yusuke1997/dblp-id-title huggingface dataset:
Task-Dependent Changes in Cross-Level Coupling between Single Neurons and Oscillatory Activity in Multiscale Networks
Internal state effects on behavioral shifts in freely behaving praying mantises (Tenodera sinensis)
The Lazy Visual Word Form Area: Computational Insights into Location-Sensitivity
Rearrangement moves on rooted phylogenetic networks
Improving policy design and epidemic response using integrated models of economic choice and disease dynamics with behavioral feedback
Parameter inference for stochastic biochemical models from perturbation experiments parallelised at the single cell level
Seasonal influenza: Modelling approaches to capture immunity propagation
Effective Design of Multifunctional Peptides by Combining Compatible Functions
The optimal spatially-dependent control measures to effectively and economically eliminate emerging infectious diseases
Sample-based modeling reveals bidirectional interplay between cell cycle progression and extrinsic apoptosis
The impact of model assumptions in interpreting cell kinetic studies
Human miRNA Precursors with Box H/ACA snoRNA Features
An Integrative Multi-Network and Multi-Classifier Approach to Predict Genetic Interactions
The development and application of bioinformatics core competencies to improve bioinformatics training and education
Understanding the impact of mobility on COVID-19 spread: A hybrid gravity-metapopulation model of COVID-19
Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli
Recombination and mutational robustness in neutral fitness landscapes
Building the Future of Bioinformatics through Student-Facilitated Conferencing
Dual Process for Intentional and Reactive Decisions
Improve the model of disease subtype heterogeneity by leveraging external summary data
Modeling and MEG evidence of early consonance processing in auditory cortex
Correction: Reconstructible Phylogenetic Networks: Do Not Distinguish the Indistinguishable
Ceramide-1-phosphate transfer protein enhances lipid transport by disrupting hydrophobic lipid-membrane contacts
Quantifying critical states of complex diseases using single-sample dynamic network biomarkers
From complete cross-docking to partners identification and binding sites predictions
A Quantitative Comparison of Anti-HIV Gene Therapy Delivered to Hematopoietic Stem Cells versus CD4+ T Cells
Beauty Is in the Eye of the Beholder: Proteins Can Recognize Binding Sites of Homologous Proteins in More than One Way
Mechanistic modeling quantifies the influence of tumor growth kinetics on the response to anti-angiogenic treatment
Membrane-Elasticity Model of Coatless Vesicle Budding Induced by ESCRT Complexes
Conformational Spread in the Flagellar Motor Switch: A Model Study
Projecting social contact matrices in 152 countries using contact surveys and demographic data
Adaptive search space pruning in complex strategic problems
Age-dependent ventilator-induced lung injury: Mathematical modeling, experimental data, and statistical analysis
Building clone-consistent ecosystem models
Active Dendrites Enhance Neuronal Dynamic Range
Impacts of observation frequency on proximity contact data and modeled transmission dynamics
FamSeq: A Variant Calling Program for Family-Based Sequencing Data Using Graphics Processing Units
Does High-Dose Antimicrobial Chemotherapy Prevent the Evolution of Resistance?
Maximum entropy and population heterogeneity in continuous cell cultures
Assessing the impact of lateral flow testing strategies on within-school SARS-CoV-2 transmission and absences: A modelling study
Evolution of Gene Regulatory Networks by Fluctuating Selection and Intrinsic Constraints
The Two Sides of Complement C3d: Evolution of Electrostatics in a Link between Innate and Adaptive Immunity
Molecular dynamics shows complex interplay and long-range effects of post-translational modifications in yeast protein interactions
Credibility assessment of patient-specific computational modeling using patient-specific cardiac modeling as an exemplar
Clustering gene expression time series data using an infinite Gaussian process mixture model
Systematic interrogation of diverse Omic data reveals interpretable, robust, and generalizable transcriptomic features of clinically successful therapeutic targets
Deciding Not to Decide: Computational and Neural Evidence for Hidden Behavior in Sequential Choice
Active dendrites regulate the spatiotemporal spread of signaling microdomains
The catecholamine precursor Tyrosine reduces autonomic arousal and decreases decision thresholds in reinforcement learning and temporal discounting
Phenotypic Mutation Rates and the Abundance of Abnormal Proteins in Yeast
Synchronization and Random Triggering of Lymphatic Vessel Contractions
A reconstruction theory of relational schema induction
Model-Based Therapeutic Correction of Hypothalamic-Pituitary-Adrenal Axis Dysfunction
NRV: An open framework for in silico evaluation of peripheral nerve electrical stimulation strategies
In vitro machine learning-based CAR T immunological synapse quality measurements correlate with patient clinical outcomes
How does date-rounding affect phylodynamic inference for public health?
