yusuke1997/dblp-id-title huggingface dataset:
Autonomous emergence of connectivity assemblies via spike triplet interactions
Within-Host Stochastic Emergence Dynamics of Immune-Escape Mutants
SARS-CoV-2 viral dynamics in non-human primates
In silico identification of potential calcium dynamics and sarcomere targets for recovering left ventricular function in rat heart failure with preserved ejection fraction
Correction: Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model
linus: Conveniently explore, share, and present large-scale biological trajectory data in a web browser
Crawling Cells Can Close Wounds without Purse Strings or Signaling
Quantification of HTLV-1 Clonality and TCR Diversity
Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production
Epigenetic cell memory: The gene's inner chromatin modification circuit
Nine quick tips for trustworthy machine learning in the biomedical sciences
Identifying locations of re-entrant drivers from patient-specific distribution of fibrosis in the left atrium
The Statistical Determinants of the Speed of Motor Learning
Gradients and Modulation of K + Channels Optimize Temporal Accuracy in Networks of Auditory Neurons
Examining the efficacy of localised gemcitabine therapy for the treatment of pancreatic cancer using a hybrid agent-based model
Optimizing therapeutic outcomes with Mechanotherapy and Ultrasound Sonopermeation in solid tumors
ChIPulate: A comprehensive ChIP-seq simulation pipeline
A semi-supervised Bayesian approach for simultaneous protein sub-cellular localisation assignment and novelty detection
HemoMIPs - Automated analysis and result reporting pipeline for targeted sequencing data
Dissecting the links between reward and loss, decision-making, and self-reported affect using a computational approach
A Unified View of "How Allostery Works"
Altered expression response upon repeated gene repression in single yeast cells
Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA
Information Flow Analysis of Interactome Networks
Sequence learning, prediction, and replay in networks of spiking neurons
Spatial Stochastic Dynamics Enable Robust Cell Polarization
Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities
A free-boundary model of a motile cell explains turning behavior
A model for hydrophobic protrusions on peripheral membrane proteins
NFTsim: Theory and Simulation of Multiscale Neural Field Dynamics
Role of Autoregulation and Relative Synthesis of Operon Partners in Alternative Sigma Factor Networks
A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family
Isofunctional Protein Subfamily Detection Using Data Integration and Spectral Clustering
Detection of focal source and arrhythmogenic substrate from body surface potentials to guide atrial fibrillation ablation
AIRRscape: An interactive tool for exploring B-cell receptor repertoires and antibody responses
A deep convolutional neural network for classification of red blood cells in sickle cell anemia
Ten simple rules and a template for creating workflows-as-applications
Optimal Stimulus Shapes for Neuronal Excitation
Similar Impact of CD8+ T Cell Responses on Early Virus Dynamics during SIV Infections of Rhesus Macaques and Sooty Mangabeys
Discriminative feature of cells characterizes cell populations of interest by a small subset of genes
Heritable tumor cell division rate heterogeneity induces clonal dominance
Influence of Low-Level Stimulus Features, Task Dependent Factors, and Spatial Biases on Overt Visual Attention
Tension and Robustness in Multitasking Cellular Networks
High-Fidelity Coding with Correlated Neurons
Automated and modular protein binder design with BinderFlow
Predicting Allosteric Effects from Orthosteric Binding in Hsp90-Ligand Interactions: Implications for Fragment-Based Drug Design
Bistability of Mitochondrial Respiration Underlies Paradoxical Reactive Oxygen Species Generation Induced by Anoxia
A modular framework for multiscale, multicellular, spatiotemporal modeling of acute primary viral infection and immune response in epithelial tissues and its application to drug therapy timing and effectiveness
Emergent multilevel selection in a simple spatial model of the evolution of altruism
Intrinsic Neuronal Properties Switch the Mode of Information Transmission in Networks
Exon level machine learning analyses elucidate novel candidate miRNA targets in an avian model of fetal alcohol spectrum disorder
Mechanistic characterization of oscillatory patterns in unperturbed tumor growth dynamics: The interplay between cancer cells and components of tumor microenvironment
Cell geometry determines symmetric and asymmetric division plane selection in Arabidopsis early embryos
The Role of Symmetric Stem Cell Divisions in Tissue Homeostasis
