yusuke1997/dblp-id-title huggingface dataset:
Modulation of working memory duration by synaptic and astrocytic mechanisms
Estimating the Location and Spatial Extent of a Covert Anthrax Release
Early and Real-Time Detection of Seasonal Influenza Onset
Using Functional Signatures to Identify Repositioned Drugs for Breast, Myelogenous Leukemia and Prostate Cancer
Lassa viral dynamics in non-human primates treated with favipiravir or ribavirin
Lobe Specific Ca 2+ -Calmodulin Nano-Domain in Neuronal Spines: A Single Molecule Level Analysis
G-Quadruplex DNA Sequences Are Evolutionarily Conserved and Associated with Distinct Genomic Features in Saccharomyces cerevisiae
Quantifying dose-, strain-, and tissue-specific kinetics of parainfluenza virus infection
Universal or Specific? A Modeling-Based Comparison of Broad-Spectrum Influenza Vaccines against Conventional, Strain-Matched Vaccines
The Distinct Conformational Dynamics of K-Ras and H-Ras A59G
Expectancy-based rhythmic entrainment as continuous Bayesian inference
Fragmentation modes and the evolution of life cycles
Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection
Little Italy: An Agent-Based Approach to the Estimation of Contact Patterns- Fitting Predicted Matrices to Serological Data
The effect of inhibition on rate code efficiency indicators
Characterization of RNA polymerase II trigger loop mutations using molecular dynamics simulations and machine learning
A Parsimonious Model of the Rabbit Action Potential Elucidates the Minimal Physiological Requirements for Alternans and Spiral Wave Breakup
Sizing Up Allometric Scaling Theory
Chaste: An Open Source C++ Library for Computational Physiology and Biology
A Network Approach to Analyzing Highly Recombinant Malaria Parasite Genes
A mathematical model of potassium homeostasis: Effect of feedforward and feedback controls
Uncovering specific mechanisms across cell types in dynamical models
Modelling transmission thresholds and hypoendemic stability for onchocerciasis elimination
Surfactant delivery in rat lungs: Comparing 3D geometrical simulation model with experimental instillation
Neurally-constrained modeling of human gaze strategies in a change blindness task
Twelve quick tips for deploying a Beacon
Multiregional integration in the brain during resting-state fMRI activity
Non-equilibrium landscape and flux reveal the stability-flexibility-energy tradeoff in working memory
Tumor cell intrinsic and extrinsic features predict prognosis in estrogen receptor positive breast cancer
Protein drift-diffusion in membranes with non-equilibrium fluctuations arising from gradients in concentration or temperature
Combined computational modeling and experimental analysis integrating chemical and mechanical signals suggests possible mechanism of shoot meristem maintenance
A simulation of the random and directed motion of dendritic cells in chemokine fields
PoweREST: Statistical power estimation for spatial transcriptomics experiments to detect differentially expressed genes between two conditions
A Spatially Detailed Model of Isometric Contraction Based on Competitive Binding of Troponin I Explains Cooperative Interactions between Tropomyosin and Crossbridges
DCMD: Distance-based classification using mixture distributions on microbiome data
Comprehensive mouse microbiota genome catalog reveals major difference to its human counterpart
Measuring the repertoire of age-related behavioral changes in Drosophila melanogaster
Practical Approaches for Detecting Selection in Microbial Genomes
Model-based analysis of response and resistance factors of cetuximab treatment in gastric cancer cell lines
Mutation severity spectrum of rare alleles in the human genome is predictive of disease type
Graph-Based Analysis of the Metabolic Exchanges between Two Co-Resident Intracellular Symbionts, Baumannia cicadellinicola and Sulcia muelleri , with Their Insect Host, Homalodisca coagulata
Chapter 8: Biological Knowledge Assembly and Interpretation
Thalamocortical and intracortical laminar connectivity determines sleep spindle properties
Cooperative Transition between Open and Closed Conformations in Potassium Channels
Understanding the mechanism of facilitation in hoverfly TSDNs
Ten simple rules to initiate and run a postdoctoral association
Constraint and Contingency in Multifunctional Gene Regulatory Circuits
A Knowledge-Based System for Display and Prediction of O-Glycosylation Network Behaviour in Response to Enzyme Knockouts
RIDDEN: Data-driven inference of receptor activity from transcriptomic data
Bottleneck Genes and Community Structure in the Cell Cycle Network of S. pombe
Ten simple rules for socially responsible science
Learning and teaching biological data science in the Bioconductor community
Discarding Functional Residues from the Substitution Table Improves Predictions of Active Sites within Three-Dimensional Structures
Models of Self-Peptide Sampling by Developing T Cells Identify Candidate Mechanisms of Thymic Selection
Spontaneous cortical activity is transiently poised close to criticality
Termination of Ca 2+ Release for Clustered IP 3 R Channels
Robustness under Functional Constraint: The Genetic Network for Temporal Expression in Drosophila Neurogenesis
Conversion of spikers to bursters in pituitary cell networks: Is it better to disperse for maximum exposure or circle the wagons?
