yusuke1997/dblp-id-title huggingface dataset:
Standard Anatomical and Visual Space for the Mouse Retina: Computational Reconstruction and Transformation of Flattened Retinae with the Retistruct Package
Linking structure and activity in nonlinear spiking networks
Correction: Inferring on the Intentions of Others by Hierarchical Bayesian Learning
Interpretation of correlated neural variability from models of feed-forward and recurrent circuits
Predicting synchronous firing of large neural populations from sequential recordings
Polycation-π Interactions Are a Driving Force for Molecular Recognition by an Intrinsically Disordered Oncoprotein Family
Mechanics of Undulatory Swimming in a Frictional Fluid
Transmembrane Topology and Signal Peptide Prediction Using Dynamic Bayesian Networks
Mechanical evolution of DNA double-strand breaks in the nucleosome
Contextual cues are not unique for motor learning: Task-dependant switching of feedback controllers
In Silico Knockout Studies of Xenophagic Capturing of Salmonella
Learning with Slight Forgetting Optimizes Sensorimotor Transformation in Redundant Motor Systems
Sequential exploration in the Iowa gambling task: Validation of a new computational model in a large dataset of young and old healthy participants
Computational estimates of mechanical constraints on cell migration through the extracellular matrix
Ten simple rules for getting the most out of a summer laboratory internship
An implementation framework to improve the transparency and reproducibility of computational models of infectious diseases
How epigenome drives chromatin folding and dynamics, insights from efficient coarse-grained models of chromosomes
Coordinating Role of RXRα in Downregulating Hepatic Detoxification during Inflammation Revealed by Fuzzy-Logic Modeling
Stochastic activity in low-rank recurrent neural networks
Modelling the effectiveness of Integrated Pest Management strategies for the control of Septoria tritici blotch
Rapid target foraging with reach or gaze: The hand looks further ahead than the eye
The tuning of tuning: How adaptation influences single cell information transfer
Histone posttranslational modifications predict specific alternative exon subtypes in mammalian brain
Comparison of Immunogen Designs That Optimize Peptide Coverage: Reply to Fischer et al
An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins
Host heterogeneity and epistasis explain punctuated evolution of SARS-CoV-2
A Computational Model for the Analysis of Lipoprotein Distributions in the Mouse: Translating FPLC Profiles to Lipoprotein Metabolism
Getting higher on rugged landscapes: Inversion mutations open access to fitter adaptive peaks in NK fitness landscapes
Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota
Transcriptomic correlates of electrophysiological and morphological diversity within and across excitatory and inhibitory neuron classes
Stress and Strain Provide Positional and Directional Cues in Development
Computational simulations of tumor growth and treatment response: Benefits of high-frequency, low-dose drug regimens and concurrent vascular normalization
A New Tool to Quantify Receptor Recruitment to Cell Contact Sites during Host-Pathogen Interaction
Even a good influenza forecasting model can benefit from internet-based nowcasts, but those benefits are limited
A Quick Guide for Building a Successful Bioinformatics Community
Size Does Matter: An Integrative In Vivo - In Silico Approach for the Treatment of Critical Size Bone Defects
What Can Causal Networks Tell Us about Metabolic Pathways?
