PLOS Computational Biology

2005 - 2022

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Volume 3, issue 12, 2007

Social Interactions in Myxobacterial Swarming pp. 1-13

Yilin Wu, Yi Jiang, Dale Kaiser and Mark Alber

Operating Regimes of Signaling Cycles: Statics, Dynamics, and Noise Filtering pp. 1-11

Carlos Gomez-Uribe, George C Verghese and Leonid A Mirny

The Long and Thorny Road to Publication in Quality Journals pp. 1-1

Thomas C Erren

The Modular Organization of Domain Structures: Insights into Protein–Protein Binding pp. 1-10

Antonio del Sol and Pablo Carbonell

Getting Started in Probabilistic Graphical Models pp. 1-5

Edoardo M Airoldi

Volume 3, issue 11, 2007

Meta-Analysis of Drosophila Circadian Microarray Studies Identifies a Novel Set of Rhythmically Expressed Genes pp. 1-1

Kevin P Keegan, Suraj Pradhan, Ji-Ping Wang and Ravi Allada

Predicting Gene Expression from Sequence: A Reexamination pp. 1-7

Yuan Yuan, Lei Guo, Lei Shen and Jun S Liu

From Inverse Problems in Mathematical Physiology to Quantitative Differential Diagnoses pp. 1-15

Sven Zenker, Jonathan Rubin and Gilles Clermont

MORPH: Probabilistic Alignment Combined with Hidden Markov Models of cis-Regulatory Modules pp. 1-15

Saurabh Sinha and Xin He

CATHEDRAL: A Fast and Effective Algorithm to Predict Folds and Domain Boundaries from Multidomain Protein Structures pp. 1-15

Oliver C Redfern, Andrew Harrison, Tim Dallman, Frances M G Pearl and Christine A Orengo

A Dynamical Systems Hypothesis of Schizophrenia pp. 1-11

Marco Loh, Edmund T Rolls and Gustavo Deco

Where Have All the Interactions Gone? Estimating the Coverage of Two-Hybrid Protein Interaction Maps pp. 1-20

Hailiang Huang, Bruno M Jedynak and Joel S Bader

Computational Biology in Cuba: An Opportunity to Promote Science in a Developing Country pp. 1-5

Tirso Pons, Luis A Montero and Juan P Febles

Ten Simple Rules for Graduate Students pp. 1-2

Jenny Gu and Philip E Bourne

Self-organizing Mechanism for Development of Space-filling Neuronal Dendrites pp. 1-12

Kaoru Sugimura, Kohei Shimono, Tadashi Uemura and Atsushi Mochizuki

In Silico Elucidation of the Molecular Mechanism Defining the Adverse Effect of Selective Estrogen Receptor Modulators pp. 1-9

Lei Xie, Jian Wang and Philip E Bourne

Stochastic Noise and Synchronisation during Dictyostelium Aggregation Make cAMP Oscillations Robust pp. 1-9

Jongrae Kim, Pat Heslop-Harrison, Ian Postlethwaite and Declan G Bates

A Nucleosome-Guided Map of Transcription Factor Binding Sites in Yeast pp. 1-10

Leelavati Narlikar, Raluca Gordân and Alexander J Hartemink

Direct Inference of SNP Heterozygosity Rates and Resolution of LOH Detection pp. 1-10

Xiaohong Li, Steven G Self, Patricia C Galipeau, Thomas G Paulson and Brian J Reid

Volume 3, issue 10, 2007

Construction, Visualisation, and Clustering of Transcription Networks from Microarray Expression Data pp. 1-11

Tom C Freeman, Leon Goldovsky, Markus Brosch, Stijn van Dongen, Pierre Mazière, Russell J Grocock, Shiri Freilich, Janet Thornton and Anton J Enright

Landscape as a Model: The Importance of Geometry pp. 1-14

E Penelope Holland, James N Aegerter, Calvin Dytham and Graham C Smith

Brightness and Darkness as Perceptual Dimensions pp. 1-10

Tony Vladusich, Marcel P Lucassen and Frans W Cornelissen

A Statistical Framework for Modeling HLA-Dependent T Cell Response Data pp. 1-8

Jennifer Listgarten, Nicole Frahm, Carl Kadie, Christian Brander and David Heckerman

