yusuke1997/dblp-id-title huggingface dataset:
Harnessing Diversity towards the Reconstructing of Large Scale Gene Regulatory Networks
RNAcontext: A New Method for Learning the Sequence and Structure Binding Preferences of RNA-Binding Proteins
Change in Allosteric Network Affects Binding Affinities of PDZ Domains: Analysis through Perturbation Response Scanning
Evolutionary Establishment of Moral and Double Moral Standards through Spatial Interactions
Molecular signatures of silencing suppression degeneracy from a complex RNA virus
DSCN: Double-target selection guided by CRISPR screening and network
Establishment of computational biology in Greece and Cyprus: Past, present, and future
Computational Design of a PDZ Domain Peptide Inhibitor that Rescues CFTR Activity
HaploCart: Human mtDNA haplogroup classification using a pangenomic reference graph
Feedback Control Architecture and the Bacterial Chemotaxis Network
Integrated Information Increases with Fitness in the Evolution of Animats
Estimating the Stoichiometry of HIV Neutralization
Real-time resolution of short-read assembly graph using ONT long reads
Towards the prediction of non-peptidic epitopes
An integrated framework for building trustworthy data-driven epidemiological models: Application to the COVID-19 outbreak in New York City
Data-dependent visualization of biological networks in the web-browser with NDExEdit
Quantitative Analysis of Genetic and Neuronal Multi-Perturbation Experiments
Amplification of Asynchronous Inhibition-Mediated Synchronization by Feedback in Recurrent Networks
Astrocytic Mechanisms Explaining Neural-Activity-Induced Shrinkage of Extraneuronal Space
The Need for Centralization of Computational Biology Resources
Correction: Signatures of criticality arise from random subsampling in simple population models
In-silico simultaneous respiratory and circulatory measurement during voluntary breathing, exercise, and mental stress: A computational approach
Ten Simple Rules for Organizing a Scientific Meeting
Beware batch culture: Seasonality and niche construction predicted to favor bacterial adaptive diversification
The Effect of Sustained Compression on Oxygen Metabolic Transport in the Intervertebral Disc Decreases with Degenerative Changes
Regulation of replication timing in Saccharomyces cerevisiae
ToxoNet: A high confidence map of protein-protein interactions in Toxoplasma gondii
Contribution of Network Connectivity in Determining the Relationship between Gene Expression and Metabolite Concentration Changes
Efficient neural decoding of self-location with a deep recurrent network
Relating Structure and Function in the Human Brain: Relative Contributions of Anatomy, Stationary Dynamics, and Non-stationarities
Induced Fit in Protein Multimerization: The HFBI Case
Bridging structure and function: A model of sequence learning and prediction in primary visual cortex
A Comprehensive Model of the Spatio-Temporal Stem Cell and Tissue Organisation in the Intestinal Crypt
Speed Controls in Translating Secretory Proteins in Eukaryotes - an Evolutionary Perspective
A Model of Stimulus-Specific Neural Assemblies in the Insect Antennal Lobe
Network Self-Organization Explains the Statistics and Dynamics of Synaptic Connection Strengths in Cortex
Dynamical Modeling of Collective Behavior from Pigeon Flight Data: Flock Cohesion and Dispersion
Context-Dependent Encoding of Fear and Extinction Memories in a Large-Scale Network Model of the Basal Amygdala
Analysis of protrusion dynamics in amoeboid cell motility by means of regularized contour flows
Organization of Cellular Receptors into a Nanoscale Junction during HIV-1 Adhesion
Tag-Trigger-Consolidation: A Model of Early and Late Long-Term-Potentiation and Depression
DeepDynaForecast: Phylogenetic-informed graph deep learning for epidemic transmission dynamic prediction
Tracing the Evolution of Lineage-Specific Transcription Factor Binding Sites in a Birth-Death Framework
Predicting the diversity of photosynthetic light-harvesting using thermodynamics and machine learning
pyTFM: A tool for traction force and monolayer stress microscopy
A Coarse-Grained Biophysical Model of E. coli and Its Application to Perturbation of the rRNA Operon Copy Number
Ten simple rules for reporting information on species interactions
The Development of Computational Biology in South Africa: Successes Achieved and Lessons Learnt
Genetic Progression and the Waiting Time to Cancer
Cytoskeleton polarity is essential in determining orientational order in basal bodies of multi-ciliated cells
Gamma Oscillations of Spiking Neural Populations Enhance Signal Discrimination
