Journal: PLoS Computational Biology

Volume 14, Issue 10

0 -- 0Braden A. W. Brinkman, Fred Rieke, Eric Shea-Brown, Michael A. Buice. Predicting how and when hidden neurons skew measured synaptic interactions
0 -- 0Joseph A. Lombardo, Matthew V. Macellaio, Bing Liu, Stephanie E. Palmer, Leslie C. Osborne. State dependence of stimulus-induced variability tuning in macaque MT
0 -- 0Eduardo Garrido, Juan Lázaro, Montserrat Jaumot, Neus Agell, Jaime Rubio-Martinez. Modeling and subtleties of K-Ras and Calmodulin interaction
0 -- 0Maximilian Schmidt, Rembrandt Bakker, Kelly Shen, Gleb Bezgin, Markus Diesmann, Sacha Jennifer van Albada. A multi-scale layer-resolved spiking network model of resting-state dynamics in macaque visual cortical areas
0 -- 0Robin Moss, Frank B. Sachse, Eloy G. Moreno-Galindo, Ricardo A. Navarro-Polanco, Martin Tristani-Firouzi, Gunnar Seemann. Modeling effects of voltage dependent properties of the cardiac muscarinic receptor on human sinus node function
0 -- 0Fabian A. Soto, Lauren Vucovich, F. Gregory Ashby. Linking signal detection theory and encoding models to reveal independent neural representations from neuroimaging data
0 -- 0Richard A. Erickson, Michael N. Fienen, S. Grace McCalla, Emily L. Weiser, Melvin L. Bower, Jonathan M. Knudson, Greg Thain. Wrangling distributed computing for high-throughput environmental science: An introduction to HTCondor
0 -- 0Katharina Nöh, Sebastian Niedenführ, Martin Beyß, Wolfgang Wiechert. A Pareto approach to resolve the conflict between information gain and experimental costs: Multiple-criteria design of carbon labeling experiments
0 -- 0Philippa J. Karoly, Levin Kuhlmann, Daniel Soudry, David B. Grayden, Mark J. Cook, Dean R. Freestone. Seizure pathways: A model-based investigation
0 -- 0Ying-Chih Chiang, Olesya Levsh, Chun Kei Lam, Jing-Ke Weng, Yi Wang. Structural and dynamic basis of substrate permissiveness in hydroxycinnamoyltransferase (HCT)
0 -- 0Ik-Soo Huh, Isabel Mendizabal, Taesung Park, Soojin V. Yi. Functional conservation of sequence determinants at rapidly evolving regulatory regions across mammals
0 -- 0Ivan Tomic, Paul M. Bays. Internal but not external noise frees working memory resources
0 -- 0Kanika Bansal, John D. Medaglia, Danielle S. Bassett, Jean M. Vettel, Sarah Feldt Muldoon. Data-driven brain network models differentiate variability across language tasks
0 -- 0Vasileios Vavourakis, Triantafyllos Stylianopoulos, Peter A. Wijeratne. In-silico dynamic analysis of cytotoxic drug administration to solid tumours: Effect of binding affinity and vessel permeability
0 -- 0Lars Ole Schwen, Sabrina Rueschenbaum. Ten quick tips for getting the most scientific value out of numerical data
0 -- 0Hao Wang, Simonas Marcisauskas, Benjamín J. Sánchez, Iván Domenzain, Daniel Hermansson, Rasmus Agren, Jens Nielsen, Eduard J. Kerkhoven. RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor
0 -- 0Michael A. Skinnider, R. Greg Stacey, Leonard J. Foster. Genomic data integration systematically biases interactome mapping
0 -- 0Frank S. Heldt, Reece Lunstone, John J. Tyson, Béla Novák. Dilution and titration of cell-cycle regulators may control cell size in budding yeast
0 -- 0Prithwish Chakraborty, Bryan L. Lewis, Stephen G. Eubank, John S. Brownstein, Madhav Marathe, Naren Ramakrishnan. What to know before forecasting the flu
0 -- 0Miguel Fribourg, Diomedes E. Logothetis, Javier González-Maeso, Stuart C. Sealfon, Belén Galocha-Iragüen, Fernando Las-Heras Andrés, Vladimir Brezina. Correction: Elucidation of molecular kinetic schemes from macroscopic traces using system identification
0 -- 0Erki Aun, Age Brauer, Veljo Kisand, Tanel Tenson, Maido Remm. A k-mer-based method for the identification of phenotype-associated genomic biomarkers and predicting phenotypes of sequenced bacteria
0 -- 0Istvan T. Kleijn, Laurens H. J. Krah, Rutger Hermsen. Noise propagation in an integrated model of bacterial gene expression and growth
0 -- 0Sandra Giuliani, Arthur C. Silva, Joyce V. V. B. Borba, Pablo I. P. Ramos, Ross A. Paveley, Eugene N. Muratov, Carolina Horta Andrade, Nicholas Furnham. Computationally-guided drug repurposing enables the discovery of kinase targets and inhibitors as new schistosomicidal agents
0 -- 0Dominik Wodarz, Pamela J. Skinner, David N. Levy, Elizabeth Connick. Virus and CTL dynamics in the extrafollicular and follicular tissue compartments in SIV-infected macaques
0 -- 0Andreas Solbrå, Aslak Wigdahl Bergersen, Jonas van den Brink, Anders Malthe-Sørenssen, Gaute T. Einevoll, Geir Halnes. A Kirchhoff-Nernst-Planck framework for modeling large scale extracellular electrodiffusion surrounding morphologically detailed neurons
