yusuke1997/dblp-id-title huggingface dataset:
Observing others give & take: A computational account of bystanders' feelings and actions
Flux Balance Analysis of Mycolic Acid Pathway: Targets for Anti-Tubercular Drugs
Firing rate homeostasis counteracts changes in stability of recurrent neural networks caused by synapse loss in Alzheimer's disease
Optimal control of multiple myeloma assuming drug resistance and off-target effects
Recombulator-X: A fast and user-friendly tool for estimating X chromosome recombination rates in forensic genetics
DARPP-32 Is a Robust Integrator of Dopamine and Glutamate Signals
The Genomic Pattern of tDNA Operon Expression in E. coli
Accessible High-Throughput Virtual Screening Molecular Docking Software for Students and Educators
Estimating Relative Changes of Metabolic Fluxes
Feedback Loops of the Mammalian Circadian Clock Constitute Repressilator
A Systems Approach Uncovers Restrictions for Signal Interactions Regulating Genome-wide Responses to Nutritional Cues in Arabidopsis
Parameter estimation in a whole-brain network model of epilepsy: Comparison of parallel global optimization solvers
Optimal Prediction of Moving Sound Source Direction in the Owl
SurvivalPath:A R package for conducting personalized survival path mapping based on time-series survival data
Spatial transcriptome-guided multi-scale framework connects P. aeruginosa metabolic states to oxidative stress biofilm microenvironment
Patterns of Proliferative Activity in the Colonic Crypt Determine Crypt Stability and Rates of Somatic Evolution
Phylogenetic Dependency Networks: Inferring Patterns of CTL Escape and Codon Covariation in HIV-1 Gag
Deep convolutional networks do not classify based on global object shape
Meta-control of social learning strategies
Evidence of a Double-Lid Movement in Pseudomonas aeruginosa Lipase: Insights from Molecular Dynamics Simulations
Unsupervised Learning of Visual Features through Spike Timing Dependent Plasticity
EMULSION: Transparent and flexible multiscale stochastic models in human, animal and plant epidemiology
Near-random connections support top-down feature-based attentional modulations in early sensory cortex
Estimating epidemiological parameters from experiments in vector access to host plants, the method of matching gradients
HiSV: A control-free method for structural variation detection from Hi-C data
OmniSegger: A time-lapse image analysis pipeline for bacterial cells
Estimating Time of Infection Using Prior Serological and Individual Information Can Greatly Improve Incidence Estimation of Human and Wildlife Infections
Identification of Genome-Scale Metabolic Network Models Using Experimentally Measured Flux Profiles
Augmenting Microarray Data with Literature-Based Knowledge to Enhance Gene Regulatory Network Inference
The Evolution of Two-Component Systems in Bacteria Reveals Different Strategies for Niche Adaptation
Barriers to Cooperation Aid Ideological Rigidity and Threaten Societal Collapse
Correction: A model for the origin and development of visual orientation selectivity
Cellular morphodynamics as quantifiers for functional states of resident tissue macrophages in vivo
A unified model library maps how neuromodulation reshapes the excitability landscape of neurons across the brain
Comprehensive computational modelling of the development of mammalian cortical connectivity underlying an architectonic type principle
RosettaSurf - A surface-centric computational design approach
Expansion of Protein Domain Repeats
Improved prediction of smoking status via isoform-aware RNA-seq deep learning models
Nano-motion Dynamics are Determined by Surface-Tethered Selectin Mechanokinetics and Bond Formation
Stealth Proteins: In Silico Identification of a Novel Protein Family Rendering Bacterial Pathogens Invisible to Host Immune Defense
Mathematical models of tissue stem and transit target cell divisions and the risk of radiation- or smoking-associated cancer
Small subpopulations of β-cells do not drive islet oscillatory [Ca2+] dynamics via gap junction communication
Correction: Minimal model of interictal and ictal discharges "Epileptor-2"
Decoding Structural Properties of a Partially Unfolded Protein Substrate: En Route to Chaperone Binding
Transmission Selects for HIV-1 Strains of Intermediate Virulence: A Modelling Approach
NEMix: Single-cell Nested Effects Models for Probabilistic Pathway Stimulation
Modeling the role of the thalamus in resting-state functional connectivity: Nature or structure
Estimation of temporal covariances in pathogen dynamics using Bayesian multivariate autoregressive models
Capsule networks as recurrent models of grouping and segmentation
Ten Simple Rules for Organizing a Virtual Conference - Anywhere
Exploring Early Stages of the Chemical Unfolding of Proteins at the Proteome Scale
