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phoenixzxls library [162 articles]

Senaste artiklarna i phoenixzxls bibliotek ordnat efter prioritet.
  • A Maximum Likelihood Method for Detecting Directional Evolution in Protein Sequences and its Application to Influenza A Virus.
    Molecular biology and evolution (29 May 2008)
    by Sergei L L Kosakovsky Pond, Art F Y F Poon, Andrew J J Leigh Brown, Simon D W D Frost
    posted to evolution influenza mle peruse by phoenixzxl on 2008-08-15 07:45:37 as ***** along with 2 people and 1 group stajich zwang Berkeley Mycology
  • Whole-cell simulation: a grand challenge of the 21st century.
    Trends Biotechnol, Vol. 19, No. 6. (June 2001), pp. 205-210.
    by M Tomita
    posted to simulation by phoenixzxl on 2008-06-16 08:42:07 as ***** along with 4 people wnpx Doug josepe fishtank
  • PLoS Computational Biology: A Primer on Learning in Bayesian Networks for Computational Biology
    posted to tutorial bayesian by phoenixzxl on 2008-03-14 07:11:39 as *****
  • BNFinder: Exact and efficient method for learning Bayesian networks
    Bioinformatics (30 September 2008), btn505.
    by Bartek Wilczynski, Norbert Dojer
    posted to soft bayesian by phoenixzxl on 2008-10-06 03:18:27 as **** along with 3 people grahamc rdiaz renatomilani
  • Predicting PDZ domain–peptide interactions from primary sequences
    Nature Biotechnology, Vol. 26, No. 9. (17 August 2008), pp. 1041-1045.
    by Jiunn R Chen, Bryan H Chang, John E Allen, Michael A Stiffler, Gavin Macbeath
    posted to prediction_ddi by phoenixzxl on 2008-09-27 04:53:16 as **** along with 3 people jyuh cabbagesofdoom zwang
  • Evolution of Complex Modular Biological Networks.
    PLoS Comput Biol, Vol. 4, No. 2. (8 February 2008)
    by Arend Hintze, Christoph Adami
    posted to network_evolution robustness by phoenixzxl on 2008-08-29 14:06:09 as **** along with 4 people grahamc laughcry rcaze alhufton
  • Robustness Can Evolve Gradually in Complex Regulatory Gene Networks with Varying Topology
    PLoS Computational Biology, Vol. 3, No. 2. (1 February 2007), e15.
    by Stefano Ciliberti, Olivier C Martin, Andreas Wagner
    posted to network_evolution robustness by phoenixzxl on 2008-08-29 14:05:37 as **** along with 15 people and 5 groups eldan ccots indigoviolet emilyhare malcook entropy nickluscombe aswin kengg dolhuis timflutre grahamc shigepong kynn carneiro EisenLab EBI-regulation SNE ParkinsonLab_at_MaRS Plantandetc
  • A Protein Domain-Based Interactome Network for C. elegans Early Embryogenesis
    Cell, Vol. 134, No. 3. (8 August 2008), pp. 534-545.
    by Mike Boxem, Zoltan Maliga, Niels Klitgord, Na Li, Irma Lemmens, Miyeko Mana, Lorenzo de Lichtervelde, Joram D Mul, Diederik van de Peut, Maxime Devos, Nicolas Simonis, Muhammed A Yildirim, Murat Cokol, Huey-Ling Kao, Anne-Sophie de Smet, Haidong Wang, Anne-Lore Schlaitz, Tong Hao, Stuart Milstein, Changyu Fan, Mike Tipsword, Kevin Drew, Matilde Galli, Kahn Rhrissorrakrai, David Drechsel, Daphne Koller, Frederick P Roth, Lilia M Iakoucheva, Keith A Dunker, Richard Bonneau, Kristin C Gunsalus, David E Hill, Fabio Piano, Jan Tavernier, Sander van den Heuvel, Anthony A Hyman, Marc Vidal
    posted to data domain insight network_ppi by phoenixzxl on 2008-08-11 14:01:58 as **** along with 4 people cerca grahamc chad_davis zwang
  • Studying complex biological systems using multifactorial perturbation.