Parametric Copula-GP model for analyzing multidimensional neuronal and behavioral relationships
Ten simple rules for engaging with artificial intelligence in biomedicine
A Single Mechanism Can Account for Human Perception of Depth in Mixed Correlation Random Dot Stereograms
PLoS Computational Biology: A New Community Journal
Older adults select different but not simpler strategies than younger adults in risky choice
Learning causal networks with latent variables from multivariate information in genomic data
Landscape as a Model: The Importance of Geometry
Cancer classification based on chromatin accessibility profiles with deep adversarial learning model
Phasic Burst Stimulation: A Closed-Loop Approach to Tuning Deep Brain Stimulation Parameters for Parkinson's Disease
Functional diversity among sensory neurons from efficient coding principles
Phase-locking patterns underlying effective communication in exact firing rate models of neural networks
On the effects of alternative optima in context-specific metabolic model predictions
Comprehensive DNA Signature Discovery and Validation
Signal Propagation in Proteins and Relation to Equilibrium Fluctuations
MMTF - An efficient file format for the transmission, visualization, and analysis of macromolecular structures
Post-Turing tissue pattern formation: Advent of mechanochemistry
Global importance analysis: An interpretability method to quantify importance of genomic features in deep neural networks
Human visual grouping based on within- and cross-area temporal correlations
Encoding in Balanced Networks: Revisiting Spike Patterns and Chaos in Stimulus-Driven Systems
Ten quick tips for sequence-based prediction of protein properties using machine learning
powerTCR: A model-based approach to comparative analysis of the clone size distribution of the T cell receptor repertoire
Exploring Fold Space Preferences of New-born and Ancient Protein Superfamilies
Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article
Robust inference of population size histories from genomic sequencing data
Filament Compliance Influences Cooperative Activation of Thin Filaments and the Dynamics of Force Production in Skeletal Muscle
Ten simple rules for international short-term research stays
Computational Fitness Landscape for All Gene-Order Permutations of an RNA Virus
What drives the perceptual change resulting from speech motor adaptation? Evaluation of hypotheses in a Bayesian modeling framework
Quantification of Diabetes Comorbidity Risks across Life Using Nation-Wide Big Claims Data
Input-Dependent Frequency Modulation of Cortical Gamma Oscillations Shapes Spatial Synchronization and Enables Phase Coding
ChromaFactor: Deconvolution of single-molecule chromatin organization with non-negative matrix factorization
Block sparse Bayes-based fuzzy system for RNA N6-methyladenosine sites prediction
Anatomical-electrical coupling of cardiac axes: Definitions and population variability for advancing personalised ECG interpretation
Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections
Coping with Viral Diversity in HIV Vaccine Design
A BMP-FGF Morphogen Toggle Switch Drives the Ultrasensitive Expression of Multiple Genes in the Developing Forebrain
The Decay of Motor Memories Is Independent of Context Change Detection
Limits of Feedback Control in Bacterial Chemotaxis
Flow Cytometry Bioinformatics
A first-takes-all model of centriole copy number control based on cartwheel elongation
A Review of 2008 for PLoS Computational Biology
Automated minute scale RNA-seq of pluripotent stem cell differentiation reveals early divergence of human and mouse gene expression kinetics
Astrocytes as a mechanism for contextually-guided network dynamics and function
The extent of ribosome queuing in budding yeast
Epidemic management and control through risk-dependent individual contact interventions
The Emergence of Up and Down States in Cortical Networks
A Change in Vaccine Efficacy and Duration of Protection Explains Recent Rises in Pertussis Incidence in the United States
Multiple factors influence the morphology of the bipolar electrogram: An in silico modeling study
A Computational Investigation on the Connection between Dynamics Properties of Ribosomal Proteins and Ribosome Assembly
Colocalization of Protein Kinase A with Adenylyl Cyclase Enhances Protein Kinase A Activity during Induction of Long-Lasting Long-Term-Potentiation
Dynamic Phenotypic Clustering in Noisy Ecosystems
Relating simulation studies by provenance - Developing a family of Wnt signaling models
Symbiotic Cell Differentiation and Cooperative Growth in Multicellular Aggregates
The metastable brain associated with autistic-like traits of typically developing individuals
