yusuke1997/dblp-id-title huggingface dataset:
Optimizing the depth and the direction of prospective planning using information values
The Internal Dynamics of Fibrinogen and Its Implications for Coagulation and Adsorption
Towards constructing a generalized structural 3D breathing human lung model based on experimental volumes, pressures, and strains
Modeling within-host and aerosol dynamics of SARS-CoV-2: The relationship with infectiousness
Defining the Nature of Thermal Intermediate in 3 State Folding Proteins: Apoflavodoxin, a Study Case
BharatSim: An agent-based modelling framework for India
Why is Real-World Visual Object Recognition Hard?
Retinal Wave Behavior through Activity-Dependent Refractory Periods
Linking Macroscopic with Microscopic Neuroanatomy Using Synthetic Neuronal Populations
Crowdsourced identification of multi-target kinase inhibitors for RET- and TAU- based disease: The Multi-Targeting Drug DREAM Challenge
Propagating Waves of Directionality and Coordination Orchestrate Collective Cell Migration
Facilitating bioinformatics reproducibility with QIIME 2 Provenance Replay
Adaptive social contact rates induce complex dynamics during epidemics
Human perception of self-motion and orientation during galvanic vestibular stimulation and physical motion
Effects of incomplete inter-hospital network data on the assessment of transmission dynamics of hospital-acquired infections
JASPER: A fast genome polishing tool that improves accuracy of genome assemblies
How Molecular Motors Are Arranged on a Cargo Is Important for Vesicular Transport
Using test positivity and reported case rates to estimate state-level COVID-19 prevalence and seroprevalence in the United States
Evolution enhances mutational robustness and suppresses the emergence of a new phenotype: A new computational approach for studying evolution
Compression-based inference of network motif sets
Predicting pathogenicity behavior in Escherichia coli population through a state dependent model and TRS profiling
Interrogating and Predicting Tolerated Sequence Diversity in Protein Folds: Application to E. elaterium Trypsin Inhibitor-II Cystine-Knot Miniprotein
Computational Inference of Neural Information Flow Networks
Uncovering and characterizing splice variants associated with survival in lung cancer patients
Criticality Is an Emergent Property of Genetic Networks that Exhibit Evolvability
A feedforward mechanism for human-like contour integration
Biases in the Experimental Annotations of Protein Function and Their Effect on Our Understanding of Protein Function Space
Modeling the structure of the frameshift-stimulatory pseudoknot in SARS-CoV-2 reveals multiple possible conformers
Multidimensional Epistasis and the Transitory Advantage of Sex
Designing microbial communities to maximize the thermodynamic driving force for the production of chemicals
On the stability and dynamics of stochastic spiking neuron models: Nonlinear Hawkes process and point process GLMs
Modelling Reveals Kinetic Advantages of Co-Transcriptional Splicing
Correction: Estimation of the dispersal distances of an aphid-borne virus in a patchy landscape
Annotation-free delineation of prokaryotic homology groups
Protons in small spaces: Discrete simulations of vesicle acidification
MHC binding affects the dynamics of different T-cell receptors in different ways
Growth rules for the repair of Asynchronous Irregular neuronal networks after peripheral lesions
Improved Statistical Methods Enable Greater Sensitivity in Rhythm Detection for Genome-Wide Data
Genomic Hallmarks of Genes Involved in Chromosomal Translocations in Hematological Cancer
Quantitative Modeling of GRK-Mediated β2AR Regulation
The Many Faces of Protein-Protein Interactions: A Compendium of Interface Geometry
Transition to Quorum Sensing in an Agrobacterium Population: A Stochastic Model
Ten simple rules for navigating the reference letter seeking process
De novo protein fold families expand the designable ligand binding site space
Ten Simple Rules for the Care and Feeding of Scientific Data
Regression Analysis for Constraining Free Parameters in Electrophysiological Models of Cardiac Cells
Conditional probabilistic diffusion model driven synthetic radiogenomic applications in breast cancer
Dynamic cues for whisker-based object localization: An analytical solution to vibration during active whisker touch
Allosteric conformational change cascade in cytoplasmic dynein revealed by structure-based molecular simulations
Identifying functional groups among the diverse, recombining antigenic var genes of the malaria parasite Plasmodium falciparum from a local community in Ghana
The Canadian Open Neuroscience Platform - An open science framework for the neuroscience community
Cell size and selection for stress-induced cell fusion in unicellular eukaryotes
