yusuke1997/dblp-id-title huggingface dataset:
Compressive stress gradients direct mechanoregulation of anisotropic growth in the zebrafish jaw joint
Structural Insights into the Inhibition of Actin-Capping Protein by Interactions with Phosphatidic Acid and Phosphatidylinositol (4, 5)-Bisphosphate
Multi-Population Classical HLA Type Imputation
Excitatory and inhibitory effects of HCN channel modulation on excitability of layer V pyramidal cells
LAP: Liability Antibody Profiler by sequence & structural mapping of natural and therapeutic antibodies
A comprehensive computational model of animal biosonar signal processing
New methods for computational decomposition of whole-mount in situ images enable effective curation of a large, highly redundant collection of Xenopus images
Multitask learning of a biophysically-detailed neuron model
Fast uncertainty quantification for dynamic flux balance analysis using non-smooth polynomial chaos expansions
Dynamic Simulations on the Arachidonic Acid Metabolic Network
Boolean model of growth signaling, cell cycle and apoptosis predicts the molecular mechanism of aberrant cell cycle progression driven by hyperactive PI3K
Sequence features of viral and human Internal Ribosome Entry Sites predictive of their activity
Temporal Adaptation Enhances Efficient Contrast Gain Control on Natural Images
Current Practice in Software Development for Computational Neuroscience and How to Improve It
Self-regulation strategy, feedback timing and hemodynamic properties modulate learning in a simulated fMRI neurofeedback environment
Cell-type-specific firing patterns in a V1 cortical column model depend on feedforward and feedback-driven states
Membrane Mechanics of Endocytosis in Cells with Turgor
Biphasic effects on human atrial arrhythmogenicity of L-type calcium channel mutations associated with a Brugada/Short QT overlap syndrome - insights from a multiscale simulation study
F-BIAS: Towards a distributed national core facility for bioimage analysis †
Art in Science Competition invites artworks to the annual exhibition on ISMB 2018 in Chicago
Computational Models of the Notch Network Elucidate Mechanisms of Context-dependent Signaling
Neighbor-Dependent Ramachandran Probability Distributions of Amino Acids Developed from a Hierarchical Dirichlet Process Model
A linear perception-action mapping accounts for response range-dependent biases in heading estimation from optic flow
Fine-grained, nonlinear registration of live cell movies reveals spatiotemporal organization of diffuse molecular processes
Activity in Inferior Parietal and Medial Prefrontal Cortex Signals the Accumulation of Evidence in a Probability Learning Task
Ten Simple Rules for Reproducible Computational Research
InteracTor: Feature engineering and explainable AI for profiling protein structure-interaction-function relationships
Proteome Sampling by the HLA Class I Antigen Processing Pathway
FluTE, a Publicly Available Stochastic Influenza Epidemic Simulation Model
A novel network control model for identifying personalized driver genes in cancer
Electric Imaging through Evolution, a Modeling Study of Commonalities and Differences
Uncovering Interactions in the Frequency Domain
Depth-dependent flow and pressure characteristics in cortical microvascular networks
Comparison of REST Cistromes across Human Cell Types Reveals Common and Context-Specific Functions
Transcriptome Profiling of Giardia intestinalis Using Strand-specific RNA-Seq
Computing with Neural Synchrony
Simulation and Theory of Antibody Binding to Crowded Antigen-Covered Surfaces
Understanding patient-derived tumor organoid growth through an integrated imaging and mathematical modeling framework
The impact of sparsity in low-rank recurrent neural networks
Bayesian calibration of a stochastic, multiscale agent-based model for predicting in vitro tumor growth
Network topology metrics explaining enrichment of hybrid epithelial/mesenchymal phenotypes in metastasis
Optimization hardness constrains ecological transients
Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities
Autonomous Targeting of Infectious Superspreaders Using Engineered Transmissible Therapies
Reconciling high-throughput gene essentiality data with metabolic network reconstructions
A Minimal Model of Metabolism-Based Chemotaxis
Correction: PPM-Decay: A computational model of auditory prediction with memory decay
Genome Majority Vote Improves Gene Predictions
Interactions between calmodulin and neurogranin govern the dynamics of CaMKII as a leaky integrator
Improved Prediction of Non-methylated Islands in Vertebrates Highlights Different Characteristic Sequence Patterns
Shared spatiotemporal category representations in biological and artificial deep neural networks
LncRNAs of Saccharomyces cerevisiae bypass the cell cycle arrest imposed by ethanol stress
Probing neural networks for dynamic switches of communication pathways
Network-assisted target identification for haploinsufficiency and homozygous profiling screens
Heat Shock Response in CHO Mammalian Cells Is Controlled by a Nonlinear Stochastic Process
