yusuke1997/dblp-id-title huggingface dataset:
Long Non-Coding RNA and Alternative Splicing Modulations in Parkinson's Leukocytes Identified by RNA Sequencing
MiMeNet: Exploring microbiome-metabolome relationships using neural networks
Spectral tuning of adaptation supports coding of sensory context in auditory cortex
Hybrid Models and Biological Model Reduction with PyDSTool
Fast Statistical Alignment
Sharpness of Spike Initiation in Neurons Explained by Compartmentalization
"Bioinformatics: Introduction and Methods, " a Bilingual Massive Open Online Course (MOOC) as a New Example for Global Bioinformatics Education
Dynamics from Seconds to Hours in Hodgkin-Huxley Model with Time-Dependent Ion Concentrations and Buffer Reservoirs
Quantitative prediction of ensemble dynamics, shapes and contact propensities of intrinsically disordered proteins
Dynamic coupling of residues within proteins as a mechanistic foundation of many enigmatic pathogenic missense variants
Robust Brain-Machine Interface Design Using Optimal Feedback Control Modeling and Adaptive Point Process Filtering
Ten simple rules for reading a scientific paper
Stem Cell Proliferation and Quiescence - Two Sides of the Same Coin
Extrapolating Weak Selection in Evolutionary Games
Interference and Shaping in Sensorimotor Adaptations with Rewards
Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data
Mathematical modeling of N-803 treatment in SIV-infected non-human primates
Perceptual learning improves discrimination but does not reduce distortions in appearance
Developmental Self-Construction and -Configuration of Functional Neocortical Neuronal Networks
Is My Network Module Preserved and Reproducible?
Predicted Molecular Effects of Sequence Variants Link to System Level of Disease
A Spatial Model of Mosquito Host-Seeking Behavior
Approximate Inference for Time-Varying Interactions and Macroscopic Dynamics of Neural Populations
The Spatial Resolution of Epidemic Peaks
Learning divisive normalization in primary visual cortex
Thalamic regulation of frontal interactions in human cognitive flexibility
Correction: Epidemiological and health economic implications of symptom propagation in respiratory pathogens: A mathematical modelling investigation
Human Genome Replication Proceeds through Four Chromatin States
Contact-Inhibited Chemotaxis in De Novo and Sprouting Blood-Vessel Growth
Refractory density model of cortical direction selectivity: Lagged-nonlagged, transient-sustained, and On-Off thalamic neuron-based mechanisms and intracortical amplification
Functional States of the Genome-Scale Escherichia Coli Transcriptional Regulatory System
Neuroprosthetic Decoder Training as Imitation Learning
Using information theory to optimise epidemic models for real-time prediction and estimation
Identifying robust hysteresis in networks
Network Events on Multiple Space and Time Scales in Cultured Neural Networks and in a Stochastic Rate Model
Soft-bound Synaptic Plasticity Increases Storage Capacity
Role of actin filaments and cis binding in cadherin clustering and patterning
Let's Make Those Book Chapters Open Too!
Atypical structural tendencies among low-complexity domains in the Protein Data Bank proteome
Sparsity in an artificial neural network predicts beauty: Towards a model of processing-based aesthetics
ASGCL: Adaptive Sparse Mapping-based graph contrastive learning network for cancer drug response prediction
Modelling T cell proliferation: Dynamics heterogeneity depending on cell differentiation, age, and genetic background
A state space approach for piecewise-linear recurrent neural networks for identifying computational dynamics from neural measurements
Evolutionarily Conserved Substrate Substructures for Automated Annotation of Enzyme Superfamilies
Mathematical Description of Bacterial Traveling Pulses
Gap junctions set the speed and nucleation rate of stage I retinal waves
Hierarchical Processing of Auditory Objects in Humans
Effective mechanical potential of cell-cell interaction explains three-dimensional morphologies during early embryogenesis
Noise leads to the perceived increase in evolutionary rates over short time scales
Characterizing superspreading potential of infectious disease: Decomposition of individual transmissibility
Network Modeling Identifies Molecular Functions Targeted by miR-204 to Suppress Head and Neck Tumor Metastasis
Rapid detection and recognition of whole brain activity in a freely behaving Caenorhabditis elegans
An Extended Normalization Model of Attention Accounts for Feature-Based Attentional Enhancement of Both Response and Coherence Gain
Aggregating multiple test results to improve medical decision-making
As Simple As Possible, but Not Simpler: Exploring the Fidelity of Coarse-Grained Protein Models for Simulated Force Spectroscopy
