yusuke1997/dblp-id-title huggingface dataset:
Autoencoder based local T cell repertoire density can be used to classify samples and T cell receptors
A mixture of sparse coding models explaining properties of face neurons related to holistic and parts-based processing
Passive Dendrites Enable Single Neurons to Compute Linearly Non-separable Functions
Speed of phototransduction in the microvillus regulates the accuracy and bandwidth of the rhabdomeric photoreceptor
Gambling in the Visual Periphery: A Conjoint-Measurement Analysis of Human Ability to Judge Visual Uncertainty
Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud
Ion Channel Density Regulates Switches between Regular and Fast Spiking in Soma but Not in Axons
PPARα siRNA-Treated Expression Profiles Uncover the Causal Sufficiency Network for Compound-Induced Liver Hypertrophy
Control of Ca2+ Influx and Calmodulin Activation by SK-Channels in Dendritic Spines
The hydrophobic effect characterises the thermodynamic signature of amyloid fibril growth
Functional Genomics Complements Quantitative Genetics in Identifying Disease-Gene Associations
A graph-based evidence synthesis approach to detecting outbreak clusters: An application to dog rabies
Brightness and Darkness as Perceptual Dimensions
Multidimensional analysis of immune responses identified biomarkers of recent Mycobacterium tuberculosis infection
No Evidence for an Item Limit in Change Detection
MitoTNT: Mitochondrial Temporal Network Tracking for 4D live-cell fluorescence microscopy data
Extracting multi-way chromatin contacts from Hi-C data
Dependence of Bacterial Chemotaxis on Gradient Shape and Adaptation Rate
Shape Similarity, Better than Semantic Membership, Accounts for the Structure of Visual Object Representations in a Population of Monkey Inferotemporal Neurons
Three types of remapping with linear decoders: A population-geometric perspective
Unravelling the γ-butyrolactone network in Streptomyces coelicolor by computational ensemble modelling
Novel Developmental Analyses Identify Longitudinal Patterns of Early Gut Microbiota that Affect Infant Growth
Building a mechanistic mathematical model of hepatitis C virus entry
Partially Glycosylated Dendrimers Block MD-2 and Prevent TLR4-MD-2-LPS Complex Mediated Cytokine Responses
A Dynamic View of Domain-Motif Interactions
Formation and Dynamics of Waves in a Cortical Model of Cholinergic Modulation
Differences in Reactivation of Tuberculosis Induced from Anti-TNF Treatments Are Based on Bioavailability in Granulomatous Tissue
Estimating neuronal firing density: A quantitative analysis of firing rate map algorithms
Ten Simple Rules for Graduate Students
Correction: Quantification of nematic cell polarity in three-dimensional tissues
A computational model for angular velocity integration in a locust heading circuit
Maximally efficient prediction in the early fly visual system may support evasive flight maneuvers
Oncodomains: A protein domain-centric framework for analyzing rare variants in tumor samples
Evolution of interface binding strengths in simplified model of protein quaternary structure
Energy landscapes of peptide-MHC binding
Personalized brain stimulation for effective neurointervention across participants
A General Shear-Dependent Model for Thrombus Formation
Trade-off between Positive and Negative Design of Protein Stability: From Lattice Models to Real Proteins
Ten simple rules for attending your first conference
Drug-Induced Regulation of Target Expression
Genesis of the αβ T-cell receptor
Deciphering Interactions in Moving Animal Groups
Extracellular loops of BtuB facilitate transport of vitamin B12 through the outer membrane of E. coli
Proportionality: A Valid Alternative to Correlation for Relative Data
Simulation of angiogenesis in three dimensions: Application to cerebral cortex
Silent Synapses, LTP, and the Indirect Parallel-Fibre Pathway: Computational Consequences of Optimal Cerebellar Noise-Processing
Molecular source attribution
Directed migration shapes cooperation in spatial ecological public goods games
Realistic modeling of mesoscopic ephaptic coupling in the human brain
Balanced Excitatory and Inhibitory Synaptic Currents Promote Efficient Coding and Metabolic Efficiency
