Journal: PLoS Computational Biology

Volume 14, Issue 4

0 -- 0Benjamin Schott, Manuel Traub, Cornelia Schlagenhauf, Masanari Takamiya, Thomas Antritter, Andreas Bartschat, Katharina Löffler, Denis Blessing, Jens C. Otte, Andrei Kobitski, G. Ulrich Nienhaus, Uwe Strähle, Ralf Mikut, Johannes Stegmaier. EmbryoMiner: A new framework for interactive knowledge discovery in large-scale cell tracking data of developing embryos
0 -- 0William Marshall, Larissa Albantakis, Giulio Tononi. Black-boxing and cause-effect power
0 -- 0Falk Lieder, Amitai Shenhav, Sebastian Musslick, Thomas L. Griffiths. Rational metareasoning and the plasticity of cognitive control
0 -- 0Nicola De Maio, Colin J. Worby, Daniel J. Wilson, Nicole Stoesser. Bayesian reconstruction of transmission within outbreaks using genomic variants
0 -- 0Itziar Irurzun-Arana, Alvaro Janda, Sergio Ardanza-Trevijano, Iñaki F. Trocóniz. Optimal dynamic control approach in a multi-objective therapeutic scenario: Application to drug delivery in the treatment of prostate cancer
0 -- 0Sneha Mitra, Anushua Biswas, Leelavati Narlikar. DIVERSITY in binding, regulation, and evolution revealed from high-throughput ChIP
0 -- 0Michael F. Bonner, Russell A. Epstein. Computational mechanisms underlying cortical responses to the affordance properties of visual scenes
0 -- 0Guillaume Drion, Julie Dethier, Alessio Franci, Rodolphe Sepulchre. Switchable slow cellular conductances determine robustness and tunability of network states
0 -- 0Jana Wäldchen, Michael Rzanny, Marco Seeland, Patrick Mäder. Automated plant species identification - Trends and future directions
0 -- 0Jian-Geng Chiou, Samuel A. Ramirez, Timothy C. Elston, Thomas P. Witelski, David G. Schaeffer, Daniel J. Lew. Principles that govern competition or co-existence in Rho-GTPase driven polarization
0 -- 0Annie M. Westerlund, Lucie Delemotte. Effect of Ca2+ on the promiscuous target-protein binding of calmodulin
0 -- 0Reuben M. Buckley, R. Daniel Kortschak, David L. Adelson. Divergent genome evolution caused by regional variation in DNA gain and loss between human and mouse
0 -- 0Travers Ching, Xun Zhu, Lana X. Garmire. Cox-nnet: An artificial neural network method for prognosis prediction of high-throughput omics data
0 -- 0Mark Reppell, John Novembre. Using pseudoalignment and base quality to accurately quantify microbial community composition
0 -- 0Fatemeh Khatami, Markus Wöhr, Heather L. Read, Monty A. Escabí. Origins of scale invariance in vocalization sequences and speech
0 -- 0Bronac Flanagan, Liam McDaid, John J. Wade, KongFatt Wong-Lin, Jim Harkin. A computational study of astrocytic glutamate influence on post-synaptic neuronal excitability
0 -- 0J. Swaroop Guntupalli, Feilong Ma, James V. Haxby. A computational model of shared fine-scale structure in the human connectome
0 -- 0Stefan Sellman, Kimberly Tsao, Michael J. Tildesley, Peter Brommesson, Colleen Webb, Uno Wennergren, Matt J. Keeling, Tom Lindström. Need for speed: An optimized gridding approach for spatially explicit disease simulations
0 -- 0Martin Weigert, Kaushikaram Subramanian, Sebastian T. Bundschuh, Eugene W. Myers, Moritz Kreysing. Biobeam - Multiplexed wave-optical simulations of light-sheet microscopy
0 -- 0Loup Rimbaud, Julien Papaïx, Jean-François Rey, Luke G. Barrett, Peter H. Thrall. Assessing the durability and efficiency of landscape-based strategies to deploy plant resistance to pathogens