The Mechanistic Basis of Myxococcus xanthus Rippling Behavior and Its Physiological Role during Predation
On the effect of phylogenetic correlations in coevolution-based contact prediction in proteins
Increased T cell trafficking as adjunct therapy for HIV-1
Information-theoretic analyses of neural data to minimize the effect of researchers' assumptions in predictive coding studies
Cooperation of dual modes of cell motility promotes epithelial stress relaxation to accelerate wound healing
Canard analysis reveals why a large Ca2+ window current promotes early afterdepolarizations in cardiac myocytes
CATHEDRAL: A Fast and Effective Algorithm to Predict Folds and Domain Boundaries from Multidomain Protein Structures
Spike-Threshold Adaptation Predicted by Membrane Potential Dynamics In Vivo
Exploring the Universe of Protein Structures beyond the Protein Data Bank
Clonal heterogeneity and antigenic stimulation shape persistence of the latent reservoir of HIV
Cortically-Controlled Population Stochastic Facilitation as a Plausible Substrate for Guiding Sensory Transfer across the Thalamic Gateway
Ten simple rules for leading a successful undergraduate-intensive research lab
Dynamic metabolic modeling of heterotrophic and mixotrophic microalgal growth on fermentative wastes
Structural Properties of the Caenorhabditis elegans Neuronal Network
A Computational and Experimental Study of the Regulatory Mechanisms of the Complement System
A Quick Guide for Computer-Assisted Instruction in Computational Biology and Bioinformatics
From Escherichia coli mutant 13C labeling data to a core kinetic model: A kinetic model parameterization pipeline
Physical constraints on accuracy and persistence during breast cancer cell chemotaxis
Induced Effects of Sodium Ions on Dopaminergic G-Protein Coupled Receptors
A history-dependent approach for accurate initial condition estimation in epidemic models
A mechanistic, stigmergy model of territory formation in solitary animals: Territorial behavior can dampen disease prevalence but increase persistence
Characterization and Identification of MicroRNA Core Promoters in Four Model Species
Modeling the diverse effects of divisive normalization on noise correlations
Physical modeling of ribosomes along messenger RNA: Estimating kinetic parameters from ribosome profiling experiments using a ballistic model
Ten simple rules to improve academic work-life balance
VarSCAT: A computational tool for sequence context annotations of genomic variants
Correction: Environmental Statistics and Optimal Regulation
A Simple Iterative Model Accurately Captures Complex Trapline Formation by Bumblebees Across Spatial Scales and Flower Arrangements
Inferring Regulatory Networks from Experimental Morphological Phenotypes: A Computational Method Reverse-Engineers Planarian Regeneration
Ten simple rules for managing laboratory information
Locations and structures of influenza A virus packaging-associated signals and other functional elements via an in silico pipeline for predicting constrained features in RNA viruses
Multiscale modelling of desquamation in the interfollicular epidermis
Diversity Waves in Collapse-Driven Population Dynamics
Trained recurrent neural networks develop phase-locked limit cycles in a working memory task
Mathematical Model for Length Control by the Timing of Substrate Switching in the Type III Secretion System
Experimentally guided computational antibody affinity maturation with de novo docking, modelling and rational design
Oscillation-Induced Signal Transmission and Gating in Neural Circuits
Integrative Multi-omics Module Network Inference with Lemon-Tree
Characterizing Dynamic Changes in the Human Blood Transcriptional Network
How Protein Stability and New Functions Trade Off
Leveraging Hypoxia-Activated Prodrugs to Prevent Drug Resistance in Solid Tumors
Identifying human diamine sensors for death related putrescine and cadaverine molecules
Human Cancer Protein-Protein Interaction Network: A Structural Perspective
Probing the Flexibility of Large Conformational Changes in Protein Structures through Local Perturbations
An electrodiffusive, ion conserving Pinsky-Rinzel model with homeostatic mechanisms
From correlation to causation: Estimating effective connectivity from zero-lag covariances of brain signals
Integrated Stochastic Model of DNA Damage Repair by Non-homologous End Joining and p53/p21- Mediated Early Senescence Signalling
Inference of Transmission Network Structure from HIV Phylogenetic Trees
Stimulus-choice (mis)alignment in primate area MT
Stochastic Differential Equation Model for Cerebellar Granule Cell Excitability
Cooperation Prevails When Individuals Adjust Their Social Ties
Combined Evidence Annotation of Transposable Elements in Genome Sequences
