Journal: PLoS Computational Biology

Volume 13, Issue 1

0 -- 0James M. Kunert, Pedro D. Maia, J. Nathan Kutz. Functionality and Robustness of Injured Connectomic Dynamics in C. elegans: Linking Behavioral Deficits to Neural Circuit Damage
0 -- 0Mohammadkarim Saeedghalati, Farnoush Farahpour, Bettina Budeus, Anja Lange, Astrid M. Westendorf, Marc Seifert, Ralf Küppers, Daniel Hoffmann. Quantitative Comparison of Abundance Structures of Generalized Communities: From B-Cell Receptor Repertoires to Microbiomes
0 -- 0Ignacio A. Rodriguez-Brenes, Andrew Hofacre, Hung Fan, Dominik Wodarz. Complex Dynamics of Virus Spread from Low Infection Multiplicities: Implications for the Spread of Oncolytic Viruses
0 -- 0Aysima Hacisuleyman, Burak Erman. Entropy Transfer between Residue Pairs and Allostery in Proteins: Quantifying Allosteric Communication in Ubiquitin
0 -- 0Iris Reuveni, Sourav Ghosh, Edi Barkai. Real Time Multiplicative Memory Amplification Mediated by Whole-Cell Scaling of Synaptic Response in Key Neurons
0 -- 0Oded Barzelay, Miriam Furst, Omri Barak. A New Approach to Model Pitch Perception Using Sparse Coding
0 -- 0David Lamparter, Daniel Marbach, Rico Rueedi, Sven Bergmann, Zoltan Kutalik. Genome-Wide Association between Transcription Factor Expression and Chromatin Accessibility Reveals Regulators of Chromatin Accessibility
0 -- 0Mina A. Khoei, Guillaume S. Masson, Laurent U. Perrinet. The Flash-Lag Effect as a Motion-Based Predictive Shift
0 -- 0Gianluigi Rossi, Giulio A. De Leo, Stefano Pongolini, Silvano Natalini, Luca Zarenghi, Matteo Ricchi, Luca Bolzoni. The Potential Role of Direct and Indirect Contacts on Infection Spread in Dairy Farm Networks
0 -- 0Heiner Stuke, Hannes Stuke, Veith Andreas Weilnhammer, Katharina Schmack. Psychotic Experiences and Overhasty Inferences Are Related to Maladaptive Learning
0 -- 0Federica Giardina, Ethan O. Romero-Severson, Jan Albert, Tom Britton, Thomas Leitner. Inference of Transmission Network Structure from HIV Phylogenetic Trees
0 -- 0Abby Tabor, Michael A. Thacker, G. Lorimer Moseley, Konrad P. Körding. Pain: A Statistical Account
0 -- 0Bethany Levick, Andy South, Ian M. Hastings. A Two-Locus Model of the Evolution of Insecticide Resistance to Inform and Optimise Public Health Insecticide Deployment Strategies
0 -- 0Christian Donner, Klaus Obermayer, Hideaki Shimazaki. Approximate Inference for Time-Varying Interactions and Macroscopic Dynamics of Neural Populations
0 -- 0Hualou Liang, Hongbin Wang. Structure-Function Network Mapping and Its Assessment via Persistent Homology
0 -- 0Cox Lwaka Tamba, Yuan-Li Ni, Yuan-Ming Zhang. Iterative sure independence screening EM-Bayesian LASSO algorithm for multi-locus genome-wide association studies
0 -- 0Antonella Paladino, Monica Civera, Laura Belvisi, Giorgio Colombo. High Affinity vs. Native Fibronectin in the Modulation of αvβ3 Integrin Conformational Dynamics: Insights from Computational Analyses and Implications for Molecular Design
0 -- 0Luca Cardelli, Rosa D. Hernansaiz-Ballesteros, Neil Dalchau, Attila Csikász-Nagy. Efficient Switches in Biology and Computer Science
0 -- 0Mary Regina Boland, Konrad J. Karczewski, Nicholas P. Tatonetti. Ten Simple Rules to Enable Multi-site Collaborations through Data Sharing
0 -- 0Gabrielle Stetz, Gennady M. Verkhivker. Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication
0 -- 0Kristin Verena Kaltdorf, Katja Schulze, Frederik Helmprobst, Philip Kollmannsberger, Thomas Dandekar, Christian Stigloher. FIJI Macro 3D ART VeSElecT: 3D Automated Reconstruction Tool for Vesicle Structures of Electron Tomograms
0 -- 0Richard John Wheeler. Use of chiral cell shape to ensure highly directional swimming in trypanosomes
0 -- 0Hoyon Hwang, Jiou Wang. Effect of mutation mechanisms on variant composition and distribution in Caenorhabditis elegans
0 -- 0Veronika Koren, Sophie Denève. Computational Account of Spontaneous Activity as a Signature of Predictive Coding
0 -- 0Fabian Fröhlich, Barbara Kaltenbacher, Fabian J. Theis, Jan Hasenauer. Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks
0 -- 0Oliver Pohl, Marius Hintsche, Zahra Alirezaeizanjani, Maximilian Seyrich, Carsten Beta, Holger Stark. Inferring the Chemotactic Strategy of P. putida and E. coli Using Modified Kramers-Moyal Coefficients
0 -- 0Christopher M. Siwy, Christopher Lockhart, Dmitri K. Klimov. Is the Conformational Ensemble of Alzheimer's Aβ10-40 Peptide Force Field Dependent?
