PLOS Computational Biology
2005 - 2025
From Public Library of Science Bibliographic data for series maintained by ploscompbiol (). Access Statistics for this journal.
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Volume 5, issue 12, 2009
- Population Structure Induces a Symmetry Breaking Favoring the Emergence of Cooperation pp. 1-7

- Jorge M Pacheco, Flávio Pinheiro and Francisco C Santos
- Calculating Evolutionary Dynamics in Structured Populations pp. 1-7

- Charles G Nathanson, Corina E Tarnita and Martin A Nowak
- Bayesian Integration and Non-Linear Feedback Control in a Full-Body Motor Task pp. 1-9

- Ian H Stevenson, Hugo L Fernandes, Iris Vilares, Kunlin Wei and Konrad P Körding
- Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies pp. 1-13

- Alexandra M Schnoes, Shoshana D Brown, Igor Dodevski and Patricia C Babbitt
- Meta-analysis of Inter-species Liver Co-expression Networks Elucidates Traits Associated with Common Human Diseases pp. 1-16

- Kai Wang, Manikandan Narayanan, Hua Zhong, Martin Tompa, Eric E Schadt and Jun Zhu
- Hyperbolic Planforms in Relation to Visual Edges and Textures Perception pp. 1-16

- Pascal Chossat and Olivier Faugeras
- Effective Reduced Diffusion-Models: A Data Driven Approach to the Analysis of Neuronal Dynamics pp. 1-10

- Gustavo Deco, Daniel Martí, Anders Ledberg, Ramon Reig and Maria V Sanchez Vives
- Nano-motion Dynamics are Determined by Surface-Tethered Selectin Mechanokinetics and Bond Formation pp. 1-19

- Brian J Schmidt, Jason A Papin and Michael B Lawrence
- Identifying Drug Effects via Pathway Alterations using an Integer Linear Programming Optimization Formulation on Phosphoproteomic Data pp. 1-11

- Alexander Mitsos, Ioannis N Melas, Paraskeuas Siminelakis, Aikaterini D Chairakaki, Julio Saez-Rodriguez and Leonidas G Alexopoulos
- Evolutionary Plasticity and Innovations in Complex Metabolic Reaction Networks pp. 1-11

- João F Matias Rodrigues and Andreas Wagner
- Model of Transcriptional Activation by MarA in Escherichia coli pp. 1-11

- Michael E Wall, David A Markowitz, Judah L Rosner and Robert G Martin
- Inferring Binding Energies from Selected Binding Sites pp. 1-8

- Yue Zhao, David Granas and Gary D Stormo
- Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure pp. 1-18

- John A Capra, Roman A Laskowski, Janet M Thornton, Mona Singh and Thomas A Funkhouser
Volume 5, issue 11, 2009
- A Hidden Markov Model for Single Particle Tracks Quantifies Dynamic Interactions between LFA-1 and the Actin Cytoskeleton pp. 1-16

- Raibatak Das, Christopher W Cairo and Daniel Coombs
- Evaluation of the Oscillatory Interference Model of Grid Cell Firing through Analysis and Measured Period Variance of Some Biological Oscillators pp. 1-16

- Eric A Zilli, Motoharu Yoshida, Babak Tahvildari, Lisa M Giocomo and Michael E Hasselmo
- A Novel Extended Granger Causal Model Approach Demonstrates Brain Hemispheric Differences during Face Recognition Learning pp. 1-13

- Tian Ge, Keith M Kendrick and Jianfeng Feng
- Attention Increases the Temporal Precision of Conscious Perception: Verifying the Neural-ST2 Model pp. 1-13

- Srivas Chennu, Patrick Craston, Brad Wyble and Howard Bowman
- Analyzing Short-Term Noise Dependencies of Spike-Counts in Macaque Prefrontal Cortex Using Copulas and the Flashlight Transformation pp. 1-13

- Arno Onken, Steffen Grünewälder, Matthias H J Munk and Klaus Obermayer
- Discovery of Regulatory Elements is Improved by a Discriminatory Approach pp. 1-8

- Eivind Valen, Albin Sandelin, Ole Winther and Anders Krogh
- Optimal Experimental Design for Parameter Estimation of a Cell Signaling Model pp. 1-12