Predicting Functional Gene Links from Phylogenetic-Statistical Analyses of Whole Genomes
In silico mutagenesis of human ACE2 with S protein and translational efficiency explain SARS-CoV-2 infectivity in different species
Radial and Spiral Stream Formation in Proteus mirabilis Colonies
Establishing a Successful Bioinformatics Core Facility Team
SpikeShip: A method for fast, unsupervised discovery of high-dimensional neural spiking patterns
Estimating fine age structure and time trends in human contact patterns from coarse contact data: The Bayesian rate consistency model
Hydrophobic Compounds Reshape Membrane Domains
Estimation of regional polygenicity from GWAS provides insights into the genetic architecture of complex traits
Ten simple rules for faculty members building just and equitable environments in academic science
Ten simple rules for leveraging virtual interaction to build higher-level learning into bioinformatics short courses
Mechanical properties of tubulin intra- and inter-dimer interfaces and their implications for microtubule dynamic instability
Identifying topologically associating domains using differential kernels
Correction: The Role of Compensatory Mutations in the Emergence of Drug Resistance
Ten simple rules to run a successful BioHackathon
Synaptic Plasticity Controls Sensory Responses through Frequency-Dependent Gamma Oscillation Resonance
Detectability of runs of homozygosity is influenced by analysis parameters and population-specific demographic history
Identification of structures for ion channel kinetic models
A Discretized Overlap Resolution Algorithm (DORA) for resolving spatial overlaps in individual-based models of microbes
Self-organised criticality in the evolution of a thermodynamic model of rodent thermoregulatory huddling
An approximate stochastic optimal control framework to simulate nonlinear neuro-musculoskeletal models in the presence of noise
Interrogating Emergent Transport Properties for Molecular Motor Ensembles: A Semi-analytical Approach
PEX5 and Ubiquitin Dynamics on Mammalian Peroxisome Membranes
ChromaSig: A Probabilistic Approach to Finding Common Chromatin Signatures in the Human Genome
Finding a Needle in a Haystack: The Role of Electrostatics in Target Lipid Recognition by PH Domains
Design of field trials for the evaluation of transmissible vaccines in animal populations
A new method for the analysis of access period experiments, illustrated with whitefly-borne cassava mosaic begomovirus
Inference for Stochastic Chemical Kinetics Using Moment Equations and System Size Expansion
How does Sec63 affect the conformation of Sec61 in yeast?
Transferable deep generative modeling of intrinsically disordered protein conformations
Conventional analysis of trial-by-trial adaptation is biased: Empirical and theoretical support using a Bayesian estimator
A Self-Organising Model of Thermoregulatory Huddling
Confidence-based Somatic Mutation Evaluation and Prioritization
Epidemic Spreading Model to Characterize Misfolded Proteins Propagation in Aging and Associated Neurodegenerative Disorders
iHerd: an integrative hierarchical graph representation learning framework to quantify network changes and prioritize risk genes in disease
Coding with transient trajectories in recurrent neural networks
Understanding photosynthetic biofilm productivity and structure through 2D simulation
Computational investigation of blood cell transport in retinal microaneurysms
Computational modelling of cell motility modes emerging from cell-matrix adhesion dynamics
Multidimensional analysis and detection of informative features in human brain white matter
A Network-based Approach for Predicting Missing Pathway Interactions
Modeling of Kidney Hemodynamics: Probability-Based Topology of an Arterial Network
The Effects of Dominance on Leadership and Energetic Gain: A Dynamic Game between Pairs of Social Foragers
Integrative Computational and Experimental Approaches to Establish a Post-Myocardial Infarction Knowledge Map
Inferring Evolutionary Histories of Pathway Regulation from Transcriptional Profiling Data
Exhaustive Analysis of a Genotype Space Comprising 10 15 Central Carbon Metabolisms Reveals an Organization Conducive to Metabolic Innovation
Beyond homogeneity: Assessing the validity of the Michaelis-Menten rate law in spatially heterogeneous environments
Ten Simple Rules for Cultivating Open Science and Collaborative R&D
A data-driven semi-parametric model of SARS-CoV-2 transmission in the United States
Kilohertz waveforms optimized to produce closed-state Na+ channel inactivation eliminate onset response in nerve conduction block
Epigenetic instability may alter cell state transitions and anticancer drug resistance
Human discrimination and modeling of high-frequency complex tones shed light on the neural codes for pitch