    Nat Rev Genet, Vol. 4, No. 2. (February 2003), pp. 145-151.
    by RC Jansen
    posted to data_integration review simulation by phoenixzxl on 2008-08-06 08:12:52 as **** along with 5 people snuppepuppan tmmurali jfr samal qfwills
  • Modern computational approaches for analysing molecular genetic variation data
    Nature Reviews Genetics, Vol. 7, No. 10., pp. 759-770.
    by Paul Marjoram, Simon Tavaré
    posted to data_integration review statistical tutorial by phoenixzxl on 2008-08-06 08:11:53 as **** along with 4 people psique jyuh jermth ramakris
  • MISSENSE MEANDERINGS IN SEQUENCE SPACE: A BIOPHYSICAL VIEW OF PROTEIN EVOLUTION
    Nat Rev Genet, Vol. 6, No. 9. (2005), pp. 678-687.
    by Mark A Depristo, Daniel M Weinreich, Daniel L Hartl
    posted to evolution protein by phoenixzxl on 2008-08-05 07:43:57 as **** along with 2 people and 1 group penka mingzhi Nie
  • Optimization of specificity in a cellular protein interaction network by negative selection.
    Nature, Vol. 426, No. 6967. (11 December 2003), pp. 676-680.
    by A Zarrinpar, SH Park, WA Lim
    posted to evolution specificity by phoenixzxl on 2008-07-31 07:59:32 as **** along with 4 people and 2 groups barry grahamc cjeans paolomarcatili structural_bioinformatics Bioinformatics
  • Cooperativity in macromolecular assembly
    Nat Chem Biol, Vol. 4, No. 8. (2008), pp. 458-465.
    by James R Williamson
    posted to assembly cooperativity by phoenixzxl on 2008-07-23 07:55:40 as **** along with 1 person paulschlesinger
  • Stochastic dynamics of macromolecular-assembly networks.
    Mol Syst Biol, Vol. 2 (2006)
    by L Saiz, JM Vilar
    posted to assembly dynamics network_dynamic by phoenixzxl on 2008-07-23 07:51:30 as **** along with 1 person wilsoros
  • Analyzing Protein Interaction Networks Using Structural Information
    Annual Review of Biochemistry, Vol. 77, No. 1. (2008)
    by Christina Kiel, Pedro Beltrao, Luis Serrano
    posted to network_ppi structure_aided by phoenixzxl on 2008-07-16 02:09:43 as **** along with 8 people and 1 group chad_davis Borelli bicko neils Evangelia grahamc paolomarcatili zwang structural_bioinformatics
  • Integrating Diverse Data for Structure Determination of Macromolecular Assemblies.
    Annu Rev Biochem (4 March 2008)
    by Frank Alber, Friedrich Förster, Dmitry Korkin, Maya Topf, Andrej Sali
    posted to complex data_integration review by phoenixzxl on 2008-07-16 02:08:04 as **** along with 1 person chad_davis
  • Assessing the limits of genomic data integration for predicting protein networks.
    Genome Res, Vol. 15, No. 7. (July 2005), pp. 945-953.
    by LJ Lu, Y Xia, A Paccanaro, H Yu, M Gerstein
    posted to data_integration insight network_ppi by phoenixzxl on 2008-06-28 09:13:00 as **** along with 13 people and 2 groups okarsligil lfriedl balajis maryee opheliav wnpx mbeautru eukfn grahamc nedwards brianb iris_2001 carlk kdl Bioinformatics
  • Assembly reflects evolution of protein complexes
    Nature (18 June 2008)
    by Emmanuel D Levy, Elisabetta B Erba, Carol V Robinson, Sarah A Teichmann
    posted to assembly complex evolution by phoenixzxl on 2008-06-27 12:06:08 as **** along with 7 people psique marck paulschlesinger neils jwm zwang faion
  • A theoretical framework for specificity in cell signaling
    Molecular Systems Biology, Vol. 1, No. 1. (18 October 2005), pp. msb4100031-E1-msb4100031-E5.
    by Natalia L Komarova, Xiufen Zou, Qing Nie, Lee Bardwell
    posted to specificity by phoenixzxl on 2008-06-24 07:24:12 as **** along with 1 person and 1 group arne dIEMoSIRIS
  • Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis
    Science, Vol. 320, No. 5883. (20 June 2008), pp. 1632-1635.
    by Ari Loytynoja, Nick Goldman
    posted to evolution sequence_alignment by phoenixzxl on 2008-06-20 04:08:46 as **** along with 22 people and 3 groups marti bpcusack chad_davis hpaces dinnes gjuggler djkt ArtemPankin jago marck imtechnology aprasad zwang bmaust bpb michaelbarton Schmidtc AbnerCYH gulsacan emptyhb jlgreen nuin Khavkin's lab iSEEM Green Lab
  • Modeling and simulation of genetic regulatory systems: a literature review.
