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tale's library [57 articles]

Recent papers added to tale's library.
  • Distribution and intensity of constraint in mammalian genomic sequence.
    Genome Res, Vol. 15, No. 7. (July 2005), pp. 901-913.
    by GM Cooper, EA Stone, G Asimenos, ED Green, S Batzoglou, A Sidow
    posted to no-tag by tale on 2007-10-31 21:58:55 as ** along with 5 people operon aprasad nirfriedman JeffR100 Garamonfok
  • Inference of functional regions in proteins by quantification of evolutionary constraints.
    Proc Natl Acad Sci U S A, Vol. 99, No. 5. (5 March 2002), pp. 2912-2917.
    by AL Simon, EA Stone, A Sidow
    posted to no-tag by tale on 2007-10-31 21:47:44 as ** along with 1 person nirfriedman
  • A fast algorithm for joint reconstruction of ancestral amino acid sequences.
    Mol Biol Evol, Vol. 17, No. 6. (June 2000), pp. 890-896.
    by T Pupko, I Pe'er, R Shamir, D Graur
    posted to no-tag by tale on 2007-10-31 21:30:02 as **
  • Evolutionary tree reconstruction using structural expectation maximization and homotopy
    Genet. Mol. Res., Vol. 6, No. 3. (September 2007), pp. 522-533.
    by J Li, M Guo
    posted to no-tag by tale on 2007-10-31 20:37:35 as **
  • A structural EM algorithm for phylogenetic inference.
    J Comput Biol, Vol. 9, No. 2. (2002), pp. 331-353.
    by N Friedman, M Ninio, I Pe'er, T Pupko
    posted to no-tag by tale on 2007-10-31 20:25:06 as ** along with 2 people wenhan Garamonfok
  • Site-to-Site Variation of Synonymous Substitution Rates
    Molecular Biology and Evolution, Vol. 22, No. 12. (December 2005), pp. 2375-2385.
    by Sergei K Pond, Spencer V Muse
    posted to no-tag by tale on 2007-10-31 18:26:33 as ** along with 2 people and 1 group stevanspringer operon FAB-lab
  • The power of phylogenetic comparison in revealing protein function.
    Proc Natl Acad Sci U S A (22 February 2005)
    by Ziheng Yang
    posted to no-tag by tale on 2007-10-31 18:25:16 as ** along with 5 people and 1 group bpcusack mdimmic stevanspringer bpb BioNica FAB-lab
  • Codon-Substitution Models for Heterogeneous Selection Pressure at Amino Acid Sites
    Genetics, Vol. 155, No. 1. (1 May 2000), pp. 431-449.
    by Ziheng Yang, Rasmus Nielsen, Nick Goldman, Anne-Mette K Pedersen
    posted to no-tag by tale on 2007-10-31 18:23:25 as ** along with 7 people fernan BioNica Natasha dylan77 Garamonfok gjuggler emptyhb
  • Towards realistic codon models: among site variability and dependency of synonymous and non-synonymous rates
    Bioinformatics, Vol. 23, No. 13. (1 July 2007), pp. i319-327.
    by Itay Mayrose, Adi Doron-Faigenboim, Eran Bacharach, Tal Pupko
    posted to no-tag by tale on 2007-10-31 18:18:28 as ** along with 1 person operon
  • Bayesian network analysis of resistance pathways against HIV-1 protease inhibitors
    Infection, Genetics and Evolution, Vol. 7, No. 3. (June 2007), pp. 382-390.
    by K Deforche, R Camacho, Z Grossman, T Silander, MA Soares, Y Moreau, RW Shafer, K Van Laethem, AP Carvalho, B Wynhoven, P Cane, J Snoeck, J Clarke, S Sirivichayakul, K Ariyoshi, A Holguin, H Rudich, R Rodrigues, MB Bouzas, P Cahn, LF Brigido, V Soriano, W Sugiura, P Phanuphak, L Morris, J Weber, D Pillay, A Tanuri, PR Harrigan, JM Shapiro, DA Katzenstein, R Kantor, AM Vandamme
    posted to no-tag by tale on 2007-10-31 15:00:21 as **
  • Bayesian network analysis of resistance pathways against protease inhibitors.
    posted to no-tag by tale on 2007-10-31 14:58:52 as **
  • Graphical Models
    posted to no-tag by tale on 2007-10-31 14:46:41 as **
  • Correlated mutations contain information about protein-protein interaction.