2015 ISCB Overton Prize Awarded to Curtis Huttenhower
Demonstrating aspects of multiscale modeling by studying the permeation pathway of the human ZnT2 zinc transporter
Characterization of Growth and Metabolism of the Haloalkaliphile Natronomonas pharaonis
Benchmarking of tools for axon length measurement in individually-labeled projection neurons
Deconvolving multiplexed protease signatures with substrate reduction and activity clustering
Ten simple rules for organizations to support research data sharing
The structural effects of indel polymorphisms outside the binding site on RNA-protein interactions are shaped by selection
ASAP-SML: An antibody sequence analysis pipeline using statistical testing and machine learning
Multilevel selection favors fragmentation modes that maintain cooperative interactions in multispecies communities
Enabling interpretable machine learning for biological data with reliability scores
Minimization of Biosynthetic Costs in Adaptive Gene Expression Responses of Yeast to Environmental Changes
Dynamic Redox Regulation of IL-4 Signaling
Lévy movements and a slowly decaying memory allow efficient collective learning in groups of interacting foragers
Bayesian Phylogeography Finds Its Roots
Hands-on training about overfitting
Reconstructing the course of the COVID-19 epidemic over 2020 for US states and counties: Results of a Bayesian evidence synthesis model
Heterogeneous, delayed-onset killing by multiple-hitting T cells: Stochastic simulations to assess methods for analysis of imaging data
Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression
PathoRM: Computational inference of pathogenic RNA methylation sites by incorporating multi-view features
The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization
The RNA Silencing Pathway: The Bits and Pieces That Matter
Ten simple rules for getting started with statistics in graduate school
β-Methylamino-L-alanine substitution of serine in SOD1 suggests a direct role in ALS etiology
Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method
The effects of the post-delay epochs on working memory error reduction
Cyclin and DNA Distributed Cell Cycle Model for GS-NS0 Cells
The Effect of Macromolecular Crowding, Ionic Strength and Calcium Binding on Calmodulin Dynamics
Identification of excitatory-inhibitory links and network topology in large-scale neuronal assemblies from multi-electrode recordings
A systematic evaluation of deep learning methods for the prediction of drug synergy in cancer
Putting benchmarks in their rightful place: The heart of computational biology
A theory of how active behavior stabilises neural activity: Neural gain modulation by closed-loop environmental feedback
Intrinsic Disorder Is a Common Feature of Hub Proteins from Four Eukaryotic Interactomes
Artificial neural networks for model identification and parameter estimation in computational cognitive models
Rapid automated 3-D pose estimation of larval zebrafish using a physical model-trained neural network
Molecular Evolution of Peptide Ligands with Custom-Tailored Characteristics for Targeting of Glycostructures
FINDSITE LHM : A Threading-Based Approach to Ligand Homology Modeling
Predicting Shine-Dalgarno Sequence Locations Exposes Genome Annotation Errors
Robust Network Topologies for Generating Switch-Like Cellular Responses
: Comprehensive Sieve Analysis of Breakthrough HIV-1 Sequences in the RV144 Vaccine Efficacy Trial
HER2+ Cancer Cell Dependence on PI3K vs. MAPK Signaling Axes Is Determined by Expression of EGFR, ERBB3 and CDKN1B
Conformational plasticity and dynamic interactions of the N-terminal domain of the chemokine receptor CXCR1
Using random forests to uncover the predictive power of distance-varying cell interactions in tumor microenvironments
Long-read sequencing transcriptome quantification with lr-kallisto
Comparing individual-based approaches to modelling the self-organization of multicellular tissues
Hydrogen-Bond Driven Loop-Closure Kinetics in Unfolded Polypeptide Chains
Vertex models capturing subcellular scales in epithelial tissues
HGCLAMIR: Hypergraph contrastive learning with attention mechanism and integrated multi-view representation for predicting miRNA-disease associations
Quasispecies Made Simple
Predicting peak spectral sensitivities of vertebrate cone visual pigments using atomistic molecular simulations
