Computer & Information Sciences
PLOS Computational Biology: Methods
The PLOS Computational Biology Methods Section was launched in 2013 and
has given computational method development a dedicated space in the journal.
Handled by our Methods Editors, Methods articles present outstanding
contributions of innovative computational methods for highly relevant
biological problems. The methods are expected to be thoroughly validated
on real (and, in addition, possibly artificial) data and to be generally
available for download or as web services.
Image Credit: Van Valen et al.
Editorial
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PLOS Computational Biology New Methods Section in PLOS Computational Biology
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PLOS Computational Biology How to Write a Presubmission Inquiry
Research
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PLOS Computational Biology DOT: Gene-set analysis by combining decorrelated association statistics
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PLOS Computational Biology DeLTA: Automated cell segmentation, tracking, and lineage reconstruction using deep learning
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PLOS Computational Biology DRAMS: A tool to detect and re-align mixed-up samples for integrative studies of multi-omics data
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PLOS Computational Biology Localized semi-nonnegative matrix factorization (LocaNMF) of widefield calcium imaging data
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PLOS Computational Biology Climbing Escher’s stairs: A way to approximate stability landscapes in multidimensional systems
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PLOS Computational Biology Comparison of methods for rhythm analysis of complex animals’ acoustic signals
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PLOS Computational Biology 3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries
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PLOS Computational Biology MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data
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PLOS Computational Biology The use of mixture density networks in the emulation of complex epidemiological individual-based models
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PLOS Computational Biology Deconvolution of calcium imaging data using marked point processes
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PLOS Computational Biology Parallel Tempering with Lasso for model reduction in systems biology
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PLOS Computational Biology The Beacon Calculus: A formal method for the flexible and concise modelling of biological systems
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PLOS Computational Biology A computational framework for a Lyapunov-enabled analysis of biochemical reaction networks
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PLOS Computational Biology Graph-based description of tertiary lymphoid organs at single-cell level
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PLOS Computational Biology SuperFreq: Integrated mutation detection and clonal tracking in cancer
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PLOS Computational Biology A system for tracking whisker kinematics and whisker shape in three dimensions
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PLOS Computational Biology Computational optimization of associative learning experiments
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PLOS Computational Biology Estimation of temporal covariances in pathogen dynamics using Bayesian multivariate autoregressive models
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PLOS Computational Biology From energy to cellular forces in the Cellular Potts Model: An algorithmic approach
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PLOS Computational Biology CDSeq: A novel complete deconvolution method for dissecting heterogeneous samples using gene expression data
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PLOS Computational Biology Clustering-independent analysis of genomic data using spectral simplicial theory
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PLOS Computational Biology Uncovering the subtype-specific temporal order of cancer pathway dysregulation
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PLOS Computational Biology Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences
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PLOS Computational Biology Bayesian inference of neuronal assemblies
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PLOS Computational Biology SCMarker: Ab initio marker selection for single cell transcriptome profiling
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PLOS Computational Biology Ancestral reconstruction of protein interaction networks
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PLOS Computational Biology SourceSet: A graphical model approach to identify primary genes in perturbed biological pathways
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PLOS Computational Biology Detecting distant-homology protein structures by aligning deep neural-network based contact maps
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PLOS Computational Biology Prepaid parameter estimation without likelihoods
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PLOS Computational Biology Executable pathway analysis using ensemble discrete-state modeling for large-scale data
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PLOS Computational Biology Integrating Hi-C links with assembly graphs for chromosome-scale assembly
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PLOS Computational Biology FAMoS: A Flexible and dynamic Algorithm for Model Selection to analyse complex systems dynamics
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PLOS Computational Biology Reappraising the utility of Google Flu Trends
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PLOS Computational Biology Ensemble of decision tree reveals potential miRNA-disease associations
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PLOS Computational Biology Assessing key decisions for transcriptomic data integration in biochemical networks
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PLOS Computational Biology Information-theoretic analysis of multivariate single-cell signaling responses
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PLOS Computational Biology PrediTALE: A novel model learned from quantitative data allows for new perspectives on TALE targeting
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PLOS Computational Biology Disease gene prediction for molecularly uncharacterized diseases
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PLOS Computational Biology Hierarchical Bayesian inference for concurrent model fitting and comparison for group studies