    J Mol Biol, Vol. 271, No. 4. (29 August 1997), pp. 511-523.
    by F Pazos, M Helmer-Citterich, G Ausiello, A Valencia
    posted to no-tag by tale on 2007-10-31 14:01:23 as ** along with 2 people gurkanbebek cjeans
  • RNA secondary structure and compensatory evolution
    posted to no-tag by tale on 2007-10-31 11:21:41 as **
  • On evolutionary conservation of thermodynamic coupling in proteins.
    J Biol Chem, Vol. 279, No. 18. (30 April 2004), pp. 19046-19050.
    by AA Fodor, RW Aldrich
    posted to no-tag by tale on 2007-10-31 11:13:30 as ** along with 6 people and 2 groups ca3295 friendpine ana barry gbart cjeans structural_bioinformatics Bioinformatics
  • Determination of network of residues that regulate allostery in protein families using sequence analysis.
    Protein Sci, Vol. 15, No. 2. (February 2006), pp. 258-268.
    by RI Dima, D Thirumalai
    posted to no-tag by tale on 2007-10-31 11:10:54 as ** along with 5 people and 1 group xdeupi gbart nirfriedman choonpeng mingzhi LabCompMed
  • A new algorithm for detecting low-complexity regions in protein sequences
    Bioinformatics, Vol. 21, No. 2. (January 2005), pp. 160-170.
    by Sung W Shin, Sam M Kim
    posted to no-tag by tale on 2007-10-31 11:08:03 as ** along with 6 people nearora sdvillal rdiaz florianleitner Bc91 Evangelia
  • Correlated mutations: Advances and limitations. A study on fusion proteins and on the Cohesin-Dockerin families.
    Proteins (28 February 2006)
    by Inbal Halperin, Haim Wolfson, Ruth Nussinov
    posted to coevolution by tale on 2007-10-31 10:31:03 as ** along with 6 people bicko gbart ramensky cjeans mingzhi friendpine
  • Detecting the Coevolution of Biosequences An Example of RNA Interaction Prediction
    Mol Biol Evol, Vol. 24, No. 9. (1 September 2007), pp. 2119-2131.
    by Chen-Hsiang Yeang, Jeremy F Darot, Harry F Noller, David Haussler
    posted to no-tag by tale on 2007-10-30 15:16:10 as ** along with 3 people cjeans dandaman friendpine
  • Dependence among Sites in RNA Evolution
    Mol Biol Evol, Vol. 23, No. 8. (1 August 2006), pp. 1525-1537.
    by Jiaye Yu, Jeffrey L Thorne
    posted to no-tag by tale on 2007-06-13 13:11:11 as **
  • Combining protein evolution and secondary structure.
    Mol Biol Evol, Vol. 13, No. 5. (May 1996), pp. 666-673.
    by JL Thorne, N Goldman, DT Jones
    posted to no-tag by tale on 2007-06-11 17:21:47 as ** along with 1 person chrn
  • A Hidden Markov Model approach to variation among sites in rate of evolution.
    Mol Biol Evol, Vol. 13, No. 1. (January 1996), pp. 93-104.
    by J Felsenstein, GA Churchill
    posted to no-tag by tale on 2007-06-11 17:20:27 as ** along with 3 people balicea gennaro zmasek
  • A Space-Time Process Model for the Evolution of DNA Sequences
    Genetics, Vol. 139, No. 2. (1 February 1995), pp. 993-1005.
    by Z Yang
    posted to no-tag by tale on 2007-06-11 17:19:30 as ** along with 3 people pradiptaray bpb friendpine
  • Interrogating protein interaction networks through structural biology.
    Proc Natl Acad Sci U S A, Vol. 99, No. 9. (30 April 2002), pp. 5896-5901.
    by P Aloy, RB Russell
    posted to no-tag by tale on 2007-06-10 13:36:47 as ** along with 10 people and 3 groups ana barry baaden bicko lfriedl chad_davis henschel ruvido cjeans Evangelia structural_bioinformatics kdl Bioinformatics
  • Computational redesign of protein-protein interaction specificity.