Evolutionary Capacitance and Control of Protein Stability in Protein-Protein Interaction Networks
Early exposure to broadly neutralizing antibodies may trigger a dynamical switch from progressive disease to lasting control of SHIV infection
Stimulus-Dependent State Transition between Synchronized Oscillation and Randomly Repetitive Burst in a Model Cerebellar Granular Layer
Correction: The Equivalence of Information-Theoretic and Likelihood-Based Methods for Neural Dimensionality Reduction
Ten Simple Rules for Reducing Overoptimistic Reporting in Methodological Computational Research
A Model of Ant Route Navigation Driven by Scene Familiarity
Flexible resonance in prefrontal networks with strong feedback inhibition
Host Mobility Drives Pathogen Competition in Spatially Structured Populations
A local measure of symmetry and orientation for individual spikes of grid cells
The Carbon Assimilation Network in Escherichia coli Is Densely Connected and Largely Sign-Determined by Directions of Metabolic Fluxes
Avalanches in a Stochastic Model of Spiking Neurons
The Young PI Buzz: Learning from the Organizers of the Junior Principal Investigator Meeting at ISMB-ECCB 2013
Approximate distance correlation for selecting highly interrelated genes across datasets
Structural Investigation of MscL Gating Using Experimental Data and Coarse Grained MD Simulations
An integrated calcium imaging processing toolbox for the analysis of neuronal population dynamics
An expert judgment model to predict early stages of the COVID-19 pandemic in the United States
Time Scales in Epigenetic Dynamics and Phenotypic Heterogeneity of Embryonic Stem Cells
Protection promotes energetically efficient structures in marine communities
Probing the link between vision and language in material perception using psychophysics and unsupervised learning
Handling Uncertainty in Dynamic Models: The Pentose Phosphate Pathway in Trypanosoma brucei
Host phenotype classification from human microbiome data is mainly driven by the presence of microbial taxa
An efficient moments-based inference method for within-host bacterial infection dynamics
A Virtual Mixture Approach to the Study of Multistate Equilibrium: Application to Constant pH Simulation in Explicit Water
Benchmarking interpretability of deep learning for predictive genomics: Recall, precision, and variability of feature attribution
Web-Based Computational Chemistry Education with CHARMMing II: Coarse-Grained Protein Folding
Biophysical Network Modelling of the dLGN Circuit: Different Effects of Triadic and Axonal Inhibition on Visual Responses of Relay Cells
Noise suppression in stochastic genetic circuits using PID controllers
Towards Systematic Discovery of Signaling Networks in Budding Yeast Filamentous Growth Stress Response Using Interventional Phosphorylation Data
How Evolving Heterogeneity Distributions of Resource Allocation Strategies Shape Mortality Patterns
Analysis of a Gene Regulatory Cascade Mediating Circadian Rhythm in Zebrafish
A dual regulation mechanism of histidine kinase CheA identified by combining network-dynamics modeling and system-level input-output data
Spatially resolved simulations of the spread of COVID-19 in three European countries
Quantitative Protein Localization Signatures Reveal an Association between Spatial and Functional Divergences of Proteins
Fast and Accurate Learning When Making Discrete Numerical Estimates
Multiscale modelization in a small virus: Mechanism of proton channeling and its role in triggering capsid disassembly
A model of anaerobic tissue perfusion during trauma - Lactate trajectory curvature can determine recovery
Ten simple rules for designing and conducting undergraduate replication projects
Network models of protein phosphorylation, acetylation, and ubiquitination connect metabolic and cell signaling pathways in lung cancer
Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes
Molecular dynamics simulations reveal how vinculin refolds partially unfolded talin rod helices to stabilize them against mechanical force
Phase Resetting Reveals Network Dynamics Underlying a Bacterial Cell Cycle
Computational Modeling and Analysis of Iron Release from Macrophages
Nucleoid-Associated Proteins Affect Mutation Dynamics in E. coli in a Growth Phase-Specific Manner