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PLOS Computational Biology Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome
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PLOS Computational Biology Uncovering functional signature in neural systems via random matrix theory
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PLOS Computational Biology A Bayesian model of acquisition and clearance of bacterial colonization incorporating within-host variation
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PLOS Computational Biology Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm
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PLOS Computational Biology Inferring neural circuit structure from datasets of heterogeneous tuning curves
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PLOS Computational Biology Bayes-optimal estimation of overlap between populations of fixed size
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PLOS Computational Biology Identification of pathways associated with chemosensitivity through network embedding
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PLOS Computational Biology Computational geometry for modeling neural populations: From visualization to simulation
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PLOS Computational Biology Integration of single-cell RNA-seq data into population models to characterize cancer metabolism
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PLOS Computational Biology CoPhosK: A method for comprehensive kinase substrate annotation using co-phosphorylation analysis
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PLOS Computational Biology Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes
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PLOS Computational Biology Identifying individual risk rare variants using protein structure guided local tests (POINT)
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PLOS Computational Biology A local measure of symmetry and orientation for individual spikes of grid cells
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PLOS Computational Biology Multi-study inference of regulatory networks for more accurate models of gene regulation
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PLOS Computational Biology OpenCASA: A new open-source and scalable tool for sperm quality analysis
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PLOS Computational Biology Statistical investigations of protein residue direct couplings
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PLOS Computational Biology SFPEL-LPI: Sequence-based Feature Projection Ensemble Learning for Predicting LncRNA-Protein Interactions
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PLOS Computational Biology PremPDI estimates and interprets the effects of missense mutations on protein-DNA interactions
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PLOS Computational Biology Identifying (un)controllable dynamical behavior in complex networks
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PLOS Computational Biology Detection and analysis of spatiotemporal patterns in brain activity
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PLOS Computational Biology Motif-Aware PRALINE: Improving the alignment of motif regions
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PLOS Computational Biology Efficient pedigree recording for fast population genetics simulation
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PLOS Computational Biology SIG-DB: Leveraging homomorphic encryption to securely interrogate privately held genomic databases
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PLOS Computational Biology An automated approach to the quantitation of vocalizations and vocal learning in the songbird
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PLOS Computational Biology MDHGI: Matrix Decomposition and Heterogeneous Graph Inference for miRNA-disease association prediction
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PLOS Computational Biology Rare-event sampling of epigenetic landscapes and phenotype transitions
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PLOS Computational Biology Crowdsourcing image analysis for plant phenomics to generate ground truth data for machine learning
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PLOS Computational Biology FusionPathway: Prediction of pathways and therapeutic targets associated with gene fusions in cancer
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PLOS Computational Biology Cancerin: A computational pipeline to infer cancer-associated ceRNA interaction networks
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PLOS Computational Biology miRAW: A deep learning-based approach to predict microRNA targets by analyzing whole microRNA transcripts
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PLOS Computational Biology Solving the RNA design problem with reinforcement learning
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PLOS Computational Biology Simulations to benchmark time-varying connectivity methods for fMRI
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PLOS Computational Biology Automated evaluation of quaternary structures from protein crystals
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PLOS Computational Biology RosettaAntibodyDesign (RAbD): A general framework for computational antibody design
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PLOS Computational Biology Correcting for batch effects in case-control microbiome studies
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PLOS Computational Biology A modelling approach for exploring muscle dynamics during cyclic contractions
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PLOS Computational Biology Using pseudoalignment and base quality to accurately quantify microbial community composition
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PLOS Computational Biology Model-based analysis of competing-endogenous pathways (MACPath) in human cancers
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PLOS Computational Biology 4Cin: A computational pipeline for 3D genome modeling and virtual Hi-C analyses from 4C data
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PLOS Computational Biology Method for the simulation of blood platelet shape and its evolution during activation
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PLOS Computational Biology Imaging of neural oscillations with embedded inferential and group prevalence statistics
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PLOS Computational Biology Clustering gene expression time series data using an infinite Gaussian process mixture model
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PLOS Computational Biology Improving pairwise comparison of protein sequences with domain co-occurrence
