Journal: PLoS Computational Biology

Volume 13, Issue 3

0 -- 0Matthew B. Biggs, Jason A. Papin. Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA
0 -- 0Johannes Friedrich, Pengcheng Zhou, Liam Paninski. Fast online deconvolution of calcium imaging data
0 -- 0Cibele Vieira Falkenberg, Evren U. Azeloglu, Mark Stothers, Thomas J. Deerinck, Yibang Chen, John C. He, Mark H. Ellisman, James C. Hone, Ravi Iyengar, Leslie M. Loew. Fragility of foot process morphology in kidney podocytes arises from chaotic spatial propagation of cytoskeletal instability
0 -- 0Andrew F. Brouwer, Rafael Meza, Marisa C. Eisenberg. Parameter estimation for multistage clonal expansion models from cancer incidence data: A practical identifiability analysis
0 -- 0David C. Farrow, Logan C. Brooks, Sangwon Hyun, Ryan J. Tibshirani, Donald S. Burke, Roni Rosenfeld. A human judgment approach to epidemiological forecasting
0 -- 0Rashmi Priya, Guillermo A. Gomez, Srikanth Budnar, Bipul R. Acharya, Andras Czirok, Alpha S. Yap, Zoltan Neufeld. Bistable front dynamics in a contractile medium: Travelling wave fronts and cortical advection define stable zones of RhoA signaling at epithelial adherens junctions
0 -- 0Alexander Byers Brummer, Van M. Savage, Brian J. Enquist. A general model for metabolic scaling in self-similar asymmetric networks
0 -- 0Polydefkis Diamantis, Oliver T. Unke, Markus Meuwly. Migration of small ligands in globins: Xe diffusion in truncated hemoglobin N
0 -- 0Krzysztof J. Gorgolewski, Fidel Alfaro-Almagro, Tibor Auer, Pierre Bellec, Mihai Capota, M. Mallar Chakravarty, Nathan William Churchill, Alexander L. Cohen, R. Cameron Craddock, Gabriel A. Devenyi, Anders Eklund, Oscar Esteban, Guillaume Flandin, Satrajit S. Ghosh, J. Swaroop Guntupalli, Mark Jenkinson, Anisha Keshavan, Gregory Kiar, Franziskus Liem, Pradeep Reddy Raamana, David Raffelt, Christopher J. Steele, Pierre-Olivier Quirion, Robert E. Smith 0002, Stephen C. Strother, Gaël Varoquaux, Yida Wang, Tal Yarkoni, Russell A. Poldrack. BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods
0 -- 0Christopher J. Lortie. Ten simple rules for short and swift presentations
0 -- 0Xuejin Li, E. Du, Ming Dao, Subra Suresh, George E. Karniadakis. Patient-specific modeling of individual sickle cell behavior under transient hypoxia
0 -- 0Joris Paijmans, David K. Lubensky, Pieter Rein ten Wolde. A thermodynamically consistent model of the post-translational Kai circadian clock
0 -- 0Paul M. Bays, Ben A. Dowding. Fidelity of the representation of value in decision-making
0 -- 0Matthew Zook, Solon Barocas, Danah Boyd, Kate Crawford 0002, Emily Keller, Seeta Peña Gangadharan, Alyssa Goodman, Rachelle Hollander, Barbara König 0002, Jacob Metcalf, Arvind Narayanan, Alondra Nelson, Frank Pasquale. Ten simple rules for responsible big data research
0 -- 0Julien Vibert, Veronique Thomas-Vaslin. Modelling T cell proliferation: Dynamics heterogeneity depending on cell differentiation, age, and genetic background
0 -- 0Daniele Caligiore, Francesco Mannella, Michael A. Arbib, Gianluca Baldassarre. Dysfunctions of the basal ganglia-cerebellar-thalamo-cortical system produce motor tics in Tourette syndrome
0 -- 0Etay Hay, Petra Ritter, Nancy J. Lobaugh, Anthony R. McIntosh. Multiregional integration in the brain during resting-state fMRI activity
0 -- 0Lindsay E. Clegg, Feilim Mac Gabhann. A computational analysis of in vivo VEGFR activation by multiple co-expressed ligands
0 -- 0Carlos Pulido-Quetglas, Estel Aparicio-Prat, Carme Arnan, Taisia Polidori, Toni Hermoso, Emilio Palumbo, Julia V. Ponomarenko, Roderic Guigó, Rory Johnson. Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion
0 -- 0David A. Rasmussen, Roger D. Kouyos, Huldrych F. Günthard, Tanja Stadler. Phylodynamics on local sexual contact networks
0 -- 0Junjiajia Long, Steven W. Zucker, Thierry Emonet. Feedback between motion and sensation provides nonlinear boost in run-and-tumble navigation
0 -- 0Kiwon Jang, Kwoneel Kim, Ara Cho, Insuk Lee, Jung Kyoon Choi. Network perturbation by recurrent regulatory variants in cancer
0 -- 0Mauricio González-Forero, Timm Faulwasser, Laurent Lehmann. A model for brain life history evolution
0 -- 0Amir Bitran, Wei-Yin Chiang, Erel Levine, Mara Prentiss. Mechanisms of fast and stringent search in homologous pairing of double-stranded DNA
