yusuke1997/dblp-id-title huggingface dataset:
Sensory modulation of gait characteristics in human locomotion: A neuromusculoskeletal modeling study
Measuring the impact of gene prediction on gene loss estimates in Eukaryotes by quantifying falsely inferred absences
Brain dynamics for confidence-weighted learning
Simulated Epidemics in an Empirical Spatiotemporal Network of 50, 185 Sexual Contacts
Predicting the Distribution of Spiral Waves from Cell Properties in a Developmental-Path Model of Dictyostelium Pattern Formation
MVHGCN: Predicting circRNA-disease associations with multi-view heterogeneous graph convolutional neural networks
Animal Cell Differentiation Patterns Suppress Somatic Evolution
Noise improves the association between effects of local stimulation and structural degree of brain networks
The FACTS model of speech motor control: Fusing state estimation and task-based control
Rethinking Transcriptional Activation in the Arabidopsis Circadian Clock
Mechanics of Channel Gating of the Nicotinic Acetylcholine Receptor
Dynamic Allostery Mediated by a Conserved Tryptophan in the Tec Family Kinases
Order and Stochastic Dynamics in Drosophila Planar Cell Polarity
Frequency-Dependent Selection Predicts Patterns of Radiations and Biodiversity
A network diffusion approach to inferring sample-specific function reveals functional changes associated with breast cancer
Empirical model for short-time prediction of COVID-19 spreading
Deducing the Kinetics of Protein Synthesis In Vivo from the Transition Rates Measured In Vitro
Sources of Variability in a Synthetic Gene Oscillator
Image-based parameter inference for epithelial mechanics
Personality variation is eroded by simple social behaviours in collective foragers
Systematic Analysis of Head-to-Head Gene Organization: Evolutionary Conservation and Potential Biological Relevance
A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism
Network Model of Immune Responses Reveals Key Effectors to Single and Co-infection Dynamics by a Respiratory Bacterium and a Gastrointestinal Helminth
Predicting the Extension of Biomedical Ontologies
Multi-feature fusion network with marginal focal dice loss for multi-label therapeutic peptide prediction
Slowness: An Objective for Spike-Timing-Dependent Plasticity?
Matrix prior for data transfer between single cell data types in latent Dirichlet allocation
Multicellular model of neuroblastoma proposes unconventional therapy based on multiple roles of p53
History dependence in insect flight decisions during odor tracking
MUMmer4: A fast and versatile genome alignment system
Dissecting the roles of calcium cycling and its coupling with voltage in the genesis of early afterdepolarizations in cardiac myocyte models
A Forced Damped Oscillation Framework for Undulatory Swimming Provides New Insights into How Propulsion Arises in Active and Passive Swimming
Lifespan Differences in Hematopoietic Stem Cells are Due to Imperfect Repair and Unstable Mean-Reversion
Antigenic Diversity, Transmission Mechanisms, and the Evolution of Pathogens
Symmetric Allosteric Mechanism of Hexameric Escherichia coli Arginine Repressor Exploits Competition between L-Arginine Ligands and Resident Arginine Residues
Automated Querying of Genome Databases
A neural network model predicts community-level signaling states in a diverse microbial community
Activity-mediated accumulation of potassium induces a switch in firing pattern and neuronal excitability type
Temporal precision of regulated gene expression
Structure Prediction of RNA Loops with a Probabilistic Approach
Wham: Identifying Structural Variants of Biological Consequence
Understanding multivariate brain activity: Evaluating the effect of voxelwise noise correlations on population codes in functional magnetic resonance imaging
Trackplot: A flexible toolkit for combinatorial analysis of genomic data
Tumor-immune partitioning and clustering algorithm for identifying tumor-immune cell spatial interaction signatures within the tumor microenvironment
Allostery: An Overview of Its History, Concepts, Methods, and Applications
Combined translational and rotational perturbations of standing balance reveal contributions of reduced reciprocal inhibition to balance impairments in children with cerebral palsy
A novel theoretical framework for simultaneous measurement of excitatory and inhibitory conductances
Controlling astrocyte-mediated synaptic pruning signals for schizophrenia drug repurposing with deep graph networks