0 -- 0Michael A. Henson, Poonam Phalak. Suboptimal community growth mediated through metabolite crossfeeding promotes species diversity in the gut microbiota
0 -- 0Misbah Razzaq, Loïc Paulevé, Anne Siegel, Julio Saez-Rodriguez, Jérémie Bourdon, Carito Guziolowski. Computational discovery of dynamic cell line specific Boolean networks from multiplex time-course data
0 -- 0Todd C. Peterson, Sofie R. Kleppner, Crystal M. Botham. Ten simple rules for scientists: Improving your writing productivity
0 -- 0Song Xu, Sanggu Kim, Irvin S. Y. Chen, Tom Chou. Modeling large fluctuations of thousands of clones during hematopoiesis: The role of stem cell self-renewal and bursty progenitor dynamics in rhesus macaque
0 -- 0Ling Chen, Alexandra E. Fish, John A. Capra. Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties
0 -- 0Xinjian Mao, Sarah McManaway, Jagdish K. Jaiswal, Priyanka B. Patel, William R. Wilson, Kevin O. Hicks, Gib Bogle. An agent-based model for drug-radiation interactions in the tumour microenvironment: Hypoxia-activated prodrug SN30000 in multicellular tumour spheroids
0 -- 0Ruohan Zhang, Shun Zhang, Matthew H. Tong, Yuchen Cui, Constantin A. Rothkopf, Dana H. Ballard, Mary M. Hayhoe. Modeling sensory-motor decisions in natural behavior
0 -- 0Philip E. Bourne. Ten simple rules when considering retirement
0 -- 0Sahar Gelfman, Quanli Wang, Yi-Fan Lu, Diana Hall, Christopher D. Bostick, Ryan Dhindsa, Matt Halvorsen, K. Melodi McSweeney, Ellese Cotterill, Tom Edinburgh, Michael A. Beaumont, Wayne N. Frankel, Slave Petrovski, Andrew S. Allen, Michael J. Boland, David B. Goldstein, Stephen J. Eglen. meaRtools: An R package for the analysis of neuronal networks recorded on microelectrode arrays
0 -- 0Francisco Y. Cai, Thomas Fussell, Sarah Cobey, Marc Lipsitch. Use of an individual-based model of pneumococcal carriage for planning a randomized trial of a whole-cell vaccine
0 -- 0Tycho Bismeijer, Sander Canisius, Lodewyk F. A. Wessels. Molecular characterization of breast and lung tumors by integration of multiple data types with functional sparse-factor analysis
0 -- 0Andreas Handel, Yan Li, Brian McKay, Kasia A. Pawelek, Veronika Zarnitsyna, Rustom Antia. Exploring the impact of inoculum dose on host immunity and morbidity to inform model-based vaccine design
0 -- 0Toshitake Asabuki, Naoki Hiratani, Tomoki Fukai. Interactive reservoir computing for chunking information streams
0 -- 0Adrian Jinich, Avi I. Flamholz, Haniu Ren, Sungjin Kim, Benjamin Sanchez-Lengeling, Charles A. R. Cotton, Elad Noor, Alán Aspuru-Guzik, Arren Bar-Even. Quantum chemistry reveals thermodynamic principles of redox biochemistry
0 -- 0Daniel Strömbom, Audrey Dussutour. Self-organized traffic via priority rules in leaf-cutting ants
0 -- 0Daniel S. Moore, Conor Brines, Heather Jewhurst, John P. Dalton, Irina G. Tikhonova. Steered molecular dynamics simulations reveal critical residues for (un)binding of substrates, inhibitors and a product to the malarial M1 aminopeptidase
0 -- 0Marcos Méndez. Ten simple rules for developing good reading habits during graduate school and beyond
0 -- 0Huy Tran, Jonathan Desponds, Carmina Perez Romero, Mathieu Coppey, Cecile Fradin, Nathalie Dostatni, Aleksandra M. Walczak. Precision in a rush: Trade-offs between reproducibility and steepness of the hunchback expression pattern
0 -- 0Scott W. Simpkins, Justin Nelson, Raamesh Deshpande, Sheena C. Li, Jeff S. Piotrowski, Erin H. Wilson, Abraham A. Gebre, Hamid Safizadeh, Reika Okamoto, Mami Yoshimura, Michael Costanzo, Yoko Yashiroda, Yoshikazu Ohya, Hiroyuki Osada, Minoru Yoshida, Charles Boone, Chad L. Myers. Predicting bioprocess targets of chemical compounds through integration of chemical-genetic and genetic interactions
0 -- 0Amrit Dhar, Kristian Davidsen, Frederick A. Matsen IV, Vladimir N. Minin. Predicting B cell receptor substitution profiles using public repertoire data
0 -- 0Ioannis Kalfas, Kasper Vinken, Rufin Vogels. Representations of regular and irregular shapes by deep Convolutional Neural Networks, monkey inferotemporal neurons and human judgments
0 -- 0Michael F. Staddon, Dapeng Bi, A. Pasha Tabatabai, Visar Ajeti, Michael P. Murrell, Shiladitya Banerjee. Cooperation of dual modes of cell motility promotes epithelial stress relaxation to accelerate wound healing
0 -- 0Ernest C. Y. Ho, Juan Nicolas Malagón, Abha Ahuja, Rama Singh, Ellen Larsen. Rotation of sex combs in Drosophila melanogaster requires precise and coordinated spatio-temporal dynamics from forces generated by epithelial cells