yusuke1997/dblp-id-title huggingface dataset:
From whole-organ imaging to in-silico blood flow modeling: A new multi-scale network analysis for revisiting tissue functional anatomy
Spatial and temporal invasion dynamics of the 2014-2017 Zika and chikungunya epidemics in Colombia
A Dynamical Role for Acetylcholine in Synaptic Renormalization
Biophysical Basis for Three Distinct Dynamical Mechanisms of Action Potential Initiation
Controlling gene expression timing through gene regulatory architecture
Dynamic Finite Size Effects in Spiking Neural Networks
Quantitative modeling of signaling in aggressive B cell lymphoma unveils conserved core network
VAMPr: VAriant Mapping and Prediction of antibiotic resistance via explainable features and machine learning
Optimal number of spacers in CRISPR arrays
Direction-selective motion discrimination by traveling waves in visual cortex
Computational principles of neural adaptation for binaural signal integration
Non-synaptic interactions between olfactory receptor neurons, a possible key feature of odor processing in flies
m6A-Driver: Identifying Context-Specific mRNA m6A Methylation-Driven Gene Interaction Networks
Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens
Population bursts in a modular neural network as a mechanism for synchronized activity in KNDy neurons
Training diversity promotes absolute-value-guided choice
STDP in a Bistable Synapse Model Based on CaMKII and Associated Signaling Pathways
Modification of Gene Duplicability during the Evolution of Protein Interaction Network
An evolutionary learning and network approach to identifying key metabolites for osteoarthritis
Quantitative Predictions of Binding Free Energy Changes in Drug-Resistant Influenza Neuraminidase
Design of Multi-Specificity in Protein Interfaces
Modeling of the axon plasma membrane structure and its effects on protein diffusion
Mapping of morpho-electric features to molecular identity of cortical inhibitory neurons
Relationships between Th1 or Th2 iNKT Cell Activity and Structures of CD1d-Antigen Complexes: Meta-analysis of CD1d-Glycolipids Dynamics Simulations
Elementary vectors and autocatalytic sets for resource allocation in next-generation models of cellular growth
Optimal structure of metaplasticity for adaptive learning
Hybrid Automata Library: A flexible platform for hybrid modeling with real-time visualization
Molecular dynamics study of differential effects of serotonin-2A-receptor (5-HT2AR) modulators
Testing predictive coding theories of autism spectrum disorder using models of active inference
Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions
Detecting Remote Evolutionary Relationships among Proteins by Large-Scale Semantic Embedding
Large scale analyses of genotype-phenotype relationships of glycine decarboxylase mutations and neurological disease severity
Modeling craniofacial development reveals spatiotemporal constraints on robust patterning of the mandibular arch
Humans decompose tasks by trading off utility and computational cost
Unifying Time to Contact Estimation and Collision Avoidance across Species
Predicting Cellular Growth from Gene Expression Signatures
Detecting Presymptomatic Infection Is Necessary to Forecast Major Epidemics in the Earliest Stages of Infectious Disease Outbreaks
Phylogenetic inference of the emergence of sequence modules and protein-protein interactions in the ADAMTS-TSL family
Inference for Nonlinear Epidemiological Models Using Genealogies and Time Series
Galaxy and Apollo as a biologist-friendly interface for high-quality cooperative phage genome annotation
Human motor learning dynamics in high-dimensional tasks
Is mammography screening beneficial: An individual-based stochastic model for breast cancer incidence and mortality
A large-scale brain network mechanism for increased seizure propensity in Alzheimer's disease
Regulation of harvester ant foraging as a closed-loop excitable system
Host Resistance, Population Structure and the Long-Term Persistence of Bubonic Plague: Contributions of a Modelling Approach in the Malagasy Focus
Using normative modeling and machine learning for detecting mild traumatic brain injury from magnetoencephalography data
Quantifying the impact of contact tracing interview prioritisation strategies on disease transmission: A modelling study
RNANetMotif: Identifying sequence-structure RNA network motifs in RNA-protein binding sites
eXplainable Artificial Intelligence (XAI) for the identification of biologically relevant gene expression patterns in longitudinal human studies, insights from obesity research
Efficient coding of natural scenes improves neural system identification
Swimming in Light: A Large-Scale Computational Analysis of the Metabolism of Dinoroseobacter shibae
Chromatin phase separated nanoregions explored by polymer cross-linker models and reconstructed from single particle trajectories
