yusuke1997/dblp-id-title huggingface dataset:
Heterogeneous firing responses predict diverse couplings to presynaptic activity in mice layer V pyramidal neurons
Optimal Behavioral Hierarchy
A Toolbox for Representational Similarity Analysis
Dynamic combination of sensory and reward information under time pressure
A Kinetic Model of Dopamine- and Calcium-Dependent Striatal Synaptic Plasticity
Mathematical Modeling of Heterogeneous Electrophysiological Responses in Human β -Cells
Scalable and flexible inference framework for stochastic dynamic single-cell models
Branch Mode Selection during Early Lung Development
Patterning the insect eye: From stochastic to deterministic mechanisms
Systems Biology of Coagulation Initiation: Kinetics of Thrombin Generation in Resting and Activated Human Blood
The Origin of Minus-end Directionality and Mechanochemistry of Ncd Motors
Modular Design of Artificial Tissue Homeostasis: Robust Control through Synthetic Cellular Heterogeneity
Evolutionary footprint of epistasis
Assessing the Accuracy of Ancestral Protein Reconstruction Methods
Structural Reorganisation and Potential Toxicity of Oligomeric Species Formed during the Assembly of Amyloid Fibrils
Computational Models Describing Possible Mechanisms for Generation of Excessive Beta Oscillations in Parkinson's Disease
EAT-Rice: A predictive model for flanking gene expression of T-DNA insertion activation-tagged rice mutants by machine learning approaches
Finding driver mutations in cancer: Elucidating the role of background mutational processes
Domino-like transient dynamics at seizure onset in epilepsy
A Unified Model of Heading and Path Perception in Primate MSTd
Bayesian Inference of Pathogen Phylogeography using the Structured Coalescent Model
Optimality principles reveal a complex interplay of intermediate toxicity and kinetic efficiency in the regulation of prokaryotic metabolism
Generative Embedding for Model-Based Classification of fMRI Data
Colony entropy - Allocation of goods in ant colonies
Design Principles for Riboswitch Function
Helicobacter pylori Evolution: Lineage- Specific Adaptations in Homologs of Eukaryotic Sel1-Like Genes
Community composition exceeds area as a predictor of long-term conservation value
Comparing Families of Dynamic Causal Models
Long-Lasting Sparks: Multi-Metastability and Release Competition in the Calcium Release Unit Network
Stochastic simulations of self-organized elastogenesis in the developing lung
Proteostasis signatures in human diseases
Self-Organization of Muscle Cell Structure and Function
Model-based translation of DNA damage signaling dynamics across cell types
Topological Phenotypes Constitute a New Dimension in the Phenotypic Space of Leaf Venation Networks
DeepCME: A deep learning framework for computing solution statistics of the chemical master equation
Ten simple rules for providing a meaningful research experience to high school students
The evolution of behavioral cues and signaling in displaced communication
Slow manifolds within network dynamics encode working memory efficiently and robustly
Possible Role of Interleukin-1β in Type 2 Diabetes Onset and Implications for Anti-inflammatory Therapy Strategies
Slow Feature Analysis on Retinal Waves Leads to V1 Complex Cells
A Condensation-Ordering Mechanism in Nanoparticle-Catalyzed Peptide Aggregation
Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors
A unifying model for the propagation of prion proteins in yeast brings insight into the [PSI+] prion
ReproPhylo: An Environment for Reproducible Phylogenomics
ESPRIT-Forest: Parallel clustering of massive amplicon sequence data in subquadratic time
Ten Simple Rules for Creating a Good Data Management Plan
Amplifiers of selection for the Moran process with both Birth-death and death-Birth updating
Modelling continual learning in humans with Hebbian context gating and exponentially decaying task signals
A marginalized two-part Beta regression model for microbiome compositional data
Stability Curve Prediction of Homologous Proteins Using Temperature-Dependent Statistical Potentials
Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit
Modeling diffusive search by non-adaptive sperm: Empirical and computational insights
Prospective Optimization with Limited Resources
Role of diffusion and reaction of the constituents in spreading of histone modification marks
Generalizing to generalize: Humans flexibly switch between compositional and conjunctive structures during reinforcement learning
Mechanistic multiscale modelling of energy metabolism in human astrocytes reveals the impact of morphology changes in Alzheimer's Disease
Synaptic Plasticity in Neural Networks Needs Homeostasis with a Fast Rate Detector
