yusuke1997/dblp-id-title huggingface dataset:
Modelling the Emergence and Dynamics of Perceptual Organisation in Auditory Streaming
In silico investigation of the mechanisms underlying atrial fibrillation due to impaired Pitx2
Chapter 17: Bioimage Informatics for Systems Pharmacology
Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns
Distribution of the Fittest Individuals and the Rate of Muller's Ratchet in a Model with Overlapping Generations
Modeling NaV1.1/SCN1A sodium channel mutations in a microcircuit with realistic ion concentration dynamics suggests differential GABAergic mechanisms leading to hyperexcitability in epilepsy and hemiplegic migraine
The Effects of Alignment Quality, Distance Calculation Method, Sequence Filtering, and Region on the Analysis of 16S rRNA Gene-Based Studies
The Dominant Folding Route Minimizes Backbone Distortion in SH3
An integrated, modular approach to data science education in microbiology
Mesoscopic Model of Actin-Based Propulsion
Molecular Origin of Polyglutamine Aggregation in Neurodegenerative Diseases
Correction: A system for tracking whisker kinematics and whisker shape in three dimensions
Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data
Spatial Generalization in Operant Learning: Lessons from Professional Basketball
CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data
Common data models to streamline metabolomics processing and annotation, and implementation in a Python pipeline
Social evolution under demographic stochasticity
Benchmarking the negatives: Effect of negative data generation on the classification of miRNA-mRNA interactions
Alternative Splicing Events Identified in Human Embryonic Stem Cells and Neural Progenitors
A multiscale model via single-cell transcriptomics reveals robust patterning mechanisms during early mammalian embryo development
Circuits with broken fibration symmetries perform core logic computations in biological networks
A Tale of Two Stories: Astrocyte Regulation of Synaptic Depression and Facilitation
The Role of Adaptation in Bacterial Speed Races
A model for the intrinsic limit of cancer therapy: Duality of treatment-induced cell death and treatment-induced stemness
Directing Experimental Biology: A Case Study in Mitochondrial Biogenesis
Interplay between Pleiotropy and Secondary Selection Determines Rise and Fall of Mutators in Stress Response
Tellurium notebooks - An environment for reproducible dynamical modeling in systems biology
The Dynamics of Supply and Demand in mRNA Translation
Evidence for Model-based Computations in the Human Amygdala during Pavlovian Conditioning
Long distance calls: Negligible information loss of little auk social vocalisations due to high frequency propagation losses
A Model of Reward- and Effort-Based Optimal Decision Making and Motor Control
Functionality and Robustness of Injured Connectomic Dynamics in C. elegans: Linking Behavioral Deficits to Neural Circuit Damage
Molecular Dynamics of "Fuzzy" Transcriptional Activator-Coactivator Interactions
Ten simple rules to host an inclusive conference
Different antigenic distance metrics generate similar predictions of influenza vaccine response breadth despite moderate correlation
Action planning and control under uncertainty emerge through a desirability-driven competition between parallel encoding motor plans
STDP and the distribution of preferred phases in the whisker system
More pests but less pesticide applications: Ambivalent effect of landscape complexity on conservation biological control
Bifurcations and bursting in the Epileptor
Computational Biology and Bioinformatics in Nigeria
Color improves edge classification in human vision
Non-degradative Ubiquitination of Protein Kinases
It's about time: Analysing simplifying assumptions for modelling multi-step pathways in systems biology
Competing endogenous RNA crosstalk at system level
Quantifying Differences and Similarities in Whole-Brain White Matter Architecture Using Local Connectome Fingerprints
Machine learning modeling of family wide enzyme-substrate specificity screens
Oxidized Calmodulin Kinase II Regulates Conduction Following Myocardial Infarction: A Computational Analysis
Modeling Viral Evolutionary Dynamics after Telaprevir-Based Treatment
Cytofkit: A Bioconductor Package for an Integrated Mass Cytometry Data Analysis Pipeline
Sparse Regression Based Structure Learning of Stochastic Reaction Networks from Single Cell Snapshot Time Series
A behavioral and modeling study of control algorithms underlying the translational optomotor response in larval zebrafish with implications for neural circuit function
Ten simple rules to power drug discovery with data science
The Changing Geometry of a Fitness Landscape Along an Adaptive Walk