Dynamic Control of Selectivity in the Ubiquitination Pathway Revealed by an ASP to GLU Substitution in an Intra-Molecular Salt-Bridge Network
GrowMatch: An Automated Method for Reconciling In Silico / In Vivo Growth Predictions
Leadership and Path Characteristics during Walks Are Linked to Dominance Order and Individual Traits in Dogs
Emergence of the Mitochondrial Reticulum from Fission and Fusion Dynamics
Modelling the mechanics of exploration in larval Drosophila
A Quantitative Model of Transcriptional Regulation Reveals the Influence of Binding Location on Expression
Efficient Partitioning of Memory Systems and Its Importance for Memory Consolidation
Rare-event sampling analysis uncovers the fitness landscape of the genetic code
Whole genomes define concordance of matched primary, xenograft, and organoid models of pancreas cancer
Unified feature association networks through integration of transcriptomic and proteomic data
Analysis of localized cAMP perturbations within a tissue reveal the effects of a local, dynamic gap junction state on ERK signaling
An Exploration of the Universe of Polyglutamine Structures
Distributed Dynamical Computation in Neural Circuits with Propagating Coherent Activity Patterns
Positive and Negative Design in Stability and Thermal Adaptation of Natural Proteins
The Potential Role of Direct and Indirect Contacts on Infection Spread in Dairy Farm Networks
Nonlinear visuoauditory integration in the mouse superior colliculus
High-Performance Drug Discovery: Computational Screening by Combining Docking and Molecular Dynamics Simulations
Ten Simple Rules for Finishing Your PhD
Individualised aspiration dynamics: Calculation by proofs
Toward a 3D model of phyllotaxis based on a biochemically plausible auxin-transport mechanism
Interspecific comparison of gene expression profiles using machine learning
Pyranose Dehydrogenase Ligand Promiscuity: A Generalized Approach to Simulate Monosaccharide Solvation, Binding, and Product Formation
Tuning Promoter Strength through RNA Polymerase Binding Site Design in Escherichia coli
Heterodimer-heterotetramer formation mediates enhanced sensor activity in a biophysical model for BMP signaling
Mechanisms for dysregulation of excitatory-inhibitory balance underlying allodynia in dorsal horn neural subcircuits
DeepGenePrior: A deep learning model for prioritizing genes affected by copy number variants
A new paradigm considering multicellular adhesion, repulsion and attraction represent diverse cellular tile patterns
This Déjà Vu Feeling - Analysis of Multidomain Protein Evolution in Eukaryotic Genomes
Fusing an agent-based model of mosquito population dynamics with a statistical reconstruction of spatio-temporal abundance patterns
Bringing bioinformatics to schools with the 4273pi project
MetaNovo: An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets
Variation in plastic responses to light results from selection in different competitive environments - A game theoretical approach using virtual plants
Joint modeling of choices and reaction times based on Bayesian contextual behavioral control
Applying a GAN-based classifier to improve transcriptome-based prognostication in breast cancer
Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response
RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestion
GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training
Quantifying Chaperone-Mediated Transitions in the Proteostasis Network of E. coli
Measuring impact of vaccination among wildlife: The case of bait vaccine campaigns for classical swine fever epidemic among wild boar in Japan
An Optimal Free Energy Dissipation Strategy of the MinCDE Oscillator in Regulating Symmetric Bacterial Cell Division
Optimality Conditions for Cell-Fate Heterogeneity That Maximize the Effects of Growth Factors in PC12 Cells
Machine and deep learning meet genome-scale metabolic modeling
Structural Evolution of the Protein Kinase-Like Superfamily
Traveling Pulses for a Two-Species Chemotaxis Model
A novel batch-effect correction method for scRNA-seq data based on Adversarial Information Factorization
Growth and adaptation mechanisms of tumour spheroids with time-dependent oxygen availability
Noise Management by Molecular Networks
Estimating short-term synaptic plasticity from pre- and postsynaptic spiking
Ten simple rules for developing good reading habits during graduate school and beyond
The geometric evolution of aortic dissections: Predicting surgical success using fluctuations in integrated Gaussian curvature
Ten Simple Rules for Running Interactive Workshops
Dynamic decomposition of spatiotemporal neural signals
Experimental and Computational Analysis of a Large Protein Network That Controls Fat Storage Reveals the Design Principles of a Signaling Network
An efficient and flexible framework for inferring global sensitivity of agent-based model parameters
