yusuke1997/dblp-id-title huggingface dataset:
A stochastic simulation of skeletal muscle calcium transients in a structurally realistic sarcomere model using MCell
Structural and Dynamic Requirements for Optimal Activity of the Essential Bacterial Enzyme Dihydrodipicolinate Synthase
Neuro-cognitive multilevel causal modeling: A framework that bridges the explanatory gap between neuronal activity and cognition
Stochastic Noise and Synchronisation during Dictyostelium Aggregation Make cAMP Oscillations Robust
Natural Isotopic Signatures of Variations in Body Nitrogen Fluxes: A Compartmental Model Analysis
The size-weight illusion and beyond: A new model of perceived weight
HiCImpute: A Bayesian hierarchical model for identifying structural zeros and enhancing single cell Hi-C data
Multi-study Integration of Brain Cancer Transcriptomes Reveals Organ-Level Molecular Signatures
State-aware detection of sensory stimuli in the cortex of the awake mouse
Short-term neuronal and synaptic plasticity act in synergy for deviance detection in spiking networks
The Emotional Gatekeeper: A Computational Model of Attentional Selection and Suppression through the Pathway from the Amygdala to the Inhibitory Thalamic Reticular Nucleus
Measured Dynamic Social Contact Patterns Explain the Spread of H1N1v Influenza
Ancestral reconstruction of protein interaction networks
Acoustic traits of bat-pollinated flowers compared to flowers of other pollination syndromes and their echo-based classification using convolutional neural networks
Correction: Infectious reactivation of cytomegalovirus explaining age- and sex-specific patterns of seroprevalence
Integrating Phylodynamics and Epidemiology to Estimate Transmission Diversity in Viral Epidemics
Systematic Prediction of Pharmacodynamic Drug-Drug Interactions through Protein-Protein-Interaction Network
Climbing Fiber Burst Size and Olivary Sub-threshold Oscillations in a Network Setting
Optimal prediction with resource constraints using the information bottleneck
Ten simple rules for being a co-author on a many-author non-empirical paper
Discerning evolutionary trends in post-translational modification and the effect of intrinsic disorder: Analysis of methylation, acetylation and ubiquitination sites in human proteins
Gaze-dependent evidence accumulation predicts multi-alternative risky choice behaviour
Decision prioritization and causal reasoning in decision hierarchies
Metamodelling of a two-population spiking neural network
The impact of interactions on invasion and colonization resistance in microbial communities
Significant associations between driver gene mutations and DNA methylation alterations across many cancer types
Ten simple rules for collaboratively writing a multi-authored paper
Forecasting unprecedented ecological fluctuations
In silico analysis of antibiotic-induced Clostridium difficile infection: Remediation techniques and biological adaptations
Learning and Generalization under Ambiguity: An fMRI Study
PARROT: Prediction of enzyme abundances using protein-constrained metabolic models
Capturing the songs of mice with an improved detection and classification method for ultrasonic vocalizations (BootSnap)
Adaptive multi-objective control explains how humans make lateral maneuvers while walking
Inferring assembly-curving trends of bacterial micro-compartment shell hexamers from crystal structure arrangements
Density Dependence Triggers Runaway Selection of Reduced Senescence
A method to quantify mechanobiologic forces during zebrafish cardiac development using 4-D light sheet imaging and computational modeling
Understanding Voltage Gating of Providencia stuartii Porins at Atomic Level
Facilitating pathway and network based analysis of RNA-Seq data with pathlinkR
Mechanical forces control the valency of the malaria adhesin VAR2CSA by exposing cryptic glycan binding sites
Structural Bridges through Fold Space
Inferring synaptic transmission from the stochastic dynamics of the quantal content: An analytical approach
Specialization Can Drive the Evolution of Modularity
Reprogramming of macrophages employing gene regulatory and metabolic network models
A Dual Model for Prioritizing Cancer Mutations in the Non-coding Genome Based on Germline and Somatic Events
Bayesian inference of structured latent spaces from neural population activity with the orthogonal stochastic linear mixing model
Stochastic optimal feedforward-feedback control determines timing and variability of arm movements with or without vision
Computationally Derived Points of Fragility of a Human Cascade Are Consistent with Current Therapeutic Strategies
Equation-Free Analysis of Two-Component System Signalling Model Reveals the Emergence of Co-Existing Phenotypes in the Absence of Multistationarity
Why aphid virus retention needs more attention: Modelling aphid behaviour and virus manipulation in non-persistent plant virus transmission
