yusuke1997/dblp-id-title huggingface dataset:
Overlap matrix completion for predicting drug-associated indications
On Side-Chain Conformational Entropy of Proteins
Collaborating with our community to increase code sharing
Inferential Structure Determination of Chromosomes from Single-Cell Hi-C Data
Integrative Analysis of Circadian Transcriptome and Metabolic Network Reveals the Role of De Novo Purine Synthesis in Circadian Control of Cell Cycle
Modeling neuronal avalanches and long-range temporal correlations at the emergence of collective oscillations: Continuously varying exponents mimic M/EEG results
Where's Whaledo: A software toolkit for array localization of animal vocalizations
High-order epistasis shapes evolutionary trajectories
Landscape Epidemiology and Control of Pathogens with Cryptic and Long-Distance Dispersal: Sudden Oak Death in Northern Californian Forests
Global and gene-specific translational regulation in Escherichia coli across different conditions
Selection of Target Sites for Mobile DNA Integration in the Human Genome
Costs of task allocation with local feedback: Effects of colony size and extra workers in social insects and other multi-agent systems
How Attention Can Create Synaptic Tags for the Learning of Working Memories in Sequential Tasks
DoGNet: A deep architecture for synapse detection in multiplexed fluorescence images
Generative FDG-PET and MRI Model of Aging and Disease Progression in Alzheimer's Disease
Protein loop structure prediction by community-based deep learning and its application to antibody CDR H3 loop modeling
PERIOD-TIMELESS Interval Timer May Require an Additional Feedback Loop
Understanding narwhal diving behaviour using Hidden Markov Models with dependent state distributions and long range dependence
A Bayesian method for identifying associations between response variables and bacterial community composition
Intrinsically Disordered Proteins Display No Preference for Chaperone Binding In Vivo
Nonequilibrium brain dynamics elicited as the origin of perturbative complexity
Fly-QMA: Automated analysis of mosaic imaginal discs in Drosophila
Comparing human and model-based forecasts of COVID-19 in Germany and Poland
A mesoscopic simulator to uncover heterogeneity and evolutionary dynamics in tumors
Sensorimotor Learning Biases Choice Behavior: A Learning Neural Field Model for Decision Making
Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action
Mixture-of-Experts Variational Autoencoder for clustering and generating from similarity-based representations on single cell data
Linear discriminant analysis reveals hidden patterns in NMR chemical shifts of intrinsically disordered proteins
Pan-cancer association of a centrosome amplification gene expression signature with genomic alterations and clinical outcome
A model of thalamo-cortical interaction for incremental binding in mental contour-tracing
Predictive Feedback Can Account for Biphasic Responses in the Lateral Geniculate Nucleus
Bayesian inference of protein conformational ensembles from limited structural data
HIV-1 Polymerase Inhibition by Nucleoside Analogs: Cellular- and Kinetic Parameters of Efficacy, Susceptibility and Resistance Selection
STDP Installs in Winner-Take-All Circuits an Online Approximation to Hidden Markov Model Learning
A single reaction-diffusion equation for the multifarious eruptions of urticaria
Quantifying infectious disease epidemic risks: A practical approach for seasonal pathogens
Nonlinear decoding of a complex movie from the mammalian retina
A Model for the Origin and Properties of Flicker-Induced Geometric Phosphenes
Dual Dimensionality Reduction Reveals Independent Encoding of Motor Features in a Muscle Synergy for Insect Flight Control
XPRESSyourself: Enhancing, standardizing, and automating ribosome profiling computational analyses yields improved insight into data
Pooled testing of traced contacts under superspreading dynamics
Multiple protein-DNA interfaces unravelled by evolutionary information, physico-chemical and geometrical properties
Bayesian adaptive dual control of deep brain stimulation in a computational model of Parkinson's disease
Reconstruction of Genome-Scale Active Metabolic Networks for 69 Human Cell Types and 16 Cancer Types Using INIT
An Integrative Approach for Modeling and Simulation of Heterocyst Pattern Formation in Cyanobacteria Filaments
Reinforcement Learning of Linking and Tracing Contours in Recurrent Neural Networks
Structure and Dynamics of the Membrane-Bound Cytochrome P450 2C9
Evolutionary Modeling of Rate Shifts Reveals Specificity Determinants in HIV-1 Subtypes
Geometry of population activity in spiking networks with low-rank structure
Evolving generalists in switching rugged landscapes
Ten Simple Rules for Developing Public Biological Databases
Live Imaging-Based Model Selection Reveals Periodic Regulation of the Stochastic G1/S Phase Transition in Vertebrate Axial Development
Fluid mechanics of the zebrafish embryonic heart trabeculation