COPS: A novel platform for multi-omic disease subtype discovery via robust multi-objective evaluation of clustering algorithms
Balance between asymmetry and abundance in multi-domain DNA-binding proteins may regulate the kinetics of their binding to DNA
High CO2 adaptation mechanisms revealed in the miR156-regulated flowering time pathway
SimPep and OP-AND: A deep learning framework and curated database for predicting osteogenic peptides
Large self-assembled clathrin lattices spontaneously disassemble without sufficient adaptor proteins
Deciphering the regulation of P2X4 receptor channel gating by ivermectin using Markov models
Identifying Causal Genes and Dysregulated Pathways in Complex Diseases
From spikes to intercellular waves: Tuning intercellular calcium signaling dynamics modulates organ size control
Validated Predictions of Metabolic Energy Consumption for Submaximal Effort Movement
Diffusive mediator feedbacks control the health-to-disease transition of skin inflammation
Accurate Prediction of Peptide Binding Sites on Protein Surfaces
The evolutionary dynamics of metabolic protocells
The Thalidomide-Binding Domain of Cereblon Defines the CULT Domain Family and Is a New Member of the β-Tent Fold
WORMHOLE: Novel Least Diverged Ortholog Prediction through Machine Learning
Scalable nonlinear programming framework for parameter estimation in dynamic biological system models
Model-Based Evaluation of Spontaneous Tumor Regression in Pilocytic Astrocytoma
Traditional Biomolecular Structure Determination by NMR Spectroscopy Allows for Major Errors
Modelling plant disease spread and containment: Simulation and approximate Bayesian Computation for Xylella fastidiosa in Puglia, Italy
Transcriptional Regulation of Lineage Commitment - A Stochastic Model of Cell Fate Decisions
Optimizing Metabolite Production Using Periodic Oscillations
Transmission delays and frequency detuning can regulate information flow between brain regions
Epidemiological and health economic implications of symptom propagation in respiratory pathogens: A mathematical modelling investigation
Differential regulatory network-based quantification and prioritization of key genes underlying cancer drug resistance based on time-course RNA-seq data
Novel non-invasive algorithm to identify the origins of re-entry and ectopic foci in the atria from 64-lead ECGs: A computational study
Ten simple rules to make computable knowledge shareable and reusable
Transcriptional Regulation by Competing Transcription Factor Modules
Splicing-aware scRNA-Seq resolution reveals execution-ready programs in effector Tregs
NullSeq: A Tool for Generating Random Coding Sequences with Desired Amino Acid and GC Contents
A joint modeling approach for longitudinal microbiome data improves ability to detect microbiome associations with disease
Targeting operational regimes of interest in recurrent neural networks
Structural spine plasticity: Learning and forgetting of odor-specific subnetworks in the olfactory bulb
MDHGI: Matrix Decomposition and Heterogeneous Graph Inference for miRNA-disease association prediction
A multi-layer mean-field model of the cerebellum embedding microstructure and population-specific dynamics
Asymmetric and adaptive reward coding via normalized reinforcement learning
Molecular Predictors of 3D Morphogenesis by Breast Cancer Cell Lines in 3D Culture
Adaptive proximity to criticality underlies amplification of ultra-slow fluctuations during free recall
Packaging contests between viral RNA molecules and kinetic selectivity
Quantitative Predictions of Peptide Binding to Any HLA-DR Molecule of Known Sequence: NetMHCIIpan
Eleven quick tips for data cleaning and feature engineering
Topological descriptors of the parameter region of multistationarity: Deciding upon connectivity
A Markov chain for numerical chromosomal instability in clonally expanding populations
Bacteria use structural imperfect mimicry to hijack the host interactome
Scalable workflow for characterization of cell-cell communication in COVID-19 patients
Model-based analysis of competing-endogenous pathways (MACPath) in human cancers
Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data
SPINDLE: End-to-end learning from EEG/EMG to extrapolate animal sleep scoring across experimental settings, labs and species
Decreasing-Rate Pruning Optimizes the Construction of Efficient and Robust Distributed Networks
Simulating the Mammalian Blastocyst - Molecular and Mechanical Interactions Pattern the Embryo
There are no equal opportunity infectors: Epidemiological modelers must rethink our approach to inequality in infection risk
Collective Learning and Optimal Consensus Decisions in Social Animal Groups
Simulation insights on the compound action potential in multifascicular nerves
Addressing delayed case reporting in infectious disease forecast modeling