Universally Sloppy Parameter Sensitivities in Systems Biology Models pp. 1-8

Ryan N Gutenkunst, Joshua J Waterfall, Fergal P Casey, Kevin S Brown, Christopher R Myers and James P Sethna

Heat Shock Response in CHO Mammalian Cells Is Controlled by a Nonlinear Stochastic Process pp. 1-12

Ovidiu Lipan, Jean-Marc Navenot, Zixuan Wang, Lei Huang and Stephen C Peiper

Volume 3, issue 9, 2007

Bistability and Oscillations in the Huang-Ferrell Model of MAPK Signaling pp. 1-8

Liang Qiao, Robert B Nachbar, Ioannis G Kevrekidis and Stanislav Y Shvartsman

Reply to “Ten Simple Rules for Getting Published” pp. 1-2

Eric Grosch

From Pathways Databases to Network Models of Switching Behavior pp. 1-5

Baltazar D Aguda and Andrew B Goryachev

Structural Reorganisation and Potential Toxicity of Oligomeric Species Formed during the Assembly of Amyloid Fibrils pp. 1-12

Mookyung Cheon, Iksoo Chang, Sandipan Mohanty, Leila M Luheshi, Christopher M Dobson, Michele Vendruscolo and Giorgio Favrin

Signal Propagation in Proteins and Relation to Equilibrium Fluctuations pp. 1-11

Chakra Chennubhotla and Ivet Bahar

Structure-Templated Predictions of Novel Protein Interactions from Sequence Information pp. 1-7

Doron Betel, Kevin E Breitkreuz, Ruth Isserlin, Danielle Dewar-Darch, Mike Tyers and Christopher W V Hogue

Volume 3, issue 8, 2007

Functional Representation of Enzymes by Specific Peptides pp. 1-10

Vered Kunik, Yasmine Meroz, Zach Solan, Ben Sandbank, Uri Weingart, Eytan Ruppin and David Horn

Recent Evolutions of Multiple Sequence Alignment Algorithms pp. 1-4

Cédric Notredame

Slowness and Sparseness Lead to Place, Head-Direction, and Spatial-View Cells pp. 1-18

Mathias Franzius, Henning Sprekeler and Laurenz Wiskott

An Information-Theoretic Characterization of the Optimal Gradient Sensing Response of Cells pp. 1-9

Burton W Andrews and Pablo A Iglesias

PERIOD–TIMELESS Interval Timer May Require an Additional Feedback Loop pp. 1-9

Robert S Kuczenski, Kevin C Hong, Jordi García-Ojalvo and Kelvin H Lee

Automated Discovery of Functional Generality of Human Gene Expression Programs pp. 1-15

Georg K Gerber, Robin D Dowell, Tommi S Jaakkola and David K Gifford

Mechanisms of Firing Patterns in Fast-Spiking Cortical Interneurons pp. 1-15

David Golomb, Karnit Donner, Liron Shacham, Dan Shlosberg, Yael Amitai and David Hansel

A Numerical Approach to Ion Channel Modelling Using Whole-Cell Voltage-Clamp Recordings and a Genetic Algorithm pp. 1-15

Meron Gurkiewicz and Alon Korngreen

A Primer on Learning in Bayesian Networks for Computational Biology pp. 1-8

Chris J Needham, James R Bradford, Andrew J Bulpitt and David R Westhead

Image-Based Modeling Reveals Dynamic Redistribution of DNA Damage into Nuclear Sub-Domains pp. 1-12

Sylvain V Costes, Artem Ponomarev, James L Chen, David Nguyen, Francis A Cucinotta and Mary Helen Barcellos-Hoff

Automated Protein Subfamily Identification and Classification pp. 1-13

Duncan P Brown, Nandini Krishnamurthy and Kimmen Sjölander

Elucidating the Altered Transcriptional Programs in Breast Cancer using Independent Component Analysis pp. 1-16

Andrew E Teschendorff, Michel Journée, Pierre A Absil, Rodolphe Sepulchre and Carlos Caldas

