Journal: PLoS Computational Biology

Volume 13, Issue 2

0 -- 0Angela F. Harper, Janelle B. Leuthaeuser, Patricia C. Babbitt, John H. Morris, Thomas E. Ferrin, Leslie B. Poole, Jacquelyn S. Fetrow. An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins
0 -- 0Zachary S. L. Foster, Thomas J. Sharpton, Niklaus J. Grünwald. Metacoder: An R package for visualization and manipulation of community taxonomic diversity data
0 -- 0David Henriques, Alejandro Fernández Villaverde, Miguel Rocha, Julio Saez-Rodriguez, Julio R. Banga. Data-driven reverse engineering of signaling pathways using ensembles of dynamic models
0 -- 0Stephanie Evans, Kieran Alden, Lourdes Cucurull-Sanchez, Christopher Larminie, Mark Coles, Marika C. Kullberg, Jon Timmis. ASPASIA: A toolkit for evaluating the effects of biological interventions on SBML model behaviour
0 -- 0Didac Santesmasses, Marco Mariotti, Roderic Guigó. Computational identification of the selenocysteine tRNA (tRNASec) in genomes
0 -- 0Guillaume Lajoie, Nedialko I. Krouchev, John F. Kalaska, Adrienne L. Fairhall, Eberhard E. Fetz. Correlation-based model of artificially induced plasticity in motor cortex by a bidirectional brain-computer interface
0 -- 0Luca Ponzoni, Giulia Rossetti, Luca Maggi, Alejandro Giorgetti, Paolo Carloni, Cristian Micheletti. Unifying view of mechanical and functional hotspots across class A GPCRs
0 -- 0Jannis Schuecker, Maximilian Schmidt, Sacha J. van Albada, Markus Diesmann, Moritz Helias. Fundamental Activity Constraints Lead to Specific Interpretations of the Connectome
0 -- 0Miguel Won, Manuel Marques-Pita, Carlota Louro, Joana Gonçalves-Sá. Early and Real-Time Detection of Seasonal Influenza Onset
0 -- 0Yen-Fu Chen, Hsiu-Chuan Lin, Kai-Neng Chuang, Chih-Hsu Lin, Hsueh-Chi S. Yen, Chen-Hsiang Yeang. A quantitative model for the rate-limiting process of UGA alternative assignments to stop and selenocysteine codons
0 -- 0Yihao Zhang, Krithika Abiraman, He Li, David M. Pierce, Anastasios V. Tzingounis, George Lykotrafitis. Modeling of the axon membrane skeleton structure and implications for its mechanical properties
0 -- 0Pierre Millard, Kieran Smallbone, Pedro Mendes. Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli
0 -- 0Jarred R. Mondoñedo, Béla Suki. Predicting Structure-Function Relations and Survival following Surgical and Bronchoscopic Lung Volume Reduction Treatment of Emphysema
0 -- 0Jan Ewald, Martin Bartl, Thomas Dandekar, Christoph Kaleta. Optimality principles reveal a complex interplay of intermediate toxicity and kinetic efficiency in the regulation of prokaryotic metabolism
0 -- 0Olga K. Kamneva. Genome composition and phylogeny of microbes predict their co-occurrence in the environment
0 -- 0Vinal V. Lakhani, Timothy C. Elston. Testing the limits of gradient sensing
0 -- 0Naomi V. Bradbury, William J. M. Probert, Katriona Shea, Michael C. Runge, Christopher Fonnesbeck, Matt J. Keeling, Matthew J. Ferrari, Michael J. Tildesley. Quantifying the Value of Perfect Information in Emergency Vaccination Campaigns
0 -- 0John F. Magnotti, Michael S. Beauchamp. A Causal Inference Model Explains Perception of the McGurk Effect and Other Incongruent Audiovisual Speech
0 -- 0Julia V. Ponomarenko, Romina Garrido, Roderic Guigó. Ten Simple Rules on How to Organize a Scientific Retreat
0 -- 0Vivek Charu, Scott Zeger, Julia R. Gog, Ottar N. Bjørnstad, Stephen Kissler, Lone Simonsen, Bryan T. Grenfell, Cécile Viboud. Human mobility and the spatial transmission of influenza in the United States
0 -- 0Arno Klein, Satrajit S. Ghosh, Forrest Sheng Bao, Joachim Giard, Yrjö Häme, Eliezer Stavsky, Noah Lee, Brian Rossa, Martin Reuter 0001, Elias Chaibub Neto, Anisha Keshavan. Mindboggling morphometry of human brains
0 -- 0Tracey M. Filzen, Peter S. Kutchukian, Jeffrey D. Hermes, Jing Li, Matthew Tudor. Representing high throughput expression profiles via perturbation barcodes reveals compound targets
0 -- 0Qian Qin, Jianxing Feng. Imputation for transcription factor binding predictions based on deep learning
0 -- 0Johannes Burge, Priyank Jaini. Accuracy Maximization Analysis for Sensory-Perceptual Tasks: Computational Improvements, Filter Robustness, and Coding Advantages for Scaled Additive Noise
0 -- 0James M. Osborne, Alexander G. Fletcher, Joe Pitt-Francis, Philip K. Maini, David J. Gavaghan. Comparing individual-based approaches to modelling the self-organization of multicellular tissues
