yusuke1997/dblp-id-title huggingface dataset:
Developing a Molecular Roadmap of Drug-Food Interactions
Mathematical models of developmental vascular remodelling: A review
A retrospective assessment of forecasting the peak of the SARS-CoV-2 Omicron BA.1 wave in England
The inhibitory control of traveling waves in cortical networks
TSCCA: A tensor sparse CCA method for detecting microRNA-gene patterns from multiple cancers
Personalized pulse wave propagation modeling to improve vasopressor dosing management in patients with severe traumatic brain injury
From skylight input to behavioural output: A computational model of the insect polarised light compass
Identifying Network Perturbation in Cancer
Confirmation bias in human reinforcement learning: Evidence from counterfactual feedback processing
A Two-Locus Model of the Evolution of Insecticide Resistance to Inform and Optimise Public Health Insecticide Deployment Strategies
Homeostatic Scaling of Excitability in Recurrent Neural Networks
Computations that sustain neural feature selectivity across processing stages
CNAViz: An interactive webtool for user-guided segmentation of tumor DNA sequencing data
Uncovering the Dynamics of Cardiac Systems Using Stochastic Pacing and Frequency Domain Analyses
The Statistical Neuroanatomy of Frontal Networks in the Macaque
Shared Protein Complex Subunits Contribute to Explaining Disrupted Co-occurrence
Dose-dependent thresholds of dexamethasone destabilize CAR T-cell treatment efficacy
Mixtures of strategies underlie rodent behavior during reversal learning
Emergence of social inequality in the spatial harvesting of renewable public goods
Protein Scaffolds Can Enhance the Bistability of Multisite Phosphorylation Systems
Factors affecting basket catheter detection of real and phantom rotors in the atria: A computational study
Spatiotemporal network coding of physiological mossy fiber inputs by the cerebellar granular layer
Ensemble dynamics and information flow deduction from whole-brain imaging data
Learning massive interpretable gene regulatory networks of the human brain by merging Bayesian networks
Using evolutionary context to classify difficult protein folds
Hypercycle
Contributions of cell behavior to geometric order in embryonic cartilage
Ten simple rules for writing a Registered Report
Gain Control Network Conditions in Early Sensory Coding
Stochastic model of vesicular stomatitis virus replication reveals mutational effects on virion production
A likelihood approach to testing hypotheses on the co-evolution of epigenome and genome
Suppressed Expression of T-Box Transcription Factors Is Involved in Senescence in Chronic Obstructive Pulmonary Disease
Modern technologies and algorithms for scaffolding assembled genomes
Prediction of Functional Sites Based on the Fuzzy Oil Drop Model
Understanding the Adaptive Growth Strategy of Lactobacillus plantarum by In Silico Optimisation
Stereochemical Criteria for Prediction of the Effects of Proline Mutations on Protein Stability
A Dynamical Phyllotaxis Model to Determine Floral Organ Number
Tuning the Mammalian Circadian Clock: Robust Synergy of Two Loops
Non-uniform distribution of myosin-mediated forces governs red blood cell membrane curvature through tension modulation
ON/OFF and Beyond - A Boolean Model of Apoptosis
A Model Analysis of Arterial Oxygen Desaturation during Apnea in Preterm Infants
From Sensory Signals to Modality-Independent Conceptual Representations: A Probabilistic Language of Thought Approach
Dynamical differential expression (DyDE) reveals the period control mechanisms of the Arabidopsis circadian oscillator
Transcriptional Dynamics Reveal Critical Roles for Non-coding RNAs in the Immediate-Early Response
Nonnegative Matrix Factorization: An Analytical and Interpretive Tool in Computational Biology
Correction: Structure-Based Druggability Assessment of the Mammalian Structural Proteome with Inclusion of Light Protein Flexibility
Determinants of Protein Abundance and Translation Efficiency in S. cerevisiae
Transcriptional Profiling of the Dose Response: A More Powerful Approach for Characterizing Drug Activities
Graphical integrity issues in open access publications: Detection and patterns of proportional ink violations
OneNet - One network to rule them all: Consensus network inference from microbiome data
Understanding thromboembolus transport patterns in the brain for stroke in the presence of carotid artery stenosis
Pneumococcal population dynamics: Investigating vaccine-induced changes through multiscale modelling
Mesoscopic Segregation of Excitation and Inhibition in a Brain Network Model
Analysis of the docking property of host variants of hACE2 for SARS-CoV-2 in a large cohort
A diurnal flux balance model of Synechocystis sp. PCC 6803 metabolism
A copula based topology preserving graph convolution network for clustering of single-cell RNA-seq data
Dynamic Fluctuations Provide the Basis of a Conformational Switch Mechanism in Apo Cyclic AMP Receptor Protein
Efficient population coding depends on stimulus convergence and source of noise
Localized semi-nonnegative matrix factorization (LocaNMF) of widefield calcium imaging data
Identification of a Kinase Profile that Predicts Chromosome Damage Induced by Small Molecule Kinase Inhibitors
Deceleration of Fusion-Fission Cycles Improves Mitochondrial Quality Control during Aging
GOOGA: A platform to synthesize mapping experiments and identify genomic structural diversity
Scuphr: A probabilistic framework for cell lineage tree reconstruction
Metabolic network reconstruction as a resource for analyzing Salmonella Typhimurium SL1344 growth in the mouse intestine
Molecular Dynamics Simulations Reveal Proton Transfer Pathways in Cytochrome C-Dependent Nitric Oxide Reductase
Identifying T Cell Receptors from High-Throughput Sequencing: Dealing with Promiscuity in TCRα and TCRβ Pairing
Where did you come from, where did you go: Refining metagenomic analysis tools for horizontal gene transfer characterisation
What makes or breaks a campaign to stop an invading plant pathogen?