Prediction of Drug Combinations by Integrating Molecular and Pharmacological Data
Phylogeographic reconstruction using air transportation data and its application to the 2009 H1N1 influenza A pandemic
Solving the RNA design problem with reinforcement learning
The Role of Adherence and Retreatment in De Novo Emergence of MDR-TB
Interaction of the human erythrocyte Band 3 anion exchanger 1 (AE1, SLC4A1) with lipids and glycophorin A: Molecular organization of the Wright (Wr) blood group antigen
Adaptable Functionality of Transcriptional Feedback in Bacterial Two-Component Systems
PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems
Computation in Dynamically Bounded Asymmetric Systems
A Stochastic Model of the Yeast Cell Cycle Reveals Roles for Feedback Regulation in Limiting Cellular Variability
Ten quick tips for creating an effective lesson
Positive interactions within and between populations decrease the likelihood of evolutionary rescue
A metabolic core model elucidates how enhanced utilization of glucose and glutamine, with enhanced glutamine-dependent lactate production, promotes cancer cell growth: The WarburQ effect
Paying attention to attention: High attention sites as indicators of protein family and function in language models
Complementary computational and experimental evaluation of missense variants in the ROMK potassium channel
Task-evoked activity quenches neural correlations and variability across cortical areas
Ten simple rules for getting started with command-line bioinformatics
MGDrivE 2: A simulation framework for gene drive systems incorporating seasonality and epidemiological dynamics
Particle-based simulations reveal two positive feedback loops allow relocation and stabilization of the polarity site during yeast mating
iModulonMiner and PyModulon: Software for unsupervised mining of gene expression compendia
Encoding of Natural Sounds at Multiple Spectral and Temporal Resolutions in the Human Auditory Cortex
MicrobiomeCensus estimates human population sizes from wastewater samples based on inter-individual variability in gut microbiomes
A predictive coding account of bistable perception - a model-based fMRI study
A Signature of Attractor Dynamics in the CA3 Region of the Hippocampus
A stochastic model for simulating ribosome kinetics in vivo
A phylogenetic method linking nucleotide substitution rates to rates of continuous trait evolution
Conditional prediction of consecutive tumor evolution using cancer progression models: What genotype comes next?
Estimating Location without External Cues
Spatial Stereoresolution for Depth Corrugations May Be Set in Primary Visual Cortex
New Maximum Likelihood Estimators for Eukaryotic Intron Evolution
When shared concept cells support associations: Theory of overlapping memory engrams
Allele-Specific Network Reveals Combinatorial Interaction That Transcends Small Effects in Psoriasis GWAS
Lateralised memory networks may explain the use of higher-order visual features in navigating insects
Coincident glutamatergic depolarizations enhance GABAA receptor-dependent Cl- influx in mature and suppress Cl- efflux in immature neurons
DelaySSA: stochastic simulation of biochemical systems and gene regulatory networks with or without time delays
The Underlying Molecular and Network Level Mechanisms in the Evolution of Robustness in Gene Regulatory Networks
A Switching Mechanism in Doxorubicin Bioactivation Can Be Exploited to Control Doxorubicin Toxicity
A Toolbox Model of Evolution of Metabolic Pathways on Networks of Arbitrary Topology
EUP: Enhanced cross-species prediction of ubiquitination sites via a conditional variational autoencoder network based on ESM2
Understanding dual process cognition via the minimum description length principle
Modeling cross-regulatory influences on monolignol transcripts and proteins under single and combinatorial gene knockdowns in Populus trichocarpa
Rates of CTL Killing in Persistent Viral Infection In Vivo
Collective predator evasion: Putting the criticality hypothesis to the test
Changes in Dynamics upon Oligomerization Regulate Substrate Binding and Allostery in Amino Acid Kinase Family Members
Comparative mapping of crawling-cell morphodynamics in deep learning-based feature space
The ins and outs of vanillyl alcohol oxidase: Identification of ligand migration paths
A deep learning model for prediction of autism status using whole-exome sequencing data
SynToxProfiler: An interactive analysis of drug combination synergy, toxicity and efficacy
The Shape of an Auxin Pulse, and What It Tells Us about the Transport Mechanism
Precise determination of input-output mapping for multimodal gene circuits using data from transient transfection