Computer Simulation of Cellular Patterning Within the Drosophila Pupal Eye
Manifold transform by recurrent cortical circuit enhances robust encoding of familiar stimuli
XDream: Finding preferred stimuli for visual neurons using generative networks and gradient-free optimization
In vitro-in silico correlation of three-dimensional turbulent flows in an idealized mouth-throat model
Correction: Grey-box modeling and hypothesis testing of functional near-infrared spectroscopy-based cerebrovascular reactivity to anodal high-definition tDCS in healthy humans
Essential Plasticity and Redundancy of Metabolism Unveiled by Synthetic Lethality Analysis
IOCBIO Kinetics: An open-source software solution for analysis of data traces
Effective Harmonic Potentials: Insights into the Internal Cooperativity and Sequence-Specificity of Protein Dynamics
A theoretical single-parameter model for urbanisation to study infectious disease spread and interventions
Weak electric fields promote resonance in neuronal spiking activity: Analytical results from two-compartment cell and network models
Enhancer Responses to Similarly Distributed Antagonistic Gradients in Development
ISCB Honors David Haussler and Aviv Regev
A Dynamical Systems Hypothesis of Schizophrenia
Transcriptome-wide root causal inference
Punishment and inspection for governing the commons in a feedback-evolving game
Investigate channel rectifications and neural dynamics by an electrodiffusive Gauss-Nernst-Planck approach
Role of genetic heterogeneity in determining the epidemiological severity of H1N1 influenza
Trade-off between local transmission and long-range dispersal drives infectious disease outbreak size in spatially structured populations
Learning How to Run a Lab: Interviews with Principal Investigators
Modeling the Amplification Dynamics of Human Alu Retrotransposons
Molecular Mechanics of the α-Actinin Rod Domain: Bending, Torsional, and Extensional Behavior
Age density patterns in patients medical conditions: A clustering approach
The intrinsically disordered N-terminus of the voltage-dependent anion channel
On the role of extrinsic noise in microRNA-mediated bimodal gene expression
Learning "graph-mer" Motifs that Predict Gene Expression Trajectories in Development
Biomolecular Events in Cancer Revealed by Attractor Metagenes
Cell cycle time series gene expression data encoded as cyclic attractors in Hopfield systems
Mutational signature dynamics indicate SARS-CoV-2's evolutionary capacity is driven by host antiviral molecules
Neural Network Mechanisms Underlying Stimulus Driven Variability Reduction
Discovering cis- Regulatory RNAs in Shewanella Genomes by Support Vector Machines
Sustained Firing of Model Central Auditory Neurons Yields a Discriminative Spectro-temporal Representation for Natural Sounds
Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli
The Structural Basis of ATP as an Allosteric Modulator
Stabilization of diastolic calcium signal via calcium pump regulation of complex local calcium releases and transient decay in a computational model of cardiac pacemaker cell with individual release channels
Being noisy in a crowd: Differential selective pressure on gene expression noise in model gene regulatory networks
Automated visualization of rule-based models
Significance of trends in gait dynamics
Designing a Nanotube Using Naturally Occurring Protein Building Blocks
Modeling influenza seasonality in the tropics and subtropics
A Primer on Metagenomics
Ribavirin-Induced Anemia in Hepatitis C Virus Patients Undergoing Combination Therapy
Evolution of the F 0 F 1 ATP Synthase Complex in Light of the Patchy Distribution of Different Bioenergetic Pathways across Prokaryotes
The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum
Decoding the language of microbiomes using word-embedding techniques, and applications in inflammatory bowel disease
Charting the spatial dynamics of early SARS-CoV-2 transmission in Washington state
Toward a Census of Bacteria in Soil
Fast Coding of Orientation in Primary Visual Cortex
Longitudinal wastewater sampling in buildings reveals temporal dynamics of metabolites
The Maximum Entropy Fallacy Redux?