Integrative single-cell omics analyses reveal epigenetic heterogeneity in mouse embryonic stem cells
Implications of diffusion and time-varying morphogen gradients for the dynamic positioning and precision of bistable gene expression boundaries
The visual cortex produces gamma band echo in response to broadband visual flicker
Probabilistic Approach to Predicting Substrate Specificity of Methyltransferases
Flux-sum coupling analysis of metabolic network models
Contact networks have small metric backbones that maintain community structure and are primary transmission subgraphs
Bacteria face trade-offs in the decomposition of complex biopolymers
Isolating and quantifying the role of developmental noise in generating phenotypic variation
Ten simple rules for designing learning experiences that involve enhancing computational biology Wikipedia articles
The Rates of Protein Synthesis and Degradation Account for the Differential Response of Neurons to Spaced and Massed Training Protocols
Evolution of chemokine receptors is driven by mutations in the sodium binding site
Learning, Memory, and the Role of Neural Network Architecture
Positional Information Generated by Spatially Distributed Signaling Cascades
Spartan : A Comprehensive Tool for Understanding Uncertainty in Simulations of Biological Systems
Inference of Quantitative Models of Bacterial Promoters from Time-Series Reporter Gene Data
Enhancing predictive performance for spectroscopic studies in wildlife science through a multi-model approach: A case study for species classification of live amphibians
Computational and Experimental Analysis of Redundancy in the Central Metabolism of Geobacter sulfurreducens
OptMDFpathway: Identification of metabolic pathways with maximal thermodynamic driving force and its application for analyzing the endogenous CO2 fixation potential of Escherichia coli
Efficient inference and identifiability analysis for differential equation models with random parameters
Differential mobility and local variation in infection attack rate
Distinguishing between different percolation regimes in noisy dynamic networks with an application to epileptic seizures
Designing Focused Chemical Libraries Enriched in Protein-Protein Interaction Inhibitors using Machine-Learning Methods
Relevance of intra-hospital patient movements for the spread of healthcare-associated infections within hospitals - a mathematical modeling study
RecPD: A Recombination-aware measure of phylogenetic diversity
A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies
Self-assembly coupled to liquid-liquid phase separation
Spatio-temporal modeling of the crowding conditions and metabolic variability in microbial communities
Defectors Can Create Conditions That Rescue Cooperation
OptRAM: In-silico strain design via integrative regulatory-metabolic network modeling
Engineering a More Thermostable Blue Light Photo Receptor Bacillus subtilis YtvA LOV Domain by a Computer Aided Rational Design Method
Leveraging epigenomes and three-dimensional genome organization for interpreting regulatory variation
Predicting Chemical Environments of Bacteria from Receptor Signaling
Response to comment on: Toward an optimal contraception dosing strategy
Crosstalk and ultrasensitivity in protein degradation pathways
Noise and Robustness in Phyllotaxis
Ten simple rules for establishing a mentorship programme
Spatiotemporal spread of Plasmodium falciparum mutations for resistance to sulfadoxine-pyrimethamine across Africa, 1990-2020
Margination and adhesion dynamics of tumor cells in a real microvascular network
Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance
The role of spatial heterogeneity in the evolution of local and global infections of viruses
Chromophore Protonation State Controls Photoswitching of the Fluoroprotein asFP595
Intrinsic Noise Profoundly Alters the Dynamics and Steady State of Morphogen-Controlled Bistable Genetic Switches
Age polyethism can emerge from social learning: A game-theoretic investigation
Scalable Rule-Based Modelling of Allosteric Proteins and Biochemical Networks
A Computational Approach to Analyze the Mechanism of Action of the Kinase Inhibitor Bafetinib
Reliable ligand discrimination in stochastic multistep kinetic proofreading: First passage time vs. product counting strategies
Comparing efficacies of moxifloxacin, levofloxacin and gatifloxacin in tuberculosis granulomas using a multi-scale systems pharmacology approach
A conserved expression signature predicts growth rate and reveals cell & lineage-specific differences
Reaction-diffusion models in weighted and directed connectomes
Correction: In Search of the Biological Significance of Modular Structures in Protein Networks
MIiSR: Molecular Interactions in Super-Resolution Imaging Enables the Analysis of Protein Interactions, Dynamics and Formation of Multi-protein Structures
The Effects of Theta Precession on Spatial Learning and Simplicial Complex Dynamics in a Topological Model of the Hippocampal Spatial Map
Do Brain Networks Evolve by Maximizing Their Information Flow Capacity?