0 -- 0Sean M. Gibbons, Sean M. Kearney, Chris S. Smillie, Eric J. Alm. Two dynamic regimes in the human gut microbiome
0 -- 0Miguel A. Fortuna, Luis Zaman, Charles Ofria, Andreas Wagner. The genotype-phenotype map of an evolving digital organism
0 -- 0Jung-Min Han, Akihiko Tanimura, Vivien Kirk, James Sneyd. A mathematical model of calcium dynamics in HSY cells
0 -- 0Dong Ping Yang, Hai-Jun Zhou, Changsong Zhou. Co-emergence of multi-scale cortical activities of irregular firing, oscillations and avalanches achieves cost-efficient information capacity
0 -- 0Hojjat Bazzazi, Aleksander S. Popel. Computational investigation of sphingosine kinase 1 (SphK1) and calcium dependent ERK1/2 activation downstream of VEGFR2 in endothelial cells
0 -- 0William Poole, Kalle Leinonen, Ilya Shmulevich, Theo A. Knijnenburg, Brady Bernard. Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression
0 -- 0Mark P. Little, Jolyon H. Hendry. Mathematical models of tissue stem and transit target cell divisions and the risk of radiation- or smoking-associated cancer
0 -- 0Alexander Miguel Monzon, Diego J. Zea, María Silvina Fornasari, Tadeo E. Saldaño, Sebastian Fernandez Alberti, Silvio C. E. Tosatto, Gustavo D. Parisi. Conformational diversity analysis reveals three functional mechanisms in proteins
0 -- 0Alice R. Walker, Pavel Silvestrov, Tina A. Müller, Robert Podolsky, Gregory Dyson, Robert P. Hausinger, Gerardo Andrés Cisneros. ALKBH7 Variant Related to Prostate Cancer Exhibits Altered Substrate Binding
0 -- 0Mark Roper, Chrisantha Fernando, Lars Chittka. Insect Bio-inspired Neural Network Provides New Evidence on How Simple Feature Detectors Can Enable Complex Visual Generalization and Stimulus Location Invariance in the Miniature Brain of Honeybees
0 -- 0Daniel Magee, Marc A. Suchard, Matthew Scotch. Bayesian phylogeography of influenza A/H3N2 for the 2014-15 season in the United States using three frameworks of ancestral state reconstruction
0 -- 0Berta Verd, Anton Crombach, Johannes Jaeger. Dynamic Maternal Gradients Control Timing and Shift-Rates for Drosophila Gap Gene Expression
0 -- 0Miguel Fribourg, Diomedes E. Logothetis, Javier González-Maeso, Stuart C. Sealfon, Belén Galocha-Iragüen, Fernando Las-Heras Andrés, Vladimir Brezina. Elucidation of molecular kinetic schemes from macroscopic traces using system identification
0 -- 0Christoph Thiel, Henrik Cordes, Lorenzo Fabbri, Hélène Eloise Aschmann, Vanessa Baier, Ines Smit, Francis Atkinson, Lars Mathias Blank, Lars Kuepfer. A Comparative Analysis of Drug-Induced Hepatotoxicity in Clinically Relevant Situations
0 -- 0Dyoni M. de Oliveira, Marcos S. Buckeridge, Wanderley Dantas dos Santos. Ten Simple Rules for Developing a Successful Research Proposal in Brazil
0 -- 0Julia Chifman, Seda Arat, Zhiyong Deng, Erica Lemler, James C. Pino, Leonard A. Harris, Michael A. Kochen, Carlos F. Lopez, Steven A. Akman, Frank M. Torti, Suzy V. Torti, Reinhard C. Laubenbacher. Activated Oncogenic Pathway Modifies Iron Network in Breast Epithelial Cells: A Dynamic Modeling Perspective
0 -- 0Franziska Oschmann, Konstantin Mergenthaler, Evelyn Jungnickel, Klaus Obermayer. Spatial separation of two different pathways accounting for the generation of calcium signals in astrocytes
0 -- 0Franca Schmid, Philbert S. Tsai, David Kleinfeld, Patrick Jenny, Bruno Weber. Depth-dependent flow and pressure characteristics in cortical microvascular networks
0 -- 0Sophie K. Kay, Heather A. Harrington, Sarah Shepherd, Keith Brennan, Trevor Dale, James M. Osborne, David J. Gavaghan, Helen M. Byrne. The role of the Hes1 crosstalk hub in Notch-Wnt interactions of the intestinal crypt
0 -- 0Jerome M. Karp, Samuel Sparks, David Cowburn. Effects of FGFR2 kinase activation loop dynamics on catalytic activity
0 -- 0Felipe Gerhard, Moritz Deger, Wilson Truccolo. On the stability and dynamics of stochastic spiking neuron models: Nonlinear Hawkes process and point process GLMs
0 -- 0Dongjun Chung, Hang J. Kim, Hongyu Zhao. graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture
0 -- 0István Bartha, Paul J. Mclaren, Chanson J. Brumme, P. Richard Harrigan, Amalio Telenti, Jacques Fellay. Estimating the Respective Contributions of Human and Viral Genetic Variation to HIV Control