Optogenetic Stimulation Shifts the Excitability of Cerebral Cortex from Type I to Type II: Oscillation Onset and Wave Propagation
Integrating Extrinsic and Intrinsic Cues into a Minimal Model of Lineage Commitment for Hematopoietic Progenitors
Ten simple rules to make your publication look better
Inter-nucleosomal communication between histone modifications for nucleosome phasing
Evolution and Phenotypic Selection of Cancer Stem Cells
The permeation mechanism of organic cations through a CNG mimic channel
Functional duality in group criticality via ambiguous interactions
Identifying promoter sequence architectures via a chunking-based algorithm using non-negative matrix factorisation
CoVar: A generalizable machine learning approach to identify the coordinated regulators driving variational gene expression
Computational Phenotyping of Two-Person Interactions Reveals Differential Neural Response to Depth-of-Thought
Dissecting recurrent waves of pertussis across the boroughs of London
Soft Skills: An Important Asset Acquired from Organizing Regional Student Group Activities
RNA editing regulates lncRNA splicing in human early embryo development
Dynamics of chromosomal target search by a membrane-integrated one-component receptor
Spatial and Functional Heterogeneities Shape Collective Behavior of Tumor-Immune Networks
Real-time forecasting of COVID-19-related hospital strain in France using a non-Markovian mechanistic model
The Serotype Distribution among Healthy Carriers before Vaccination Is Essential for Predicting the Impact of Pneumococcal Conjugate Vaccine on Invasive Disease
SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution
Physiologically based pharmacokinetic/pharmacodynamic model for the prediction of morphine brain disposition and analgesia in adults and children
Causes and Consequences of Hyperexcitation in Central Clock Neurons
Semi-automated 3D Leaf Reconstruction and Analysis of Trichome Patterning from Light Microscopic Images
Investigating differential abundance methods in microbiome data: A benchmark study
Predicting Human Nucleosome Occupancy from Primary Sequence
Integrating Flux Balance Analysis into Kinetic Models to Decipher the Dynamic Metabolism of Shewanella oneidensis MR-1
Protein prediction models support widespread post-transcriptional regulation of protein abundance by interacting partners
Ten Simple Rules To Commercialize Scientific Research
A particle-based computational model to analyse remodelling of the red blood cell cytoskeleton during malaria infections
A Multiscale Model to Investigate Circadian Rhythmicity of Pacemaker Neurons in the Suprachiasmatic Nucleus
A Healthy Fear of the Unknown: Perspectives on the Interpretation of Parameter Fits from Computational Models in Neuroscience
Scalable multi-sample single-cell data analysis by Partition-Assisted Clustering and Multiple Alignments of Networks
TIPP3 and TIPP3-fast: Improved abundance profiling in metagenomics
Decoding brain activity using a large-scale probabilistic functional-anatomical atlas of human cognition
Prediction and Dissection of Widely-Varying Association Rate Constants of Actin-Binding Proteins
serojump: A Bayesian tool for inferring infection timing and antibody kinetics from longitudinal serological data
Information Routing Driven by Background Chatter in a Signaling Network
Positional SHAP (PoSHAP) for Interpretation of machine learning models trained from biological sequences
AC-PCoA: Adjustment for confounding factors using principal coordinate analysis
Bayesian Inference for Genomic Data Integration Reduces Misclassification Rate in Predicting Protein-Protein Interactions
Correction: Bayesian parameter estimation for dynamical models in systems biology
Large Scale Characterization of the LC13 TCR and HLA-B8 Structural Landscape in Reaction to 172 Altered Peptide Ligands: A Molecular Dynamics Simulation Study
Target Prediction for an Open Access Set of Compounds Active against Mycobacterium tuberculosis
Data-driven reverse engineering of signaling pathways using ensembles of dynamic models
Dorsal and median raphe neuronal firing dynamics characterized by nonlinear measures
Structural diversity of B-cell receptor repertoires along the B-cell differentiation axis in humans and mice
Modeling CRISPR gene drives for suppression of invasive rodents using a supervised machine learning framework
Task-Based Core-Periphery Organization of Human Brain Dynamics
Global disruption in excitation-inhibition balance can cause localized network dysfunction and Schizophrenia-like context-integration deficits
Structural organization and energy storage in crosslinked actin assemblies
Why do eukaryotic proteins contain more intrinsically disordered regions?
