yusuke1997/dblp-id-title huggingface dataset:
Natural Selection on Functional Modules, a Genome-Wide Analysis
Control of βAR- and N -methyl- D -aspartate (NMDA) Receptor-Dependent cAMP Dynamics in Hippocampal Neurons
Robust expansion of phylogeny for fast-growing genome sequence data
Genome replication in asynchronously growing microbial populations
Structural identifiability of biomolecular controller motifs with and without flow measurements as model output
Learning to Estimate Dynamical State with Probabilistic Population Codes
A Stevedore's Protein Knot
Simulations to benchmark time-varying connectivity methods for fMRI
Inferring a spatial code of cell-cell interactions across a whole animal body
Targeted Molecular Dynamics Study of C-Loop Closure and Channel Gating in Nicotinic Receptors
ISMB 2014 - The Premier Conference for the World's Computational Biologists
A computational model of pig ventricular cardiomyocyte electrophysiology and calcium handling: Translation from pig to human electrophysiology
Model-checking ecological state-transition graphs
Ten simple rules for forming a scientific professional society
Sampling bias and model choice in continuous phylogeography: Getting lost on a random walk
Rosetta design with co-evolutionary information retains protein function
CTD: An information-theoretic algorithm to interpret sets of metabolomic and transcriptomic perturbations in the context of graphical models
Conflict and competition between model-based and model-free control
Detecting polynucleotide motifs: Pentads, hexads, and beyond
Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist
Ten Simple Rules for Reviewers
Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity
Intrinsic Disorder in the Human Spliceosomal Proteome
Implications of localized charge for human influenza A H1N1 hemagglutinin evolution: Insights from deep mutational scans
Evolution of Cooperation in Social Dilemmas on Complex Networks
Efficiency of protein synthesis inhibition depends on tRNA and codon compositions
Yielding Elastic Tethers Stabilize Robust Cell Adhesion
Stable, Precise, and Reproducible Patterning of Bicoid and Hunchback Molecules in the Early Drosophila Embryo
Estimating orientation in natural scenes: A spiking neural network model of the insect central complex
Astrocyte-mediated spike-timing-dependent long-term depression modulates synaptic properties in the developing cortex
Dynamic recycling of extracellular ATP in human epithelial intestinal cells
A detailed kinetic model of Eastern equine encephalitis virus replication in a susceptible host cell
Learning gene networks underlying clinical phenotypes using SNP perturbation
Thalamic deep brain stimulation paradigm to reduce consciousness: Cortico-striatal dynamics implicated in mechanisms of consciousness
Mapping molar shapes on signaling pathways
Use of an individual-based model of pneumococcal carriage for planning a randomized trial of a whole-cell vaccine
A direct interaction of cholesterol with the dopamine transporter prevents its out-to-inward transition
Quantitative Analysis of Mechanisms That Govern Red Blood Cell Age Structure and Dynamics during Anaemia
Spontaneous Decoding of the Timing and Content of Human Object Perception from Cortical Surface Recordings Reveals Complementary Information in the Event-Related Potential and Broadband Spectral Change
A Multiscale Model Evaluates Screening for Neoplasia in Barrett's Esophagus
Thermodynamic modeling of genome-wide nucleosome depleted regions in yeast
Towards a Molecular Understanding of the Link between Imatinib Resistance and Kinase Conformational Dynamics
Multistationary and Oscillatory Modes of Free Radicals Generation by the Mitochondrial Respiratory Chain Revealed by a Bifurcation Analysis
Stress-Induced Impairment of a Working Memory Task: Role of Spiking Rate and Spiking History Predicted Discharge
Allostery in the dynamic coactivator domain KIX occurs through minor conformational micro-states
Motility Enhancement through Surface Modification Is Sufficient for Cyanobacterial Community Organization during Phototaxis
RosettaAntibodyDesign (RAbD): A general framework for computational antibody design
A simple kit to use computational notebooks for more openness, reproducibility, and productivity in research
Prospects for detecting early warning signals in discrete event sequence data: Application to epidemiological incidence data