Variable habitat conditions drive species covariation in the human microbiota
Mixture models reveal multiple positional bias types in RNA-Seq data and lead to accurate transcript concentration estimates
Individualized genetic network analysis reveals new therapeutic vulnerabilities in 6, 700 cancer genomes
Finding the balance between model complexity and performance: Using ventral striatal oscillations to classify feeding behavior in rats
Inferring tumor progression in large datasets
Synaptic Learning Rules and Sparse Coding in a Model Sensory System
Differential Repression of Alternative Transcripts: A Screen for miRNA Targets
Linking Myometrial Physiology to Intrauterine Pressure; How Tissue-Level Contractions Create Uterine Contractions of Labor
Approximate Bayesian Computation
During haptic communication, the central nervous system compensates distinctly for delay and noise
Amplitude cancellation influences the association between frequency components in the neural drive to muscle and the rectified EMG signal
Revealing and reshaping attractor dynamics in large networks of cortical neurons
GINI: From ISH Images to Gene Interaction Networks
Comparing and linking machine learning and semi-mechanistic models for the predictability of endemic measles dynamics
Modeling microbial metabolic trade-offs in a chemostat
Value-complexity tradeoff explains mouse navigational learning
Statistical regularities in natural scenes that support figure-ground segregation by neural populations
Inferring parameters of cancer evolution in chronic lymphocytic leukemia
PBMDA: A novel and effective path-based computational model for miRNA-disease association prediction
Spike-Based Population Coding and Working Memory
A mechanistic modeling framework reveals the key principles underlying tumor metabolism
A computational study of astrocytic glutamate influence on post-synaptic neuronal excitability
Widespread Compensatory Evolution Conserves DNA-Encoded Nucleosome Organization in Yeast
IQCELL: A platform for predicting the effect of gene perturbations on developmental trajectories using single-cell RNA-seq data
Estimation of Directed Effective Connectivity from fMRI Functional Connectivity Hints at Asymmetries of Cortical Connectome
Determining Host Metabolic Limitations on Viral Replication via Integrated Modeling and Experimental Perturbation
Synchronous Chaos and Broad Band Gamma Rhythm in a Minimal Multi-Layer Model of Primary Visual Cortex
The Presence of Nuclear Cactus in the Early Drosophila Embryo May Extend the Dynamic Range of the Dorsal Gradient
Uncertainty reduction in biochemical kinetic models: Enforcing desired model properties
From space to time: Spatial inhomogeneities lead to the emergence of spatiotemporal sequences in spiking neuronal networks
Comparative Genomics and Disorder Prediction Identify Biologically Relevant SH3 Protein Interactions
PF 2 fit : Polar Fast Fourier Matched Alignment of Atomistic Structures with 3D Electron Microscopy Maps
Mining folded proteomes in the era of accurate structure prediction
Protein superfolds are characterised as frustration-free topologies: A case study of pure parallel β-sheet topologies
Model design choices impact biological insight: Unpacking the broad landscape of spatial-temporal model development decisions
Optimal Noise Filtering in the Chemotactic Response of Escherichia coli
Mechanisms of human dynamic object recognition revealed by sequential deep neural networks
Multivariate classification of neuroimaging data with nested subclasses: Biased accuracy and implications for hypothesis testing
Design of nanobody targeting SARS-CoV-2 spike glycoprotein using CDR-grafting assisted by molecular simulation and machine learning
A Molecular Clock Infers Heterogeneous Tissue Age Among Patients with Barrett's Esophagus
Music in Our Ears: The Biological Bases of Musical Timbre Perception
Computational modeling of blood component transport related to coronary artery thrombosis in Kawasaki disease
Mining Host-Pathogen Protein Interactions to Characterize Burkholderia mallei Infectivity Mechanisms
Spike-Timing Theory of Working Memory
Navigation task and action space drive the emergence of egocentric and allocentric spatial representations
Replication Fork Polarity Gradients Revealed by Megabase-Sized U-Shaped Replication Timing Domains in Human Cell Lines
Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes
Predicting the mechanism and rate of H-NS binding to AT-rich DNA
Comparing T cell receptor repertoires using optimal transport
Modelling ribosome kinetics and translational control on dynamic mRNA
Sequence specificity despite intrinsic disorder: How a disease-associated Val/Met polymorphism rearranges tertiary interactions in a long disordered protein
Local and collective transitions in sparsely-interacting ecological communities
CODON - Software to manual curation of prokaryotic genomes
Outlook on Thailand's Genomics and Computational Biology Research and Development
MGSurvE: A framework to optimize trap placement for genetic surveillance of mosquito populations
Effect of Ca2+ on the promiscuous target-protein binding of calmodulin
Improving the Caenorhabditis elegans Genome Annotation Using Machine Learning
Steered molecular dynamics simulations reveal critical residues for (un)binding of substrates, inhibitors and a product to the malarial M1 aminopeptidase
Assessing criticality in pre-seizure single-neuron activity of human epileptic cortex
A Computational Approach to Finding Novel Targets for Existing Drugs
The Social Bayesian Brain: Does Mentalizing Make a Difference When We Learn?
