Journal: PLoS Computational Biology

Volume 12, Issue 4

0 -- 0Wendy J. Adams. The Development of Audio-Visual Integration for Temporal Judgements
0 -- 0Konstantin Popov, James Komianos, Garegin A. Papoian. MEDYAN: Mechanochemical Simulations of Contraction and Polarity Alignment in Actomyosin Networks
0 -- 0Christian Diener, Georgina Garza Ramos Martínez, Daniel Moreno Blas, David A. Castillo González, Gerardo Corzo, Susana Castro-Obregon, Gabriel del Rio. Effective Design of Multifunctional Peptides by Combining Compatible Functions
0 -- 0Maryam M. Shanechi, Amy L. Orsborn, Jose M. Carmena. Robust Brain-Machine Interface Design Using Optimal Feedback Control Modeling and Adaptive Point Process Filtering
0 -- 0Andrew Wight, Doo Yang, Ilya Ioshikhes, Andrew P. Makrigiannis. Nucleosome Presence at AML-1 Binding Sites Inversely Correlates with Ly49 Expression: Revelations from an Informatics Analysis of Nucleosomes and Immune Cell Transcription Factors
0 -- 0Eric Talevich, A. Hunter Shain, Thomas Botton, Boris C. Bastian. CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing
0 -- 0Yohai Bar-Sinai, Jean-Daniel Julien, Eran Sharon, Shahaf Armon, Naomi Nakayama, Mokhtar Adda-Bedia, Arezki Boudaoud. Mechanical Stress Induces Remodeling of Vascular Networks in Growing Leaves
0 -- 0Brian Granger, Yi-Chien Chang, Yan Wang, Charles DeLisi, Daniel Segrè, Zhenjun Hu. Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0
0 -- 0Evgeni V. Nikolaev, Eduardo D. Sontag. Quorum-Sensing Synchronization of Synthetic Toggle Switches: A Design Based on Monotone Dynamical Systems Theory
0 -- 0Antonio L. C. Gomes, Harris H. Wang. The Role of Genome Accessibility in Transcription Factor Binding in Bacteria
0 -- 0Natalia Szostak, Szymon Wasik, Jacek Blazewicz. Hypercycle
0 -- 0Mark Shein-Idelson, Gilad Cohen, Eshel Ben-Jacob, Yael Hanein. Modularity Induced Gating and Delays in Neuronal Networks
0 -- 0Samuel P. C. Brand, Kat S. Rock, Matt J. Keeling. The Interaction between Vector Life History and Short Vector Life in Vector-Borne Disease Transmission and Control
0 -- 0Yilun Zhang, Tatyana O. Sharpee. A Robust Feedforward Model of the Olfactory System
0 -- 0Simeone Marino, Hannah P. Gideon, Chang-Gong, Shawn Mankad, John T. McCrone, Philana Ling Lin, Jennifer J. Linderman, JoAnne L. Flynn, Denise E. Kirschner. Computational and Empirical Studies Predict Mycobacterium tuberculosis-Specific T Cells as a Biomarker for Infection Outcome
0 -- 0Steven C. Bagley, Marina Sirota, Richard O. Chen, Atul J. Butte, Russ B. Altman. Constraints on Biological Mechanism from Disease Comorbidity Using Electronic Medical Records and Database of Genetic Variants
0 -- 0Yotam Luz, Maoz Shamir. Oscillations via Spike-Timing Dependent Plasticity in a Feed-Forward Model
0 -- 0Kendall Gillies, Stephen M. Krone, James J. Nagler, Irvin R. Schultz. A Computational Model of the Rainbow Trout Hypothalamus-Pituitary-Ovary-Liver Axis
0 -- 0Jolene Atia, Conor McCloskey, Anatoly S. Shmygol, David A. Rand, Hugo Antonius van den Berg, Andrew M. Blanks. Reconstruction of Cell Surface Densities of Ion Pumps, Exchangers, and Channels from mRNA Expression, Conductance Kinetics, Whole-Cell Calcium, and Current-Clamp Voltage Recordings, with an Application to Human Uterine Smooth Muscle Cells
0 -- 0Raul Rodriguez-Esteban. A Drug-Centric View of Drug Development: How Drugs Spread from Disease to Disease
0 -- 0Adam N. Sanborn, Ulrik R. Beierholm. Fast and Accurate Learning When Making Discrete Numerical Estimates