Specificity of Loxosceles α clade phospholipase D enzymes for choline-containing lipids: Role of a conserved aromatic cage
Identifying metabolic adaptations characteristic of cardiotoxicity using paired transcriptomics and metabolomics data integrated with a computational model of heart metabolism
How public reaction to disease information across scales and the impacts of vector control methods influence disease prevalence and control efficacy
Ten simple rules for increased lab resilience
Bidirectional de novo peptide sequencing using a transformer model
Secuer: Ultrafast, scalable and accurate clustering of single-cell RNA-seq data
Successful cardiac resynchronization therapy reduces negative septal work in patient-specific models of dyssynchronous heart failure
Deep Neural Networks as a Computational Model for Human Shape Sensitivity
Mutation bias interacts with composition bias to influence adaptive evolution
Dynamics and Control of Diseases in Networks with Community Structure
A quantitative description of light-limited cyanobacterial growth using flux balance analysis
Pan-cancer characterization of ncRNA synergistic competition uncovers potential carcinogenic biomarkers
Surface Dynamics in Allosteric Regulation of Protein-Protein Interactions: Modulation of Calmodulin Functions by Ca 2+
The use of ambient humidity conditions to improve influenza forecast
Evolutionary information helps understand distinctive features of the angiotensin II receptors AT1 and AT2 in amniota
Correction: Low-dimensional controllability of brain networks
Tracking the contribution of inductive bias to individualised internal models
Reliability of Transcriptional Cycles and the Yeast Cell-Cycle Oscillator
High Resolution Models of Transcription Factor-DNA Affinities Improve In Vitro and In Vivo Binding Predictions
Natural, Persistent Oscillations in a Spatial Multi-Strain Disease System with Application to Dengue
Extensive Decoupling of Metabolic Genes in Cancer
Age-dependent Pavlovian biases influence motor decision-making
Correction: A Combination of Transcriptional and MicroRNA Regulation Improves the Stability of the Relative Concentrations of Target Genes
Optimal Vaccine Allocation for the Early Mitigation of Pandemic Influenza
Multi-cell ECM compaction is predictable via superposition of nonlinear cell dynamics linearized in augmented state space
Calibrating spatiotemporal models of microbial communities to microscopy data: A review
Viscoelastic properties of wheat gluten in a molecular dynamics study
A normative model of peripersonal space encoding as performing impact prediction
COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions
Analysis of emergent patterns in crossing flows of pedestrians reveals an invariant of 'stripe' formation in human data
Efficient "Shotgun" Inference of Neural Connectivity from Highly Sub-sampled Activity Data
Glutamate-Bound NMDARs Arising from In Vivo -like Network Activity Extend Spatio-temporal Integration in a L5 Cortical Pyramidal Cell Model
Knotted vs. Unknotted Proteins: Evidence of Knot-Promoting Loops
In vivo Conditions Induce Faithful Encoding of Stimuli by Reducing Nonlinear Synchronization in Vestibular Sensory Neurons
Muscle Synergies Heavily Influence the Neural Control of Arm Endpoint Stiffness and Energy Consumption
Phylogenetic Diversity Theory Sheds Light on the Structure of Microbial Communities
The origin of biological homochirality along with the origin of life
Effects of recombination on multi-drug resistance evolution in Plasmodium falciparum malaria
PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph
Investigating key cell types and molecules dynamics in PyMT mice model of breast cancer through a mathematical model
High Accuracy Decoding of Dynamical Motion from a Large Retinal Population
Controlled Measurement and Comparative Analysis of Cellular Components in E . coli Reveals Broad Regulatory Changes in Response to Glucose Starvation
A model-based evaluation of the efficacy of COVID-19 social distancing, testing and hospital triage policies
The Effect of Gap Junctional Coupling on the Spatiotemporal Patterns of Ca2+ Signals and the Harmonization of Ca2+-Related Cellular Responses
Estimation of heterogeneous instantaneous reproduction numbers with application to characterize SARS-CoV-2 transmission in Massachusetts counties
Quantifying the clusterness and trajectoriness of single-cell RNA-seq data
Causal Modeling of Cancer-Stromal Communication Identifies PAPPA as a Novel Stroma-Secreted Factor Activating NFκB Signaling in Hepatocellular Carcinoma
Bridging the Resolution Gap in Structural Modeling of 3D Genome Organization
Cooltools: Enabling high-resolution Hi-C analysis in Python
Metabolic Factors Limiting Performance in Marathon Runners
Computation and measurement of cell decision making errors using single cell data
Suboptimal Criterion Learning in Static and Dynamic Environments