Multiscale modeling of influenza A virus replication in cell cultures predicts infection dynamics for highly different infection conditions
Distinguishing shadows from surface boundaries using local achromatic cues
Average Is Optimal: An Inverted-U Relationship between Trial-to-Trial Brain Activity and Behavioral Performance
A mentorship and incubation program using project-based learning to build a professional bioinformatics pipeline in Kenya
Cortical oscillations support sampling-based computations in spiking neural networks
On the validity of electric brain signal predictions based on population firing rates
SMetABF: A rapid algorithm for Bayesian GWAS meta-analysis with a large number of studies included
Spatial constraints and stochastic seeding subvert microbial arms race
In silico study of multicellular automaticity of heterogeneous cardiac cell monolayers: Effects of automaticity strength and structural linear anisotropy
What Is Stochastic Resonance? Definitions, Misconceptions, Debates, and Its Relevance to Biology
The Molecular Basis of Polyunsaturated Fatty Acid Interactions with the Shaker Voltage-Gated Potassium Channel
Arrhythmogenic effects of ultra-long and bistable cardiac action potentials
BETASCAN: Probable β-amyloids Identified by Pairwise Probabilistic Analysis
Inferring oscillatory modulation in neural spike trains
Learning as filtering: Implications for spike-based plasticity
Telling ecological networks apart by their structure: A computational challenge
Chirality provides a direct fitness advantage and facilitates intermixing in cellular aggregates
Identifying individual risk rare variants using protein structure guided local tests (POINT)
GPMelt: A hierarchical Gaussian process framework to explore the dark meltome of thermal proteome profiling experiments
Mathematical model and tool to explore shorter multi-drug therapy options for active pulmonary tuberculosis
Sperm chemotaxis in marine species is optimal at physiological flow rates according theory of filament surfing
Growth of bacteria in 3-d colonies
A computational framework for cortical microtubule dynamics in realistically shaped plant cells
Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock
Response to comment on "Identifying patterns differing between high-dimensional datasets with generalized contrastive PCA"
Control fast or control smart: When should invading pathogens be controlled?
Chaotic and stochastic dynamics of epileptiform-like activities in sclerotic hippocampus resected from patients with pharmacoresistant epilepsy
Insect Bio-inspired Neural Network Provides New Evidence on How Simple Feature Detectors Can Enable Complex Visual Generalization and Stimulus Location Invariance in the Miniature Brain of Honeybees
Ensemble of decision tree reveals potential miRNA-disease associations
Identifying the engagement of a brain network during a targeted tDCS-fMRI experiment using a machine learning approach
XA4C: eXplainable representation learning via Autoencoders revealing Critical genes
Shining a Light on Dark Sequencing: Characterising Errors in Ion Torrent PGM Data
MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics
Comment on "A comprehensive overview and evaluation of circular RNA detection tools"
Neural Dynamics as Sampling: A Model for Stochastic Computation in Recurrent Networks of Spiking Neurons
Comorbidities in the diseasome are more apparent than real: What Bayesian filtering reveals about the comorbidities of depression
A computational framework for modelling infectious disease policy based on age and household structure with applications to the COVID-19 pandemic
Conformational diversity analysis reveals three functional mechanisms in proteins
Adaptation across the 2D population code explains the spatially distributive nature of motor learning
Characterization and clustering of kinase isoform expression in metastatic melanoma
Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB's Education Committee)
Wide-Field Motion Integration in Fly VS Cells: Insights from an Inverse Approach
Optimizing global COVID-19 vaccine allocation: An agent-based computational model of 148 countries
Enhanced production of heterologous proteins by a synthetic microbial community: Conditions and trade-offs
Regulatory context drives conservation of glycine riboswitch aptamers
Mechanistic insight into the functional role of human sinoatrial node conduction pathways and pacemaker compartments heterogeneity: A computer model analysis
Multi-scale Inference of Interaction Rules in Animal Groups Using Bayesian Model Selection
Rescuing Loading Induced Bone Formation at Senescence
Accurate, high-coverage assignment of in vivo protein kinases to phosphosites from in vitro phosphoproteomic specificity data