Enhanced perfusion following exposure to radiotherapy: A theoretical investigation
A bio-mimetic miniature drone for real-time audio based short-range tracking
An exact method for quantifying the reliability of end-of-epidemic declarations in real time
Bayesian identification of differentially expressed isoforms using a novel joint model of RNA-seq data
Evolution at 'Sutures' and 'Centers': Recombination Can Aid Adaptation of Spatially Structured Populations on Rugged Fitness Landscapes
Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences
Integrating deep learning with microfluidics for biophysical classification of sickle red blood cells adhered to laminin
Axonal Noise as a Source of Synaptic Variability
Agent-Based Model of Therapeutic Adipose-Derived Stromal Cell Trafficking during Ischemia Predicts Ability To Roll on P-Selectin
The Morphological Identity of Insect Dendrites
The number of active metabolic pathways is bounded by the number of cellular constraints at maximal metabolic rates
Ten simple rules towards healthier research labs
Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors
Brain Rhythms Reveal a Hierarchical Network Organization
Integrating AlphaFold2 models and clinical data to improve the assessment of Short Linear Motifs (SLiMs) and their variants' pathogenicity
Drug Discovery Using Chemical Systems Biology: Repositioning the Safe Medicine Comtan to Treat Multi-Drug and Extensively Drug Resistant Tuberculosis
Prediction of Amyloidogenic and Disordered Regions in Protein Chains
Modulation of antigen discrimination by duration of immune contacts in a kinetic proofreading model of T cell activation with extreme statistics
Model-Free Reconstruction of Excitatory Neuronal Connectivity from Calcium Imaging Signals
A systematic machine learning and data type comparison yields metagenomic predictors of infant age, sex, breastfeeding, antibiotic usage, country of origin, and delivery type
Predictive model identifies key network regulators of cardiomyocyte mechano-signaling
Testing the limits of gradient sensing
Stabilizing patterns in time: Neural network approach
Modeling visual-based pitch, lift and speed control strategies in hoverflies
A Reaction-Diffusion Model of ROS-Induced ROS Release in a Mitochondrial Network
The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data
Ten simple rules to make your computing more environmentally sustainable
Force variability is mostly not motor noise: Theoretical implications for motor control
From kill the winner to eliminate the winner in open phage-bacteria systems
The effect of non-linear signal in classification problems using gene expression
A Cervid Vocal Fold Model Suggests Greater Glottal Efficiency in Calling at High Frequencies
Positive Evolutionary Selection of an HD Motif on Alzheimer Precursor Protein Orthologues Suggests a Functional Role
PanoView: An iterative clustering method for single-cell RNA sequencing data
A kinetic model of the central carbon metabolism for acrylic acid production in Escherichia coli
BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data
Optimal density of bacterial cells
Orchard: Building large cancer phylogenies using stochastic combinatorial search
Prediction of Human Disease Genes by Human-Mouse Conserved Coexpression Analysis
Reinforcement learning when your life depends on it: A neuro-economic theory of learning
Robust pleiotropy-decomposed polygenic scores identify distinct contributions to elevated coronary artery disease polygenic risk
A spatio-temporal model to reveal oscillator phenotypes in molecular clocks: Parameter estimation elucidates circadian gene transcription dynamics in single-cells
Determinants of combination GM-CSF immunotherapy and oncolytic virotherapy success identified through in silico treatment personalization
Capturing continuous, long timescale behavioral changes in Drosophila melanogaster postural data
Time-dependent computational model of post-traumatic osteoarthritis to estimate how mechanoinflammatory mechanisms impact cartilage aggrecan content
Transcription Factor Map Alignment of Promoter Regions
PLoS Computational Biology Conference Postcards from ISMB/ECCB 2011
Multi-scale approaches for high-speed imaging and analysis of large neural populations
Genome-Wide Identification of Human Functional DNA Using a Neutral Indel Model
A computational framework for the morpho-elastic development of molluskan shells by surface and volume growth
Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments
Evolution of Resistance to Targeted Anti-Cancer Therapies during Continuous and Pulsed Administration Strategies
Dual STDP processes at Purkinje cells contribute to distinct improvements in accuracy and speed of saccadic eye movements
Investigating the deregulation of metabolic tasks via Minimum Network Enrichment Analysis (MiNEA) as applied to nonalcoholic fatty liver disease using mouse and human omics data
Grasping Objects with Environmentally Induced Position Uncertainty
Ten simple rules for short and swift presentations
Predicting neuronal firing from calcium imaging using a control theoretic approach
