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biehls library [61 articles]

Senaste artiklarna i biehls bibliotek.
  • Constraints imposed by non-functional protein-protein interactions on gene expression and proteome size
    Mol Syst Biol, Vol. 4 (2008)
    by Jingshan Zhang, Sergei Maslov, Eugene I Shakhnovich
    posted to no-tag by biehl on 2008-08-26 15:03:56 as ** along with 2 people zwang Ema
  • Wiley InterScience :: Article :: HTML Full Text
    posted to toread_whenprinted by biehl on 2008-08-19 12:26:55 as **
  • Revisiting the Saccharomyces cerevisiae predicted ORFeome
    Genome Res. (23 May 2008), gr.076661.108.
    by Qian-Ru Li, Anne-Ruxandra Carvunis, Haiyuan Yu, Jing-Dong J Han, Quan Zhong, Nicolas Simonis, Stanley Tam, Tong Hao, Niels J Klitgord, Denis Dupuy, Danny Mou, Ilan Wapinski, Aviv Regev, David E Hill, Michael E Cusick, Marc Vidal
    posted to yeast by biehl on 2008-07-11 13:20:52 as ** along with 4 people and 1 group jyuh nklee stajich dbensasson Berkeley Mycology
  • Comparative proteogenomics: Combining mass spectrometry and comparative genomics to analyze multiple genomes
    Genome Res., Vol. 18, No. 7. (1 July 2008), pp. 1133-1142.
    by Nitin Gupta, Jamal Benhamida, Vipul Bhargava, Daniel Goodman, Elisabeth Kain, Ian Kerman, Ngan Nguyen, Noah Ollikainen, Jesse Rodriguez, Jian Wang, Mary S Lipton, Margaret Romine, Vineet Bafna, Richard D Smith, Pavel A Pevzner
    posted to proteomics by biehl on 2008-07-07 10:52:29 as **** along with 2 people and 1 group Neeperando stajich Berkeley Mycology
  • A generative, probabilistic model of local protein structure
    Proceedings of the National Academy of Sciences, Vol. 105, No. 26. (1 July 2008), pp. 8932-8937.
    by Wouter Boomsma, Kanti V Mardia, Charles C Taylor, Jesper Ferkinghoff-Borg, Anders Krogh, Thomas Hamelryck
    posted to structure by biehl on 2008-07-02 09:23:54 as ***** along with 3 people mijam apaydin zwang
  • Large-scale modulation of thermodynamic protein folding barriers linked to electrostatics
    Proceedings of the National Academy of Sciences, Vol. 105, No. 25. (24 June 2008), pp. 8625-8630.
    by Oyvind Halskau, Raul Perez-Jimenez, Beatriz Ibarra-Molero, Jarl Underhaug, Victor Munoz, Aurora Martinez, Jose M Sanchez-Ruiz
    posted to folding by biehl on 2008-06-26 11:19:20 as **
  • Optimization in computational systems biology
    BMC Systems Biology, Vol. 2, No. 1. (2008)
    by Julio Banga
    posted to toread_whenprinted by biehl on 2008-06-11 09:44:12 as ** along with 5 people balicea phoenixzxl reyez jrbanga tmmurali
  • Dead-Time Free Measurement of Dipole-Dipole Interactions between Electron Spins
    Journal of Magnetic Resonance, Vol. 142, No. 2. (February 2000), pp. 331-340.
    by M Pannier, S Veit, A Godt, G Jeschke, HW Spiess
    posted to nmr by biehl on 2008-05-28 10:25:34 as ** along with 2 people viktor21614 EvaKaltenborn
  • Development of a Physics-Based Force Field for the Scoring and Refinement of Protein Models
    Biophys. J. (4 January 2008), biophysj.107.121947.
    by Liliana Wroblewska, Anna Jagielska, Jeffrey Skolnick
    posted to forcefield by biehl on 2008-05-23 14:25:06 as ** along with 1 person paulschlesinger
  • Ten-microsecond MD simulation of a fast-folding WW domain
    Biophys. J. (13 March 2008), biophysj.108.131565.