Correction: The contribution of the basal ganglia and cerebellum to motor learning: A neuro-computational approach
Chemotaxis Receptor Complexes: From Signaling to Assembly
Inferring gene regulatory networks using transcriptional profiles as dynamical attractors
Cost-efficient vaccination protocols for network epidemiology
Detecting Key Structural Features within Highly Recombined Genes
Annealed Importance Sampling for Neural Mass Models
Atlases of cognition with large-scale human brain mapping
Genetic Selection for Context-Dependent Stochastic Phenotypes: Sp1 and TATA Mutations Increase Phenotypic Noise in HIV-1 Gene Expression
A machine learning and network framework to discover new indications for small molecules
CAncer bioMarker Prediction Pipeline (CAMPP) - A standardized framework for the analysis of quantitative biological data
CHOmics: A web-based tool for multi-omics data analysis and interactive visualization in CHO cell lines
Approximate Bayesian estimation of coevolutionary arms races
Why Genes Evolve Faster on Secondary Chromosomes in Bacteria
Correlations from structure and phylogeny combine constructively in the inference of protein partners from sequences
Denoising diffusion probabilistic models for generation of realistic fully-annotated microscopy image datasets
Optimal anti-amyloid-beta therapy for Alzheimer's disease via a personalized mathematical model
scBoolSeq: Linking scRNA-seq statistics and Boolean dynamics
Deterministic response strategies in a trial-and-error learning task
Prediction of cccDNA dynamics in hepatitis B patients by a combination of serum surrogate markers
CystiHuman: A model of human neurocysticercosis
Frequency-Invariant Representation of Interaural Time Differences in Mammals
Accuracy of real-time multi-model ensemble forecasts for seasonal influenza in the U.S
Two stages of bandwidth scaling drives efficient neural coding of natural sounds
Bounded rational decision-making models suggest capacity-limited concurrent motor planning in human posterior parietal and frontal cortex
Loregic: A Method to Characterize the Cooperative Logic of Regulatory Factors
One Size Doesn't Fit All - RefEditor: Building Personalized Diploid Reference Genome to Improve Read Mapping and Genotype Calling in Next Generation Sequencing Studies
Sampling the Solution Space in Genome-Scale Metabolic Networks Reveals Transcriptional Regulation in Key Enzymes
Structural Modeling of Protein Interactions by Analogy: Application to PSD-95
Correction: SDImpute: A statistical block imputation method based on cell-level and gene-level information for dropouts in single-cell RNA-seq data
A data-driven approach for constructing mutation categories for mutational signature analysis
NeKo: A tool for automatic network construction from prior knowledge
PreMLS: The undersampling technique based on ClusterCentroids to predict multiple lysine sites
Unsupervised Feature Learning Improves Prediction of Human Brain Activity in Response to Natural Images
Interplay of Intrinsic and Synaptic Conductances in the Generation of High-Frequency Oscillations in Interneuronal Networks with Irregular Spiking
The dynamics of motor learning through the formation of internal models
Flux Balance Analysis of Cyanobacterial Metabolism: The Metabolic Network of Synechocystis sp. PCC 6803
An in vitro quantitative systems pharmacology approach for deconvolving mechanisms of drug-induced, multilineage cytopenias
Structure Modeling of All Identified G Protein-Coupled Receptors in the Human Genome
Improved estimation of time-varying reproduction numbers at low case incidence and between epidemic waves
Ras Conformational Switching: Simulating Nucleotide-Dependent Conformational Transitions with Accelerated Molecular Dynamics
Steady-state approximations for Hodgkin-Huxley cell models: Reduction of order for uterine smooth muscle cell model
Metabolic Network Topology Reveals Transcriptional Regulatory Signatures of Type 2 Diabetes
Variation in the geometry of concept manifolds across human visual cortex
Stochasticity, Bistability and the Wisdom of Crowds: A Model for Associative Learning in Genetic Regulatory Networks
Resolving Structural Variability in Network Models and the Brain
Dynamic Changes in Protein Functional Linkage Networks Revealed by Integration with Gene Expression Data
Unveiling Time in Dose-Response Models to Infer Host Susceptibility to Pathogens
Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale
DetEdit: A graphical user interface for annotating and editing events detected in long-term acoustic monitoring data
Tumor immune cell clustering and its association with survival in African American women with ovarian cancer
Supervised learning and model analysis with compositional data
Methods detecting rhythmic gene expression are biologically relevant only for strong signal
Magnitude-sensitive reaction times reveal non-linear time costs in multi-alternative decision-making
Refractoriness in Sustained Visuo-Manual Control: Is the Refractory Duration Intrinsic or Does It Depend on External System Properties?
