Journal: PLoS Computational Biology

Volume 14, Issue 12

0 -- 0Isao T. Tokuda, Daisuke Ono, Sato Honma, Ken-ichi Honma, Hanspeter Herzel. Coherency of circadian rhythms in the SCN is governed by the interplay of two coupling factors
0 -- 0Lindley Darden, Kunal Kundu, Lipika R. Pal, John Moult. Harnessing formal concepts of biological mechanism to analyze human disease
0 -- 0Agustina Razetti, Caroline Medioni, Grégoire Malandain, Florence Besse, Xavier Descombes. A stochastic framework to model axon interactions within growing neuronal populations
0 -- 0Vlad Elgart, Jia-Ren Lin, Joseph Loscalzo. Determinants of drug-target interactions at the single cell level
0 -- 0Itamar Daniel Landau, Haim Sompolinsky. Coherent chaos in a recurrent neural network with structured connectivity
0 -- 0Wang Xi, Michael A. Beer. Local epigenomic state cannot discriminate interacting and non-interacting enhancer-promoter pairs with high accuracy
0 -- 0Anne V. Brown, Jacqueline D. Campbell, Teshale Assefa, David Grant, Rex T. Nelson, Nathan T. Weeks, Steven B. Cannon. Ten quick tips for sharing open genomic data
0 -- 0John M. Jumper, Nabil F. Faruk, Karl F. Freed, Tobin R. Sosnick. Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics
0 -- 0Rory G. Townsend, Pulin Gong. Detection and analysis of spatiotemporal patterns in brain activity
0 -- 0Zhen Wah Tan, Enrico Guarnera, Igor N. Berezovsky. Exploring chromatin hierarchical organization via Markov State Modelling
0 -- 0Nicolas A. Pabon, Yan Xia, Samuel K. Estabrooks, Zhaofeng Ye, Amanda K. Herbrand, Evelyn Süß, Ricardo M. Biondi, Victoria A. Assimon, Jason E. Gestwicki, Jeffrey L. Brodsky, Carlos J. Camacho, Ziv Bar-Joseph. Predicting protein targets for drug-like compounds using transcriptomics
0 -- 0Sergio Arregui, Alberto Aleta, Joaquín Sanz, Yamir Moreno. Projecting social contact matrices to different demographic structures
0 -- 0Ho Ka Chan, Fabian Hersperger, Emiliano Marachlian, Brian H. Smith, Fernando Locatelli, Paul Szyszka, Thomas Nowotny. Odorant mixtures elicit less variable and faster responses than pure odorants
0 -- 0Nicholas Baker, Hongjing Lu, Gennady Erlikhman, Philip J. Kellman. Deep convolutional networks do not classify based on global object shape
0 -- 0Luhao Zhang, Maodong Li, Zhirong Liu. A comprehensive ensemble model for comparing the allosteric effect of ordered and disordered proteins
0 -- 0Edouard A. Hay, Raghuveer Parthasarathy. Performance of convolutional neural networks for identification of bacteria in 3D microscopy datasets
0 -- 0Jia Lu, Xiaoyi Cao, Sheng Zhong. A likelihood approach to testing hypotheses on the co-evolution of epigenome and genome
0 -- 0Aleksandr V. Zhuravlev, Oleg V. Vetrovoy, Elena V. Savvateeva-Popova. Enzymatic and non-enzymatic pathways of kynurenines' dimerization: the molecular factors for oxidative stress development
0 -- 0Murat Cokol, Chen Li, Sriram Chandrasekaran. Chemogenomic model identifies synergistic drug combinations robust to the pathogen microenvironment
0 -- 0Brian C. Lee, Daniel Jacob Tward, Partha P. Mitra, Michael I. Miller. On variational solutions for whole brain serial-section histology using a Sobolev prior in the computational anatomy random orbit model
0 -- 0Jennifer L. Wilson, Rebecca Racz, Tianyun Liu, Oluseyi Adeniyi, Jielin Sun, Anuradha Ramamoorthy, Michael Pacanowski, Russ B. Altman. PathFX provides mechanistic insights into drug efficacy and safety for regulatory review and therapeutic development
0 -- 0Nele Vandersickel, Masaya Watanabe, Qian Tao, Jan Fostier, Katja Zeppenfeld, Alexander V. Panfilov. Dynamical anchoring of distant arrhythmia sources by fibrotic regions via restructuring of the activation pattern
0 -- 0Lei Liu, Guang Shi, D. Thirumalai, Changbong Hyeon. Chain organization of human interphase chromosome determines the spatiotemporal dynamics of chromatin loci
0 -- 0Ashish B. George, Kirill S. Korolev. Chirality provides a direct fitness advantage and facilitates intermixing in cellular aggregates
0 -- 0Enrico Lavezzo, Michele Berselli, Ilaria Frasson, Rosalba Perrone, Giorgio Palù, Alessandra R. Brazzale, Sara N. Richter, Stefano Toppo. G-quadruplex forming sequences in the genome of all known human viruses: A comprehensive guide
0 -- 0Ning Zhang, Yuting Chen, Feiyang Zhao, Qing Yang, Franco L. Simonetti, Minghui Li. PremPDI estimates and interprets the effects of missense mutations on protein-DNA interactions