Global Patterns of Protein Domain Gain and Loss in Superkingdoms
Uncertainty-guided learning with scaled prediction errors in the basal ganglia
Exploration of potential novel drug targets for rheumatoid arthritis by plasma proteome screening
The Free Energy Landscape of Small Molecule Unbinding
Fides: Reliable trust-region optimization for parameter estimation of ordinary differential equation models
Reversing allosteric communication: From detecting allosteric sites to inducing and tuning targeted allosteric response
The Fragile Breakage versus Random Breakage Models of Chromosome Evolution
Measuring Granger Causality between Cortical Regions from Voxelwise fMRI BOLD Signals with LASSO
Phylogenetic Analysis Reveals That ERVs "Die Young" but HERV-H Is Unusually Conserved
Variance in C. elegans gut bacterial load suggests complex host-microbe dynamics
Methodological challenges in translational drug response modeling in cancer: A systematic analysis with FORESEE
Uncovering direct and indirect molecular determinants of chromatin loops using a computational integrative approach
The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function
Allosteric regulation in STAT3 interdomains is mediated by a rigid core: SH2 domain regulation by CCD in D170A variant
Structure, Dynamics and Implied Gating Mechanism of a Human Cyclic Nucleotide-Gated Channel
Regulatory network-based imputation of dropouts in single-cell RNA sequencing data
Deciphering Transcriptional Dynamics In Vivo by Counting Nascent RNA Molecules
An independent component analysis confounding factor correction framework for identifying broad impact expression quantitative trait loci
Correction: A musculoskeletal finite element model of rat knee joint for evaluating cartilage biomechanics during gait
Architect: A tool for aiding the reconstruction of high-quality metabolic models through improved enzyme annotation
Novel estimates reveal subnational heterogeneities in disease-relevant contact patterns in the United States
Infectious reactivation of cytomegalovirus explaining age- and sex-specific patterns of seroprevalence
The breadth of HIV-1 neutralizing antibodies depends on the conservation of key sites in their epitopes
Protein sequence optimization with a pairwise decomposable penalty for buried unsatisfied hydrogen bonds
OrganoID: A versatile deep learning platform for tracking and analysis of single-organoid dynamics
Correction: Subgraphs of functional brain networks identify dynamical constraints of cognitive control
Different Inward and Outward Conduction Mechanisms in Na V Ms Suggested by Molecular Dynamics Simulations
Risk averse reproduction numbers improve resurgence detection
Interactions between species introduce spurious associations in microbiome studies
A model explaining mRNA level fluctuations based on activity demands and RNA age
Modeling Latently Infected Cell Activation: Viral and Latent Reservoir Persistence, and Viral Blips in HIV-infected Patients on Potent Therapy
Instance-based generalization for human judgments about uncertainty
A model for the origin and development of visual orientation selectivity
Recurrent Network Models for Perfect Temporal Integration of Fluctuating Correlated Inputs
Disentangling the effects of metabolic cost and accuracy on movement speed
Adaptation optimizes sensory encoding for future stimuli
Correction: Stress generation, relaxation and size control in confined tumor growth
Understanding the hemodynamic changes in fetuses with coarctation of the aorta using a lumped model of fetal circulation
Sensory noise predicts divisive reshaping of receptive fields
Modelling the epidemiology of residual Plasmodium vivax malaria in a heterogeneous host population: A case study in the Amazon Basin
Directed attenuation to enhance vaccine immunity
A Computational Approach to Identifying Gene-microRNA Modules in Cancer
Molecular Simulations of Cotranslational Protein Folding: Fragment Stabilities, Folding Cooperativity, and Trapping in the Ribosome
Inferring Stabilizing Mutations from Protein Phylogenies: Application to Influenza Hemagglutinin
Viral Population Estimation Using Pyrosequencing
Minimal model of interictal and ictal discharges "Epileptor-2"
Neuromotor Noise Is Malleable by Amplifying Perceived Errors
Connectivity concepts in neuronal network modeling
Agent-based and continuous models of hopper bands for the Australian plague locust: How resource consumption mediates pulse formation and geometry
Temperature-driven coordination of circadian transcriptional regulation
A computational workflow for assessing drug effects on temporal signaling dynamics reveals robustness in stimulus-specific NFκB signaling
Using Biological Pathway Data with Paxtools
Dimensions of control for subthreshold oscillations and spontaneous firing in dopamine neurons