Prosthetic Avian Vocal Organ Controlled by a Freely Behaving Bird Based on a Low Dimensional Model of the Biomechanical Periphery
Coarse-Grained Simulations of Topology-Dependent Mechanisms of Protein Unfolding and Translocation Mediated by ClpY ATPase Nanomachines
Ten Simple Rules for Teaching Bioinformatics at the High School Level
Allosteric Communication in Myosin V: From Small Conformational Changes to Large Directed Movements
Modeling Fatty Acid Transfer from Artery to Cardiomyocyte
A Model for Direction Sensing in Dictyostelium discoideum: Ras Activity and Symmetry Breaking Driven by a Gβγ-Mediated, Gα2-Ric8 - Dependent Signal Transduction Network
An Evolutionary Trade-Off between Protein Turnover Rate and Protein Aggregation Favors a Higher Aggregation Propensity in Fast Degrading Proteins
3D morphology-based clustering and simulation of human pyramidal cell dendritic spines
Oscillator decomposition of infant fNIRS data
A Biophysical Model of CRISPR/Cas9 Activity for Rational Design of Genome Editing and Gene Regulation
Ten simple rules for partnering with K-12 teachers to support broader impact goals
A Model of Brain Circulation and Metabolism: NIRS Signal Changes during Physiological Challenges
Trade-off between synergy and efficacy in combinations of HIV-1 latency-reversing agents
Multiscale computational model of Achilles tendon wound healing: Untangling the effects of repair and loading
A Probabilistic Model of RNA Conformational Space
PPIDomainMiner: Inferring domain-domain interactions from multiple sources of protein-protein interactions
Revealing Pathway Dynamics in Heart Diseases by Analyzing Multiple Differential Networks
A mechanistic spatio-temporal framework for modelling individual-to-individual transmission - With an application to the 2014-2015 West Africa Ebola outbreak
Integrating Interactive Computational Modeling in Biology Curricula
Comparative study of population genomic approaches for mapping colony-level traits
In-Vivo Real-Time Control of Protein Expression from Endogenous and Synthetic Gene Networks
Sensorimotor maps can be dynamically calibrated using an adaptive-filter model of the cerebellum
adaPop: Bayesian inference of dependent population dynamics in coalescent models
Integrin Clustering Is Driven by Mechanical Resistance from the Glycocalyx and the Substrate
A Biologically Constrained, Mathematical Model of Cortical Wave Propagation Preceding Seizure Termination
Biocurators: Contributors to the World of Science
Social conformity is a heuristic when individual risky decision-making is disrupted
Finding the rhythm: Humans exploit nonlinear intrinsic dynamics of compliant systems in periodic interaction tasks
Evolution along the parasitism-mutualism continuum determines the genetic repertoire of prophages
Modeling subjective relevance in schizophrenia and its relation to aberrant salience
The Evolutionary Origins of Hierarchy
Ten simple rules for providing optimal administrative support to research teams
Replication Pauses of the Wild-Type and Mutant Mitochondrial DNA Polymerase Gamma: A Simulation Study
Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis
Deconstructing Interocular Suppression: Attention and Divisive Normalization
Identifying the genes impacted by cell proliferation in proteomics and transcriptomics studies
The Development of Computational Biology in Pakistan: Still a Long Way to Go
Detecting Genetic Association of Common Human Facial Morphological Variation Using High Density 3D Image Registration
Ten Simple Rules for Establishing International Research Collaborations
Mechanistic modeling of cell viability assays with in silico lineage tracing
Interpreting and de-noising genetically engineered barcodes in a DNA virus
Spatial and temporal patterns of nitric oxide diffusion and degradation drive emergent cerebrovascular dynamics
Dynamic Modeling of Cell Migration and Spreading Behaviors on Fibronectin Coated Planar Substrates and Micropatterned Geometries
A combined experimental-computational approach uncovers a role for the Golgi matrix protein Giantin in breast cancer progression
iPiDA-SWGCN: Identification of piRNA-disease associations based on Supplementarily Weighted Graph Convolutional Network
Metallochaperones Regulate Intracellular Copper Levels
Multidimensional phenotyping predicts lifespan and quantifies health in Caenorhabditis elegans
Integration of Genome and Chromatin Structure with Gene Expression Profiles To Predict c- MYC Recognition Site Binding and Function
Anatomically accurate model of EMG during index finger flexion and abduction derived from diffusion tensor imaging
Generalized estimating equation modeling on correlated microbiome sequencing data with longitudinal measures
Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data