0 -- 0Wen-Han Yu, Peng Zhao, Monia Draghi, Claudia Arevalo, Christina B. Karsten, Todd J. Suscovich, Bronwyn Gunn, Hendrik Streeck, Abraham L. Brass, Michael Tiemeyer, Michael S. Seaman, John R. Mascola, Lance Wells, Douglas A. Lauffenburger, Galit Alter. Exploiting glycan topography for computational design of Env glycoprotein antigenicity
0 -- 0Robin Mills, Hanno Hildenbrandt, Graham K. Taylor, Charlotte K. Hemelrijk. Physics-based simulations of aerial attacks by peregrine falcons reveal that stooping at high speed maximizes catch success against agile prey
0 -- 0Hironori Fujita, Masayoshi Kawaguchi. Spatial regularity control of phyllotaxis pattern generated by the mutual interaction between auxin and PIN1
0 -- 0Stephanie A. Ross, Nilima Nigam, James M. Wakeling. A modelling approach for exploring muscle dynamics during cyclic contractions
0 -- 0Yoram Zarai, Tamir Tuller. Computational analysis of the oscillatory behavior at the translation level induced by mRNA levels oscillations due to finite intracellular resources
0 -- 0Maria Concetta Palumbo, Micaela Morettini, Paolo Tieri, Fasma Diele, Massimo Sacchetti, Filippo Castiglione. Personalizing physical exercise in a computational model of fuel homeostasis
0 -- 0Marco Del Giudice, Stefano Bo, Silvia Grigolon, Carla Bosia. On the role of extrinsic noise in microRNA-mediated bimodal gene expression
0 -- 0Sean M. Gibbons, Claire Duvallet, Eric J. Alm. Correcting for batch effects in case-control microbiome studies
0 -- 0Kevin J. Flynn, David O. F. Skibinski, Christian Lindemann. Effects of growth rate, cell size, motion, and elemental stoichiometry on nutrient transport kinetics
0 -- 0Jacquelyn S. Fetrow, Patricia C. Babbitt. New computational approaches to understanding molecular protein function
0 -- 0Wilberforce Zachary Ouma, Katja Pogacar, Erich Grotewold. Topological and statistical analyses of gene regulatory networks reveal unifying yet quantitatively different emergent properties
0 -- 0Masataka Sawayama, Shin'ya Nishida. Material and shape perception based on two types of intensity gradient information
0 -- 0Juan Francisco Viso, Patricia Belelli, Matías R. Machado, Humberto González, Sergio Pantano, María Julia Amundarain, Fernando Zamarreño, Maria Marta Branda, Diego M. A. Guérin, Marcelo D. Costabel. Multiscale modelization in a small virus: Mechanism of proton channeling and its role in triggering capsid disassembly
0 -- 0Jared Adolf-Bryfogle, Oleksandr Kalyuzhniy, Michael Kubitz, Brian Weitzner, Xiaozhen Hu, Yumiko Adachi, William R. Schief, Roland L. Dunbrack Jr.. RosettaAntibodyDesign (RAbD): A general framework for computational antibody design
0 -- 0Arnaud Messé, Marc-Thorsten Hütt, Claus C. Hilgetag. Toward a theory of coactivation patterns in excitable neural networks
0 -- 0Nicholas T. Franklin, Michael J. Frank. Compositional clustering in task structure learning
0 -- 0Ricardo Martínez-García, Carey D. Nadell, Raimo Hartmann, Knut Drescher, Juan A. Bonachela. Cell adhesion and fluid flow jointly initiate genotype spatial distribution in biofilms
0 -- 0Wolfgang Giese, Gregor Milicic, Andreas Schröder, Edda Klipp. Spatial modeling of the membrane-cytosolic interface in protein kinase signal transduction
0 -- 0Vasyl V. Mykuliak, Alexander William M. Haining, Magdaléna von Essen, Armando del Río Hernández, Vesa P. Hytönen. Mechanical unfolding reveals stable 3-helix intermediates in talin and α-catenin