0 -- 0Tohar S. Yarden, Israel Nelken. Stimulus-specific adaptation in a recurrent network model of primary auditory cortex
0 -- 0James T. Yurkovich, Laurence Yang, Bernhard O. Palsson. Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells
0 -- 0Erick A. Perez Alday, Michael A. Colman, Philip Langley, Henggui Zhang. Novel non-invasive algorithm to identify the origins of re-entry and ectopic foci in the atria from 64-lead ECGs: A computational study
0 -- 0Mahamar Dicko, Pierre Saramito, Guy B. Blanchard, Claire M. Lye, Bénédicte Sanson, Jocelyn Étienne. Geometry can provide long-range mechanical guidance for embryogenesis
0 -- 0Anush Chiappino-Pepe, Stepan Tymoshenko, Meriç Ataman, Dominique Soldati-Favre, Vassily Hatzimanikatis. Bioenergetics-based modeling of Plasmodium falciparum metabolism reveals its essential genes, nutritional requirements, and thermodynamic bottlenecks
0 -- 0Marie Devaine, Jean Daunizeau. Learning about and from others' prudence, impatience or laziness: The computational bases of attitude alignment
0 -- 0Binwu Zhao, Martien A. Cohen Stuart, Carol K. Hall. Navigating in foldonia: Using accelerated molecular dynamics to explore stability, unfolding and self-healing of the β-solenoid structure formed by a silk-like polypeptide
0 -- 0Zhu-Hong You, Zhi-an Huang, Zexuan Zhu, Guiying Yan, Zheng-Wei Li, Zhenkun Wen, Xing Chen. PBMDA: A novel and effective path-based computational model for miRNA-disease association prediction
0 -- 0Sang Woo Park, Benjamin M. Bolker. Effects of contact structure on the transient evolution of HIV virulence
0 -- 0Bruno A. Gaëta, Javier De Las Rivas, Paul Horton, Pieter Meysman, Nicola J. Mulder, Paolo Romano 0001, Lonnie R. Welch. Ten simple rules for forming a scientific professional society
0 -- 0Charles Rocabert, Carole Knibbe, Jessika Consuegra, Dominique Schneider, Guillaume Beslon. Beware batch culture: Seasonality and niche construction predicted to favor bacterial adaptive diversification
0 -- 0Michiel J. M. Niesen, Connie Y. Wang, Reid C. Van Lehn, Thomas Miller III. Structurally detailed coarse-grained model for Sec-facilitated co-translational protein translocation and membrane integration
0 -- 0Sergey G. Aleksin, Kaiyu Zheng, Dmitri A. Rusakov, Leonid Savtchenko. ARACHNE: A neural-neuroglial network builder with remotely controlled parallel computing
0 -- 0. PLOS Computational Biology 2016 Reviewer and Editorial Board Thank You
0 -- 0Matthew J. Betts, Oliver Wichmann, Mathias Utz, Timon Andre, Evangelia Petsalaki, Pablo Minguez, Luca Parca, Frederick P. Roth, Anne-Claude Gavin, Peer Bork, Robert B. Russell. Systematic identification of phosphorylation-mediated protein interaction switches
0 -- 0Susmita Roy, Heiko Lammert, Ryan L. Hayes, Bin Chen, Regan LeBlanc, T. Kwaku Dayie, José N. Onuchic, Karissa Y. Sanbonmatsu. A magnesium-induced triplex pre-organizes the SAM-II riboswitch
0 -- 0Jeffrey Chen, Thomas MacCarthy. The preferred nucleotide contexts of the AID/APOBEC cytidine deaminases have differential effects when mutating retrotransposon and virus sequences compared to host genes
0 -- 0Swati Jain, Jonathan D. Jou, Ivelin S. Georgiev, Bruce Randall Donald. A critical analysis of computational protein design with sparse residue interaction graphs
0 -- 0Walter Basile, Oxana Sachenkova, Sara Light, Arne Elofsson. High GC content causes orphan proteins to be intrinsically disordered
0 -- 0Emma Saulnier, Olivier Gascuel, Samuel Alizon. Inferring epidemiological parameters from phylogenies using regression-ABC: A comparative study
0 -- 0Bin Huang, Mingyang Lu, Dongya Jia, Eshel Ben-Jacob, Herbert Levine, José N. Onuchic. Interrogating the topological robustness of gene regulatory circuits by randomization
0 -- 0Jonathan T. Young, Tetsuhiro S. Hatakeyama, Kunihiko Kaneko. Dynamics robustness of cascading systems
0 -- 0Aurélien Naldi, Romain M. Larive, Urszula Czerwinska, Serge Urbach, Philippe Montcourrier, Christian Roy, Jérôme Solassol, Gilles Freiss, Peter J. Coopman, Ovidiu Radulescu. Reconstruction and signal propagation analysis of the Syk signaling network in breast cancer cells
0 -- 0Daniel Howsmon, Uwe Kruger, Stepan Melnyk, S. Jill James, Juergen Hahn. Classification and adaptive behavior prediction of children with autism spectrum disorder based upon multivariate data analysis of markers of oxidative stress and DNA methylation