Biomedical Discovery Acceleration, with Applications to Craniofacial Development
Analysis of spiking synchrony in visual cortex reveals distinct types of top-down modulation signals for spatial and object-based attention
Correction: Humans adapt their anticipatory eye movements to the volatility of visual motion properties
Why Do Hubs in the Yeast Protein Interaction Network Tend To Be Essential: Reexamining the Connection between the Network Topology and Essentiality
Variant calling enhances the identification of cancer cells in single-cell RNA sequencing data
Gene communities in co-expression networks across different tissues
Membrane-Mediated Interaction between Strongly Anisotropic Protein Scaffolds
Evaluation of linear and non-linear activation dynamics models for insect muscle
Testing, tracing and isolation in compartmental models
Neuronal gain modulability is determined by dendritic morphology: A computational optogenetic study
Enhancing Human Spermine Synthase Activity by Engineered Mutations
Contextual Refinement of Regulatory Targets Reveals Effects on Breast Cancer Prognosis of the Regulome
Correction: Seasonal influenza: Modelling approaches to capture immunity propagation
New computational protein design methods for de novo small molecule binding sites
Traceability, reproducibility and wiki-exploration for "à-la-carte" reconstructions of genome-scale metabolic models
Potential Energy Landscape and Robustness of a Gene Regulatory Network: Toggle Switch
Mixed mechanism of conformational selection and induced fit as a molecular recognition process in the calreticulin family of proteins
The Long and Thorny Road to Publication in Quality Journals
Upregulation of an inward rectifying K+ channel can rescue slow Ca2+ oscillations in K(ATP) channel deficient pancreatic islets
Effect of magnitude and variability of energy of activation in multisite ultrasensitive biochemical processes
A Drug-Centric View of Drug Development: How Drugs Spread from Disease to Disease
Mycobacterium susceptibility to ivermectin by inhibition of eccD3, an ESX-3 secretion system component
Database size positively correlates with the loss of species-level taxonomic resolution for the 16S rRNA and other prokaryotic marker genes
Relating Cortical Atrophy in Temporal Lobe Epilepsy with Graph Diffusion-Based Network Models
Sparse deconvolution of cell type medleys in spatial transcriptomics
A deep learning algorithm for 3D cell detection in whole mouse brain image datasets
Red blood cell phenotyping from 3D confocal images using artificial neural networks
Robust Detection and Genotyping of Single Feature Polymorphisms from Gene Expression Data
A Bayesian hierarchical model of trial-to-trial fluctuations in decision criterion
Locally adaptive Bayesian birth-death model successfully detects slow and rapid rate shifts
Folding Very Short Peptides Using Molecular Dynamics
A Systematic Bayesian Integration of Epidemiological and Genetic Data
Chapter 5: Network Biology Approach to Complex Diseases
Low-dimensional controllability of brain networks
Synchrony, oscillations, and phase relationships in collective neuronal activity: A highly comparative overview of methods
In-silico Assessment of Protein-Protein Electron Transfer. A Case Study: Cytochrome c Peroxidase - Cytochrome c
OpenCyto: An Open Source Infrastructure for Scalable, Robust, Reproducible, and Automated, End-to-End Flow Cytometry Data Analysis
Weighted Frequent Gene Co-expression Network Mining to Identify Genes Involved in Genome Stability
A dual-feedback loop model of the mammalian circadian clock for multi-input control of circadian phase
Acetylcholine-gated current translates wake neuronal firing rate information into a spike timing-based code in Non-REM sleep, stabilizing neural network dynamics during memory consolidation
Epidemiological consequences of enduring strain-specific immunity requiring repeated episodes of infection
Scientific Software Development Is Not an Oxymoron
Ten quick tips for teaching with participatory live coding
Stability of Cross-Feeding Polymorphisms in Microbial Communities
Network-based analysis of prostate cancer cell lines reveals novel marker gene candidates associated with radioresistance and patient relapse
The properties of human disease mutations at protein interfaces
PolyUbiquitin Chain Linkage Topology Selects the Functions from the Underlying Binding Landscape
A Future Vision for PLOS Computational Biology
Efficient ReML inference in variance component mixed models using a Min-Max algorithm
Insights into the Fold Organization of TIM Barrel from Interaction Energy Based Structure Networks
Self-loops in evolutionary graph theory: Friends or foes?