Benchmarking Inverse Statistical Approaches for Protein Structure and Design with Exactly Solvable Models
Maximum entropy methods for extracting the learned features of deep neural networks
Jaxkineticmodel: Neural ordinary differential equations inspired parameterization of kinetic models
Categorical judgments do not modify sensory representations in working memory
Ten simple rules for creating a scientific web application
Pleiotropy promotes the evolution of inducible immune responses in a model of host-pathogen coevolution
Keeping up with the Joneses: Interpersonal Prediction Errors and the Correlation of Behavior in a Tandem Sequential Choice Task
SiteMotif: A graph-based algorithm for deriving structural motifs in Protein Ligand binding sites
Automated Processing of Imaging Data through Multi-tiered Classification of Biological Structures Illustrated Using Caenorhabditis elegans
Control of Whole Heart Geometry by Intramyocardial Mechano-Feedback: A Model Study
Numerical Analysis of Ca 2+ Signaling in Rat Ventricular Myocytes with Realistic Transverse-Axial Tubular Geometry and Inhibited Sarcoplasmic Reticulum
Minimum Free Energy Path of Ligand-Induced Transition in Adenylate Kinase
paramix: An R package for parameter discretisation in compartmental models, with application to calculating years of life lost
Determining travel fluxes in epidemic areas
A hierarchical multiscale model of forward and backward alpha-band traveling waves in the visual system
Model-based identification of conditionally-essential genes from transposon-insertion sequencing data
What a Plant Sounds Like: The Statistics of Vegetation Echoes as Received by Echolocating Bats
Matt: Local Flexibility Aids Protein Multiple Structure Alignment
Multivariate resilience indicators to anticipate vector-borne disease outbreaks: A West Nile virus case-study
16S rRNA sequence embeddings: Meaningful numeric feature representations of nucleotide sequences that are convenient for downstream analyses
Ten quick tips for deep learning in biology
Spike burst-pause dynamics of Purkinje cells regulate sensorimotor adaptation
Detecting adherence to the recommended childhood vaccination schedule from user-generated content in a US parenting forum
Deep learning for robust and flexible tracking in behavioral studies for C. elegans
Using genetic data to identify transmission risk factors: Statistical assessment and application to tuberculosis transmission
Characterising seasonal influenza epidemiology using primary care surveillance data
A method for analysing tissue motion and deformation during mammalian organogenesis
Network Evolution: Rewiring and Signatures of Conservation in Signaling
Mammalian Sleep Dynamics: How Diverse Features Arise from a Common Physiological Framework
Spatio-Temporal Credit Assignment in Neuronal Population Learning
Computational Analysis of Whole-Genome Differential Allelic Expression Data in Human
Hi-C implementation of genome structure for in silico models of radiation-induced DNA damage
Assessing the drivers of syphilis among men who have sex with men in Switzerland reveals a key impact of screening frequency: A modelling study
Spike-Triggered Covariance Analysis Reveals Phenomenological Diversity of Contrast Adaptation in the Retina
Integrative experimental/computational approach establishes active cellular protrusion as the primary driving force of phagocytic spreading by immune cells
Spine Calcium Transients Induced by Synaptically-Evoked Action Potentials Can Predict Synapse Location and Establish Synaptic Democracy
Live Coverage of Scientific Conferences Using Web Technologies
A generative learning model for saccade adaptation
In Silico Elucidation of the Recognition Dynamics of Ubiquitin
Automatic Morphological Subtyping Reveals New Roles of Caspases in Mitochondrial Dynamics
Measuring spectrally-resolved information transfer
Astrocytes Optimize the Synaptic Transmission of Information
Machine Learning for Characterization of Insect Vector Feeding
A computational model for gonadotropin releasing cells in the teleost fish medaka
Model-Driven Understanding of Palmitoylation Dynamics: Regulated Acylation of the Endoplasmic Reticulum Chaperone Calnexin
What does the mean mean? A simple test for neuroscience
Structural and Thermodynamic Approach to Peptide Immunogenicity
Infer global, predict local: Quantity-relevance trade-off in protein fitness predictions from sequence data
Exploring strategy differences between humans and monkeys with recurrent neural networks
Marmosets mutually compensate for differences in rhythms when coordinating vigilance
Ten Simple Rules to Achieve Conference Speaker Gender Balance
The σB alternative sigma factor circuit modulates noise to generate different types of pulsing dynamics
STRFs in primary auditory cortex emerge from masking-based statistics of natural sounds