Stochastic ordering of complexoform protein assembly by genetic circuits
Wall shear stress and pressure patterns in aortic stenosis patients with and without aortic dilation captured by high-performance image-based computational fluid dynamics
Multiplex Eukaryotic Transcription (In)activation: Timing, Bursting and Cycling of a Ratchet Clock Mechanism
Automated morphological phenotyping using learned shape descriptors and functional maps: A novel approach to geometric morphometrics
The role of Allee effect in modelling post resection recurrence of glioblastoma
Model of Transcriptional Activation by MarA in Escherichia coli
Using Sequence-Specific Chemical and Structural Properties of DNA to Predict Transcription Factor Binding Sites
CellMet: Extracting 3D shape and topology metrics from confluent cells within tissues
A dual computational and experimental strategy to enhance TSLP antibody affinity for improved asthma treatment
The interplay between age structure and cultural transmission
Mapping Gene Associations in Human Mitochondria using Clinical Disease Phenotypes
Decoding Unattended Fearful Faces with Whole-Brain Correlations: An Approach to Identify Condition-Dependent Large-Scale Functional Connectivity
Ten Simple Rules for Getting Help from Online Scientific Communities
Arrhythmia mechanisms and spontaneous calcium release: Bi-directional coupling between re-entrant and focal excitation
Structural influences on synaptic plasticity: The role of presynaptic connectivity in the emergence of E/I co-tuning
Mechanical feedback coordinates cell wall expansion and assembly in yeast mating morphogenesis
Integrated computational and in vivo models reveal Key Insights into macrophage behavior during bone healing
AI-powered simulation-based inference of a genuinely spatial-stochastic gene regulation model of early mouse embryogenesis
Adjusting Phenotypes by Noise Control
kCSD-python, reliable current source density estimation with quality control
Memory Storage Fidelity in the Hippocampal Circuit: The Role of Subregions and Input Statistics
Thermodynamic and sequential characteristics of phase separation and droplet formation for an intrinsically disordered region/protein ensemble
Synaptic balancing: A biologically plausible local learning rule that provably increases neural network noise robustness without sacrificing task performance
Lattice-Based Model of Ductal Carcinoma In Situ Suggests Rules for Breast Cancer Progression to an Invasive State
Large-Scale Off-Target Identification Using Fast and Accurate Dual Regularized One-Class Collaborative Filtering and Its Application to Drug Repurposing
A simple model for learning in volatile environments
The self-organization of plant microtubules inside the cell volume yields their cortical localization, stable alignment, and sensitivity to external cues
Stochastic Simulations Suggest that HIV-1 Survives Close to Its Error Threshold
Bayesian inference of ancestral recombination graphs
scRepertoire 2: Enhanced and efficient toolkit for single-cell immune profiling
Automated registration and clustering for enhanced localization atomic force microscopy of flexible membrane proteins
Markov Networks of Collateral Resistance: National Antimicrobial Resistance Monitoring System Surveillance Results from Escherichia coli Isolates, 2004-2012
BAGEL: Protein engineering via exploration of an energy landscape
Connectivity in the Yeast Cell Cycle Transcription Network: Inferences from Neural Networks
Communication Efficiency and Congestion of Signal Traffic in Large-Scale Brain Networks
Mathematical modeling of hepatitis C RNA replication, exosome secretion and virus release
Accelerating joint species distribution modelling with Hmsc-HPC by GPU porting
Estimating the effectiveness of non-pharmaceutical interventions against COVID-19 transmission in the Netherlands
Spatial Pattern Dynamics of 3D Stem Cell Loss of Pluripotency via Rules-Based Computational Modeling
Gene Expression Network Reconstruction by Convex Feature Selection when Incorporating Genetic Perturbations
The Role of the Frank-Starling Law in the Transduction of Cellular Work to Whole Organ Pump Function: A Computational Modeling Analysis
Reconstruction of Cell Surface Densities of Ion Pumps, Exchangers, and Channels from mRNA Expression, Conductance Kinetics, Whole-Cell Calcium, and Current-Clamp Voltage Recordings, with an Application to Human Uterine Smooth Muscle Cells
Condition-adaptive fused graphical lasso (CFGL): An adaptive procedure for inferring condition-specific gene co-expression network
Boosting GWAS using biological networks: A study on susceptibility to familial breast cancer
Neuronal Firing Sensitivity to Morphologic and Active Membrane Parameters
Ten quick tips for delivering programming lessons
