yusuke1997/dblp-id-title huggingface dataset:
Exploiting the similarity of dissimilarities for biomedical applications and enhanced machine learning
Prioritizing and characterizing functionally relevant genes across human tissues
Unsupervised extraction of epidemic syndromes from participatory influenza surveillance self-reported symptoms
Solving the influence maximization problem reveals regulatory organization of the yeast cell cycle
Computational Analysis of Viscoelastic Properties of Crosslinked Actin Networks
A Numerical Approach to Ion Channel Modelling Using Whole-Cell Voltage-Clamp Recordings and a Genetic Algorithm
Getting Started in Structural Phylogenomics
An enriched network motif family regulates multistep cell fate transitions with restricted reversibility
General Anesthetics Predicted to Block the GLIC Pore with Micromolar Affinity
Ten Simple Rules for Getting Grants
A multi-state model of the CaMKII dodecamer suggests a role for calmodulin in maintenance of autophosphorylation
Compositional Lotka-Volterra describes microbial dynamics in the simplex
Real-time single-cell characterization of the eukaryotic transcription cycle reveals correlations between RNA initiation, elongation, and cleavage
Flexibility and intrinsic disorder are conserved features of hepatitis C virus E2 glycoprotein
Physics-based tissue simulator to model multicellular systems: A study of liver regeneration and hepatocellular carcinoma recurrence
Differential equation modeling of cell population dynamics in skeletal muscle regeneration from single-cell transcriptomic data
Colocalization of Coregulated Genes: A Steered Molecular Dynamics Study of Human Chromosome 19
Divide and Conquer: Functional Segregation of Synaptic Inputs by Astrocytic Microdomains Could Alleviate Paroxysmal Activity Following Brain Trauma
Moving analytical ultracentrifugation software to a good manufacturing practices (GMP) environment
NeuroMotion: Open-source platform with neuromechanical and deep network modules to generate surface EMG signals during voluntary movement
Spike Triggered Hormone Secretion in Vasopressin Cells; a Model Investigation of Mechanism and Heterogeneous Population Function
T-shaped alignments integrating HIV-1 near full-length genome and partial pol sequences can improve phylogenetic inference of transmission clusters
A real-time feedback system stabilises the regulation of worker reproduction under various colony sizes
Calculating Evolutionary Dynamics in Structured Populations
The neglected giants: Uncovering the prevalence and functional groups of huge proteins in proteomes
Population Structure Induces a Symmetry Breaking Favoring the Emergence of Cooperation
Protein-Protein Interactions in a Crowded Environment: An Analysis via Cross-Docking Simulations and Evolutionary Information
Benchmarking network algorithms for contextualizing genes of interest
Detecting Horizontal Gene Transfer between Closely Related Taxa
Chemomechanical regulation of myosin Ic cross-bridges: Deducing the elastic properties of an ensemble from single-molecule mechanisms
Biases in neural population codes with a few active neurons
Deep learning tools and modeling to estimate the temporal expression of cell cycle proteins from 2D still images
Improving the Precision of the Structure-Function Relationship by Considering Phylogenetic Context
Electrical receptive fields of retinal ganglion cells: Influence of presynaptic neurons
What Can Systems Theory of Networks Offer to Biology?