    Nat Struct Mol Biol, Vol. 11, No. 4. (April 2004), pp. 371-379.
    by T Kortemme, LA Joachimiak, AN Bullock, AD Schuler, BL Stoddard, D Baker
    posted to no-tag by tale on 2007-06-10 13:27:41 as ** along with 6 people jteyra lna jwm bicko ruvido cjeans
  • Networks of Coevolving Sites in Structural and Functional Domains of Serpin Proteins
    Molecular Biology and Evolution, Vol. 22, No. 7. (15 July 2005), pp. 1627-1634.
    by Michael J Buck, William R Atchley
    posted to no-tag by tale on 2007-05-13 11:39:55 as ** along with 2 people friendpine cjeans
  • Continuous Representations of Time Series Gene Expression
    by Data
    posted to no-tag by tale on 2007-05-13 08:22:38 as ** along with 1 person dimatura
  • SPATIAL AND TEMPORAL CONTROL OF DIFFERENTIATION AND CELL CYCLE PROGRESSION IN CAULOBACTER CRESCENTUS - Annual Review of Microbiology, 57(1):225 - Full Text
    posted to no-tag by tale on 2007-05-11 15:23:31 as ***
  • Exploring a Phylogenetic Approach for the Detection of Correlated Substitutions in Proteins
    Mol Biol Evol, Vol. 17, No. 11. (1 November 2000), pp. 1753-1759.
    by Pierre Tuff, Pierre Darlu
    posted to no-tag by tale on 2007-05-11 13:05:23 as ** along with 1 person cjeans
  • Functional Coevolutionary Networks of the Hsp70HopHsp90 System Revealed through Computational Analyses
    Molecular Biology and Evolution, Vol. 24, No. 4. (April 2007), pp. 1032-1044.
    by Travers, AA Simon, Fares, A Mario
    posted to no-tag by tale on 2007-05-11 13:03:30 as **** along with 2 people nirfriedman mingzhi
  • Computational and Statistical Methods to Explore the Various Dimensions of Protein Evolution
    Current Bioinformatics, Vol. 1, No. 2. (May 2006), pp. 207-217.
    by Fares, A Mario
    posted to no-tag by tale on 2007-05-11 12:57:44 as ***
  • Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous
    Nature, Vol. 431, No. 7011. (21 October 2004), pp. 980-984.
    by Bryan Kolaczkowski, Joseph W Thornton
    posted to no-tag by tale on 2007-05-10 19:55:47 as ** along with 1 person aprasad
  • Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
    Nature, Vol. 447, No. 7141., pp. 167-177.
    by Tarjei S Mikkelsen, Matthew J Wakefield, Bronwen Aken, Chris T Amemiya, Jean L Chang, Shannon Duke, Manuel Garber, Andrew J Gentles, Leo Goodstadt, Andreas Heger, Jerzy Jurka, Michael Kamal, Evan Mauceli, Stephen MJ Searle, Ted Sharpe, Michelle L Baker, Mark A Batzer, Panayiotis V Benos, Katherine Belov, Michele Clamp, April Cook, James Cuff, Radhika Das, Lance Davidow, Janine E Deakin, Melissa J Fazzari, Jacob L Glass, Manfred Grabherr, John M Greally, Wanjun Gu, Timothy A Hore, Gavin A Huttley, Michael Kleber, Randy L Jirtle, Edda Koina, Jeannie T Lee, Shaun Mahony, Marco A Marra, Robert D Miller, Robert D Nicholls, Mayumi Oda, Anthony T Papenfuss, Zuly E Parra, David D Pollock, David A Ray, Jacqueline E Schein, Terence P Speed, Katherine Thompson, John L Vandeberg, Claire M Wade, Jerilyn A Walker, Paul D Waters, Caleb Webber, Jennifer R Weidman, Xiaohui Xie, Michael C Zody, Jennifer, Chris P Ponting, Matthew Breen, Paul B Samollow, Eric S Lander, Kerstin Lindblad-Toh
    posted to no-tag by tale on 2007-05-10 19:19:00 as *** along with 1 person and 2 groups dchughes G4ID Genetics-of-Gambling
  • In silico sequence evolution with site-specific interactions along phylogenetic trees
    Bioinformatics, Vol. 22, No. 6. (15 March 2006), pp. 716-722.
    by Tanja Gesell, Arndt von Haeseler
    posted to no-tag by tale on 2007-05-10 19:16:11 as ** along with 2 people and 2 groups chad_davis marcius BioinfoCIPF SGU-CIPF
  • Phylogenetic estimation of context-dependent substitution rates by maximum likelihood.