    by Peter L Freddolino, Feng Liu, Martin H Gruebele, Klaus Schulten
    posted to dynamics by biehl on 2008-05-23 13:41:40 as ** along with 3 people and 1 group samjlord skoch3 paulschlesinger Koch_Lab
  • A new protein linear motif benchmark for multiple sequence alignment software
    BMC Bioinformatics, Vol. 9 (25 April 2008), 213.
    by Emmanuel Perrodou, Claudia Chica, Olivier Poch, Toby J Gibson, Julie D Thompson
    posted to testset by biehl on 2008-05-07 10:21:53 as ** along with 2 people chad_davis niallhaslam
  • A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences
    BMC Bioinformatics, Vol. 9 (06 May 2008), 229.
    by Claudia Chica, Alberto Labarga, Cathryn M Gould, Rodrigo Lopez, Toby J Gibson
    posted to conservation by biehl on 2008-05-07 10:12:09 as read along with 2 people alanrw cabbagesofdoom
  • Bayesian estimates of free energies from nonequilibrium work data in the presence of instrument noise
    (1 Jul 2007)
    by Paul Maragakis, Felix Ritort, Carlos Bustamante, Martin Karplus, Gavin E Crooks
    posted to toread_whenprinted by biehl on 2008-04-30 15:37:48 as **
  • Calculation of protein-ligand binding free energy by using a polarizable potential
    Proceedings of the National Academy of Sciences, Vol. 105, No. 17. (29 April 2008), pp. 6290-6295.
    by Dian Jiao, Pavel A Golubkov, Thomas A Darden, Pengyu Ren
    posted to toread by biehl on 2008-04-29 18:41:31 as ** along with 3 people and 3 groups barry sobolevnrm jmccammon McCammon structural_bioinformatics baker-group
  • Cell water dynamics on multiple time scales
    Proceedings of the National Academy of Sciences, Vol. 105, No. 17. (29 April 2008), pp. 6266-6271.
    by Erik Persson, Bertil Halle
    posted to toread dynamics by biehl on 2008-04-29 18:40:51 as ** along with 1 person and 1 group sobolevnrm baker-group
  • PSAIA - Protein Structure and Interaction Analyzer
    BMC Structural Biology, Vol. 8 (09 April 2008), 21.
    by Josip Mihel, Mile Sikic, Sanja Tomic, Branko Jeren, Kristian Vlahovicek
    posted to for_anne by biehl on 2008-04-28 10:55:18 as **
  • MS-DOCK: Accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Nicolas Sauton, David Lagorce, Bruno Villoutreix, Maria Miteva
    posted to docking by biehl on 2008-04-28 10:52:35 as ** along with 1 person neils
  • Protein complexes and functional modules in molecular networks.
    Proc Natl Acad Sci U S A, Vol. 100, No. 21. (14 October 2003), pp. 12123-12128.
    by V Spirin, LA Mirny
    posted to toread by biehl on 2008-04-23 23:35:28 as **** along with 11 people and 4 groups ellakat carlk grahamc camster kentsis ujh tmmurali dragonrez karfunkel joseph_x_zhou Evangelia dbk-lab biophysics HIV_DR bioNetwork_sysBio
  • Evolvability and hierarchy in rewired bacterial gene networks
    Nature, Vol. 452, No. 7189. (17 April 2008), pp. 840-845.
    by Mark Isalan, Caroline Lemerle, Konstantinos Michalodimitrakis, Carsten Horn, Pedro Beltrao, Emanuele Raineri, Mireia Garriga-Canut, Luis Serrano
    posted to toread by biehl on 2008-04-22 22:48:10 as **** along with 18 people and 4 groups zwang michaelbarton aheilbut chad_davis austin AbnerCYH hryk margaritis cactus dbikard Garamonfok caseybrown aalibes tmmurali dullhunk neils cmzmasek josedavid BergmanLab SynBioSys Centre de Recherches Interdisciplinaires GEB
  • Intrinsic noise, dissipation cost, and robustness of cellular networks: The underlying energy landscape of MAPK signal transduction
    Proceedings of the National Academy of Sciences (17 April 2008), 0708708105.