The impact of temporal sampling resolution on parameter inference for biological transport models
Computational Protein Design Quantifies Structural Constraints on Amino Acid Covariation
A new dynamic correlation algorithm reveals novel functional aspects in single cell and bulk RNA-seq data
The MAPK/ERK channel capacity exceeds 6 bit/hour
Logic-based modeling of biological networks with Netflux
Determinants of Cell-to-Cell Variability in Protein Kinase Signaling
Computational Complementation: A Modelling Approach to Study Signalling Mechanisms during Legume Autoregulation of Nodulation
Hydrophobin Film Structure for HFBI and HFBII and Mechanism for Accelerated Film Formation
Connecting signaling and metabolic pathways in EGF receptor-mediated oncogenesis of glioblastoma
OOPS: Object-Oriented Polarization Software for analysis of fluorescence polarization microscopy images
Laminar specificity of the auditory perceptual awareness negativity: A biophysical modeling study
Predictive Dynamics of Human Pain Perception
An Integrated Approach to Reconstructing Genome-Scale Transcriptional Regulatory Networks
Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours
Dread and the Disvalue of Future Pain
How Co-translational Folding of Multi-domain Protein Is Affected by Elongation Schedule: Molecular Simulations
HELIOS: High-speed sequence alignment in optics
On the Origin of DNA Genomes: Evolution of the Division of Labor between Template and Catalyst in Model Replicator Systems
Tox_(R)CNN: Deep learning-based nuclei profiling tool for drug toxicity screening
Interactions between Connected Half-Sarcomeres Produce Emergent Mechanical Behavior in a Mathematical Model of Muscle
Quantitative theory of deep brain stimulation of the subthalamic nucleus for the suppression of pathological rhythms in Parkinson's disease
Sequential mutations in exponentially growing populations
Measuring Fisher Information Accurately in Correlated Neural Populations
Genome-Wide Analysis of Human Disease Alleles Reveals That Their Locations Are Correlated in Paralogous Proteins
Predicting Important Residues and Interaction Pathways in Proteins Using Gaussian Network Model: Binding and Stability of HLA Proteins
Decomposition of Gene Expression State Space Trajectories
Risk sensitivity and theory of mind in human coordination
The CanOE Strategy: Integrating Genomic and Metabolic Contexts across Multiple Prokaryote Genomes to Find Candidate Genes for Orphan Enzymes
Phase changes in neuronal postsynaptic spiking due to short term plasticity
Assessment of ab initio models of protein complexes by molecular dynamics
Gene expression noise can promote the fixation of beneficial mutations in fluctuating environments
Upper bounds for integrated information
Molecular Insights into the Dynamics of Pharmacogenetically Important N-Terminal Variants of the Human β 2 -Adrenergic Receptor
Signal Processing in the TGF-β Superfamily Ligand-Receptor Network
Not All Scale-Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Evolution
Deep learning approach for automatic assessment of schizophrenia and bipolar disorder in patients using R-R intervals
Use of temperature to improve West Nile virus forecasts
Torsion-Mediated Interaction between Adjacent Genes
Synthetic Lethality between Gene Defects Affecting a Single Non-essential Molecular Pathway with Reversible Steps
Hydra: A mixture modeling framework for subtyping pediatric cancer cohorts using multimodal gene expression signatures
Data-Driven Metabolic Pathway Compositions Enhance Cancer Survival Prediction
Assessing the contribution of tumor mutational phenotypes to cancer progression risk
MINT: A toolbox for the analysis of multivariate neural information coding and transmission
Model-based prioritization for acquiring protection
Scalability of Asynchronous Networks Is Limited by One-to-One Mapping between Effective Connectivity and Correlations
Correction: Organism-Adapted Specificity of the Allosteric Regulation of Pyruvate Kinase in Lactic Acid Bacteria
Quantification of Ebola virus replication kinetics in vitro
Bayesian modelling of high-throughput sequencing assays with malacoda
Expression of quasi-equivalence and capsid dimorphism in the Hepadnaviridae
The Rat Genome Database Curators: Who, What, Where, Why
The color phi phenomenon: Not so special, after all?