Digital twin predicting diet response before and after long-term fasting
A physicochemical model of odor sampling
A model of developmental canalization, applied to human cranial form
Tissue Forge: Interactive biological and biophysics simulation environment
Analyzing cancer gene expression data through the lens of normal tissue-specificity
Fidelity of the representation of value in decision-making
Uncovering population contributions to the extracellular potential in the mouse visual system using Laminar Population Analysis
Learning efficient representations of environmental priors in working memory
General object-based features account for letter perception
Individual trajectories for recovery of neocortical activity in disorders of consciousness
Neighborhood Regularized Logistic Matrix Factorization for Drug-Target Interaction Prediction
Mixed Signal Learning by Spike Correlation Propagation in Feedback Inhibitory Circuits
Understanding Genotype-Phenotype Effects in Cancer via Network Approaches
A Digital Framework to Build, Visualize and Analyze a Gene Expression Atlas with Cellular Resolution in Zebrafish Early Embryogenesis
Systematic Analysis of Pleiotropy in C. elegans Early Embryogenesis
Assembly of the Transmembrane Domain of E. coli PhoQ Histidine Kinase: Implications for Signal Transduction from Molecular Simulations
Resilience of mobility network to dynamic population response across COVID-19 interventions: Evidences from Chile
Evidence of Conformational Selection Driving the Formation of Ligand Binding Sites in Protein-Protein Interfaces
A network-based approach to integrate nutrient microenvironment in the prediction of synthetic lethality in cancer metabolism
Personalizing chemotherapy drug selection using a novel transcriptomic chemogram
Modeling Dynamics of Cell-to-Cell Variability in TRAIL-Induced Apoptosis Explains Fractional Killing and Predicts Reversible Resistance
Simulation of Soluble and Bound VEGF-stimulated in vitro Capillary-like Network Formation on Deformed Substrate
Constrained inference in sparse coding reproduces contextual effects and predicts laminar neural dynamics
Mechanics and Dynamics of X-Chromosome Pairing at X Inactivation
An in-silico analysis of experimental designs to study ventricular function: A focus on the right ventricle
Wing structure and neural encoding jointly determine sensing strategies in insect flight
Predicting neuronal dynamics with a delayed gain control model
Predicting Gene Expression from Sequence: A Reexamination
Biophysically detailed mathematical models of multiscale cardiac active mechanics
Coincidence Detection of Place and Temporal Context in a Network Model of Spiking Hippocampal Neurons
Cortical and Hippocampal Correlates of Deliberation during Model-Based Decisions for Rewards in Humans
Accurate Detection of Recombinant Breakpoints in Whole-Genome Alignments
The Beta Cell in Its Cluster: Stochastic Graphs of Beta Cell Connectivity in the Islets of Langerhans
Large-Scale Analysis of Network Bistability for Human Cancers
Ten Simple Rules for avoiding and resolving conflicts with your colleagues
microRNA Target Predictions across Seven Drosophila Species and Comparison to Mammalian Targets
Rampant Exchange of the Structure and Function of Extramembrane Domains between Membrane and Water Soluble Proteins
Modelling brain representations of abstract concepts
Mesoscopic Model and Free Energy Landscape for Protein-DNA Binding Sites: Analysis of Cyanobacterial Promoters
Symmetry Restoring Bifurcation in Collective Decision-Making
StanDep: Capturing transcriptomic variability improves context-specific metabolic models
A constructivist-based proposal for bioinformatics teaching practices during lockdown
Ligand Binding and Circular Permutation Modify Residue Interaction Network in DHFR
Estimating individuals' genetic and non-genetic effects underlying infectious disease transmission from temporal epidemic data
Reconstructing contact network structure and cross-immunity patterns from multiple infection histories
A biologically inspired repair mechanism for neuronal reconstructions with a focus on human dendrites
Correction: Generation of Binary Tree-Child phylogenetic networks
Adaptive Temperature Compensation in Circadian Oscillations
Computational and Statistical Analysis of Protein Mass Spectrometry Data
Genome composition and phylogeny of microbes predict their co-occurrence in the environment
Anomalous diffusion and asymmetric tempering memory in neutrophil chemotaxis
A Comprehensive, Quantitative, and Genome-Wide Model of Translation
Dissecting mutational allosteric effects in alkaline phosphatases associated with different Hypophosphatasia phenotypes: An integrative computational investigation
Introduction to Computational Proteomics
Exploring tumor-normal cross-talk with TranNet: Role of the environment in tumor progression
Explain Bioinformatics to Your Grandmother!