    by Saul Lapidus, Bo Han, Jin Wang
    posted to toread by biehl on 2008-04-22 22:46:52 as ** along with 4 people cactus ddcttrl margaritis jjray
  • Intrinsic Disorder and Functional Proteomics
    Biophys. J., Vol. 92, No. 5. (1 March 2007), pp. 1439-1456.
    by Predrag Radivojac, Lilia M Iakoucheva, Christopher J Oldfield, Zoran Obradovic, Vladimir N Uversky, Keith A Dunker
    posted to disorder by biehl on 2008-04-17 12:24:17 as ** along with 2 people allmensch cjeans
  • Protein-protein interaction networks and biology—what's the connection?
    Nature Biotechnology, Vol. 26, No. 1., pp. 69-72.
    by Luke Hakes, John W Pinney, David L Robertson, Simon C Lovell
    posted to toread by biehl on 2008-04-17 11:51:42 as ** along with 15 people and 1 group zdai paolomarcatili Yanno jyuh tmmurali jfr balicea dullhunk neils mikaelhuss cjeans nedwards shikin mclarenv Yumyai GeneGo
  • The backbone structure of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein is essentially identical to its mesophilic E. coli homolog
    BMC Structural Biology, Vol. 8 (28 March 2008), 20.
    by Matthew J Cuneo, Yaji Tian, Malin Allert, Homme W Hellinga
    posted to mutation structure by biehl on 2008-04-09 09:01:39 as **
  • Comparison of protein interaction networks reveals species conservation and divergence.
    BMC Bioinformatics, Vol. 7 (17 October 2006), 457.
    by Zhi Liang, Meng Xu, Maikun Teng, Liwen Niu
    posted to network penelope by biehl on 2008-04-07 16:48:38 as ** along with 3 people cerca carlk balajis
  • From time series to complex networks: The visibility graph
    Proceedings of the National Academy of Sciences, Vol. 105, No. 13. (1 April 2008), pp. 4972-4975.
    by Lucas Lacasa, Bartolo Luque, Fernando Ballesteros, Jordi Luque, Juan C Nuno
    posted to network by biehl on 2008-04-02 11:12:02 as ** along with 2 people vrich AbnerCYH
  • A multi-template combination algorithm for protein comparative modeling
    BMC Structural Biology, Vol. 8 (17 March 2008), 18.
    by Jianlin Cheng
    posted to homology by biehl on 2008-03-26 09:40:25 as **
  • Hybrid optimization method with general switching strategy for parameter estimation
    BMC Systems Biology, Vol. 2, No. 1. (2008)
    by Eva B Canto, Martin Peifer, Julio Banga, Jens Timmer, Christian Fleck
    posted to no-tag by biehl on 2008-03-26 09:36:44 as ** along with 2 people xili03 pmendes
  • From the Cover: Consistent blind protein structure generation from NMR chemical shift data
    Proceedings of the National Academy of Sciences, Vol. 105, No. 12. (25 March 2008), pp. 4685-4690.
    by Yang Shen, Oliver Lange, Frank Delaglio, Paolo Rossi, James M Aramini, Gaohua Liu, Alexander Eletsky, Yibing Wu, Kiran K Singarapu, Alexander Lemak, Alexandr Ignatchenko, Cheryl H Arrowsmith, Thomas Szyperski, Gaetano T Montelione, David Baker, Ad Bax
    posted to no-tag by biehl on 2008-03-25 18:28:15 as **** along with 5 people and 1 group dgront apaydin zwang sunhwan skoddet Nielsen group
  • Gambling for global goods
    Proceedings of the National Academy of Sciences, Vol. 105, No. 7. (19 February 2008), pp. 2261-2262.
    by Anna Dreber, Martin A Nowak
    posted to toread by biehl on 2008-02-19 22:31:24 as **
  • The Evolutionary and Developmental Foundations of Mathematics
    PLoS Biology, Vol. 6, No. 2. (1 February 2008), e19.
    by Michael J Beran
    posted to toread by biehl on 2008-02-08 10:01:24 as **** along with 3 people madhadron djkt psique
  • Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain.
