tomt21's library 123 articles Export

	Simulation-based model selection for dynamical systems in systems and population biology [My Copy] (9 Nov 2009) by Tina Toni, Michael P. H. Stumpf posted to no-tag by tomt21 on 2009-11-10 18:43:57 as along with 1 person dah
	InterPro: the integrative protein signature database. [My Copy] Nucleic acids research, Vol. 37, No. Database issue. (21 January 2009) by Sarah Hunter, Rolf Apweiler, Teresa K. Attwood, et al.Amos Bairoch, Alex Bateman, David Binns, Peer Bork, Ujjwal Das, Louise Daugherty, Lauranne Duquenne, Robert D. Finn, Julian Gough, Daniel Haft, Nicolas Hulo, Daniel Kahn, Elizabeth Kelly, Aurélie Laugraud, Ivica Letunic, David Lonsdale, Rodrigo Lopez, Martin Madera, John Maslen, Craig McAnulla, Jennifer McDowall, Jaina Mistry, Alex Mitchell, Nicola Mulder, Darren Natale, Christine Orengo, Antony F. Quinn, Jeremy D. Selengut, Christian J. Sigrist, Manjula Thimma, Paul D. Thomas, Franck Valentin, Derek Wilson, Cathy H. Wu, Corin Yeats posted to no-tag by tomt21 on 2009-11-06 13:26:41 as along with 4 people BioNica lptolik nlapalu druvus
	A fungal phylogeny based on 82 complete genomes using the composition vector method [My Copy] BMC Evolutionary Biology, Vol. 9, No. 1. (10 August 2009), 195. by Hao Wang, Zhao Xu, Lei Gao, Bailin Hao posted to no-tag by tomt21 on 2009-11-06 13:26:14 as along with 4 people and 1 group nlapalu jamselem stajich druvus Mycology
	Initial sequence and comparative analysis of the cat genome [My Copy] Genome Research, Vol. 17, No. 11. (1 November 2007), pp. 1675-1689. by Joan U. Pontius, James C. Mullikin, Douglas R. Smith, et al.Kerstin Lindblad-Toh, Sante Gnerre, Michele Clamp, Jean Chang, Robert Stephens, Beena Neelam, Natalia Volfovsky, Alejandro A. SchÃ¤ffer, Richa Agarwala, Kristina NarfstrÃ¶m, William J. Murphy, Urs Giger, Alfred L. Roca, Agostinho Antunes, Marilyn Menotti-Raymond, Naoya Yuhki, Jill Pecon-Slattery, Warren E. Johnson, Guillaume Bourque, Glenn Tesler, Stephen J. OâBrien posted to cats by tomt21 on 2009-10-28 21:58:48 as along with 4 people aprasad dchughes kmegq hpaces
	Parameter estimation for Boolean models of biological networks [My Copy] (21 Aug 2009) by Elena Dimitrova, Luis D. Garcia-Puente, Franziska Hinkelmann, et al.Abdul S. Jarrah, Reinhard Laubenbacher, Brandilyn Stigler, Michael Stillman, Paola Vera-Licona posted to no-tag by tomt21 on 2009-08-25 12:04:41 as
	Systematics Researchers Want to Fend Off Patents [My Copy] Science, Vol. 325, No. 5941. (7 August 2009), 664. by Elizabeth Pennisi posted to microsoft evil by tomt21 on 2009-08-22 09:26:58 as along with 3 people and 2 groups rdiaz dinnes jago Convention on Knowledge Commons Patent_Reform
	Spectral characteristics of network redundancy [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 80, No. 2. (2009), 026117. by Ben D. Macarthur, Rubén J. Sánchez Garc'ia posted to no-tag by tomt21 on 2009-08-20 11:24:35 as
	Inferring genetic networks: An information theoretic approach [My Copy] (2 Aug 2009) by L. Diambra posted to expression inference networks by tomt21 on 2009-08-04 21:25:18 as along with 1 person apocapoc
	Benchmarks for testing community detection algorithms on directed and weighted graphs with overlapping communities [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 80, No. 1. (2009), 016118. by Andrea Lancichinetti, Santo Fortunato posted to clustering networks by tomt21 on 2009-08-03 14:22:52 as along with 2 people deanmalmgren dpf
	Spectral partitioning with multiple eigenvectors [My Copy] Discrete Applied Mathematics, Vol. 90, No. 1-3. (15 January 1999), pp. 3-26. by C. Alpert posted to clustering networks by tomt21 on 2009-07-24 14:17:25 as
	The Principal Components Analysis of a Graph, and its Relationships to Spectral Clustering [My Copy] In Proceedings of the 15th European Conference on Machine Learning (ECML 2004). Lecture Notes in Artificial Intelligence, Vol. 3201 (2004), pp. 371-383. by Marco Saerens, François Fouss, Luh Yen, Pierre Dupont posted to clustering networks by tomt21 on 2009-07-24 14:16:37 as