- Samuel Bandara, Johannes P Schlöder, Roland Eils, Hans Georg Bock and Tobias Meyer
- A Role for Rebinding in Rapid and Reliable T Cell Responses to Antigen pp. 1-12

- Omer Dushek, Raibatak Das and Daniel Coombs
Volume 5, issue 10, 2009
- Towards a Mathematical Theory of Cortical Micro-circuits pp. 1-26

- Dileep George and Jeff Hawkins
- The Mechanism of Ubiquitination in the Cullin-RING E3 Ligase Machinery: Conformational Control of Substrate Orientation pp. 1-10

- Jin Liu and Ruth Nussinov
- ‘Glocal’ Robustness Analysis and Model Discrimination for Circadian Oscillators pp. 1-10

- Marc Hafner, Heinz Koeppl, Martin Hasler and Andreas Wagner
- Grasping Objects with Environmentally Induced Position Uncertainty pp. 1-11

- Vassilios N Christopoulos and Paul R Schrater
- Perturbation-based Markovian Transmission Model for Probing Allosteric Dynamics of Large Macromolecular Assembling: A Study of GroEL-GroES pp. 1-13

- Hsiao-Mei Lu and Jie Liang
- Mechanical Strength of 17 134 Model Proteins and Cysteine Slipknots pp. 1-15

- Mateusz Sikora, Joanna I Sułkowska and Marek Cieplak
- Getting Started in Gene Expression Microarray Analysis pp. 1-4

- Donna K Slonim and Itai Yanai
- Gene Circuit Analysis of the Terminal Gap Gene huckebein pp. 1-16

- Maksat Ashyraliyev, Ken Siggens, Hilde Janssens, Joke Blom, Michael Akam and Johannes Jaeger
Volume 5, issue 9, 2009
- Predicting Positive p53 Cancer Rescue Regions Using Most Informative Positive (MIP) Active Learning pp. 1-12

- Samuel A Danziger, Roberta Baronio, Lydia Ho, Linda Hall, Kirsty Salmon, G Wesley Hatfield, Peter Kaiser and Richard H Lathrop
- Transcriptional Profiling of the Dose Response: A More Powerful Approach for Characterizing Drug Activities pp. 1-12

- Rui-Ru Ji, Heshani de Silva, Yisheng Jin, Robert E Bruccoleri, Jian Cao, Aiqing He, Wenjun Huang, Paul S Kayne, Isaac M Neuhaus, Karl-Heinz Ott, Becky Penhallow, Mark I Cockett, Michael G Neubauer, Nathan O Siemers and Petra Ross-Macdonald
- Googling Food Webs: Can an Eigenvector Measure Species' Importance for Coextinctions? pp. 1-6

- Stefano Allesina and Mercedes Pascual
- Chemically Based Mathematical Model for Development of Cerebral Cortical Folding Patterns pp. 1-6

- Deborah A Striegel and Monica K Hurdal
- A Statistical Model to Identify Differentially Expressed Proteins in 2D PAGE Gels pp. 1-9

- Steven H Wu, Michael A Black, Robyn A North, Kelly R Atkinson and Allen G Rodrigo
- Interrogating and Predicting Tolerated Sequence Diversity in Protein Folds: Application to E. elaterium Trypsin Inhibitor-II Cystine-Knot Miniprotein pp. 1-15

- Jennifer L Lahti, Adam P Silverman and Jennifer R Cochran
- Statistical Use of Argonaute Expression and RISC Assembly in microRNA Target Identification pp. 1-15

- Stephen A Stanhope, Srikumar Sengupta, Johan den Boon, Paul Ahlquist and Michael A Newton
- A Structured Model of Video Reproduces Primary Visual Cortical Organisation pp. 1-16

- Pietro Berkes, Richard E Turner and Maneesh Sahani
- Parallel Computational Subunits in Dentate Granule Cells Generate Multiple Place Fields pp. 1-16

- Balázs Ujfalussy, Tamás Kiss and Péter Érdi
Volume 5, issue 8, 2009
- Microarray Comparative Genomic Hybridisation Analysis Incorporating Genomic Organisation, and Application to Enterobacterial Plant Pathogens pp. 1-17