Design of Multi-Specificity in Protein Interfaces pp. 1-14

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

Sergey Kryazhimskiy, Ulf Dieckmann, Simon A Levin and Jonathan Dushoff

Volume 3, issue 7, 2007

Sarcomere Lattice Geometry Influences Cooperative Myosin Binding in Muscle pp. 1-17

Bertrand C W Tanner, Thomas L Daniel and Michael Regnier

Computationally Derived Points of Fragility of a Human Cascade Are Consistent with Current Therapeutic Strategies pp. 1-13

Deyan Luan, Michael Zai and Jeffrey D Varner

Prediction of Gene Expression in Embryonic Structures of Drosophila melanogaster pp. 1-13

Anastasia A Samsonova, Mahesan Niranjan, Steven Russell and Alvis Brazma

Chemotaxis Receptor Complexes: From Signaling to Assembly pp. 1-9

Robert G Endres, Joseph J Falke and Ned S Wingreen

Novel Algorithms Reveal Streptococcal Transcriptomes and Clues about Undefined Genes pp. 1-18

Patricia A Ryan, Brian W Kirk, Chad W Euler, Raymond Schuch and Vincent A Fischetti

Optimal Timing and Duration of Induction Therapy for HIV-1 Infection pp. 1-18

Marcel E Curlin, Shyamala Iyer and John E Mittler

Not All Scale-Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Evolution pp. 1-12

Fereydoun Hormozdiari, Petra Berenbrink, Nataša Pržulj and S Cenk Sahinalp

Natively Unstructured Loops Differ from Other Loops pp. 1-12

Avner Schlessinger, Jinfeng Liu and Burkhard Rost

Protein–Protein Interaction Hotspots Carved into Sequences pp. 1-8

Yanay Ofran and Burkhard Rost

Quantitative Analysis of Cell Nucleus Organisation pp. 1-8

Carol Shiels, Niall M Adams, Suhail A Islam, David A Stephens and Paul S Freemont

Introduction to Computational Proteomics pp. 1-10

Jacques Colinge and Keiryn L Bennett

Volume 3, issue 6, 2007

Digital Signal Processing Reveals Circadian Baseline Oscillation in Majority of Mammalian Genes pp. 1-7

Andrey A Ptitsyn, Sanjin Zvonic and Jeffrey M Gimble

Machine Learning and Its Applications to Biology pp. 1-11

Adi L Tarca, Vincent J Carey, Xue-wen Chen, Roberto Romero and Sorin Drăghici

The International Society for Computational Biology 10th Anniversary pp. 1-3

Lawrence Hunter, Russ B Altman and Philip E Bourne

A Mass Conserved Reaction–Diffusion System Captures Properties of Cell Polarity pp. 1-15

Mikiya Otsuji, Shuji Ishihara, Carl Co, Kozo Kaibuchi, Atsushi Mochizuki and Shinya Kuroda

Slowness: An Objective for Spike-Timing–Dependent Plasticity? pp. 1-13

Henning Sprekeler, Christian Michaelis and Laurenz Wiskott

Hierarchical Processing of Auditory Objects in Humans pp. 1-9

Sukhbinder Kumar, Klaas E Stephan, Jason D Warren, Karl J Friston and Timothy D Griffiths

A View from the Dark Side pp. 1-4

David B Searls

Flexible and Accurate Detection of Genomic Copy-Number Changes from aCGH pp. 1-8

Oscar M Rueda and Ramón Díaz-Uriarte

Volume 3, issue 5, 2007

Ten Simple Rules for a Good Poster Presentation pp. 1-2

Thomas C Erren and Philip E Bourne

Predictive Modeling of Signaling Crosstalk during C. elegans Vulval Development pp. 1-12

Jasmin Fisher, Nir Piterman, Alex Hajnal and Thomas A Henzinger

ISMB/ECCB 2007: The Premier Conference on Computational Biology pp. 1-4

Thomas Lengauer, B J Morrison McKay and Burkhard Rost

Cooperative Gating and Spatial Organization of Membrane Proteins through Elastic Interactions pp. 1-10

