yusuke1997/dblp-id-title huggingface dataset:
DEER-PREdict: Software for efficient calculation of spin-labeling EPR and NMR data from conformational ensembles
Modelling 3D saccade generation by feedforward optimal control
Decelerating Spread of West Nile Virus by Percolation in a Heterogeneous Urban Landscape
A mathematical model for IL-6-mediated, stem cell driven tumor growth and targeted treatment
Efficient algorithms to discover alterations with complementary functional association in cancer
Cross-GWAS coherence test at the gene and pathway level
iCircDA-NEAE: Accelerated attribute network embedding and dynamic convolutional autoencoder for circRNA-disease associations prediction
Fast Bayesian Inference of Copy Number Variants using Hidden Markov Models with Wavelet Compression
Segregating Complex Sound Sources through Temporal Coherence
Dynamics and heterogeneity of brain damage in multiple sclerosis
VALERIE: Visual-based inspection of alternative splicing events at single-cell resolution
Structure-Based Predictive Models for Allosteric Hot Spots
BioAFMviewer: An interactive interface for simulated AFM scanning of biomolecular structures and dynamics
Dynamic causal modelling shows a prominent role of local inhibition in alpha power modulation in higher visual cortex
BEEM-Static: Accurate inference of ecological interactions from cross-sectional microbiome data
Classical Mathematical Models for Description and Prediction of Experimental Tumor Growth
Community interactions and spatial structure shape selection on antibiotic resistant lineages
Characterizing Protein Interactions Employing a Genome-Wide siRNA Cellular Phenotyping Screen
Exploring the inhibitory effect of membrane tension on cell polarization
Stroke Rehabilitation Reaches a Threshold
The Human Functional Brain Network Demonstrates Structural and Dynamical Resilience to Targeted Attack
Deep learning approaches to landmark detection in tsetse wing images
Modeling Inhibitory Interneurons in Efficient Sensory Coding Models
Fast- or Slow-inactivated State Preference of Na + Channel Inhibitors: A Simulation and Experimental Study
Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data
Leveraging effect size distributions to improve polygenic risk scores derived from summary statistics of genome-wide association studies
The E2.65A mutation disrupts dynamic binding poses of SB269652 at the dopamine D2 and D3 receptors
A physiologically based pharmacokinetic model to optimize the dosage regimen and withdrawal time of cefquinome in pigs
Neuromechanistic Model of Auditory Bistability
Long-range Order in Canary Song
Hydrophobic Gating of Ion Permeation in Magnesium Channel CorA
Deep Neural Networks Rival the Representation of Primate IT Cortex for Core Visual Object Recognition
Reverse-Engineering Post-Transcriptional Regulation of Gap Genes in Drosophila melanogaster
Multi-cellular network model predicts alterations in glomerular endothelial structure in diabetic kidney disease
Flexible Modeling of Epidemics with an Empirical Bayes Framework
Integrative Analysis Using Module-Guided Random Forests Reveals Correlated Genetic Factors Related to Mouse Weight
Computational prediction of drug response in short QT syndrome type 1 based on measurements of compound effect in stem cell-derived cardiomyocytes
Semantic Similarity for Automatic Classification of Chemical Compounds
Model-driven analysis of mutant fitness experiments improves genome-scale metabolic models of Zymomonas mobilis ZM4
A generative spiking neural-network model of goal-directed behaviour and one-step planning
Predicted Auxiliary Navigation Mechanism of Peritrichously Flagellated Chemotactic Bacteria
The influence of the crowding assumptions in biofilm simulations
Understanding Pitch Perception as a Hierarchical Process with Top-Down Modulation
A meta-contrastive learning approach for clinical drug-drug interaction extraction from biomedical literature
Cytoplasmic flows in starfish oocytes are fully determined by cortical contractions
Integration of Metabolic and Quorum Sensing Signals Governing the Decision to Cooperate in a Bacterial Social Trait
Ten simple rules for using public biological data for your research
Dynamical modelling of viral infection and cooperative immune protection in COVID-19 patients
Trafficking dynamics of VEGFR1, VEGFR2, and NRP1 in human endothelial cells
Global Entrainment of Transcriptional Systems to Periodic Inputs
Rhythmic Manipulation of Objects with Complex Dynamics: Predictability over Chaos
Human Leg Model Predicts Ankle Muscle-Tendon Morphology, State, Roles and Energetics in Walking
Optimal synaptic signaling connectome for locomotory behavior in Caenorhabditis elegans: Design minimizing energy cost
Are there physicochemical differences between allosteric and competitive ligands?
Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL
Order matters: How covert value updating during sequential option sampling shapes economic preference
Influence of cell type specific infectivity and tissue composition on SARS-CoV-2 infection dynamics within human airway epithelium
The G-OBIM tongue model: An accurate open-source biomechanical model of a male human tongue
Molecular dynamics simulations of human cohesin subunits identify DNA binding sites and their potential roles in DNA loop extrusion
Bayesian reconstruction of transmission within outbreaks using genomic variants
Key Role of Local Regulation in Chemosensing Revealed by a New Molecular Interaction-Based Modeling Method
Membrane Partitioning of Anionic, Ligand-Coated Nanoparticles Is Accompanied by Ligand Snorkeling, Local Disordering, and Cholesterol Depletion
Arousal state affects perceptual decision-making by modulating hierarchical sensory processing in a large-scale visual system model
Protein degradation sets the fraction of active ribosomes at vanishing growth
Non-monotonic Temporal-Weighting Indicates a Dynamically Modulated Evidence-Integration Mechanism
Tool evaluation for the detection of variably sized indels from next generation whole genome and targeted sequencing data
Enhancing antibody-antigen interaction prediction with atomic flexibility
Mathematical modeling of the Candida albicans yeast to hyphal transition reveals novel control strategies
Simulating the Complex Cell Design of Trypanosoma brucei and Its Motility
Structural dynamics of SARS-CoV-2 nucleocapsid protein induced by RNA binding
A Differentiation-Based Phylogeny of Cancer Subtypes
Amyloid pathology disrupts gliotransmitter release in astrocytes
Tracking urban human activity from mobile phone calling patterns
When do stereotypes undermine indirect reciprocity?
Ten simple rules for Global North researchers to stop perpetuating helicopter research in the Global South
Modeling age-specific incidence of colon cancer via niche competition
Distribution of calbindin-positive neurons across areas and layers of the marmoset cerebral cortex
Mathematical modeling and quantitative analysis of HIV-1 Gag trafficking and polymerization
New computational approaches to understanding molecular protein function
Preferred Supramolecular Organization and Dimer Interfaces of Opioid Receptors from Simulated Self-Association
Inferring feature importance with uncertainties with application to large genotype data
Automatic Design of Digital Synthetic Gene Circuits
Computational design of substrate selective inhibition
Dynamic Conformational Change Regulates the Protein-DNA Recognition: An Investigation on Binding of a Y-Family Polymerase to Its Target DNA
CyVerse: Cyberinfrastructure for open science
Statistical Analysis of Tract-Tracing Experiments Demonstrates a Dense, Complex Cortical Network in the Mouse
DeLTA: Automated cell segmentation, tracking, and lineage reconstruction using deep learning
Spike-Timing-Based Computation in Sound Localization
Meta-Analysis of Differentiating Mouse Embryonic Stem Cell Gene Expression Kinetics Reveals Early Change of a Small Gene Set
Embedding mRNA Stability in Correlation Analysis of Time-Series Gene Expression Data
Domes and cones: Adhesion-induced fission of membranes by ESCRT proteins
Bayesian inference of relative fitness on high-throughput pooled competition assays
Filament turnover tunes both force generation and dissipation to control long-range flows in a model actomyosin cortex
Weakly Circadian Cells Improve Resynchrony
Are we really Bayesian? Probabilistic inference shows sub-optimal knowledge transfer
Repeated games with partner choice
How Cations Can Assist DNase I in DNA Binding and Hydrolysis
Modularity of Protein Folds as a Tool for Template-Free Modeling of Structures
Machine learning liver-injuring drug interactions with non-steroidal anti-inflammatory drugs (NSAIDs) from a retrospective electronic health record (EHR) cohort
Topological Sholl descriptors for neuronal clustering and classification
Unbiased Simulations Reveal the Inward-Facing Conformation of the Human Serotonin Transporter and Na + Ion Release
Normal Modes Expose Active Sites in Enzymes
Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors
Noise-resistant developmental reproducibility in vertebrate somite formation
Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA
Critical behaviour of the stochastic Wilson-Cowan model
Parsimony, Exhaustivity and Balanced Detection in Neocortex
Temporal dynamics of short-term neural adaptation across human visual cortex
Tracking collective cell motion by topological data analysis
Vector bionomics and vectorial capacity as emergent properties of mosquito behaviors and ecology
Evolutionary Accessibility of Mutational Pathways
