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PLoS Computational Biology, Volume 11
Volume 11, Number 1, January 2015
- Aidan Budd, Holger Dinkel
, Manuel Corpas
, Jonathan C. Fuller
, Laura Rubinat
, Damien P. Devos
, Pierre H. Khoueiry
, Konrad U. Förstner
, Fotis Georgatos, Francis Rowland
, Malvika Sharan
, Janos X. Binder, Tom Grace, Karyn Traphagen, Adam Gristwood, Natasha T. Wood:
Ten Simple Rules for Organizing an Unconference. - Ruth Nussinov
:
Advancements and Challenges in Computational Biology.
- Peter D. Karp, Bonnie Berger, Diane E. Kovats, Thomas Lengauer
, Michal Linial
, Pardis Sabeti, Winston Hide
, Burkhard Rost
:
ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus.
- Eberhard O. Voit, Harald A. Martens, Stig W. Omholt:
150 Years of the Mass Action Law.
- Alboukadel Kassambara, Thierry Rème, Michel Jourdan, Thierry Fest, Dirk Hose, Karin Tarte, Bernard Klein:
GenomicScape: An Easy-to-Use Web Tool for Gene Expression Data Analysis. Application to Investigate the Molecular Events in the Differentiation of B Cells into Plasma Cells. - Ueli Rutishauser
, Jean-Jacques E. Slotine, Rodney J. Douglas:
Computation in Dynamically Bounded Asymmetric Systems. - Helen L. Ramsden, Gülsen Sürmeli
, Steven G. McDonagh, Matthew F. Nolan
:
Laminar and Dorsoventral Molecular Organization of the Medial Entorhinal Cortex Revealed by Large-scale Anatomical Analysis of Gene Expression. - Loic Matthey, Paul M. Bays
, Peter Dayan:
A Probabilistic Palimpsest Model of Visual Short-term Memory. - Erick Andres Perez-Alday, Michael A. Colman
, Philip Langley, Timothy D. Butters, Jonathan Higham
, Antony J. Workman, Jules C. Hancox, Henggui Zhang:
A New Algorithm to Diagnose Atrial Ectopic Origin from Multi Lead ECG Systems - Insights from 3D Virtual Human Atria and Torso. - Daeyong Jin, Hyunju Lee
:
A Computational Approach to Identifying Gene-microRNA Modules in Cancer. - Massimo Lai, Denis Brun, Stuart J. Edelstein, Nicolas Le Novère:
Modulation of Calmodulin Lobes by Different Targets: An Allosteric Model with Hemiconcerted Conformational Transitions. - Diana Stefan, Corinne Pinel, Stéphane Pinhal, Eugenio Cinquemani, Johannes Geiselmann
, Hidde de Jong
:
Inference of Quantitative Models of Bacterial Promoters from Time-Series Reporter Gene Data. - Michael Fauth, Florentin Wörgötter, Christian Tetzlaff:
The Formation of Multi-synaptic Connections by the Interaction of Synaptic and Structural Plasticity and Their Functional Consequences. - Nigel Stepp, Dietmar Plenz, Narayan Srinivasa:
Synaptic Plasticity Enables Adaptive Self-Tuning Critical Networks. - Emilie Montastier
, Nathalie Villa-Vialaneix, Sylvie Caspar-Bauguil
, Petr Hlavaty, Eva Tvrzicka
, Ignacio Gonzalez, Wim H. M. Saris, Dominique Langin
, Marie Kunesova, Nathalie Viguerie
:
System Model Network for Adipose Tissue Signatures Related to Weight Changes in Response to Calorie Restriction and Subsequent Weight Maintenance. - Jamie T. Griffin:
The Interaction between Seasonality and Pulsed Interventions against Malaria in Their Effects on the Reproduction Number. - Frédéric Boudon
, Jérôme Chopard, Olivier Ali
, Benjamin Gilles, Olivier Hamant
, Arezki Boudaoud
, Jan Traas, Christophe Godin:
A Computational Framework for 3D Mechanical Modeling of Plant Morphogenesis with Cellular Resolution. - Martin Rückl, Ian Parker, Jonathan S. Marchant