A Complex-Valued Firing-Rate Model That Approximates the Dynamics of Spiking Networks
Druggable Protein Interaction Sites Are More Predisposed to Surface Pocket Formation than the Rest of the Protein Surface
Asynchronous Rate Chaos in Spiking Neuronal Circuits
Folding kinetics of an entangled protein
Recombination-aware phylogeographic inference using the structured coalescent with ancestral recombination
FIMTrack: An open source tracking and locomotion analysis software for small animals
Genome-scale metabolic modelling when changes in environmental conditions affect biomass composition
Kinetic and data-driven modeling of pancreatic β-cell central carbon metabolism and insulin secretion
On the role of sparseness in the evolution of modularity in gene regulatory networks
Ten simple rules for developing bioinformatics capacity at an academic institution
A subcomponent-guided deep learning method for interpretable cancer drug response prediction
Temporal Controls of the Asymmetric Cell Division Cycle in Caulobacter crescentus
Constructing benchmark test sets for biological sequence analysis using independent set algorithms
Experimental and computational investigation of enzyme functional annotations uncovers misannotation in the EC 1.1.3.15 enzyme class
A Structured Model of Video Reproduces Primary Visual Cortical Organisation
BiomeNet: A Bayesian Model for Inference of Metabolic Divergence among Microbial Communities
A mathematical framework for understanding the spontaneous emergence of complexity applicable to growing multicellular systems
A RESTful API for Accessing Microbial Community Data for MG-RAST
Differential polarization of cortical pyramidal neuron dendrites through weak extracellular fields
Quantifying the Impact of Human Immunodeficiency Virus-1 Escape From Cytotoxic T-Lymphocytes
Correction: Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways
Dose optimization of an adjuvanted peptide-based personalized neoantigen melanoma vaccine
Comprehensive discovery of CRISPR-targeted terminally redundant sequences in the human gut metagenome: Viruses, plasmids, and more
Tuning social interactions' strength drives collective response to light intensity in schooling fish
Mutation Induced Extinction in Finite Populations: Lethal Mutagenesis and Lethal Isolation
Coevolutionary dynamics of phenotypic diversity and contingent cooperation
Predictive modeling of antibiotic eradication therapy success for new-onset Pseudomonas aeruginosa pulmonary infections in children with cystic fibrosis
Grid Cells, Place Cells, and Geodesic Generalization for Spatial Reinforcement Learning
Partitioning stable and unstable expression level variation in cell populations: A theoretical framework and its application to the T cell receptor
Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species
Fusome topology and inheritance during insect gametogenesis
Altering neuronal excitability to preserve network connectivity in a computational model of Alzheimer's disease
Alternate conformational trajectories in ribosome translocation
Evolutionary Interactions between N-Linked Glycosylation Sites in the HIV-1 Envelope
Self-replicating artificial neural networks give rise to universal evolutionary dynamics
Computational design of Periplasmic binding protein biosensors guided by molecular dynamics
Visual perception of liquids: Insights from deep neural networks
How robust are estimates of key parameters in standard viral dynamic models?
Natural Image Coding in V1: How Much Use Is Orientation Selectivity?
A Third Approach to Gene Prediction Suggests Thousands of Additional Human Transcribed Regions
BiP Clustering Facilitates Protein Folding in the Endoplasmic Reticulum
Computational Cancer Biology: An Evolutionary Perspective
A Bayesian Attractor Model for Perceptual Decision Making
MC EMiNEM Maps the Interaction Landscape of the Mediator
Dimensionality and Dynamics in the Behavior of C. elegans
A Computational Model of a Descending Mechanosensory Pathway Involved in Active Tactile Sensing
Physiological characterization of electrodermal activity enables scalable near real-time autonomic nervous system activation inference
Evolution of Function in the "Two Dinucleotide Binding Domains" Flavoproteins
Model-driven discovery of calcium-related protein-phosphatase inhibition in plant guard cell signaling
Regulatory Network Structure as a Dominant Determinant of Transcription Factor Evolutionary Rate
Bistable Dynamics Underlying Excitability of Ion Homeostasis in Neuron Models
Comparing the effectiveness of ring and block-vaccination strategies on networks
Stimulus-to-stimulus learning in RNNs with cortical inductive biases
The Role of Social Contacts and Original Antigenic Sin in Shaping the Age Pattern of Immunity to Seasonal Influenza
Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically consistent metabolic models
Why and how to set up a Bioinformatics Learning Lab (BILL)
Dynamic maximum entropy provides accurate approximation of structured population dynamics
The Stochastic Early Reaction, Inhibition, and late Action (SERIA) model for antisaccades
Temperature-robust activity patterns arise from coordinated axonal Sodium channel properties
Hierarchical Models in the Brain
Increased Brain Signal Variability Accompanies Lower Behavioral Variability in Development
Multi-region infectious disease prediction modeling based on spatio-temporal graph neural network and the dynamic model
Decoding dynamic visual scenes across the brain hierarchy
Inherent versus induced protein flexibility: Comparisons within and between apo and holo structures
Implementation of Complex Biological Logic Circuits Using Spatially Distributed Multicellular Consortia
A Nucleosome-Guided Map of Transcription Factor Binding Sites in Yeast