	Experiments on Graph Clustering Algorithms [My Copy] Algorithms - ESA 2003 (2003), pp. 568-579. by Ulrik Brandes, Marco Gaertler, Dorothea Wagner posted to clustering networks by tomt21 on 2009-07-24 14:14:59 as
	Functional cartography of complex metabolic networks [My Copy] Nature, Vol. 433, No. 7028. (24 February 2005), pp. 895-900. by Roger Guimera, Luis A. Nunes Amaral posted to clustering networks by tomt21 on 2009-07-24 14:13:28 as along with 23 people and 4 groups schwartzjmc lawraga Scis0000002 vtraag cgaugain pdelosri cswinburne camster dbk BioGeek Borelli lfriedl balajis alexg eweaver tny wnpx cjeans kdang carlk RobMills Diego_Prada marcio streptomyces dbk-lab kdl Bioinformatics
	Analysis of community structure in networks of correlated data [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 80, No. 1. (2009), 016114. by Sergio Gómez, Pablo Jensen, Alex Arenas posted to clustering networks by tomt21 on 2009-07-24 13:51:01 as along with 3 people vtraag apocapoc deanmalmgren
	Assessing the relevance of node features for network structure [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 28. (14 July 2009), pp. 11433-11438. by Ginestra Bianconi, Paolo Pin, Matteo Marsili posted to networks by tomt21 on 2009-07-15 12:52:50 as along with 12 people rdiaz daforerog Kovanen zwang apocapoc Diego_Prada winterstream trfield deanmalmgren roys tmmurali statnet
	Parameter and state estimation of experimental chaotic systems using synchronization [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 80, No. 1. (2009), 016201. by John C. Quinn, Paul H. Bryant, Daniel R. Creveling, Sallee R. Klein, Henry D. I. Abarbanel posted to no-tag by tomt21 on 2009-07-07 14:59:52 as
	Master-equation analysis of accelerating networks [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 79, No. 5. (2009), 056101. by David M. D. Smith, Jukka P. Onnela, Nick S. Jones posted to networks by tomt21 on 2009-07-06 15:31:41 as along with 1 person ocs
	Unusual percolation in simple small-world networks [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 79, No. 6. (June 2009), 066112. by Reuven Cohen, Daryush J. Dawid, Mehran Kardar, Yaneer B. Yam posted to no-tag by tomt21 on 2009-07-06 15:18:20 as along with 3 people davidecellai leonglester deanmalmgren
	Alternative approach to community detection in networks [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 79, No. 6. (2009), 066111. by A. D. Medus, C. O. Dorso posted to no-tag by tomt21 on 2009-07-06 15:16:28 as along with 3 people senseable-urb Kovanen deanmalmgren
	Shortest path discovery of complex networks [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 79, No. 6. (2009), 065101. by Attila Fekete, Gábor Vattay, Márton Pósfai posted to no-tag by tomt21 on 2009-07-06 15:15:55 as along with 2 people Kovanen deanmalmgren
	Extracting the multiscale backbone of complex weighted networks [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 16. (21 April 2009), pp. 6483-6488. by M. Ãngeles Serrano, MariÃ¡n BoguÃ±Ã¡, Alessandro Vespignani posted to networks by tomt21 on 2009-07-06 15:08:07 as along with 9 people and 1 group rdiaz edws rsantana trfield pinney deanmalmgren sobolevnrm kevinchannon kshundyak baker-group
	A Simplex Method for Function Minimization [My Copy] The Computer Journal, Vol. 7, No. 4. (1 January 1965), pp. 308-313. by J. A. Nelder, R. Mead posted to no-tag by tomt21 on 2009-06-24 01:11:19 as along with 11 people and 2 groups eyliu A_Coletta_Thesis eindermu skoch3 michelcias pcoupe deitosrafael 0pika0 granujilla aogier abrentnall Structural Biology Group TorVergata Koch_Lab
	Homotopy equivalence of isospectral graphs [My Copy] (22 Jun 2009) by Terrence Bisson, Aristide Tsemo posted to no-tag by tomt21 on 2009-06-23 18:33:16 as
	Lyapunov exponents in one-dimensional disordered systems with long-range memory [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 79, No. 6. (2009), 062102. by Alexander Iomin posted to no-tag by tomt21 on 2009-06-20 02:34:42 as