, Chamakuri Nagaiah, Friedrich W. Johenning, Sten Rüdiger:
Modulation of Elementary Calcium Release Mediates a Transition from Puffs to Waves in an IP3R Cluster Model. - Davod Alizadehrad, Timothy Krüger
, Markus Engstler, Holger Stark:
Simulating the Complex Cell Design of Trypanosoma brucei and Its Motility. - Ioannis Andrianakis, Ian R. Vernon, Nicky McCreesh
, Trevelyan J. McKinley, Jeremy E. Oakley, Rebecca N. Nsubuga, Michael Goldstein, Richard G. White
:
Bayesian History Matching of Complex Infectious Disease Models Using Emulation: A Tutorial and a Case Study on HIV in Uganda. - Regina S. Salvat, Andrew S. Parker, Yoonjoo Choi
, Chris Bailey-Kellogg, Karl E. Griswold:
Mapping the Pareto Optimal Design Space for a Functionally Deimmunized Biotherapeutic Candidate. - J. Matthew Mahoney, Jaclyn N. Taroni, Viktor Martyanov, Tammara A. Wood, Casey S. Greene
, Patricia A. Pioli, Monique E. Hinchcliff, Michael L. Whitfield:
Systems Level Analysis of Systemic Sclerosis Shows a Network of Immune and Profibrotic Pathways Connected with Genetic Polymorphisms. - Andreas Wilke, Jared Bischof, Travis Harrison, Tom Brettin, Mark D'Souza, Wolfgang Gerlach, Hunter Matthews, Tobias Paczian, Jared Wilkening, Elizabeth M. Glass, Narayan Desai, Folker Meyer:
A RESTful API for Accessing Microbial Community Data for MG-RAST. - Raimon Sabate, Frederic Rousseau, Joost Schymkowitz
, Salvador Ventura
:
What Makes a Protein Sequence a Prion? - Lu Chen, Lei Du-Cuny, Sylvestor Moses, Sabrina Dumas, Zuohe Song, Abdol Hossein Rezaeian, Hui-Kuan Lin, Emmanuelle J. Meuillet, Shuxing Zhang:
Novel Inhibitors Induce Large Conformational Changes of GAB1 Pleckstrin Homology Domain and Kill Breast Cancer Cells. - Markus Niklasson, Alexandra Ahlner, Cecilia Andresen
, Joseph A. Marsh
, Patrik Lundström:
Fast and Accurate Resonance Assignment of Small-to-Large Proteins by Combining Automated and Manual Approaches. - Andrei N. Lupas, Hongbo Zhu, Mateusz Korycinski:
The Thalidomide-Binding Domain of Cereblon Defines the CULT Domain Family and Is a New Member of the β-Tent Fold. - Eduard Porta-Pardo
, Adam Godzik
:
Analysis of Individual Protein Regions Provides Novel Insights on Cancer Pharmacogenomics. - Thomas Sakoparnig, Patrick Fried, Niko Beerenwinkel:
Identification of Constrained Cancer Driver Genes Based on Mutation Timing. - Elizabeth N. Davison, Kimberly J. Schlesinger, Danielle S. Bassett, Mary-Ellen Lynall
, Michael B. Miller, Scott T. Grafton, Jean M. Carlson:
Brain Network Adaptability across Task States. - Benjamin Simmonds, Maurice J. Chacron
:
Activation of Parallel Fiber Feedback by Spatially Diffuse Stimuli Reduces Signal and Noise Correlations via Independent Mechanisms in a Cerebellum-Like Structure. - Sadra Sadeh
, Stefan Rotter:
Orientation Selectivity in Inhibition-Dominated Networks of Spiking Neurons: Effect of Single Neuron Properties and Network Dynamics.
Volume 11, Number 2, February 2015
- Thomas C. Erren, Tracy E. Slanger, J. Valérie Groß, Philip E. Bourne, Paul Cullen:
Ten Simple Rules for Lifelong Learning, According to Hamming. - Thomas Lengauer
, Ruth Nussinov
:
How to Write a Presubmission Inquiry. - Effy Vayena, Marcel Salathé, Lawrence C. Madoff, John S. Brownstein:
Ethical Challenges of Big Data in Public Health. - Philip E. Bourne:
Confronting the Ethical Challenges of Big Data in Public Health.