Correlation of Influenza Virus Excess Mortality with Antigenic Variation: Application to Rapid Estimation of Influenza Mortality Burden
Modeling the kinetics of the neutralizing antibody response against SARS-CoV-2 variants after several administrations of Bnt162b2
Mutation Bias Favors Protein Folding Stability in the Evolution of Small Populations
Modeling Integrated Cellular Machinery Using Hybrid Petri-Boolean Networks
DAPTEV: Deep aptamer evolutionary modelling for COVID-19 drug design
Improving pairwise comparison of protein sequences with domain co-occurrence
The Role of Non-Native Interactions in the Folding of Knotted Proteins
Starling Flock Networks Manage Uncertainty in Consensus at Low Cost
Detecting differential alternative splicing events in scRNA-seq with or without Unique Molecular Identifiers
Disentangling the Roles of Approach, Activation and Valence in Instrumental and Pavlovian Responding
Characterization of the NiRAN domain from RNA-dependent RNA polymerase provides insights into a potential therapeutic target against SARS-CoV-2
Impact of Ribosomal Modification on the Binding of the Antibiotic Telithromycin Using a Combined Grand Canonical Monte Carlo/Molecular Dynamics Simulation Approach
Parallel Tempering with Lasso for model reduction in systems biology
Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories
Ten simple rules for productive lab meetings
Self-Assembly and DNA Binding of the Blocking Factor in X Chromosome Inactivation
Gap junction plasticity as a mechanism to regulate network-wide oscillations
MicrobeTrace: Retooling molecular epidemiology for rapid public health response
Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies
Explainable detection of adverse drug reaction with imbalanced data distribution
Systematic benchmarking of deep-learning methods for tertiary RNA structure prediction
Identifying essential factors for energy-efficient walking control across a wide range of velocities in reflex-based musculoskeletal systems
Mathematical modeling of multiple pathways in colorectal carcinogenesis using dynamical systems with Kronecker structure
Beyond GLMs: A Generative Mixture Modeling Approach to Neural System Identification
Performance of virtual screening against GPCR homology models: Impact of template selection and treatment of binding site plasticity
Sperm migration in the genital tract - In silico experiments identify key factors for reproductive success
Spatial clustering and common regulatory elements correlate with coordinated gene expression
Unfolding Simulations Reveal the Mechanism of Extreme Unfolding Cooperativity in the Kinetically Stable α-Lytic Protease
Two critical positions in zinc finger domains are heavily mutated in three human cancer types
"I Look in Your Eyes, Honey": Internal Face Features Induce Spatial Frequency Preference for Human Face Processing
How the Brain Decides When to Work and When to Rest: Dissociation of Implicit-Reactive from Explicit-Predictive Computational Processes
Multifunctional RNA-binding proteins influence mRNA abundance and translational efficiency of distinct sets of target genes
Visual perception of texture regularity: Conjoint measurements and a wavelet response-distribution model
Ten simple rules for writing a response to reviewers
Dose-response in modulating brain function with transcranial direct current stimulation: From local to network levels
Suprathreshold perceptual decisions constrain models of confidence
General principles of binding between cell surface receptors and multi-specific ligands: A computational study
Improving homology modeling from low-sequence identity templates in Rosetta: A case study in GPCRs
An Allosteric Signaling Pathway of Human 3-Phosphoglycerate Kinase from Force Distribution Analysis
How to write a scientific paper in fifteen steps
Kinase Inhibition Leads to Hormesis in a Dual Phosphorylation-Dephosphorylation Cycle
Novel Peptide-Mediated Interactions Derived from High-Resolution 3-Dimensional Structures
Deep self-supervised learning for biosynthetic gene cluster detection and product classification
Combining Structure and Sequence Information Allows Automated Prediction of Substrate Specificities within Enzyme Families
Inferring protein fitness landscapes from laboratory evolution experiments
Temperature Control of Fimbriation Circuit Switch in Uropathogenic Escherichia coli : Quantitative Analysis via Automated Model Abstraction
Modelling the visual world of a velvet worm
A Variant of TNFR2-Fc Fusion Protein Exhibits Improved Efficacy in Treating Experimental Rheumatoid Arthritis
Ten simple rules for building and maintaining sustainable high-performance computing infrastructure for research in resource-limited settings
Neurogenesis Drives Stimulus Decorrelation in a Model of the Olfactory Bulb