Pain: A Statistical Account
Characteristic Effects of Stochastic Oscillatory Forcing on Neural Firing: Analytical Theory and Comparison to Paddlefish Electroreceptor Data
Timing over Tuning: Overcoming the Shortcomings of a Line Attractor during a Working Memory Task
Self-organization of conducting pathways explains electrical wave propagation in cardiac tissues with high fraction of non-conducting cells
Chemical features mining provides new descriptive structure-odor relationships
ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
tension: A Python package for FORCE learning
High-Resolution Modeling of Transmembrane Helical Protein Structures from Distant Homologues
Ten simple rules for effective research data management
A Three Species Model to Simulate Application of Hyperbaric Oxygen Therapy to Chronic Wounds
M-Track: A New Software for Automated Detection of Grooming Trajectories in Mice
Predicting partner fitness based on spatial structuring in a light-driven microbial community
Genome-Scale Metabolic Modeling Elucidates the Role of Proliferative Adaptation in Causing the Warburg Effect
Accurately Measuring Recombination between Closely Related HIV-1 Genomes
Energy-Information Trade-Offs between Movement and Sensing
Learning infectious disease epidemiology in a modern framework
Flexible and Accurate Detection of Genomic Copy-Number Changes from aCGH
Protein Networks as Logic Functions in Development and Cancer
The influence of astrocytes on the width of orientation hypercolumns in visual cortex: A computational perspective
Robustness and parameter geography in post-translational modification systems
Mechanical and Assembly Units of Viral Capsids Identified via Quasi-Rigid Domain Decomposition
The Equivalence of Information-Theoretic and Likelihood-Based Methods for Neural Dimensionality Reduction
Quantitative cell-based model predicts mechanical stress response of growing tumor spheroids over various growth conditions and cell lines
Inferring decoding strategies for multiple correlated neural populations
Signaling through polymerization and degradation: Analysis and simulations of T cell activation mediated by Bcl10
Flux balance analysis predicts Warburg-like effects of mouse hepatocyte deficient in miR-122a
Game-Changing Innovations: How Culture Can Change the Parameters of Its Own Evolution and Induce Abrupt Cultural Shifts
Parsimonious Model of Vascular Patterning Links Transverse Hormone Fluxes to Lateral Root Initiation: Auxin Leads the Way, while Cytokinin Levels Out
The Computational Development of Reinforcement Learning during Adolescence
Conservation of Expression and Sequence of Metabolic Genes Is Reflected by Activity Across Metabolic States
Including Thermal Fluctuations in Actomyosin Stable States Increases the Predicted Force per Motor and Macroscopic Efficiency in Muscle Modelling
A genotype imputation method for de-identified haplotype reference information by using recurrent neural network
A Validated Multiscale In-Silico Model for Mechano-sensitive Tumour Angiogenesis and Growth
Biophysical modeling and experimental analysis of the dynamics of C. elegans body-wall muscle cells
Energy optimization induces predictive-coding properties in a multi-compartment spiking neural network model
An agent-based model of dengue virus transmission shows how uncertainty about breakthrough infections influences vaccination impact projections
Computational Identification of Mechanistic Factors That Determine the Timing and Intensity of the Inflammatory Response
Warm Body Temperature Facilitates Energy Efficient Cortical Action Potentials
Positively charged mineral surfaces promoted the accumulation of organic intermediates at the origin of metabolism
A Computational Clonal Analysis of the Developing Mouse Limb Bud
Functional and spatial rewiring principles jointly regulate context-sensitive computation
A Computational Modeling and Simulation Approach to Investigate Mechanisms of Subcellular cAMP Compartmentation
A Graphical Modelling Approach to the Dissection of Highly Correlated Transcription Factor Binding Site Profiles
Effect of Network Architecture on Synchronization and Entrainment Properties of the Circadian Oscillations in the Suprachiasmatic Nucleus
Diversity and Plasticity of Th Cell Types Predicted from Regulatory Network Modelling
Molecular mechanism for bidirectional regulation of CD44 for lipid raft affiliation by palmitoylations and PIP2
Metabolic cross-feeding interactions modulate the dynamic community structure in microbial fuel cell under variable organic loading wastewaters