- Aidan Budd, Manuel Corpas
, Michelle D. Brazas
, Jonathan C. Fuller, Jeremy Goecks, Nicola J. Mulder
, Magali Michaut
, B. F. Francis Ouellette
, Aleksandra Pawlik, Niklas Blomberg
:
A Quick Guide for Building a Successful Bioinformatics Community.
- David G. García Münzer, Margaritis Kostoglou
, Michael C. Georgiadis, Efstratios N. Pistikopoulos
, Athanasios Mantalaris:
Cyclin and DNA Distributed Cell Cycle Model for GS-NS0 Cells. - Tiberiu Tesileanu
, Lucy J. Colwell, Stanislas Leibler:
Protein Sectors: Statistical Coupling Analysis versus Conservation. - Saheed Imam, Daniel R. Noguera
, Timothy J. Donohue
:
An Integrated Approach to Reconstructing Genome-Scale Transcriptional Regulatory Networks. - J. Harry Caufield
, Marco Abreu, Christopher Wimble, Peter Uetz
:
Protein Complexes in Bacteria. - Mei Yan Lee, Scott L. Diamond:
A Human Platelet Calcium Calculator Trained by Pairwise Agonist Scanning. - Daniel M. Keenan, Amy W. Quinkert
, Donald W. Pfaff:
Stochastic Modeling of Mouse Motor Activity under Deep Brain Stimulation: The Extraction of Arousal Information. - Renaud Jolivet
, Jay S. Coggan
, Igor Allaman
, Pierre J. Magistretti
:
Multi-timescale Modeling of Activity-Dependent Metabolic Coupling in the Neuron-Glia-Vasculature Ensemble. - Benjamin J. Binder, Joanna F. Sundstrom
, Jennifer M. Gardner, Vladimir Jiranek, Stephen G. Oliver:
Quantifying Two-Dimensional Filamentous and Invasive Growth Spatial Patterns in Yeast Colonies. - Benjamin Allen
, Christine Sample, Yulia Dementieva, Ruben C. Medeiros, Christopher Paoletti, Martin A. Nowak:
The Molecular Clock of Neutral Evolution Can Be Accelerated or Slowed by Asymmetric Spatial Structure. - Benjamin A. Dunn, Maria Mørreaunet, Yasser Roudi
:
Correlations and Functional Connections in a Population of Grid Cells. - Jagannath Swaminathan, Alexander A. Boulgakov
, Edward M. Marcotte
:
A Theoretical Justification for Single Molecule Peptide Sequencing. - Ying Li, Guang Li, Benjamin Görling, Burkhard Luy
, Jiulin Du, Jun Yan
:
Integrative Analysis of Circadian Transcriptome and Metabolic Network Reveals the Role of De Novo Purine Synthesis in Circadian Control of Cell Cycle. - Yonatan Schweitzer, Michael M. Kozlov:
Membrane-Mediated Interaction between Strongly Anisotropic Protein Scaffolds. - David K. Johnson
, John Karanicolas:
Selectivity by Small-Molecule Inhibitors of Protein Interactions Can Be Driven by Protein Surface Fluctuations. - Martina Kutmon
, Martijn P. van Iersel
, Anwesha Bohler, Thomas Kelder, Nuno Nunes, Alexander R. Pico
, Chris T. A. Evelo:
PathVisio 3: An Extendable Pathway Analysis Toolbox. - Renske M. A. Vroomans, Paulien Hogeweg, Kirsten H. W. J. ten Tusscher:
Segment-Specific Adhesion as a Driver of Convergent Extension. - Christian Meisel
, Andreas Klaus
, Christian Kuehn
, Dietmar Plenz:
Critical Slowing Down Governs the Transition to Neuron Spiking. - Jorge M. Pacheco
, Vítor V. Vasconcelos
, Francisco C. Santos
, Brian Skyrms:
Co-evolutionary Dynamics of Collective Action with Signaling for a Quorum. - Andrew J. K. Conlan, Ellen Brooks-Pollock
, Trevelyan J. McKinley, Andrew P. Mitchell, Gareth J. Jones, Martin Vordermeier, James L. N. Wood:
Potential Benefits of Cattle Vaccination as a Supplementary Control for Bovine Tuberculosis. - Vladimir Potapov
, Jenifer B. Kaplan, Amy E. Keating
:
Data-Driven Prediction and Design of bZIP Coiled-Coil Interactions. - Elisa M. Tartaglia
, Nicolas Brunel, Gianluigi Mongillo
:
Modulation of Network Excitability by Persistent Activity: How Working Memory Affects the Response to Incoming Stimuli. - Johannes Eckstein
, Nikolaus Berndt
, Hermann-Georg Holzhütter
:
