yusuke1997/dblp-id-title huggingface dataset:
BioSeq-Diabolo: Biological sequence similarity analysis using Diabolo
Towards integration of time-resolved confocal microscopy of a 3D in vitro microfluidic platform with a hybrid multiscale model of tumor angiogenesis
Representation of foreseeable choice outcomes in orbitofrontal cortex triplet-wise interactions
Mapping the Conformation Space of Wildtype and Mutant H-Ras with a Memetic, Cellular, and Multiscale Evolutionary Algorithm
Inferring Strain Mixture within Clinical Plasmodium falciparum Isolates from Genomic Sequence Data
TphPMF: A microbiome data imputation method using hierarchical Bayesian Probabilistic Matrix Factorization
Computational Model of Vascular Endothelial Growth Factor Spatial Distribution in Muscle and Pro-Angiogenic Cell Therapy
Microarray Based Diagnosis Profits from Better Documentation of Gene Expression Signatures
Social dilemmas of sociality due to beneficial and costly contagion
Impact of the COVID-19 pandemic on computational biology early career researchers: A global retrospective study
Ligand Clouds around Protein Clouds: A Scenario of Ligand Binding with Intrinsically Disordered Proteins
miRAW: A deep learning-based approach to predict microRNA targets by analyzing whole microRNA transcripts
Spike-Timing Dependence of Structural Plasticity Explains Cooperative Synapse Formation in the Neocortex
Role of non-specific interactions in the phase-separation and maturation of macromolecules
Impaired Air Conditioning within the Nasal Cavity in Flat-Faced Homo
Decoding decision-making behavior from sparse neural spiking activity
Dominating lengthscales of zebrafish collective behaviour
Imbalanced amplification: A mechanism of amplification and suppression from local imbalance of excitation and inhibition in cortical circuits
Multivariate pattern dependence
Few-shot learning for classification of novel macromolecular structures in cryo-electron tomograms
Signaling Pathways Involved in Striatal Synaptic Plasticity are Sensitive to Temporal Pattern and Exhibit Spatial Specificity
Interpreting neural decoding models using grouped model reliance
Catalysis of Protein Folding by Chaperones Accelerates Evolutionary Dynamics in Adapting Cell Populations
Direct reciprocity between individuals that use different strategy spaces
Nonparametric serial interval estimation with uniform mixtures
Evolutionary and Physiological Importance of Hub Proteins
From Bytes to Bedside: Data Integration and Computational Biology for Translational Cancer Research
In Vivo Volume and Hemoglobin Dynamics of Human Red Blood Cells
Assessing the best time interval between doses in a two-dose vaccination regimen to reduce the number of deaths in an ongoing epidemic of SARS-CoV-2
Arioc: High-concurrency short-read alignment on multiple GPUs
Reward-driven changes in striatal pathway competition shape evidence evaluation in decision-making
Embedding Responses in Spontaneous Neural Activity Shaped through Sequential Learning
PyOIF: Computational tool for modelling of multi-cell flows in complex geometries
Improving the validity of neuroimaging decoding tests of invariant and configural neural representation
From Spiking Neuron Models to Linear-Nonlinear Models
LinguaPhylo: A probabilistic model specification language for reproducible phylogenetic analyses
Size and structure of the sequence space of repeat proteins
Structural and Functional Characterization of a Caenorhabditis elegans Genetic Interaction Network within Pathways
In silico modeling of directed differentiation of induced pluripotent stem cells to definitive endoderm
Fusion and Fission of Genes Define a Metric between Fungal Genomes
Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression
Chemophoresis engine: A general mechanism of ATPase-driven cargo transport
Identification and quantitation of clinically relevant microbes in patient samples: Comparison of three k-mer based classifiers for speed, accuracy, and sensitivity
Optimal algorithms for controlling infectious diseases in real time using noisy infection data
Black-boxing and cause-effect power
A Role for Both Conformational Selection and Induced Fit in Ligand Binding by the LAO Protein