Efficient Olfactory Coding in the Pheromone Receptor Neuron of a Moth
Mapping genes for human face shape: Exploration of univariate phenotyping strategies
Homeodynamic feedback inhibition control in whole-brain simulations
Choose, rate or squeeze: Comparison of economic value functions elicited by different behavioral tasks
TreeKnit: Inferring ancestral reassortment graphs of influenza viruses
Temporal Variability and Social Heterogeneity in Disease Transmission: The Case of SARS in Hong Kong
Ten simple rules for creating and sustaining antiracist graduate programs
Inherent limitations of probabilistic models for protein-DNA binding specificity
Mutation D816V Alters the Internal Structure and Dynamics of c-KIT Receptor Cytoplasmic Region: Implications for Dimerization and Activation Mechanisms
Modeling and Dynamics of the Inward-Facing State of a Na + /Cl - Dependent Neurotransmitter Transporter Homologue
β-adrenergic signaling broadly contributes to LTP induction
High GC content causes orphan proteins to be intrinsically disordered
Synergistic information supports modality integration and flexible learning in neural networks solving multiple tasks
Potentials and limitations in the application of Convolutional Neural Networks for mosquito species identification using wing images
Methods and considerations for estimating parameters in biophysically detailed neural models with simulation based inference
A regularized functional regression model enabling transcriptome-wide dosage-dependent association study of cancer drug response
Sparsity and Compressed Coding in Sensory Systems
Synapses learn to utilize stochastic pre-synaptic release for the prediction of postsynaptic dynamics
More Than 1, 001 Problems with Protein Domain Databases: Transmembrane Regions, Signal Peptides and the Issue of Sequence Homology
Integrative analysis of structural variations using short-reads and linked-reads yields highly specific and sensitive predictions
Optimal occlusion uniformly partitions red blood cells fluxes within a microvascular network
Correction: Understanding narwhal diving behaviour using Hidden Markov Models with dependent state distributions and long range dependence
Neural mass modeling of slow-fast dynamics of seizure initiation and abortion
Incorporating regulatory interactions into gene-set analyses for GWAS data: A controlled analysis with the MAGMA tool
Angiogenesis: An Adaptive Dynamic Biological Patterning Problem
Epithelial stratification shapes infection dynamics
Species abundance correlations carry limited information about microbial network interactions
Phenotypic-dependent variability and the emergence of tolerance in bacterial populations
Neuroblastoma Tyrosine Kinase Signaling Networks Involve FYN and LYN in Endosomes and Lipid Rafts
A spectrum of routing strategies for brain networks
The Flash-Lag Effect as a Motion-Based Predictive Shift
Virtual epilepsy patient cohort: Generation and evaluation
Computational models of compound nerve action potentials: Efficient filter-based methods to quantify effects of tissue conductivities, conduction distance, and nerve fiber parameters
Evolution and Selection in Yeast Promoters: Analyzing the Combined Effect of Diverse Transcription Factor Binding Sites
Prediction of Protein Binding Regions in Disordered Proteins
A comparison of EEG encoding models using audiovisual stimuli and their unimodal counterparts
Coupled Information Diffusion-Pest Dynamics Models Predict Delayed Benefits of Farmer Cooperation in Pest Management Programs
speaq 2.0: A complete workflow for high-throughput 1D NMR spectra processing and quantification
Bioinformatics Meets User-Centred Design: A Perspective
Comparing two classes of biological distribution systems using network analysis
Comparative Microbial Modules Resource: Generation and Visualization of Multi-species Biclusters
PTEN Hopping on the Cell Membrane Is Regulated via a Positively-Charged C2 Domain
Sparse connectivity for MAP inference in linear models using sister mitral cells
Slow nucleosome dynamics set the transcriptional speed limit and induce RNA polymerase II traffic jams and bursts
Modelling the impact of JNJ-1802, a first-in-class dengue inhibitor blocking the NS3-NS4B interaction, on in-vitro DENV-2 dynamics
The Influence of Synaptic Weight Distribution on Neuronal Population Dynamics
PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions
Ten simple rules for structuring papers
Pathway-based Screening Strategy for Multitarget Inhibitors of Diverse Proteins in Metabolic Pathways
Modeling driver cells in developing neuronal networks
Correction: Success-efficient/failure-safe strategy for hierarchical reinforcement motor learning