Combinatorial Pattern Discovery Approach for the Folding Trajectory Analysis of a β -Hairpin
Ten simple rules for principled simulation modelling
Receptive Field Inference with Localized Priors
Bayesian phylogeography of influenza A/H3N2 for the 2014-15 season in the United States using three frameworks of ancestral state reconstruction
Force-dependent focal adhesion assembly and disassembly: A computational study
A benchmark of computational CRISPR-Cas9 guide design methods
Testing Foundations of Biological Scaling Theory Using Automated Measurements of Vascular Networks
Epidemiological modeling of SARS-CoV-2 in white-tailed deer (Odocoileus virginianus) reveals conditions for introduction and widespread transmission
Complementarity of Spike- and Rate-Based Dynamics of Neural Systems
Utility and Limitations of Using Gene Expression Data to Identify Functional Associations
The siRNA Non-seed Region and Its Target Sequences Are Auxiliary Determinants of Off-Target Effects
Ant visual route navigation: How the fine details of behaviour promote successful route performance and convergence
A component overlapping attribute clustering (COAC) algorithm for single-cell RNA sequencing data analysis and potential pathobiological implications
Characterization of intrinsically disordered regions in proteins informed by human genetic diversity
A modular protein language modelling approach to immunogenicity prediction
On realized serial and generation intervals given control measures: The COVID-19 pandemic case
A fast lasso-based method for inferring higher-order interactions
OmnibusX: A unified platform for accessible multi-omics analysis
Brief Overview of Bioinformatics Activities in Singapore
Inferring causal connectivity from pairwise recordings and optogenetics
Logarithmic and Power Law Input-Output Relations in Sensory Systems with Fold-Change Detection
Neuronal Functional Connection Graphs among Multiple Areas of the Rat Somatosensory System during Spontaneous and Evoked Activities
Optimising and Communicating Options for the Control of Invasive Plant Disease When There Is Epidemiological Uncertainty
Ten simple rules for organizing a special session at a scientific conference
Somnotate: A probabilistic sleep stage classifier for studying vigilance state transitions
Detecting Emerging Transmissibility of Avian Influenza Virus in Human Households
Network Analysis of Breast Cancer Progression and Reversal Using a Tree-Evolving Network Algorithm
MONET: Multi-omic module discovery by omic selection
Correction: Folding Very Short Peptides Using Molecular Dynamics
What Are Lightness Illusions and Why Do We See Them?
Sensitivity Analysis of Intracellular Signaling Pathway Kinetics Predicts Targets for Stem Cell Fate Control
Dynamic Maternal Gradients Control Timing and Shift-Rates for Drosophila Gap Gene Expression
Comparison of methods for rhythm analysis of complex animals' acoustic signals
Emergence of Shared Intentionality Is Coupled to the Advance of Cumulative Culture
Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads
A Kuramoto model of self-other integration across interpersonal synchronization strategies
Dendritic Nonlinearities Reduce Network Size Requirements and Mediate ON and OFF States of Persistent Activity in a PFC Microcircuit Model
All-atom normal mode dynamics of HIV-1 capsid
LaDIVA: A neurocomputational model providing laryngeal motor control for speech acquisition and production
Why the growth of arboviral diseases necessitates a new generation of global risk maps and future projections
Generative models of birdsong learning link circadian fluctuations in song variability to changes in performance
The evolutionary origin of the universal distribution of mutation fitness effect
Infectious Disease Modeling of Social Contagion in Networks
Computational Biology in Brazil
Established Microbial Colonies Can Survive Type VI Secretion Assault
Self-Organization of Microcircuits in Networks of Spiking Neurons with Plastic Synapses
Chapter 11: Genome-Wide Association Studies
Prediction by Promoter Logic in Bacterial Quorum Sensing
One Year of PLoS Computational Biology
SPEACH_AF: Sampling protein ensembles and conformational heterogeneity with Alphafold2
The effects of base rate neglect on sequential belief updating and real-world beliefs
At the Edge of Chaos: How Cerebellar Granular Layer Network Dynamics Can Provide the Basis for Temporal Filters
Self-organizing Mechanism for Development of Space-filling Neuronal Dendrites
Dynamic Modelling of Pathways to Cellular Senescence Reveals Strategies for Targeted Interventions
Mslar: Microbial synthetic lethal and rescue database
Conditional Cooperativity of Toxin - Antitoxin Regulation Can Mediate Bistability between Growth and Dormancy