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PLOS Computational Biology LRSSLMDA: Laplacian Regularized Sparse Subspace Learning for MiRNA-Disease Association prediction
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PLOS Computational Biology Non-linear auto-regressive models for cross-frequency coupling in neural time series
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PLOS Computational Biology Strawberry: Fast and accurate genome-guided transcript reconstruction and quantification from RNA-Seq
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PLOS Computational Biology Multivariate pattern dependence
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PLOS Computational Biology An efficient moments-based inference method for within-host bacterial infection dynamics
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PLOS Computational Biology Automated visualization of rule-based models
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PLOS Computational Biology Electrical stimulus artifact cancellation and neural spike detection on large multi-electrode arrays
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PLOS Computational Biology Individual versus superensemble forecasts of seasonal influenza outbreaks in the United States
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PLOS Computational Biology Maximum entropy methods for extracting the learned features of deep neural networks
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PLOS Computational Biology Clusternomics: Integrative context-dependent clustering for heterogeneous datasets
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PLOS Computational Biology Incorporating networks in a probabilistic graphical model to find drivers for complex human diseases
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PLOS Computational Biology Vicus: Exploiting local structures to improve network-based analysis of biological data
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PLOS Computational Biology DeepPep: Deep proteome inference from peptide profiles
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PLOS Computational Biology Estimating short-term synaptic plasticity from pre- and postsynaptic spiking
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PLOS Computational Biology Neuron’s eye view: Inferring features of complex stimuli from neural responses
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PLOS Computational Biology Efficient and accurate causal inference with hidden confounders from genome-transcriptome variation data
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PLOS Computational Biology Multi-scale approaches for high-speed imaging and analysis of large neural populations
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PLOS Computational Biology Rearrangement moves on rooted phylogenetic networks
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PLOS Computational Biology Quantifying critical states of complex diseases using single-sample dynamic network biomarkers
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PLOS Computational Biology LASSIM—A network inference toolbox for genome-wide mechanistic modeling
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PLOS Computational Biology Leveraging functional annotations in genetic risk prediction for human complex diseases
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PLOS Computational Biology Dynamic decomposition of spatiotemporal neural signals
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PLOS Computational Biology On the effects of alternative optima in context-specific metabolic model predictions
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PLOS Computational Biology Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks
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PLOS Computational Biology Identifying stochastic oscillations in single-cell live imaging time series using Gaussian processes
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PLOS Computational Biology Exhaustive search of linear information encoding protein-peptide recognition
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PLOS Computational Biology PBMDA: A novel and effective path-based computational model for miRNA-disease association prediction
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PLOS Computational Biology Fast online deconvolution of calcium imaging data
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PLOS Computational Biology Imputation for transcription factor binding predictions based on deep learning
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PLOS Computational Biology Representing high throughput expression profiles via perturbation barcodes reveals compound targets
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PLOS Computational Biology Data-driven reverse engineering of signaling pathways using ensembles of dynamic models
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PLOS Computational Biology Contextual Refinement of Regulatory Targets Reveals Effects on Breast Cancer Prognosis of the Regulome
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PLOS Computational Biology A Topological Criterion for Filtering Information in Complex Brain Networks
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PLOS Computational Biology Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model
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PLOS Computational Biology Improving Phylogeny Reconstruction at the Strain Level Using Peptidome Datasets
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PLOS Computational Biology A Graph-Centric Approach for Metagenome-Guided Peptide and Protein Identification in Metaproteomics
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PLOS Computational Biology Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments
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PLOS Computational Biology The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization
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PLOS Computational Biology Structural Identifiability of Dynamic Systems Biology Models
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PLOS Computational Biology PreTIS: A Tool to Predict Non-canonical 5’ UTR Translational Initiation Sites in Human and Mouse
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PLOS Computational Biology Likelihood-Based Inference of B Cell Clonal Families
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PLOS Computational Biology SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent
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PLOS Computational Biology SUMOFLUX: A Generalized Method for Targeted 13C Metabolic Flux Ratio Analysis
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PLOS Computational Biology Efficient Reconstruction of Predictive Consensus Metabolic Network Models
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PLOS Computational Biology A Robust Actin Filaments Image Analysis Framework