0 -- 0Malgorzata Kardynska, Anna Paszek, Jaroslaw Smieja, David G. Spiller, Wieslawa Widlak, Michael R. H. White, Pawel Paszek, Marek Kimmel. Quantitative analysis reveals crosstalk mechanisms of heat shock-induced attenuation of NF-κB signaling at the single cell level
0 -- 0Justus A. Kromer, Steffen Märcker, Steffen Lange, Christel Baier, Benjamin M. Friedrich. Decision making improves sperm chemotaxis in the presence of noise
0 -- 0Kathleen Gregory, Siri Jodha Khalsa, William K. Michener, Fotis E. Psomopoulos, Anita de Waard, Mingfang Wu. Eleven quick tips for finding research data
0 -- 0Leander Schietgat, Celine Vens, Ricardo Cerri, Carlos N. Fischer, Eduardo P. Costa, Jan Ramon, Claudia M. A. Carareto, Hendrik Blockeel. A machine learning based framework to identify and classify long terminal repeat retrotransposons
0 -- 0Huanan Zhang, Catherine A. A. Lee, Zhuliu Li, John R. Garbe, Cindy R. Eide, Raphael Petegrosso, Rui Kuang, Jakub Tolar. A multitask clustering approach for single-cell RNA-seq analysis in Recessive Dystrophic Epidermolysis Bullosa
0 -- 0Laurent Dollé, Ricardo Chavarriaga, Agnès Guillot, Mehdi Khamassi. Interactions of spatial strategies producing generalization gradient and blocking: A computational approach
0 -- 0Tomás Gedeon, Bree Cummins, Shaun Harker, Konstantin Mischaikow. Identifying robust hysteresis in networks
0 -- 0Ji-Sung Kim, Xin Gao, Andrey Rzhetsky. RIDDLE: Race and ethnicity Imputation from Disease history with Deep LEarning
0 -- 0Joydeep Sarkar, Alka A. Potdar, Gerald M. Saidel. Whole-body iron transport and metabolism: Mechanistic, multi-scale model to improve treatment of anemia in chronic kidney disease
0 -- 0David R. J. Pleydell, Samuel Soubeyrand, Sylvie Dallot, Gérard Labonne, Joël Chadoeuf, Emmanuel Jacquot, Gaël Thébaud. Estimation of the dispersal distances of an aphid-borne virus in a patchy landscape
0 -- 0Geoffrey D. Hannigan, Melissa Beth Duhaime, Danai Koutra, Patrick D. Schloss. Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome
0 -- 0Florian Kaiser, Sebastian Bittrich, Sebastian Salentin, Christoph Leberecht, V. Joachim Haupt, Sarah Krautwurst, Michael Schroeder 0001, Dirk Labudde. Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases
0 -- 0Spencer Bliven, Aleix Lafita, Althea Parker, Guido Capitani, Jose M. Duarte. Automated evaluation of quaternary structures from protein crystals
0 -- 0Javier A. Caballero, Mark D. Humphries, Kevin N. Gurney. A probabilistic, distributed, recursive mechanism for decision-making in the brain
0 -- 0Russell B. Davidson, Josie Hendrix, Brian J. Geiss, Martin McCullagh. Allostery in the dengue virus NS3 helicase: Insights into the NTPase cycle from molecular simulations
0 -- 0Bart Penders. Ten simple rules for responsible referencing
0 -- 0Neil C. C. Brown, Greg Wilson. Ten quick tips for teaching programming
0 -- 0Catherine M. Byrne, Soren Gantt, Daniel Coombs. Effects of spatiotemporal HSV-2 lesion dynamics and antiviral treatment on the risk of HIV-1 acquisition
0 -- 0Jessica Ausborn, Hidehiko Koizumi, William H. Barnett, Tibin T. John, Ruli Zhang, Yaroslav I. Molkov, Jeffrey C. Smith, Ilya A. Rybak. Organization of the core respiratory network: Insights from optogenetic and modeling studies
0 -- 0Ricardo R. da Silva, Mingxun Wang, Louis-Félix Nothias, Justin J. J. van der Hooft, Andrés Mauricio Caraballo-Rodríguez, Evan Fox, Marcy J. Balunas, Jonathan L. Klassen, Norberto Peporine Lopes, Pieter C. Dorrestein. Propagating annotations of molecular networks using in silico fragmentation