    PLoS Comput Biol, Vol. 2, No. 1. (January 2006)
    by T Hou, K Chen, WA McLaughlin, B Lu, W Wang
    posted to dynamics penelope sh3 by biehl on 2008-02-07 15:01:55 as read along with 4 people jteyra neils carlescorbi Evangelia
  • SH3-SPOT: an algorithm to predict preferred ligands to different members of the SH3 gene family
    Journal of Molecular Biology, Vol. 298, No. 2. (28 April 2000), pp. 313-328.
    by Barbara Brannetti, Allegra Via, Gianluca Cestra, Gianni Cesareni, Manuela H Citterich
    posted to penelope sh3 by biehl on 2008-01-31 14:23:27 as *** along with 2 people carlescorbi Evangelia
  • Protein Interaction Networks by Proteome Peptide Scanning
    PLoS Biology, Vol. 2, No. 1. (1 January 2004), e14.
    by Christiane Landgraf, Simona Panni, Luisa Montecchi-Palazzi, Luisa Castagnoli, Jens Schneider-Mergener, Rudolf Volkmer-Engert, Gianni Cesareni
    posted to penelope sh3 by biehl on 2008-01-31 14:19:41 as *** along with 3 people eukfn Evangelia hplatero
  • In Vitro Evolution of Recognition Specificity Mediated by SH3 Domains Reveals Target Recognition Rules
    J. Biol. Chem., Vol. 277, No. 24. (7 June 2002), pp. 21666-21674.
    by Simona Panni, Luciana Dente, Gianni Cesareni
    posted to penelope sh3 by biehl on 2008-01-31 14:19:06 as *** along with 1 person matzke
  • Can we infer peptide recognition specificity mediated by SH3 domains?
    FEBS Letters, Vol. 513, No. 1. (20 February 2002), pp. 38-44.
    by Gianni Cesareni, Simona Panni, Giuliano Nardelli, Luisa Castagnoli
    posted to penelope sh3 by biehl on 2008-01-31 14:16:02 as *** along with 1 person Evangelia
  • A simple principle concerning the robustness of protein complex activity to changes in gene expression
    BMC Systems Biology, Vol. 2, No. 1. (2008)
    by Jennifer Semple, Tanya Vavouri, Ben Lehner
    posted to toread by biehl on 2008-01-30 09:23:23 as *** along with 3 people jyuh jjray Ema
  • Preservation of protein clefts in comparative models
    BMC Structural Biology, Vol. 8 (16 January 2008), 2.
    by David Piedra, Sergi Lois, Xavier
    posted to penelope toread_whenprinted by biehl on 2008-01-30 09:04:38 as ** along with 1 person dimka
  • Multiscale complex network of protein conformational fluctuations in single-molecule time series
    Proceedings of the National Academy of Sciences, Vol. 105, No. 2. (15 January 2008), pp. 536-541.
    by Chun-Biu Li, Haw Yang, Tamiki Komatsuzaki
    posted to dynamics by biehl on 2008-01-16 10:02:03 as *** along with 3 people and 1 group hsekiguc ruvido sobolevnrm baker-group
  • Petri net-based method for the analysis of the dynamics of signal propagation in signaling pathways
    Bioinformatics, Vol. 24, No. 2. (15 January 2008), pp. 209-217.
    by Simon Hardy, Pierre N Robillard
    posted to network by biehl on 2008-01-16 09:18:46 as *** along with 2 people bootsy mailund
  • Matt: Local Flexibility Aids Protein Multiple Structure Alignment
    PLoS Computational Biology, Vol. 4, No. 1. (1 January 2008), e10.
    by Matthew Menke, Bonnie Berger, Lenore Cowen
    posted to fragment penelope rmsd superposition by biehl on 2008-01-14 09:54:06 as ***** along with 1 person chad_davis
  • Can molecular dynamics simulations help in discriminating correct from erroneous protein 3D models?