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PLOS Computational Biology Inference of Ancestral Recombination Graphs through Topological Data Analysis
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PLOS Computational Biology Metagenome and Metatranscriptome Analyses Using Protein Family Profiles
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PLOS Computational Biology Inferring Strain Mixture within Clinical Plasmodium falciparum Isolates from Genomic Sequence Data
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PLOS Computational Biology Rare Variants Association Analysis in Large-Scale Sequencing Studies at the Single Locus Level
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PLOS Computational Biology Evolution-Based Functional Decomposition of Proteins
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PLOS Computational Biology Stochastic Simulation of Biomolecular Networks in Dynamic Environments
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PLOS Computational Biology Bayesian Top-Down Protein Sequence Alignment with Inferred Position-Specific Gap Penalties
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PLOS Computational Biology Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics
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PLOS Computational Biology Incomplete Lineage Sorting and Hybridization Statistics for Large-Scale Retroposon Insertion Data
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PLOS Computational Biology BIITE: A Tool to Determine HLA Class II Epitopes from T Cell ELISpot Data
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PLOS Computational Biology BinPacker: Packing-Based De Novo Transcriptome Assembly from RNA-seq Data
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PLOS Computational Biology Ensemble Tractography
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PLOS Computational Biology NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated Ribosomes
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PLOS Computational Biology Epidemic Reconstruction in a Phylogenetics Framework: Transmission Trees as Partitions of the Node Set
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PLOS Computational Biology Text Mining for Protein Docking
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PLOS Computational Biology AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility
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PLOS Computational Biology Beyond the E-Value: Stratified Statistics for Protein Domain Prediction
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PLOS Computational Biology Inferring the Clonal Structure of Viral Populations from Time Series Sequencing
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PLOS Computational Biology Temporal Gillespie Algorithm: Fast Simulation of Contagion Processes on Time-Varying Networks
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PLOS Computational Biology Extracting Diffusive States of Rho GTPase in Live Cells: Towards In Vivo Biochemistry
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PLOS Computational Biology pMD-Membrane: A Method for Ligand Binding Site Identification in Membrane-Bound Proteins
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PLOS Computational Biology Multi-scale Visualization of Molecular Architecture Using Real-Time Ambient Occlusion in Sculptor
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PLOS Computational Biology Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning
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PLOS Computational Biology Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit
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PLOS Computational Biology ApoE4-specific Misfolded Intermediate Identified by Molecular Dynamics Simulations
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PLOS Computational Biology Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling
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PLOS Computational Biology Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways
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PLOS Computational Biology Crawling and Gliding: A Computational Model for Shape-Driven Cell Migration
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PLOS Computational Biology PF2 fit: Polar Fast Fourier Matched Alignment of Atomistic Structures with 3D Electron Microscopy Maps
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PLOS Computational Biology Efficient “Shotgun” Inference of Neural Connectivity from Highly Sub-sampled Activity Data
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PLOS Computational Biology Detecting Horizontal Gene Transfer between Closely Related Taxa
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PLOS Computational Biology A Generative Statistical Algorithm for Automatic Detection of Complex Postures
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PLOS Computational Biology An Integrated Framework Advancing Membrane Protein Modeling and Design
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PLOS Computational Biology Efficient Characterization of Parametric Uncertainty of Complex (Bio)chemical Networks
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PLOS Computational Biology Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method
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PLOS Computational Biology Time-Course Gene Set Analysis for Longitudinal Gene Expression Data
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PLOS Computational Biology Automated High-Throughput Characterization of Single Neurons by Means of Simplified Spiking Models
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PLOS Computational Biology Monte Carlo Planning Method Estimates Planning Horizons during Interactive Social Exchange
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PLOS Computational Biology A Multiscale Model Evaluates Screening for Neoplasia in Barrett’s Esophagus
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PLOS Computational Biology Sharing and Specificity of Co-expression Networks across 35 Human Tissues
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PLOS Computational Biology Convex Clustering: An Attractive Alternative to Hierarchical Clustering
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PLOS Computational Biology Accurate Computation of Survival Statistics in Genome-Wide Studies
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PLOS Computational Biology Quantification of Interactions between Dynamic Cellular Network Functionalities by Cascaded Layering
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PLOS Computational Biology A Bayesian Ensemble Approach for Epidemiological Projections
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PLOS Computational Biology Quantifying Spike Train Oscillations: Biases, Distortions and Solutions