Spatiotemporal Expression Control Correlates with Intragenic Scaffold Matrix Attachment Regions (S/MARs) in Arabidopsis thaliana
Information theoretic evidence for layer- and frequency-specific changes in cortical information processing under anesthesia
Networks of High Mutual Information Define the Structural Proximity of Catalytic Sites: Implications for Catalytic Residue Identification
Hub connectivity, neuronal diversity, and gene expression in the Caenorhabditis elegans connectome
Substrate-Specific Reorganization of the Conformational Ensemble of CSK Implicates Novel Modes of Kinase Function
Uncovering the impact of infection routes on within-host MPXV dynamics: Insights from a mathematical modeling study
Bipartite Community Structure of eQTLs
Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast
Calcium Wave Propagation in Networks of Endothelial Cells: Model-based Theoretical and Experimental Study
Modeling the Impact of Lesions in the Human Brain
Correction: Critical role of deadenylation in regulating poly(A) rhythms and circadian gene expression
Classification of bursting patterns: A tale of two ducks
Escherichia coli Peptidoglycan Structure and Mechanics as Predicted by Atomic-Scale Simulations
Functional Impact of Missense Variants in BRCA1 Predicted by Supervised Learning
Integrating Antimicrobial Therapy with Host Immunity to Fight Drug-Resistant Infections: Classical vs. Adaptive Treatment
Gene Expression Variability within and between Human Populations and Implications toward Disease Susceptibility
Full scale structural, mechanical and dynamical properties of HIV-1 liposomes
The Upside of Failure: How Regional Student Groups Learn from Their Mistakes
Evolution of Intra-specific Regulatory Networks in a Multipartite Bacterial Genome
Mutualism provides a basis for biodiversity in eco-evolutionary community assembly
Elastic Energy Storage and Radial Forces in the Myofilament Lattice Depend on Sarcomere Length
Functional hierarchies in brain dynamics characterized by signal reversibility in ferret cortex
Generalizing population RT-qPCR cycle threshold values-informed estimation of epidemiological dynamics: Impact of surveillance practices and pathogen variability
Morphological Transformation and Force Generation of Active Cytoskeletal Networks
International Society for Computational Biology Welcomes Its Newest Class of Fellows
Quantification of hypoxic regions distant from occlusions in cerebral penetrating arteriole trees
A mathematical model of calcium dynamics in HSY cells
Timing the Emergence of Resistance to Anti-HIV Drugs with Large Genetic Barriers
Robust Unidirectional Airflow through Avian Lungs: New Insights from a Piecewise Linear Mathematical Model
Impact of School Cycles and Environmental Forcing on the Timing of Pandemic Influenza Activity in Mexican States, May-December 2009
Mathematical Model of Viral Kinetics In Vitro Estimates the Number of E2-CD81 Complexes Necessary for Hepatitis C Virus Entry
Advancing code sharing in the computational biology community
Sparse Distributed Representation of Odors in a Large-scale Olfactory Bulb Circuit
Limited Agreement of Independent RNAi Screens for Virus-Required Host Genes Owes More to False-Negative than False-Positive Factors
Slow diffusive dynamics in a chaotic balanced neural network
GRAFIMO: Variant and haplotype aware motif scanning on pangenome graphs
AI reveals insights into link between CD33 and cognitive impairment in Alzheimer's Disease
Point-estimating observer models for latent cause detection
Graphia: A platform for the graph-based visualisation and analysis of high dimensional data
Estimating the Fitness Cost of Escape from HLA Presentation in HIV-1 Protease and Reverse Transcriptase
Mathematical modelling reveals unexpected inheritance and variability patterns of cell cycle parameters in mammalian cells
Transcriptomic correlates of neuron electrophysiological diversity
Getting Started in Biological Pathway Construction and Analysis
Computational Analysis of Mouse piRNA Sequence and Biogenesis
Precision in a rush: Trade-offs between reproducibility and steepness of the hunchback expression pattern
Investigating Homology between Proteins using Energetic Profiles
Ten simple rules for supporting historically underrepresented students in science
Heterogeneous Network Edge Prediction: A Data Integration Approach to Prioritize Disease-Associated Genes
Envelope reconstruction of speech and music highlights stronger tracking of speech at low frequencies
Power-Law Inter-Spike Interval Distributions Infer a Conditional Maximization of Entropy in Cortical Neurons
How Merkel cells transduce mechanical stimuli: A biophysical model of Merkel cells
DeepG4: A deep learning approach to predict cell-type specific active G-quadruplex regions