The interplay between cancer type, panel size and tumor mutational burden threshold in patient selection for cancer immunotherapy
Simulated poaching affects global connectivity and efficiency in social networks of African savanna elephants - An exemplar of how human disturbance impacts group-living species
Elucidation of molecular kinetic schemes from macroscopic traces using system identification
Using 'sentinel' plants to improve early detection of invasive plant pathogens
The Aggregated Gut Viral Catalogue (AVrC): A unified resource for exploring the viral diversity of the human gut
On the choice of metric in gradient-based theories of brain function
Efficient consideration of coordinated water molecules improves computational protein-protein and protein-ligand docking discrimination
Frequency Dependence of Signal Power and Spatial Reach of the Local Field Potential
Host responses and viral traits interact to shape the impacts of climate warming on highly pathogenic avian influenza in migratory waterfowl
A multi-scale coevolutionary approach to predict interactions between protein domains
A new machine learning method for cancer mutation analysis
Multi-view fusion based on graph convolutional network with attention mechanism for predicting miRNA related to drugs
Top-down inputs drive neuronal network rewiring and context-enhanced sensory processing in olfaction
Conformational Transitions upon Ligand Binding: Holo-Structure Prediction from Apo Conformations
Resilience of three-dimensional sinusoidal networks in liver tissue
What Is the Role of Motif D in the Nucleotide Incorporation Catalyzed by the RNA-dependent RNA Polymerase from Poliovirus?
Machine learning-driven identification of drugs inhibiting cytochrome P450 2C9
Digital Signal Processing Reveals Circadian Baseline Oscillation in Majority of Mammalian Genes
Gamma Synchronization Influences Map Formation Time in a Topological Model of Spatial Learning
The information theory of developmental pruning: Optimizing global network architectures using local synaptic rules
Detecting Coevolution in and among Protein Domains
The logic of the floral transition: Reverse-engineering the switch controlling the identity of lateral organs
The Convallis Rule for Unsupervised Learning in Cortical Networks
Enzyme Localization Can Drastically Affect Signal Amplification in Signal Transduction Pathways
Ten simple rules for collaborative lesson development
Axial and Radial Forces of Cross-Bridges Depend on Lattice Spacing
A network-informed analysis of SARS-CoV-2 and hemophagocytic lymphohistiocytosis genes' interactions points to Neutrophil extracellular traps as mediators of thrombosis in COVID-19
Modeling and Classification of Kinetic Patterns of Dynamic Metabolic Biomarkers in Physical Activity
A Model of Drosophila Larva Chemotaxis
Prediction of antibiotic resistance in Escherichia coli from large-scale pan-genome data
EEG-representational geometries and psychometric distortions in approximate numerical judgment
Computational analysis of GAL pathway pinpoints mechanisms underlying natural variation
Efficient encoding of spectrotemporal information for bat echolocation
Apoptosis mapping in space and time of 3D tumor ecosystems reveals transmissibility of cytotoxic cancer death
Falling towards Forgetfulness: Synaptic Decay Prevents Spontaneous Recovery of Memory
Dynamics on Networks: The Role of Local Dynamics and Global Networks on the Emergence of Hypersynchronous Neural Activity
A mathematical model describing the localization and spread of influenza A virus infection within the human respiratory tract
A model of risk and mental state shifts during social interaction
Mathematical basis and toolchain for hierarchical optimization of biochemical networks
Modeling soybean growth: A mixed model approach
Maintaining Homeostasis by Decision-Making
Investigation of Inflammation and Tissue Patterning in the Gut Using a Spatially Explicit General-Purpose Model of Enteric Tissue (SEGMEnT)
Design and execution of a verification, validation, and uncertainty quantification plan for a numerical model of left ventricular flow after LVAD implantation
A Range-Normalization Model of Context-Dependent Choice: A New Model and Evidence
A Theoretical Model of Jigsaw-Puzzle Pattern Formation by Plant Leaf Epidermal Cells
Probing the rules of cell coordination in live tissues by interpretable machine learning based on graph neural networks
Reply to "Ten Simple Rules for Getting Published"
Low-rate firing limit for neurons with axon, soma and dendrites driven by spatially distributed stochastic synapses
Epigenetic switching as a strategy for quick adaptation while attenuating biochemical noise
SnIPRE: Selection Inference Using a Poisson Random Effects Model
Empirical Multiscale Networks of Cellular Regulation
Standing Genetic Variation and the Evolution of Drug Resistance in HIV
Mathematical Modeling Reveals Kinetics of Lymphocyte Recirculation in the Whole Organism