    Journal of Computational Biology, Vol. 9, No. 1. (2002), pp. 67-103.
    by Hidde de Jong
    posted to simulation by phoenixzxl on 2008-06-16 08:40:38 as **** along with 14 people and 3 groups eldan tmmurali bayesian balicea Happybene wnpx kengg noano sstoma josepe dagmar jo_davies roys maburkitt VirtualPlants Plantandetc compneur
  • How to succeed in science: a concise guide for young biomedical scientists. Part II: making discoveries.
    Nature reviews. Molecular cell biology (10 April 2008)
    by Jonathan W W Yewdell
    posted to others by phoenixzxl on 2008-06-07 02:12:58 as **** along with 6 people psique jyuh iramjohn tayzerhouse05 renatomilani sci91078
  • How to succeed in science: a concise guide for young biomedical scientists. Part I: taking the plunge
    Nat Rev Mol Cell Biol, Vol. 9, No. 5. (May 2008), pp. 413-416.
    by Jonathan W Yewdell
    posted to others by phoenixzxl on 2008-06-07 02:11:00 as **** along with 10 people and 1 group psique lp2 GeeSharpMinor jyuh kengg tayzerhouse05 iramjohn sobolevnrm bmaust sci91078 baker-group
  • A map of human protein interactions derived from co-expression of human mRNAs and their orthologs
    Mol Syst Biol, Vol. 4 (15 April 2008)
    by Arun K Ramani, Zhihua Li, Traver G Hart, Mark W Carlson, Daniel R Boutz, Edward M Marcotte
    posted to data_integration gene_expression prediction_ppi by phoenixzxl on 2008-04-16 02:12:11 as **** along with 7 people and 1 group tmmurali biomcgary zwang giovanni grahamc ardalby ptrobajo OPIG
  • Relating three-dimensional structures to protein networks provides evolutionary insights.
    Science, Vol. 314, No. 5807. (22 December 2006), pp. 1938-1941.
    by PM Kim, LJ Lu, Y Xia, MB Gerstein
    posted to dynamics network_dynamic network_evolution network_ppi prediction_interface by phoenixzxl on 2008-04-06 05:22:52 as **** along with 18 people and 2 groups cerca bicko lfriedl chad_davis Einat tny choonpeng timflutre grahamc ramensky massivemayhem efge lpfernandes cdeane Pao-Yang carlk paolomarcatili saket structural_bioinformatics kdl
  • Protein networks in disease
    Genome Res., Vol. 18, No. 4. (1 April 2008), pp. 644-652.
    by Trey Ideker, Roded Sharan
    posted to network_evolution network_ppi by phoenixzxl on 2008-04-03 09:32:03 as **** along with 20 people giovenko jyuh balicea tmmurali Borelli jwdietrich frohike bootsy nedwards roys mclarenv brianb schuylrp jfr paolomarcatili gracio thomaskelder ptrobajo raiyar zwang
  • Predicting gene expression from sequence.
    Cell, Vol. 117, No. 2. (16 April 2004), pp. 185-198.
    by MA Beer, S Tavazoie
    posted to bayesian gene_expression peruse by phoenixzxl on 2008-03-14 06:57:33 as **** along with 9 people and 5 groups tharris ana xwbcn adepace nickluscombe noano koller jrest klo C. elegans / WormBase structural_bioinformatics Bioinformatics EisenLab EBI-regulation
  • Bayesian learning of biological pathways on genomic data assimilation
    Bioinformatics (25 September 2008), btn483.
    by Ryo Yoshida, Masao Nagasaki, Rui Yamaguchi, Seiya Imoto, Satoru Miyano, Tomoyuki Higuchi
    posted to simulation data_integration bayesian by phoenixzxl on 2008-10-06 03:23:30 as *** along with 2 people rdiaz renatomilani
  • The intrinsic conformational propensities of the 20 naturally occurring amino acids and reflection of these propensities in proteins
    Proceedings of the National Academy of Sciences, Vol. 105, No. 34. (2008), pp. 12259-12264.
    by David A Beck, Darwin O Alonso, Daigo Inoyama, Valerie Daggett
    posted to science simulation by phoenixzxl on 2008-08-27 09:05:33 as *** along with 2 people paulschlesinger zwang
  • Evolutionary cores of domain co-occurrence networks.