Interplay of multiple pathways and activity-dependent rules in STDP
Ten simple rules for avoiding predatory publishing scams
Correction: Exploring the miRNA Regulatory Network Using Evolutionary Correlations
Revealing Posttranscriptional Regulatory Elements Through Network-Level Conservation
Systems biology predicts that fibrosis in tuberculous granulomas may arise through macrophage-to-myofibroblast transformation
Automated Analysis of a Diverse Synapse Population
PremPS: Predicting the impact of missense mutations on protein stability
DRAMS: A tool to detect and re-align mixed-up samples for integrative studies of multi-omics data
ScRDAVis: An R shiny application for single-cell transcriptome data analysis and visualization
Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations
ProInfer: An interpretable protein inference tool leveraging on biological networks
Towards Predicting the Response of a Solid Tumour to Chemotherapy and Radiotherapy Treatments: Clinical Insights from a Computational Model
BiComp-DTA: Drug-target binding affinity prediction through complementary biological-related and compression-based featurization approach
Uncovering drivers of dose-dependence and individual variation in malaria infection outcomes
Correction: MaxHiC: A robust background correction model to identify biologically relevant chromatin interactions in Hi-C and capture Hi-C experiments
Predicting Disease Risk Using Bootstrap Ranking and Classification Algorithms
Identification of gene specific cis-regulatory elements during differentiation of mouse embryonic stem cells: An integrative approach using high-throughput datasets
Post-processing and weighted combination of infectious disease nowcasts
Micro-dissection and integration of long and short reads to create a robust catalog of kidney compartment-specific isoforms
SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models
Searching for Collective Behavior in a Large Network of Sensory Neurons
A toolkit for the dynamic study of air sacs in siamang and other elastic circular structures
A Model for the Self-Organization of Vesicular Flux and Protein Distributions in the Golgi Apparatus
Plausible pathway for a host-parasite molecular replication network to increase its complexity through Darwinian evolution
Evaluating targeted COVID-19 vaccination strategies with agent-based modeling
Spatio-temporal Model of Endogenous ROS and Raft-Dependent WNT/Beta-Catenin Signaling Driving Cell Fate Commitment in Human Neural Progenitor Cells
Informing Optimal Environmental Influenza Interventions: How the Host, Agent, and Environment Alter Dominant Routes of Transmission
CodonTest: Modeling Amino Acid Substitution Preferences in Coding Sequences
Point process analysis of noise in early invertebrate vision
Mathematical modeling of malaria vaccination with seasonality and immune feedback
Measuring Global Credibility with Application to Local Sequence Alignment
Anticipatory coadaptation of ankle stiffness and sensorimotor gain for standing balance
Burst control: Synaptic conditions for burst generation in cortical layer 5 pyramidal neurons
Stochastic gene expression in proliferating cells: Differing noise intensity in single-cell and population perspectives
A transfer learning approach to identify Plasmodium in microscopic images
Effects of tDCS of the DLPFC on brain networks: A hybrid brain modeling study
Refinement and Pattern Formation in Neural Circuits by the Interaction of Traveling Waves with Spike-Timing Dependent Plasticity
The Evolution of Collective Restraint: Policing and Obedience among Non-conjugative Plasmids
Correction: In-silico dynamic analysis of cytotoxic drug administration to solid tumours: Effect of binding affinity and vessel permeability
Pathfinder: Protein folding pathway prediction based on conformational sampling
novoStoic2.0: An integrated framework for pathway synthesis, thermodynamic evaluation, and enzyme selection
Mechanism of Iron-Dependent Repressor (IdeR) Activation and DNA Binding: A Molecular Dynamics and Protein Structure Network Study
Important miRs of Pathways in Different Tumor Types
Temperature-Dependent Model of Multi-step Transcription Initiation in Escherichia coli Based on Live Single-Cell Measurements
Statistics of Knots, Geometry of Conformations, and Evolution of Proteins
Attractive internuclear force drives the collective behavior of nuclear arrays in Drosophila embryos
Infection patterns in simple and complex contagion processes on networks
Mathematical modeling of intratumoral immunotherapy yields strategies to improve the treatment outcomes
Categorical encoding of decision variables in orbitofrontal cortex
Neural encoding of biomechanically (im)possible human movements in occipitotemporal cortex
Extracellular matrix density regulates the formation of tumour spheroids through cell migration
Immune selection suppresses the emergence of drug resistance in malaria parasites but facilitates its spread
Reproducibility efforts as a teaching tool: A pilot study
Mechanisms of fast and stringent search in homologous pairing of double-stranded DNA
Increased Vulnerability of Human Ventricle to Re-entrant Excitation in hERG-linked Variant 1 Short QT Syndrome