The Role of Response Elements Organization in Transcription Factor Selectivity: The IFN-β Enhanceosome Example
Model of neural induction in the ascidian embryo
Self-Organized Criticality in Developing Neuronal Networks
Spatial modeling of the membrane-cytosolic interface in protein kinase signal transduction
Adaptive oscillators support Bayesian prediction in temporal processing
Connectivity and dynamics in the olfactory bulb
Accurate Distinction of Pathogenic from Benign CNVs in Mental Retardation
Evolutionary Genomics Suggests That CheV Is an Additional Adaptor for Accommodating Specific Chemoreceptors within the Chemotaxis Signaling Complex
Metabolic modeling of sex-specific liver tissue suggests mechanism of differences in toxicological responses
Controlling seizure propagation in large-scale brain networks
Herbivore community function shapes resilience and bistability of coral reefs
Locust Collective Motion and Its Modeling
A Quick Guide to Genomics and Bioinformatics Training for Clinical and Public Audiences
PathFX provides mechanistic insights into drug efficacy and safety for regulatory review and therapeutic development
Spatial and Topological Organization of DNA Chains Induced by Gene Co-localization
The Multilayer Connectome of Caenorhabditis elegans
Spatial inequities in access to medications for treatment of opioid use disorder highlight scarcity of methadone providers under counterfactual scenarios
A Predictive Model for Yeast Cell Polarization in Pheromone Gradients
Prioritising older individuals for COVID-19 booster vaccination leads to optimal public health outcomes in a range of socio-economic settings
Theta-gamma coupling emerges from spatially heterogeneous cholinergic neuromodulation
Combining Evolutionary Information and an Iterative Sampling Strategy for Accurate Protein Structure Prediction
Causal network inference from gene transcriptional time-series response to glucocorticoids
Maintaining maximal metabolic flux by gene expression control
Interpretable online network dictionary learning for inferring long-range chromatin interactions
Efficient Physical Embedding of Topologically Complex Information Processing Networks in Brains and Computer Circuits
A modelling approach for exploring muscle dynamics during cyclic contractions
The ability of transcription factors to differentially regulate gene expression is a crucial component of the mechanism underlying inversion, a frequently observed genetic interaction pattern
A Bayesian Approach to the Evolution of Metabolic Networks on a Phylogeny
Automated plant species identification - Trends and future directions
Changes in Lysozyme Flexibility upon Mutation Are Frequent, Large and Long-Ranged
Memory Switches in Chemical Reaction Space
GenomicScape: An Easy-to-Use Web Tool for Gene Expression Data Analysis. Application to Investigate the Molecular Events in the Differentiation of B Cells into Plasma Cells
Elucidating the Altered Transcriptional Programs in Breast Cancer using Independent Component Analysis
Efficient encoding of motion is mediated by gap junctions in the fly visual system
Energy Landscape of All-Atom Protein-Protein Interactions Revealed by Multiscale Enhanced Sampling
Glycoside Hydrolases across Environmental Microbial Communities
Divisive Gain Modulation with Dynamic Stimuli in Integrate-and-Fire Neurons
A Model of Binocular Rivalry and Cross-orientation Suppression
The Role of Genome Accessibility in Transcription Factor Binding in Bacteria
Bayesian Comparison of Neurovascular Coupling Models Using EEG-fMRI
Efficient Optimization of Stimuli for Model-Based Design of Experiments to Resolve Dynamical Uncertainty
The Essential Complexity of Auditory Receptive Fields
Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data
Improving the reliability of model-based decision-making estimates in the two-stage decision task with reaction-times and drift-diffusion modeling
Beyond Statistical Significance: Implications of Network Structure on Neuronal Activity
Persisting Viral Sequences Shape Microbial CRISPR-based Immunity
Sensorimotor Model of Obstacle Avoidance in Echolocating Bats
A new index for characterizing micro-bead motion in a flow induced by ciliary beating: Part I, experimental analysis
Bud-Localization of CLB2 mRNA Can Constitute a Growth Rate Dependent Daughter Sizer
Optimizing tuberculosis treatment efficacy: Comparing the standard regimen with Moxifloxacin-containing regimens
A Bayesian model of distance perception from ocular convergence
A Bayesian Ensemble Approach for Epidemiological Projections
Gene Expression in the Rodent Brain is Associated with Its Regional Connectivity
Information-theoretic analysis of realistic odor plumes: What cues are useful for determining location?