ECD-CDGI: An efficient energy-constrained diffusion model for cancer driver gene identification
Deep Sequencing of Protease Inhibitor Resistant HIV Patient Isolates Reveals Patterns of Correlated Mutations in Gag and Protease
Ephaptic coupling in white matter fibre bundles modulates axonal transmission delays
Dynamics and turnover of memory CD8 T cell responses following yellow fever vaccination
ClassTR: Classifying Within-Host Heterogeneity Based on Tandem Repeats with Application to Mycobacterium tuberculosis Infections
In Remembrance: Reinhart Heinrich 1946-2006
A new index for characterizing micro-bead motion in a flow induced by ciliary beating: Part II, modeling
A computational model for how cells choose temporal or spatial sensing during chemotaxis
Dominant Glint Based Prey Localization in Horseshoe Bats: A Possible Strategy for Noise Rejection
Humans adapt their anticipatory eye movements to the volatility of visual motion properties
Dynamical Allocation of Cellular Resources as an Optimal Control Problem: Novel Insights into Microbial Growth Strategies
Memory, innovation and vertical learning
Maximum-Likelihood Model Averaging To Profile Clustering of Site Types across Discrete Linear Sequences
Sensitive Detection of Viral Transcripts in Human Tumor Transcriptomes
Cardinal features of involuntary force variability can arise from the closed-loop control of viscoelastic afferented muscles
Improving Contact Prediction along Three Dimensions
Automatic Adaptation to Fast Input Changes in a Time-Invariant Neural Circuit
A neural network model for the evolution of learning in changing environments
Spread of hospital-acquired infections: A comparison of healthcare networks
A kinetic model for USP14 regulated substrate degradation in 26S proteasome
Quantifying ecosystem states and state transitions of the Upper Mississippi River System using topological data analysis
In vitro and in silico multidimensional modeling of oncolytic tumor virotherapy dynamics
Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics
Genome-Wide Functional Divergence after the Symbiosis of Proteobacteria with Insects Unraveled through a Novel Computational Approach
Cerebellar Motor Learning: When Is Cortical Plasticity Not Enough?
Experimental Studies and Dynamics Modeling Analysis of the Swimming and Diving of Whirligig Beetles ( Coleoptera: Gyrinidae )
SpaMWGDA: Identifying spatial domains of spatial transcriptomes using multi-view weighted fusion graph convolutional network and data augmentation
Brain-wide connectome inferences using functional connectivity MultiVariate Pattern Analyses (fc-MVPA)
Metabolic Constraint-Based Refinement of Transcriptional Regulatory Networks
Rapid Prediction of Bacterial Heterotrophic Fluxomics Using Machine Learning and Constraint Programming
Simple Topological Features Reflect Dynamics and Modularity in Protein Interaction Networks
Network Signatures of Survival in Glioblastoma Multiforme
Identification of Functional Subclasses in the DJ-1 Superfamily Proteins
Trading Speed and Accuracy by Coding Time: A Coupled-circuit Cortical Model
Operant conditioning of stochastic chemical reaction networks
Food Web Assembly Rules for Generalized Lotka-Volterra Equations
Computational redesign of a fluorogen activating protein with Rosetta
From trainees to trainers to instructors: Sustainably building a national capacity in bioinformatics training
PyRates - A code-generation tool for modeling dynamical systems in biology and beyond
Co-emergence of multi-scale cortical activities of irregular firing, oscillations and avalanches achieves cost-efficient information capacity
How single neuron properties shape chaotic dynamics and signal transmission in random neural networks
Comparison of FORCE trained spiking and rate neural networks shows spiking networks learn slowly with noisy, cross-trial firing rates
NuSeT: A deep learning tool for reliably separating and analyzing crowded cells
Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model
Putting Theory to the Test: Which Regulatory Mechanisms Can Drive Realistic Growth of a Root?