- Leighton Pritchard, Hui Liu, Clare Booth, Emma Douglas, Patrice François, Jacques Schrenzel, Peter E Hedley, Paul R J Birch and Ian K Toth
- Nash Equilibria in Multi-Agent Motor Interactions pp. 1-8

- Daniel A Braun, Pedro A Ortega and Daniel M Wolpert
- Evolutionary Triplet Models of Structured RNA pp. 1-20

- Robert K Bradley and Ian Holmes
- Qualia: The Geometry of Integrated Information pp. 1-24

- David Balduzzi and Giulio Tononi
- Accurate Prediction of DnaK-Peptide Binding via Homology Modelling and Experimental Data pp. 1-9

- Joost Van Durme, Sebastian Maurer-Stroh, Rodrigo Gallardo, Hannah Wilkinson, Frederic Rousseau and Joost Schymkowitz
- Detection of Functional Modes in Protein Dynamics pp. 1-13

- Jochen S Hub and Bert L de Groot
- Investigating CTL Mediated Killing with a 3D Cellular Automaton pp. 1-12

- Frederik Graw and Roland R Regoes
- FLORA: A Novel Method to Predict Protein Function from Structure in Diverse Superfamilies pp. 1-12

- Oliver C Redfern, Benoît H Dessailly, Timothy J Dallman, Ian Sillitoe and Christine A Orengo
- A Generalized Framework for Quantifying the Dynamics of EEG Event-Related Desynchronization pp. 1-10

- Steven Lemm, Klaus-Robert Müller and Gabriel Curio
- Geometric De-noising of Protein-Protein Interaction Networks pp. 1-10

- Oleksii Kuchaiev, Marija Rašajski, Desmond J Higham and Nataša Pržulj
- Computation of Conformational Coupling in Allosteric Proteins pp. 1-10

- Brian A Kidd, David Baker and Wendy E Thomas
- A Self-Organizing Algorithm for Modeling Protein Loops pp. 1-11

- Pu Liu, Fangqiang Zhu, Dmitrii N Rassokhin and Dimitris K Agrafiotis
Volume 5, issue 7, 2009
- Predicting the Distribution of Spiral Waves from Cell Properties in a Developmental-Path Model of Dictyostelium Pattern Formation pp. 1-10

- Daniel Geberth and Marc-Thorsten Hütt
- Dynamic Modeling of Vaccinating Behavior as a Function of Individual Beliefs pp. 1-10

- Flávio Codeço Coelho and Claudia T Codeço
- Identification of a Kinase Profile that Predicts Chromosome Damage Induced by Small Molecule Kinase Inhibitors pp. 1-10

- Andrew J Olaharski, Nina Gonzaludo, Hans Bitter, David Goldstein, Stephan Kirchner, Hirdesh Uppal and Kyle Kolaja
- Semantic Similarity in Biomedical Ontologies pp. 1-12

- Catia Pesquita, Daniel Faria, André O Falcão, Phillip Lord and Francisco M Couto
- Bistable Perception Modeled as Competing Stochastic Integrations at Two Levels pp. 1-9

- Guido Gigante, Maurizio Mattia, Jochen Braun and Paolo Del Giudice
Volume 5, issue 6, 2009
- The Effect of Ongoing Exposure Dynamics in Dose Response Relationships pp. 1-12

- Josep M Pujol, Joseph E Eisenberg, Charles N Haas and James S Koopman
- Integrating Statistical Predictions and Experimental Verifications for Enhancing Protein-Chemical Interaction Predictions in Virtual Screening pp. 1-11

- Nobuyoshi Nagamine, Takayuki Shirakawa, Yusuke Minato, Kentaro Torii, Hiroki Kobayashi, Masaya Imoto and Yasubumi Sakakibara
- A Probabilistic Model of RNA Conformational Space pp. 1-11

- Jes Frellsen, Ida Moltke, Martin Thiim, Kanti V Mardia, Jesper Ferkinghoff-Borg and Thomas Hamelryck
- Taking the Lag out of Jet Lag through Model-Based Schedule Design pp. 1-14

- Dennis A Dean , II, Daniel B Forger and Elizabeth B Klerman
- Maximum-Likelihood Model Averaging To Profile Clustering of Site Types across Discrete Linear Sequences pp. 1-14