Neural adaptation and fractional dynamics as a window to underlying neural excitability
Electrical stimulus artifact cancellation and neural spike detection on large multi-electrode arrays
Interpreting T-cell search "strategies" in the light of evolution under constraints
Data integration uncovers the metabolic bases of phenotypic variation in yeast
Reconstruction of Protein Backbones from the BriX Collection of Canonical Protein Fragments
Sparse high-dimensional decomposition of non-primary auditory cortical receptive fields
Computational Biomarker Pipeline from Discovery to Clinical Implementation: Plasma Proteomic Biomarkers for Cardiac Transplantation
Probabilistic Learning by Rodent Grid Cells
A graph neural network-based spatial multi-omics data integration method for deciphering spatial domains
Ictal wavefront propagation in slices and simulations with conductance-based refractory density model
Differential sustained and transient temporal processing across visual streams
Object detection through search with a foveated visual system
Spatial regularity control of phyllotaxis pattern generated by the mutual interaction between auxin and PIN1
Detection of Alpha-Rod Protein Repeats Using a Neural Network and Application to Huntingtin
Interpreting Metabolomic Profiles using Unbiased Pathway Models
Assessing the Relative Stability of Dimer Interfaces in G Protein-Coupled Receptors
Breaking the circularity in circular analyses: Simulations and formal treatment of the flattened average approach
Multiscale modelling shows how cell-ECM interactions impact ECM fibre alignment and cell detachment
The Morphology of the Rat Vibrissal Array: A Model for Quantifying Spatiotemporal Patterns of Whisker-Object Contact
Program Bytes: Satellite Meetings, SIGs, and AKEs at ISMB 2016
Avalanches during epithelial tissue growth; Uniform Growth and a drosophila eye disc model
Poisson balanced spiking networks
Stoichiometric Representation of Gene-Protein-Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction
A method for achieving complete microbial genomes and improving bins from metagenomics data
Optimal dynamic control approach in a multi-objective therapeutic scenario: Application to drug delivery in the treatment of prostate cancer
A Look Inside HIV Resistance through Retroviral Protease Interaction Maps
REDCRAFT: A computational platform using residual dipolar coupling NMR data for determining structures of perdeuterated proteins in solution
Correction: Signal Propagation in Proteins and Relation to Equilibrium Fluctuations
Stimulating at the right time to recover network states in a model of the cortico-basal ganglia-thalamic circuit
Dopamine Neurons Change the Type of Excitability in Response to Stimuli
Effect of Global Cardiac Ischemia on Human Ventricular Fibrillation: Insights from a Multi-scale Mechanistic Model of the Human Heart
Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism
Computational Analyses of Synergism in Small Molecular Network Motifs
Ensembles of Spiking Neurons with Noise Support Optimal Probabilistic Inference in a Dynamically Changing Environment
Prediction of DNA Methylation based on Multi-dimensional feature encoding and double convolutional fully connected convolutional neural network
Predicting antimicrobial mechanism-of-action from transcriptomes: A generalizable explainable artificial intelligence approach
Mechanism of Focal Adhesion Kinase Mechanosensing
Recalibrating probabilistic forecasts of epidemics
Collective intelligence defines biological functions in Wikipedia as communities in the hidden protein connection network
Fostering accessible online education using Galaxy as an e-learning platform
How stimulation frequency and intensity impact on the long-lasting effects of coordinated reset stimulation
Design of an adaptable intrafascicular electrode (AIR) for selective nerve stimulation by model-based optimization
Challenges of COVID-19 Case Forecasting in the US, 2020-2021
ReaDDy 2: Fast and flexible software framework for interacting-particle reaction dynamics
Quantifying the risk of spillover reduction programs for human health
Information integration and collective motility in phototactic cyanobacteria
Network-Based Integration of Disparate Omic Data To Identify "Silent Players" in Cancer
Patterns of asymmetry and energy cost generated from predictive simulations of hemiparetic gait
Evidence of Influence of Genomic DNA Sequence on Human X Chromosome Inactivation
Continuous action with a neurobiologically inspired computational approach reveals the dynamics of selection history
Accelerating prediction of chemical shift of protein structures on GPUs: Using OpenACC
A Bayesian Framework to Identify Methylcytosines from High-Throughput Bisulfite Sequencing Data
Compositional clustering in task structure learning
Promoter Complexity and Tissue-Specific Expression of Stress Response Components in Mytilus galloprovincialis , a Sessile Marine Invertebrate Species
Disease Surveillance on Complex Social Networks
LMSM: A modular approach for identifying lncRNA related miRNA sponge modules in breast cancer
Classification and phylogeny for the annotation of novel eukaryotic GNAT acetyltransferases
Segmentation-Less, Automated, Vascular Vectorization
Environmental dynamics shape perceptual decision bias
Synaptic Plasticity Can Produce and Enhance Direction Selectivity
Excalibur: A new ensemble method based on an optimal combination of aggregation tests for rare-variant association testing for sequencing data
Integration of single-cell RNA-seq data into population models to characterize cancer metabolism
Machine Learning Assisted Design of Highly Active Peptides for Drug Discovery
Buffering and total calcium levels determine the presence of oscillatory regimes in cardiac cells
Statistical Mechanics Provides Novel Insights into Microtubule Stability and Mechanism of Shrinkage
Emergence and maintenance of modularity in neural networks with Hebbian and anti-Hebbian inhibitory STDP
Geometrically Repatterned Immunological Synapses Uncover Formation Mechanisms
Ten simple rules for open human health research
coiaf: Directly estimating complexity of infection with allele frequencies
G4SNVHunter: An R/Bioconductor Package for Evaluating SNV-Induced Disruption of G-Quadruplex Structures Leveraging the G4Hunter Algorithm
Effective Stimuli for Constructing Reliable Neuron Models
A proactive/reactive mass screening approach with uncertain symptomatic cases
Structure of Spontaneous UP and DOWN Transitions Self-Organizing in a Cortical Network Model
How are estimated cellular turnover rates influenced by the dynamics of a source population?