0 -- 0Takumi Higaki, Natsumaro Kutsuna, Kae Akita, Hisako Takigawa-Imamura, Kenji Yoshimura, Takashi Miura. A Theoretical Model of Jigsaw-Puzzle Pattern Formation by Plant Leaf Epidermal Cells
0 -- 0Phuong Dao, Damian Wójtowicz, Steevenson Nelson, David Levens, Teresa M. Przytycka. Ups and Downs of Poised RNA Polymerase II in B-Cells
0 -- 0Sara Ballouz, Jesse A. Gillis. AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression
0 -- 0Rumen Kostadinov, Carlo C. Maley, Mary K. Kuhner. Bulk Genotyping of Biopsies Can Create Spurious Evidence for Hetereogeneity in Mutation Content
0 -- 0Erida Gjini, Patricia H. Brito. Integrating Antimicrobial Therapy with Host Immunity to Fight Drug-Resistant Infections: Classical vs. Adaptive Treatment
0 -- 0Jie Wang, Shuli Xia, Brian Arand, Heng Zhu, Raghu Machiraju, Kun Huang 0001, Hongkai Ji, Jiang Qian. Single-Cell Co-expression Analysis Reveals Distinct Functional Modules, Co-regulation Mechanisms and Clinical Outcomes
0 -- 0Nick W. Ruktanonchai, Patrick De Leenheer, Andrew J. Tatem, Victor A. Alegana, T. Trevor Caughlin, Elisabeth Zu Erbach-Schoenberg, Christopher Lourenço, Corrine W. Ruktanonchai, David L. Smith. Identifying Malaria Transmission Foci for Elimination Using Human Mobility Data
0 -- 0Casimir Emako, Charlène Gayrard, Axel Buguin, Luís Neves de Almeida, Nicolas Vauchelet. Traveling Pulses for a Two-Species Chemotaxis Model
0 -- 0Jonas Kubilius, Stefania Bracci, Hans P. Op de Beeck. Deep Neural Networks as a Computational Model for Human Shape Sensitivity
0 -- 0Nicolas Muller, Matthieu Piel, Vincent Calvez, Raphael Voituriez, Joana Gonçalves-Sá, Chin-Lin Guo, Xingyu Jiang, Andrew Murray, Nicolas Meunier. A Predictive Model for Yeast Cell Polarization in Pheromone Gradients
0 -- 0Paola Malerba, Giri P. Krishnan, Jean-Marc Fellous, Maxim Bazhenov. Hippocampal CA1 Ripples as Inhibitory Transients
0 -- 0Jonas Schluter, Armin P. Schoech, Kevin R. Foster, Sara Mitri. The Evolution of Quorum Sensing as a Mechanism to Infer Kinship
0 -- 0Matias I. Maturana, Nicholas V. Apollo, Alex E. Hadjinicolaou, David J. Garrett, Shaun L. Cloherty, Tatiana Kameneva, David B. Grayden, Michael R. Ibbotson, Hamish Meffin. A Simple and Accurate Model to Predict Responses to Multi-electrode Stimulation in the Retina
0 -- 0Philipp J. Albert, Ulrich S. Schwarz. Dynamics of Cell Ensembles on Adhesive Micropatterns: Bridging the Gap between Single Cell Spreading and Collective Cell Migration
0 -- 0Enrico Sandro Colizzi, Paulien Hogeweg. Parasites Sustain and Enhance RNA-Like Replicators through Spatial Self-Organisation
0 -- 0Maulik K. Nariya, Johnny Israeli, Jack J. Shi, Eric J. Deeds. Mathematical Model for Length Control by the Timing of Substrate Switching in the Type III Secretion System
0 -- 0Kashif Mahfooz, Mahendra Singh, Robert Renden, John F. Wesseling. A Well-Defined Readily Releasable Pool with Fixed Capacity for Storing Vesicles at Calyx of Held
0 -- 0Andrew G. McDonald, Keith F. Tipton, Gavin P. Davey. A Knowledge-Based System for Display and Prediction of O-Glycosylation Network Behaviour in Response to Enzyme Knockouts
0 -- 0Robin N. Thompson, Christopher A. Gilligan, Nik J. Cunniffe. Detecting Presymptomatic Infection Is Necessary to Forecast Major Epidemics in the Earliest Stages of Infectious Disease Outbreaks
0 -- 0Victor Trevino, Alberto Cassese, Zsuzsanna Nagy, Xiaodong Zhuang, John M. Herbert, Philipp Antzack, Kim Clarke, Nicholas Davies, Ayesha Rahman, Moray J. Campbell, Michele Guindani, Roy Bicknell, Marina Vannucci, Francesco Falciani. A Network Biology Approach Identifies Molecular Cross-Talk between Normal Prostate Epithelial and Prostate Carcinoma Cells