The SAMBA tool uses long reads to improve the contiguity of genome assemblies
Micelle-like clusters in phase-separated Nanog condensates: A molecular simulation study
A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets
Deep autoencoder-based behavioral pattern recognition outperforms standard statistical methods in high-dimensional zebrafish studies
Individual identity information persists in learned calls of introduced parrot populations
RNA-Seq Mapping and Detection of Gene Fusions with a Suffix Array Algorithm
Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases
Failure of Adaptive Self-Organized Criticality during Epileptic Seizure Attacks
Exploring the mono-/bistability range of positively autoregulated signaling systems in the presence of competing transcription factor binding sites
Mechanical Cell-Matrix Feedback Explains Pairwise and Collective Endothelial Cell Behavior In Vitro
Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets
Computational and robotic modeling reveal parsimonious combinations of interactions between individuals in schooling fish
A mechanistic integrative computational model of macrophage polarization: Implications in human pathophysiology
Repeatability and timing of tropical influenza epidemics
STGIC: A graph and image convolution-based method for spatial transcriptomic clustering
The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species
Identification of a Functional Connectome for Long-Term Fear Memory in Mice
Critical Role of Transient Activity of MT1-MMP for ECM Degradation in Invadopodia
Systematic clustering algorithm for chromatin accessibility data and its application to hematopoietic cells
A Characterization of Scale Invariant Responses in Enzymatic Networks
Differential contribution to gene expression prediction of histone modifications at enhancers or promoters
Brain-optimized extraction of complex sound features that drive continuous auditory perception
FunOrder: A robust and semi-automated method for the identification of essential biosynthetic genes through computational molecular co-evolution
Ten simple rules for writing a popular science book
Modeling Protective Anti-Tumor Immunity via Preventative Cancer Vaccines Using a Hybrid Agent-based and Delay Differential Equation Approach
MTMol-GPT: De novo multi-target molecular generation with transformer-based generative adversarial imitation learning
Ten steps to investigate a cellular system with mathematical modeling
Mechanistic basis of post-treatment control of SIV after anti-α4β7 antibody therapy
The impact of surveillance and control on highly pathogenic avian influenza outbreaks in poultry in Dhaka division, Bangladesh
The correlation between cell and nucleus size is explained by an eukaryotic cell growth model
Dorsal anterior cingulate-brainstem ensemble as a reinforcement meta-learner
Improving the workflow to crack Small, Unbalanced, Noisy, but Genuine (SUNG) datasets in bioacoustics: The case of bonobo calls
Measurements of the Impact of 3′ End Sequences on Gene Expression Reveal Wide Range and Sequence Dependent Effects
Conflicting Biomedical Assumptions for Mathematical Modeling: The Case of Cancer Metastasis
Molecular Mechanism of Allosteric Communication in Hsp70 Revealed by Molecular Dynamics Simulations
Prediction by Graph Theoretic Measures of Structural Effects in Proteins Arising from Non-Synonymous Single Nucleotide Polymorphisms
Genome scale metabolic network modelling for metabolic profile predictions
Novel Computational Protocols for Functionally Classifying and Characterising Serine Beta-Lactamases
Characterizing the dynamics, reactivity and controllability of moods in depression with a Kalman filter
Workshops: A Great Way to Enhance and Supplement a Degree
Mapping the gene network landscape of Alzheimer's disease through integrating genomics and transcriptomics
Macroscopic phase resetting-curves determine oscillatory coherence and signal transfer in inter-coupled neural circuits
Human mobility and the spatial transmission of influenza in the United States
Developmental Robustness by Obligate Interaction of Class B Floral Homeotic Genes and Proteins
Estimating the cumulative incidence of SARS-CoV-2 with imperfect serological tests: Exploiting cutoff-free approaches
A DIseAse MOdule Detection (DIAMOnD) Algorithm Derived from a Systematic Analysis of Connectivity Patterns of Disease Proteins in the Human Interactome
A multivalent binding model infers antibody Fc species from systems serology
What is the nature of motor adaptation to dynamic perturbations?