Learning the statistics and landscape of somatic mutation-induced insertions and deletions in antibodies
Predictive Coding of Dynamical Variables in Balanced Spiking Networks
A randomization-based causal inference framework for uncovering environmental exposure effects on human gut microbiota
Sequential inference as a mode of cognition and its correlates in fronto-parietal and hippocampal brain regions
Model Constrained by Visual Hierarchy Improves Prediction of Neural Responses to Natural Scenes
XENet: Using a new graph convolution to accelerate the timeline for protein design on quantum computers
Quantification of long-term doxorubicin response dynamics in breast cancer cell lines to direct treatment schedules
VCF2CAPS-A high-throughput CAPS marker design from VCF files and its test-use on a genotyping-by-sequencing (GBS) dataset
Supercoiled DNA and non-equilibrium formation of protein complexes: A quantitative model of the nucleoprotein ParBS partition complex
Integrating Quantitative Knowledge into a Qualitative Gene Regulatory Network
The Natural Statistics of Audiovisual Speech
A flexible and generalizable model of online latent-state learning
Measuring context dependency in birdsong using artificial neural networks
A Semi-Quantitative, Synteny-Based Method to Improve Functional Predictions for Hypothetical and Poorly Annotated Bacterial and Archaeal Genes
Modeling spatial evolution of multi-drug resistance under drug environmental gradients
Prediction of amphipathic helix - membrane interactions with Rosetta
Education in Computational Biology Today and Tomorrow
Computational geometry for modeling neural populations: From visualization to simulation
Genotype networks of 80 quantitative Arabidopsis thaliana phenotypes reveal phenotypic evolvability despite pervasive epistasis
Optimization of echinococcosis control measures based on system dynamics
Evolution of tunnels in α/β-hydrolase fold proteins - What can we learn from studying epoxide hydrolases?
Active probing to highlight approaching transitions to ictal states in coupled neural mass models
Data-driven identification of biological systems using multi-scale analysis
Existence and Control of Go/No-Go Decision Transition Threshold in the Striatum
Membrane Interaction of Bound Ligands Contributes to the Negative Binding Cooperativity of the EGF Receptor
TransMarker: Unveiling dynamic network biomarkers in cancer progression through cross-state graph alignment and optimal transport
Predictive Features of Persistent Activity Emergence in Regular Spiking and Intrinsic Bursting Model Neurons
Finding Associations among Histone Modifications Using Sparse Partial Correlation Networks
Cooperative coding of continuous variables in networks with sparsity constraint
Validation of DBFOLD: An efficient algorithm for computing folding pathways of complex proteins
Emergence of Recombinant Forms of HIV: Dynamics and Scaling
Efficient Reverse-Engineering of a Developmental Gene Regulatory Network
PESSA: A web tool for pathway enrichment score-based survival analysis in cancer
Biomarker Discovery by Sparse Canonical Correlation Analysis of Complex Clinical Phenotypes of Tuberculosis and Malaria
Correction: Learning Gene Networks under SNP Perturbations Using eQTL Datasets
Charles Bonnet Syndrome: Evidence for a Generative Model in the Cortex?
Imputation of spatially-resolved transcriptomes by graph-regularized tensor completion
Multiphysics and multiscale modeling of microthrombosis in COVID-19
Sensory Agreement Guides Kinetic Energy Optimization of Arm Movements during Object Manipulation
10 simple rules for teaching wet-lab experimentation to computational biology students, i.e., turning computer mice into lab rats
Dendritic Pooling of Noisy Threshold Processes Can Explain Many Properties of a Collision-Sensitive Visual Neuron
Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes
Insights on the impact of mitochondrial organisation on bioenergetics in high-resolution computational models of cardiac cell architecture
PyFibers: An open-source NEURON-Python package to simulate responses of model nerve fibers to electrical stimulation
ATPase Subdomain IA Is a Mediator of Interdomain Allostery in Hsp70 Molecular Chaperones
Optimal control methods for nonlinear parameter estimation in biophysical neuron models
Determinants of Sexual Network Structure and Their Impact on Cumulative Network Measures
Functional Inference of Complex Anatomical Tendinous Networks at a Macroscopic Scale via Sparse Experimentation
Local Geometry and Evolutionary Conservation of Protein Surfaces Reveal the Multiple Recognition Patches in Protein-Protein Interactions
Fast and general tests of genetic interaction for genome-wide association studies
Ten simple rules for making training materials FAIR