0 -- 0Danesh Moradigaravand, Martin Palm, Anne Farewell, Ville Mustonen, Jonas Warringer, Leopold Parts. Prediction of antibiotic resistance in Escherichia coli from large-scale pan-genome data
0 -- 0Iris I. A. Groen, Sara Jahfari, Noor Seijdel, Sennay Ghebreab, Victor A. F. Lamme, H. Steven Scholte. Scene complexity modulates degree of feedback activity during object detection in natural scenes
0 -- 0Jordan C. Rozum, Réka Albert. Identifying (un)controllable dynamical behavior in complex networks
0 -- 0Benjamin D. Lee. Ten simple rules for documenting scientific software
0 -- 0Anna Bochicchio, Miroslav Krepl, Fan Yang, Gabriele Varani, Jirí Sponer, Paolo Carloni. Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study
0 -- 0Kellen Chen, Xiao Hu, Silvia S. Blemker, Jeffrey W. Holmes. Multiscale computational model of Achilles tendon wound healing: Untangling the effects of repair and loading
0 -- 0Peter Neri. The empirical characteristics of human pattern vision defy theoretically-driven expectations
0 -- 0Daniel H. Blustein, Ahmed W. Shehata, Kevin B. Englehart, Jonathon W. Sensinger. Conventional analysis of trial-by-trial adaptation is biased: Empirical and theoretical support using a Bayesian estimator
0 -- 0Shouryadipta Ghosh, Kenneth Tran, Lea M. D. Delbridge, Anthony Hickey, Eric Hanssen, Edmund J. Crampin, Vijay Rajagopal. Insights on the impact of mitochondrial organisation on bioenergetics in high-resolution computational models of cardiac cell architecture
0 -- 0Nicholas A. Rossi, Thierry Mora, Aleksandra M. Walczak, Mary J. Dunlop. Active degradation of MarA controls coordination of its downstream targets
0 -- 0Andrew F. Neuwald, Stephen F. Altschul. Statistical investigations of protein residue direct couplings
0 -- 0Marius Somveille, Josh A. Firth, Lucy M. Aplin, Damien Farine, Ben C. Sheldon, Robin N. Thompson. Movement and conformity interact to establish local behavioural traditions in animal populations
0 -- 0Hayden Tronnolone, Jennifer M. Gardner, Joanna F. Sundstrom, Vladimir Jiranek, Stephen G. Oliver, Benjamin J. Binder. TAMMiCol: Tool for analysis of the morphology of microbial colonies
0 -- 0Michael Moutoussis, Edward T. Bullmore, Ian M. Goodyer, Peter Fonagy, Peter B. Jones, Raymond J. Dolan, Peter Dayan. Change, stability, and instability in the Pavlovian guidance of behaviour from adolescence to young adulthood
0 -- 0Logan L. Grado, Matthew D. Johnson, Theoden I. Netoff. Bayesian adaptive dual control of deep brain stimulation in a computational model of Parkinson's disease
0 -- 0Kemal Eren, Steven Weaver, Robert Ketteringham, Morné Valentyn, Melissa Laird Smith, Venkatesh Kumar, Sanjay Mohan, Sergei L. Kosakovsky Pond, Ben Murrell. Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons
0 -- 0Wojciech Potrzebowski, Jill Trewhella, Ingemar Andre. Bayesian inference of protein conformational ensembles from limited structural data
0 -- 0Gina Polo, Carlos Mera Acosta, Marcelo B. Labruna, Fernando Ferreira, Dirk Brockmann. Hosts mobility and spatial spread of Rickettsia rickettsii
0 -- 0Philip E. Bourne, Fran Lewitter, Scott Markel, Jason A. Papin. One thousand simple rules
0 -- 0John M. Jumper, Nabil F. Faruk, Karl F. Freed, Tobin R. Sosnick. Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours
0 -- 0Anne Cori, Pierre Nouvellet, Tini Garske, Hervé Bourhy, Emmanuel Nakouné, Thibaut Jombart. A graph-based evidence synthesis approach to detecting outbreak clusters: An application to dog rabies
0 -- 0Mengrou Shan, David Dai, Arunodai Vudem, Jeffrey D. Varner, Abraham Duncan Stroock. Multi-scale computational study of the Warburg effect, reverse Warburg effect and glutamine addiction in solid tumors
0 -- 0Renato Pagliara, Deborah M. Gordon, Naomi Ehrich Leonard. Regulation of harvester ant foraging as a closed-loop excitable system
0 -- 0Aleksandra Tarkowska, Denise Carvalho-Silva, Charles E. Cook, Edd Turner, Robert D. Finn, Andrew D. Yates. Eleven quick tips to build a usable REST API for life sciences
0 -- 0Michiel W. H. Remme, John Rinzel, Susanne Schreiber. Function and energy consumption constrain neuronal biophysics in a canonical computation: Coincidence detection
0 -- 0Wen Zhang 0008, Xiang Yue, Guifeng Tang, Wenjian Wu, Feng Huang, Xining Zhang. SFPEL-LPI: Sequence-based feature projection ensemble learning for predicting LncRNA-protein interactions