A First Look at ARFome: Dual-Coding Genes in Mammalian Genomes
Epigenetics is all you need: A transformer to decode chromatin structural compartments from the epigenome
Differential temperature sensitivity of synaptic and firing processes in a neural mass model of epileptic discharges explains heterogeneous response of experimental epilepsy to focal brain cooling
DDGWizard: Integration of feature calculation resources for analysis and prediction of changes in protein thermostability upon point mutations
Preprocessing choices affect RNA velocity results for droplet scRNA-seq data
Key residues in TLR4-MD2 tetramer formation identified by free energy simulations
Role of non-native electrostatic interactions in the coupled folding and binding of PUMA with Mcl-1
Flow-Based Network Analysis of the Caenorhabditis elegans Connectome
Adaptive multi-view multi-label learning for identifying disease-associated candidate miRNAs
Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor
Identification of Low-Complexity Domains by Compositional Signatures Reveals Class-Specific Frequencies and Functions Across the Domains of Life
Enhancement of Transport Selectivity through Nano-Channels by Non-Specific Competition
Efficient "Communication through Coherence" Requires Oscillations Structured to Minimize Interference between Signals
Highly Sensitive and Specific Detection of Rare Variants in Mixed Viral Populations from Massively Parallel Sequence Data
Negative feedback may suppress variation to improve collective foraging performance
Reciprocal Regulation as a Source of Ultrasensitivity in Two-Component Systems with a Bifunctional Sensor Kinase
Systematic, network-based characterization of therapeutic target inhibitors
Genome Landscapes and Bacteriophage Codon Usage
Detecting shifts in nonlinear dynamics using Empirical Dynamic Modeling with Nested-Library Analysis
Brain signal predictions from multi-scale networks using a linearized framework
Chromatin-enriched RNAs mark active and repressive cis-regulation: An analysis of nuclear RNA-seq
NIBBS-Search for Fast and Accurate Prediction of Phenotype-Biased Metabolic Systems
Dissecting peripheral protein-membrane interfaces
Machine learning identification of Pseudomonas aeruginosa strains from colony image data
Lipid Receptor S1P 1 Activation Scheme Concluded from Microsecond All-Atom Molecular Dynamics Simulations
Avoiding the bullies: The resilience of cooperation among unequals
Diffusion model predicts the geometry of actin cytoskeleton from cell morphology
A Neurocomputational Model of Stimulus-Specific Adaptation to Oddball and Markov Sequences
Analysis of 11, 430 recombinant protein production experiments reveals that protein yield is tunable by synonymous codon changes of translation initiation sites
Testing Biochemistry Revisited: How In Vivo Metabolism Can Be Understood from In Vitro Enzyme Kinetics
Bat detective - Deep learning tools for bat acoustic signal detection
Quantifying the roles of vomiting, diarrhea, and residents vs. staff in norovirus transmission in U.S. nursing home outbreaks
Fitness models provide accurate short-term forecasts of SARS-CoV-2 variant frequency
Combining Experiments and Simulations Using the Maximum Entropy Principle
A new method for inferring timetrees from temporally sampled molecular sequences
Effects of FGFR2 kinase activation loop dynamics on catalytic activity
Fast and near-optimal monitoring for healthcare acquired infection outbreaks
Nonlinear Muscles, Passive Viscoelasticity and Body Taper Conspire To Create Neuromechanical Phase Lags in Anguilliform Swimmers
AutoDockFR : Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility
Simulation atomic force microscopy for atomic reconstruction of biomolecular structures from resolution-limited experimental images
An overview of bioinformatics courses delivered at the academic level in Italy: Reflections and recommendations from BITS
A Three-Threshold Learning Rule Approaches the Maximal Capacity of Recurrent Neural Networks
Exploring Off-Targets and Off-Systems for Adverse Drug Reactions via Chemical-Protein Interactome - Clozapine-Induced Agranulocytosis as a Case Study
Characterizing the Transmission Potential of Zoonotic Infections from Minor Outbreaks
Ten simple rules for succeeding as an underrepresented STEM undergraduate
Sparse Coding Can Predict Primary Visual Cortex Receptive Field Changes Induced by Abnormal Visual Input
Circadian distribution of epileptiform discharges in epilepsy: Candidate mechanisms of variability
Nonoptimal Component Placement, but Short Processing Paths, due to Long-Distance Projections in Neural Systems
Correction: Facilitating the propagation of spiking activity in feedforward networks by including feedback
Scrutinizing MHC-I Binding Peptides and Their Limits of Variation
Perceptual clustering in auditory streaming
Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web
Systematic perturbation of an artificial neural network: A step towards quantifying causal contributions in the brain