Impact of Network Structure and Cellular Response on Spike Time Correlations
A Model for Sigma Factor Competition in Bacterial Cells
Strawberry: Fast and accurate genome-guided transcript reconstruction and quantification from RNA-Seq
Benchmarking uncertainty quantification for protein engineering
Systematic design of pulse dosing to eradicate persister bacteria
Expression-Guided In Silico Evaluation of Candidate Cis Regulatory Codes for Drosophila Muscle Founder Cells
Molecular Basis of Calcium-Sensitizing and Desensitizing Mutations of the Human Cardiac Troponin C Regulatory Domain: A Multi-Scale Simulation Study
Macroscopic resting state model predicts theta burst stimulation response: A randomized trial
Structure-based Molecular Simulations Reveal the Enhancement of Biased Brownian Motions in Single-headed Kinesin
Representation of Time-Varying Stimuli by a Network Exhibiting Oscillations on a Faster Time Scale
SPIN-CGNN: Improved fixed backbone protein design with contact map-based graph construction and contact graph neural network
Unveiling the role of local metabolic constraints on the structure and activity of spiking neural networks
Assessing predictors for new post translational modification sites: A case study on hydroxylation
Cooperative DNA Recognition Modulated by an Interplay between Protein-Protein Interactions and DNA-Mediated Allostery
Phase-Coherence Transitions and Communication in the Gamma Range between Delay-Coupled Neuronal Populations
SiGMoiD: A super-statistical generative model for binary data
Feedback parameters for a closed-loop multiple-input multiple-output model of the upper limb
Consistent Estimation of Gibbs Energy Using Component Contributions
Noise-Induced Min Phenotypes in E. coli
Correction: Baseline CD4+ T Cell Counts Correlates with HIV-1 Synonymous Rate in HLA-B*5701 Subjects with Different Risk of Disease Progression
Optimal control of agent-based models via surrogate modeling
GenoTriplo: A SNP genotype calling method for triploids
MDCK Cystogenesis Driven by Cell Stabilization within Computational Analogues
RNACOREX - RNA coregulatory network explorer and classifier
A Bayesian approach to modelling heterogeneous calcium responses in cell populations
Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model
The role of cell geometry and cell-cell communication in gradient sensing
An Electrostatic Funnel in the GABA-Binding Pathway
Evolutionary dynamics of paroxysmal nocturnal hemoglobinuria
Thermodynamic model of gene regulation for the Or59b olfactory receptor in Drosophila
Decorrelation of Neural-Network Activity by Inhibitory Feedback
PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny
Conflicting effects of recombination on the evolvability and robustness in neutrally evolving populations
The Emergence of Alternative 3′ and 5′ Splice Site Exons from Constitutive Exons
Impact of Limited Solvent Capacity on Metabolic Rate, Enzyme Activities, and Metabolite Concentrations of S. cerevisiae Glycolysis
The dopamine circuit as a reward-taxis navigation system
Bayesian inference and comparison of stochastic transcription elongation models
The effect of spatial randomness on the average fixation time of mutants
An ensemble n-sub-epidemic modeling framework for short-term forecasting epidemic trajectories: Application to the COVID-19 pandemic in the USA
Global and Local Architecture of the Mammalian microRNA-Transcription Factor Regulatory Network
Short Term Synaptic Depression Imposes a Frequency Dependent Filter on Synaptic Information Transfer
Estimating a novel stochastic model for within-field disease dynamics of banana bunchy top virus via approximate Bayesian computation
Bridging from single to collective cell migration: A review of models and links to experiments
Multiscale analysis of autotroph-heterotroph interactions in a high-temperature microbial community
A Bayesian model based computational analysis of the relationship between bisulfite accessible single-stranded DNA in chromatin and somatic hypermutation of immunoglobulin genes
Genetic Architecture Promotes the Evolution and Maintenance of Cooperation
Isolating single cycles of neural oscillations in population spiking
When do correlations increase with firing rates in recurrent networks?