Alterations in Brain Connectivity Underlying Beta Oscillations in Parkinsonism
Interaction of the Antimicrobial Peptide Polymyxin B1 with Both Membranes of E . coli : A Molecular Dynamics Study
Bringing Molecules Back into Molecular Evolution
McComedy: A user-friendly tool for next-generation individual-based modeling of microbial consumer-resource systems
On the Origins of Suboptimality in Human Probabilistic Inference
Perturbation Variability Does Not Influence Implicit Sensorimotor Adaptation
BMDD: A probabilistic framework for accurate imputation of zero-inflated microbiome sequencing data
Theoretical perspectives on central chemosensitivity: CO2/H+-sensitive neurons in the locus coeruleus
Ten simple rules for organizing a webinar series
Evolutionary Dynamics on Protein Bi-stability Landscapes can Potentially Resolve Adaptive Conflicts
Senescent Cells in Growing Tumors: Population Dynamics and Cancer Stem Cells
Parasites Sustain and Enhance RNA-Like Replicators through Spatial Self-Organisation
Benchmarking multi-ancestry prostate cancer polygenic risk scores in a real-world cohort
Ab Initio Modeling of the Herpesvirus VP26 Core Domain Assessed by CryoEM Density
A Comprehensive Benchmark of Kernel Methods to Extract Protein-Protein Interactions from Literature
2017 ISCB Accomplishment by a Senior Scientist Award given to Pavel Pevzner
Maps of variability in cell lineage trees
Linking Microscopic Spatial Patterns of Tissue Destruction in Emphysema to Macroscopic Decline in Stiffness Using a 3D Computational Model
Topological state-space estimation of functional human brain networks
A Computational Analysis of ATP Binding of SV40 Large Tumor Antigen Helicase Motor
Adaptation supports short-term memory in a visual change detection task
Comparing mutational pathways to lopinavir resistance in HIV-1 subtypes B versus C
Protein-Protein Interaction Hotspots Carved into Sequences
CINner: Modeling and simulation of chromosomal instability in cancer at single-cell resolution
A fibrin enhanced thrombosis model for medical devices operating at low shear regimes or large surface areas
A data-driven interactome of synergistic genes improves network-based cancer outcome prediction
Multi-scale modelling of location- and frequency-dependent synaptic plasticity induced by repetitive magnetic stimulation in the dendrites of pyramidal neurons
A deep learning approach to real-time HIV outbreak detection using genetic data
A genome-wide comprehensive analysis of nucleosome positioning in yeast
How adaptive plasticity evolves when selected against
The Organization of Local and Distant Functional Connectivity in the Human Brain
Label-free deep learning-based species classification of bacteria imaged by phase-contrast microscopy
Bayesian integrative analysis of epigenomic and transcriptomic data identifies Alzheimer's disease candidate genes and networks
The Trigger Factor Chaperone Encapsulates and Stabilizes Partial Folds of Substrate Proteins
Electrodiffusion dynamics in the cardiomyocyte dyad at nano-scale resolution using the Poisson-Nernst-Planck (PNP) equations
Dose-to-Duration Encoding and Signaling beyond Saturation in Intracellular Signaling Networks
Can a time varying external drive give rise to apparent criticality in neural systems?
Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study
OpenABC enables flexible, simplified, and efficient GPU accelerated simulations of biomolecular condensates
Computational Lipidology: Predicting Lipoprotein Density Profiles in Human Blood Plasma
Model-based and phylogenetically adjusted quantification of metabolic interaction between microbial species
Phylogenetic inference of changes in amino acid propensities with single-position resolution
Evolution of a Signaling Nexus Constrained by Protein Interfaces and Conformational States
The role of oscillations in grid cells' toroidal topology
The interplay of SARS-CoV-2 evolution and constraints imposed by the structure and functionality of its proteins
A Computational Pipeline for High- Throughput Discovery of cis -Regulatory Noncoding RNA in Prokaryotes
Evaluating reproducibility of AI algorithms in digital pathology with DAPPER
Predicting Peptide Structures in Native Proteins from Physical Simulations of Fragments
NeuroML-DB: Sharing and characterizing data-driven neuroscience models described in NeuroML
The shadowing effect of initial expectation on learning asymmetry
Localized Lipid Packing of Transmembrane Domains Impedes Integrin Clustering
A Probabilistic Model to Predict Clinical Phenotypic Traits from Genome Sequencing
Active Vertex Model for cell-resolution description of epithelial tissue mechanics
Multilevel Selection in Models of Prebiotic Evolution II: A Direct Comparison of Compartmentalization and Spatial Self-Organization
Accounting for reporting delays in real-time phylodynamic analyses with preferential sampling
Modeling the Evolution of Regulatory Elements by Simultaneous Detection and Alignment with Phylogenetic Pair HMMs
SUMOFLUX: A Generalized Method for Targeted 13C Metabolic Flux Ratio Analysis
Computational design of improved standardized chemotherapy protocols for grade II oligodendrogliomas
Accurate cancer phenotype prediction with AKLIMATE, a stacked kernel learner integrating multimodal genomic data and pathway knowledge
Determinants of Beat-to-Beat Variability of Repolarization Duration in the Canine Ventricular Myocyte: A Computational Analysis
Organization of Physical Interactomes as Uncovered by Network Schemas
Mathematical Modeling of the Phoenix Rising Pathway
Protein-Protein Interactions More Conserved within Species than across Species
Tensor decomposition of multi-dimensional splicing events across multiple tissues to identify splicing-mediated risk genes associated with complex traits
Designing optimal allocations for cancer screening using queuing network models
From Spontaneous Motor Activity to Coordinated Behaviour: A Developmental Model
LabOps: A flexible self-hosted workflow of open source tools for efficient collaboration within research laboratories
Optimizing mitochondrial maintenance in extended neuronal projections
Dedicated transcriptomics combined with power analysis lead to functional understanding of genes with weak phenotypic changes in knockout lines
Recursive MAGUS: Scalable and accurate multiple sequence alignment
Geometric analysis enables biological insight from complex non-identifiable models using simple surrogates
SourceSet: A graphical model approach to identify primary genes in perturbed biological pathways
Segregation and Crosstalk of D1 Receptor-Mediated Activation of ERK in Striatal Medium Spiny Neurons upon Acute Administration of Psychostimulants
Comprehensively benchmarking applications for detecting copy number variation
Robust averaging protects decisions from noise in neural computations
Phenomenological Model for Predicting the Catabolic Potential of an Arbitrary Nutrient
Bilinearity in Spatiotemporal Integration of Synaptic Inputs
Long-Range Intra-Protein Communication Can Be Transmitted by Correlated Side-Chain Fluctuations Alone
A multi-approach and multi-scale platform to model CD4+ T cells responding to infections
Conformal prediction for uncertainty quantification in dynamic biological systems
UV-Induced Mutagenesis in Escherichia coli SOS Response: A Quantitative Model
Emergence of Spatial Structure in Cell Groups and the Evolution of Cooperation
Fragility of foot process morphology in kidney podocytes arises from chaotic spatial propagation of cytoskeletal instability
Predicting how and when hidden neurons skew measured synaptic interactions
RAINBOW: Haplotype-based genome-wide association study using a novel SNP-set method
Expanding the Druggable Space of the LSD1/CoREST Epigenetic Target: New Potential Binding Regions for Drug-Like Molecules, Peptides, Protein Partners, and Chromatin
Amino acid composition predicts prion activity
Computational Modeling, Formal Analysis, and Tools for Systems Biology
Cross-Over between Discrete and Continuous Protein Structure Space: Insights into Automatic Classification and Networks of Protein Structures
Dynamics of Mutant Cells in Hierarchical Organized Tissues
A transcriptome-based classifier to determine molecular subtypes in medulloblastoma
Missing data in amortized simulation-based neural posterior estimation
Bayesian Estimation of Mixture Models with Prespecified Elements to Compare Drug Resistance in Treatment-Naïve and Experienced Tuberculosis Cases
A Novel Computational Method Identifies Intra- and Inter-Species Recombination Events in Staphylococcus aureus and Streptococcus pneumoniae
Multiobjective optimization identifies cancer-selective combination therapies