A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts
Modular Composition of Gene Transcription Networks
Predicting Epidemic Risk from Past Temporal Contact Data
Capabilities and Limitations of Tissue Size Control through Passive Mechanical Forces
Separability of Human Motor Memories during reaching adaptation with force cues
NMDA receptor inhibition increases, synchronizes, and stabilizes the collective pancreatic beta cell activity: Insights through multilayer network analysis
Brain and Behavior in Decision-Making
Identifying Tightly Regulated and Variably Expressed Networks by Differential Rank Conservation (DIRAC)
Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models?
Biophysics and population size constrains speciation in an evolutionary model of developmental system drift
Molecular basis of Arginine and Lysine DNA sequence-dependent thermo-stability modulation
Forecasting upper respiratory tract infection burden using high-dimensional time series data and forecast combinations
Comparison of fluctuations in global network topology of modeled and empirical brain functional connectivity
Radical triads, not pairs, may explain effects of hypomagnetic fields on neurogenesis
Penalised regression improves imputation of cell-type specific expression using RNA-seq data from mixed cell populations compared to domain-specific methods
Digital Atlasing and Standardization in the Mouse Brain
Sampling effects and measurement overlap can bias the inference of neuronal avalanches
Analyzing and Synthesizing Phylogenies Using Tree Alignment Graphs
CRISPR-M: Predicting sgRNA off-target effect using a multi-view deep learning network
Fold Designability, Distribution, and Disease
CStone: A de novo transcriptome assembler for short-read data that identifies non-chimeric contigs based on underlying graph structure
Binding of Two Intrinsically Disordered Peptides to a Multi-Specific Protein: A Combined Monte Carlo and Molecular Dynamics Study
Topological data analysis distinguishes parameter regimes in the Anderson-Chaplain model of angiogenesis
Forecasting the 2013-2014 Influenza Season Using Wikipedia
Estimated Comparative Integration Hotspots Identify Different Behaviors of Retroviral Gene Transfer Vectors
Bayesian History Matching of Complex Infectious Disease Models Using Emulation: A Tutorial and a Case Study on HIV in Uganda
Impact of increased diagnosis of early HIV infection and immediate antiretroviral treatment initiation on HIV transmission among men who have sex with men in the Netherlands
Orbit Image Analysis: An open-source whole slide image analysis tool
A Novel Extended Granger Causal Model Approach Demonstrates Brain Hemispheric Differences during Face Recognition Learning
Correction: The specious art of single-cell genomics
Novel Inhibitors Induce Large Conformational Changes of GAB1 Pleckstrin Homology Domain and Kill Breast Cancer Cells
Learning, visualizing and exploring 16S rRNA structure using an attention-based deep neural network
Optimization of Muscle Activity for Task-Level Goals Predicts Complex Changes in Limb Forces across Biomechanical Contexts
A computational modeling approach for predicting multicell spheroid patterns based on signaling-induced differential adhesion
iCRBP-LKHA: Large convolutional kernel and hybrid channel-spatial attention for identifying circRNA-RBP interaction sites
Non-ohmic tissue conduction in cardiac electrophysiology: Upscaling the non-linear voltage-dependent conductance of gap junctions
Model-based spatial navigation in the hippocampus-ventral striatum circuit: A computational analysis
Scene complexity modulates degree of feedback activity during object detection in natural scenes
A Neurocomputational Model of the Mismatch Negativity
A Network Convergence Zone in the Hippocampus
Metapopulation Persistence in Random Fragmented Landscapes
Correction: clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets
Flux balance analysis of the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC19718 unravels specific metabolic activities while degrading toxic compounds
Nonlinear eco-evolutionary games with global environmental fluctuations and local environmental feedbacks
Estimating the cumulative incidence of COVID-19 in the United States using influenza surveillance, virologic testing, and mortality data: Four complementary approaches
Towards a System Level Understanding of Non-Model Organisms Sampled from the Environment: A Network Biology Approach
Calculation of the force field required for nucleus deformation during cell migration through constrictions
Modeling the effects of Aedes aegypti's larval environment on adult body mass at emergence
A Thalamocortical Neural Mass Model of the EEG during NREM Sleep and Its Response to Auditory Stimulation
Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies
Reactive Oxygen Species Production by Forward and Reverse Electron Fluxes in the Mitochondrial Respiratory Chain
Alkylpurine Glycosylase D Employs DNA Sculpting as a Strategy to Extrude and Excise Damaged Bases