Learning clinical networks from medical records based on information estimates in mixed-type data
Predicting kinase inhibitors using bioactivity matrix derived informer sets
MitoScape: A big-data, machine-learning platform for obtaining mitochondrial DNA from next-generation sequencing data
Divergent genome evolution caused by regional variation in DNA gain and loss between human and mouse
Swarm: A federated cloud framework for large-scale variant analysis
aiSEGcell: User-friendly deep learning-based segmentation of nuclei in transmitted light images
Demonstration of three-dimensional contact point determination and contour reconstruction during active whisking behavior of an awake rat
Memory functions reveal structural properties of gene regulatory networks
Repetitive training enhances the pattern recognition capability of cultured neural networks
A conceptual and computational framework for modelling and understanding the non-equilibrium gene regulatory networks of mouse embryonic stem cells
Development of Genomic Sciences in Mexico: A Good Start and a Long Way to Go
The tumour histopathology "glossary" for AI developers
Loop analysis of blood pressure/volume homeostasis
Designing Molecular Dynamics Simulations to Shift Populations of the Conformational States of Calmodulin
Memory shapes microbial populations
Bayesian Computation Emerges in Generic Cortical Microcircuits through Spike-Timing-Dependent Plasticity
A mathematical model coupling polarity signaling to cell adhesion explains diverse cell migration patterns
LASSI: A lattice model for simulating phase transitions of multivalent proteins
(A)Symmetric Stem Cell Replication and Cancer
Hemodynamic Traveling Waves in Human Visual Cortex
Data-driven discovery and parameter estimation of mathematical models in biological pattern formation
Inferring a simple mechanism for alpha-blocking by fitting a neural population model to EEG spectra
Effects of Electrical and Structural Remodeling on Atrial Fibrillation Maintenance: A Simulation Study
An Introduction to Programming for Bioscientists: A Python-Based Primer
Developmental trajectory of Caenorhabditis elegans nervous system governs its structural organization
Sparse and Compositionally Robust Inference of Microbial Ecological Networks
Reduction in social learning and increased policy uncertainty about harmful intent is associated with pre-existing paranoid beliefs: Evidence from modelling a modified serial dictator game
Versatility and Invariance in the Evolution of Homologous Heteromeric Interfaces
The Role of Flexibility and Conformational Selection in the Binding Promiscuity of PDZ Domains
Augmenting subnetwork inference with information extracted from the scientific literature
Increased Aggregation Is More Frequently Associated to Human Disease-Associated Mutations Than to Neutral Polymorphisms
DMFpred: Predicting protein disorder molecular functions based on protein cubic language model
Mathematical model of oxygen, nutrient, and drug transport in tuberculosis granulomas
DNFE: Directed network flow entropy for detecting tipping points during biological processes
Correction of copy number induced false positives in CRISPR screens
Binding-induced functional-domain motions in the Argonaute characterized by adaptive advanced sampling
Effects of contact structure on the transient evolution of HIV virulence
Rosetta FunFolDes - A general framework for the computational design of functional proteins
Robust spatial memory maps encoded by networks with transient connections
DEXOM: Diversity-based enumeration of optimal context-specific metabolic networks
Rational Engineering of Enzyme Allosteric Regulation through Sequence Evolution Analysis
Superhelical Destabilization in Regulatory Regions of Stress Response Genes
On Expression Patterns and Developmental Origin of Human Brain Regions
Correction: Neural adaptation and fractional dynamics as a window to underlying neural excitability
Cell Shape Dynamics: From Waves to Migration
Diminished Self-Chaperoning Activity of the ΔF508 Mutant of CFTR Results in Protein Misfolding
Mathematical Model of a Telomerase Transcriptional Regulatory Network Developed by Cell-Based Screening: Analysis of Inhibitor Effects and Telomerase Expression Mechanisms
A Structural Model of Truncated Gaussia princeps Luciferase Elucidating the Crucial Catalytic Function of No.76 Arginine towards Coelenterazine Oxidation
How MicroRNA and Transcription Factor Co-regulatory Networks Affect Osteosarcoma Cell Proliferation
Intra-vector infection dynamics challenge how to model the extrinsic incubation period for major arboviruses: dengue, Zika, and chikungunya
Inferring Viral Dynamics in Chronically HCV Infected Patients from the Spatial Distribution of Infected Hepatocytes
Modeling Meiotic Chromosomes Indicates a Size Dependent Contribution of Telomere Clustering and Chromosome Rigidity to Homologue Juxtaposition
The Influence of Hydroxylation on Maintaining CpG Methylation Patterns: A Hidden Markov Model Approach
EFMouse: A toolbox to model stimulation-induced electric fields in the mouse brain
Separable actions of acetylcholine and noradrenaline on neuronal ensemble formation in hippocampal CA3 circuits
Is Model Fitting Necessary for Model-Based fMRI?