- Zhang Zhang and Jeffrey P Townsend
- Exploring the Free Energy Landscape: From Dynamics to Networks and Back pp. 1-9

- Diego Prada-Gracia, Jesús Gómez-Gardeñes, Pablo Echenique and Fernando Falo
- Ten Simple Rules for Choosing between Industry and Academia pp. 1-4

- David B Searls
Volume 5, issue 5, 2009
- Smoothing of, and Parameter Estimation from, Noisy Biophysical Recordings pp. 1-16

- Quentin J M Huys and Liam Paninski
- A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family pp. 1-16

- Gregory D Friedland, Nils-Alexander Lakomek, Christian Griesinger, Jens Meiler and Tanja Kortemme
- How to Get the Most out of Your Curation Effort pp. 1-13

- Andrey Rzhetsky, Hagit Shatkay and W John Wilbur
- Fast Statistical Alignment pp. 1-15

- Robert K Bradley, Adam Roberts, Michael Smoot, Sudeep Juvekar, Jaeyoung Do, Colin Dewey, Ian Holmes and Lior Pachter
- SHRiMP: Accurate Mapping of Short Color-space Reads pp. 1-11

- Stephen M Rumble, Phil Lacroute, Adrian V Dalca, Marc Fiume, Arend Sidow and Michael Brudno
- Functional Brain Networks Develop from a “Local to Distributed” Organization pp. 1-14

- Damien A Fair, Alexander L Cohen, Jonathan D Power, Nico U F Dosenbach, Jessica A Church, Francis M Miezin, Bradley L Schlaggar and Steven E Petersen
- Prediction of Protein Binding Regions in Disordered Proteins pp. 1-18

- Bálint Mészáros, István Simon and Zsuzsanna Dosztányi
- Pairwise Maximum Entropy Models for Studying Large Biological Systems: When They Can Work and When They Can't pp. 1-18

- Yasser Roudi, Sheila Nirenberg and Peter E Latham
Volume 5, issue 4, 2009
- Divisive Gain Modulation with Dynamic Stimuli in Integrate-and-Fire Neurons pp. 1-12

- Cheng Ly and Brent Doiron
- Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples pp. 1-11

- James Robert White, Niranjan Nagarajan and Mihai Pop
- Ten Simple Rules To Combine Teaching and Research pp. 1-2

- Quentin Vicens and Philip E Bourne
- Natural Image Coding in V1: How Much Use Is Orientation Selectivity? pp. 1-16

- Jan Eichhorn, Fabian Sinz and Matthias Bethge
- Webb Miller and Trey Ideker To Receive Top International Bioinformatics Awards for 2009 from the International Society for Computational Biology pp. 1-4

- B J Morrison McKay and Clare Sansom
- Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL pp. 1-21

- Zheng Yang, Peter Májek and Ivet Bahar
- Polymorphism Data Can Reveal the Origin of Species Abundance Statistics pp. 1-6

- Yosef E Maruvka and Nadav M Shnerb
- Towards Prediction of Metabolic Products of Polyketide Synthases: An In Silico Analysis pp. 1-14

- Gitanjali Yadav, Rajesh S Gokhale and Debasisa Mohanty
Volume 5, issue 3, 2009
- Cross-Over between Discrete and Continuous Protein Structure Space: Insights into Automatic Classification and Networks of Protein Structures pp. 1-20

- Alberto Pascual-García, David Abia, Ángel R Ortiz and Ugo Bastolla
- BETASCAN: Probable β-amyloids Identified by Pairwise Probabilistic Analysis pp. 1-11

- Allen W Bryan, Matthew Menke, Lenore J Cowen, Susan L Lindquist and Bonnie Berger
- Directing Experimental Biology: A Case Study in Mitochondrial Biogenesis pp. 1-12

- Matthew A Hibbs, Chad L Myers, Curtis Huttenhower, David C Hess, Kai Li, Amy A Caudy and Olga G Troyanskaya
- A Systems Approach Uncovers Restrictions for Signal Interactions Regulating Genome-wide Responses to Nutritional Cues in Arabidopsis pp. 1-12

- Gabriel Krouk, Daniel Tranchina, Laurence Lejay, Alexis A Cruikshank, Dennis Shasha, Gloria M Coruzzi and Rodrigo A Gutiérrez
- Toward a Detailed Description of the Thermally Induced Dynamics of the Core Promoter pp. 1-10