0 -- 0Markus List, Peter Ebert, Felipe Albrecht. Ten Simple Rules for Developing Usable Software in Computational Biology
0 -- 0Andrea Insabato, Mario Pannunzi, Gustavo Deco. Multiple Choice Neurodynamical Model of the Uncertain Option Task
0 -- 0Tamara Carla Bidone, Wonyeong Jung, Daniel Maruri, Carlos Borau, Roger D. Kamm, Taeyoon Kim. Morphological Transformation and Force Generation of Active Cytoskeletal Networks
0 -- 0Christoph Zimmer, Reza Yaesoubi, Ted Cohen. A Likelihood Approach for Real-Time Calibration of Stochastic Compartmental Epidemic Models
0 -- 0Erik Andrews, Yue Wang, Tian Xia, Wenqing Cheng, Chao Cheng. Contextual Refinement of Regulatory Targets Reveals Effects on Breast Cancer Prognosis of the Regulome
0 -- 0Nicholas A. Rossi, Mary J. Dunlop. Customized Regulation of Diverse Stress Response Genes by the Multiple Antibiotic Resistance Activator MarA
0 -- 0Stewart Heitmann, Michael Rule, Wilson Truccolo, Bard Ermentrout. Optogenetic Stimulation Shifts the Excitability of Cerebral Cortex from Type I to Type II: Oscillation Onset and Wave Propagation
0 -- 0Nikolay Chenkov, Henning Sprekeler, Richard Kempter. Memory replay in balanced recurrent networks
0 -- 0Ruth Nussinov, Jason A. Papin, Ilya A. Vakser. Computing the Dynamic Supramolecular Structural Proteome
0 -- 0Ilan Y. Smoly, Netta Shemesh, Michal Ziv-Ukelson, Anat Ben-Zvi, Esti Yeger Lotem. An Asymmetrically Balanced Organization of Kinases versus Phosphatases across Eukaryotes Determines Their Distinct Impacts
0 -- 0Marie Amalric, Liping Wang, Pierre Pica, Santiago Figueira, Mariano Sigman, Stanislas Dehaene. The language of geometry: Fast comprehension of geometrical primitives and rules in human adults and preschoolers
0 -- 0William R. Holmes, Nabora de Mochel, Qixuan Wang, Huijing Du, Tao Peng, Michael Chiang, Olivier Cinquin, Ken Cho, Qing Nie. Gene Expression Noise Enhances Robust Organization of the Early Mammalian Blastocyst
0 -- 0Kaitlyn M. Gayvert, Omar Aly, James Platt, Marcus W. Bosenberg, David F. Stern, Olivier Elemento. A Computational Approach for Identifying Synergistic Drug Combinations
0 -- 0Eric Jonas, Konrad Paul Körding. Could a Neuroscientist Understand a Microprocessor?