    Mol Biol Evol, Vol. 21, No. 3. (March 2004), pp. 468-488.
    by A Siepel, D Haussler
    posted to no-tag by tale on 2007-05-10 15:53:41 as ** along with 4 people mdimmic penka djkt uwe
  • Assessing Site-Interdependent Phylogenetic Models of Sequence Evolution
    Mol Biol Evol, Vol. 23, No. 9. (1 September 2006), pp. 1762-1775.
    by Nicolas Rodrigue, Herve Philippe, Nicolas Lartillot
    posted to coevolution by tale on 2007-05-10 15:48:21 as ** along with 2 people penka redelings
  • A Dependent-Rates Model and an MCMC-Based Methodology for the Maximum-Likelihood Analysis of Sequences with Overlapping Reading Frames
    Mol Biol Evol, Vol. 18, No. 5. (1 May 2001), pp. 763-776.
    by Anne-Mette K Pedersen, Jens L Jensen
    posted to coevolution by tale on 2007-05-10 15:33:30 as ***
  • Identification and Classification of Conserved RNA Secondary Structures in the Human Genome.
    PLoS Comput Biol, Vol. 2, No. 4. (21 April 2006)
    by Jakob Skou S Pedersen, Gill Bejerano, Adam Siepel, Kate Rosenbloom, Kerstin Lindblad-Toh, Eric S S Lander, Jim Kent, Webb Miller, David Haussler
    posted to no-tag by tale on 2007-05-10 15:12:17 as ** along with 11 people and 2 groups hpaces marcius eckart_bindewald tardigrade arcticrasta tabu mtagaya Eonwe ilh djkt raylim BioinfoCIPF SGU-CIPF
  • Analysis of covariation in an SH3 domain sequence alignment: applications in tertiary contact prediction and the design of compensating hydrophobic core substitutions.
    J Mol Biol, Vol. 303, No. 3. (27 October 2000), pp. 433-446.
    by SM Larson, AA Di Nardo, AR Davidson
    posted to no-tag by tale on 2007-05-10 12:39:09 as ** along with 6 people and 2 groups ana gbart analogAI Haggan cjeans bethbromley structural_bioinformatics Bioinformatics
  • An Evolutionary Space-Time Model with Varying Among-Site Dependencies
    Molecular Biology and Evolution, Vol. 23, No. 2. (20 February 2006), pp. 392-400.
    by Adi Stern, Tal Pupko
    posted to no-tag by tale on 2007-05-10 12:23:27 as **
  • Protein Evolution with Dependence Among Codons Due to Tertiary Structure
    Mol Biol Evol, Vol. 20, No. 10. (1 October 2003), pp. 1692-1704.
    by Douglas M Robinson, David T Jones, Hirohisa Kishino, Nick Goldman, Jeffrey L Thorne
    posted to no-tag by tale on 2007-05-10 12:19:00 as ** along with 2 people penka redelings
  • Evolutionary rate in the protein interaction network.
    Science, Vol. 296, No. 5568. (26 April 2002), pp. 750-752.
    by HB Fraser, AE Hirsh, LM Steinmetz, C Scharfe, MW Feldman
    posted to evolution by tale on 2007-05-10 11:54:19 as ** along with 4 people friendpine dragonrez bjorns timflutre
  • In silico two-hybrid system for the selection of physically interacting protein pairs
    Proteins: Structure, Function, and Genetics, Vol. 47, No. 2. (2002), pp. 219-227.
    by Florencio Pazos, Alfonso Valencia
    posted to coevolution by tale on 2007-05-10 11:31:33 as **
  • Evolution of Two-Component Signal Transduction
    Mol Biol Evol, Vol. 17, No. 12. (1 December 2000), pp. 1956-1970.
    by Kristin K Koretke, Andrei N Lupas, Patrick V Warren, Martin Rosenberg, James R Brown
    posted to no-tag by tale on 2007-05-09 14:44:10 as **** along with 1 person cjeans
  • A Novel Method for Detecting Intramolecular Coevolution: Adding a Further Dimension to Selective Constraints Analyses
    Genetics, Vol. 173, No. 1. (1 May 2006), pp. 9-23.
