Biology & Life Sciences
PLOS Computational Biology Top 10%
PLOS Computational Biology is home to research on living systems at all scales—from molecules and cells, to patient populations and ecosystems—through the application of computational methods. Each year, we celebrate the impact our authors have had in these fields and share out the body of work that has earned the top 10% of citations. We hope you enjoy exploring this Collection.
Image Credit: RNA videogame issue image
2014
-
PLOS Computational Biology Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data
-
PLOS Computational Biology Evolutionary Game Dynamics in Populations with Heterogenous Structures
-
PLOS Computational Biology Enumeration of Smallest Intervention Strategies in Genome-Scale Metabolic Networks
-
PLOS Computational Biology Spatial Transmission of 2009 Pandemic Influenza in the US
-
PLOS Computational Biology Inferring on the Intentions of Others by Hierarchical Bayesian Learning
-
PLOS Computational Biology Thermodynamic Costs of Information Processing in Sensory Adaptation
-
PLOS Computational Biology Resolving Structural Variability in Network Models and the Brain
-
PLOS Computational Biology Mechanisms of Zero-Lag Synchronization in Cortical Motifs
-
PLOS Computational Biology Chromatin Loops as Allosteric Modulators of Enhancer-Promoter Interactions
-
PLOS Computational Biology Comparison of Filtering Methods for the Modeling and Retrospective Forecasting of Influenza Epidemics
-
PLOS Computational Biology Spectral Signatures of Reorganised Brain Networks in Disorders of Consciousness
-
PLOS Computational Biology Integrating Diverse Datasets Improves Developmental Enhancer Prediction
-
PLOS Computational Biology Mechanical Cell-Matrix Feedback Explains Pairwise and Collective Endothelial Cell Behavior In Vitro
-
PLOS Computational Biology k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design
-
PLOS Computational Biology Fast Reconstruction of Compact Context-Specific Metabolic Network Models
-
PLOS Computational Biology Encoding of Natural Sounds at Multiple Spectral and Temporal Resolutions in the Human Auditory Cortex
-
PLOS Computational Biology Are Current Atomistic Force Fields Accurate Enough to Study Proteins in Crowded Environments?
-
PLOS Computational Biology On the Use of Human Mobility Proxies for Modeling Epidemics
-
PLOS Computational Biology Collective Behaviour without Collective Order in Wild Swarms of Midges
-
PLOS Computational Biology VBA: A Probabilistic Treatment of Nonlinear Models for Neurobiological and Behavioural Data
-
PLOS Computational Biology Wikipedia Usage Estimates Prevalence of Influenza-Like Illness in the United States in Near Real-Time
-
PLOS Computational Biology Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns
-
PLOS Computational Biology Searching for Collective Behavior in a Large Network of Sensory Neurons
-
PLOS Computational Biology ECOD: An Evolutionary Classification of Protein Domains
-
PLOS Computational Biology Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism
-
PLOS Computational Biology A Taxonomy of Bacterial Microcompartment Loci Constructed by a Novel Scoring Method
-
PLOS Computational Biology Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration
-
PLOS Computational Biology Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies
-
PLOS Computational Biology rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids
-
PLOS Computational Biology Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features
-
PLOS Computational Biology Classical Mathematical Models for Description and Prediction of Experimental Tumor Growth
-
PLOS Computational Biology Deep Neural Networks Rival the Representation of Primate IT Cortex for Core Visual Object Recognition
-
PLOS Computational Biology SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution
-
PLOS Computational Biology A Toolbox for Representational Similarity Analysis
-
PLOS Computational Biology From the Phenomenology to the Mechanisms of Consciousness: Integrated Information Theory 3.0
-
PLOS Computational Biology PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations
-
PLOS Computational Biology Deep Supervised, but Not Unsupervised, Models May Explain IT Cortical Representation
-
PLOS Computational Biology iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections
-
PLOS Computational Biology Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible
-
PLOS Computational Biology BEAST 2: A Software Platform for Bayesian Evolutionary Analysis
2015
-
PLOS Computational Biology Multi-timescale Modeling of Activity-Dependent Metabolic Coupling in the Neuron-Glia-Vasculature Ensemble
-
PLOS Computational Biology Partial Unwrapping and Histone Tail Dynamics in Nucleosome Revealed by Coarse-Grained Molecular Simulations
-
PLOS Computational Biology Membrane-Mediated Interaction between Strongly Anisotropic Protein Scaffolds
-
PLOS Computational Biology Transcriptional Bursting in Gene Expression: Analytical Results for General Stochastic Models
-
PLOS Computational Biology Asynchronous Rate Chaos in Spiking Neuronal Circuits
-
PLOS Computational Biology What Makes a Protein Sequence a Prion?