A General Framework for Thermodynamically Consistent Parameterization and Efficient Sampling of Enzymatic Reactions
The Effect of Heterogeneity on Invasion in Spatial Epidemics: From Theory to Experimental Evidence in a Model System
A Proposal for a Coordinated Effort for the Determination of Brainwide Neuroanatomical Connectivity in Model Organisms at a Mesoscopic Scale
From ideal to practical: Heterogeneity of student-generated variant lists highlights hidden reproducibility gaps
Hybrid Equation/Agent-Based Model of Ischemia-Induced Hyperemia and Pressure Ulcer Formation Predicts Greater Propensity to Ulcerate in Subjects with Spinal Cord Injury
Dilution and titration of cell-cycle regulators may control cell size in budding yeast
Ten simple rules for teaching an introduction to R
Brain Anatomical Network and Intelligence
The Dynamics of T-Cell Receptor Repertoire Diversity Following Thymus Transplantation for DiGeorge Anomaly
International Society for Computational Biology Honors David Eisenberg with 2013 Accomplishment by a Senior Scientist Award
Multi-scale simulations of the T cell receptor reveal its lipid interactions, dynamics and the arrangement of its cytoplasmic region
Human Visual Search Does Not Maximize the Post-Saccadic Probability of Identifying Targets
ECOD: An Evolutionary Classification of Protein Domains
Performance of early warning signals for disease re-emergence: A case study on COVID-19 data
Decipher the Mechanisms of Protein Conformational Changes Induced by Nucleotide Binding through Free-Energy Landscape Analysis: ATP Binding to Hsp70
The Role of Incoherent MicroRNA-Mediated Feedforward Loops in Noise Buffering
Temporal pattern separation in hippocampal neurons through multiplexed neural codes
Post-transcriptional regulation across human tissues
Inference of Genotype-Phenotype Relationships in the Antigenic Evolution of Human Influenza A (H3N2) Viruses
Identifying Malaria Transmission Foci for Elimination Using Human Mobility Data
Mathematical modelling of the antibiotic-induced morphological transition of Pseudomonas aeruginosa
Invasion and effective size of graph-structured populations
Mathematical Modelling of DNA Replication Reveals a Trade-off between Coherence of Origin Activation and Robustness against Rereplication
The Interaction between Vector Life History and Short Vector Life in Vector-Borne Disease Transmission and Control
An ensemble forecast system for tracking dynamics of dengue outbreaks and its validation in China
Federated learning for COVID-19 mortality prediction in a multicentric sample of 21 hospitals
Multiscale Simulations Suggest a Mechanism for the Association of the Dok7 PH Domain with PIP-Containing Membranes
Predictability of Evolutionary Trajectories in Fitness Landscapes
A numerical framework for mechano-regulated tendon healing - Simulation of early regeneration of the Achilles tendon
Predicting Binding to P-Glycoprotein by Flexible Receptor Docking
Circuits and mechanisms for TMS-induced corticospinal waves: Connecting sensitivity analysis to the network graph
Allocating limited surveillance effort for outbreak detection of endemic foot and mouth disease
Conformational Coupling between Receptor and Kinase Binding Sites through a Conserved Salt Bridge in a Signaling Complex Scaffold Protein
Structural and energetic profiling of SARS-CoV-2 receptor binding domain antibody recognition and the impact of circulating variants
Novel mRNA-specific effects of ribosome drop-off on translation rate and polysome profile
Universal Pacemaker of Genome Evolution
Ensemble-Based Computational Approach Discriminates Functional Activity of p53 Cancer and Rescue Mutants
From "What Is?" to "What Isn't?" Computational Biology
Spectrally specific temporal analyses of spike-train responses to complex sounds: A unifying framework
Recall DNA methylation levels at low coverage sites using a CNN model in WGBS
Foraging in a non-foraging task: Fitness maximization explains human risk preference dynamics under changing environment
Spike Correlations in a Songbird Agree with a Simple Markov Population Model
Migration of small ligands in globins: Xe diffusion in truncated hemoglobin N
Contrasting mechanisms for hidden hearing loss: Synaptopathy vs myelin defects
Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density
Webb Miller and Trey Ideker To Receive Top International Bioinformatics Awards for 2009 from the International Society for Computational Biology
The limitations, dangers, and benefits of simple methods for testing identifiability
Identification of the Proliferation/Differentiation Switch in the Cellular Network of Multicellular Organisms
Structure of Protein Interaction Networks and Their Implications on Drug Design
Intrinsically Disordered Regions May Lower the Hydration Free Energy in Proteins: A Case Study of Nudix Hydrolase in the Bacterium Deinococcus radiodurans
How To Record a Million Synaptic Weights in a Hippocampal Slice
Phase Transitions in the Multi-cellular Regulatory Behavior of Pancreatic Islet Excitability
Chapter 13: Mining Electronic Health Records in the Genomics Era
The role of spatial structure in the evolution of viral innate immunity evasion: A diffusion-reaction cellular automaton model