Bacterial Temporal Dynamics Enable Optimal Design of Antibiotic Treatment
High-affinity P2Y2 and low-affinity P2X7 receptor interaction modulates ATP-mediated calcium signaling in murine osteoblasts
Effect of Ionic Diffusion on Extracellular Potentials in Neural Tissue
Rational social distancing policy during epidemics with limited healthcare capacity
Synaptic Size Dynamics as an Effectively Stochastic Process
Tissue-Specific Functional Networks for Prioritizing Phenotype and Disease Genes
NGS-PrimerPlex: High-throughput primer design for multiplex polymerase chain reactions
Beyond advertising: New infrastructures for publishing integrated research objects
Mathematical modeling and simulation of tumor-induced angiogenesis in retinal hemangioblastoma
Shape-specific characterization of colorectal adenoma growth and transition to cancer with stochastic cell-based models
RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor
Confidence resets reveal hierarchical adaptive learning in humans
Systematic modelling of the development of laminar projection origins in the cerebral cortex: Interactions of spatio-temporal patterns of neurogenesis and cellular heterogeneity
Elementary Growth Modes provide a molecular description of cellular self-fabrication
Electron Transfer Interactome of Cytochrome c
Synchronization-Induced Rhythmicity of Circadian Oscillators in the Suprachiasmatic Nucleus
A Brain-Machine Interface for Control of Medically-Induced Coma
Biological network growth in complex environments: A computational framework
Bayesian inference for spatio-temporal stochastic transmission of plant disease in the presence of roguing: A case study to characterise the dispersal of Flavescence dorée
Broadband Criticality of Human Brain Network Synchronization
Strange attractor of a narwhal (Monodon monoceros)
Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions
OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions
Details in the evaluation of circular RNA detection tools: Reply to Chen and Chuang
RAFFT: Efficient prediction of RNA folding pathways using the fast Fourier transform
Transition state characteristics during cell differentiation
Perturbations both trigger and delay seizures due to generic properties of slow-fast relaxation oscillators
Combining biomarker and virus phylogenetic models improves HIV-1 epidemiological source identification
Small RNAs Originated from Pseudogenes: cis - or trans -Acting?
Computational modeling of color perception with biologically plausible spiking neural networks
Forward and Backward Inference in Spatial Cognition
The Time Scale of Evolutionary Innovation
Phylodynamic Inference for Structured Epidemiological Models
In Silico Analysis of Cell Cycle Synchronisation Effects in Radiotherapy of Tumour Spheroids
Pruning deep neural networks generates a sparse, bio-inspired nonlinear controller for insect flight
Tumor-Immune Interaction, Surgical Treatment, and Cancer Recurrence in a Mathematical Model of Melanoma
Mathematical Modelling of Molecular Pathways Enabling Tumour Cell Invasion and Migration
Role of Lipids in Spheroidal High Density Lipoproteins
Quantification of Local Morphodynamics and Local GTPase Activity by Edge Evolution Tracking
Resource diversity and supply drive colonization resistance
Optimal Workloop Energetics of Muscle-Actuated Systems: An Impedance Matching View
State dependence of stimulus-induced variability tuning in macaque MT
Computational Modeling of the Hematopoietic Erythroid-Myeloid Switch Reveals Insights into Cooperativity, Priming, and Irreversibility
Memes: A motif analysis environment in R using tools from the MEME Suite
How pupil responses track value-based decision-making during and after reinforcement learning
Intuitive physical reasoning about objects' masses transfers to a visuomotor decision task consistent with Newtonian physics
The Modular Organization of Protein Interactions in Escherichia coli
Adaptive feature detection from differential processing in parallel retinal pathways
Dose-dependent interaction of parasites with tiers of host defense predicts "wormholes" that prolong infection at intermediate inoculum sizes
Molecular Dynamics Study of the Opening Mechanism for DNA Polymerase I
Indirect reciprocity with stochastic and dual reputation updates
A Novel Bayesian Method for Detection of APOBEC3-Mediated Hypermutation and Its Application to Zoonotic Transmission of Simian Foamy Viruses
Spatial Acuity and Prey Detection in Weakly Electric Fish
Modeling and Inferring Cleavage Patterns in Proliferating Epithelia