yusuke1997/dblp-id-title huggingface dataset:
Comprehensive Meta-analysis of Ontology Annotated 16S rRNA Profiles Identifies Beta Diversity Clusters of Environmental Bacterial Communities
Computationally Efficient Implementation of a Novel Algorithm for the General Unified Threshold Model of Survival (GUTS)
Unsupervised Learning of Cone Spectral Classes from Natural Images
Mindboggling morphometry of human brains
Bayesian inference of state feedback control parameters for fo perturbation responses in cerebellar ataxia
Integrative Approach to Pain Genetics Identifies Pain Sensitivity Loci across Diseases
Sensorimotor integration enhances temperature stimulus processing
AI-driven discovery of novel extracellular matrix biomarkers in pelvic organ prolapse
The Hydrophobic Temperature Dependence of Amino Acids Directly Calculated from Protein Structures
Extracting the fingerprints of sequences of random rhythmic auditory stimuli from electrophysiological data
Correction: All2: A tool for selecting mosaic mutations from comprehensive multi-cell comparisons
Eradication of Chronic Myeloid Leukemia Stem Cells: A Novel Mathematical Model Predicts No Therapeutic Benefit of Adding G-CSF to Imatinib
Exploring the inhibition mechanism of adenylyl cyclase type 5 by n-terminal myristoylated Gαi1
Structure learning for gene regulatory networks
Neural crest streaming as an emergent property of tissue interactions during morphogenesis
Likelihood-free nested sampling for parameter inference of biochemical reaction networks
Visual social information use in collective foraging
A Simple Histone Code Opens Many Paths to Epigenetics
Convex Clustering: An Attractive Alternative to Hierarchical Clustering
On convolutional neural networks for selection inference: Revealing the effect of preprocessing on model learning and the capacity to discover novel patterns
Signatures of neutral evolution in exponentially growing tumors: A theoretical perspective
scRNMF: An imputation method for single-cell RNA-seq data by robust and non-negative matrix factorization
Finding landmarks - An investigation of viewing behavior during spatial navigation in VR using a graph-theoretical analysis approach
Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes
It is theoretically possible to avoid misfolding into non-covalent lasso entanglements using small molecule drugs
Four guiding principles for effective trainee-led STEM community engagement through high school outreach
Optimizing strategies for slowing the spread of invasive species
How do (perceptual) distracters distract?
The primacy model and the structure of olfactory space
SUITOR: Selecting the number of mutational signatures through cross-validation
Detection and segmentation of morphologically complex eukaryotic cells in fluorescence microscopy images via feature pyramid fusion
Epigenetic regulation of cell fate reprogramming in aging and disease: A predictive computational model
Frequent Gain and Loss of Functional Transcription Factor Binding Sites
Distinguishing Antimicrobial Models with Different Resistance Mechanisms via Population Pharmacodynamic Modeling
Shape analysis of gamma rhythm supports a superlinear inhibitory regime in an inhibition-stabilized network
Metabolic plasticity in synthetic lethal mutants: Viability at higher cost
Modeling and Simulation of Mucus Flow in Human Bronchial Epithelial Cell Cultures - Part I: Idealized Axisymmetric Swirling Flow
Transforming the study of organisms: Phenomic data models and knowledge bases
Conformational Changes in Protein Loops and Helices Induced by Post-Translational Phosphorylation
Reversible and Noisy Progression towards a Commitment Point Enables Adaptable and Reliable Cellular Decision-Making
Fitting dynamic measles models to subnational case notification data from Ethiopia: Methodological challenges and key considerations
In silico co-factor balance estimation using constraint-based modelling informs metabolic engineering in Escherichia coli
Contrasting model mechanisms of alanine aminotransferase (ALT) release from damaged and necrotic hepatocytes as an example of general biomarker mechanisms
Inferring repeat-protein energetics from evolutionary information
Automated Discovery of Tissue-Targeting Enhancers and Transcription Factors from Binding Motif and Gene Function Data
Subunit promotion energies for channel opening in heterotetrameric olfactory CNG channels
Rapid memory encoding in a recurrent network model with behavioral time scale synaptic plasticity