Inferred expression regulator activities suggest genes mediating cardiometabolic genetic signals
Evolution of Self-Organized Task Specialization in Robot Swarms
Collective Dynamics Underlying Allosteric Transitions in Hemoglobin
Probabilistic transmission models incorporating sequencing data for healthcare-associated Clostridioides difficile outperform heuristic rules and identify strain-specific differences in transmission
Impact of Dendritic Size and Dendritic Topology on Burst Firing in Pyramidal Cells
In silico prediction of ARB resistance: A first step in creating personalized ARB therapy
How ecological feedbacks between human population and land cover influence sustainability
The Construction and Use of Log-Odds Substitution Scores for Multiple Sequence Alignment
Cheater suppression and stochastic clearance through quorum sensing
Mathematical analysis of robustness of oscillations in models of the mammalian circadian clock
Modelling the impact of vaccination on COVID-19 in African countries
Theoretical Model for Cellular Shapes Driven by Protrusive and Adhesive Forces
Dopamine encoding of novelty facilitates efficient uncertainty-driven exploration
Evolution of heterogeneous perceptual limits and indifference in competitive foraging
Model-based inference of cell cycle dynamics captures alterations of the DNA replication programme
Integrative modeling of diverse protein-peptide systems using CABS-dock
Getting Started in Gene Orthology and Functional Analysis
Comparing Algorithms That Reconstruct Cell Lineage Trees Utilizing Information on Microsatellite Mutations
Atomistic simulation of protein evolution reveals sequence covariation and time-dependent fluctuations of site-specific substitution rates
A computationally tractable birth-death model that combines phylogenetic and epidemiological data
Computing the Local Field Potential (LFP) from Integrate-and-Fire Network Models
Circadian Phase Resetting via Single and Multiple Control Targets
Structured environments foster competitor coexistence by manipulating interspecies interfaces
iPiDA-LTR: Identifying piwi-interacting RNA-disease associations based on Learning to Rank
Epigenetics Decouples Mutational from Environmental Robustness. Did It Also Facilitate Multicellularity?
Identification of allosteric inhibitors of the ecto-5'-nucleotidase (CD73) targeting the dimer interface
Binding pocket dynamics along the recovery stroke of human β-cardiac myosin
A hydro-osmotic coarsening theory of biological cavity formation
Identifying important parameters in the inflammatory process with a mathematical model of immune cell influx and macrophage polarization
Catecholaminergic Regulation of Learning Rate in a Dynamic Environment
Computational modeling suggests binding-induced expansion of Epsin disordered regions upon association with AP2
Ensemble Tractography
Inter-paralog amino acid inversion events in large phylogenies of duplicated proteins
meaRtools: An R package for the analysis of neuronal networks recorded on microelectrode arrays
A Sparse Coding Model with Synaptically Local Plasticity and Spiking Neurons Can Account for the Diverse Shapes of V1 Simple Cell Receptive Fields
Inferring Aggregated Functional Traits from Metagenomic Data Using Constrained Non-negative Matrix Factorization: Application to Fiber Degradation in the Human Gut Microbiota
Synthetic method of analogues for emerging infectious disease forecasting
Progression of Diabetic Capillary Occlusion: A Model
Ups and Downs of Poised RNA Polymerase II in B-Cells
A Generic Mechanism of Emergence of Amyloid Protofilaments from Disordered Oligomeric Aggregates
Task-Driven Activity Reduces the Cortical Activity Space of the Brain: Experiment and Whole-Brain Modeling
Radical pairs may explain reactive oxygen species-mediated effects of hypomagnetic field on neurogenesis
Liebig's law of the minimum in the TGF-β/SMAD pathway
From dawn till dusk: Time-adaptive bayesian optimization for neurostimulation
Effects of spatiotemporal HSV-2 lesion dynamics and antiviral treatment on the risk of HIV-1 acquisition
A benchmark-driven approach to reconstruct metabolic networks for studying cancer metabolism
Explaining the Determinants of First Phase HIV Decay Dynamics through the Effects of Stage-dependent Drug Action
Hierarchy and control of ageing-related methylation networks
Computational simulation of the reactive oxygen species and redox network in the regulation of chloroplast metabolism
Pulmonary drug delivery and retention: A computational study to identify plausible parameters based on a coupled airway-mucus flow model
Competing evolutionary paths in growing populations with applications to multidrug resistance
Maintaining a Cognitive Map in Darkness: The Need to Fuse Boundary Knowledge with Path Integration
Correlations and Functional Connections in a Population of Grid Cells
Population-level toggling of T cell immune escape at human leukocyte antigen anchor residues in SARS-CoV-2 Spike proteins, in an ethnically diverse population region
An optimal normalization method for high sparse compositional microbiome data
Ten simple rules for fostering creativity in research labs
A semi-automated algorithm for image analysis of respiratory organoids
Multi-Scale Modeling of HIV Infection in vitro and APOBEC3G-Based Anti-Retroviral Therapy
The limitations of phenotype prediction in metabolism