Continuous evaluation of denoising strategies in resting-state fMRI connectivity using fMRIPrep and Nilearn
An Analytically Solvable Model for Rapid Evolution of Modular Structure
Revealing Molecular Mechanisms by Integrating High-Dimensional Functional Screens with Protein Interaction Data
Malaria Incidence Rates from Time Series of 2-Wave Panel Surveys
Validation-based model selection for 13C metabolic flux analysis with uncertain measurement errors
Grouping promotes both partnership and rivalry with long memory in direct reciprocity
Dynamic predictive coding: A model of hierarchical sequence learning and prediction in the neocortex
Atomistic Picture for the Folding Pathway of a Hybrid-1 Type Human Telomeric DNA G-quadruplex
Protein Topology Determines Cysteine Oxidation Fate: The Case of Sulfenyl Amide Formation among Protein Families
Web-Based Computational Chemistry Education with CHARMMing III: Reduction Potentials of Electron Transfer Proteins
Evolutionary analysis of polyproline motifs in Escherichia coli reveals their regulatory role in translation
How Haptic Size Sensations Improve Distance Perception
Current Estimates for HIV-1 Production Imply Rapid Viral Clearance in Lymphoid Tissues
The (In)dependence of Alternative Splicing and Gene Duplication
Decoupled contrastive multi-view clustering with adaptive false negative elimination for cancer subtyping
Reward-predictive representations generalize across tasks in reinforcement learning
Ten simple rules for delivering live distance training in bioinformatics across the globe using webinars
Machine learning mathematical models for incidence estimation during pandemics
Evolution of Integrated Causal Structures in Animats Exposed to Environments of Increasing Complexity
A Computational Model Predicting Disruption of Blood Vessel Development
Short-Term Memory Trace in Rapidly Adapting Synapses of Inferior Temporal Cortex
Molecular Dynamics Simulations of Forced Unbending of Integrin α V β 3
PLUS: Predicting cancer metastasis potential based on positive and unlabeled learning
Modeling Chemotaxis Reveals the Role of Reversed Phosphotransfer and a Bi-Functional Kinase-Phosphatase
About Dice, Bouldering, and Team Empowerment: Running the CompOmics Group at VIB and Ghent University, Belgium
Ten Simple Rules for Developing a Successful Research Proposal in Brazil
A Stochastic Model of Latently Infected Cell Reactivation and Viral Blip Generation in Treated HIV Patients
Differences in the consolidation by spontaneous and evoked ripples in the presence of active dendrites
Rational Design and Adaptive Management of Combination Therapies for Hepatitis C Virus Infection
Hybrid simulation modelling of networks of heterogeneous care homes and the inter-facility spread of Covid-19 by sharing staff
Discriminating External and Internal Causes for Heading Changes in Freely Flying Drosophila
Deciphering the Code for Retroviral Integration Target Site Selection
Networks of necessity: Simulating COVID-19 mitigation strategies for disabled people and their caregivers
SyBLaRS: A web service for laying out, rendering and mining biological maps in SBGN, SBML and more
Rare-event sampling of epigenetic landscapes and phenotype transitions
Implementation Considerations, Not Topological Differences, Are the Main Determinants of Noise Suppression Properties in Feedback and Incoherent Feedforward Circuits
The mechanical influence of densification on epithelial architecture
Dysregulation of excitatory neural firing replicates physiological and functional changes in aging visual cortex
Modeling the circadian regulation of the immune system: Sexually dimorphic effects of shift work
Visually guided homing of bumblebees in ambiguous situations: A behavioural and modelling study
Characterizing chromatin folding coordinate and landscape with deep learning
Inferring microbial interactions with their environment from genomic and metagenomic data
Modelling the potential use of pre-exposure prophylaxis to reduce nosocomial SARS-CoV-2 transmission
Compact Modeling of Allosteric Multisite Proteins: Application to a Cell Size Checkpoint
B Cell Activation Triggered by the Formation of the Small Receptor Cluster: A Computational Study
ISCB Honors Michael S. Waterman and Mathieu Blanchette
Expression Profile of the Schistosoma japonicum Degradome Reveals Differential Protease Expression Patterns and Potential Anti-schistosomal Intervention Targets
Analysis of Gene Regulatory Networks in the Mammalian Circadian Rhythm
Mechanisms underlying a thalamocortical transformation during active tactile sensation
Glycolysis Is Governed by Growth Regime and Simple Enzyme Regulation in Adherent MDCK Cells
Bulk Genotyping of Biopsies Can Create Spurious Evidence for Hetereogeneity in Mutation Content
What Makes Ribosome-Mediated Transcriptional Attenuation Sensitive to Amino Acid Limitation?