- Boian S Alexandrov, Vladimir Gelev, Sang Wook Yoo, Alan R Bishop, Kim Ø Rasmussen and Anny Usheva
- Ras Conformational Switching: Simulating Nucleotide-Dependent Conformational Transitions with Accelerated Molecular Dynamics pp. 1-10

- Barry J Grant, Alemayehu A Gorfe and J Andrew McCammon
- Accurate Prediction of Peptide Binding Sites on Protein Surfaces pp. 1-10

- Evangelia Petsalaki, Alexander Stark, Eduardo García-Urdiales and Robert B Russell
- Understanding Pitch Perception as a Hierarchical Process with Top-Down Modulation pp. 1-15

- Emili Balaguer-Ballester, Nicholas R Clark, Martin Coath, Katrin Krumbholz and Susan L Denham
- Probabilistic Interaction Network of Evidence Algorithm and its Application to Complete Labeling of Peak Lists from Protein NMR Spectroscopy pp. 1-15

- Arash Bahrami, Amir H Assadi, John L Markley and Hamid R Eghbalnia
- Steady-State Kinetic Modeling Constrains Cellular Resting States and Dynamic Behavior pp. 1-9

- Jeremy E Purvis, Ravi Radhakrishnan and Scott L Diamond
- Broadband Criticality of Human Brain Network Synchronization pp. 1-13

- Manfred G Kitzbichler, Marie L Smith, Søren R Christensen and Ed Bullmore
- Accurate Detection of Recombinant Breakpoints in Whole-Genome Alignments pp. 1-13

- Oscar Westesson and Ian Holmes
- “I Look in Your Eyes, Honey”: Internal Face Features Induce Spatial Frequency Preference for Human Face Processing pp. 1-13

- Matthias S Keil
- Estimation of Thalamocortical and Intracortical Network Models from Joint Thalamic Single-Electrode and Cortical Laminar-Electrode Recordings in the Rat Barrel System pp. 1-24

- Patrick Blomquist, Anna Devor, Ulf G Indahl, Istvan Ulbert, Gaute T Einevoll and Anders M Dale
- T-Cell Epitope Prediction: Rescaling Can Mask Biological Variation between MHC Molecules pp. 1-7

- Aidan MacNamara, Ulrich Kadolsky, Charles R M Bangham and Becca Asquith
Volume 5, issue 2, 2009
- The Temporal Winner-Take-All Readout pp. 1-13

- Maoz Shamir
- Allosteric Communication Occurs via Networks of Tertiary and Quaternary Motions in Proteins pp. 1-14

- Michael D Daily and Jeffrey J Gray
- Statistical Dynamics of Flowing Red Blood Cells by Morphological Image Processing pp. 1-10

- John M Higgins, David T Eddington, Sangeeta N Bhatia and L Mahadevan
Volume 5, issue 1, 2009
- Efficient Network Reconstruction from Dynamical Cascades Identifies Small-World Topology of Neuronal Avalanches pp. 1-20

- Sinisa Pajevic and Dietmar Plenz
- Estimating the Location and Spatial Extent of a Covert Anthrax Release pp. 1-9

- Judith Legrand, Joseph R Egan, Ian M Hall, Simon Cauchemez, Steve Leach and Neil M Ferguson
- Partial Order Optimum Likelihood (POOL): Maximum Likelihood Prediction of Protein Active Site Residues Using 3D Structure and Sequence Properties pp. 1-15

- Wenxu Tong, Ying Wei, Leonel F Murga, Mary Jo Ondrechen and Ronald J Williams
- Action Potential Initiation in the Hodgkin-Huxley Model pp. 1-7

- Lucy J Colwell and Michael P Brenner
- Shape, Size, and Robustness: Feasible Regions in the Parameter Space of Biochemical Networks pp. 1-12

- Adel Dayarian, Madalena Chaves, Eduardo D Sontag and Anirvan M Sengupta
- Evolutionary Sequence Modeling for Discovery of Peptide Hormones pp. 1-12

- Kemal Sonmez, Naunihal T Zaveri, Ilan A Kerman, Sharon Burke, Charles R Neal, Xinmin Xie, Stanley J Watson and Lawrence Toll
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