Emergence of Emotion Selectivity in Deep Neural Networks Trained to Recognize Visual Objects
Genome-Scale Metabolic Network Validation of Shewanella oneidensis Using Transposon Insertion Frequency Analysis
Autonomous Optimization of Targeted Stimulation of Neuronal Networks
Latching dynamics as a basis for short-term recall
Systematic Planning of Genome-Scale Experiments in Poorly Studied Species
mdciao: Accessible Analysis and Visualization of Molecular Dynamics Simulation Data
THLANet: A deep learning framework for predicting TCR-pHLA binding in immunotherapy applications
Infrastructure for bioinformatics applications in Tanzania: Lessons from the Sickle Cell Programme
ToPS: A Framework to Manipulate Probabilistic Models of Sequence Data
Self-organization in Balanced State Networks by STDP and Homeostatic Plasticity
NeuroML: A Language for Describing Data Driven Models of Neurons and Networks with a High Degree of Biological Detail
The role of chromatin state in intron retention: A case study in leveraging large scale deep learning models
How Random Is Social Behaviour? Disentangling Social Complexity through the Study of a Wild House Mouse Population
Modulation transfer functions for audiovisual speech
Predictions of time to HIV viral rebound following ART suspension that incorporate personal biomarkers
Rare Variants Association Analysis in Large-Scale Sequencing Studies at the Single Locus Level
Evolutionary Conserved Positions Define Protein Conformational Diversity
Quantification of the Relative Importance of CTL, B Cell, NK Cell, and Target Cell Limitation in the Control of Primary SIV-Infection
Surrogate modeling of Cellular-Potts agent-based models as a segmentation task using the U-Net neural network architecture
Fundamental Limits to Position Determination by Concentration Gradients
Identifying influential neighbors in animal flocking
HAL-X: Scalable hierarchical clustering for rapid and tunable single-cell analysis
Data-driven model discovery and model selection for noisy biological systems
Speciation trajectories in recombining bacterial species
PAIRUP-MS: Pathway analysis and imputation to relate unknowns in profiles from mass spectrometry-based metabolite data
Modelling the interaction between stem cells derived cardiomyocytes patches and host myocardium to aid non-arrhythmic engineered heart tissue design
Scoring protein-ligand binding structures through learning atomic graphs with inter-molecular adjacency
Host Control of Malaria Infections: Constraints on Immune and Erythropoeitic Response Kinetics
Inference of RNA Polymerase II Transcription Dynamics from Chromatin Immunoprecipitation Time Course Data
Simulation-based validation of a method to detect changes in SARS-CoV-2 reinfection risk
PRIMAL: Fast and Accurate Pedigree-based Imputation from Sequence Data in a Founder Population
ggsashimi: Sashimi plot revised for browser- and annotation-independent splicing visualization
Quantifying the effects of antiangiogenic and chemotherapy drug combinations on drug delivery and treatment efficacy
Social Contact Networks and Disease Eradicability under Voluntary Vaccination
VBA: A Probabilistic Treatment of Nonlinear Models for Neurobiological and Behavioural Data
Chemical Reaction Network Theory elucidates sources of multistability in interferon signaling
Doubting what you already know: Uncertainty regarding state transitions is associated with obsessive compulsive symptoms
Energetic Selection of Topology in Ferredoxins
Genes for highly abundant proteins in Escherichia coli avoid 5' codons that promote ribosomal initiation
From energy to cellular forces in the Cellular Potts Model: An algorithmic approach
Stimulus Design for Model Selection and Validation in Cell Signaling
Inference of R 0 and Transmission Heterogeneity from the Size Distribution of Stuttering Chains
Reconciling kinetic and thermodynamic models of bacterial transcription
Fast and flexible processing of large FRET image stacks using the FRET-IBRA toolkit
Deep6mA: A deep learning framework for exploring similar patterns in DNA N6-methyladenine sites across different species
Differential methods for assessing sensitivity in biological models
Profiling transcription factor activity dynamics using intronic reads in time-series transcriptome data
Microenvironmental Variables Must Influence Intrinsic Phenotypic Parameters of Cancer Stem Cells to Affect Tumourigenicity
Hydrophobicity and Charge Shape Cellular Metabolite Concentrations
Fast estimation of time-varying infectious disease transmission rates
Predicting functional effects of ion channel variants using new phenotypic machine learning methods