Characterizing and dissociating multiple time-varying modulatory computations influencing neuronal activity
The Beacon Calculus: A formal method for the flexible and concise modelling of biological systems
Linear motifs regulating protein secretion, sorting and autophagy in Leishmania parasites are diverged with respect to their host equivalents
Tissue-Specificity of Gene Expression Diverges Slowly between Orthologs, and Rapidly between Paralogs
Cell Assembly Dynamics of Sparsely-Connected Inhibitory Networks: A Simple Model for the Collective Activity of Striatal Projection Neurons
Parametric Alignment of Drosophila Genomes
A Model of Cardiovascular Disease Giving a Plausible Mechanism for the Effect of Fractionated Low-Dose Ionizing Radiation Exposure
Feedbacks, Bifurcations, and Cell Fate Decision-Making in the p53 System
Protein Complexes are Central in the Yeast Genetic Landscape
How to fit in: The learning principles of cell differentiation
multi-GPA-Tree: Statistical approach for pleiotropy informed and functional annotation tree guided prioritization of GWAS results
Phenome-Wide Association Studies on a Quantitative Trait: Application to TPMT Enzyme Activity and Thiopurine Therapy in Pharmacogenomics
Persistent thermal input controls steering behavior in Caenorhabditis elegans
Speeding Up Ecological and Evolutionary Computations in R; Essentials of High Performance Computing for Biologists
Cooperative stochastic binding and unbinding explain synaptic size dynamics and statistics
Predicting lung aging using scRNA-Seq data
Multiple Genetic Interaction Experiments Provide Complementary Information Useful for Gene Function Prediction
Segregation of the Brain into Gray and White Matter: A Design Minimizing Conduction Delays
Biomathematical enzyme kinetics model of prebiotic autocatalytic RNA networks: degenerating parasite-specific hyperparasite catalysts confer parasite resistance and herald the birth of molecular immunity
Shared input and recurrency in neural networks for metabolically efficient information transmission
Nucleosome positioning sequence patterns as packing or regulatory
Cell-Cycle Dependence of Transcription Dominates Noise in Gene Expression
TeXP: Deconvolving the effects of pervasive and autonomous transcription of transposable elements
Ten simple rules for innovative dissemination of research
Quorum-Sensing Synchronization of Synthetic Toggle Switches: A Design Based on Monotone Dynamical Systems Theory
Statistical Computations Underlying the Dynamics of Memory Updating
Induction of Wnt-Inducible Signaling Protein-1 Correlates with Invasive Breast Cancer Oncogenesis and Reduced Type 1 Cell-Mediated Cytotoxic Immunity: A Retrospective Study
Ten simple rules to aid in achieving a vision
Tracking progress towards malaria elimination in China: Individual-level estimates of transmission and its spatiotemporal variation using a diffusion network approach
Systems Approaches to the Eukaryotic Stress Response
Patient Referral Patterns and the Spread of Hospital-Acquired Infections through National Health Care Networks
Morphological and Stress Vulnerability Indices for Human Coronary Plaques and Their Correlations with Cap Thickness and Lipid Percent: An IVUS-Based Fluid-Structure Interaction Multi-patient Study
I_MDS: an inflammatory bowel disease molecular activity score to classify patients with differing disease-driving pathways and therapeutic response to anti-TNF treatment
Knowledge graph embedding for profiling the interaction between transcription factors and their target genes
Analysis of Individual Protein Regions Provides Novel Insights on Cancer Pharmacogenomics
The International Society for Computational Biology 10th Anniversary
Genome-scale metabolic modeling reveals metabolic trade-offs associated with lipid production in Rhodotorula toruloides
Adhesion-regulated junction slippage controls cell intercalation dynamics in an Apposed-Cortex Adhesion Model
Viral Phylodynamics
Computational Prediction and Experimental Assessment of Secreted/Surface Proteins from Mycobacterium tuberculosis H37Rv
Accurate contact-based modelling of repeat proteins predicts the structure of new repeats protein families
Moving Education Forward
3-way Networks: Application of Hypergraphs for Modelling Increased Complexity in Comparative Genomics
MGAE-DC: Predicting the synergistic effects of drug combinations through multi-channel graph autoencoders
Reactive Searching and Infotaxis in Odor Source Localization
Neurocomputational mechanism of controllability inference under a multi-agent setting
A Latent Markov Modelling Approach to the Evaluation of Circulating Cathodic Antigen Strips for Schistosomiasis Diagnosis Pre- and Post-Praziquantel Treatment in Uganda
Achieving Optimal Growth through Product Feedback Inhibition in Metabolism