Exploring a diverse world of effector domains and amyloid signaling motifs in fungal NLR proteins
Theoretical Analysis of the Stress Induced B-Z Transition in Superhelical DNA
Quantitative drug susceptibility testing for Mycobacterium tuberculosis using unassembled sequencing data and machine learning
PEtab - Interoperable specification of parameter estimation problems in systems biology
sumSTAAR: A flexible framework for gene-based association studies using GWAS summary statistics
Ten quick tips for ensuring machine learning model validity
Encoding of Naturalistic Stimuli by Local Field Potential Spectra in Networks of Excitatory and Inhibitory Neurons
Structural Drift: The Population Dynamics of Sequential Learning
Multiple morphogens and rapid elongation promote segmental patterning during development
Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO)
Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons
A nowcasting framework for correcting for reporting delays in malaria surveillance
Ten simple rules for implementing a successful field season
Viral Perturbations of Host Networks Reflect Disease Etiology
A multiscale electro-metabolic model of a rat neocortical circuit reveals the impact of ageing on central cortical layers
The biomechanics of chewing and suckling in the infant: A potential mechanism for physiologic metopic suture closure
A variational deep-learning approach to modeling memory T cell dynamics
Motion prediction enables simulated MR-imaging of freely moving model organisms
A new method for the joint estimation of instantaneous reproductive number and serial interval during epidemics
Pulse transit time estimation of aortic pulse wave velocity and blood pressure using machine learning and simulated training data
Bioinformatics Education - Perspectives and Challenges
A Novel Drug-Mouse Phenotypic Similarity Method Detects Molecular Determinants of Drug Effects
Breast cancer is marked by specific, Public T-cell receptor CDR3 regions shared by mice and humans
Making Biomolecular Simulations Accessible in the Post-Nobel Prize Era
Deciphering the Arginine-Binding Preferences at the Substrate-Binding Groove of Ser/Thr Kinases by Computational Surface Mapping
Self versus Environment Motion in Postural Control
Susceptibility to Superhelically Driven DNA Duplex Destabilization: A Highly Conserved Property of Yeast Replication Origins
CRISPR-Analytics (CRISPR-A): A platform for precise analytics and simulations for gene editing
Using de novo assembly to identify structural variation of eight complex immune system gene regions
Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes
The relation between crosstalk and gene regulation form revisited
A computational model of shared fine-scale structure in the human connectome
Computation of Steady-State Probability Distributions in Stochastic Models of Cellular Networks
Network approaches and applications in biology
Models of SIV rebound after treatment interruption that involve multiple reactivation events
TIBA: A web application for the visual analysis of temporal occurrences, interactions, and transitions of animal behavior
Stochastic Ion Channel Gating in Dendritic Neurons: Morphology Dependence and Probabilistic Synaptic Activation of Dendritic Spikes
Correction: Spatiotemporal Expression Control Correlates with Intragenic Scaffold Matrix Attachment Regions (S/MARs) in Arabidopsis thaliana
Coupling and heterogeneity modulate pacemaking capability in healthy and diseased two-dimensional sinoatrial node tissue models
Recent Evolutions of Multiple Sequence Alignment Algorithms
Effects of Specular Highlights on Perceived Surface Convexity
Discovering adaptation-capable biological network structures using control-theoretic approaches
Combination treatment optimization using a pan-cancer pathway model
An Epigenomic fingerprint of human cancers by landscape interrogation of super enhancers at the constituent level
Determining the interaction status and evolutionary fate of duplicated homomeric proteins
Predicting gene expression in the human malaria parasite Plasmodium falciparum using histone modification, nucleosome positioning, and 3D localization features
Generalizing biological surround suppression based on center surround similarity via deep neural network models
Scelestial: Fast and accurate single-cell lineage tree inference based on a Steiner tree approximation algorithm
SubClonal Hierarchy Inference from Somatic Mutations: Automatic Reconstruction of Cancer Evolutionary Trees from Multi-region Next Generation Sequencing