Computational Biology Resources Lack Persistence and Usability
Towards Reproducible Descriptions of Neuronal Network Models
RNAtango: Analysing and comparing RNA 3D structures via torsional angles
Stimulus uncertainty and relative reward rates determine adaptive responding in perceptual decision-making
scMSI: Accurately inferring the sub-clonal Micro-Satellite status by an integrated deconvolution model on length spectrum
The LUX Score: A Metric for Lipidome Homology
Computational modeling of rhythmic expectations: Perspectives, pitfalls, and prospects
Mechanistic Mathematical Modeling Tests Hypotheses of the Neurovascular Coupling in fMRI
Exploring the sequence fitness landscape of a bridge between protein folds
Correction: Single Sample Expression-Anchored Mechanisms Predict Survival in Head and Neck Cancer
The hierarchical packing of euchromatin domains can be described as multiplicative cascades
Interspike intervals within retinal spike bursts combinatorially encode multiple stimulus features
Global Motions of the Nuclear Pore Complex: Insights from Elastic Network Models
A Single-Rate Context-Dependent Learning Process Underlies Rapid Adaptation to Familiar Object Dynamics
Origami: Single-cell 3D shape dynamics oriented along the apico-basal axis of folding epithelia from fluorescence microscopy data
A triple distinction of cerebellar function for oculomotor learning and fatigue compensation
Accurate Prediction of DnaK-Peptide Binding via Homology Modelling and Experimental Data
Macroecological patterns in experimental microbial communities
Remarkable structural transformations of actin bundles are driven by their initial polarity, motor activity, crosslinking, and filament treadmilling
Ten Simple Rules for Making Good Oral Presentations
Global Quantitative Modeling of Chromatin Factor Interactions
Accurate Quantification of Functional Analogy among Close Homologs
Evaluating the Adequacy of Gravity Models as a Description of Human Mobility for Epidemic Modelling
A mechanism for punctuating equilibria during mammalian vocal development
Joint Ancestry and Association Testing in Admixed Individuals
A hierarchy of metabolite exchanges in metabolic models of microbial species and communities
Properties of winning Iterated Prisoner's Dilemma strategies
TASmania: A bacterial Toxin-Antitoxin Systems database
Explaining Diversity in Metagenomic Datasets by Phylogenetic-Based Feature Weighting
A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways
Creating cell-specific computational models of stem cell-derived cardiomyocytes using optical experiments
Mechanical feedback and robustness of apical constrictions in Drosophila embryo ventral furrow formation
Probability Fluxes and Transition Paths in a Markovian Model Describing Complex Subunit Cooperativity in HCN2 Channels
In silico analyses identify sequence contamination thresholds for Nanopore-generated SARS-CoV-2 sequences
Backtracking: Improved methods for identifying the source of a deliberate release of Bacillus anthracis from the temporal and spatial distribution of cases
A stochastic framework to model axon interactions within growing neuronal populations
Statistical Dynamics of Flowing Red Blood Cells by Morphological Image Processing
TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions
Nonlinear Hebbian Learning as a Unifying Principle in Receptive Field Formation
Evolution of the nonsense-mediated decay pathway is associated with decreased cytolytic immune infiltration
Synaptic reshaping of plastic neuronal networks by periodic multichannel stimulation with single-pulse and burst stimuli
Cross-fitted instrument: A blueprint for one-sample Mendelian randomization
Ion dynamics at the energy-deprived tripartite synapse
Correction: Demonstrating aspects of multiscale modeling by studying the permeation pathway of the human ZnT2 zinc transporter
Hotspot Mutations in KIT Receptor Differentially Modulate Its Allosterically Coupled Conformational Dynamics: Impact on Activation and Drug Sensitivity
Coordinating cell polarization and morphogenesis through mechanical feedback
Modelling the Effects of Electrical Coupling between Unmyelinated Axons of Brainstem Neurons Controlling Rhythmic Activity
Modeling the daily rhythm of human pain processing in the dorsal horn
lra: A long read aligner for sequences and contigs
Integrating information from historical data into mechanistic models for influenza forecasting
Mutual Inactivation of Notch Receptors and Ligands Facilitates Developmental Patterning
OrgaCCC: Orthogonal graph autoencoders for constructing cell-cell communication networks on spatial transcriptomics data
How does a small molecule bind at a cryptic binding site?
