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PLOS Computational Biology

2005 - 2025

From Public Library of Science
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Volume 3, issue 12, 2007

Getting Started in Probabilistic Graphical Models pp. 1-5 Downloads
Edoardo M Airoldi

Volume 3, issue 11, 2007

Where Have All the Interactions Gone? Estimating the Coverage of Two-Hybrid Protein Interaction Maps pp. 1-20 Downloads
Hailiang Huang, Bruno M Jedynak and Joel S Bader
Meta-Analysis of Drosophila Circadian Microarray Studies Identifies a Novel Set of Rhythmically Expressed Genes pp. 1-1 Downloads
Kevin P Keegan, Suraj Pradhan, Ji-Ping Wang and Ravi Allada
Self-organizing Mechanism for Development of Space-filling Neuronal Dendrites pp. 1-12 Downloads
Kaoru Sugimura, Kohei Shimono, Tadashi Uemura and Atsushi Mochizuki
A Nucleosome-Guided Map of Transcription Factor Binding Sites in Yeast pp. 1-10 Downloads
Leelavati Narlikar, Raluca Gordân and Alexander J Hartemink
Direct Inference of SNP Heterozygosity Rates and Resolution of LOH Detection pp. 1-10 Downloads
Xiaohong Li, Steven G Self, Patricia C Galipeau, Thomas G Paulson and Brian J Reid
Predicting Gene Expression from Sequence: A Reexamination pp. 1-7 Downloads
Yuan Yuan, Lei Guo, Lei Shen and Jun S Liu
Ten Simple Rules for Graduate Students pp. 1-2 Downloads
Jenny Gu and Philip E Bourne
From Inverse Problems in Mathematical Physiology to Quantitative Differential Diagnoses pp. 1-15 Downloads
Sven Zenker, Jonathan Rubin and Gilles Clermont
MORPH: Probabilistic Alignment Combined with Hidden Markov Models of cis-Regulatory Modules pp. 1-15 Downloads
Saurabh Sinha and Xin He

Volume 3, issue 10, 2007

Construction, Visualisation, and Clustering of Transcription Networks from Microarray Expression Data pp. 1-11 Downloads
Tom C Freeman, Leon Goldovsky, Markus Brosch, Stijn van Dongen, Pierre Mazière, Russell J Grocock, Shiri Freilich, Janet Thornton and Anton J Enright
Brightness and Darkness as Perceptual Dimensions pp. 1-10 Downloads
Tony Vladusich, Marcel P Lucassen and Frans W Cornelissen
Heat Shock Response in CHO Mammalian Cells Is Controlled by a Nonlinear Stochastic Process pp. 1-12 Downloads
Ovidiu Lipan, Jean-Marc Navenot, Zixuan Wang, Lei Huang and Stephen C Peiper
A Statistical Framework for Modeling HLA-Dependent T Cell Response Data pp. 1-8 Downloads
Jennifer Listgarten, Nicole Frahm, Carl Kadie, Christian Brander and David Heckerman
Universally Sloppy Parameter Sensitivities in Systems Biology Models pp. 1-8 Downloads
Ryan N Gutenkunst, Joshua J Waterfall, Fergal P Casey, Kevin S Brown, Christopher R Myers and James P Sethna
Landscape as a Model: The Importance of Geometry pp. 1-14 Downloads
E Penelope Holland, James N Aegerter, Calvin Dytham and Graham C Smith

Volume 3, issue 9, 2007

Bistability and Oscillations in the Huang-Ferrell Model of MAPK Signaling pp. 1-8 Downloads
Liang Qiao, Robert B Nachbar, Ioannis G Kevrekidis and Stanislav Y Shvartsman
Signal Propagation in Proteins and Relation to Equilibrium Fluctuations pp. 1-11 Downloads
Chakra Chennubhotla and Ivet Bahar
Structural Reorganisation and Potential Toxicity of Oligomeric Species Formed during the Assembly of Amyloid Fibrils pp. 1-12 Downloads
Mookyung Cheon, Iksoo Chang, Sandipan Mohanty, Leila M Luheshi, Christopher M Dobson, Michele Vendruscolo and Giorgio Favrin
Structure-Templated Predictions of Novel Protein Interactions from Sequence Information pp. 1-7 Downloads
Doron Betel, Kevin E Breitkreuz, Ruth Isserlin, Danielle Dewar-Darch, Mike Tyers and Christopher W V Hogue
From Pathways Databases to Network Models of Switching Behavior pp. 1-5 Downloads
Baltazar D Aguda and Andrew B Goryachev

