Journal: PLoS Computational Biology

Volume 13, Issue 7

0 -- 0Peter Eastman, Jason M. Swails, John D. Chodera, Robert McGibbon, Yutong Zhao, Kyle Beauchamp, Lee-Ping Wang, Andrew C. Simmonett, Matthew P. Harrigan, Chaya D. Stern, Rafal P. Wiewiora, Bernard R. Brooks, Vijay S. Pande. OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
0 -- 0Warren D. Anderson, Danielle DeCicco, James S. Schwaber, Rajanikanth Vadigepalli. A data-driven modeling approach to identify disease-specific multi-organ networks driving physiological dysregulation
0 -- 0John H. C. Palmer, Adam Keane, Pulin Gong. Learning and executing goal-directed choices by internally generated sequences in spiking neural circuits
0 -- 0Xinxian Shao, Andrew Mugler, Justin Kim, Ha Jun Jeong, Bruce R. Levin, Ilya Nemenman. Growth of bacteria in 3-d colonies
0 -- 0Murodzhon Akhmedov, Amanda J. Kedaigle, Renan Escalante Chong, Roberto Montemanni, Francesco Bertoni, Ernest Fraenkel, Ivo Kwee. PCSF: An R-package for network-based interpretation of high-throughput data
0 -- 0Yang Li, Alexis A. Jourdain, Sarah E. Calvo, Jun S. Liu, Vamsi K. Mootha. CLIC, a tool for expanding biological pathways based on co-expression across thousands of datasets
0 -- 0Roman A. Sandler, Dustin Fetterhoff, Robert E. Hampson, Sam A. Deadwyler, Vasilis Z. Marmarelis. Cannabinoids disrupt memory encoding by functionally isolating hippocampal CA1 from CA3
0 -- 0Gamze Gürsoy, Yun Xu, Jie Liang. Spatial organization of the budding yeast genome in the cell nucleus and identification of specific chromatin interactions from multi-chromosome constrained chromatin model
0 -- 0András Szabó, Roeland M. H. Merks. Blood vessel tortuosity selects against evolution of aggressive tumor cells in confined tissue environments: A modeling approach
0 -- 0Vehpi Yildirim, Suryakiran Vadrevu, Benjamin Thompson, Leslie S. Satin, Richard Bertram. Upregulation of an inward rectifying K+ channel can rescue slow Ca2+ oscillations in K(ATP) channel deficient pancreatic islets
0 -- 0Joni Vuorio, Ilpo Vattulainen, Hector Martinez-Seara. Atomistic fingerprint of hyaluronan-CD44 binding
0 -- 0Dariusz Matlak, Ewa Szczurek. Epistasis in genomic and survival data of cancer patients
0 -- 0Davide Lonardoni, Hayder Amin, Stefano Di Marco, Alessandro Maccione, Luca Berdondini, Thierry Nieus. Recurrently connected and localized neuronal communities initiate coordinated spontaneous activity in neuronal networks
0 -- 0Saeed Omidi, Mihaela Zavolan, Mikhail Pachkov, Jeremie Breda, Severin Berger, Erik van Nimwegen. Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors
0 -- 0Xiaoping Liu, Xiao Chang, Rui Liu, Xiangtian Yu, Luonan Chen, Kazuyuki Aihara. Quantifying critical states of complex diseases using single-sample dynamic network biomarkers
0 -- 0Zixuan Cang, Guo-Wei Wei. TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions
0 -- 0Pekka Marttinen, William P. Hanage. Speciation trajectories in recombining bacterial species
0 -- 0Meriç Ataman, Daniel F. Hernandez Gardiol, Georgios Fengos, Vassily Hatzimanikatis. redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models
0 -- 0Juliana C. Wortman, Marcos Nahmad, Pengcheng Zhang, Arthur D. Lander, Clare C. Yu. Expanding signaling-molecule wavefront model of cell polarization in the Drosophila wing primordium
0 -- 0Jonathan Diamond, Daniel M. Wolpert, J. Randall Flanagan. Rapid target foraging with reach or gaze: The hand looks further ahead than the eye
0 -- 0Mathieu Bottier, Sylvain Blanchon, Gabriel Pelle, Emilie Bequignon, Daniel Isabey, André Coste, Estelle Escudier, James B. Grotberg, Jean-François Papon, Marcel Filoche, Bruno Louis. A new index for characterizing micro-bead motion in a flow induced by ciliary beating: Part I, experimental analysis
0 -- 0Connor Sharp, James E. Bray, Nicholas G. Housden, Martin C. J. Maiden, Colin Kleanthous. Diversity and distribution of nuclease bacteriocins in bacterial genomes revealed using Hidden Markov Models
0 -- 0Marta Lukacisinová, Sebastian Novak, Tiago Paixão. Stress-induced mutagenesis: Stress diversity facilitates the persistence of mutator genes
0 -- 0Oliver J. Maclaren, Aimée Parker, Carmen Pin, Simon R. Carding, Alastair J. M. Watson, Alexander G. Fletcher, Helen M. Byrne, Philip K. Maini. A hierarchical Bayesian model for understanding the spatiotemporal dynamics of the intestinal epithelium
0 -- 0Lukas Bartonek, Bojan Zagrovic. mRNA/protein sequence complementarity and its determinants: The impact of affinity scales
0 -- 0Hua-Qing Wu, Mei-Ling Cheng, Jin-mei Lai, Hsuan-Hui Wu, Meng-Chun Chen, Wen-Huan Liu, Wu Hsiung Wu, Peter Mu-Hsin Chang, Chi-Ying F. Huang, Ann-Ping Tsou, Ming-Shi Shiao, Feng-Sheng Wang. Flux balance analysis predicts Warburg-like effects of mouse hepatocyte deficient in miR-122a