Indirect punishment can outperform direct punishment in promoting cooperation in structured populations
HighDimMixedModels.jl: Robust high-dimensional mixed-effects models across omics data
Iterative Reconstruction of Transcriptional Regulatory Networks: An Algorithmic Approach
Ten simple rules on how to create open access and reproducible molecular simulations of biological systems
Depth in convolutional neural networks solves scene segmentation
A dynamical systems approach for estimating phase interactions between rhythms of different frequencies from experimental data
Hybrid stochastic framework predicts efficacy of prophylaxis against HIV: An example with different dolutegravir prophylaxis schemes
Statistical perspective on functional and causal neural connectomics: The Time-Aware PC algorithm
Adaptive Synaptogenesis Constructs Neural Codes That Benefit Discrimination
Ten simple rules for writing a cover letter to accompany a job application for an academic position
A data-driven modeling approach to identify disease-specific multi-organ networks driving physiological dysregulation
Differences between joint-space and musculoskeletal estimations of metabolic rate time profiles
Estimating the Respective Contributions of Human and Viral Genetic Variation to HIV Control
Predicting Peptide-Mediated Interactions on a Genome-Wide Scale
Manifold Based Optimization for Single-Cell 3D Genome Reconstruction
A new computational model illuminates the extraordinary eyes of Phronima
Ubiquitin Dynamics in Complexes Reveal Molecular Recognition Mechanisms Beyond Induced Fit and Conformational Selection
Phylodynamics on local sexual contact networks
Improvement in Protein Domain Identification Is Reached by Breaking Consensus, with the Agreement of Many Profiles and Domain Co-occurrence
Integration of sleep homeostasis and navigation in Drosophila
Minimum Criteria for DNA Damage-Induced Phase Advances in Circadian Rhythms
Genomic Variability within an Organism Exposes Its Cell Lineage Tree
Reward from Punishment Does Not Emerge at All Costs
Advanced vision transformers and open-set learning for robust mosquito classification: A novel approach to entomological studies
Reservoir Computing Properties of Neural Dynamics in Prefrontal Cortex
Enchained growth and cluster dislocation: A possible mechanism for microbiota homeostasis
Organism-Adapted Specificity of the Allosteric Regulation of Pyruvate Kinase in Lactic Acid Bacteria
Optimal evaluation of energy yield and driving force in microbial metabolic pathway variants
The Rough Guide to In Silico Function Prediction, or How To Use Sequence and Structure Information To Predict Protein Function
Representations of regular and irregular shapes by deep Convolutional Neural Networks, monkey inferotemporal neurons and human judgments
Modelling the spatiotemporal dynamics of senescent cells in wound healing, chronic wounds, and fibrosis
Rule-Based Cell Systems Model of Aging using Feedback Loop Motifs Mediated by Stress Responses
Estimation of country-level basic reproductive ratios for novel Coronavirus (SARS-CoV-2/COVID-19) using synthetic contact matrices
Network Clustering Revealed the Systemic Alterations of Mitochondrial Protein Expression
Protein Family Expansions and Biological Complexity
Simulating the effect of ankle plantarflexion and inversion-eversion exoskeleton torques on center of mass kinematics during walking
Short-term activity cycles impede information transmission in ant colonies
Tactile stimulations reduce or promote the segregation of auditory streams: psychophysics and modeling
Convergent Transmission of RNAi Guide-Target Mismatch Information across Argonaute Internal Allosteric Network
Inference of transmission dynamics and retrospective forecast of invasive meningococcal disease
Using Combined Diagnostic Test Results to Hindcast Trends of Infection from Cross-Sectional Data
Temporal Encoding in a Nervous System
Computational Analysis of Rho GTPase Cycling
Ten simple rules for the sharing of bacterial genotype - Phenotype data on antimicrobial resistance
Network potential identifies therapeutic miRNA cocktails in Ewing sarcoma
From Birdsong to Human Speech Recognition: Bayesian Inference on a Hierarchy of Nonlinear Dynamical Systems
A Systematic Framework for Molecular Dynamics Simulations of Protein Post-Translational Modifications
Modelling Vesicular Release at Hippocampal Synapses
Tamping Ramping: Algorithmic, Implementational, and Computational Explanations of Phasic Dopamine Signals in the Accumbens
Correction: Bayesian regression explains how human participants handle parameter uncertainty
A mixture of attention experts-embedded flow-based generative model to create synthetic cells in single-cell RNA-Seq datasets
Analyzing Short-Term Noise Dependencies of Spike-Counts in Macaque Prefrontal Cortex Using Copulas and the Flashlight Transformation
