| | Education A Primer on Regression Methods for Decoding cis-Regulatory Logic Debopriya Das, Matteo Pellegrini, and Joe W. Gray PLoS Comput Biol. 2009 January; 5(1): e1000269. Published online 2009 January 30. doi: 10.1371/journal.pcbi.1000269.PMCID: PMC2607548 Editorial A Review of 2008 for PLoS Computational
Biology Evie Browne, Rosemary Dickin, and Philip E. Bourne PLoS Comput Biol. 2009 January; 5(1): e1000275. Published online 2009 January 30. doi: 10.1371/journal.pcbi.1000275.PMCID: PMC2613517 Message from ISCB Microblogging the ISMB: A New Approach to Conference Reporting Neil Saunders, Pedro Beltrão, Lars Jensen, Daniel Jurczak, Roland Krause, Michael Kuhn, and Shirley Wu PLoS Comput Biol. 2009 January; 5(1): e1000263. Published online 2009 January 30. doi: 10.1371/journal.pcbi.1000263.PMCID: PMC2612753 Research Articles Questioning the Ubiquity of Neofunctionalization Todd A. Gibson and Debra S. Goldberg PLoS Comput Biol. 2009 January; 5(1): e1000252. Published online 2009 January 2. doi: 10.1371/journal.pcbi.1000252.PMCID: PMC2597716 Polyamine Sharing between Tubulin Dimers Favours Microtubule
Nucleation and Elongation via Facilitated Diffusion Alain Mechulam, Konstantin G. Chernov, Elodie Mucher, Loic Hamon, Patrick A. Curmi, and David Pastré PLoS Comput Biol. 2009 January; 5(1): e1000255. Published online 2009 January 2. doi: 10.1371/journal.pcbi.1000255.PMCID: PMC2599886 Shape, Size, and Robustness: Feasible Regions in the Parameter Space of Biochemical Networks Adel Dayarian, Madalena Chaves, Eduardo D. Sontag, and Anirvan M. Sengupta PLoS Comput Biol. 2009 January; 5(1): e1000256. Published online 2009 January 2. doi: 10.1371/journal.pcbi.1000256.PMCID: PMC2599888 Predicting Cellular Growth from Gene Expression Signatures Edoardo M. Airoldi, Curtis Huttenhower, David Gresham, Charles Lu, Amy A. Caudy, Maitreya J. Dunham, James R. Broach, David Botstein, and Olga G. Troyanskaya PLoS Comput Biol. 2009 January; 5(1): e1000257. Published online 2009 January 2. doi: 10.1371/journal.pcbi.1000257.PMCID: PMC2599889 Evolutionary Sequence Modeling for Discovery of Peptide Hormones Kemal Sonmez, Naunihal T. Zaveri, Ilan A. Kerman, Sharon Burke, Charles R. Neal, Xinmin Xie, Stanley J. Watson, and Lawrence Toll PLoS Comput Biol. 2009 January; 5(1): e1000258. Published online 2009 January 9. doi: 10.1371/journal.pcbi.1000258.PMCID: PMC2603333 State Based Model of Long-Term Potentiation and Synaptic Tagging and
Capture Adam B. Barrett, Guy O. Billings, Richard G. M. Morris, and Mark C. W. van Rossum PLoS Comput Biol. 2009 January; 5(1): e1000259. Published online 2009 January 16. doi: 10.1371/journal.pcbi.1000259.PMCID: PMC2603667 Deterministic Mechanical Model of T-Killer Cell Polarization
Reproduces the Wandering of Aim between Simultaneously Engaged Targets Mun Ju Kim and Ivan V. Maly PLoS Comput Biol. 2009 January; 5(1): e1000260. Published online 2009 January 9. doi: 10.1371/journal.pcbi.1000260.PMCID: PMC2603019 An Analysis of Enzyme Kinetics Data for Mitochondrial DNA Strand Termination by Nucleoside Reverse Transcription Inhibitors Katherine V. Wendelsdorf, Zhuo Song, Yang Cao, and David C. Samuels PLoS Comput Biol. 2009 January; 5(1): e1000261. Published online 2009 January 9. doi: 10.1371/journal.pcbi.1000261.PMCID: PMC2603287 Phylogenetic and Functional Assessment of Orthologs Inference
Projects and Methods Adrian M. Altenhoff and Christophe Dessimoz PLoS Comput Biol. 2009 January; 5(1): e1000262. Published online 2009 January 16. doi: 10.1371/journal.pcbi.1000262.PMCID: PMC2612752 Developmental Robustness by Obligate Interaction of Class B Floral Homeotic Genes and Proteins Thorsten Lenser, Günter Theißen, and Peter Dittrich PLoS Comput Biol. 2009 January; 5(1): e1000264. Published online 2009 January 16. doi: 10.1371/journal.pcbi.1000264.PMCID: PMC2612583 Action Potential Initiation in the Hodgkin-Huxley Model Lucy J. Colwell and Michael P. Brenner PLoS Comput Biol. 2009 January; 5(1): e1000265. Published online 2009 January 16. doi: 10.1371/journal.pcbi.1000265.PMCID: PMC2607014 Partial Order Optimum Likelihood (POOL): Maximum Likelihood Prediction of Protein Active Site Residues Using 3D Structure and Sequence Properties Wenxu Tong, Ying Wei, Leonel F. Murga, Mary Jo Ondrechen, and Ronald J. Williams PLoS Comput Biol. 2009 January; 5(1): e1000266. Published online 2009 January 16. doi: 10.1371/journal.pcbi.1000266.PMCID: PMC2612599 Joint Evolutionary Trees: A Large-Scale Method To Predict Protein