-
PLOS Computational Biology A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces
-
PLOS Computational Biology The Sense of Confidence during Probabilistic Learning: A Normative Account
-
PLOS Computational Biology AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility
-
PLOS Computational Biology Cell-Specific Cardiac Electrophysiology Models
-
PLOS Computational Biology Spatial Heterogeneity in Drug Concentrations Can Facilitate the Emergence of Resistance to Cancer Therapy
-
PLOS Computational Biology Evolution of Bow-Tie Architectures in Biology
-
PLOS Computational Biology An Integrated Framework Advancing Membrane Protein Modeling and Design
-
PLOS Computational Biology Multiscale Embedded Gene Co-expression Network Analysis
-
PLOS Computational Biology Maximizing Sensory Dynamic Range by Tuning the Cortical State to Criticality
-
PLOS Computational Biology Steering Evolution with Sequential Therapy to Prevent the Emergence of Bacterial Antibiotic Resistance
-
PLOS Computational Biology Computing the Local Field Potential (LFP) from Integrate-and-Fire Network Models
-
PLOS Computational Biology Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling
-
PLOS Computational Biology Mechanism of Focal Adhesion Kinase Mechanosensing
-
PLOS Computational Biology Brain Network Adaptability across Task States
-
PLOS Computational Biology Model-based Traction Force Microscopy Reveals Differential Tension in Cellular Actin Bundles
-
PLOS Computational Biology Embodied Choice: How Action Influences Perceptual Decision Making
-
PLOS Computational Biology Inference of Network Dynamics and Metabolic Interactions in the Gut Microbiome
-
PLOS Computational Biology FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants
-
PLOS Computational Biology Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method
-
PLOS Computational Biology A Computational Framework for 3D Mechanical Modeling of Plant Morphogenesis with Cellular Resolution
-
PLOS Computational Biology Forecasting the 2013–2014 Influenza Season Using Wikipedia
-
PLOS Computational Biology Sharing and Specificity of Co-expression Networks across 35 Human Tissues
-
PLOS Computational Biology General Relationship of Global Topology, Local Dynamics, and Directionality in Large-Scale Brain Networks
-
PLOS Computational Biology Cell Fate Reprogramming by Control of Intracellular Network Dynamics
-
PLOS Computational Biology A Functional Cartography of Cognitive Systems
-
PLOS Computational Biology Proportionality: A Valid Alternative to Correlation for Relative Data
-
PLOS Computational Biology Dynamic Network Drivers of Seizure Generation, Propagation and Termination in Human Neocortical Epilepsy
-
PLOS Computational Biology High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED
-
PLOS Computational Biology Predicting Anticancer Drug Responses Using a Dual-Layer Integrated Cell Line-Drug Network Model
-
PLOS Computational Biology A Bayesian Model of Category-Specific Emotional Brain Responses
-
PLOS Computational Biology SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis
-
PLOS Computational Biology Resting-State Temporal Synchronization Networks Emerge from Connectivity Topology and Heterogeneity
-
PLOS Computational Biology BASiCS: Bayesian Analysis of Single-Cell Sequencing Data
-
PLOS Computational Biology The Roles of Post-translational Modifications in the Context of Protein Interaction Networks
-
PLOS Computational Biology Combining Search, Social Media, and Traditional Data Sources to Improve Influenza Surveillance
-
PLOS Computational Biology VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires
-
PLOS Computational Biology PathVisio 3: An Extendable Pathway Analysis Toolbox
-
PLOS Computational Biology Sparse and Compositionally Robust Inference of Microbial Ecological Networks
-
PLOS Computational Biology ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
-
PLOS Computational Biology MAGMA: Generalized Gene-Set Analysis of GWAS Data
2016
-
PLOS Computational Biology Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities
-