Antimicrobial Peptides Design by Evolutionary Multiobjective Optimization
Reconstructing the Three-Dimensional GABAergic Microcircuit of the Striatum
Viral RNA Degradation and Diffusion Act as a Bottleneck for the Influenza A Virus Infection Efficiency
Fostering bioinformatics education through skill development of professors: Big Genomic Data Skills Training for Professors
Generating correlated data for omics simulation
Sensing Membrane Stresses by Protein Insertions
Roles and interplay of reinforcement-based and error-based processes during reaching and gait in neurotypical adults and individuals with Parkinson's disease
A Mathematical Model for the Reciprocal Differentiation of T Helper 17 Cells and Induced Regulatory T Cells
PCSF: An R-package for network-based interpretation of high-throughput data
Particle-based simulations of polarity establishment reveal stochastic promotion of Turing pattern formation
COMSUC: A web server for the identification of consensus molecular subtypes of cancer based on multiple methods and multi-omics data
Rapid interpretation of small-angle X-ray scattering data
CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures
Data-driven segmentation of cortical calcium dynamics
Analyzing histone ChIP-seq data with a bin-based probability of being signal
On the preservation of vessel bifurcations during flow-mediated angiogenic remodelling
A software ecosystem for brain tractometry processing, analysis, and insight
Landscape and variation of novel retroduplications in 26 human populations
Modular analysis of the control of flagellar Ca2+-spike trains produced by CatSper and CaV channels in sea urchin sperm
Correction: Cell Type Specific Alterations in Interchromosomal Networks across the Cell Cycle
Specificity and tunability of efflux pumps: A new role for the proton gradient?
Distal Loop Flexibility of a Regulatory Domain Modulates Dynamics and Activity of C-Terminal Src Kinase (Csk)
Emergent Synchronous Bursting of Oxytocin Neuronal Network
Maximizing multi-reaction dependencies provides more accurate and precise predictions of intracellular fluxes than the principle of parsimony
Mathematical model predicts anti-adhesion-antibiotic-debridement combination therapies can clear an antibiotic resistant infection
Modeling the START transition in the budding yeast cell cycle
Library size-stabilized metacells construction enhances co-expression network analysis in single-cell data
Voxelized simulation of cerebral oxygen perfusion elucidates hypoxia in aged mouse cortex
Modularity and Dynamics of Cellular Networks
Coupling of Lever Arm Swing and Biased Brownian Motion in Actomyosin
Flow mechanisms of the air-blood barrier
Constraint-Based Model of Shewanella oneidensis MR-1 Metabolism: A Tool for Data Analysis and Hypothesis Generation
In Silico Screening of the Key Cellular Remodeling Targets in Chronic Atrial Fibrillation
Effect of Promoter Architecture on the Cell-to-Cell Variability in Gene Expression
mPPases create a conserved anionic membrane fingerprint as identified via multi-scale simulations
Hierarchical semantic composition of biosimulation models using bond graphs
Motif-Aware PRALINE: Improving the alignment of motif regions
Seriation in Paleontological Data Using Markov Chain Monte Carlo Methods
Cell signaling model for arterial mechanobiology
Cost-benefit trade-offs in decision-making and learning
Behavioral Modeling of Human Choices Reveals Dissociable Effects of Physical Effort and Temporal Delay on Reward Devaluation
Modeling the Afferent Dynamics of the Baroreflex Control System
Reappraising the utility of Google Flu Trends
Correction: A Biophysical Model of the Mitochondrial Respiratory System and Oxidative Phosphorylation
Using Structure to Explore the Sequence Alignment Space of Remote Homologs
MEDYAN: Mechanochemical Simulations of Contraction and Polarity Alignment in Actomyosin Networks
How Dendrites Affect Online Recognition Memory
Quantifying Global Tolerance of Biochemical Systems: Design Implications for Moiety-Transfer Cycles
Practical sampling of constraint-based models: Optimized thinning boosts CHRR performance
Correction: Impact of Different Oseltamivir Regimens on Treating Influenza A Virus Infection and Resistance Emergence: Insights from a Modelling Study
Scale free topology as an effective feedback system
Modelling cell shape in 3D structured environments: A quantitative comparison with experiments
Loads Bias Genetic and Signaling Switches in Synthetic and Natural Systems
Ten simple rules for working with other people's code
miRScore: A rapid and precise microRNA validation tool
Within-host mechanisms of immune regulation explain the contrasting dynamics of two helminth species in both single and dual infections
Burst-Time-Dependent Plasticity Robustly Guides ON/OFF Segregation in the Lateral Geniculate Nucleus