Parameters in Dynamic Models of Complex Traits are Containers of Missing Heritability
Transition from Persistent to Anti-Persistent Correlations in Postural Sway Indicates Velocity-Based Control
A low-threshold potassium current enhances sparseness and reliability in a model of avian auditory cortex
TGF-M: Topology-augmented geometric features enhance molecular property prediction
A Model for the Epigenetic Switch Linking Inflammation to Cell Transformation: Deterministic and Stochastic Approaches
Ten simple rules for leading a many-author non-empirical paper
Biomedical Cloud Computing With Amazon Web Services
Functional Maps of Protein Complexes from Quantitative Genetic Interaction Data
Linear viscoelastic properties of the vertex model for epithelial tissues
The role of curvature feedback in the energetics and dynamics of lamprey swimming: A closed-loop model
Emotional Valence and the Free-Energy Principle
Computer Simulations Imply Forelimb-Dominated Underwater Flight in Plesiosaurs
OpenSim Moco: Musculoskeletal optimal control
Simulation enabled search for explanatory mechanisms of the fracture healing process
Reduction in Learning Rates Associated with Anterograde Interference Results from Interactions between Different Timescales in Motor Adaptation
Nucleotide-time alignment for molecular recorders
A Method to Constrain Genome-Scale Models with 13 C Labeling Data
Grandmothering and cognitive resources are required for the emergence of menopause and extensive post-reproductive lifespan
The influence of cross-border mobility on the COVID-19 epidemic in Nordic countries
Segmentation and Tracking of Adherens Junctions in 3D for the Analysis of Epithelial Tissue Morphogenesis
Leveraging structure-informed machine learning for fast steric zipper propensity prediction across whole proteomes
Optimal Screening Strategies for Healthcare Associated Infections in a Multi-Institutional Setting
Networks of Causal Linkage Between Eigenmodes Characterize Behavioral Dynamics of Caenorhabditis elegans
Comprehensive analysis of lectin-glycan interactions reveals determinants of lectin specificity
Allosteric mechanism of the circadian protein Vivid resolved through Markov state model and machine learning analysis
A549 in-silico 1.0: A first computational model to simulate cell cycle dependent ion current modulation in the human lung adenocarcinoma
High Stimulus-Related Information in Barrel Cortex Inhibitory Interneurons
Robust Inference of Cell-to-Cell Expression Variations from Single- and K-Cell Profiling
A Community Resource Benchmarking Predictions of Peptide Binding to MHC-I Molecules
From Functional Genomics to Functional Immunomics: New Challenges, Old Problems, Big Rewards
Comparative Analyses of Fundamental Differences in Membrane Transport Capabilities in Prokaryotes and Eukaryotes
Mapping the dynamics of visual feature coding: Insights into perception and integration
Tensile force-induced cytoskeletal remodeling: Mechanics before chemistry
Correction: From Inverse Problems in Mathematical Physiology to Quantitative Differential Diagnoses
Exploring Massive, Genome Scale Datasets with the GenometriCorr Package
Managing and Analyzing Next-Generation Sequence Data
The Modular Organization of Domain Structures: Insights into Protein-Protein Binding
Cancer molecular subtyping using limited multi-omics data with missingness
Correction: Reactive Searching and Infotaxis in Odor Source Localization
Models of Purkinje cell dendritic tree selection during early cerebellar development
The Spirit of Competition: To Win or Not To Win
Signalling and the Evolution of Cooperative Foraging in Dynamic Environments
The Affective Ising Model: A computational account of human affect dynamics
Cortical Gamma Rhythms Modulate NMDAR-Mediated Spike Timing Dependent Plasticity in a Biophysical Model
Alterations of the interactome of Bcl-2 proteins in breast cancer at the transcriptional, mutational and structural level
Mapping the learning curves of deep learning networks
Differences in olfactory bulb mitral cell spiking with ortho- and retronasal stimulation revealed by data-driven models
Complex spatiotemporal oscillations emerge from transverse instabilities in large-scale brain networks
Action Potential Initiation in the Hodgkin-Huxley Model
Formation of phage lysis patterns and implications on co-propagation of phages and motile host bacteria
Challenges Predicting Ligand-Receptor Interactions of Promiscuous Proteins: The Nuclear Receptor PXR
Reframing dopamine: A controlled controller at the limbic-motor interface
Estimating behavioural relaxation induced by COVID-19 vaccines in the first months of their rollout
Predicting Achievable Fundamental Frequency Ranges in Vocalization Across Species
Stereotypical Escape Behavior in Caenorhabditis elegans Allows Quantification of Effective Heat Stimulus Level
Establishing brain states in neuroimaging data
Membrane perturbing properties of toxin mycolactone from Mycobacterium ulcerans
Depletion of the Chromatin Looping Proteins CTCF and Cohesin Causes Chromatin Compaction: Insight into Chromatin Folding by Polymer Modelling
Determinants of drug-target interactions at the single cell level