	Coexistence in stochastic spatial models [My Copy] (12 Jun 2009) by Rick Durrett posted to no-tag by tomt21 on 2009-06-20 02:25:59 as
	Introduction To Mathematical Methods In Bioinformatics (Universitext) [My Copy] (16 October 2004) by Alexander Isaev posted to no-tag by tomt21 on 2009-06-01 14:25:35 as along with 1 person and 1 group fsilvestri InformationRetrieval
	Parameter inference and model selection in signaling pathway models [My Copy] (27 May 2009) by Tina Toni, Michael P. H. Stumpf posted to inference model parameter selection by tomt21 on 2009-06-01 13:18:47 as along with 1 person dah
	Aligning graphs and finding substructures by message passing [My Copy] (12 May 2009) by S. Bradde, A. Braunstein, H. Mahmoudi, F. Tria, M. Weigt, R. Zecchina posted to alignment networks by tomt21 on 2009-05-13 13:05:09 as along with 1 person marinari
	Quantifying stochastic effects in biochemical reaction networks using partitioned leaping [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 79, No. 5. (2009), 051906. by Leonard A. Harris, Aaron M. Piccirilli, Emily R. Majusiak, Paulette Clancy posted to dynamics by tomt21 on 2009-05-13 12:54:32 as
	Past-future information bottleneck in dynamical systems [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 79, No. 4. (2009), 041925. by Felix Creutzig, Amir Globerson, Naftali Tishby posted to no-tag by tomt21 on 2009-04-28 14:59:38 as
	Geometry and stability of dynamical systems [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 79, No. 4. (2009), 046606. by Raffaele Punzi, Mattias N. R. Wohlfarth posted to dynamics by tomt21 on 2009-04-15 14:44:31 as
	A Dimension Reduction Method for Inferring Biochemical Networks [My Copy] (25 Feb 2009) by Gheorghe Craciun, Casian Pantea, Grzegorz A. Rempala posted to dynamics by tomt21 on 2009-02-26 15:02:19 as
	Spontaneous Emergence of Modularity in a Model of Evolving Individuals and in Real Networks [My Copy] (23 Feb 2009) by Jiankui He, Jun Sun, Michael W. Deem posted to networks by tomt21 on 2009-02-25 13:03:58 as along with 3 people phreeza agutfraind deanmalmgren
	A presentation of the category of stochastic matrices [My Copy] (16 Feb 2009) by Tobias Fritz posted to cats by tomt21 on 2009-02-17 02:17:51 as along with 1 person jrw
	Information-theoretic approach to network modularity. [My Copy] Phys Rev E Stat Nonlin Soft Matter Phys, Vol. 71, No. 4 Pt 2. (Apr 2005) by Etay Ziv, Manuel Middendorf, Chris H. Wiggins posted to algorithms analysis bacterial bibtex biophysics carlo coli computer escherichia genetic method models monte networks neural physiology simulation statistical systems theory transcription by tomt21 on 2009-02-11 12:13:55 as
	Genomic analysis of essentiality within protein networks. [My Copy] Trends Genet, Vol. 20, No. 6. (Jun 2004), pp. 227-231. by Haiyuan Yu, Dov Greenbaum, Hao X. Lu, Xiaowei Zhu, Mark Gerstein posted to animals bibtex expression factors gene genes genetic genomics humans proteins regulation regulator transcription by tomt21 on 2009-02-11 12:13:55 as
	Functional and topological characterization of protein interaction networks. [My Copy] Proteomics, Vol. 4, No. 4. (Apr 2004), pp. 928-942. by Soon H. Yook, Zoltán N. Oltvai, Albert L. Barabási posted to algorithms bibtex biology cerevisiae computational databases macromolecular protein proteome saccharomyces substances by tomt21 on 2009-02-11 12:13:55 as
	Using complexity measure factor to predict protein subcellular location. [My Copy] Amino Acids, Vol. 28, No. 1. (Feb 2005), pp. 57-61. by X. Xiao, S. Shao, Y. Ding, Z. Huang, Y. Huang, K. C. Chou posted to acids algorithms amino bibtex biological fractions models proteins subcellular by tomt21 on 2009-02-11 12:13:55 as
	DIP: the database of interacting proteins. [My Copy] Nucleic Acids Res, Vol. 28, No. 1. (Jan 2000), pp. 289-291. by I. Xenarios, D. W. Rice, L. Salwinski, M. K. Baron, E. M. Marcotte, D. Eisenberg posted to bibtex binding databases factual protein proteins by tomt21 on 2009-02-11 12:13:55 as