Facilitated Variation: How Evolution Learns from Past Environments To Generalize to New Environments
Models that learn how humans learn: The case of decision-making and its disorders
Transmission of temporally correlated spike trains through synapses with short-term depression
Apparent Motion Suppresses Responses in Early Visual Cortex: A Population Code Model
Competition-driven evolution of organismal complexity
Meta-analysis of transcriptomic data reveals clusters of consistently deregulated gene and disease ontologies in Down syndrome
Unbiased and efficient log-likelihood estimation with inverse binomial sampling
Task-Specific Response Strategy Selection on the Basis of Recent Training Experience
OperonSEQer: A set of machine-learning algorithms with threshold voting for detection of operon pairs using short-read RNA-sequencing data
Efficient sampling-based Bayesian Active Learning for synaptic characterization
The decay of motor adaptation to novel movement dynamics reveals an asymmetry in the stability of motion state-dependent learning
Seizure and redox rescue in a model of glucose transport deficiency
fluEvidenceSynthesis: An R package for evidence synthesis based analysis of epidemiological outbreaks
Combined Changes in Chloride Regulation and Neuronal Excitability Enable Primary Afferent Depolarization to Elicit Spiking without Compromising its Inhibitory Effects
Sarcomere Lattice Geometry Influences Cooperative Myosin Binding in Muscle
Entropy Measures Quantify Global Splicing Disorders in Cancer
Integration of social cues and individual experiences during instrumental avoidance learning
Robust dynamic experiments for the precise estimation of respiration and fermentation parameters of fruit and vegetables
Modelling how plant cell-cycle progression leads to cell size regulation
Non-monotonic effects of GABAergic synaptic inputs on neuronal firing
A systems-level model reveals that 1, 2-Propanediol utilization microcompartments enhance pathway flux through intermediate sequestration
Contradictory Behavioral Biases Result from the Influence of Past Stimuli on Perception
Correction: PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph
Eco-evolutionary Model of Rapid Phenotypic Diversification in Species-Rich Communities
Correction: Perturbing low dimensional activity manifolds in spiking neuronal networks
Ten simple rules for documenting scientific software
Tipping the Balance: Robustness of Tip Cell Selection, Migration and Fusion in Angiogenesis
High-dimensional mediation analysis in survival models
The functional logic of odor information processing in the Drosophila antennal lobe
Data-driven modelling makes quantitative predictions regarding bacteria surface motility
Partial label learning for automated classification of single-cell transcriptomic profiles
Modeling the impact of single-cell stochasticity and size control on the population growth rate in asymmetrically dividing cells
Correction: Atrial arrhythmogenicity of KCNJ2 mutations in short QT syndrome: Insights from virtual human atria
Prioritizing Therapeutics for Lung Cancer: An Integrative Meta-analysis of Cancer Gene Signatures and Chemogenomic Data
MicroRNAs Form Triplexes with Double Stranded DNA at Sequence-Specific Binding Sites; a Eukaryotic Mechanism via which microRNAs Could Directly Alter Gene Expression
rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids
Funneled Landscape Leads to Robustness of Cell Networks: Yeast Cell Cycle
Uncertainty-Dependent Extinction of Fear Memory in an Amygdala-mPFC Neural Circuit Model
Optimal control of the spatial allocation of COVID-19 vaccines: Italy as a case study
Customized Regulation of Diverse Stress Response Genes by the Multiple Antibiotic Resistance Activator MarA
Exploiting the geometry of the solution space to reduce sensitivity to neuromotor noise
Evolutionary analyses of intrinsically disordered regions reveal widespread signals of conservation
Dimensionality in recurrent spiking networks: Global trends in activity and local origins in connectivity
The geometry of efficient codes: How rate-distortion trade-offs distort the latent representations of generative models
Ranking of cell clusters in a single-cell RNA-sequencing analysis framework using prior knowledge
iDREM: Interactive visualization of dynamic regulatory networks
Learning Pitch with STDP: A Computational Model of Place and Temporal Pitch Perception Using Spiking Neural Networks
Scalable, trustworthy generative model for virtual multi-staining from H&E whole slide images
Ten simple rules for organizing a data science workshop