Bioinformatics Goes to School - New Avenues for Teaching Contemporary Biology
Systems Biology-Based Investigation of Cellular Antiviral Drug Targets Identified by Gene-Trap Insertional Mutagenesis
A computational analysis of dynamic, multi-organ inflammatory crosstalk induced by endotoxin in mice
Identifying Crucial Parameter Correlations Maintaining Bursting Activity
Prediction of opioid-related outcomes in a medicaid surgical population: Evidence to guide postoperative opiate therapy and monitoring
Blockade of Neuronal α7-nAChR by α-Conotoxin ImI Explained by Computational Scanning and Energy Calculations
Inferring Horizontal Gene Transfer
Modeling Contact Inhibition of Locomotion of Colliding Cells Migrating on Micropatterned Substrates
Intracellular Information Processing through Encoding and Decoding of Dynamic Signaling Features
Ten simple rules for writing a career development award proposal
Vessel network extraction and analysis of mouse pulmonary vasculature via X-ray micro-computed tomographic imaging
Unsupervised learning reveals interpretable latent representations for translucency perception
Chapter 2: Data-Driven View of Disease Biology
GCSENet: A GCN, CNN and SENet ensemble model for microRNA-disease association prediction
The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies
Structural Characteristics of Novel Protein Folds
Coexistence rules for small, antagonistically interacting microbial communities
wavess: An R package for simulation of adaptive within-host virus sequence evolution
Ten simple rules when considering retirement
Identification of a Novel Class of Farnesylation Targets by Structure-Based Modeling of Binding Specificity
Synonymous Substitution Rates Predict HIV Disease Progression as a Result of Underlying Replication Dynamics
Integrating Cellular Metabolism into a Multiscale Whole-Body Model
A Continuum Model for Metabolic Gas Exchange in Pear Fruit
Modeling the functions of condensin in chromosome shaping and segregation
A Bayesian inference method to estimate transmission trees with multiple introductions; applied to SARS-CoV-2 in Dutch mink farms
A multimodal Transformer Network for protein-small molecule interactions enhances predictions of kinase inhibition and enzyme-substrate relationships
Evolutionary Triplet Models of Structured RNA
Investigations of Oligonucleotide Usage Variance Within and Between Prokaryotes
Gause's Principle and the Effect of Resource Partitioning on the Dynamical Coexistence of Replicating Templates
Evolution of Genetic Potential
Identification of Hammerhead Ribozymes in All Domains of Life Reveals Novel Structural Variations
The role of sensory uncertainty in simple contour integration
The Roles of Post-translational Modifications in the Context of Protein Interaction Networks
The computational relationship between reinforcement learning, social inference, and paranoia
Effectiveness of Ultra-Low Volume insecticide spraying to prevent dengue in a non-endemic metropolitan area of Brazil
Canonical Response Parameterization: Quantifying the structure of responses to single-pulse intracranial electrical brain stimulation
Efficient representations of tumor diversity with paired DNA-RNA aberrations
Rigid-body fitting to atomic force microscopy images for inferring probe shape and biomolecular structure
Synchronization of Firing in Cortical Fast-Spiking Interneurons at Gamma Frequencies: A Phase-Resetting Analysis
2010 ISCB Overton Prize Awarded to Steven E. Brenner
Ten simple rules for writing a PLOS Computational Biology quick tips article
Intercellular Variability in Protein Levels from Stochastic Expression and Noisy Cell Cycle Processes
Next-generation yeast-two-hybrid analysis with Y2H-SCORES identifies novel interactors of the MLA immune receptor
Fundamentals of FAIR biomedical data analyses in the cloud using custom pipelines
Diverse mutant selection windows shape spatial heterogeneity in evolving populations
Strength-dependent perturbation of whole-brain model working in different regimes reveals the role of fluctuations in brain dynamics
Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA
Ten simple rules for providing effective bioinformatics research support
Interneuronal network model of theta-nested fast oscillations predicts differential effects of heterogeneity, gap junctions and short term depression for hyperpolarizing versus shunting inhibition
Cortical cell assemblies and their underlying connectivity: An in silico study
Model supports asymmetric regulation across the intercellular junction for collective cell polarization
High-integrity human intervention in ecosystems: Tracking self-organization modes
High-throughput Interpretation of Killer-cell Immunoglobulin-like Receptor Short-read Sequencing Data with PING
A strategy for mapping biophysical to abstract neuronal network models applied to primary visual cortex