Correction: From space to time: Spatial inhomogeneities lead to the emergence of spatiotemporal sequences in spiking neuronal networks
Accumulation of continuously time-varying sensory evidence constrains neural and behavioral responses in human collision threat detection
BioJava 5: A community driven open-source bioinformatics library
Atorvastatin-mediated rescue of cancer-related cognitive changes in combined anticancer therapies
A Computational Model of Hepatic Energy Metabolism: Understanding Zonated Damage and Steatosis in NAFLD
Encoding of Spatio-Temporal Input Characteristics by a CA1 Pyramidal Neuron Model
Optimal Sequential Immunization Can Focus Antibody Responses against Diversity Loss and Distraction
Antagonistic Coevolution Drives Whack-a-Mole Sensitivity in Gene Regulatory Networks
Estimating the number of genetic mutations (hits) required for carcinogenesis based on the distribution of somatic mutations
Stochastic dynamics of Francisella tularensis infection and replication
Inferring Clonal Composition from Multiple Sections of a Breast Cancer
Single-cell analysis reveals the pan-cancer invasiveness-associated transition of adipose-derived stromal cells into COL11A1-expressing cancer-associated fibroblasts
Learning from the past: A short term forecast method for the COVID-19 incidence curve
A neural network model for the orbitofrontal cortex and task space acquisition during reinforcement learning
In silico prediction of HIV-1-host molecular interactions and their directionality
Modelling the spatial dynamics of oncolytic virotherapy in the presence of virus-resistant tumour cells
Sm/Lsm Genes Provide a Glimpse into the Early Evolution of the Spliceosome
Mathematical modeling reveals ferritin as the strongest cellular driver of dietary iron transfer block in enterocytes
The Role of Ongoing Dendritic Oscillations in Single-Neuron Dynamics
A Likelihood-Based Approach to Identifying Contaminated Food Products Using Sales Data: Performance and Challenges
Computation of Conformational Coupling in Allosteric Proteins
Phenotypic Signatures Arising from Unbalanced Bacterial Growth
Improved Estimation and Interpretation of Correlations in Neural Circuits
Calibration of individual-based models to epidemiological data: A systematic review
Two types of critical cell density for mechanical elimination of abnormal cell clusters from epithelial tissue
An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data
A computational account of multiple motives guiding context-dependent prosocial behavior
Collective Signal Processing in Cluster Chemotaxis: Roles of Adaptation, Amplification, and Co-attraction in Collective Guidance
A Network Inference Method for Large-Scale Unsupervised Identification of Novel Drug-Drug Interactions
Inferring latent temporal progression and regulatory networks from cross-sectional transcriptomic data of cancer samples
A Structural Systems Biology Approach for Quantifying the Systemic Consequences of Missense Mutations in Proteins
Engineering gene overlaps to sustain genetic constructs in vivo
Hemodynamics-driven mathematical model of first and second heart sound generation
The challenge of chromatin model comparison and validation: A project from the first international 4D Nucleome Hackathon
A Balance Equation Determines a Switch in Neuronal Excitability
A New Fiji-Based Algorithm That Systematically Quantifies Nine Synaptic Parameters Provides Insights into Drosophila NMJ Morphometry
Spikelets in Pyramidal Neurons: Action Potentials Initiated in the Axon Initial Segment That Do Not Activate the Soma
Docking cholesterol to integral membrane proteins with Rosetta
The Effects of Temperature on the Stability of a Neuronal Oscillator
Enhanced Methods for Local Ancestry Assignment in Sequenced Admixed Individuals
ODE Constrained Mixture Modelling: A Method for Unraveling Subpopulation Structures and Dynamics
PLoS Computational Biology Conference Postcards from ISMB 2010
Quantitative Analyses of Circadian Gene Expression in Mammalian Cell Cultures
Invariant recognition drives neural representations of action sequences
A Mechanistic View of the Role of E3 in Sumoylation
Ten simple rules for using large language models in science, version 1.0
The COVID-19 outbreak in Sichuan, China: Epidemiology and impact of interventions
Segment-Specific Adhesion as a Driver of Convergent Extension
In-silico dynamic analysis of cytotoxic drug administration to solid tumours: Effect of binding affinity and vessel permeability
Lévy Walks Suboptimal under Predation Risk
Information transmission from NFkB signaling dynamics to gene expression
Flux-Based Transport Enhancement as a Plausible Unifying Mechanism for Auxin Transport in Meristem Development
Correction: Ten simple rules to colorize biological data visualization
Neighbor-enhanced diffusivity in dense, cohesive cell populations
A Normative Theory of Forgetting: Lessons from the Fruit Fly