Correction: Dynamic metabolic adaptation can promote species coexistence in competitive microbial communities
Neural mechanisms of flexible perceptual inference
The genome-scale metabolic model for the purple non-sulfur bacterium Rhodopseudomonas palustris Bis A53 accurately predicts phenotypes under chemoheterotrophic, chemoautotrophic, photoheterotrophic, and photoautotrophic growth conditions
Early Characterization of the Severity and Transmissibility of Pandemic Influenza Using Clinical Episode Data from Multiple Populations
Stochastic neural field model of stimulus-dependent variability in cortical neurons
Network analysis of toxin production in Clostridioides difficile identifies key metabolic dependencies
Strong association between genomic 3D structure and CRISPR cleavage efficiency
Identification of pathways associated with chemosensitivity through network embedding
A mathematical model of flagellar gene regulation and construction in Salmonella enterica
Software for Computing and Annotating Genomic Ranges
Entrainment of the Mammalian Cell Cycle by the Circadian Clock: Modeling Two Coupled Cellular Rhythms
Embedding optimization reveals long-lasting history dependence in neural spiking activity
A dual graph neural network for drug-drug interactions prediction based on molecular structure and interactions
Fourteen quick tips for crowdsourcing geographically linked data for public health advocacy
Impact on backpropagation of the spatial heterogeneity of sodium channel kinetics in the axon initial segment
Nanoscale organization of ryanodine receptor distribution and phosphorylation pattern determines the dynamics of calcium sparks
Biomedical Data Commons (BMDC) prioritizes B-lymphocyte non-coding genetic variants in Type 1 Diabetes
Neurobiological Models of Two-Choice Decision Making Can Be Reduced to a One-Dimensional Nonlinear Diffusion Equation
Ten simple rules for surviving an interdisciplinary PhD
A unitary mechanism underlies adaptation to both local and global environmental statistics in time perception
A Mathematical Model for Neutrophil Gradient Sensing and Polarization
Red Queen Processes Drive Positive Selection on Major Histocompatibility Complex (MHC) Genes
Whole-cell modeling of E. coli colonies enables quantification of single-cell heterogeneity in antibiotic responses
Inferring ongoing cancer evolution from single tumour biopsies using synthetic supervised learning
Energy Landscape Reveals That the Budding Yeast Cell Cycle Is a Robust and Adaptive Multi-stage Process
Stress-induced mutagenesis: Stress diversity facilitates the persistence of mutator genes
Immunization strategies in networks with missing data
Improved gene regulatory network inference from single cell data with dropout augmentation
Assessing the Nature of Lipid Raft Membranes
Comparative RNA-seq Analysis in the Unsequenced Axolotl: The Oncogene Burst Highlights Early Gene Expression in the Blastema
Identification of Constrained Cancer Driver Genes Based on Mutation Timing
Insights into the dynamic trajectories of protein filament division revealed by numerical investigation into the mathematical model of pure fragmentation
Constraint-Based Modeling of Carbon Fixation and the Energetics of Electron Transfer in Geobacter metallireducens
Near Equilibrium Calculus of Stem Cells in Application to the Airway Epithelium Lineage
Ten quick tips for protecting health data using de-identification and perturbation of structured datasets
End-to-end sequence-structure-function meta-learning predicts genome-wide chemical-protein interactions for dark proteins
Quantitative Analysis of Cell Nucleus Organisation
Predicting regrowth of low-grade gliomas after radiotherapy
On measuring selection in cancer from subclonal mutation frequencies
OpenSim: Simulating musculoskeletal dynamics and neuromuscular control to study human and animal movement
A Covering Method for Detecting Genetic Associations between Rare Variants and Common Phenotypes
Hebbian learning with elasticity explains how the spontaneous motor tempo affects music performance synchronization
Scaffolding the cup-shaped double membrane in autophagy
Contrasting the impact of cytotoxic and cytostatic drug therapies on tumour progression
An extended and generalized framework for the calculation of metabolic intervention strategies based on minimal cut sets
Dynamics of adaptive immunity against phage in bacterial populations
Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties
Temporal dynamics of a CSF1R signaling gene regulatory network involved in epilepsy