Catalytic promiscuity in the RNA World may have aided the evolution of prebiotic metabolism
Stability of Neuronal Networks with Homeostatic Regulation
Interplay between mobility, multi-seeding and lockdowns shapes COVID-19 local impact
A new clustering and nomenclature for beta turns derived from high-resolution protein structures
Unlocking plant health survey data: An approach to quantify the sensitivity and specificity of visual inspections
SIG-DB: Leveraging homomorphic encryption to securely interrogate privately held genomic databases
Beyond core object recognition: Recurrent processes account for object recognition under occlusion
Predicting the pathogenicity of novel variants in mitochondrial tRNA with MitoTIP
Correction: Collective Cell Motion in an Epithelial Sheet Can be Quantitatively Described by a Stochastic Interacting Particle Model
Reconstructible Phylogenetic Networks: Do Not Distinguish the Indistinguishable
Parameter estimation in behavioral epidemic models with endogenous societal risk-response
Large scale paired antibody language models
Molecular determinants for the thermodynamic and functional divergence of uniporter GLUT1 and proton symporter XylE
Large-scale cortical travelling waves predict localized future cortical signals
Bioinformatics Projects Supporting Life-Sciences Learning in High Schools
Quantitative Analysis of Immune Response and Erythropoiesis during Rodent Malarial Infection
The unbiased estimation of the fraction of variance explained by a model
A Family of Algorithms for Computing Consensus about Node State from Network Data
Degenerate T-cell Recognition of Peptides on MHC Molecules Creates Large Holes in the T-cell Repertoire
Physical constraints on early blastomere packings
Ten simple rules to make your research more sustainable
State-Space Analysis of Time-Varying Higher-Order Spike Correlation for Multiple Neural Spike Train Data
Neural Modularity Helps Organisms Evolve to Learn New Skills without Forgetting Old Skills
COVID-19 in schools: Mitigating classroom clusters in the context of variable transmission
Nonlinear fusion is optimal for a wide class of multisensory tasks
Enzyme Sequestration as a Tuning Point in Controlling Response Dynamics of Signalling Networks
Excitatory/inhibitory ratio disruption modulates neural synchrony and flow directions in a cortical microcircuit
Refinement of the Central Steps of Substrate Transport by the Aspartate Transporter GltPh: Elucidating the Role of the Na2 Sodium Binding Site
Exploring the impact of inoculum dose on host immunity and morbidity to inform model-based vaccine design
Insertion of the Ca 2+ -Independent Phospholipase A 2 into a Phospholipid Bilayer via Coarse-Grained and Atomistic Molecular Dynamics Simulations
Flexibility to contingency changes distinguishes habitual and goal-directed strategies in humans
Conditions for the Evolution of Gene Clusters in Bacterial Genomes
One Rule to Grow Them All: A General Theory of Neuronal Branching and Its Practical Application
Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism
scDSSC: Deep Sparse Subspace Clustering for scRNA-seq Data
Optimal immune specificity at the intersection of host life history and parasite epidemiology
Human Motor Cortical Activity Is Selectively Phase-Entrained on Underlying Rhythms
Bioactivity assessment of natural compounds using machine learning models trained on target similarity between drugs
Decision making improves sperm chemotaxis in the presence of noise
A data-informed mean-field approach to mapping of cortical parameter landscapes
High Degree of Heterogeneity in Alzheimer's Disease Progression Patterns
Statistical inference in ensemble modeling of cellular metabolism
A Semi-Supervised Method for Predicting Transcription Factor-Gene Interactions in Escherichia coli
Tracking human skill learning with a hierarchical Bayesian sequence model
Robust Identification of Noncoding RNA from Transcriptomes Requires Phylogenetically-Informed Sampling
Abnormal Cortical Networks in Mild Cognitive Impairment and Alzheimer's Disease
Movement Timing and Invariance Arise from Several Geometries
How Force Might Activate Talin's Vinculin Binding Sites: SMD Reveals a Structural Mechanism
ApoE4-specific Misfolded Intermediate Identified by Molecular Dynamics Simulations
Environmental and State-Level Regulatory Factors Affect the Incidence of Autism and Intellectual Disability
A hierarchical stochastic model for bistable perception
Sour grapes and sweet victories: How actions shape preferences
A regression based approach to phylogenetic reconstruction from multi-sample bulk DNA sequencing of tumors
Sparse Codes for Speech Predict Spectrotemporal Receptive Fields in the Inferior Colliculus
Learning from animals: How to Navigate Complex Terrains
Deciphering the RRM-RNA recognition code: A computational analysis