0 -- 0Laurent Mackay, Hana Zemkova, Stanko S. Stojilkovic, Arthur Sherman, Anmar Khadra. Deciphering the regulation of P2X4 receptor channel gating by ivermectin using Markov models
0 -- 0Carla Aimé, Jean-Baptiste André, Michel Raymond. Grandmothering and cognitive resources are required for the emergence of menopause and extensive post-reproductive lifespan
0 -- 0Sang-Woo Lee, Yoshihiro Morishita. Possible roles of mechanical cell elimination intrinsic to growing tissues from the perspective of tissue growth efficiency and homeostasis
0 -- 0Mathieu Bottier, Marta Peña Fernández, Gabriel Pelle, Daniel Isabey, Bruno Louis, James B. Grotberg, Marcel Filoche. A new index for characterizing micro-bead motion in a flow induced by ciliary beating: Part II, modeling
0 -- 0Ethan Oblak, Jarrod A. Lewis-Peacock, James S. Sulzer. Self-regulation strategy, feedback timing and hemodynamic properties modulate learning in a simulated fMRI neurofeedback environment
0 -- 0Shuxiang Ruan, Gary D. Stormo. Inherent limitations of probabilistic models for protein-DNA binding specificity
0 -- 0Cesare V. Parise, Marc O. Ernst. Noise, multisensory integration, and previous response in perceptual disambiguation
0 -- 0Joanna Jedrzejewska-Szmek, Vincent Luczak, Ted Abel, Kim T. Blackwell. β-adrenergic signaling broadly contributes to LTP induction
0 -- 0Muhammet Uzuntarla, Ernest Barreto, Joaquín J. Torres. Inverse stochastic resonance in networks of spiking neurons
0 -- 0Aseel Shomar, Lukas Geyrhofer, Noam E. Ziv, Naama Brenner. Cooperative stochastic binding and unbinding explain synaptic size dynamics and statistics
0 -- 0Christopher Finn McQuaid, Frank van den Bosch, Anna Szyniszewska, Titus Alicai, Anthony Pariyo, Patrick Chiza Chikoti, Christopher A. Gilligan. Spatial dynamics and control of a crop pathogen with mixed-mode transmission
0 -- 0Koon-Kiu Yan, Shaoke Lou, Mark Gerstein. MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions
0 -- 0Joshua G. A. Cashaback, Heather R. McGregor, Ayman Mohatarem, Paul L. Gribble. Dissociating error-based and reinforcement-based loss functions during sensorimotor learning
0 -- 0Giorgos Minas, David A. Rand. Long-time analytic approximation of large stochastic oscillators: Simulation, analysis and inference
0 -- 0Shihao Yang, Samuel C. Kou, Fred Lu, John S. Brownstein, Nicholas Brooke, Mauricio Santillana. Advances in using Internet searches to track dengue
0 -- 0Haruo Hosoya, Aapo Hyvärinen. A mixture of sparse coding models explaining properties of face neurons related to holistic and parts-based processing
0 -- 0Johan D. Carlin, Nikolaus Kriegeskorte. Adjudicating between face-coding models with individual-face fMRI responses
0 -- 0Kamran Kaveh, Yutaka Takahashi, Michael Farrar, Guy Storme, Marcucci Guido, Jamie Piepenburg, Jackson Penning, Jasmine Foo, Kevin Leder, Susanta K. Hui. Combination therapeutics of Nilotinib and radiation in acute lymphoblastic leukemia as an effective method against drug-resistance
0 -- 0William Gilpin, Marcus W. Feldman. A phase transition induces chaos in a predator-prey ecosystem with a dynamic fitness landscape
0 -- 0Magdalena Zwierzyna, John P. Overington. Classification and analysis of a large collection of in vivo bioassay descriptions
0 -- 0François Serra, Davide Baù, Mike Goodstadt, David Castillo, Guillaume J. Filion, Marc A. Martí-Renom. Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors
0 -- 0Alexandra Vormberg, Felix Effenberger, Julia Muellerleile, Hermann Cuntz. Universal features of dendrites through centripetal branch ordering
0 -- 0James R. H. Cooke, Arjan C. ter Horst, Robert J. van Beers, W. Pieter Medendorp. Effect of depth information on multiple-object tracking in three dimensions: A probabilistic perspective
0 -- 0Nick Fyson, Jerry King, Thomas Belcher, Andrew Preston, Caroline Colijn. A curated genome-scale metabolic model of Bordetella pertussis metabolism
0 -- 0Mikhail V. Pogorelyy, Yuval Elhanati, Quentin Marcou, Anastasiia L. Sycheva, Ekaterina Komech, Vadim I. Nazarov, Olga V. Britanova, Dmitry M. Chudakov, Ilgar Mamedov, Yury Lebedev, Thierry Mora, Aleksandra M. Walczak. Persisting fetal clonotypes influence the structure and overlap of adult human T cell receptor repertoires
0 -- 0Meriç Ataman, Vassily Hatzimanikatis. lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites
0 -- 0Wilsaan M. Joiner, Gary C. Sing, Maurice A. Smith. Temporal specificity of the initial adaptive response in motor adaptation
0 -- 0Bin Shao, Haiyu Yuan, Rongfei Zhang, Xuan Wang, Shuwen Zhang, Qi Ouyang, Nan Hao, Chunxiong Luo. Reconstructing the regulatory circuit of cell fate determination in yeast mating response
0 -- 0Franz Hamilton, Alun L. Lloyd, Kevin B. Flores. Hybrid modeling and prediction of dynamical systems