PLOS Computational Biology Intercellular Variability in Protein Levels from Stochastic Expression and Noisy Cell Cycle Processes
-
PLOS Computational Biology The Computational Development of Reinforcement Learning during Adolescence
-
PLOS Computational Biology Residual Viremia in Treated HIV+ Individuals
-
PLOS Computational Biology The Evolutionary Origins of Hierarchy
-
PLOS Computational Biology SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent
-
PLOS Computational Biology Ensemble Tractography
-
PLOS Computational Biology Inference for Stochastic Chemical Kinetics Using Moment Equations and System Size Expansion
-
PLOS Computational Biology Pathway-Based Genomics Prediction using Generalized Elastic Net
-
PLOS Computational Biology 4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments
-
PLOS Computational Biology Evolution-Based Functional Decomposition of Proteins
-
PLOS Computational Biology Reconstruction of Tissue-Specific Metabolic Networks Using CORDA
-
PLOS Computational Biology Dynamic Cholesterol-Conditioned Dimerization of the G Protein Coupled Chemokine Receptor Type 4
-
PLOS Computational Biology Measuring Integrated Information from the Decoding Perspective
-
PLOS Computational Biology Reservoir Computing Properties of Neural Dynamics in Prefrontal Cortex
-
PLOS Computational Biology A Biophysical Model of CRISPR/Cas9 Activity for Rational Design of Genome Editing and Gene Regulation
-
PLOS Computational Biology Using an Insect Mushroom Body Circuit to Encode Route Memory in Complex Natural Environments
-
PLOS Computational Biology BinPacker: Packing-Based De Novo Transcriptome Assembly from RNA-seq Data
-
PLOS Computational Biology The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization
-
PLOS Computational Biology Constrained Allocation Flux Balance Analysis
-
PLOS Computational Biology Structural Identifiability of Dynamic Systems Biology Models
-
PLOS Computational Biology Deep Neural Networks as a Computational Model for Human Shape Sensitivity
-
PLOS Computational Biology Does High-Dose Antimicrobial Chemotherapy Prevent the Evolution of Resistance?
-
PLOS Computational Biology Identifying Malaria Transmission Foci for Elimination Using Human Mobility Data
-
PLOS Computational Biology Deep Learning for Population Genetic Inference
-
PLOS Computational Biology Quantifying Clonal and Subclonal Passenger Mutations in Cancer Evolution
-
PLOS Computational Biology Neighborhood Regularized Logistic Matrix Factorization for Drug-Target Interaction Prediction
-
PLOS Computational Biology The Multilayer Connectome of Caenorhabditis elegans
-
PLOS Computational Biology Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments
-
PLOS Computational Biology SMOG 2: A Versatile Software Package for Generating Structure-Based Models
-
PLOS Computational Biology Cytofkit: A Bioconductor Package for an Integrated Mass Cytometry Data Analysis Pipeline
-
PLOS Computational Biology Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights
-
PLOS Computational Biology Stimulation-Based Control of Dynamic Brain Networks
-
PLOS Computational Biology Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes
-
PLOS Computational Biology NLLSS: Predicting Synergistic Drug Combinations Based on Semi-supervised Learning
-
PLOS Computational Biology Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics
-
PLOS Computational Biology CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing
-
PLOS Computational Biology MEGAN Community Edition – Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data
2017
-
PLOS Computational Biology A Computational Approach for Identifying Synergistic Drug Combinations
-
PLOS Computational Biology Intrinsically-generated fluctuating activity in excitatory-inhibitory networks
-
PLOS Computational Biology Erroneous energy-generating cycles in published genome scale metabolic networks: Identification and removal
-
PLOS Computational Biology ROTS: An R package for reproducibility-optimized statistical testing
-
PLOS Computational Biology An optimal strategy for epilepsy surgery: Disruption of the rich-club?