Insights into the Coupling of Duplication Events and Macroevolution from an Age Profile of Animal Transmembrane Gene Families
Tuned inhibition in perceptual decision-making circuits can explain seemingly suboptimal confidence behavior
DeepCellState: An autoencoder-based framework for predicting cell type specific transcriptional states induced by drug treatment
Maintenance of delay-period activity in working memory task is modulated by local network structure
Fast Protein Loop Sampling and Structure Prediction Using Distance-Guided Sequential Chain-Growth Monte Carlo Method
Simulation-based inference for non-parametric statistical comparison of biomolecule dynamics
Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models
Predicting lncRNA-disease associations based on heterogeneous graph convolutional generative adversarial network
Spatiotemporal Feedback and Network Structure Drive and Encode Caenorhabditis elegans Locomotion
Folding Pathways of a Knotted Protein with a Realistic Atomistic Force Field
Stabilized marker gene identification and functional annotation from single-cell transcriptomic data
Modelling Hair Follicle Growth Dynamics as an Excitable Medium
Network perturbation by recurrent regulatory variants in cancer
AI-first structural identification of pathogenic protein target interfaces
Positive Selection, Relaxation, and Acceleration in the Evolution of the Human and Chimp Genome
Waveform distortion for temperature compensation and synchronization in circadian rhythms: An approach based on the renormalization group method
Material and shape perception based on two types of intensity gradient information
Multiple nutrient transporters enable cells to mitigate a rate-affinity tradeoff
Inferring a complete genotype-phenotype map from a small number of measured phenotypes
Bridging the gap between mechanistic biological models and machine learning surrogates
The Emergence of Synaesthesia in a Neuronal Network Model via Changes in Perceptual Sensitivity and Plasticity
Force encoding in muscle spindles during stretch of passive muscle
Combining Search, Social Media, and Traditional Data Sources to Improve Influenza Surveillance
A generative growth model for thalamocortical axonal branching in primary visual cortex
Chemotactic Response and Adaptation Dynamics in Escherichia coli
Unraveling the mechanisms of surround suppression in early visual processing
Ab Initio Prediction of Transcription Factor Targets Using Structural Knowledge
CoRE-ATAC: A deep learning model for the functional classification of regulatory elements from single cell and bulk ATAC-seq data
Pulsatile contractions and pattern formation in excitable actomyosin cortex
Ten simple rules for making a vocabulary FAIR
Genome-Scale Reconstruction of Escherichia coli 's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization
Whisker Movements Reveal Spatial Attention: A Unified Computational Model of Active Sensing Control in the Rat
Paving the Way Towards a Successful and Fulfilling Career in Computational Biology
Clustered Desynchronization from High-Frequency Deep Brain Stimulation
Bistability in fatty-acid oxidation resulting from substrate inhibition
Retracing Micro-Epidemics of Chagas Disease Using Epicenter Regression
Genetic Co-Occurrence Network across Sequenced Microbes
ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis
deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data
TAMC: A deep-learning approach to predict motif-centric transcriptional factor binding activity based on ATAC-seq profile
The Universal Statistical Distributions of the Affinity, Equilibrium Constants, Kinetics and Specificity in Biomolecular Recognition
System Model Network for Adipose Tissue Signatures Related to Weight Changes in Response to Calorie Restriction and Subsequent Weight Maintenance
Effects of Ligand Binding on the Mechanical Properties of Ankyrin Repeat Protein Gankyrin
Convolutional neural networks can identify brain interactions involved in decoding spatial auditory attention
Leveraging eQTLs to identify individual-level tissue of interest for a complex trait
Prediction of Drug-Target Interactions and Drug Repositioning via Network-Based Inference
Computational prediction of protein interactions in single cells by proximity sequencing
Investigation of hemodynamic bulk flow patterns caused by aortic stenosis using a combined 4D Flow MRI-CFD framework
A Dynamic Network Approach for the Study of Human Phenotypes
Agent-Based Modeling of Oxygen-Responsive Transcription Factors in Escherichia coli
Network trade-offs and homeostasis in Arabidopsis shoot architectures
Accelerated Profile HMM Searches
Coordination of Rapid Sphingolipid Responses to Heat Stress in Yeast
Evolutionary Evidence for Alternative Structure in RNA Sequence Co-variation
Non-linear Membrane Properties in Entorhinal Cortical Stellate Cells Reduce Modulation of Input-Output Responses by Voltage Fluctuations
Correction: Dynamic Maternal Gradients Control Timing and Shift-Rates for Drosophila Gap Gene Expression
How multi-scale modeling can help examine social determinants of health and resulting disparities
A weak coupling mechanism for the early steps of the recovery stroke of myosin VI: A free energy simulation and string method analysis
Computational Thinking in Life Science Education
The Force at the Tip - Modelling Tension and Proliferation in Sprouting Angiogenesis