Computer Simulations Suggest a Key Role of Membranous Nanodomains in Biliary Lipid Secretion. - Renaud Bastien, Stéphane Douady, Bruno Moulia:
A Unified Model of Shoot Tropism in Plants: Photo-, Gravi- and Propio-ception. - Guangyou Duan, Dirk Walther
:
The Roles of Post-translational Modifications in the Context of Protein Interaction Networks. - Edward J. Banigan
, Tajie H. Harris
, David A. Christian, Christopher A. Hunter, Andrea J. Liu
:
Heterogeneous CD8+ T Cell Migration in the Lymph Node in the Absence of Inflammation Revealed by Quantitative Migration Analysis. - Ishutesh Jain, Mandar M. Inamdar, Ranjith Padinhateeri:
Statistical Mechanics Provides Novel Insights into Microtubule Stability and Mechanism of Shrinkage. - Adrián Ponce-Alvarez
, Gustavo Deco
, Patric Hagmann, Gian Luca Romani, Dante Mantini
, Maurizio Corbetta
:
Resting-State Temporal Synchronization Networks Emerge from Connectivity Topology and Heterogeneity. - Laura R. González-Ramírez, Omar J. Ahmed, Sydney S. Cash, C. Eugene Wayne, Mark A. Kramer:
A Biologically Constrained, Mathematical Model of Cortical Wave Propagation Preceding Seizure Termination. - Eric Bonnet, Laurence Calzone
, Tom Michoel
:
Integrative Multi-omics Module Network Inference with Lemon-Tree. - Eric Lowet, Mark J. Roberts
, Avgis Hadjipapas
, Alina Peter, Jan van der Eerden, Peter De Weerd:
Input-Dependent Frequency Modulation of Cortical Gamma Oscillations Shapes Spatial Synchronization and Enables Phase Coding. - Ignacia Echeverria, Garegin A. Papoian
:
DNA Exit Ramps Are Revealed in the Binding Landscapes Obtained from Simulations in Helical Coordinates. - Xavier Didelot
, Daniel J. Wilson
:
ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes. - Daniel Malagarriga, Alessandro E. P. Villa
, Jordi García-Ojalvo
, Antonio J. Pons Rivero
:
Mesoscopic Segregation of Excitation and Inhibition in a Brain Network Model. - Kasper Jensen, Yueqiong Ni, Gianni Panagiotou, Irene Kouskoumvekaki
:
Developing a Molecular Roadmap of Drug-Food Interactions. - Yoonji Lee
, Sun Choi
, Changbong Hyeon
:
Communication over the Network of Binary Switches Regulates the Activation of A2A Adenosine Receptor. - Hanna Julienne
, Benjamin Audit
, Alain Arneodo
:
Embryonic Stem Cell Specific "Master" Replication Origins at the Heart of the Loss of Pluripotency. - Claude Gérard, John J. Tyson, Damien Coudreuse
, Béla Novák:
Cell Cycle Control by a Minimal Cdk Network. - Bence Ferdinandy
, Enys Mones
, Tamás Vicsek, Viktor Müller
:
HIV Competition Dynamics over Sexual Networks: First Comer Advantage Conserves Founder Effects. - Paul Thatcher Edlefsen, Morgane Rolland, Tomer Hertz
, Sodsai Tovanabutra, Andrew J. Gartland, Allan C. deCamp, Craig A. Magaret, Hasan Ahmed, Raphael Gottardo
, Michal Juraska, Connor McCoy, Brendan B. Larsen, Eric Sanders-Buell, Chris Carrico, Sergey Menis, Meera Bose, Miguel A. Arroyo, Robert J. O'Connell, Sorachai Nitayaphan, Punnee Pitisuttithum, Jaranit Kaewkungwal
, Supachai Rerks-Ngarm, Merlin L. Robb, Tatsiana Kirys, Ivelin Georgiev, Peter D. Kwong, Konrad Scheffler
, Sergei L. Kosakovsky Pond, Jonathan M. Carlson, Nelson Michael, William R. Schief, James I. Mullins, Jerome H. Kim, Peter B. Gilbert:
: Comprehensive Sieve Analysis of Breakthrough HIV-1 Sequences in the RV144 Vaccine Efficacy Trial. - Hinrich Arnoldt, Shuwen Chang
, Sven Jahnke, Birk Urmersbach, Holger Taschenberger
, Marc Timme
:
When Less Is More: Non-monotonic Spike Sequence Processing in Neurons. - Julien Jorda, Yu Liu, Thomas A. Bobik, Todd O. Yeates
:
Exploring Bacterial Organelle Interactomes: A Model of the Protein-Protein Interaction Network in the Pdu Microcompartment.