    BMC Evol Biol, Vol. 5, No. 1. (2005)
    by S Wuchty, E Almaas
    posted to network_evolution by phoenixzxl on 2008-08-27 08:25:44 as *** along with 4 people agustinarce tny neils stajich
  • PRINCESS: a PRotein INteraction Confidence Evaluation System with multiple data Sources.
    Mol Cell Proteomics (29 January 2008)
    by Dong Li, Wanlin Liu, Zhongyang Liu, Jian Wang, Qijun Liu, Yunping Zhu, Fuchu He
    posted to bayesian data_integration by phoenixzxl on 2008-08-27 08:10:06 as *** along with 2 people jyuh kluck
  • Functional coherence in domain interaction networks
    Bioinformatics, Vol. 24, No. 16. (15 August 2008), pp. i28-34.
    by Jayesh Pandey, Mehmet Koyuturk, Shankar Subramaniam, Ananth Grama
    posted to network_ppi prediction_ddi prediction_function by phoenixzxl on 2008-08-11 03:53:04 as *** along with 1 person zwang
  • The evolution of epidemic influenza
    Nature Reviews Genetics, Vol. 8, No. 3. (30 January 2007), pp. 196-205.
    by Martha I Nelson, Edward C Holmes
    posted to evolution influenza review by phoenixzxl on 2008-08-06 08:13:51 as *** along with 1 person friendpine
  • An integrated view of protein evolution
    Nature Reviews Genetics, Vol. 7, No. 5., pp. 337-348.
    by Csaba Pál, Balázs Papp, Martin J Lercher
    posted to data_integration evolution protein review by phoenixzxl on 2008-08-06 08:00:42 as *** along with 7 people and 2 groups icases dayjm tny entropy markbothwell BioNica mingzhi Bothwellab TNT
  • THE BAYESIAN REVOLUTION IN GENETICS
    Nat Rev Genet, Vol. 5, No. 4. (April 2004), pp. 251-261.
    by Mark A Beaumont, Bruce Rannala
    posted to bayesian review by phoenixzxl on 2008-08-06 07:59:30 as *** along with 8 people and 2 groups garyfeng okarsligil Borelli Ayest dlr kt ichbins81 bmaust ReadingLab Bioinformatics
  • Predicting Pathway Membership via Domain Signatures
    Bioinformatics (1 August 2008), btn403.
    by Holger Frohlich, Mark Fellmann, Holger Sultmann, Annemarie Poustka, Tim Beissbarth
    posted to data_integration machine_learning structure_aided svm by phoenixzxl on 2008-08-04 07:17:20 as *** along with 4 people barriot ptrobajo mdstobbe jyuh
  • Deciphering Protein–Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners
    PLoS Computational Biology, Vol. 3, No. 4. (1 April 2007), e43.
    by Benjamin A Shoemaker, Anna R Panchenko
    posted to prediction_ddi prediction_ppi tutorial by phoenixzxl on 2008-07-31 03:29:35 as *** along with 14 people Yanno jyuh aalibes bicko jfr chad_davis cjeans iris_2001 zwang lpfernandes groepl carlk Evangelia higueruelo
  • Cooperativity and biological complexity
    Nat Chem Biol, Vol. 4, No. 8. (2008), pp. 435-439.
    by Adrian Whitty
    posted to cooperativity by phoenixzxl on 2008-07-23 07:58:57 as *** along with 2 people higueruelo paulschlesinger
  • Message-Passing Algorithms for the Prediction of Protein Domain Interactions from Protein-Protein Interaction Data
    Bioinformatics (17 July 2008), btn366.
    by Mudassar Iqbal, Alex A Freitas, Colin G Johnson, Massimo Vergassola
    posted to prediction_ddi by phoenixzxl on 2008-07-21 07:20:25 as *** along with 5 people grahamc afon zwang reyez iris_2001
  • A stringent test for hydrophobicity scales: Two proteins with 88% sequence identity but different structure and function
    Proceedings of the National Academy of Sciences (30 June 2008), 0803264105.