    BMC Bioinformatics, Vol. 9 (07 January 2008), 6.
    by Jean-Francois Taly, Antoine Marin, Jean-Francois Gibrat
    posted to dynamics by biehl on 2008-01-09 09:22:42 as **** along with 1 person LamBras
  • The Modular Organization of Domain Structures: Insights into Protein–Protein Binding
    PLoS Computational Biology, Vol. 3, No. 12. (1 December 2007), e239.
    by Del, Pablo Carbonell
    posted to no-tag by biehl on 2008-01-02 15:24:08 as read along with 9 people carlk bicko chad_davis choonpeng grahamc cjeans zwang niallhaslam marti
  • Getting Started in Probabilistic Graphical Models
    PLoS Computational Biology, Vol. 3, No. 12. (1 December 2007), e252.
    by Edoardo M Airoldi
    posted to no-tag by biehl on 2008-01-02 13:49:47 as read along with 12 people and 1 group jfr jyuh balicea AbnerCYH stajich cjeans GustavoLacerda GeeSharpMinor sobolevnrm cabbagezs nklee softsimu baker-group
  • Background frequencies for residue variability estimates: BLOSUM revisited
    BMC Bioinformatics, Vol. 8 (27 December 2007), 488.
    by I Mihalek, I Res, O Lichtarge
    posted to toread by biehl on 2008-01-02 13:47:35 as ** along with 5 people and 1 group bicko chad_davis gokhan rabio laughcry structural_bioinformatics
  • Illuminating the mechanistic roles of enzyme conformational dynamics
    Proceedings of the National Academy of Sciences, Vol. 104, No. 46. (13 November 2007), pp. 18055-18060.
    by Jeffrey A Hanson, Karl Duderstadt, Lucas P Watkins, Sucharita Bhattacharyya, Jason Brokaw, Jhih-Wei Chu, Haw Yang
    posted to toread by biehl on 2007-12-12 17:32:13 as ** along with 1 person and 1 group sobolevnrm baker-group
  • A modular network model of aging
    Mol Syst Biol, Vol. 3 (4 December 2007)
    by Huiling Xue, Bo Xian, Dong Dong, Kai Xia, Shanshan Zhu, Zhongnan Zhang, Lei Hou, Qingpeng Zhang, Yi Zhang, Jing-Dong J Han
    posted to toread by biehl on 2007-12-12 17:32:03 as ** along with 8 people tmmurali muraken grahamc cjeans zwang mingzhi renatomilani dap5087
  • Introduction to Lambda Calculus
    (1988)
    by HP Barendregt
    posted to programming by biehl on 2007-12-05 22:48:10 as *** along with 11 people and 2 groups MikolkaMikolka enochguimond SamB JeffreyPalmer yallop pintman glaubersp robertoalamino namin mvermaat d23 logics of knowledge Lambda the Ultimate
  • A consensus view of protein dynamics.
    Proc Natl Acad Sci U S A (10 January 2007)
    by Manuel Rueda, Carles Ferrer-Costa, Tim Meyer, Alberto Pérez, Jordi Camps, Adam Hospital, Josep Lluis L Gelpí, Modesto Orozco
    posted to dynamics by biehl on 2007-12-05 14:53:04 as ** along with 12 people and 2 groups LamBras lna dimka aqeel aswin rabio grahamc hmk zwang Ema phoenixzxl ras ParkinsonLab_at_MaRS The BMM Dome
  • RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs.
    BMC Bioinformatics, Vol. 3 (16 May 2002)
    by CM Zmasek, SR Eddy
    posted to homology penelope by biehl on 2007-11-16 13:56:31 as *** along with 2 people and 1 group indigoviolet cjeans EisenLab
  • Atomic-level characterization of disordered protein ensembles
    Current Opinion in Structural Biology, Vol. 17, No. 1. (February 2007), pp. 3-14.
    by Tanja Mittag, Julie D Forman-Kay
    posted to unfolded by biehl on 2007-11-13 16:56:51 as *** along with 4 people and 1 group allmensch apaydin xdeupi cactus LabCompMed
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