Sensing and Integration of Erk and PI3K Signals by Myc
A machine learning pipeline for classification of cetacean echolocation clicks in large underwater acoustic datasets
Mathematical properties of optimal fluxes in cellular reaction networks at balanced growth
C-reactive protein upregulates the whole blood expression of CD59 - an integrative analysis
Biodiversity is enhanced by sequential resource utilization and environmental fluctuations via emergent temporal niches
Robust transmission of rate coding in the inhibitory Purkinje cell to cerebellar nuclei pathway in awake mice
Under-Dominance Constrains the Evolution of Negative Autoregulation in Diploids
Explicit Kinetic Heterogeneity: Mathematical Models for Interpretation of Deuterium Labeling of Heterogeneous Cell Populations
Mathematical modeling of the microtubule detyrosination/tyrosination cycle for cell-based drug screening design
RNA covariation at helix-level resolution for the identification of evolutionarily conserved RNA structure
Random Wiring, Ganglion Cell Mosaics, and the Functional Architecture of the Visual Cortex
Virus-host interactions predictor (VHIP): Machine learning approach to resolve microbial virus-host interaction networks
Incorporating networks in a probabilistic graphical model to find drivers for complex human diseases
Call detail record aggregation methodology impacts infectious disease models informed by human mobility
OpenABM-Covid19 - An agent-based model for non-pharmaceutical interventions against COVID-19 including contact tracing
Oscillations in working memory and neural binding: A mechanism for multiple memories and their interactions
Statistics of correlated percolation in a bacterial community
Ten simple rules to make the most out of your undergraduate research career
What can we learn when fitting a simple telegraph model to a complex gene expression model?
A whole-task brain model of associative recognition that accounts for human behavior and neuroimaging data
Asymmetric and transient properties of reciprocal activity of antagonists during the paw-shake response in the cat
Genetic Correlations Greatly Increase Mutational Robustness and Can Both Reduce and Enhance Evolvability
An Emerging Allee Effect Is Critical for Tumor Initiation and Persistence
From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints
Shadow enhancers mediate trade-offs between transcriptional noise and fidelity
Correcting motion induced fluorescence artifacts in two-channel neural imaging
Ten simple rules for teaching yourself R
A Coarse-Grained Elastic Network Atom Contact Model and Its Use in the Simulation of Protein Dynamics and the Prediction of the Effect of Mutations
LTS and FS Inhibitory Interneurons, Short-Term Synaptic Plasticity, and Cortical Circuit Dynamics
Bayesian phylodynamic inference with complex models
Lipid Clustering Correlates with Membrane Curvature as Revealed by Molecular Simulations of Complex Lipid Bilayers
A Network Model to Describe the Terminal Differentiation of B Cells
PhyloGibbs-MP: Module Prediction and Discriminative Motif-Finding by Gibbs Sampling
Relations between large-scale brain connectivity and effects of regional stimulation depend on collective dynamical state
Modeling the impact of xenointoxication in dogs to halt Trypanosoma cruzi transmission
Computational Model of the Insect Pheromone Transduction Cascade
Stochastically Gating Ion Channels Enable Patterned Spike Firing through Activity-Dependent Modulation of Spike Probability
PEDF, a pleiotropic WTC-LI biomarker: Machine learning biomarker identification and validation
Finding, visualizing, and quantifying latent structure across diverse animal vocal repertoires
Human decision making anticipates future performance in motor learning
Neurally Encoding Time for Olfactory Navigation
Bacteria-Human Somatic Cell Lateral Gene Transfer Is Enriched in Cancer Samples
Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm
Optimising age coverage of seasonal influenza vaccination in England: A mathematical and health economic evaluation
The impact of local assembly rules on RNA packaging in a T = 1 satellite plant virus
Galaxy-ML: An accessible, reproducible, and scalable machine learning toolkit for biomedicine
Twelve quick steps for genome assembly and annotation in the classroom
Inferring Visuomotor Priors for Sensorimotor Learning
Large benefits to youth-focused HIV treatment-as-prevention efforts in generalized heterosexual populations: An agent-based simulation model
Identifying parameter regions for multistationarity
Viral escape-inspired framework for structure-guided dual bait protein biosensor design
Prioritizing Genomic Drug Targets in Pathogens: Application to Mycobacterium tuberculosis
Functional Alignment of Regulatory Networks: A Study of Temperate Phages
Chapter 1: Biomedical Knowledge Integration
Influence of surprise on reinforcement learning in younger and older adults
Cooperativity Dominates the Genomic Organization of p53-Response Elements: A Mechanistic View
A Simulated Intermediate State for Folding and Aggregation Provides Insights into ΔN6 β 2 -Microglobulin Amyloidogenic Behavior