Multi-Scale Simulations Provide Supporting Evidence for the Hypothesis of Intramolecular Protein Translocation in GroEL/GroES Complexes
The Fate of Cooperation during Range Expansions
Multiscale Modeling of Red Blood Cell Mechanics and Blood Flow in Malaria
Ten simple rules for navigating the computational aspect of an interdisciplinary PhD
A Petri Net Model of Granulomatous Inflammation: Implications for IL-10 Mediated Control of Leishmania donovani Infection
How the storage effect and the number of temporal niches affect biodiversity in stochastic and seasonal environments
A Robust Actin Filaments Image Analysis Framework
Disentangling and modeling interactions in fish with burst-and-coast swimming reveal distinct alignment and attraction behaviors
Inference and design of antibody specificity: From experiments to models and back
An integrative network approach for longitudinal stratification in Parkinson's disease
Single Sample Expression-Anchored Mechanisms Predict Survival in Head and Neck Cancer
Using virtual patient cohorts to uncover immune response differences in cancer and immunosuppressed COVID-19 patients
Building momentum: A computational account of persistence toward long-term goals
Differences in boundary behavior in the 3D vertex and Voronoi models
Automated C. elegans behavior analysis via deep learning-based detection and tracking
Frequency spectrum of chemical fluctuation: A probe of reaction mechanism and dynamics
Functional Characterization of Transcription Factor Motifs Using Cross-species Comparison across Large Evolutionary Distances
Mechanobiological model for simulation of injured cartilage degradation via pro-inflammatory cytokines and mechanical stimulus
Data-driven analysis of fine-scale badger movement in the UK
Reduced model to predict thrombin and fibrin during thrombosis on collagen/tissue factor under venous flow: Roles of γ'-fibrin and factor XIa
Age-Dependent Evolution of the Yeast Protein Interaction Network Suggests a Limited Role of Gene Duplication and Divergence
The C. elegans Connectome Consists of Homogenous Circuits with Defined Functional Roles
2014 ISCB Accomplishment by a Senior Scientist Award: Gene Myers
A Detailed History of Intron-rich Eukaryotic Ancestors Inferred from a Global Survey of 100 Complete Genomes
Immersed Boundary Models for Quantifying Flow-Induced Mechanical Stimuli on Stem Cells Seeded on 3D Scaffolds in Perfusion Bioreactors
Combined multiplex panel test results are a poor estimate of disease prevalence without adjustment for test error
Reduced level of docosahexaenoic acid shifts GPCR neuroreceptors to less ordered membrane regions
Gene regulation by a protein translation factor at the single-cell level
Group testing as a strategy for COVID-19 epidemiological monitoring and community surveillance
Crawling and Gliding: A Computational Model for Shape-Driven Cell Migration
Human online adaptation to changes in prior probability
A hierarchical process model links behavioral aging and lifespan in C. elegans
Spatial Metrics of Tumour Vascular Organisation Predict Radiation Efficacy in a Computational Model
A probabilistic model for the ultradian timing of REM sleep in mice
Agent-based model predicts that layered structure and 3D movement work synergistically to reduce bacterial load in 3D in vitro models of tuberculosis granuloma
Genetic drift and selection in many-allele range expansions
The Making of the Women in Biology Forum (WiB) at Bioclues
Time-series modeling of epidemics in complex populations: Detecting changes in incidence volatility over time
Restricted N-glycan Conformational Space in the PDB and Its Implication in Glycan Structure Modeling
Increased decision thresholds enhance information gathering performance in juvenile Obsessive-Compulsive Disorder (OCD)
Auditory Frequency and Intensity Discrimination Explained Using a Cortical Population Rate Code
Predicting mean ribosome load for 5'UTR of any length using deep learning
Innate Immunity and the Inter-exposure Interval Determine the Dynamics of Secondary Influenza Virus Infection and Explain Observed Viral Hierarchies
Porcupine: A visual pipeline tool for neuroimaging analysis
The kinetic landscape of nucleosome assembly: A coarse-grained molecular dynamics study
ORN: Inferring patient-specific dysregulation status of pathway modules in cancer with OR-gate Network
Mesoscopic description of hippocampal replay and metastability in spiking neural networks with short-term plasticity