0 -- 0Daniel C. Kirouac, Jinyan Du, Johanna Lahdenranta, Matthew D. Onsum, Ulrik B. Nielsen, Birgit Schoeberl, Charlotte F. McDonagh. HER2+ Cancer Cell Dependence on PI3K vs. MAPK Signaling Axes Is Determined by Expression of EGFR, ERBB3 and CDKN1B
0 -- 0Daniela Börnigen, Svitlana Tyekucheva, Xiaodong Wang, Jennifer R. Rider, Gwo-Shu Lee, Lorelei A. Mucci, Christopher Sweeney, Curtis Huttenhower. Computational Reconstruction of NFκB Pathway Interaction Mechanisms during Prostate Cancer
0 -- 0Robert Kalescky, Hongyu Zhou, Jin Liu, Peng Tao. Rigid Residue Scan Simulations Systematically Reveal Residue Entropic Roles in Protein Allostery
0 -- 0Nurcan Tuncbag, Sara J. C. Gosline, Amanda J. Kedaigle, Anthony R. Soltis, Anthony Gitter, Ernest Fraenkel. Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package
0 -- 0Ali Farshchiansadegh, Alejandro Melendez-Calderon, Rajiv Ranganathan, Todd D. Murphey, Ferdinando A. Mussa-Ivaldi. Sensory Agreement Guides Kinetic Energy Optimization of Arm Movements during Object Manipulation
0 -- 0Amit Upadhyay, Aaron D. Fleetwood, Ogun Adebali, Robert D. Finn, Igor B. Zhulin. Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes
0 -- 0Timothy S. Carpenter, Felice C. Lightstone. An Electrostatic Funnel in the GABA-Binding Pathway
0 -- 0Carles Foguet, Silvia Marin, Vitaly A. Selivanov, Eric Fanchon, Wai-Nang Paul Lee, Joan J. Guinovart, Pedro de Atauri, Marta Cascante. HepatoDyn: A Dynamic Model of Hepatocyte Metabolism That Integrates 13C Isotopomer Data
0 -- 0Francesco Donnarumma, Domenico Maisto, Giovanni Pezzulo. Problem Solving as Probabilistic Inference with Subgoaling: Explaining Human Successes and Pitfalls in the Tower of Hanoi
0 -- 0David N. Quan, Chen-Yu Tsao, Hsuan-Chen Wu, William E. Bentley. Quorum Sensing Desynchronization Leads to Bimodality and Patterned Behaviors
0 -- 0Tatiana Maximova, Ryan Moffatt, Buyong Ma, Ruth Nussinov, Amarda Shehu. Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics
0 -- 0Nafise Erfanian Saeedi, Peter J. Blamey, Anthony N. Burkitt, David B. Grayden. Learning Pitch with STDP: A Computational Model of Place and Temporal Pitch Perception Using Spiking Neural Networks
0 -- 0Ingrid Paine, Arnaud Chauviere, John Landua, Amulya Sreekumar, Vittorio Cristini, Jeffrey M. Rosen, Michael T. Lewis. A Geometrically-Constrained Mathematical Model of Mammary Gland Ductal Elongation Reveals Novel Cellular Dynamics within the Terminal End Bud
0 -- 0Stephen Gang Wu, Yuxuan Wang, Wu Jiang, Tolutola Oyetunde, Ruilian Yao, Xuehong Zhang, Kazuyuki Shimizu, Yinjie J. Tang, Forrest Sheng Bao. Rapid Prediction of Bacterial Heterotrophic Fluxomics Using Machine Learning and Constraint Programming
0 -- 0Melanie Laßek, Jens Weingarten, Martin Wegner, Benjamin F. Mueller, Marion Rohmer, Dominic Baeumlisberger, Tabiwang N. Arrey, Meike Hick, Jörg Ackermann 0001, Amparo Acker-Palmer, Ina Koch, Ulrike Müller, Michael Karas, Walter Volknandt. APP Is a Context-Sensitive Regulator of the Hippocampal Presynaptic Active Zone
0 -- 0Lorenzo Asti, Guido Uguzzoni, Paolo Marcatili, Andrea Pagnani. Maximum-Entropy Models of Sequenced Immune Repertoires Predict Antigen-Antibody Affinity
0 -- 0Eben Kenah, Tom Britton, M. Elizabeth Halloran, Ira M. Longini Jr.. Molecular Infectious Disease Epidemiology: Survival Analysis and Algorithms Linking Phylogenies to Transmission Trees
0 -- 0Yael Steuerman, Irit Gat-Viks. Exploiting Gene-Expression Deconvolution to Probe the Genetics of the Immune System