    by Mario A Fares, Simon A Travers
    posted to no-tag by tale on 2007-05-09 14:43:13 as ** along with 5 people and 3 groups stevanspringer operon caporaso breden cjeans FAB-lab biomedical-nlp SFUAntibodyResearch
  • Phylogenetic Methodology for Detecting Protein Interactions
    Mol Biol Evol, Vol. 24, No. 3. (1 March 2007), pp. 650-659.
    by Peter J Waddell, Hirohisa Kishino, Rissa Ota
    posted to no-tag by tale on 2007-05-09 14:39:22 as ** along with 2 people and 1 group stevanspringer zwang FAB-lab
  • Coevolving protein residues: maximum likelihood identification and relationship to structure
    Journal of Molecular Biology, Vol. 287, No. 1. (19 March 1999), pp. 187-198.
    by David D Pollock, William R Taylor, Nick Goldman
    posted to no-tag by tale on 2007-05-09 14:33:23 as ****
  • Similarity of phylogenetic trees as indicator of protein-protein interaction.
    Protein Eng, Vol. 14, No. 9. (September 2001), pp. 609-614.
    by F Pazos, A Valencia
    posted to no-tag by tale on 2007-05-08 13:29:35 as ** along with 4 people ca3295 balajis IbnBio selrac
  • Simultaneous amino acid substitutions at antigenic sites drive influenza A hemagglutinin evolution
    PNAS, Vol. 104, No. 15. (10 April 2007), pp. 6283-6288.
    by Arthur C Shih, Tzu-Chang Hsiao, Mei-Shang Ho, Wen-Hsiung Li
    posted to no-tag by tale on 2007-05-08 11:17:38 as ** along with 2 people lshaw saru
  • Detecting the Dependent Evolution of Biosequences
    by Darot
    posted to no-tag by tale on 2007-05-08 11:13:33 as **** along with 701 people and 131 groups fernand0 dperkel egh jyuh samth sora florine ladygoat hopm hellige parmentierf ssn mortimer tinkha V plaugg ansobol mjaz berthelemy eldan pdlug zephoria carloscabanillas Janos bkliethermes nazareno elsantosneto januadiaboli yaroslavvb jurijmlotman geomblog srl bigga treycausey CSG mcphee chandrashekar denns matzke sherrivokey sona cassj lijil hlovise coolger incites bigmagpie alicetiara yorgos johannsen cavlec smbrower viller jenmy mlzafron tymmail sedging davidr macowell eimaj42jdp Flit BenWillems agallet hawesie sngourlay jolilius rmagf acer ville garyfeng danifazzio willwade gantlord melanieramage mgregg cwb neteler carneym crispinb rdlong lillekatt davemack agarza carsonr imcdnzl tjimenez Tolik lna dmikurube szityu michmill P2324548 jpbenda Vaccine tadm mkwalker anar grzegorz japple planetoid okarsligil stormybriggs UWerplab nbr inbetweener pafmon stina pgastrein xiruela kutabar jfr xamde kliether mleis jshahin cmunson lfriedl sharonhoward ccots terraces czlamer brent_lance subhradeep jjray Jellyfish cmmorel bayesian benavides ghsalazar manuelpq sekulerlab jmaryott kristina chad_davis Ayest thens austin RMGraze e2holmes JAShapiro contradictoryben lrodero jamesfournie nybon hawkestein diegolino_veneziano rvosa Schmidtc lyongu ricmilne KarinaFigueroa jfmenudet cdmilligan great_apes brthz juliajumeau gloinf billwolff mrkrause halsnalle pintman yish mkcerusky cyph3r idm smithco ruudvanleeuwen BarrosH aelva harshpshah earnoux princessbritty Laki kupopo ryang eustatic daqing balicea stain matts ram frankgrimes Pfaff9 locatellimp seawidget ianli kate_waxlyrical rherring ThomasEtEckert cliona shaun gregnishihara harmonjt Happybene jklugman mwyarbro rburnett prabakaran nperrin tystl gugek NicolasNeubauer gytisc Nele pedagogicapprentice dlouzeck phillipkent emerson rafamayo arichar6 pasion sadsackmac gbae redcourgette sunilbajpai JJNonesuch heintz BuckeyePhysicist 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