Tristan Ursell, Kerwyn Casey Huang, Eric Peterson and Rob Phillips

“Simple Rules for Editors”? Here is One Rule to Tackle Neglected Problems of Publishing pp. 1-1

Thomas C Erren and Michael Erren

Integrated Mechanisms of Anticipation and Rate-of-Change Computations in Cortical Circuits pp. 1-13

Gabriel D Puccini, Maria V Sanchez-Vives and Albert Compte

The Human Genomic Melting Map pp. 1-13

Fang Liu, Eivind Tøstesen, Jostein K Sundet, Tor-Kristian Jenssen, Christoph Bock, Geir Ivar Jerstad, William G Thilly and Eivind Hovig

Binding Site Graphs: A New Graph Theoretical Framework for Prediction of Transcription Factor Binding Sites pp. 1-11

Timothy E Reddy, Charles DeLisi and Boris E Shakhnovich

Volume 3, issue 4, 2007

Patterns of Mesenchymal Condensation in a Multiscale, Discrete Stochastic Model pp. 1-11

Scott Christley, Mark S Alber and Stuart A Newman

Ten Simple Rules for Making Good Oral Presentations pp. 1-2

Philip E Bourne

Cell Size at S Phase Initiation: An Emergent Property of the G1/S Network pp. 1-18

Matteo Barberis, Edda Klipp, Marco Vanoni and Lilia Alberghina

Deciphering Protein–Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners pp. 1-7

Benjamin A Shoemaker and Anna R Panchenko

Volume 3, issue 3, 2007

Measures of Clade Confidence Do Not Correlate with Accuracy of Phylogenetic Trees pp. 1-9

Barry G Hall and Stephen J Salipante

Ten Simple Rules for a Successful Collaboration pp. 1-2

Quentin Vicens and Philip E Bourne

Global Discriminative Learning for Higher-Accuracy Computational Gene Prediction pp. 1-10

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

Oliver Sander, Tobias Sing, Ingolf Sommer, Andrew J Low, Peter K Cheung, P Richard Harrigan, Thomas Lengauer and Francisco S Domingues

DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies pp. 1-14

Shaun Mahony, Philip E Auron and Panayiotis V Benos

Dose Response Relationship in Anti-Stress Gene Regulatory Networks pp. 1-19

Qiang Zhang and Melvin E Andersen

Query-Dependent Banding (QDB) for Faster RNA Similarity Searches pp. 1-15

Eric P Nawrocki and Sean R Eddy

Potential Energy Landscape and Robustness of a Gene Regulatory Network: Toggle Switch pp. 1-13

Keun-Young Kim and Jin Wang

Volume 3, issue 2, 2007

Functional Impact of Missense Variants in BRCA1 Predicted by Supervised Learning pp. 1-14

Rachel Karchin, Alvaro N A Monteiro, Sean V Tavtigian, Marcelo A Carvalho and Andrej Sali

From Bytes to Bedside: Data Integration and Computational Biology for Translational Cancer Research pp. 1-11

Jomol P Mathew, Barry S Taylor, Gary D Bader, Saiju Pyarajan, Marco Antoniotti, Arul M Chinnaiyan, Chris Sander, Steven J Burakoff and Bud Mishra

Repressor Dimerization in the Zebrafish Somitogenesis Clock pp. 1-11

Olivier Cinquin

Robustness Can Evolve Gradually in Complex Regulatory Gene Networks with Varying Topology pp. 1-10

Stefano Ciliberti, Olivier C Martin and Andreas Wagner

Volume 3, issue 1, 2007

In Remembrance: Reinhart Heinrich 1946–2006 pp. 1-1

Thomas Höfer

Moving Education Forward pp. 1-2

Fran Lewitter

Computational Aspects of Feedback in Neural Circuits pp. 1-20

Wolfgang Maass, Prashant Joshi and Eduardo D Sontag

Nitric Oxide Regulates Input Specificity of Long-Term Depression and Context Dependence of Cerebellar Learning pp. 1-13

Hideaki Ogasawara, Tomokazu Doi, Kenji Doya and Mitsuo Kawato