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ORCIDPLoS 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.