Comparative structural dynamic analysis of GTPases
Bi-stability in cooperative transport by ants in the presence of obstacles
StellarPath: Hierarchical-vertical multi-omics classifier synergizes stable markers and interpretable similarity networks for patient profiling
Synaptic reorganization of synchronized neuronal networks with synaptic weight and structural plasticity
Adaptive Landscape by Environment Interactions Dictate Evolutionary Dynamics in Models of Drug Resistance
Beyond Muscles Stiffness: Importance of State-Estimation to Account for Very Fast Motor Corrections
An evolutionary approach to predict the orientation of CRISPR arrays
Human-like monocular depth biases in deep neural networks
Coupling water fluxes with cell wall mechanics in a multicellular model of plant development
Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes
Timing of Neuropeptide Coupling Determines Synchrony and Entrainment in the Mammalian Circadian Clock
Boolean analysis reveals systematic interactions among low-abundance species in the human gut microbiome
A recurrent neural network framework for flexible and adaptive decision making based on sequence learning
A Unified Model of Shoot Tropism in Plants: Photo-, Gravi- and Propio-ception
Inverse folding based pre-training for the reliable identification of intrinsic transcription terminators
Dynamic integration of forward planning and heuristic preferences during multiple goal pursuit
Exhaustive search of linear information encoding protein-peptide recognition
Prokaryotic virus host prediction with graph contrastive augmentaion
A multispecies framework for modeling adaptive immunity and immunotherapy in cancer
Cyclic transitions between higher order motifs underlie sustained asynchronous spiking in sparse recurrent networks
Non-asymptotic transients away from steady states determine cellular responsiveness to dynamic spatial-temporal signals
Neural diffusivity and pre-emptive epileptic seizure intervention
PrediTALE: A novel model learned from quantitative data allows for new perspectives on TALE targeting
Formation of Regulatory Modules by Local Sequence Duplication
From Morphology to Neural Information: The Electric Sense of the Skate
Interrogation of the Protein-Protein Interactions between Human BRCA2 BRC Repeats and RAD51 Reveals Atomistic Determinants of Affinity
Transcranial direct current stimulation of cerebellum alters spiking precision in cerebellar cortex: A modeling study of cellular responses
How large is the universe of RNA-like motifs? A clustering analysis of RNA graph motifs using topological descriptors
pyPAGE: A framework for Addressing biases in gene-set enrichment analysis - A case study on Alzheimer's disease
The quarantine hospital strategy as a way to reduce both community and nosocomial transmission in the context of a COVID-like epidemic
Localizing Genes to Cerebellar Layers by Classifying ISH Images
Mechanism of collagen folding propagation studied by Molecular Dynamics simulations
Correction: Task-Based Core-Periphery Organization of Human Brain Dynamics
The role of competition versus cooperation in microbial community coalescence
Modelling the acclimation capacity of coral reefs to a warming ocean
Physicochemical and metabolic constraints for thermodynamics-based stoichiometric modelling under mesophilic growth conditions
Ten simple rules for women principal investigators during a pandemic
Systematic discovery of the functional impact of somatic genome alterations in individual tumors through tumor-specific causal inference
Ten simple rules for training by researchers for researchers in a rapidly evolving workforce
Generating functional protein variants with variational autoencoders
Correction: Comprehensively benchmarking applications for detecting copy number variation
The very early evolution of protein translocation across membranes
Individualized network analysis reveals a link between the gut microbiome, diet intervention and Gestational Diabetes Mellitus
PIEZO1 regulates leader cell formation and cellular coordination during collective keratinocyte migration
Next-Generation Sequencing of Human Mitochondrial Reference Genomes Uncovers High Heteroplasmy Frequency
Elastic analysis bridges structure and dynamics of an AAA+ molecular motor
The folded X-pattern is not necessarily a statistical signature of decision confidence
When does humoral memory enhance infection?