Regulation of adenylyl cyclase 5 in striatal neurons confers the ability to detect coincident neuromodulatory signals
Predicting protein targets for drug-like compounds using transcriptomics
Mathematical Model of a Cell Size Checkpoint
The Dynamics of Human Body Weight Change
Investigating the representation of uncertainty in neuronal circuits
Comprehensive Repertoire of Foldable Regions within Whole Genomes
Modelling of malaria risk, rates, and trends: A spatiotemporal approach for identifying and targeting sub-national areas of high and low burden
A Circadian Clock-Regulated Toggle Switch Explains AtGRP7 and AtGRP8 Oscillations in Arabidopsis thaliana
Text Mining Genotype-Phenotype Relationships from Biomedical Literature for Database Curation and Precision Medicine
Machine Learning Methods Enable Predictive Modeling of Antibody Feature: Function Relationships in RV144 Vaccinees
Template-based mapping of dynamic motifs in tissue morphogenesis
Post-lockdown abatement of COVID-19 by fast periodic switching
Predicting B cell receptor substitution profiles using public repertoire data
Combinations of low-level and high-level neural processes account for distinct patterns of context-dependent choice
Efficient computation of adjoint sensitivities at steady-state in ODE models of biochemical reaction networks
Network Inference Algorithms Elucidate Nrf2 Regulation of Mouse Lung Oxidative Stress
Signaling Logic of Activity-Triggered Dendritic Protein Synthesis: An mTOR Gate But Not a Feedback Switch
Intergenic and Repeat Transcription in Human, Chimpanzee and Macaque Brains Measured by RNA-Seq
Structural Consensus among Antibodies Defines the Antigen Binding Site
Challenging a paradigm: Staggered versus single-pulse mass dog vaccination strategy for rabies elimination
Beyond the Binding Site: The Role of the β2 - β3 Loop and Extra-Domain Structures in PDZ Domains
Simulation-based Reconstructed Diffusion unveils the effect of aging on protein diffusion in Escherichia coli
Potential Benefits of Cattle Vaccination as a Supplementary Control for Bovine Tuberculosis
Independent component analysis recovers consistent regulatory signals from disparate datasets
Simultaneous Clustering of Multiple Gene Expression and Physical Interaction Datasets
Spontaneous Quaternary and Tertiary T-R Transitions of Human Hemoglobin in Molecular Dynamics Simulation
Inferring the nature of linguistic computations in the brain
A multi-label learning model for predicting drug-induced pathology in multi-organ based on toxicogenomics data
Modeling suggests that virion production cycles within individual cells is key to understanding acute hepatitis B virus infection kinetics
Genome-scale metabolic modeling of the human gut bacterium Bacteroides fragilis strain 638R
A unified framework for inferring the multi-scale organization of chromatin domains from Hi-C
Primate protein-ligand interfaces exhibit significant conservation and unveil human-specific evolutionary drivers
Detecting interaction networks in the human microbiome with conditional Granger causality
Redundant representations are required to disambiguate simultaneously presented complex stimuli
Metabolic modelling as a powerful tool to identify critical components of Pneumocystis growth medium
Ten Simple Rules for the Open Development of Scientific Software
Refining Protein Subcellular Localization
Ten simple rules for researchers who want to develop web apps
A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for Next-Generation Sequencing Data
Emergence of Switch-Like Behavior in a Large Family of Simple Biochemical Networks