0 -- 0Qixuan Wang, William R. Holmes, Julian Sosnik, Thomas Schilling, Qing Nie. Cell Sorting and Noise-Induced Cell Plasticity Coordinate to Sharpen Boundaries between Gene Expression Domains
0 -- 0Chen Zhao, Jeffrey S. Isenberg, Aleksander S. Popel. Transcriptional and Post-Transcriptional Regulation of Thrombospondin-1 Expression: A Computational Model
0 -- 0Emanuel J. V. Gonçalves, Zrinka Raguz Nakic, Mattia Zampieri, Omar Wagih, David Ochoa, Uwe Sauer, Pedro Beltrão, Julio Saez-Rodriguez. Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast
0 -- 0Edward S. Lee, Paul G. Thomas, Jeff E. Mold, Andrew J. Yates. Identifying T Cell Receptors from High-Throughput Sequencing: Dealing with Promiscuity in TCRα and TCRβ Pairing
0 -- 0Martina Michalikova, Michiel W. H. Remme, Richard Kempter. Spikelets in Pyramidal Neurons: Action Potentials Initiated in the Axon Initial Segment That Do Not Activate the Soma
0 -- 0Shenshen Wang. Optimal Sequential Immunization Can Focus Antibody Responses against Diversity Loss and Distraction
0 -- 0Hilje M. Doekes, Christophe Fraser, Katrina A. Lythgoe. Effect of the Latent Reservoir on the Evolution of HIV at the Within- and Between-Host Levels
0 -- 0Hsiao-Han Chang, Colin J. Worby, Adoke Yeka, Joaniter Nankabirwa, Moses R. Kamya, Sarah G. Staedke, Grant Dorsey, Maxwell Murphy, Daniel E. Neafsey, Anna E. Jeffreys, Christina Hubbart, Kirk A. Rockett, Roberto Amato, Dominic Kwiatkowski, Caroline O. Buckee, Bryan Greenhouse. THE REAL McCOIL: A method for the concurrent estimation of the complexity of infection and SNP allele frequency for malaria parasites
0 -- 0Austin W. T. Chiang, Walt Y. L. Wu, Ting Wang, Ming-Jing Hwang. Identification of Entry Factors Involved in Hepatitis C Virus Infection Based on Host-Mimicking Short Linear Motifs
0 -- 0Sheng Wang 0001, Siqi Sun, Zhen Li, Renyu Zhang, Jinbo Xu. Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model
0 -- 0Sylvain Prigent, Clémence Frioux, Simon M. Dittami, Sven Thiele, Abdelhalim Larhlimi, Guillaume Collet, Fabien Gutknecht, Jeanne Got, Damien Eveillard, Jérémie Bourdon, Frédéric Plewniak, Thierry Tonon, Anne Siegel. Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks
0 -- 0Alireza Yazdani, He Li, Jay D. Humphrey, George E. Karniadakis. A General Shear-Dependent Model for Thrombus Formation
0 -- 0Weikang Wang, Kuan Tao, Jing Wang, Gen Yang, Qi Ouyang, Yugang Wang, Lei Zhang, Feng Liu. Exploring the inhibitory effect of membrane tension on cell polarization
0 -- 0Stuart P. Wilson. Self-organised criticality in the evolution of a thermodynamic model of rodent thermoregulatory huddling
0 -- 0Pia Abel zur Wiesch, Fabrizio Clarelli, Ted Cohen. Using Chemical Reaction Kinetics to Predict Optimal Antibiotic Treatment Strategies
0 -- 0Max Hinne, Annet Meijers, Rembrandt Bakker, Paul H. E. Tiesinga, Morten Mørup, Marcel A. J. van Gerven. The missing link: Predicting connectomes from noisy and partially observed tract tracing data
0 -- 0Te Wu, Long Wang 0001, Feng Fu. Coevolutionary dynamics of phenotypic diversity and contingent cooperation
0 -- 0Luc E. Coffeng, Cornelus Hermsen, Robert W. Sauerwein, Sake J. de Vlas. The Power of Malaria Vaccine Trials Using Controlled Human Malaria Infection
0 -- 0James M. Kunert, Joshua L. Proctor, Steven L. Brunton, J. Nathan Kutz. Spatiotemporal Feedback and Network Structure Drive and Encode Caenorhabditis elegans Locomotion
0 -- 0Yaroslav Pollak, Sarah Goldberg, Roee Amit. A Looping-Based Model for Quenching Repression
0 -- 0Tanmay A. Gokhale, Jong M. Kim, Robert D. Kirkton, Nenad Bursac, Craig S. Henriquez. Modeling an Excitable Biosynthetic Tissue with Inherent Variability for Paired Computational-Experimental Studies
0 -- 0Gaurav Bajpai, Ishutesh Jain, Mandar M. Inamdar, Dibyendu Das 0004, Ranjith Padinhateeri. Binding of DNA-bending non-histone proteins destabilizes regular 30-nm chromatin structure
0 -- 0Mihaela Enculescu, Christoph Metzendorf, Richard Sparla, Maximilian Hahnel, Johannes G. Bode, Martina U. Muckenthaler, Stefan Legewie. Modelling Systemic Iron Regulation during Dietary Iron Overload and Acute Inflammation: Role of Hepcidin-Independent Mechanisms
0 -- 0Elyse H. Norton, Stephen M. Fleming, Nathaniel D. Daw, Michael S. Landy. Suboptimal Criterion Learning in Static and Dynamic Environments