Quantification of spatial and phenotypic heterogeneity in an agent-based model of tumour-macrophage interactions
Unified tumor growth mechanisms from multimodel inference and dataset integration
MetGEMs Toolbox: Metagenome-scale models as integrative toolbox for uncovering metabolic functions and routes of human gut microbiome
The Evolution of Quorum Sensing as a Mechanism to Infer Kinship
Architecture of the brain's visual system enhances network stability and performance through layers, delays, and feedback
Alignment and Prediction of cis -Regulatory Modules Based on a Probabilistic Model of Evolution
Seven quick tips for analysis scripts in neuroimaging
PPI-ID: Streamlining protein-protein interaction prediction through domain and SLiM mapping
Ten Simple Rules on How to Organize a Scientific Retreat
Mathematical modeling of dopamine rhythms and timing of dopamine reuptake inhibitors
Bayesian comparison of explicit and implicit causal inference strategies in multisensory heading perception
Systems-level network modeling of Small Cell Lung Cancer subtypes identifies master regulators and destabilizers
Exploring the Evolution of Novel Enzyme Functions within Structurally Defined Protein Superfamilies
Sparse balance: Excitatory-inhibitory networks with small bias currents and broadly distributed synaptic weights
Using the drug-protein interactome to identify anti-ageing compounds for humans
Performance assessment of sample-specific network control methods for bulk and single-cell biological data analysis
Dynamics and Mechanical Stability of the Developing Dorsoventral Organizer of the Wing Imaginal Disc
Twelve quick tips for designing sound dynamical models for bioprocesses
In Silico Analysis of the Apolipoprotein E and the Amyloid β Peptide Interaction: Misfolding Induced by Frustration of the Salt Bridge Network
Bayesian refinement of protein structures and ensembles against SAXS data using molecular dynamics
Comparison of in silico predictions of action potential duration in response to inhibition of IKr and ICaL with new human ex vivo recordings
A novel stochastic simulation approach enables exploration of mechanisms for regulating polarity site movement
Global Analysis of Small Molecule Binding to Related Protein Targets
Cholinergic neuromodulation of inhibitory interneurons facilitates functional integration in whole-brain models
Synaptic Homeostasis and Restructuring across the Sleep-Wake Cycle
Ten Simple Rules for Writing a Literature Review
Ten simple rules for choosing a PhD supervisor
Neural energy coding patterns of dopaminergic neural microcircuit and its impairment in major depressive disorder: A computational study
Top-Down Analysis of Temporal Hierarchy in Biochemical Reaction Networks
Mechanistic computational modeling of sFLT1 secretion dynamics
Similarity in Shape Dictates Signature Intrinsic Dynamics Despite No Functional Conservation in TIM Barrel Enzymes
A system for tracking whisker kinematics and whisker shape in three dimensions
The Impact of Oxygen on Metabolic Evolution: A Chemoinformatic Investigation
Bayesian nowcasting with leading indicators applied to COVID-19 fatalities in Sweden
On the Growth of Scientific Knowledge: Yeast Biology as a Case Study
The Na+/K+-ATPase generically enables deterministic bursting in class I neurons by shearing the spike-onset bifurcation structure
Limited synapse overproduction can speed development but sometimes with long-term energy and discrimination penalties
ClustAll: An R package for patient stratification in complex diseases
Allele imputation for the killer cell immunoglobulin-like receptor KIR3DL1/S1
A Two-Stage Cascade Model of BOLD Responses in Human Visual Cortex
What we can and what we cannot see with extracellular multielectrodes
Quantifying Transmission Investment in Malaria Parasites
MGDrivE 3: A decoupled vector-human framework for epidemiological simulation of mosquito genetic control tools and their surveillance
Insights on cross-species transmission of SARS-CoV-2 from structural modeling
Ten simple rules for switching from face-to-face to remote conference: An opportunity to estimate the reduction in GHG emissions
Intra-Tumour Signalling Entropy Determines Clinical Outcome in Breast and Lung Cancer
A magnesium-induced triplex pre-organizes the SAM-II riboswitch
How Informative Are Spatial CA3 Representations Established by the Dentate Gyrus?