Trial-by-trial learning of successor representations in human behavior
Theta oscillations optimize a speed-precision trade-off in phase coding neurons
Taking the Lag out of Jet Lag through Model-Based Schedule Design
Comprehensive Analysis of Affymetrix Exon Arrays Using BioConductor
Optimizing clinical dosing of combination broadly neutralizing antibodies for HIV prevention
Rigidity Emerges during Antibody Evolution in Three Distinct Antibody Systems: Evidence from QSFR Analysis of Fab Fragments
The Evolution of Multivariate Maternal Effects
Modeling an Evolutionary Conserved Circadian Cis -Element
Structural Model of RNA Polymerase II Elongation Complex with Complete Transcription Bubble Reveals NTP Entry Routes
Computational Modeling of Seizure Dynamics Using Coupled Neuronal Networks: Factors Shaping Epileptiform Activity
Size regulation of multiple organelles competing for a limiting subunit pool
Time scales and wave formation in non-linear spatial public goods games
Increased A-to-I RNA editing in atherosclerosis and cardiomyopathies
Interpreting the CTCF-mediated sequence grammar of genome folding with AkitaV2
Heterogeneity and Convergence of Olfactory First-Order Neurons Account for the High Speed and Sensitivity of Second-Order Neurons
Cell Size at S Phase Initiation: An Emergent Property of the G 1 /S Network
Removal of reinforcement improves instrumental performance in humans by decreasing a general action bias rather than unmasking learnt associations
Differentially Expressed RNA from Public Microarray Data Identifies Serum Protein Biomarkers for Cross-Organ Transplant Rejection and Other Conditions
How Modeling Can Reconcile Apparently Discrepant Experimental Results: The Case of Pacemaking in Dopaminergic Neurons
Predicting the Functions and Specificity of Triterpenoid Synthases: A Mechanism-Based Multi-intermediate Docking Approach
The location of the axon initial segment affects the bandwidth of spike initiation dynamics
Learning action-oriented models through active inference
The Natural History of Biocatalytic Mechanisms
Adaptive Spike Threshold Enables Robust and Temporally Precise Neuronal Encoding
Maximal Extraction of Biological Information from Genetic Interaction Data
Category-specific perceptual learning of robust object recognition modelled using deep neural networks
Optimal Balance of the Striatal Medium Spiny Neuron Network
Use of compressed sensing to expedite high-throughput diagnostic testing for COVID-19 and beyond
Spatial models of pattern formation during phagocytosis
Pairwise Maximum Entropy Models for Studying Large Biological Systems: When They Can Work and When They Can't
Ten simple rules for creating a global network in computational biology
Leveraging Prior Information to Detect Causal Variants via Multi-Variant Regression
Combined Model of Intrinsic and Extrinsic Variability for Computational Network Design with Application to Synthetic Biology
Cluster size distribution of cells disseminating from a primary tumor
Primary Visual Cortex as a Saliency Map: A Parameter-Free Prediction and Its Test by Behavioral Data
Overlaid positive and negative feedback loops shape dynamical properties of PhoPQ two-component system
How Anacetrapib Inhibits the Activity of the Cholesteryl Ester Transfer Protein? Perspective through Atomistic Simulations
Drivers of Inter-individual Variation in Dengue Viral Load Dynamics
DySCo: A general framework for dynamic functional connectivity
Comments on "Human Dominant Disease Genes Are Enriched in Paralogs Originating from Whole Genome Duplication"
Examining the controllability of sepsis using genetic algorithms on an agent-based model of systemic inflammation
A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology
Adaptation of metabolite leakiness leads to symbiotic chemical exchange and to a resilient microbial ecosystem
Predicting Co-Complexed Protein Pairs from Heterogeneous Data
Default mode network connectivity predicts individual differences in long-term forgetting: Evidence for storage degradation, not retrieval failure
Imaging with spatio-temporal modelling to characterize the dynamics of plant-pathogen lesions
An aggregation-removal model for the formation and size determination of post-synaptic scaffold domains
Mechanical network equivalence between the katydid and mammalian inner ears
A Role for Rebinding in Rapid and Reliable T Cell Responses to Antigen
Rhythm Generation through Period Concatenation in Rat Somatosensory Cortex
Projecting social contact matrices to different demographic structures
Modeling and subtleties of K-Ras and Calmodulin interaction
Predicting the causative pathogen among children with pneumonia using a causal Bayesian network
Correction: Graph neural fields: A framework for spatiotemporal dynamical models on the human connectome
Ten quick tips to get you started with Bayesian statistics