Emergence of Functional Specificity in Balanced Networks with Synaptic Plasticity
Retinal optic flow during natural locomotion
Interacting active surfaces: A model for three-dimensional cell aggregates
Phi fluctuates with surprisal: An empirical pre-study for the synthesis of the free energy principle and integrated information theory
A coupled-oscillator model of olfactory bulb gamma oscillations
Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome
Hybrid predictive coding: Inferring, fast and slow
Cancer cell sedimentation in 3D cultures reveals active migration regulated by self-generated gradients and adhesion sites
In Silico Elucidation of the Molecular Mechanism Defining the Adverse Effect of Selective Estrogen Receptor Modulators
Open Access: Taking Full Advantage of the Content
Optimizing circadian drug infusion schedules towards personalized cancer chronotherapy
Convergent perturbation of the human domain-resolved interactome by viruses and mutations inducing similar disease phenotypes
Dynamic Structure Formation of Peripheral Membrane Proteins
Statistical Inference for Multi-Pathogen Systems
ARTreeFormer: A faster attention-based autoregressive model for phylogenetic inference
The Energy Landscape, Folding Pathways and the Kinetics of a Knotted Protein
The Effect of Ongoing Exposure Dynamics in Dose Response Relationships
Electrical synapses regulate both subthreshold integration and population activity of principal cells in response to transient inputs within canonical feedforward circuits
Modular, focused data science education improves biomedical learners' abilities: A study of the Data and Analytics for Research Training (DART) program
AutoEdge-CCP: A novel approach for predicting cancer-associated circRNAs and drugs based on automated edge embedding
Using early detection data to estimate the date of emergence of an epidemic outbreak
Information transmission in a cell monolayer: A numerical study
Same but not alike: Structure, flexibility and energetics of domains in multi-domain proteins are influenced by the presence of other domains
Neural activity induces strongly coupled electro-chemo-mechanical interactions and fluid flow in astrocyte networks and extracellular space - A computational study
Humans account for cognitive costs when finding shortcuts: An information-theoretic analysis of navigation
Quorum Sensing Desynchronization Leads to Bimodality and Patterned Behaviors
Gate-based quantum computing for protein design
Mate Choice and the Origin of Menopause
Across-subjects classification of stimulus modality from human MEG high frequency activity
Sequence learning recodes cortical representations instead of strengthening initial ones
Dendritic Spikes Amplify the Synaptic Signal to Enhance Detection of Motion in a Simulation of the Direction-Selective Ganglion Cell
Covering Hierarchical Dirichlet Mixture Models on binary data to enhance genomic stratifications in onco-hematology
The Long and Viscous Road: Uncovering Nuclear Diffusion Barriers in Closed Mitosis
VIRify: An integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models
Regulated bacterial interaction networks: A mathematical framework to describe competitive growth under inclusion of metabolite cross-feeding
LASSIM - A network inference toolbox for genome-wide mechanistic modeling
Wisdom of crowds in computational biology
Adaptive algorithms for shaping behavior
Correction: A new model for simultaneous dimensionality reduction and time-varying functional connectivity estimation
Ten simple rules for recognizing data and software contributions in hiring, promotion, and tenure
The role of children in the spread of COVID-19: Using household data from Bnei Brak, Israel, to estimate the relative susceptibility and infectivity of children
Ten simple rules for carrying out and writing meta-analyses
ProteinHistorian: Tools for the Comparative Analysis of Eukaryote Protein Origin
Personalized pathology test for Cardio-vascular disease: Approximate Bayesian computation with discriminative summary statistics learning
Functional triplet motifs underlie accurate predictions of single-trial responses in populations of tuned and untuned V1 neurons
PLOS Computational Biology 2015 Reviewer Thank You
Probing the Mutational Interplay between Primary and Promiscuous Protein Functions: A Computational-Experimental Approach
A modular approach for modeling the cell cycle based on functional response curves
Enhanced Sensitivity to Rapid Input Fluctuations by Nonlinear Threshold Dynamics in Neocortical Pyramidal Neurons
Ten practical tips and tricks to improve the effectiveness of biological network alignment
Resist or perish: Fate of a microbial population subjected to a periodic presence of antimicrobial
Autonomous epithelial folding induced by an intracellular mechano-polarity feedback loop
Inferring Growth Control Mechanisms in Growing Multi-cellular Spheroids of NSCLC Cells from Spatial-Temporal Image Data
Estimating Costs and Benefits of CTL Escape Mutations in SIV/HIV Infection
Computational study on ratio-sensing in yeast galactose utilization pathway
Deep inference of seabird dives from GPS-only records: Performance and generalization properties