Appropriate relaxation of non-pharmaceutical interventions minimizes the risk of a resurgence in SARS-CoV-2 infections in spite of the Delta variant
Clusternomics: Integrative context-dependent clustering for heterogeneous datasets
An AP Endonuclease 1-DNA Polymerase β Complex: Theoretical Prediction of Interacting Surfaces
APP Is a Context-Sensitive Regulator of the Hippocampal Presynaptic Active Zone
Parallel synapses with transmission nonlinearities enhance neuronal classification capacity
Inferring Hypotheses on Functional Relationships of Genes: Analysis of the Arabidopsis thaliana Subtilase Gene Family
Recurrence risk stratification of hepatocellular carcinomas based on immune gene expression and features extracted from pathological images
Identifying the Rules of Engagement Enabling Leukocyte Rolling, Activation, and Adhesion
Circadian Clocks Are Resounding in Peripheral Tissues
On the Origins and Control of Community Types in the Human Microbiome
An information theoretic treatment of sequence-to-expression modeling
Universal features of dendrites through centripetal branch ordering
A stochastic and dynamical view of pluripotency in mouse embryonic stem cells
Hybrid modeling and prediction of dynamical systems
Dynamic Modelling under Uncertainty: The Case of Trypanosoma brucei Energy Metabolism
Crossing Borders for Science
Identifying Cognate Binding Pairs among a Large Set of Paralogs: The Case of PE/PPE Proteins of Mycobacterium tuberculosis
Combinatorial Clustering of Residue Position Subsets Predicts Inhibitor Affinity across the Human Kinome
Nonlinear effects of intrinsic dynamics on temporal encoding in a model of avian auditory cortex
Modelling interference between vectors of non-persistently transmitted plant viruses to identify effective control strategies
The quantitative basis for the redistribution of immobile bacterial lipoproteins to division septa
Radial Frequency Analysis of Contour Shapes in the Visual Cortex
Communication over the Network of Binary Switches Regulates the Activation of A 2A Adenosine Receptor
Integrating across neuroimaging modalities boosts prediction accuracy of cognitive ability
Multiple Estimates of Transmissibility for the 2009 Influenza Pandemic Based on Influenza-like-Illness Data from Small US Military Populations
Modeling Structure-Function Relationships in Synthetic DNA Sequences using Attribute Grammars
Inferring the ancestry of parents and grandparents from genetic data
The Amino Acid Alphabet and the Architecture of the Protein Sequence-Structure Map. I. Binary Alphabets
A Bayesian Model of Category-Specific Emotional Brain Responses
Intricate Knots in Proteins: Function and Evolution
The eBioKit, a stand-alone educational platform for bioinformatics
Robust point-process Granger causality analysis in presence of exogenous temporal modulations and trial-by-trial variability in spike trains
Differential roles of sleep spindles and sleep slow oscillations in memory consolidation
Quantifying the impact of COVID-19 control measures using a Bayesian model of physical distancing
Replicability of bulk RNA-Seq differential expression and enrichment analysis results for small cohort sizes
Modeling the dynamics of oligodendrocyte precursor cells and the genesis of gliomas
Ten Simple Rules To Combine Teaching and Research
Predicting cryptic links in host-parasite networks
Correction: Decoding the language of microbiomes using word-embedding techniques, and applications in inflammatory bowel disease
GPRuler: Metabolic gene-protein-reaction rules automatic reconstruction
Influence of Rotational Nucleosome Positioning on Transcription Start Site Selection in Animal Promoters
Phylogenies from dynamic networks
Patient groups in Rheumatoid arthritis identified by deep learning respond differently to biologic or targeted synthetic DMARDs
Pushing Structural Information into the Yeast Interactome by High-Throughput Protein Docking Experiments
Predicting therapeutic drugs for hepatocellular carcinoma based on tissue-specific pathways
A computational approach to distinguish somatic vs. germline origin of genomic alterations from deep sequencing of cancer specimens without a matched normal
An in silico framework for the rational design of vaginal probiotic therapy
Pooling strategies in V1 can account for the functional and structural diversity across species
Estimating Mycobacterium tuberculosis transmission in a South African clinic: Spatiotemporal model based on person movements
What Can Interaction Webs Tell Us About Species Roles?