Mate selection: A useful approach to maximize genetic gain and control inbreeding in genomic and conventional oil palm (Elaeis guineensis Jacq.) hybrid breeding
Atrial Heterogeneity Generates Re-entrant Substrate during Atrial Fibrillation and Anti-arrhythmic Drug Action: Mechanistic Insights from Canine Atrial Models
Neural manifold under plasticity in a goal driven learning behaviour
Comparison of metabolic states using genome-scale metabolic models
Interpretable pairwise distillations for generative protein sequence models
Dynamic properties of internal noise probed by modulating binocular rivalry
Biological impact of mutually exclusive exon switching
Control of Gene Expression by RNA Binding Protein Action on Alternative Translation Initiation Sites
Age-structured non-pharmaceutical interventions for optimal control of COVID-19 epidemic
Peptide probes derived from pertuzumab by molecular dynamics modeling for HER2 positive tumor imaging
Physiological models of the lateral superior olive
A Mathematical Model of Muscle Containing Heterogeneous Half-Sarcomeres Exhibits Residual Force Enhancement
Thermodynamic Basis for the Emergence of Genomes during Prebiotic Evolution
Ten simple rules for humane data science
A Methodological Framework for the Reconstruction of Contiguous Regions of Ancestral Genomes and Its Application to Mammalian Genomes
The Signaling Petri Net-Based Simulator: A Non-Parametric Strategy for Characterizing the Dynamics of Cell-Specific Signaling Networks
Practical Measures of Integrated Information for Time-Series Data
Steered Molecular Dynamics Simulations of a Type IV Pilus Probe Initial Stages of a Force-Induced Conformational Transition
Multiscale modeling of layer formation in epidermis
Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments
ceRNAR: An R package for identification and analysis of ceRNA-miRNA triplets
Genetic buffering and potentiation in metabolism
Gene Expression Noise in Spatial Patterning: hunchback Promoter Structure Affects Noise Amplitude and Distribution in Drosophila Segmentation
Trade-off between Multiple Constraints Enables Simultaneous Formation of Modules and Hubs in Neural Systems
Automated High-Throughput Characterization of Single Neurons by Means of Simplified Spiking Models
A numerical approach for a discrete Markov model for progressing drug resistance of cancer
Linear-regression-based algorithms can succeed at identifying microbial functional groups despite the nonlinearity of ecological function
Correction: The Genome: An Outsider's View
Transcriptomics technologies
Analyzing pharmacological intervention points: A method to calculate external stimuli to switch between steady states in regulatory networks
From the Phenomenology to the Mechanisms of Consciousness: Integrated Information Theory 3.0
A functional spiking-neuron model of activity-silent working memory in humans based on calcium-mediated short-term synaptic plasticity
Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models
Role of pore dilation in molecular transport through the nuclear pore complex: Insights from polymer scaling theory
The Genome: An Outsider's View
An Integrative Genomic Approach to Uncover Molecular Mechanisms of Prokaryotic Traits
Threshold-awareness in adaptive cancer therapy
Modeling second-order boundary perception: A machine learning approach
SMOG 2: A Versatile Software Package for Generating Structure-Based Models
ACAP1 assembles into an unusual protein lattice for membrane deformation through multiple stages
Impact of Microscopic Motility on the Swimming Behavior of Parasites: Straighter Trypanosomes are More Directional
Modeling circuit mechanisms of opposing cortical responses to visual flow perturbations
Creating High-Resolution Multiscale Maps of Human Tissue Using Multi-beam SEM
Estimating and interpreting secondary attack risk: Binomial considered biased
Learning Universal Computations with Spikes
Random walk informed heterogeneity detection reveals how the lymph node conduit network influences T cells collective exploration behavior
Shaping Neural Circuits by High Order Synaptic Interactions
Ten simple rules for creating a sense of belonging in your research group
Analysis of the Protein Domain and Domain Architecture Content in Fungi and Its Application in the Search of New Antifungal Targets
Intracellular signaling in proto-eukaryotes evolves to alleviate regulatory conflicts of endosymbiosis
Criticality enhances the multilevel reliability of stimulus responses in cortical neural networks
Unifying view of mechanical and functional hotspots across class A GPCRs
Strong Inference for Systems Biology
ArcDFI: Attention regularization guided by CYP450 interactions for predicting drug-food interactions
Potassium and sodium microdomains in thin astroglial processes: A computational model study
A Taxonomy of Bacterial Microcompartment Loci Constructed by a Novel Scoring Method
Action Potential Energy Efficiency Varies Among Neuron Types in Vertebrates and Invertebrates