Volume 3, issue 8, 2007

Automated Discovery of Functional Generality of Human Gene Expression Programs pp. 1-15 Downloads
Georg K Gerber, Robin D Dowell, Tommi S Jaakkola and David K Gifford
A Numerical Approach to Ion Channel Modelling Using Whole-Cell Voltage-Clamp Recordings and a Genetic Algorithm pp. 1-15 Downloads
Meron Gurkiewicz and Alon Korngreen
An Information-Theoretic Characterization of the Optimal Gradient Sensing Response of Cells pp. 1-9 Downloads
Burton W Andrews and Pablo A Iglesias
PERIOD–TIMELESS Interval Timer May Require an Additional Feedback Loop pp. 1-9 Downloads
Robert S Kuczenski, Kevin C Hong, Jordi García-Ojalvo and Kelvin H Lee
Automated Protein Subfamily Identification and Classification pp. 1-13 Downloads
Duncan P Brown, Nandini Krishnamurthy and Kimmen Sjölander
Recent Evolutions of Multiple Sequence Alignment Algorithms pp. 1-4 Downloads
Cédric Notredame
Elucidating the Altered Transcriptional Programs in Breast Cancer using Independent Component Analysis pp. 1-16 Downloads
Andrew E Teschendorff, Michel Journée, Pierre A Absil, Rodolphe Sepulchre and Carlos Caldas
Image-Based Modeling Reveals Dynamic Redistribution of DNA Damage into Nuclear Sub-Domains pp. 1-12 Downloads
Sylvain V Costes, Artem Ponomarev, James L Chen, David Nguyen, Francis A Cucinotta and Mary Helen Barcellos-Hoff
Functional Representation of Enzymes by Specific Peptides pp. 1-10 Downloads
Vered Kunik, Yasmine Meroz, Zach Solan, Ben Sandbank, Uri Weingart, Eytan Ruppin and David Horn
A Primer on Learning in Bayesian Networks for Computational Biology pp. 1-8 Downloads
Chris J Needham, James R Bradford, Andrew J Bulpitt and David R Westhead
Design of Multi-Specificity in Protein Interfaces pp. 1-14 Downloads
Elisabeth L Humphris and Tanja Kortemme
On State-Space Reduction in Multi-Strain Pathogen Models, with an Application to Antigenic Drift in Influenza A pp. 1-1 Downloads
Sergey Kryazhimskiy, Ulf Dieckmann, Simon A Levin and Jonathan Dushoff
Slowness and Sparseness Lead to Place, Head-Direction, and Spatial-View Cells pp. 1-18 Downloads
Mathias Franzius, Henning Sprekeler and Laurenz Wiskott

Volume 3, issue 7, 2007

Protein–Protein Interaction Hotspots Carved into Sequences pp. 1-8 Downloads
Yanay Ofran and Burkhard Rost
Novel Algorithms Reveal Streptococcal Transcriptomes and Clues about Undefined Genes pp. 1-18 Downloads
Patricia A Ryan, Brian W Kirk, Chad W Euler, Raymond Schuch and Vincent A Fischetti
Prediction of Gene Expression in Embryonic Structures of Drosophila melanogaster pp. 1-13 Downloads
Anastasia A Samsonova, Mahesan Niranjan, Steven Russell and Alvis Brazma
Chemotaxis Receptor Complexes: From Signaling to Assembly pp. 1-9 Downloads
Robert G Endres, Joseph J Falke and Ned S Wingreen
Introduction to Computational Proteomics pp. 1-10 Downloads
Jacques Colinge and Keiryn L Bennett
Natively Unstructured Loops Differ from Other Loops pp. 1-12 Downloads
Avner Schlessinger, Jinfeng Liu and Burkhard Rost