CBNA: A control theory based method for identifying coding and non-coding cancer drivers
Dissociating Variability and Effort as Determinants of Coordination
Analysis of high-dimensional metabolomics data with complex temporal dynamics using RM-ASCA+
Development and validation of influenza forecasting for 64 temperate and tropical countries
Modelling the modulation of cortical Up-Down state switching by astrocytes
Predicting synthetic lethal interactions using conserved patterns in protein interaction networks
Optimizing network propagation for multi-omics data integration
Inference of Epidemiological Dynamics Based on Simulated Phylogenies Using Birth-Death and Coalescent Models
Higher-Order Synaptic Interactions Coordinate Dynamics in Recurrent Networks
Know-how of holding a Bioinformatics competition: Structure, model, overview, and perspectives
Disease Interventions Can Interfere with One Another through Disease-Behaviour Interactions
Improving Collective Estimations Using Resistance to Social Influence
scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data
Optimal Current Transfer in Dendrites
Modeling of Pharmacokinetics of Cocaine in Human Reveals the Feasibility for Development of Enzyme Therapies for Drugs of Abuse
Advances in using Internet searches to track dengue
Dynamic Rendering of the Heterogeneous Cell Response to Anticancer Treatments
Gene Expression Noise Enhances Robust Organization of the Early Mammalian Blastocyst
Generation of Binary Tree-Child phylogenetic networks
Modeling Conformational Ensembles of Slow Functional Motions in Pin1-WW
Metabolic network segmentation: A probabilistic graphical modeling approach to identify the sites and sequential order of metabolic regulation from non-targeted metabolomics data
Novel anti-malarial drug strategies to prevent artemisinin partner drug resistance: A model-based analysis
Episome partitioning and symmetric cell divisions: Quantifying the role of random events in the persistence of HPV infections
Comment on: Toward an optimal contraception dosing strategy
Polymorphism Data Can Reveal the Origin of Species Abundance Statistics
Probing the Extent of Randomness in Protein Interaction Networks
Quantitative Analysis of the Association Angle between T-cell Receptor Vα/Vβ Domains Reveals Important Features for Epitope Recognition
Restriction of S-adenosylmethionine conformational freedom by knotted protein binding sites
Complex genetic and epigenetic regulation deviates gene expression from a unifying global transcriptional program
Systems Modeling of Molecular Mechanisms Controlling Cytokine-driven CD4+ T Cell Differentiation and Phenotype Plasticity
Evolutionary Games of Multiplayer Cooperation on Graphs
Action potential propagation and synchronisation in myelinated axons
PRAS: Predicting functional targets of RNA binding proteins based on CLIP-seq peaks
You Are Not Working for Me; I Am Working with You
An Integrated Framework Advancing Membrane Protein Modeling and Design
Emergent competition shapes top-down versus bottom-up control in multi-trophic ecosystems
Differential contributions of synaptic and intrinsic inhibitory currents to speech segmentation via flexible phase-locking in neural oscillators
GDP Release Preferentially Occurs on the Phosphate Side in Heterotrimeric G-proteins
Charge Profile Analysis Reveals That Activation of Pro-apoptotic Regulators Bax and Bak Relies on Charge Transfer Mediated Allosteric Regulation
Sample size calculation for phylogenetic case linkage
Histone tails cooperate to control the breathing of genomic nucleosomes
Computer-Based Screening of Functional Conformers of Proteins
MinePath: Mining for Phenotype Differential Sub-paths in Molecular Pathways
Metabolic Adaptation Processes That Converge to Optimal Biomass Flux Distributions
Adaptive foraging of pollinators fosters gradual tipping under resource competition and rapid environmental change
On the Use of Human Mobility Proxies for Modeling Epidemics
Structural Conversion of Aβ 17-42 Peptides from Disordered Oligomers to U-Shape Protofilaments via Multiple Kinetic Pathways
Tissue-guided LASSO for prediction of clinical drug response using preclinical samples
Ten simple rules for giving an effective academic job talk
Differential Affinity and Catalytic Activity of CheZ in E. coli Chemotaxis
Notification of Republication: Modeling individual time courses of thrombopoiesis during multi-cyclic chemotherapy
The Rate of Beneficial Mutations Surfing on the Wave of a Range Expansion
Synaptic polarity and sign-balance prediction using gene expression data in the Caenorhabditis elegans chemical synapse neuronal connectome network
A master equation approach to actin polymerization applied to endocytosis in yeast
Ecological and evolutionary dynamics of cell-virus-virophage systems
Causal Inference for Spatial Constancy across Saccades