I Am Not a Scientist, I Am a Number
An Introduction to Biomolecular Graphics
Alu and B1 Repeats Have Been Selectively Retained in the Upstream and Intronic Regions of Genes of Specific Functional Classes
The stochastic logistic model with correlated carrying capacities reproduces beta-diversity metrics of microbial communities
A Guild of 45 CRISPR-Associated (Cas) Protein Families and Multiple CRISPR/Cas Subtypes Exist in Prokaryotic Genomes
Mutant fate in spatially structured populations on graphs: Connecting models to experiments
Lineage space and the propensity of bacterial cells to undergo growth transitions
The finite state projection based Fisher information matrix approach to estimate information and optimize single-cell experiments
Ad hoc efforts for advancing data science education
FAIR-USE4OS: Guidelines for creating impactful open-source software
Competitive tuning: Competition's role in setting the frequency-dependence of Ca2+-dependent proteins
Tracking Pseudomonas aeruginosa transmissions due to environmental contamination after discharge in ICUs using mathematical models
Elucidating multi-input processing 3-node gene regulatory network topologies capable of generating striped gene expression patterns
Derivation and simulation of a computational model of active cell populations: How overlap avoidance, deformability, cell-cell junctions and cytoskeletal forces affect alignment
Unusual Intron Conservation near Tissue-Regulated Exons Found by Splicing Microarrays
Integrating thermodynamic and sequence contexts improves protein-RNA binding prediction
Treatment-Mediated Alterations in HIV Fitness Preserve CD4 + T Cell Counts but Have Minimal Effects on Viral Load
All-atom simulation of the HET-s prion replication
Representational structure or task structure? Bias in neural representational similarity analysis and a Bayesian method for reducing bias
High-Accuracy HLA Type Inference from Whole-Genome Sequencing Data Using Population Reference Graphs
Coordinated Optimization of Visual Cortical Maps (I) Symmetry-based Analysis
Learning to integrate parts for whole through correlated neural variability
The condition for dynamic stability in humans walking with feedback control
Radiation necrosis after radiation therapy treatment of brain metastases: A computational approach
Disentangling Abstraction from Statistical Pattern Matching in Human and Machine Learning
Computer-guided binding mode identification and affinity improvement of an LRR protein binder without structure determination
Extended ensemble simulations of a SARS-CoV-2 nsp1-5'-UTR complex
Dynamic Alignment Models for Neural Coding
Visual Data Mining of Biological Networks: One Size Does Not Fit All
A model of how depth facilitates scene-relative object motion perception
Vulnerability-Based Critical Neurons, Synapses, and Pathways in the Caenorhabditis elegans Connectome
Direct coupling analysis of epistasis in allosteric materials
How Sensitive Is the Human Visual System to the Local Statistics of Natural Images?
Comparisons of Allergenic and Metazoan Parasite Proteins: Allergy the Price of Immunity
Machine learning prediction of malaria vaccine efficacy based on antibody profiles
The role of adaptation in generating monotonic rate codes in auditory cortex
Ten Simple Rules to becoming a principal investigator
Ancestral Reconstruction
A Robust Feedforward Model of the Olfactory System
Spatiotemporal orchestration of calcium-cAMP oscillations on AKAP/AC nanodomains is governed by an incoherent feedforward loop
Parallel Representation of Value-Based and Finite State-Based Strategies in the Ventral and Dorsal Striatum
Establishment and Validation of Computational Model for MT1-MMP Dependent ECM Degradation and Intervention Strategies
teemi: An open-source literate programming approach for iterative design-build-test-learn cycles in bioengineering
MaxComp: Predicting single-cell chromatin compartments from 3D chromosome structures
Factors affecting aerosol SARS-CoV-2 transmission via HVAC systems; a modeling study
Ten simple rules for establishing an experimental lab
Minor variations in multicellular life cycles have major effects on adaptation
A Low Dimensional Description of Globally Coupled Heterogeneous Neural Networks of Excitatory and Inhibitory Neurons
Inference of Disease-Related Molecular Logic from Systems-Based Microarray Analysis
Regulating synchronous oscillations of cerebellar granule cells by different types of inhibition
Linear Motif-Mediated Interactions Have Contributed to the Evolution of Modularity in Complex Protein Interaction Networks
Avoidance of non-localizable obstacles in echolocating bats: A robotic model
Local motion adaptation enhances the representation of spatial structure at EMD arrays
Genome Complexity Browser: Visualization and quantification of genome variability
A Multi-Compartment Model for Interneurons in the Dorsal Lateral Geniculate Nucleus
A MAPK-Driven Feedback Loop Suppresses Rac Activity to Promote RhoA-Driven Cancer Cell Invasion
Qualitative Dynamical Modelling Can Formally Explain Mesoderm Specification and Predict Novel Developmental Phenotypes
Predicted Functions of MdmX in Fine-Tuning the Response of p53 to DNA Damage
Are There Rearrangement Hotspots in the Human Genome?