Identification of Networks of Co-Occurring, Tumor-Related DNA Copy Number Changes Using a Genome-Wide Scoring Approach
Distal Spike Initiation Zone Location Estimation by Morphological Simulation of Ionic Current Filtering Demonstrated in a Novel Model of an Identified Drosophila Motoneuron
Bistability in Apoptosis by Receptor Clustering
GENERALIST: A latent space based generative model for protein sequence families
Simulation of the Undiseased Human Cardiac Ventricular Action Potential: Model Formulation and Experimental Validation
Adaptive Gain Modulation in V1 Explains Contextual Modifications during Bisection Learning
Examining Variable Domain Orientations in Antigen Receptors Gives Insight into TCR-Like Antibody Design
Speed, Sensitivity, and Bistability in Auto-activating Signaling Circuits
A Feedback Quenched Oscillator Produces Turing Patterning with One Diffuser
Slow Noise in the Period of a Biological Oscillator Underlies Gradual Trends and Abrupt Transitions in Phasic Relationships in Hybrid Neural Networks
Sensor-based localization of epidemic sources on human mobility networks
Structure-Guided Comparative Analysis of Proteins: Principles, Tools, and Applications for Predicting Function
Patient contrastive learning: A performant, expressive, and practical approach to electrocardiogram modeling
Better together: Elements of successful scientific software development in a distributed collaborative community
Identifying Currents in the Gene Pool for Bacterial Populations Using an Integrative Approach
Using Entropy Maximization to Understand the Determinants of Structural Dynamics beyond Native Contact Topology
A Multiscale Approach to Modelling Drug Metabolism by Membrane-Bound Cytochrome P450 Enzymes
Contact-number-driven virus evolution: A multi-level modeling framework for the evolution of acute or persistent RNA virus infection
Synchrony is more than its top-down and climatic parts: interacting Moran effects on phytoplankton in British seas
Computational translation of genomic responses from experimental model systems to humans
Low Probability of Initiating nirS Transcription Explains Observed Gas Kinetics and Growth of Bacteria Switching from Aerobic Respiration to Denitrification
A Nonlinear Dynamic Approach Reveals a Long-Term Stroke Effect on Cerebral Blood Flow Regulation at Multiple Time Scales
Network feature-based phenotyping of leaf venation robustly reconstructs the latent space
Analysis of the Free-Energy Surface of Proteins from Reversible Folding Simulations
Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0
Computational Design of the Affinity and Specificity of a Therapeutic T Cell Receptor
Mechanism of MicroRNA-Target Interaction: Molecular Dynamics Simulations and Thermodynamics Analysis
A theory of memory for binary sequences: Evidence for a mental compression algorithm in humans
The SKMT Algorithm: A method for assessing and comparing underlying protein entanglement
Epydemix: An open-source Python package for epidemic modeling with integrated approximate Bayesian calibration
Arterial Stiffening Provides Sufficient Explanation for Primary Hypertension
Whole community invasions and the integration of novel ecosystems
Epistasis in genomic and survival data of cancer patients
The Impact of Different Sources of Fluctuations on Mutual Information in Biochemical Networks
Accuracy of the Lotka-Volterra model fails in strongly coupled microbial consumer-resource systems
Shrinking the Metabolic Solution Space Using Experimental Datasets
Preferentially Quantized Linker DNA Lengths in Saccharomyces cerevisiae
Dual Delayed Feedback Provides Sensitivity and Robustness to the NF- κ B Signaling Module
Expectation generation and its effect on subsequent pain and visual perception
Network-State Modulation of Power-Law Frequency-Scaling in Visual Cortical Neurons
Protrusive Push versus Enveloping Embrace: Computational Model of Phagocytosis Predicts Key Regulatory Role of Cytoskeletal Membrane Anchors
Identifying cell states in single-cell RNA-seq data at statistically maximal resolution
Binding of Nucleoid-Associated Protein Fis to DNA Is Regulated by DNA Breathing Dynamics
Modelling the Effects of Population Structure on Childhood Disease: The Case of Varicella
An Integrated Computational/Experimental Model of Lymphoma Growth
Yeast Mating and Image-Based Quantification of Spatial Pattern Formation
mbkmeans: Fast clustering for single cell data using mini-batch k-means
The Dynamic Brain: From Spiking Neurons to Neural Masses and Cortical Fields