Limits on amplifiers of natural selection under death-Birth updating
Full Design Automation of Multi-State RNA Devices to Program Gene Expression Using Energy-Based Optimization
Why are viral genomes so fragile? The bottleneck hypothesis
Optimizing Experimental Design for Comparing Models of Brain Function
Motor-related signals support localization invariance for stable visual perception
Stochastic principles governing alternative splicing of RNA
Precise Regulation of Gene Expression Dynamics Favors Complex Promoter Architectures
Obsessive-compulsive disorder is characterized by decreased Pavlovian influence on instrumental behavior
Deciphering Dimerization Modes of PAS Domains: Computational and Experimental Analyses of the AhR: ARNT Complex Reveal New Insights Into the Mechanisms of AhR Transformation
An Experimental and Computational Study of the Effect of ActA Polarity on the Speed of Listeria monocytogenes Actin-based Motility
Ten simple rules for getting and giving credit for data
Global Prediction of Tissue-Specific Gene Expression and Context-Dependent Gene Networks in Caenorhabditis elegans
Spatial Heterogeneity and Peptide Availability Determine CTL Killing Efficiency In Vivo
Frank-Starling mechanism, fluid responsiveness, and length-dependent activation: Unravelling the multiscale behaviors with an in silico analysis
Mechanochemical Coupling in the Myosin Motor Domain. I. Insights from Equilibrium Active-Site Simulations
Protective impacts of household-based tuberculosis contact tracing are robust across endemic incidence levels and community contact patterns
Grey-box modeling and hypothesis testing of functional near-infrared spectroscopy-based cerebrovascular reactivity to anodal high-definition tDCS in healthy humans
A dynamic attractor network model of memory formation, reinforcement and forgetting
Immuno-epidemiological Modeling of HIV-1 Predicts High Heritability of the Set-Point Virus Load, while Selection for CTL Escape Dominates Virulence Evolution
The Fitness Landscape of HIV-1 Gag: Advanced Modeling Approaches and Validation of Model Predictions by In Vitro Testing
HPVsim: An agent-based model of HPV transmission and cervical disease
Simulations of dynamically cross-linked actin networks: Morphology, rheology, and hydrodynamic interactions
The Role of Inhibition in a Computational Model of an Auditory Cortical Neuron during the Encoding of Temporal Information
Chaos in synthetic microbial communities
Quantifying the Contribution of the Liver to Glucose Homeostasis: A Detailed Kinetic Model of Human Hepatic Glucose Metabolism
Inferring neural circuit structure from datasets of heterogeneous tuning curves
A mathematical model for the role of dopamine-D2 self-regulation in the production of ultradian rhythms
Multi-scale computational study of the Warburg effect, reverse Warburg effect and glutamine addiction in solid tumors
serosim: An R package for simulating serological data arising from vaccination, epidemiological and antibody kinetics processes
Simulations of Long-Term Community Dynamics in Coral Reefs - How Perturbations Shape Trajectories
A Phylogenomic Study of Human, Dog, and Mouse
Near real-time forecasting for cholera decision making in Haiti after Hurricane Matthew
Natural variants of von Willebrand factor R1205 causing von Willebrand disease with accelerated von Willebrand factor clearance: In silico docking models and energetics of the interaction with both LRP1 and GpIb A1 domain
A multiscale model of the role of microenvironmental factors in cell segregation and heterogeneity in breast cancer development
Correction: Ten simple rules for organizing a bioinformatics training course in low- and middle-income countries
NMR Methods to Study Dynamic Allostery
The calcitron: A simple neuron model that implements many learning rules via the calcium control hypothesis
Experimental validation of computerised models of clustering of platelet glycoprotein receptors that signal via tandem SH2 domain proteins
Integrating linear optimization with structural modeling to increase HIV neutralization breadth
CIRCUST: A novel methodology for temporal order reconstruction of molecular rhythms; validation and application towards a daily rhythm gene expression atlas in humans
Deconvolution of cancer cell states by the XDec-SM method
Funneling modulatory peptide design with generative models: Discovery and characterization of disruptors of calcineurin protein-protein interactions
The value of decreasing the duration of the infectious period of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection
Model-based analysis of the acute effects of transcutaneous magnetic spinal cord stimulation on micturition after spinal cord injury in humans
Paranoia, self-deception and overconfidence
Mapping Dynamic Histone Acetylation Patterns to Gene Expression in Nanog-Depleted Murine Embryonic Stem Cells
Method for cycle detection in sparse, irregularly sampled, long-term neuro-behavioral timeseries: Basis pursuit denoising with polynomial detrending of long-term, inter-ictal epileptiform activity
Learning the structure of the world: The adaptive nature of state-space and action representations in multi-stage decision-making
Multi-strain phage induced clearance of bacterial infections
High rifampicin peak plasma concentrations accelerate the slow phase of bacterial decline in tuberculosis patients: Evidence for heteroresistance
NLLSS: Predicting Synergistic Drug Combinations Based on Semi-supervised Learning
The Temporal Winner-Take-All Readout
Cholera- and Anthrax-Like Toxins Are among Several New ADP-Ribosyltransferases
What Makes a Protein Sequence a Prion?