Synchronization of Isolated Downstates (K-Complexes) May Be Caused by Cortically-Induced Disruption of Thalamic Spindling
Morphophenotypic classification of tumor organoids as an indicator of drug exposure and penetration potential
Bayesian inference of phylogenetic networks from bi-allelic genetic markers
PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data
Ten simple rules in considering a career in academia versus government
Evolutionary Analysis of Human Immunodeficiency Virus Type 1 Therapies Based on Conditionally Replicating Vectors
Ten Simple Rules for Lifelong Learning, According to Hamming
Correction: Systematic Analysis of Head-to-Head Gene Organization: Evolutionary Conservation and Potential Biological Relevance
BIPS - A code base for designing and coding of a Phage ImmunoPrecipitation Oligo Library
Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures
The geometry of representational drift in natural and artificial neural networks
A cell-and-plasma numerical model reveals hemodynamic stress and flow adaptation in zebrafish microvessels after morphological alteration
Modelling the effectiveness of antiviral treatment strategies to prevent household transmission of acute respiratory viruses
Cargo surface fluidity can reduce inter-motor mechanical interference, promote load-sharing and enhance processivity in teams of molecular motors
Transfer learning enables prediction of CYP2D6 haplotype function
Modeling Higher-Order Correlations within Cortical Microcolumns
Polypolish: Short-read polishing of long-read bacterial genome assemblies
Two-dimensional video-based analysis of human gait using pose estimation
Time warping between main epidemic time series in epidemiological surveillance
Ten Simple Rules for Getting Published
Functional Rotation of the Transporter AcrB: Insights into Drug Extrusion from Simulations
Impact of between-tissue differences on pan-cancer predictions of drug sensitivity
Computational Fragment-Based Binding Site Identification by Ligand Competitive Saturation
Suprachiasmatic nucleus-wide estimation of oscillatory temporal dynamics
Proteostasis is adaptive: Balancing chaperone holdases against foldases
Identification of dynamical changes of rabies transmission under quarantine: Community-based measures towards rabies elimination
Firing-rate based network modeling of the dLGN circuit: Effects of cortical feedback on spatiotemporal response properties of relay cells
A General Definition and Nomenclature for Alternative Splicing Events
Neocortical Axon Arbors Trade-off Material and Conduction Delay Conservation
Optical Neuroimage Studio (OptiNiSt): Intuitive, scalable, extendable framework for optical neuroimage data analysis
Multistable Decision Switches for Flexible Control of Epigenetic Differentiation
Inhibitory neurons exhibit high controlling ability in the cortical microconnectome
Canalization of Gene Expression and Domain Shifts in the Drosophila Blastoderm by Dynamical Attractors
Application of modular response analysis to medium- to large-size biological systems
Discovering Sequence Motifs with Arbitrary Insertions and Deletions
Ten Simple Rules for Providing a Scientific Web Resource
ISMB/ECCB Rebooted: 2015 Brings Major Update to the Meeting Program
Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows
Ten simple rules for more objective decision-making
Consequences of Converting Graded to Action Potentials upon Neural Information Coding and Energy Efficiency
Characterizing the Metabolism of Dehalococcoides with a Constraint-Based Model
Large-Scale Conformational Transitions and Dimerization Are Encoded in the Amino-Acid Sequences of Hsp70 Chaperones
Visualization and quantification of coral reef soundscapes using CoralSoundExplorer software
A Theory of Rate Coding Control by Intrinsic Plasticity Effects
Multiscale community detection in Cytoscape
A dose-response model for statistical analysis of chemical genetic interactions in CRISPRi screens
Vertical Binocular Disparity is Encoded Implicitly within a Model Neuronal Population Tuned to Horizontal Disparity and Orientation
Correction: Intrinsic motivation for choice varies with individual risk attitudes and the controllability of the environment
Fast and interpretable consensus clustering via minipatch learning
In vivo and in silico dynamics of the development of Metabolic Syndrome
The FGGY Carbohydrate Kinase Family: Insights into the Evolution of Functional Specificities
Ten simple rules for reporting a bug
Multiscale Mechanical Model of the Pacinian Corpuscle Shows Depth and Anisotropy Contribute to the Receptor's Characteristic Response to Indentation
Basal leakage in oscillation: Coupled transcriptional and translational control using feed-forward loops
Active head rolls enhance sonar-based auditory localization performance
Associating lncRNAs with small molecules via bilevel optimization reveals cancer-related lncRNAs
Do Humans Optimally Exploit Redundancy to Control Step Variability in Walking?