Enhancing long-term forecasting: Learning from COVID-19 models
FLORA: A Novel Method to Predict Protein Function from Structure in Diverse Superfamilies
A computational model tracks whole-lung Mycobacterium tuberculosis infection and predicts factors that inhibit dissemination
Host factor prioritization for pan-viral genetic perturbation screens using random intercept models and network propagation
Recurrent neural networks can explain flexible trading of speed and accuracy in biological vision
Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference
Decoding Single Molecule Time Traces with Dynamic Disorder
Increasing consensus of context-specific metabolic models by integrating data-inferred cell functions
Dynamically-Driven Inactivation of the Catalytic Machinery of the SARS 3C-Like Protease by the N214A Mutation on the Extra Domain
Posttranscriptional Expression Regulation: What Determines Translation Rates?
Inflow/Outflow Boundary Conditions for Particle-Based Blood Flow Simulations: Application to Arterial Bifurcations and Trees
Glutamate Mediated Astrocytic Filtering of Neuronal Activity
A computational analysis of the role of integrins and Rho-GTPases in the emergence and disruption of apical-basal polarization in renal epithelial cells
An elasticity-curvature illusion decouples cutaneous and proprioceptive cues in active exploration of soft objects
Ten Simple Rules for Developing Usable Software in Computational Biology
Revisiting the invasion paradox: Resistance-richness relationship is driven by augmentation and displacement trends
Exploration of the Dynamic Properties of Protein Complexes Predicted from Spatially Constrained Protein-Protein Interaction Networks
Chapter 10: Mining Genome-Wide Genetic Markers
Protein Conservation and Variation Suggest Mechanisms of Cell Type-Specific Modulation of Signaling Pathways
Cross-population coupling of neural activity based on Gaussian process current source densities
Machines vs. Ensembles: Effective MAPK Signaling through Heterogeneous Sets of Protein Complexes
Parameterization of cell-free systems with time-series data using KETCHUP
A Network Biology Approach Identifies Molecular Cross-Talk between Normal Prostate Epithelial and Prostate Carcinoma Cells
Re-awakening the brain: Forcing transitions in disorders of consciousness by external in silico perturbation
No substantial change in the balance between model-free and model-based control via training on the two-step task
scPADGRN: A preconditioned ADMM approach for reconstructing dynamic gene regulatory network using single-cell RNA sequencing data
The Burr distribution as a model for the delay between key events in an individual's infection history
Primacy coding facilitates effective odor discrimination when receptor sensitivities are tuned
Asymmetric Evolutionary Games
The life history of learning: Demographic structure changes cultural outcomes
Processing Oscillatory Signals by Incoherent Feedforward Loops
Integrated Assessment and Prediction of Transcription Factor Binding
Ten Simple Rules for Writing a Reply Paper
Looking at Cerebellar Malformations through Text-Mined Interactomes of Mice and Humans
Epidemic Spread on Weighted Networks
Regulation of Early Steps of GPVI Signal Transduction by Phosphatases: A Systems Biology Approach
Rapid Sampling of Molecular Motions with Prior Information Constraints
Identifying Cell Types from Spatially Referenced Single-Cell Expression Datasets
Strain Mediated Adaptation Is Key for Myosin Mechanochemistry: Discovering General Rules for Motor Activity
Efficient and accurate causal inference with hidden confounders from genome-transcriptome variation data
Operational Principles for the Dynamics of the In Vitro ParA-ParB System
Mapping DNA sequence to transcription factor binding energy in vivo
Ten simple rules to colorize biological data visualization
SALARECON connects the Atlantic salmon genome to growth and feed efficiency
Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks
An Innovative Influenza Vaccination Policy: Targeting Last Season's Patients
Moving Forward Moving Backward: Directional Sorting of Chemotactic Cells due to Size and Adhesion Differences
Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations
The Emergence and Fate of Horizontally Acquired Genes in Escherichia coli
Spinal Mechanisms May Provide a Combination of Intermittent and Continuous Control of Human Posture: Predictions from a Biologically Based Neuromusculoskeletal Model
ΔFBA - Predicting metabolic flux alterations using genome-scale metabolic models and differential transcriptomic data
Measuring and mitigating PCR bias in microbiota datasets
What are housekeeping genes?