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PLOS Computational Biology Loregic: A Method to Characterize the Cooperative Logic of Regulatory Factors
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PLOS Computational Biology NEMix: Single-cell Nested Effects Models for Probabilistic Pathway Stimulation
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PLOS Computational Biology ConPADE: Genome Assembly Ploidy Estimation from Next-Generation Sequencing Data
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PLOS Computational Biology Cell Fate Reprogramming by Control of Intracellular Network Dynamics
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PLOS Computational Biology Proportionality: A Valid Alternative to Correlation for Relative Data
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PLOS Computational Biology Inference of Quantitative Models of Bacterial Promoters from Time-Series Reporter Gene Data
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PLOS Computational Biology Protein-Protein Docking with Dynamic Residue Protonation States
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PLOS Computational Biology Estimating Relative Changes of Metabolic Fluxes
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PLOS Computational Biology BiomeNet: A Bayesian Model for Inference of Metabolic Divergence among Microbial Communities
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PLOS Computational Biology Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns
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PLOS Computational Biology Characterizing Protein Interactions Employing a Genome-Wide siRNA Cellular Phenotyping Screen
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PLOS Computational Biology A Bayesian Framework to Identify Methylcytosines from High-Throughput Bisulfite Sequencing Data
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PLOS Computational Biology SANTA: Quantifying the Functional Content of Molecular Networks
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PLOS Computational Biology Principal Component Analysis Characterizes Shared Pathogenetics from Genome-Wide Association Studies
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PLOS Computational Biology VASP-E: Specificity Annotation with a Volumetric Analysis of Electrostatic Isopotentials
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PLOS Computational Biology Unbiased Functional Clustering of Gene Variants with a Phenotypic-Linkage Network
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PLOS Computational Biology Identification of Allelic Imbalance with a Statistical Model for Subtle Genomic Mosaicism
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PLOS Computational Biology Defining the Estimated Core Genome of Bacterial Populations Using a Bayesian Decision Model
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PLOS Computational Biology A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for Next-Generation Sequencing Data
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PLOS Computational Biology A Multiscale Approach to Modelling Drug Metabolism by Membrane-Bound Cytochrome P450 Enzymes
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PLOS Computational Biology ODE Constrained Mixture Modelling: A Method for Unraveling Subpopulation Structures and Dynamics
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PLOS Computational Biology Optimal Sampling Strategies for Detecting Zoonotic Disease Epidemics
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PLOS Computational Biology A Scalable Computational Framework for Establishing Long-Term Behavior of Stochastic Reaction Networks
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PLOS Computational Biology Historical Pedigree Reconstruction from Extant Populations Using PArtitioning of RElatives (PREPARE)
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PLOS Computational Biology An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes
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PLOS Computational Biology High-Resolution Modeling of Transmembrane Helical Protein Structures from Distant Homologues
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PLOS Computational Biology Phylogenetic Quantification of Intra-tumour Heterogeneity
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PLOS Computational Biology Enhanced Methods for Local Ancestry Assignment in Sequenced Admixed Individuals
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PLOS Computational Biology Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible
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PLOS Computational Biology Exact Hybrid Particle/Population Simulation of Rule-Based Models of Biochemical Systems
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PLOS Computational Biology MRFalign: Protein Homology Detection through Alignment of Markov Random Fields
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PLOS Computational Biology HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data
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PLOS Computational Biology Probabilistic Approach to Predicting Substrate Specificity of Methyltransferases
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PLOS Computational Biology Direct Solution of the Chemical Master Equation Using Quantized Tensor Trains
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PLOS Computational Biology Universal Count Correction for High-Throughput Sequencing
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PLOS Computational Biology In Silico Single-Molecule Manipulation of DNA with Rigid Body Dynamics
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PLOS Computational Biology Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data
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PLOS Computational Biology Fast Reconstruction of Compact Context-Specific Metabolic Network Models
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PLOS Computational Biology Enumeration of Smallest Intervention Strategies in Genome-Scale Metabolic Networks
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PLOS Computational Biology Inferring the Source of Transmission with Phylogenetic Data
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PLOS Computational Biology A Tunable Coarse-Grained Model for Ligand-Receptor Interaction
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PLOS Computational Biology Novel Methods for Analysing Bacterial Tracks Reveal Persistence in Rhodobacter sphaeroides
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PLOS Computational Biology Analyzing and Synthesizing Phylogenies Using Tree Alignment Graphs
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PLOS Computational Biology A Self-Directed Method for Cell-Type Identification and Separation of Gene Expression Microarrays
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PLOS Computational Biology Consistent Estimation of Gibbs Energy Using Component Contributions