Computing Average Passive Forces in Sarcomeres in Length-Ramp Simulations
SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent
Positive allosteric modulators of lecithin: Cholesterol acyltransferase adjust the orientation of the membrane-binding domain and alter its spatial free energy profile
Rapid 3D phenotypic analysis of neurons and organoids using data-driven cell segmentation-free machine learning
Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration
The impact of whole genome duplications on the human gene regulatory networks
Antithetic effect of interferon-α on cell-free and cell-to-cell HIV-1 infection
A structured evaluation of genome-scale constraint-based modeling tools for microbial consortia
Lipidome visualisation, comparison, and analysis in a vector space
Stochastic Model of Integrin-Mediated Signaling and Adhesion Dynamics at the Leading Edges of Migrating Cells
Strategies for Identifying RNA Splicing Regulatory Motifs and Predicting Alternative Splicing Events
BioCRNpyler: Compiling chemical reaction networks from biomolecular parts in diverse contexts
Selection for rapid uptake of scarce or fluctuating resource explains vulnerability of glycolysis to imbalance
Possible roles of mechanical cell elimination intrinsic to growing tissues from the perspective of tissue growth efficiency and homeostasis
Beyond the chemical master equation: Stochastic chemical kinetics coupled with auxiliary processes
Learning to represent signals spike by spike
Circadian KaiC Phosphorylation: A Multi-Layer Network
Synergistic epistasis among cancer drivers can rescue early tumors from the accumulation of deleterious passengers
Microbial Forensics: Predicting Phenotypic Characteristics and Environmental Conditions from Large-Scale Gene Expression Profiles
Using Network Component Analysis to Dissect Regulatory Networks Mediated by Transcription Factors in Yeast
Learning a deep language model for microbiomes: The power of large scale unlabeled microbiome data
Nonlinear stimulus representations in neural circuits with approximate excitatory-inhibitory balance
Determination of the Processes Driving the Acquisition of Immunity to Malaria Using a Mathematical Transmission Model
Discovery of novel dual adenosine A1/A2A receptor antagonists using deep learning, pharmacophore modeling and molecular docking
A curated genome-scale metabolic model of Bordetella pertussis metabolism
Critical Roles of the Direct GABAergic Pallido-cortical Pathway in Controlling Absence Seizures
ProMod3 - A versatile homology modelling toolbox
A Combination of Transcriptional and MicroRNA Regulation Improves the Stability of the Relative Concentrations of Target Genes
Multiscale model of defective interfering particle replication for influenza A virus infection in animal cell culture
Spectral Analysis of Input Spike Trains by Spike-Timing-Dependent Plasticity
Modelling of Yeast Mating Reveals Robustness Strategies for Cell-Cell Interactions
Systematic Inference of Copy-Number Genotypes from Personal Genome Sequencing Data Reveals Extensive Olfactory Receptor Gene Content Diversity
Meteorological factors and non-pharmaceutical interventions explain local differences in the spread of SARS-CoV-2 in Austria
Inhibition as a Binary Switch for Excitatory Plasticity in Pyramidal Neurons
Assessing Computational Methods of Cis-Regulatory Module Prediction
Computational Discovery of Putative Leads for Drug Repositioning through Drug-Target Interaction Prediction
Behaviors and Strategies of Bacterial Navigation in Chemical and Nonchemical Gradients
Erroneous energy-generating cycles in published genome scale metabolic networks: Identification and removal
Origins of scale invariance in vocalization sequences and speech
Predicting the Responses of Repetitively Firing Neurons to Current Noise
RSero: A user-friendly R package to reconstruct pathogen circulation history from seroprevalence studies
Action subsampling supports policy compression in large action spaces
Spatial synchronization codes from coupled rate-phase neurons
In-silico and in-vitro morphometric analysis of intestinal organoids
Mechanisms of Left-Right Coordination in Mammalian Locomotor Pattern Generation Circuits: A Mathematical Modeling View
Molecular mechanism of proton-coupled ligand translocation by the bacterial efflux pump EmrE