Testing Whether Humans Have an Accurate Model of Their Own Motor Uncertainty in a Speeded Reaching Task
Behavioral Sequence Analysis Reveals a Novel Role for ß2* Nicotinic Receptors in Exploration
Acute Effects of Sex Steroid Hormones on Susceptibility to Cardiac Arrhythmias: A Simulation Study
Learning the sequence of influenza A genome assembly during viral replication using point process models and fluorescence in situ hybridization
A functional theory of bistable perception based on dynamical circular inference
Representing high throughput expression profiles via perturbation barcodes reveals compound targets
Controlling microbial co-culture based on substrate pulsing can lead to stability through differential fitness advantages
150 Years of the Mass Action Law
A structural dynamics model for how CPEB3 binding to SUMO2 can regulate translational control in dendritic spines
BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities
Dark-matter matters: Discriminating subtle blood cancers using the darkest DNA
Connectome-based biophysical models of pathological protein spreading in neurodegenerative diseases
Accurate prediction of kinase-substrate networks using knowledge graphs
Podbat: A Novel Genomic Tool Reveals Swr1-Independent H2A.Z Incorporation at Gene Coding Sequences through Epigenetic Meta-Analysis
Vision-based collective motion: A locust-inspired reductionist model
SmartPhase: Accurate and fast phasing of heterozygous variant pairs for genetic diagnosis of rare diseases
A Model of the Spatio-temporal Dynamics of Drosophila Eye Disc Development
Co-evolutionary Dynamics of Collective Action with Signaling for a Quorum
Quantifying Spike Train Oscillations: Biases, Distortions and Solutions
Robust switches in thalamic network activity require a timescale separation between sodium and T-type calcium channel activations
MobsPy: A programming language for biochemical reaction networks
Interplay of Gene Expression Noise and Ultrasensitive Dynamics Affects Bacterial Operon Organization
Inferring transmission heterogeneity using virus genealogies: Estimation and targeted prevention
Human behavioral complexity peaks at age 25
Dynamic Change of Global and Local Information Processing in Propofol-Induced Loss and Recovery of Consciousness
Universal risk phenotype of US counties for flu-like transmission to improve county-specific COVID-19 incidence forecasts
Polymodal allosteric regulation of Type 1 Serine/Threonine Kinase Receptors via a conserved electrostatic lock
Determinants of early afterdepolarization properties in ventricular myocyte models
Contrasting factors associated with COVID-19-related ICU admission and death outcomes in hospitalised patients by means of Shapley values
EpiBeds: Data informed modelling of the COVID-19 hospital burden in England
A new model for simultaneous dimensionality reduction and time-varying functional connectivity estimation
The evolutionary origins of Lévy walk foraging
Behavioural Contagion Explains Group Cohesion in a Social Crustacean
Mathematical model of a personalized neoantigen cancer vaccine and the human immune system
Simplified internal models in human control of complex objects
Dynamic Reweighting of Auditory Modulation Filters
Striking Similarities in the Genomic Distribution of Tandemly Arrayed Genes in Arabidopsis and Rice
ASPASIA: A toolkit for evaluating the effects of biological interventions on SBML model behaviour
Model based planners reflect on their model-free propensities
An Ovol2-Zeb1 Mutual Inhibitory Circuit Governs Bidirectional and Multi-step Transition between Epithelial and Mesenchymal States
Improving Breast Cancer Survival Analysis through Competition-Based Multidimensional Modeling
Computational Predictions Provide Insights into the Biology of TAL Effector Target Sites
Learning to synchronize: How biological agents can couple neural task modules for dealing with the stability-plasticity dilemma
Dynamic Changes in Subgraph Preference Profiles of Crucial Transcription Factors
Systematic identification of phosphorylation-mediated protein interaction switches
An image-computable model of human visual shape similarity
Geometry of the Gene Expression Space of Individual Cells
Inferring TF activation order in time series scRNA-Seq studies
Novel travel time aware metapopulation models and multi-layer waning immunity for late-phase epidemic and endemic scenarios
Scedar: A scalable Python package for single-cell RNA-seq exploratory data analysis
Spatially distributed infection increases viral load in a computational model of SARS-CoV-2 lung infection
Exploring of the feature space of de novo developed post-transcriptional riboregulators
Ten simple rules for improving research data discovery
Protein Molecular Function Prediction by Bayesian Phylogenomics
Dynamic Allostery in the Methionine Repressor Revealed by Force Distribution Analysis
Numerical knockouts-In silico assessment of factors predisposing to thoracic aortic aneurysms