Volume 11, Number 3, March 2015
- Marco D. Visser, Sean M. McMahon, Cory Merow, Philip M. Dixon, Sydne Record
, Eelke Jongejans
:
Speeding Up Ecological and Evolutionary Computations in R; Essentials of High Performance Computing for Biologists. - Tomás Helikar
, Christine E. Cutucache, Lauren M. Dahlquist, Tyler A. Herek, Joshua J. Larson, Jim A. Rogers:
Integrating Interactive Computational Modeling in Biology Curricula.
- Dimitri Yatsenko, Kresimir Josic, Alexander S. Ecker
, Emmanouil Froudarakis
, R. James Cotton
, Andreas S. Tolias:
Improved Estimation and Interpretation of Correlations in Neural Circuits. - Jérémie Sibille
, Khanh Dao Duc
, David Holcman
, Nathalie Rouach
:
The Neuroglial Potassium Cycle during Neurotransmission: Role of Kir4.1 Channels. - Yu-Chen Lo, Silvia Senese, Chien-Ming Li, Qiyang Hu, Yong Huang, Robert Damoiseaux, Jorge Z. Torres
:
Large-Scale Chemical Similarity Networks for Target Profiling of Compounds Identified in Cell-Based Chemical Screens. - Davide Provasi, Mustafa Burak Boz, Jennifer M. Johnston, Marta Filizola
:
Preferred Supramolecular Organization and Dimer Interfaces of Opioid Receptors from Simulated Self-Association. - Maxim Volgushev
, Vladimir Ilin
, Ian H. Stevenson
:
Identifying and Tracking Simulated Synaptic Inputs from Neuronal Firing: Insights from In Vitro Experiments. - Adrian M. Haith, David M. Huberdeau
, John W. Krakauer:
Hedging Your Bets: Intermediate Movements as Optimal Behavior in the Context of an Incomplete Decision. - Deborah A. Weighill, Daniel A. Jacobson:
3-way Networks: Application of Hypergraphs for Modelling Increased Complexity in Comparative Genomics. - Alistair M. Senior, Michael A. Charleston
, Mathieu Lihoreau, Jérôme Buhl, David Raubenheimer
, Stephen J. Simpson
:
Evolving Nutritional Strategies in the Presence of Competition: A Geometric Agent-Based Model. - Miriam C. Klein-Flügge
, Steven W. Kennerley
, Ana C. Saraiva, Will D. Penny
, Sven Bestmann
:
Behavioral Modeling of Human Choices Reveals Dissociable Effects of Physical Effort and Temporal Delay on Reward Devaluation. - Carson C. Chow, Kelsey K. Finn, Geoffery B. Storchan, Xinping Lu, Xiaoyan Sheng, S. Stoney Simons Jr.:
Kinetically-Defined Component Actions in Gene Repression. - Alejandro Torres-Sánchez
, Jesús Gómez-Gardeñes
, Fernando Falo
:
An Integrative Approach for Modeling and Simulation of Heterocyst Pattern Formation in Cyanobacteria Filaments. - Francisco Martínez-Jiménez
, Marc A. Martí-Renom
:
Ligand-Target Prediction by Structural Network Biology Using nAnnoLyze. - Bruno B. Averbeck:
Theory of Choice in Bandit, Information Sampling and Foraging Tasks. - Loes C. J. van Dam
, Marc O. Ernst
:
Mapping Shape to Visuomotor Mapping: Learning and Generalisation of Sensorimotor Behaviour Based on Contextual Information. - Davide Albanese
, Carlotta De Filippo
, Duccio Cavalieri
, Claudio Donati
:
Explaining Diversity in Metagenomic Datasets by Phylogenetic-Based Feature Weighting. - Luca Giuggioli