Modeling the Seasonal Adaptation of Circadian Clocks by Changes in the Network Structure of the Suprachiasmatic Nucleus
A neural network model enables worm tracking in challenging conditions and increases signal-to-noise ratio in phenotypic screens
Perturbation-Expression Analysis Identifies RUNX1 as a Regulator of Human Mammary Stem Cell Differentiation
Mistakes can stabilise the dynamics of rock-paper-scissors games
Bioenergetics-based modeling of Plasmodium falciparum metabolism reveals its essential genes, nutritional requirements, and thermodynamic bottlenecks
An electrophysiological and kinematic model of Paramecium, the "swimming neuron"
Ten simple rules for a successful international consortium in big data omics
Identifying Anatomical Origins of Coexisting Oscillations in the Cortical Microcircuit
Distributed network flows generate localized category selectivity in human visual cortex
Neurobiologically Realistic Determinants of Self-Organized Criticality in Networks of Spiking Neurons
In vivo neural activity of electrosensory pyramidal cells: Biophysical characterization and phenomenological modeling
Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks
Assessing Computational Methods for Transcription Factor Target Gene Identification Based on ChIP-seq Data
Transcriptome diversity is a systematic source of variation in RNA-sequencing data
Natural Selection Fails to Optimize Mutation Rates for Long-Term Adaptation on Rugged Fitness Landscapes
Population Heterogeneity in the Epithelial to Mesenchymal Transition Is Controlled by NFAT and Phosphorylated Sp1
Formal Models of the Network Co-occurrence Underlying Mental Operations
Nuclear plasticity increases susceptibility to damage during confined migration
Bioinformatics for the Human Microbiome Project
Drug Discovery Using Chemical Systems Biology: Weak Inhibition of Multiple Kinases May Contribute to the Anti-Cancer Effect of Nelfinavir
DGCyTOF: Deep learning with graphic cluster visualization to predict cell types of single cell mass cytometry data
A motor unit-based model of muscle fatigue
Inferring Contacting Residues within and between Proteins: What Do the Probabilities Mean?
An associative memory Hamiltonian model for DNA and nucleosomes
Ten Simple Rules for Choosing between Industry and Academia
Insights into muscle metabolic energetics: Modelling muscle-tendon mechanics and metabolic rates during walking across speeds
Protein Design Using Continuous Rotamers
Ten simple rules for good research practice
Anticipation and Choice Heuristics in the Dynamic Consumption of Pain Relief
Ten simple rules for managing communications with a large number of coauthors
Bioinformatics in Jordan: Status, challenges, and future directions
The evolutionary maintenance of Lévy flight foraging
Differential disruptions in population coding along the dorsal-ventral axis of CA1 in the APP/PS1 mouse model of Aβ pathology
Mouse Hair Cycle Expression Dynamics Modeled as Coupled Mesenchymal and Epithelial Oscillators
Realistic assumptions about spatial locations and clustering of premises matter for models of foot-and-mouth disease spread in the United States
In-silico EEG biomarkers of reduced inhibition in human cortical microcircuits in depression
Ultrasensitization: Switch-Like Regulation of Cellular Signaling by Transcriptional Induction
Dual-purpose dynamics emerge from a heterogeneous cell population in Drosophila metamorphosis
Effects of growth rate, cell size, motion, and elemental stoichiometry on nutrient transport kinetics
Getting Started in Probabilistic Graphical Models
Nuclear export is a limiting factor in eukaryotic mRNA metabolism
Interface-Resolved Network of Protein-Protein Interactions
Reinforcement Learning Using a Continuous Time Actor-Critic Framework with Spiking Neurons
Deriving fine-scale models of human mobility from aggregated origin-destination flow data
Protein charge distribution in proteomes and its impact on translation
Electrosensory Midbrain Neurons Display Feature Invariant Responses to Natural Communication Stimuli
Nine quick tips for pathway enrichment analysis
On the usage of artificial intelligence in leprosy care: A systematic literature review
Disease-Associated Mutations Disrupt Functionally Important Regions of Intrinsic Protein Disorder
Cell Surface Receptors for Signal Transduction and Ligand Transport: A Design Principles Study
The Cultural Brain Hypothesis: How culture drives brain expansion, sociality, and life history
Teaching students to R3eason, not merely to solve problem sets: The role of philosophy and visual data communication in accessible data science education
A Kinetic Platform to Determine the Fate of Nitric Oxide in Escherichia coli
Identifying properties of pattern completion neurons in a computational model of the visual cortex