Comprehensive analysis of cancer breakpoints reveals signatures of genetic and epigenetic contribution to cancer genome rearrangements
Seasonally Dependent Relationships between Indicators of Malaria Transmission and Disease Provided by Mathematical Model Simulations
Neutral Models of Microbiome Evolution
Characterizing the Impact of Category Uncertainty on Human Auditory Categorization Behavior
Machine learning on multiple epigenetic features reveals H3K27Ac as a driver of gene expression prediction across patients with glioblastoma
Universally valid reduction of multiscale stochastic biochemical systems using simple non-elementary propensities
Phylogenetic reconciliation
Molecular Constraints on Synaptic Tagging and Maintenance of Long-Term Potentiation: A Predictive Model
Managing disease outbreaks: The importance of vector mobility and spatially heterogeneous control
Advancements and Challenges in Computational Biology
Integrated meta-analysis of colorectal cancer public proteomic datasets for biomarker discovery and validation
Success of prophylactic antiviral therapy for SARS-CoV-2: Predicted critical efficacies and impact of different drug-specific mechanisms of action
Stimulus presentation can enhance spiking irregularity across subcortical and cortical regions
Electrostatically Accelerated Encounter and Folding for Facile Recognition of Intrinsically Disordered Proteins
Leveraging a physiologically-based quantitative translational modeling platform for designing B cell maturation antigen-targeting bispecific T cell engagers for treatment of multiple myeloma
A biophysical model of dynamic balancing of excitation and inhibition in fast oscillatory large-scale networks
Correction: Expectancy-based rhythmic entrainment as continuous Bayesian inference
How Entorhinal Grid Cells May Learn Multiple Spatial Scales from a Dorsoventral Gradient of Cell Response Rates in a Self-organizing Map
Establishing and Managing a Global Student Network
Selective inhibition in CA3: A mechanism for stable pattern completion through heterosynaptic plasticity
DeepDeconUQ estimates malignant cell fraction prediction intervals in bulk RNA-seq tissue
Understanding heterogeneous mechanisms of heart failure with preserved ejection fraction through cardiorenal mathematical modeling
Winter is coming: Pathogen emergence in seasonal environments
Genome-Wide Detection and Analysis of Multifunctional Genes
Algorithms to Model Single Gene, Single Chromosome, and Whole Genome Copy Number Changes Jointly in Tumor Phylogenetics
The Contribution of High-Order Metabolic Interactions to the Global Activity of a Four-Species Microbial Community
Updating age-specific contact structures to match evolving demography in a dynamic mathematical model of tuberculosis vaccination
Optimal transport reveals dynamic gene regulatory networks via gene velocity estimation
Classifying RNA-Binding Proteins Based on Electrostatic Properties
Predicting gait adaptations due to ankle plantarflexor muscle weakness and contracture using physics-based musculoskeletal simulations
A Hidden Feedback in Signaling Cascades Is Revealed
Dimensionality reduction of longitudinal 'omics data using modern tensor factorizations
Correction: Sequential inference as a mode of cognition and its correlates in fronto-parietal and hippocampal brain regions
Unsupervised learning for robust working memory
Correction: Elucidation of molecular kinetic schemes from macroscopic traces using system identification
Predicting knee adduction moment response to gait retraining with minimal clinical data
Perturbation biology links temporal protein changes to drug responses in a melanoma cell line
Effect of Dedifferentiation on Time to Mutation Acquisition in Stem Cell-Driven Cancers
Building Disease-Specific Drug-Protein Connectivity Maps from Molecular Interaction Networks and PubMed Abstracts
Non-Centered Spike-Triggered Covariance Analysis Reveals Neurotrophin-3 as a Developmental Regulator of Receptive Field Properties of ON-OFF Retinal Ganglion Cells
Teaching Bioinformatics in Concert