Volume 3, issue 6, 2007

Flexible and Accurate Detection of Genomic Copy-Number Changes from aCGH pp. 1-8 Downloads
Oscar M Rueda and Ramón Díaz-Uriarte
The International Society for Computational Biology 10th Anniversary pp. 1-3 Downloads
Lawrence Hunter, Russ B Altman and Philip E Bourne
Machine Learning and Its Applications to Biology pp. 1-11 Downloads
Adi L Tarca, Vincent J Carey, Xue-wen Chen, Roberto Romero and Sorin Drăghici
A View from the Dark Side pp. 1-4 Downloads
David B Searls
Slowness: An Objective for Spike-Timing–Dependent Plasticity? pp. 1-13 Downloads
Henning Sprekeler, Christian Michaelis and Laurenz Wiskott
Hierarchical Processing of Auditory Objects in Humans pp. 1-9 Downloads
Sukhbinder Kumar, Klaas E Stephan, Jason D Warren, Karl J Friston and Timothy D Griffiths
Digital Signal Processing Reveals Circadian Baseline Oscillation in Majority of Mammalian Genes pp. 1-7 Downloads
Andrey A Ptitsyn, Sanjin Zvonic and Jeffrey M Gimble

Volume 3, issue 5, 2007

Cooperative Gating and Spatial Organization of Membrane Proteins through Elastic Interactions pp. 1-10 Downloads
Tristan Ursell, Kerwyn Casey Huang, Eric Peterson and Rob Phillips
Binding Site Graphs: A New Graph Theoretical Framework for Prediction of Transcription Factor Binding Sites pp. 1-11 Downloads
Timothy E Reddy, Charles DeLisi and Boris E Shakhnovich
Ten Simple Rules for a Good Poster Presentation pp. 1-2 Downloads
Thomas C Erren and Philip E Bourne
Integrated Mechanisms of Anticipation and Rate-of-Change Computations in Cortical Circuits pp. 1-13 Downloads
Gabriel D Puccini, Maria V Sanchez-Vives and Albert Compte
The Human Genomic Melting Map pp. 1-13 Downloads
Fang Liu, Eivind Tøstesen, Jostein K Sundet, Tor-Kristian Jenssen, Christoph Bock, Geir Ivar Jerstad, William G Thilly and Eivind Hovig
“Simple Rules for Editors”? Here is One Rule to Tackle Neglected Problems of Publishing pp. 1-1 Downloads
Thomas C Erren and Michael Erren

Volume 3, issue 4, 2007

Deciphering Protein–Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners pp. 1-7 Downloads
Benjamin A Shoemaker and Anna R Panchenko
Ten Simple Rules for Making Good Oral Presentations pp. 1-2 Downloads
Philip E Bourne

Volume 3, issue 3, 2007

DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies pp. 1-14 Downloads
Shaun Mahony, Philip E Auron and Panayiotis V Benos
Global Discriminative Learning for Higher-Accuracy Computational Gene Prediction pp. 1-10 Downloads
Axel Bernal, Koby Crammer, Artemis Hatzigeorgiou and Fernando Pereira
Structural Descriptors of gp120 V3 Loop for the Prediction of HIV-1 Coreceptor Usage pp. 1-10 Downloads
Oliver Sander, Tobias Sing, Ingolf Sommer, Andrew J Low, Peter K Cheung, P Richard Harrigan, Thomas Lengauer and Francisco S Domingues
Query-Dependent Banding (QDB) for Faster RNA Similarity Searches pp. 1-15 Downloads
Eric P Nawrocki and Sean R Eddy
Measures of Clade Confidence Do Not Correlate with Accuracy of Phylogenetic Trees pp. 1-9 Downloads
Barry G Hall and Stephen J Salipante
Potential Energy Landscape and Robustness of a Gene Regulatory Network: Toggle Switch pp. 1-13 Downloads
Keun-Young Kim and Jin Wang

Volume 3, issue 2, 2007

Robustness Can Evolve Gradually in Complex Regulatory Gene Networks with Varying Topology pp. 1-10 Downloads
Stefano Ciliberti, Olivier C Martin and Andreas Wagner
Functional Impact of Missense Variants in BRCA1 Predicted by Supervised Learning pp. 1-14 Downloads
Rachel Karchin, Alvaro N A Monteiro, Sean V Tavtigian, Marcelo A Carvalho and Andrej Sali

Volume 3, issue 1, 2007

Moving Education Forward pp. 1-2 Downloads
Fran Lewitter
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