Order Under Uncertainty: Robust Differential Expression Analysis Using Probabilistic Models for Pseudotime Inference
Noncommutative Biology: Sequential Regulation of Complex Networks
A Mechanistic Model for Cooperative Behavior of Co-transcribing RNA Polymerases
Ten simple rules for failing successfully in academia
Prediction of off-target specificity and cell-specific fitness of CRISPR-Cas System using attention boosted deep learning and network-based gene feature
From Cellular Characteristics to Disease Diagnosis: Uncovering Phenotypes with Supercells
A deep generative model of 3D single-cell organization
Evolution and Optimality of Similar Neural Mechanisms for Perception and Action during Search
STL-based Analysis of TRAIL-induced Apoptosis Challenges the Notion of Type I/Type II Cell Line Classification
Evolutionary history of calcium-sensing receptors unveils hyper/hypocalcemia-causing mutations
Computational characterization of the xanthan gum glycosyltransferase GumK
Correction: cytoNet: Spatiotemporal network analysis of cell communities
CLIC, a tool for expanding biological pathways based on co-expression across thousands of datasets
Differential Chromosome Conformations as Hallmarks of Cellular Identity Revealed by Mathematical Polymer Modeling
Oscillations in an artificial neural network convert competing inputs into a temporal code
CrossLabFit: A novel framework for integrating qualitative and quantitative data across multiple labs for model calibration
Slower Visuomotor Corrections with Unchanged Latency are Consistent with Optimal Adaptation to Increased Endogenous Noise in the Elderly
Integrated Mechanisms of Anticipation and Rate-of-Change Computations in Cortical Circuits
Can Molecular Motors Drive Distance Measurements in Injured Neurons?
Transcriptomic landscape around wound bed defines regenerative versus non-regenerative outcomes in mouse digit amputation
A low-dimensional approximation of optimal confidence
POMAShiny: A user-friendly web-based workflow for metabolomics and proteomics data analysis
AI-Aristotle: A physics-informed framework for systems biology gray-box identification
Transformation of Context-dependent Sensory Dynamics into Motor Behavior
New model of glucose-insulin regulation characterizes effects of physical activity and facilitates personalized treatment evaluation in children and adults with type 1 diabetes
A Factor Graph Nested Effects Model To Identify Networks from Genetic Perturbations
Ten quick tips for avoiding pitfalls in multi-omics data integration analyses
CRIMSON: An open-source software framework for cardiovascular integrated modelling and simulation
Blood vessel tortuosity selects against evolution of aggressive tumor cells in confined tissue environments: A modeling approach
Use of Raman and Raman optical activity to extract atomistic details of saccharides in aqueous solution
JBrowse Connect: A server API to connect JBrowse instances and users
Mechanistic Modelling and Bayesian Inference Elucidates the Variable Dynamics of Double-Strand Break Repair
Evolution of Stress Response in the Face of Unreliable Environmental Signals
Dissecting Dynamic Genetic Variation That Controls Temporal Gene Response in Yeast
Forgetting in Reinforcement Learning Links Sustained Dopamine Signals to Motivation
Subthreshold moment analysis of neuronal populations driven by synchronous synaptic inputs
An information theoretic method to resolve millisecond-scale spike timing precision in a comprehensive motor program
Estimating genetic variance contributed by a quantitative trait locus: A random model approach
Learning what matters: Synaptic plasticity with invariance to second-order input correlations
"Guilt by Association" Is the Exception Rather Than the Rule in Gene Networks
Dynamics of Cellular Responses to Radiation
Correction: Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences
Chromatin accessibility of primary human cancers ties regional mutational processes and signatures with tissues of origin
Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast
Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible
Asymmetrical Damage Partitioning in Bacteria: A Model for the Evolution of Stochasticity, Determinism, and Genetic Assimilation
Assimilating Seizure Dynamics
Fine-scale estimation of effective reproduction numbers for dengue surveillance
Emergence of spontaneous assembly activity in developing neural networks without afferent input
A spatio-temporal individual-based network framework for West Nile virus in the USA: Spreading pattern of West Nile virus
Quantifying the strength of quorum sensing crosstalk within microbial communities
Extracting Message Inter-Departure Time Distributions from the Human Electroencephalogram
Simple Plans or Sophisticated Habits? State, Transition and Learning Interactions in the Two-Step Task
Automated Protein Subfamily Identification and Classification
Ten simple rules in biomedical engineering to improve healthcare equity
Signatures of hierarchical temporal processing in the mouse visual system
A reaction-diffusion network model predicts a dual role of Cactus/IκB to regulate Dorsal/NFκB nuclear translocation in Drosophila
Fused Regression for Multi-source Gene Regulatory Network Inference
A recurrent neural network model of prefrontal brain activity during a working memory task
How does feedback from phage infections influence the evolution of phase variation in Campylobacter?
