), pp. 340-342.
    by PN Pusey, W van Megen
    posted to colloidal diffusion fluorescence qualifier by kedmond on 2007-05-18 08:13:31 as read along with 4 people and 1 group cgguido waitonhill weeks dchen WeeksLab
  • Viscosity and Structural Relaxation in Suspensions of Hard-Sphere Colloids
    Physical Review Letters, Vol. 75 (31 July 1995), 958.
    by PN Segrè, SP Meeker, PN Pusey, WCK Poon
    posted to colloidal diffusion qualifier structure by kedmond on 2007-07-11 21:14:14 as ***** along with 2 people weeks dchen
  • Direct Visualization of Colloidal Rod Assembly by Confocal Microscopy
    Langmuir, Vol. 21, No. 12. (7 June 2005), pp. 5298-5306.
    by A Mohraz, MJ Solomon
    posted to colloidal microscopy monodisperse qualifier rotation synthesis by kedmond on 2007-06-25 03:35:37 as *** along with 2 people kdesmond weeks
  • Relation between the Widom line and the breakdown of the Stokes-Einstein relation in supercooled water
    PNAS, Vol. 104, No. 23. (5 June 2007), pp. 9575-9579.
    by Pradeep Kumar, SV Buldyrev, SR Becker, PH Poole, FW Starr, HE Stanley
    posted to diffusion qualifier supercooled by kedmond on 2007-08-09 19:45:51 as **
  • CHEMISTRY: Colloidal Molecules and Beyond
    Science, Vol. 301, No. 5632. (25 July 2003), pp. 470-471.
    by Alfons van Blaaderen
    posted to colloidal microscopy monodisperse qualifier rotation self-assembly structure by kedmond on 2007-04-04 09:26:31 as **** along with 1 person dchen
  • notes Spatially heterogeneous dynamics in supercooled liquids.
    Annu Rev Phys Chem, Vol. 51 (2000), pp. 99-128.
    by MD Ediger
    posted to qualifier review structure supercooled by kedmond on 2007-05-22 21:17:49 as read along with 2 people weeks dchen
  • Rotational diffusion in a chain of particles
    Journal of Physics: Condensed Matter, Vol. 17, No. 45. (2005), pp. S3631-S3637.
    by Holger Stark, Michael Reichert, Jérome Bibette
    posted to diffusion qualifier rotation theory by kedmond on 2007-06-30 23:43:54 as ** along with 1 person and 1 group rodney Kopelman_Group
  • Fractional Stokes-Einstein and Debye-Stokes-Einstein Relations in a Network-Forming Liquid
    Physical Review Letters, Vol. 97, No. 5. (2006)
    by Stephen R Becker, Peter H Poole, Francis W Starr
    posted to diffusion qualifier rotation simulation theory by kedmond on 2007-06-30 18:35:55 as read along with 1 person weeks
  • Confocal microscopy of colloids
    Journal of Physics: Condensed Matter, Vol. 19, No. 11. (2007)
    by Semwogerere, Eric R Weeks
    posted to colloidal microscopy qualifier by kedmond on 2007-07-27 11:53:39 as read along with 2 people and 1 group rodney dchen Kopelman_Group
  • notes Preparation of Doublet, Triangular, and Tetrahedral Colloidal Clusters by Controlled Emulsification
    Langmuir, Vol. 22, No. 1. (3 January 2006), pp. 57-62.
    by D Zerrouki, B Rotenberg, S Abramson, J Baudry, C Goubault, F Leal-Calderon, DJ Pine, J Bibette
    posted to colloidal emulsions monodisperse qualifier self-assembly by kedmond on 2007-06-14 04:53:18 as ****
  • notes Length Scale of Dynamic Heterogeneities at the Glass Transition Determined by Multidimensional Nuclear Magnetic Resonance
    Physical Review Letters, Vol. 81, No. 13. (1998), 2727.
    by U Tracht, M Wilhelm, A Heuer, H Feng, K Schmidt-Rohr, HW Spiess
    posted to glass molecular qualifier supercooled by kedmond on 2007-05-18 07:45:34 as read along with 1 person dchen
  • notes The microscopic dynamics of freezing in supercooled colloidal fluids
    The Journal of Chemical Physics, Vol. 100, No. 12. (1994), pp. 9088-9095.
    by David G Grier, Cherry A Murray
    posted to colloidal qualifier structure supercooled by kedmond on 2007-06-09 23:29:04 as ****
  • Change in crystallization mechanism at the glass transition of colloidal spheres
    Nature, Vol. 362, No. 6421. (15 April 1993), pp. 616-618.
    by W van Megen, SM Underwood
    posted to colloidal crystals glass qualifier structure by kedmond on 2007-06-10 00:25:17 as *** along with 1 person and 1 group cgguido WeeksLab
  • notes Glass transition in colloidal hard spheres: Measurement and mode-coupling-theory analysis of the coherent intermediate scattering function
    Physical Review E, Vol. 49, No. 5. (May 1994), 4206.
    by W van Megen, SM Underwood
    posted to colloidal glass qualifier by kedmond on 2007-05-18 08:16:42 as **** along with 2 people weeks dchen
  • Shape-Induced Frustration of Hexagonal Order in Polyhedral Colloids
    Physical Review Letters, Vol. 96, No. 2. (2006)
    by Roel PA Dullens, Maurice CD Mourad, Dirk GAL Aarts, Jacob P Hoogenboom, Willem K Kegel
    posted to colloidal glass qualifier structure by kedmond on 2007-06-25 03:30:51 as ***
  • Translation-rotation paradox for diffusion in fragile glass-forming liquids
    Physical Review E, Vol. 50, No. 3. (1994), 2064.
    by Frank H Stillinger, Jennifer A Hodgdon
    posted to diffusion glass qualifier rotation theory by kedmond on 2007-04-01 04:02:56 as read along with 1 person weeks
  • Nature of the divergence in low shear viscosity of colloidal hard-sphere dispersions
    Physical Review E, Vol. 65, No. 4. (April 2002), 041405.
    by Zhengdong Cheng, Jixiang Zhu, Paul M Chaikin, See-Eng Phan, William B Russel
    posted to colloidal diffusion qualifier structure supercooled by kedmond on 2007-07-11 21:45:05 as **** along with 3 people ghunter weeks dchen
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