Emergent Behaviors from a Cellular Automaton Model for Invasive Tumor Growth in Heterogeneous Microenvironments
Intrinsic motivation for choice varies with individual risk attitudes and the controllability of the environment
Dynamic compensation, parameter identifiability, and equivariances
Analysis of a Splice Array Experiment Elucidates Roles of Chromatin Elongation Factor Spt4-5 in Splicing
PhyDOSE: Design of follow-up single-cell sequencing experiments of tumors
A Universal Trend of Reduced mRNA Stability near the Translation-Initiation Site in Prokaryotes and Eukaryotes
A Phenomenological Theory of Spatially Structured Local Synaptic Connectivity
Efficient Bayesian inference for stochastic agent-based models
Spatial dynamics and control of a crop pathogen with mixed-mode transmission
Modeling effects of voltage dependent properties of the cardiac muscarinic receptor on human sinus node function
Feature blindness: A challenge for understanding and modelling visual object recognition
Gene expression bias between the subgenomes of allopolyploid hybrids is an emergent property of the kinetics of expression
Improving the understanding of cytoneme-mediated morphogen gradients by in silico modeling
Modelling the Spread of HIV Immune Escape Mutants in a Vaccinated Population
The Human Genomic Melting Map
Hypoxic pulmonary vasoconstriction as a regulator of alveolar-capillary oxygen flux: A computational model of ventilation-perfusion matching
Evidence for Composite Cost Functions in Arm Movement Planning: An Inverse Optimal Control Approach
Delay Selection by Spike-Timing-Dependent Plasticity in Recurrent Networks of Spiking Neurons Receiving Oscillatory Inputs
Spike-timing dependent plasticity partially compensates for neural delays in a multi-layered network of motion-sensitive neurons
Risk Maps for the Spread of Highly Pathogenic Avian Influenza in Poultry
Communication through Resonance in Spiking Neuronal Networks
Trajectory inference from single-cell genomics data with a process time model
Galaxy Training: A powerful framework for teaching!
The benefits of insect-swarm hunting to echolocating bats, and its influence on the evolution of bat echolocation signals
Evolution of multicellular life cycles under costly fragmentation
Mechanical Stress Inference for Two Dimensional Cell Arrays
Ten simple rules for supporting a temporary online pivot in higher education
Parameters and determinants of responses to selection in antibody libraries
Parallel development of object recognition in newborn chicks and deep neural networks
Dissection of Regulatory Networks that Are Altered in Disease via Differential Co-expression
PSICIC: Noise and Asymmetry in Bacterial Division Revealed by Computational Image Analysis at Sub-Pixel Resolution
A new framework for assessing subject-specific whole brain circulation and perfusion using MRI-based measurements and a multi-scale continuous flow model
A machine learning approach for predicting CRISPR-Cas9 cleavage efficiencies and patterns underlying its mechanism of action
Embodied decisions as active inference
Single Nucleotide Polymorphisms Can Create Alternative Polyadenylation Signals and Affect Gene Expression through Loss of MicroRNA-Regulation
Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome
Evidence for Finely-Regulated Asynchronous Growth of Toxoplasma gondii Cysts Based on Data-Driven Model Selection
Relaxing restrictions at the pace of vaccination increases freedom and guards against further COVID-19 waves
Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution
DPCfam: Unsupervised protein family classification by Density Peak Clustering of large sequence datasets
Evolutionary Epidemiology of Drug-Resistance in Space
Correction: Biophysically grounded mean-field models of neural populations under electrical stimulation
Modelling Negative Feedback Networks for Activating Transcription Factor 3 Predicts a Dominant Role for miRNAs in Immediate Early Gene Regulation
Exploring the Contextual Sensitivity of Factors that Determine Cell-to-Cell Variability in Receptor-Mediated Apoptosis
EpiFusion: Joint inference of the effective reproduction number by integrating phylodynamic and epidemiological modelling with particle filtering
CustOmics: A versatile deep-learning based strategy for multi-omics integration
Compensation for Changing Motor Uncertainty
Recombination Enhances HIV-1 Envelope Diversity by Facilitating the Survival of Latent Genomic Fragments in the Plasma Virus Population
Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation
Design and implementation of an asynchronous online course-based undergraduate research experience (CURE) in computational genomics
Construction of disease-specific cytokine profiles by associating disease genes with immune responses