Putting computational models of immunity to the test - An invited challenge to predict B.pertussis vaccination responses
Stochastic Theory of Early Viral Infection: Continuous versus Burst Production of Virions
Combinatorial Modeling of Chromatin Features Quantitatively Predicts DNA Replication Timing in Drosophila
Different forms of superspreading lead to different outcomes: Heterogeneity in infectiousness and contact behavior relevant for the case of SARS-CoV-2
Chemogenomic model identifies synergistic drug combinations robust to the pathogen microenvironment
Mass spectrometry and machine learning for the accurate diagnosis of benzylpenicillin and multidrug resistance of Staphylococcus aureus in bovine mastitis
Identifying predictors and assessing causal effect on hypertension risk among adults using Double Machine Learning models: Insights from Bangladesh Demographic and Health Survey
Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping
Ten quick tips for staying safe online
A Systems Approach to Predict Oncometabolites via Context-Specific Genome-Scale Metabolic Networks
Using Likelihood-Free Inference to Compare Evolutionary Dynamics of the Protein Networks of H. pylori and P. falciparum
PyLDM - An open source package for lifetime density analysis of time-resolved spectroscopic data
ROTS: An R package for reproducibility-optimized statistical testing
Relating local connectivity and global dynamics in recurrent excitatory-inhibitory networks
A network modelling approach to assess non-pharmaceutical disease controls in a worker population: An application to SARS-CoV-2
STENCIL: A web templating engine for visualizing and sharing life science datasets
Differences in Cell Division Rates Drive the Evolution of Terminal Differentiation in Microbes
Why Open Drug Discovery Needs Four Simple Rules for Licensing Data and Models
An antigenic diversification threshold for falciparum malaria transmission at high endemicity
CytoSpatio: Learning cell type spatial relationships using multirange, multitype point process models
Evaluation of Objective Uncertainty in the Visual System
Zipf's Law Arises Naturally When There Are Underlying, Unobserved Variables
Ten Quick Tips for Using the Gene Ontology
Identifying the mechanism for superdiffusivity in mouse fibroblast motility
Natural variability in bee brain size and symmetry revealed by micro-CT imaging and deep learning
Playbook workflow builder: Interactive construction of bioinformatics workflows
Phosphorylation Variation during the Cell Cycle Scales with Structural Propensities of Proteins
Storage of Correlated Patterns in Standard and Bistable Purkinje Cell Models
Quantifying Aggregated Uncertainty in Plasmodium falciparum Malaria Prevalence and Populations at Risk via Efficient Space-Time Geostatistical Joint Simulation
Adaptive representations of sound for automatic insect recognition
Evolving Nutritional Strategies in the Presence of Competition: A Geometric Agent-Based Model
Measures of Clade Confidence Do Not Correlate with Accuracy of Phylogenetic Trees
Robustness of DNA Repair through Collective Rate Control
Delayed skeletal muscle repair following inflammatory damage in simulated agent-based models of muscle regeneration
Investigating the structural changes due to adenosine methylation of the Kaposi's sarcoma-associated herpes virus ORF50 transcript
Stochastic De-repression of Rhodopsins in Single Photoreceptors of the Fly Retina
Modeling enculturated bias in entrainment to rhythmic patterns
Evaluation of the Oscillatory Interference Model of Grid Cell Firing through Analysis and Measured Period Variance of Some Biological Oscillators
Ten Simple Rules for Organizing an Unconference
clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets
Evaluation of parameters affecting performance and reliability of machine learning-based antibiotic susceptibility testing from whole genome sequencing data
Multiple Choice Neurodynamical Model of the Uncertain Option Task
Sequence Similarity Network Reveals Common Ancestry of Multidomain Proteins
Connectivity, reproduction number, and mobility interact to determine communities' epidemiological superspreader potential in a metapopulation network
A topological data analytic approach for discovering biophysical signatures in protein dynamics
Effect of cellular rearrangement time delays on the rheology of vertex models for confluent tissues
Deciphering Protein-Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners
Coupling plankton and cholera dynamics: Insights into outbreak prediction and practical disease management
Reassessing Google Flu Trends Data for Detection of Seasonal and Pandemic Influenza: A Comparative Epidemiological Study at Three Geographic Scales