	A likelihood approach to analysis of network data. [My Copy] Proc Natl Acad Sci U S A, Vol. 103, No. 20. (May 2006), pp. 7566-7570. by Carsten Wiuf, Markus Brameier, Oskar Hagberg, Michael P. H. Stumpf posted to animals bibtex caenorhabditis data elegans functions information interpretation likelihood mathematics models nerve net proteins services social statistical support theoretical by tomt21 on 2009-02-11 12:13:55 as
	Collective dynamics of 'small-world' networks. [My Copy] Nature, Vol. 393, No. 6684. (Jun 1998), pp. 440-442. by D. J. Watts, S. H. Strogatz posted to animals bibtex biological caenorhabditis communicable diseases elegans experimental games models nerve net neurological theoretical by tomt21 on 2009-02-11 12:13:55 as
	Detecting putative orthologs. [My Copy] Bioinformatics, Vol. 19, No. 13. (Sep 2003), pp. 1710-1711. by D. P. Wall, H. B. Fraser, A. E. Hirsh posted to albicans algorithms alignment bibtex candida cerevisiae evolution functions likelihood molecular saccharomyces sequence by tomt21 on 2009-02-11 12:13:55 as
	The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. [My Copy] Mol Biol Evol, Vol. 18, No. 7. (Jul 2001), pp. 1283-1292. by A. Wagner posted to bibtex cerevisiae duplication evolution factors fungal gene genes genetic models molecular proteins saccharomyces system techniques time two-hybrid by tomt21 on 2009-02-11 12:13:55 as
	A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. [My Copy] Nature, Vol. 403, No. 6770. (Feb 2000), pp. 623-627. by P. Uetz, L. Giot, G. Cagney, et al.T. A. Mansfield, R. S. Judson, J. R. Knight, D. Lockshon, V. Narayan, M. Srinivasan, P. Pochart, Qureshi A. Emili, Y. Li, B. Godwin, D. Conover, T. Kalbfleisch, G. Vijayadamodar, M. Yang, M. Johnston, S. Fields, J. M. Rothberg posted to bibtex binding cerevisiae frames fungal library open peptide protein proteins reading saccharomyces structure system techniques tertiary two-hybrid by tomt21 on 2009-02-11 12:13:55 as
	Towards an understanding of complex protein networks. [My Copy] Trends Cell Biol, Vol. 11, No. 3. (Mar 2001), pp. 102-106. by C. L. Tucker, J. F. Gera, P. Uetz posted to bibtex biological biology cell cells cerevisiae computational cycle mapping models peptide proteins proteome saccharomyces system techniques two-hybrid by tomt21 on 2009-02-11 12:13:54 as
	Generating Confidence Intervals on Networks [My Copy] To Appear (2006) by Tom Thorne, Michael Stumpf posted to bibtex by tomt21 on 2009-02-11 12:13:54 as
	The Plasmodium protein network diverges from those of other eukaryotes. [My Copy] Nature, Vol. 438, No. 7064. (Nov 2005), pp. 108-112. by Silpa Suthram, Taylor Sittler, Trey Ideker posted to animals bibtex binding caenorhabditis cells cerevisiae conserved drosophila elegans eukaryotic falciparum helicobacter melanogaster phylogeny plasmodium protein proteins protozoan pylori saccharomyces sequence species specificity system techniques two-hybrid by tomt21 on 2009-02-11 12:13:54 as
	Subnets of scale-free networks are not scale-free: sampling properties of networks. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 12. (Mar 2005), pp. 4221-4224. by Michael P. H. Stumpf, Carsten Wiuf, Robert M. May posted to bibtex by tomt21 on 2009-02-11 12:13:54 as
	Statistical Model Selection Methods Applied to Biological Networks [My Copy] In Transactions on Computational Systems Biology III (2005) by Michael Stumpf, Piers Ingram, Ian Nouvel, Carsten Wiuf posted to bibtex by tomt21 on 2009-02-11 12:13:54 as
	A model of large-sacle proteome evolution [My Copy] Advances in Complex Systems, Vol. 5 (2002), pp. 43-54. by Ricard Sole, Romualdo P. Satorras, Eric Smith, Thomas Kepler posted to bibtex by tomt21 on 2009-02-11 12:13:54 as

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tomt21's library 123 articles Export

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