Optimal Population-Level Infection Detection Strategies for Malaria Control and Elimination in a Spatial Model of Malaria Transmission
The Impact of Cortical Lesions on Thalamo-Cortical Network Dynamics after Acute Ischaemic Stroke: A Combined Experimental and Theoretical Study
Independent working memory resources for egocentric and allocentric spatial information
Credibility assessment of in silico clinical trials for medical devices
Training in High-Throughput Sequencing: Common Guidelines to Enable Material Sharing, Dissemination, and Reusability
Statistical analysis of 3D localisation microscopy images for quantification of membrane protein distributions in a platelet clot model
Distributed Representations Accelerate Evolution of Adaptive Behaviours
Mutual Repression Enhances the Steepness and Precision of Gene Expression Boundaries
Somato-dendritic Synaptic Plasticity and Error-backpropagation in Active Dendrites
CRISPRbuilder-TB: "CRISPR-builder for tuberculosis". Exhaustive reconstruction of the CRISPR locus in mycobacterium tuberculosis complex using SRA
Ten Simple Rules for Internship in a Pharmaceutical Company
Cholesterol binding to the sterol-sensing region of Niemann Pick C1 protein confines dynamics of its N-terminal domain
Modelling optimal vaccination strategy for SARS-CoV-2 in the UK
Reliable B Cell Epitope Predictions: Impacts of Method Development and Improved Benchmarking
bmdrc: Python package for quantifying phenotypes from chemical exposures with benchmark dose modeling
Exploring the transmission of cognitive task information through optimal brain pathways
The Evolutionary Dynamics of a Rapidly Mutating Virus within and between Hosts: The Case of Hepatitis C Virus
An expandable synthetic library of human paired antibody sequences
Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models
Managing spatio-temporal heterogeneity of susceptibles by embedding it into an homogeneous model: A mechanistic and deep learning study
Modeling cell biological features of meiotic chromosome pairing to study interlock resolution
Cell type-specific mechanisms of information transfer in data-driven biophysical models of hippocampal CA3 principal neurons
Modeling time-varying brain networks with a self-tuning optimized Kalman filter
Dimensionality of Carbon Nanomaterials Determines the Binding and Dynamics of Amyloidogenic Peptides: Multiscale Theoretical Simulations
Coevolving residues inform protein dynamics profiles and disease susceptibility of nSNVs
Model-Based Analysis for Qualitative Data: An Application in Drosophila Germline Stem Cell Regulation
Evolution of major histocompatibility complex gene copy number
Impact of oxygen and glucose availability on the viability and connectivity of islet cells: A computational study of reconstructed avascular human islets
Weak Noise in Neurons May Powerfully Inhibit the Generation of Repetitive Spiking but Not Its Propagation
Neuron's eye view: Inferring features of complex stimuli from neural responses
Optimization of experimental designs for biological rhythm discovery
Optimizing Provider Recruitment for Influenza Surveillance Networks
Deep learning as a tool for neural data analysis: Speech classification and cross-frequency coupling in human sensorimotor cortex
Predicting Transmembrane Helix Packing Arrangements using Residue Contacts and a Force-Directed Algorithm
Risk-Sensitivity in Bayesian Sensorimotor Integration
Phenotypes to remember: Evolutionary developmental memory capacity and robustness
Gene Network Homology in Prokaryotes Using a Similarity Search Approach: Queries of Quorum Sensing Signal Transduction
The Eighth Annual Bio-Ontologies Meeting
Dimensional reduction in networks of non-Markovian spiking neurons: Equivalence of synaptic filtering and heterogeneous propagation delays
Increasing growth rate slows adaptation when genotypes compete for diffusing resources
A Neural Computational Model of Incentive Salience
Conformational Changes and Slow Dynamics through Microsecond Polarized Atomistic Molecular Simulation of an Integral Kv1.2 Ion Channel
Correction: A dynamic genetic-hormonal regulatory network model explains multiple cellular behaviors of the root apical meristem of Arabidopsis thaliana
Estimating the probabilities of rare arrhythmic events in multiscale computational models of cardiac cells and tissue
Roles of mTOR in thoracic aortopathy understood by complex intracellular signaling interactions
Multi-scale model suggests the trade-off between protein and ATP demand as a driver of metabolic changes during yeast replicative ageing
Mapping Shape to Visuomotor Mapping: Learning and Generalisation of Sensorimotor Behaviour Based on Contextual Information
Ten simple rules for running a successful women-in-STEM organization on an academic campus
Subbarrel Patterns in Somatosensory Cortical Barrels Can Emerge from Local Dynamic Instabilities
Identification of New IκBα Complexes by an Iterative Experimental and Mathematical Modeling Approach
A mathematical model of the role of aggregation in sonic hedgehog signalling
Smart Swarms of Bacteria-Inspired Agents with Performance Adaptable Interactions
Why do G-quadruplexes dimerize through the 5'-ends? Driving forces for G4 DNA dimerization examined in atomic detail
Unsupervised learning of perceptual feature combinations
Knots: Attractive Places with High Path Tortuosity in Mouse Open Field Exploration
The Invariance Hypothesis Implies Domain-Specific Regions in Visual Cortex
Genetic programming based models in plant tissue culture: An addendum to traditional statistical approach
A maximum-entropy model for predicting chromatin contacts
Allosteric modulation of proton binding confers Cl- activation and glutamate selectivity to vesicular glutamate transporters
Correction: Mathematical modeling of the molecular switch of TNFR1-mediated signaling pathways applying Petri net formalism and in silico knockout analysis
Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity
Age-differentiated incentives for adaptive behavior during epidemics produce oscillatory and chaotic dynamics
HIV Promoter Integration Site Primarily Modulates Transcriptional Burst Size Rather Than Frequency