, Thomas J. McKetterick, Marc Holderied
:
Delayed Response and Biosonar Perception Explain Movement Coordination in Trawling Bats. - Amanda Miguel, Jen Hsin, Tianyun Liu, Grace W. Tang, Russ B. Altman
, Kerwyn Casey Huang:
Variations in the Binding Pocket of an Inhibitor of the Bacterial Division Protein FtsZ across Genotypes and Species. - Vassilios N. Christopoulos, James Bonaiuto
, Richard A. Andersen:
A Biologically Plausible Computational Theory for Value Integration and Action Selection in Decisions with Competing Alternatives. - Tamar Friedlander
, Avraham E. Mayo
, Tsvi Tlusty
, Uri Alon:
Evolution of Bow-Tie Architectures in Biology. - Giles W. Story, Ivo Vlaev, Peter Dayan, Ben Seymour
, Ara Darzi, Raymond J. Dolan
:
Anticipation and Choice Heuristics in the Dynamic Consumption of Pain Relief. - Adrien Wohrer, Christian K. Machens
:
On the Number of Neurons and Time Scale of Integration Underlying the Formation of Percepts in the Brain. - Alan L. Hutchison
, Mark Maienschein-Cline, Andrew H. Chiang, S. M. Ali Tabei, Herman Gudjonson, Neil Bahroos, Ravi Allada, Aaron R. Dinner:
Improved Statistical Methods Enable Greater Sensitivity in Rhythm Detection for Genome-Wide Data. - Fiete Haack, Heiko Lemcke, Roland Ewald, Tareck Rharass
, Adelinde M. Uhrmacher:
Spatio-temporal Model of Endogenous ROS and Raft-Dependent WNT/Beta-Catenin Signaling Driving Cell Fate Commitment in Human Neural Progenitor Cells. - Christopher R. S. Banerji, Simone Severini, Carlos Caldas
, Andrew E. Teschendorff:
Intra-Tumour Signalling Entropy Determines Clinical Outcome in Breast and Lung Cancer. - Omar Al Hammal
, David Alonso
, Rampal S. Etienne
, Stephen J. Cornell:
When Can Species Abundance Data Reveal Non-neutrality? - James A. Geraets
, Eric C. Dykeman, Peter G. Stockley
, Neil A. Ranson
, Reidun Twarock
:
Asymmetric Genome Organization in an RNA Virus Revealed via Graph-Theoretical Analysis of Tomographic Data. - Fan Yang, Evangelia Petsalaki
, Thomas Rolland
, David E. Hill, Marc Vidal, Frederick P. Roth
:
Protein Domain-Level Landscape of Cancer-Type-Specific Somatic Mutations. - Cheng Lv
, Xiaoguang Li, Fangting Li, Tiejun Li:
Energy Landscape Reveals That the Budding Yeast Cell Cycle Is a Robust and Adaptive Multi-stage Process. - Feng Fu, Martin A. Nowak, Sebastian Bonhoeffer
:
Spatial Heterogeneity in Drug Concentrations Can Facilitate the Emergence of Resistance to Cancer Therapy. - Thomas Obadia, Romain Silhol
, Lulla Opatowski
, Laura Temime
, Judith Legrand, Anne C. M. Thiébaut, Jean-Louis Herrmann
, Eric Fleury, Didier Guillemot
, Pierre-Yves Boëlle
:
Detailed Contact Data and the Dissemination of Staphylococcus aureus in Hospitals. - Kristen Fortney, Joshua Griesman, Max Kotlyar, Chiara Pastrello, Marc Angeli
, Ming-Sound Tsao
, Igor Jurisica:
Prioritizing Therapeutics for Lung Cancer: An Integrative Meta-analysis of Cancer Gene Signatures and Chemogenomic Data.