A Neutrophil Phenotype Model for Extracorporeal Treatment of Sepsis
Prediction of graft loss in living donor liver transplantation during the early postoperative period
Evaluating COVID-19 vaccination policy in Québec (Canada) using a data-driven dynamic transmission model
An Asymmetrically Balanced Organization of Kinases versus Phosphatases across Eukaryotes Determines Their Distinct Impacts
Pluripotency, Differentiation, and Reprogramming: A Gene Expression Dynamics Model with Epigenetic Feedback Regulation
Correction: Beyond Muscles Stiffness: Importance of State-Estimation to Account for Very Fast Motor Corrections
Resolving Anatomical and Functional Structure in Human Brain Organization: Identifying Mesoscale Organization in Weighted Network Representations
Uncovering temperature sensitivity of West Nile virus transmission: Novel computational approaches to mosquito-pathogen trait responses
Automated deconvolution of structured mixtures from heterogeneous tumor genomic data
Simultaneously determining regional heterogeneity and connection directionality from neural activity and symmetric connection
Moderate confirmation bias enhances decision-making in groups of reinforcement-learning agents
Enzyme Kinetics of the Mitochondrial Deoxyribonucleoside Salvage Pathway Are Not Sufficient to Support Rapid mtDNA Replication
Dose Response Relationship in Anti-Stress Gene Regulatory Networks
Revisiting the importance of model fitting for model-based fMRI: It does matter in computational psychiatry
Pre- and postsynaptically expressed spike-timing-dependent plasticity contribute differentially to neuronal learning
Protein ensembles link genotype to phenotype
A Density-Dependent Switch Drives Stochastic Clustering and Polarization of Signaling Molecules
Using Multiple Microenvironments to Find Similar Ligand-Binding Sites: Application to Kinase Inhibitor Binding
Neuromotor Noise, Error Tolerance and Velocity-Dependent Costs in Skilled Performance
Coding Efficiency of Fly Motion Processing Is Set by Firing Rate, Not Firing Precision
Correction: Accounting for non-stationarity in epidemiology by embedding time-varying parameters in stochastic models
Structure-based prediction of nucleic acid binding residues by merging deep learning- and template-based approaches
Extraction of Transcript Diversity from Scientific Literature
Effects of Heterogeneous and Clustered Contact Patterns on Infectious Disease Dynamics
Tipping the Scale from Disorder to Alpha-helix: Folding of Amphiphilic Peptides in the Presence of Macroscopic and Molecular Interfaces
Dissecting the Calcium-Induced Differentiation of Human Primary Keratinocytes Stem Cells by Integrative and Structural Network Analyses
A Maximum Entropy Test for Evaluating Higher-Order Correlations in Spike Counts
Unbiased Functional Clustering of Gene Variants with a Phenotypic-Linkage Network
The Opponent Channel Population Code of Sound Location Is an Efficient Representation of Natural Binaural Sounds
Rhythmidia: A modern tool for circadian period analysis of filamentous fungi
Mathematical framework for place coding in the auditory system
Traveling waves in the human visual cortex: An MEG-EEG model-based approach
Simple models including energy and spike constraints reproduce complex activity patterns and metabolic disruptions
Modeling HIV-1 infection in the brain
Microblogging the ISMB: A New Approach to Conference Reporting
New Insights into the Genetic Control of Gene Expression using a Bayesian Multi-tissue Approach
Efficient Network Reconstruction from Dynamical Cascades Identifies Small-World Topology of Neuronal Avalanches
Assessing computational genomics skills: Our experience in the H3ABioNet African bioinformatics network
Reconstructing the regulatory circuit of cell fate determination in yeast mating response
PARE: A framework for removal of confounding effects from any distance-based dimension reduction method
Integration, coincidence detection and resonance in networks of spiking neurons expressing Gamma oscillations and asynchronous states
Humans Can Adopt Optimal Discounting Strategy under Real-Time Constraints
A dynamic foot model for predictive simulations of human gait reveals causal relations between foot structure and whole-body mechanics
RNAtranslator: Modeling protein-conditional RNA design as sequence-to-sequence natural language translation
Establishing a computational biology flipped classroom
Role of connectivity anisotropies in the dynamics of cultured neuronal networks
Stochastic Simulations on the Reliability of Action Potential Propagation in Thin Axons
Early Transcriptome Signatures from Immunized Mouse Dendritic Cells Predict Late Vaccine-Induced T-Cell Responses
Phyletic Profiling with Cliques of Orthologs Is Enhanced by Signatures of Paralogy Relationships