    by Alexander E Kister, James C Phillips
    posted to insight prediction_structure by phoenixzxl on 2008-07-01 02:04:44 as *** along with 1 person bcondon
  • Optimization in computational systems biology
    BMC Systems Biology, Vol. 2, No. 1. (2008)
    by Julio Banga
    posted to insight system_biology by phoenixzxl on 2008-06-30 01:35:09 as *** along with 7 people mazloom jyuh tmmurali reyez jrbanga biehl balicea
  • Automated design of specificity in molecular recognition.
    Nat Struct Biol, Vol. 10, No. 1. (January 2003), pp. 45-52.
    by JJ Havranek, PB Harbury
    posted to coiled_coil protein_design specificity by phoenixzxl on 2008-06-24 02:54:54 as *** along with 1 person bethbromley
  • Specificity and Evolvability in Eukaryotic Protein Interaction Networks
    PLoS Computational Biology, Vol. 3, No. 2. (1 February 2007), e25.
    by Pedro Beltrao, Luis Serrano
    posted to network_evolution network_ppi specificity by phoenixzxl on 2008-06-23 10:57:55 as *** along with 1 person pedrobeltrao
  • Evolutionary conservation of domain-domain interactions
    Genome Biology, Vol. 7 (21 December 2006), R125.
    by Zohar Itzhaki, Eyal Akiva, Yael Altuvia, Hanah Margalit
    posted to evolution prediction_ddi by phoenixzxl on 2008-05-16 09:42:25 as *** along with 3 people and 2 groups tharris grahamc winterschlaefer C. elegans / WormBase ParkinsonLab_at_MaRS
  • Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Andrew Bordner, Andrey Gorin
    posted to complex data_integration prediction_interface by phoenixzxl on 2008-05-13 07:28:04 as *** along with 4 people chad_davis jyuh neils bicko
  • notes Tracking the ends: a dynamic protein network controls the fate of microtubule tips
    Nature Reviews Molecular Cell Biology, Vol. 9, No. 4. (05 March 2008), pp. 309-322.
    by Anna Akhmanova, Michel O Steinmetz
    posted to coiled_coil network_dynamic network_ppi review by phoenixzxl on 2008-04-08 13:20:39 as *** along with 1 person lechristophe
  • Coiled-Coil Irregularities and Instabilities in Group A Streptococcus M1 Are Required for Virulence
    Science, Vol. 319, No. 5868. (7 March 2008), pp. 1405-1408.
    by Case Mcnamara, Annelies S Zinkernagel, Pauline Macheboeuf, Madeleine W Cunningham, Victor Nizet, Partho Ghosh
    posted to coiled_coil by phoenixzxl on 2008-03-25 02:40:09 as *** along with 1 person davidlott
  • Interaction-Site Prediction for Protein Complexes: a Critical Assessment
    Bioinformatics (22 June 2007), btm323.
    by Huan-Xiang Zhou, Sanbo Qin
    posted to machine_learning prediction_interface prediction_ppi review by phoenixzxl on 2008-03-19 06:03:59 as *** along with 10 people tjimenez bicko malcook zwang cabbagezs niallhaslam carlescorbi marti higueruelo kintoki
  • Specificity in protein interactions and its relationship with sequence diversity and coevolution.
    Proc Natl Acad Sci U S A (27 April 2007)
    by Luke Hakes, Simon C C Lovell, Stephen G G Oliver, David L L Robertson
    posted to co-evolution specificity by phoenixzxl on 2008-03-19 01:33:32 as *** along with 9 people and 2 groups stevanspringer bjorns cjeans zwang Garamonfok cursonivel1 tale winterschlaefer chrys FAB-lab cursonivel1
  • Characterization of Domain-Peptide Interaction Interface: A Case Study on the Amphiphysin-1 SH3 Domain
    Journal of Molecular Biology, Vol. 376, No. 4. (29 February 2008), pp. 1201-1214.
    by Tingjun Hou, Wei Zhang, David A Case, Wei Wang
    posted to prediction_interface by phoenixzxl on 2008-03-17 12:11:01 as ***
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