Interfaces Based on Sequence Sampling Stefan Engelen, Ladislas A. Trojan, Sophie Sacquin-Mora, Richard Lavery, and Alessandra Carbone PLoS Comput Biol. 2009 January; 5(1): e1000267. Published online 2009 January 23. doi: 10.1371/journal.pcbi.1000267.PMCID: PMC2613531 Computational Modeling of the Hematopoietic Erythroid-Myeloid Switch Reveals Insights into Cooperativity, Priming, and Irreversibility Vijay Chickarmane, Tariq Enver, and Carsten Peterson PLoS Comput Biol. 2009 January; 5(1): e1000268. Published online 2009 January 23. doi: 10.1371/journal.pcbi.1000268.PMCID: PMC2613533 Coordinated Concentration Changes of Transcripts and Metabolites in Saccharomyces cerevisiae Patrick H. Bradley, Matthew J. Brauer, Joshua D. Rabinowitz, and Olga G. Troyanskaya PLoS Comput Biol. 2009 January; 5(1): e1000270. Published online 2009 January 30. doi: 10.1371/journal.pcbi.1000270.PMCID: PMC2614473 Efficient Network Reconstruction from Dynamical Cascades Identifies
Small-World Topology of Neuronal Avalanches Sinisa Pajevic and Dietmar Plenz PLoS Comput Biol. 2009 January; 5(1): e1000271. Published online 2009 January 30. doi: 10.1371/journal.pcbi.1000271.PMCID: PMC2615076 Astrocytic Mechanisms Explaining Neural-Activity-Induced Shrinkage of Extraneuronal Space Ivar Østby, Leiv Øyehaug, Gaute T. Einevoll, Erlend A. Nagelhus, Erik Plahte, Thomas Zeuthen, Catherine M. Lloyd, Ole P. Ottersen, and Stig W. Omholt PLoS Comput Biol. 2009 January; 5(1): e1000272. Published online 2009 January 23. doi: 10.1371/journal.pcbi.1000272.PMCID: PMC2613522 Model-Based Therapeutic Correction of Hypothalamic-Pituitary-Adrenal Axis Dysfunction Amos Ben-Zvi, Suzanne D. Vernon, and Gordon Broderick PLoS Comput Biol. 2009 January; 5(1): e1000273. Published online 2009 January 23. doi: 10.1371/journal.pcbi.1000273.PMCID: PMC2613527 A Factor Graph Nested Effects Model To Identify Networks from Genetic Perturbations Charles J. Vaske, Carrie House, Truong Luu, Bryan Frank, Chen-Hsiang Yeang, Norman H. Lee, and Joshua M. Stuart PLoS Comput Biol. 2009 January; 5(1): e1000274. Published online 2009 January 30. doi: 10.1371/journal.pcbi.1000274.PMCID: PMC2613752 Cohesive versus Flexible Evolution of Functional Modules in Eukaryotes Like Fokkens and Berend Snel PLoS Comput Biol. 2009 January; 5(1): e1000276. Published online 2009 January 30. doi: 10.1371/journal.pcbi.1000276.PMCID: PMC2615111 Poisson-Nernst-Planck Models of Nonequilibrium Ion Electrodiffusion through a Protegrin Transmembrane Pore Dan S. Bolintineanu, Abdallah Sayyed-Ahmad, H. Ted Davis, and Yiannis N. Kaznessis PLoS Comput Biol. 2009 January; 5(1): e1000277. Published online 2009 January 30. doi: 10.1371/journal.pcbi.1000277.PMCID: PMC2614469 Prediction of Protein–Protein Interaction Sites in Sequences and 3D Structures by Random Forests Mile Šikić, Sanja Tomić, and Kristian Vlahoviček PLoS Comput Biol. 2009 January; 5(1): e1000278. Published online 2009 January 30. doi: 10.1371/journal.pcbi.1000278.PMCID: PMC2621338 Precise Regulation of Gene Expression Dynamics Favors Complex Promoter Architectures Dirk Müller and Jörg Stelling PLoS Comput Biol. 2009 January; 5(1): e1000279. Published online 2009 January 30. doi: 10.1371/journal.pcbi.1000279.PMCID: PMC2615112 Corrections Correction: A Novel Three-Phase Model of Brain Tissue Microstructure Jana L. Gevertz and Salvatore Torquato PLoS Comput Biol. 2009 January; 5(1): 10.1371/annotation/c9faa83b-3c7b-4f38-8d74-1a4309403688. Published online 2009 January 6. doi: 10.1371/annotation/c9faa83b-3c7b-4f38-8d74-1a4309403688.PMCID: PMC2665010 Corrects: Jana L. Gevertz, et al. A Novel Three-Phase Model of Brain Tissue Microstructure. PLoS Comput Biol. 2008 August; 4(8): e1000152. Correction: Silent Synapses, LTP, and the Indirect Parallel-Fibre Pathway: Computational Consequences of Optimal Cerebellar Noise-Processing John Porrill and Paul Dean PLoS Comput Biol. 2009 January; 5(1): 10.1371/annotation/349e7f3a-c9ce-4de2-b369-254ae8ab76cd. Published online 2009 January 24. doi: 10.1371/annotation/349e7f3a-c9ce-4de2-b369-254ae8ab76cd.PMCID: PMC2641020 Corrects: John Porrill, et al. Silent Synapses, LTP, and the Indirect Parallel-Fibre Pathway: Computational Consequences of Optimal Cerebellar Noise-Processing. PLoS Comput Biol. 2008 May; 4(5): e1000085. |