Springs vs. motors: Ideal assistance in the lower limbs during walking at different speeds
Surprise-minimization as a solution to the structural credit assignment problem
Inverse stochastic resonance in networks of spiking neurons
Extracting Gene Networks for Low-Dose Radiation Using Graph Theoretical Algorithms
Semantic influences on object detection: Drift diffusion modeling provides insights regarding mechanism
A Peptide Filtering Relation Quantifies MHC Class I Peptide Optimization
The Origins of Specificity in Polyketide Synthase Protein Interactions
Ten simple rules for aspiring graduate students
Circadian rhythm shows potential for mRNA efficiency and self-organized division of labor in multinucleate cells
VarPPUD: Pinpointing diagnostic variants from sets of prioritized, strong candidate variants
Lipid Exchange Mechanism of the Cholesteryl Ester Transfer Protein Clarified by Atomistic and Coarse-grained Simulations
Ten (not so) simple rules for clinical trial data-sharing
Evaluation of the Phase-Dependent Rhythm Control of Human Walking Using Phase Response Curves
Design of optimal nonlinear network controllers for Alzheimer's disease
Using Hawkes Processes to model imported and local malaria cases in near-elimination settings
Modeling Electrophysiological Coupling and Fusion between Human Mesenchymal Stem Cells and Cardiomyocytes
Modality independent or modality specific? Common computations underlie confidence judgements in visual and auditory decisions
Ranbow: A fast and accurate method for polyploid haplotype reconstruction
Deconvolution of the Cellular Force-Generating Subsystems that Govern Cytokinesis Furrow Ingression
Elastic energy savings and active energy cost in a simple model of running
The role of cryptic ancestral symmetry in histone folding mechanisms across Eukarya and Archaea
Ten simple rules for how you can help make your lab a better place as a graduate student or postdoc
The Regional Student Group Program of the ISCB Student Council: Stories from the Road
Can subjective pain be inferred from objective physiological data? Evidence from patients with sickle cell disease
Ten simple rules for research with humans
Structured Pathway across the Transition State for Peptide Folding Revealed by Molecular Dynamics Simulations
Correlation-based model of artificially induced plasticity in motor cortex by a bidirectional brain-computer interface
Revealing mechanisms of infectious disease spread through empirical contact networks
Saccadic Momentum and Facilitation of Return Saccades Contribute to an Optimal Foraging Strategy
Site-Specific Phosphorylation of VEGFR2 Is Mediated by Receptor Trafficking: Insights from a Computational Model
Rise and Demise of Bioinformatics? Promise and Progress
Transcription factor competition facilitates self-sustained oscillations in single gene genetic circuits
Mechanistic computational modeling of monospecific and bispecific antibodies targeting interleukin-6/8 receptors
FamPipe: An Automatic Analysis Pipeline for Analyzing Sequencing Data in Families for Disease Studies
Selection upon Genome Architecture: Conservation of Functional Neighborhoods with Changing Genes
Comparison and benchmark of deep learning methods for non-coding RNA classification
Meet-U: Educating through research immersion
Heterogeneous Host Susceptibility Enhances Prevalence of Mixed-Genotype Micro-Parasite Infections
Natively Unstructured Loops Differ from Other Loops
Correction: Recentrifuge: Robust comparative analysis and contamination removal for metagenomics
A Mass Conserved Reaction-Diffusion System Captures Properties of Cell Polarity
Mouse visual cortex as a limited resource system that self-learns an ecologically-general representation
The Elementary Operations of Human Vision Are Not Reducible to Template-Matching
A Generalized Allosteric Mechanism for cis -Regulated Cyclic Nucleotide Binding Domains
Impact of Fast Sodium Channel Inactivation on Spike Threshold Dynamics and Synaptic Integration
Tuning Curves for Arm Posture Control in Motor Cortex Are Consistent with Random Connectivity
netgsa: Fast computation and interactive visualization for topology-based pathway enrichment analysis
Maximizing the Information Content of Experiments in Systems Biology
Mathematical modeling suggests 14-3-3 proteins modulate RAF paradoxical activation
Entropic Stabilization of Proteins and Its Proteomic Consequences
Robustness and Fragility in Immunosenescence
Machine Learning and Its Applications to Biology
Accuracy of Answers to Cell Lineage Questions Depends on Single-Cell Genomics Data Quality and Quantity
Non-destructive classification of unlabeled cells: Combining an automated benchtop magnetic resonance scanner and artificial intelligence
The Role of Oligomerization and Cooperative Regulation in Protein Function: The Case of Tryptophan Synthase
Computational Assessment of the Cooperativity between RNA Binding Proteins and MicroRNAs in Transcript Decay
Resonant learning in scale-free networks
Computational simulations and Ca2+ imaging reveal that slow synaptic depolarizations (slow EPSPs) inhibit fast EPSP evoked action potentials for most of their time course in enteric neurons
Spatial kinetics and immune control of murine cytomegalovirus infection in the salivary glands
Biomarkers of mRNA vaccine efficacy derived from mechanistic modeling of tumor-immune interactions
Balancing central control and sensory feedback produces adaptable and robust locomotor patterns in a spiking, neuromechanical model of the salamander spinal cord
Information-theoretic analysis of multivariate single-cell signaling responses
rtestim: Time-varying reproduction number estimation with trend filtering
Leveraging functional annotations in genetic risk prediction for human complex diseases
Visual physiology of the layer 4 cortical circuit in silico