Short-wavelength-sensitive 2 (Sws2) visual photopigment models combined with atomistic molecular simulations to predict spectral peaks of absorbance
A computational model of epithelial solute and water transport along a human nephron
ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus
Impact of waning immunity against SARS-CoV-2 severity exacerbated by vaccine hesitancy
Host population structure impedes reversion to drug sensitivity after discontinuation of treatment
Predictive reward-prediction errors of climbing fiber inputs integrate modular reinforcement learning with supervised learning
ECOD domain classification of 48 whole proteomes from AlphaFold Structure Database using DPAM2
Tracking bacteria at high density with FAST, the Feature-Assisted Segmenter/Tracker
Correction: Improving the Precision of the Structure-Function Relationship by Considering Phylogenetic Context
Predictive Modeling of Signaling Crosstalk during C. elegans Vulval Development
Emergent effects of synaptic connectivity on the dynamics of global and local slow waves in a large-scale thalamocortical network model of the human brain
Stability Properties of Underdominance in Finite Subdivided Populations
Evaluating Spatial Interaction Models for Regional Mobility in Sub-Saharan Africa
A Sensorimotor Model for Computing Intended Reach Trajectories
Verification and reproducible curation of the BioModels repository
EAGLE: An algorithm that utilizes a small number of genomic features to predict tissue/cell type-specific enhancer-gene interactions
Digital twin for sex-specific identification of class III antiarrhythmic drugs based on in vitro measurements, computer models, and machine learning tools
Noise during Rest Enables the Exploration of the Brain's Dynamic Repertoire
Competing ParA Structures Space Bacterial Plasmids Equally over the Nucleoid
Benchmarking the predictive capability of human gait simulations
Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics
Spatial organization of the budding yeast genome in the cell nucleus and identification of specific chromatin interactions from multi-chromosome constrained chromatin model
The Ability of Flux Balance Analysis to Predict Evolution of Central Metabolism Scales with the Initial Distance to the Optimum
Thermodynamics and H 2 Transfer in a Methanogenic, Syntrophic Community
Linear Superposition and Prediction of Bacterial Promoter Activity Dynamics in Complex Conditions
Discovering differential genome sequence activity with interpretable and efficient deep learning
Achieving Occam's razor: Deep learning for optimal model reduction
The mechanism of MinD stability modulation by MinE in Min protein dynamics
A Cell-based Computational Modeling Approach for Developing Site-Directed Molecular Probes
magpie: A power evaluation method for differential RNA methylation analysis in N6-methyladenosine sequencing
Monte Carlo Planning Method Estimates Planning Horizons during Interactive Social Exchange
Ligand discrimination in immune cells: Signal processing insights into immune dysfunction in ER+ breast cancer
Network and Atomistic Simulations Unveil the Structural Determinants of Mutations Linked to Retinal Diseases
Coding and Decoding with Adapting Neurons: A Population Approach to the Peri-Stimulus Time Histogram
Deterministic Mechanical Model of T-Killer Cell Polarization Reproduces the Wandering of Aim between Simultaneously Engaged Targets
Physics-based modeling provides predictive understanding of selectively promiscuous substrate binding by Hsp70 chaperones
Transient chromatin properties revealed by polymer models and stochastic simulations constructed from Chromosomal Capture data
Estimating the Probability of Polyreactive Antibodies 4E10 and 2F5 Disabling a gp41 Trimer after T Cell-HIV Adhesion
Estimates of the basic reproduction number for rubella using seroprevalence data and indicator-based approaches
Modeling geographic vaccination strategies for COVID-19 in Norway
Characterizing collaborative transcription regulation with a graph-based deep learning approach
BinPacker: Packing-Based De Novo Transcriptome Assembly from RNA-seq Data
Practical Strategies for Discovering Regulatory DNA Sequence Motifs
Correction: Individual-based model highlights the importance of trade-offs for virus-host population dynamics and long-term co-existence
IPScan: Detecting novel intronic PolyAdenylation events with RNA-seq data
Stochastic Regulation of her1/7 Gene Expression Is the Source of Noise in the Zebrafish Somite Clock Counteracted by Notch Signalling
Effects of Transcriptional Pausing on Gene Expression Dynamics
Drug-Class Specific Impact of Antivirals on the Reproductive Capacity of HIV
"Broadband" Bioinformatics Skills Transfer with the Knowledge Transfer Programme (KTP): Educational Model for Upliftment and Sustainable Development