Incorporating the speciation process into species delimitation
A Mechanical Design Principle for Tissue Structure and Function in the Airway Tree
Probability Matching as a Computational Strategy Used in Perception
Variations in the Binding Pocket of an Inhibitor of the Bacterial Division Protein FtsZ across Genotypes and Species
A molecular odorant transduction model and the complexity of spatio-temporal encoding in the Drosophila antenna
CeleST: Computer Vision Software for Quantitative Analysis of C. elegans Swim Behavior Reveals Novel Features of Locomotion
Network-guided prediction of aromatase inhibitor response in breast cancer
An Adapting Auditory-motor Feedback Loop Can Contribute to Generating Vocal Repetition
Mesoscale simulations predict the role of synergistic cerebellar plasticity during classical eyeblink conditioning
Towards Identifying and Reducing the Bias of Disease Information Extracted from Search Engine Data
Strong intracellular signal inactivation produces sharper and more robust signaling from cell membrane to nucleus
Revealing cancer driver genes through integrative transcriptomic and epigenomic analyses with Moonlight
Measuring distance through dense weighted networks: The case of hospital-associated pathogens
Connectivity Homology Enables Inter-Species Network Models of Synthetic Lethality
Dynamic filopodial forces induce accumulation, damage, and plastic remodeling of 3D extracellular matrices
Phase-Locked Signals Elucidate Circuit Architecture of an Oscillatory Pathway
Calcium modeling of spine apparatus-containing human dendritic spines demonstrates an "all-or-nothing" communication switch between the spine head and dendrite
Global diversity and balancing selection of 23 leading Plasmodium falciparum candidate vaccine antigens
To what extent naringenin binding and membrane depolarization shape mitoBK channel gating - A machine learning approach
Spherical harmonics texture extraction for versatile analysis of biological objects
One thousand simple rules
Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants
NanoMethViz: An R/Bioconductor package for visualizing long-read methylation data
Ten Simple Rules for Taking Advantage of Git and GitHub
Spatiotemporal Computations of an Excitable and Plastic Brain: Neuronal Plasticity Leads to Noise-Robust and Noise-Constructive Computations
Ten simple rules for writing Dockerfiles for reproducible data science
A computational study of co-inhibitory immune complex assembly at the interface between T cells and antigen presenting cells
A Quick Guide to Teaching R Programming to Computational Biology Students
Optimal Schedules of Light Exposure for Rapidly Correcting Circadian Misalignment
Inter-domain Communication Mechanisms in an ABC Importer: A Molecular Dynamics Study of the MalFGK 2 E Complex
Towards a Mathematical Theory of Cortical Micro-circuits
BrainIAK tutorials: User-friendly learning materials for advanced fMRI analysis
Histologic and biochemical alterations predict pulmonary mechanical dysfunction in aging mice with chronic lung inflammation
Knowledge-Based Analysis for Detecting Key Signaling Events from Time-Series Phosphoproteomics Data
Optimal control prevents itself from eradicating stochastic disease epidemics
Human Monogenic Disease Genes Have Frequently Functionally Redundant Paralogs
In the Multi-domain Protein Adenylate Kinase, Domain Insertion Facilitates Cooperative Folding while Accommodating Function at Domain Interfaces
scHiCTools: A computational toolbox for analyzing single-cell Hi-C data
Optimal Learning Rules for Discrete Synapses
Genome Comparison of Human and Non-Human Malaria Parasites Reveals Species Subset-Specific Genes Potentially Linked to Human Disease
Correction: Quantitative Analysis of Glycerol Accumulation, Glycolysis and Growth under Hyper Osmotic Stress
The R-loop grammar predicts R-loop formation under different topological constraints
Prediction of Microbial Growth Rate versus Biomass Yield by a Metabolic Network with Kinetic Parameters
Invariant Distribution of Promoter Activities in Escherichia coli
Nine quick tips for efficient bioinformatics curriculum development and training
Characteristics of measles epidemics in China (1951-2004) and implications for elimination: A case study of three key locations
Ten simple rules for running a summer research program
Comparative Analysis of Yeast Metabolic Network Models Highlights Progress, Opportunities for Metabolic Reconstruction
Freedom to choose between public resources promotes cooperation
Oligomers of Heat-Shock Proteins: Structures That Don't Imply Function