Dynamical Organization of Syntaxin-1A at the Presynaptic Active Zone
A curriculum learning approach to training antibody language models
Functional asymmetry and plasticity of electrical synapses interconnecting neurons through a 36-state model of gap junction channel gating
Harnessing the flexibility of neural networks to predict dynamic theoretical parameters underlying human choice behavior
Emergent Patterns of Social Affiliation in Primates, a Model
BayFlux: A Bayesian method to quantify metabolic Fluxes and their uncertainty at the genome scale
Cellular Architecture Regulates Collective Calcium Signaling and Cell Contractility
Signaling models for dopamine-dependent temporal contiguity in striatal synaptic plasticity
Recognizing Sequences of Sequences
Lipid-driven alignment and binding of p7 dimers in early oligomer assembly
Identification and Rational Redesign of Peptide Ligands to CRIP1, A Novel Biomarker for Cancers
Co-operation between Polymerases and Nucleotide Synthetases in the RNA World
Cancerin: A computational pipeline to infer cancer-associated ceRNA interaction networks
A computational grid-to-place-cell transformation model indicates a synaptic driver of place cell impairment in early-stage Alzheimer's Disease
The Role of Thalamic Population Synchrony in the Emergence of Cortical Feature Selectivity
A multi-scale layer-resolved spiking network model of resting-state dynamics in macaque visual cortical areas
Correction: Personalized glucose forecasting for type 2 diabetes using data assimilation
Modelling disease mitigation at mass gatherings: A case study of COVID-19 at the 2022 FIFA World Cup
MIGGRI: A multi-instance graph neural network model for inferring gene regulatory networks for Drosophila from spatial expression images
Homeostatic bidirectional plasticity in upbound and downbound micromodules in a model of the olivocerebellar loop
IL6-mediated HCoV-host interactome regulatory network and GO/Pathway enrichment analysis
Myxococcus xanthus Gliding Motors Are Elastically Coupled to the Substrate as Predicted by the Focal Adhesion Model of Gliding Motility
Three-dimensional topology optimization model to simulate the external shapes of bone
Modeling of Wnt-mediated tissue patterning in vertebrate embryogenesis
Estimation of Vaccine Efficacy and Critical Vaccination Coverage in Partially Observed Outbreaks
Modeling the sequence dependence of differential antibody binding in the immune response to infectious disease
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
Conformational coupling by trans-phosphorylation in calcium calmodulin dependent kinase II
Viral surface geometry shapes influenza and coronavirus spike evolution through antibody pressure
NUFEB: A massively parallel simulator for individual-based modelling of microbial communities
HAPP: High-accuracy pipeline for processing deep metabarcoding data
Identification of Biochemical Network Modules Based on Shortest Retroactive Distances
Early transmission of sensitive strain slows down emergence of drug resistance in Plasmodium vivax
The Role of Elastic Stresses on Leaf Venation Morphogenesis
Spatially Pooled Contrast Responses Predict Neural and Perceptual Similarity of Naturalistic Image Categories
Detecting critical slowing down in high-dimensional epidemiological systems
GABAergic neurons can facilitate the propagation of cortical spreading depolarization: experiments in mouse neocortical slices and a novel neural field computational model
Developmental hourglass: Verification by numerical evolution and elucidation by dynamical-systems theory
Determination of effective synaptic conductances using somatic voltage clamp
Clonal dominance and transplantation dynamics in hematopoietic stem cell compartments
Kinetic modeling of H2O2 dynamics in the mitochondria of HeLa cells
Spatial distribution of cytoskeleton-mediated feedback controls cell polarization: A computational study
In silico assessment of genetic variation in KCNA5 reveals multiple mechanisms of human atrial arrhythmogenesis
Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5'-Phosphate Production in E . coli
Best practices for estimating and reporting epidemiological delay distributions of infectious diseases
Recovering Protein-Protein and Domain-Domain Interactions from Aggregation of IP-MS Proteomics of Coregulator Complexes
DeepChIA-PET: Accurately predicting ChIA-PET from Hi-C and ChIP-seq with deep dilated networks
Importance of Electrostatic Interactions in the Association of Intrinsically Disordered Histone Chaperone Chz1 and Histone H2A.Z-H2B
Automated Tracking of Whiskers in Videos of Head Fixed Rodents
Temporal Gillespie Algorithm: Fast Simulation of Contagion Processes on Time-Varying Networks
An open source tool to infer epidemiological and immunological dynamics from serological data: serosolver
Stochastic Simulation of Biomolecular Networks in Dynamic Environments
Functional mechanisms underlie the emergence of a diverse range of plasticity phenomena
Beyond ℓ1 sparse coding in V1
PPM-Decay: A computational model of auditory prediction with memory decay
Correction: Assessment of ab initio models of protein complexes by molecular dynamics