-
PLOS Computational Biology Spontaneous cortical activity is transiently poised close to criticality
-
PLOS Computational Biology Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks
-
PLOS Computational Biology Imputation for transcription factor binding predictions based on deep learning
-
PLOS Computational Biology Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment
-
PLOS Computational Biology Hard real-time closed-loop electrophysiology with the Real-Time eXperiment Interface (RTXI)
-
PLOS Computational Biology Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks
-
PLOS Computational Biology Inverse stochastic resonance in networks of spiking neurons
-
PLOS Computational Biology Depth-dependent flow and pressure characteristics in cortical microvascular networks
-
PLOS Computational Biology Projecting social contact matrices in 152 countries using contact surveys and demographic data
-
PLOS Computational Biology Dose-response relationships for environmentally mediated infectious disease transmission models
-
PLOS Computational Biology Two dynamic regimes in the human gut microbiome
-
PLOS Computational Biology A Topological Criterion for Filtering Information in Complex Brain Networks
-
PLOS Computational Biology High-order epistasis shapes evolutionary trajectories
-
PLOS Computational Biology Predictive representations can link model-based reinforcement learning to model-free mechanisms
-
PLOS Computational Biology Dysfunctions of the basal ganglia-cerebellar-thalamo-cortical system produce motor tics in Tourette syndrome
-
PLOS Computational Biology Quantifying critical states of complex diseases using single-sample dynamic network biomarkers
-
PLOS Computational Biology A General Shear-Dependent Model for Thrombus Formation
-
PLOS Computational Biology Persisting fetal clonotypes influence the structure and overlap of adult human T cell receptor repertoires
-
PLOS Computational Biology Widespread position-specific conservation of synonymous rare codons within coding sequences
-
PLOS Computational Biology Post-transcriptional regulation across human tissues
-
PLOS Computational Biology Mindboggling morphometry of human brains
-
PLOS Computational Biology Interrogating the topological robustness of gene regulatory circuits by randomization
-
PLOS Computational Biology SteadyCom: Predicting microbial abundances while ensuring community stability
-
PLOS Computational Biology Comparing individual-based approaches to modelling the self-organization of multicellular tissues
-
PLOS Computational Biology Human mobility and the spatial transmission of influenza in the United States
-
PLOS Computational Biology A deep convolutional neural network for classification of red blood cells in sickle cell anemia
-
PLOS Computational Biology Fast online deconvolution of calcium imaging data
-
PLOS Computational Biology Towards a theory of cortical columns: From spiking neurons to interacting neural populations of finite size
-
PLOS Computational Biology Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks
-
PLOS Computational Biology BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods
-
PLOS Computational Biology BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities
-
PLOS Computational Biology Active Vertex Model for cell-resolution description of epithelial tissue mechanics
-
PLOS Computational Biology Could a Neuroscientist Understand a Microprocessor?
-
PLOS Computational Biology Metacoder: An R package for visualization and manipulation of community taxonomic diversity data
-
PLOS Computational Biology LRSSLMDA: Laplacian Regularized Sparse Subspace Learning for MiRNA-Disease Association prediction
-
PLOS Computational Biology PBMDA: A novel and effective path-based computational model for miRNA-disease association prediction
-
PLOS Computational Biology OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
-
PLOS Computational Biology Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model
-
PLOS Computational Biology mixOmics: An R package for ‘omics feature selection and multiple data integration
-
PLOS Computational Biology Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads