yusuke1997/dblp-id-title huggingface dataset:
A Micellar On-Pathway Intermediate Step Explains the Kinetics of Prion Amyloid Formation
IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis
Multiple Spike Time Patterns Occur at Bifurcation Points of Membrane Potential Dynamics
Assessing key decisions for transcriptomic data integration in biochemical networks
MouseNet: A biologically constrained convolutional neural network model for the mouse visual cortex
VASP: A Volumetric Analysis of Surface Properties Yields Insights into Protein-Ligand Binding Specificity
Towards a molecular basis of ubiquitin signaling: A dual-scale simulation study of ubiquitin dimers
When Does Model-Based Control Pay Off?
A mathematical model of local and global attention in natural scene viewing
The structural coverage of the human proteome before and after AlphaFold
Intrinsic Disorder in Protein Interactions: Insights From a Comprehensive Structural Analysis
Modeling the temporal dynamics of the gut microbial community in adults and infants
Teaching the Fundamentals of Biological Data Integration Using Classroom Games
Predicting yield of individual field-grown rapeseed plants from rosette-stage leaf gene expression
Reliability-enhanced data cleaning in biomedical machine learning using inductive conformal prediction
Bioinformatics calls the school: Use of smartphones to introduce Python for bioinformatics in high schools
Leading a Statistical Bioinformatics Lab: It's All About Finding Balance
Three-Dimensional Gradients of Cytokine Signaling between T Cells
Combining flipped-classroom and spaced-repetition learning in a master-level bioinformatics course
Neural Population Dynamics during Reaching Are Better Explained by a Dynamical System than Representational Tuning
Long-Range Periodic Patterns in Microbial Genomes Indicate Significant Multi-Scale Chromosomal Organization
The physiological variability of channel density in hippocampal CA1 pyramidal cells and interneurons explored using a unified data-driven modeling workflow
Towards a data-driven characterization of behavioral changes induced by the seasonal flu
Model-Based Analysis of Cell Cycle Responses to Dynamically Changing Environments
Influence of Wiring Cost on the Large-Scale Architecture of Human Cortical Connectivity
Ten Simple Rules for Experiments' Provenance
Statistical Analysis of 3D Images Detects Regular Spatial Distributions of Centromeres and Chromocenters in Animal and Plant Nuclei
Controlling brain dynamics: Landscape and transition path for working memory
Rational inattention and tonic dopamine
The Effects of City Streets on an Urban Disease Vector
Probabilistic neural transfer function estimation with Bayesian system identification
Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues
How conformity can lead to polarised social behaviour
All2: A tool for selecting mosaic mutations from comprehensive multi-cell comparisons
Particle-based model shows complex rearrangement of tissue mechanical properties are needed for roots to grow in hard soil
GeM-LR: Discovering predictive biomarkers for small datasets in vaccine studies
Correction: Effects of Darwinian Selection and Mutability on Rate of Broadly Neutralizing Antibody Evolution during HIV-1 Infection
Cooperative adaptation to therapy (CAT) confers resistance in heterogeneous non-small cell lung cancer
A metric for evaluating biological information in gene sets and its application to identify co-expressed gene clusters in PBMC
Index analysis: An approach to understand signal transduction with application to the EGFR signalling pathway
PyPhi: A toolbox for integrated information theory
Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks
Comparison of Insertional RNA Editing in Myxomycetes
Mechanism of Bacterial Signal Transduction Revealed by Molecular Dynamics of Tsr Dimers and Trimers of Dimers in Lipid Vesicles
Interaction of Motility, Directional Sensing, and Polarity Modules Recreates the Behaviors of Chemotaxing Cells
Kinetic and thermodynamic insights into sodium ion translocation through the μ-opioid receptor from molecular dynamics and machine learning analysis
Electrotonic Signals along Intracellular Membranes May Interconnect Dendritic Spines and Nucleus
Maynard Smith revisited: A multi-agent reinforcement learning approach to the coevolution of signalling behaviour
Biophysically grounded mean-field models of neural populations under electrical stimulation
Role of the reaction-structure coupling in temperature compensation of the KaiABC circadian rhythm
Using topic modeling to detect cellular crosstalk in scRNA-seq
Disease-Aging Network Reveals Significant Roles of Aging Genes in Connecting Genetic Diseases
Relating Neuronal Firing Patterns to Functional Differentiation of Cerebral Cortex
Stability of working memory in continuous attractor networks under the control of short-term plasticity
Patterns of Subnet Usage Reveal Distinct Scales of Regulation in the Transcriptional Regulatory Network of Escherichia coli
SteatoNet: The First Integrated Human Metabolic Model with Multi-layered Regulation to Investigate Liver-Associated Pathologies
Deciphering Protein-Protein Interactions. Part I. Experimental Techniques and Databases
Discovering molecular features of intrinsically disordered regions by using evolution for contrastive learning
CoPhosK: A method for comprehensive kinase substrate annotation using co-phosphorylation analysis
Welcome to PLoS Computational Biology "Education"
Text Mining for Protein Docking
A Deterministic Model Predicts the Properties of Stochastic Calcium Oscillations in Airway Smooth Muscle Cells
k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design
Pre-training artificial neural networks with spontaneous retinal activity improves motion prediction in natural scenes
Relatively slow stochastic gene-state switching in the presence of positive feedback significantly broadens the region of bimodality through stabilizing the uninduced phenotypic state
ChromoTrace: Computational reconstruction of 3D chromosome configurations for super-resolution microscopy
Modulation of the dynamics of cerebellar Purkinje cells through the interaction of excitatory and inhibitory feedforward pathways
Pairwise Analysis Can Account for Network Structures Arising from Spike-Timing Dependent Plasticity
Bayesian reconstruction of memories stored in neural networks from their connectivity
Microtubule-based nucleation results in a large sensitivity to cell geometry of the plant cortical array
The Representation of Prediction Error in Auditory Cortex
Nutritional Systems Biology Modeling: From Molecular Mechanisms to Physiology
A Network Characteristic That Correlates Environmental and Genetic Robustness
Molecular Mechanical Differences between Isoforms of Contractile Actin in the Presence of Isoforms of Smooth Muscle Tropomyosin
Prediction of Cell Penetrating Peptides by Support Vector Machines
Bioschemas training profiles: A set of specifications for standardizing training information to facilitate the discovery of training programs and resources
Bistability versus Bimodal Distributions in Gene Regulatory Processes from Population Balance
Modeling large fluctuations of thousands of clones during hematopoiesis: The role of stem cell self-renewal and bursty progenitor dynamics in rhesus macaque
Classification and adaptive behavior prediction of children with autism spectrum disorder based upon multivariate data analysis of markers of oxidative stress and DNA methylation
Socioeconomic determinants of protective behaviors and contact patterns in the post-COVID-19 pandemic era: A cross-sectional study in Italy
Mathematical modeling indicates that regulatory inhibition of CD8+ T cell cytotoxicity can limit efficacy of IL-15 immunotherapy in cases of high pre-treatment SIV viral load
Learning a Weighted Sequence Model of the Nucleosome Core and Linker Yields More Accurate Predictions in Saccharomyces cerevisiae and Homo sapiens
Uncertainty-aware traction force microscopy
Ten simple rules for writing compelling recommendation letters
Control of filament length by a depolymerizing gradient
maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks
Assessing the potential impact of transmission during prolonged viral shedding on the effect of lockdown relaxation on COVID-19
Integrative Analysis of Transgenic Alfalfa ( Medicago sativa L.) Suggests New Metabolic Control Mechanisms for Monolignol Biosynthesis
Simple biochemical networks allow accurate sensing of multiple ligands with a single receptor
Correction: Contrasting mechanisms for hidden hearing loss: Synaptopathy vs myelin defects
Early Warning Signals for Critical Transitions: A Generalized Modeling Approach
Modeling disordered protein interactions from biophysical principles
Minimal Size of Cell Assemblies Coordinated by Gamma Oscillations
Gene regulatory network structure informs the distribution of perturbation effects
Amyloidogenesis Abolished by Proline Substitutions but Enhanced by Lipid Binding
Bayesian Inference of Spatial Organizations of Chromosomes
OneProt: Towards multi-modal protein foundation models via latent space alignment of sequence, structure, binding sites and text encoders
Traffic Instabilities in Self-Organized Pedestrian Crowds
A Thermodynamic Model of Monovalent Cation Homeostasis in the Yeast Saccharomyces cerevisiae
The Spatial Dynamics of Predators and the Benefits and Costs of Sharing Information
Physiology of Layer 5 Pyramidal Neurons in Mouse Primary Visual Cortex: Coincidence Detection through Bursting
Ten Simple Rules for a Bioinformatics Journal Club
Fixation dynamics on hypergraphs
Reward Bases: A simple mechanism for adaptive acquisition of multiple reward types
Tissue-adjusted pathway analysis of cancer (TPAC): A novel approach for quantifying tumor-specific gene set dysregulation relative to normal tissue
What Evidence Is There for the Homology of Protein-Protein Interactions?
Distinct Timing Mechanisms Produce Discrete and Continuous Movements
Quantifying the Relative Contributions of Divisive and Subtractive Feedback to Rhythm Generation
A Theory of Cheap Control in Embodied Systems
Epithelial organ shape is generated by patterned actomyosin contractility and maintained by the extracellular matrix
RgCop-A regularized copula based method for gene selection in single-cell RNA-seq data
Investigating microscale patchiness of motile microbes under turbulence in a simulated convective mixed layer
Computational Analysis and Prediction of the Binding Motif and Protein Interacting Partners of the Abl SH3 Domain
Estimating the Continuous-Time Dynamics of Energy and Fat Metabolism in Mice
Semantic prioritization of novel causative genomic variants
Humans combine value learning and hypothesis testing strategically in multi-dimensional probabilistic reward learning
Purely STDP-based assembly dynamics: Stability, learning, overlaps, drift and aging
Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli
UNNT: A novel Utility for comparing Neural Net and Tree-based models
An agent-based model for drug-radiation interactions in the tumour microenvironment: Hypoxia-activated prodrug SN30000 in multicellular tumour spheroids
Discrete mechanical model of lamellipodial actin network implements molecular clutch mechanism and generates arcs and microspikes
The importance of mechanical constraints for proper polarization and psuedo-cleavage furrow generation in the early Caenorhabditis elegans embryo
A Generalized Framework for Quantifying the Dynamics of EEG Event-Related Desynchronization
Correlated Electrostatic Mutations Provide a Reservoir of Stability in HIV Protease
Harmony-based data integration for distributed single-cell multi-omics data
Correction: Inferring Loss-of-Heterozygosity from Unpaired Tumors Using High-Density Oligonucleotide SNP Arrays
Finding branched pathways in metabolic network via atom group tracking
A mathematical model for persistent post-CSD vasoconstriction
Target-agnostic drug prediction integrated with medical record analysis uncovers differential associations of statins with increased survival in COVID-19 patients
Global nonlinear approach for mapping parameters of neural mass models
The Genealogical Population Dynamics of HIV-1 in a Large Transmission Chain: Bridging within and among Host Evolutionary Rates
A minimally invasive neurostimulation method for controlling abnormal synchronisation in the neuronal activity
SILGGM: An extensive R package for efficient statistical inference in large-scale gene networks
Ten simple rules for building an enthusiastic iGEM team
Evolution-Based Functional Decomposition of Proteins
AnophelesModel: An R package to interface mosquito bionomics, human exposure and intervention effects with models of malaria intervention impact
Trip duration drives shift in travel network structure with implications for the predictability of spatial disease spread
Computational model of integrin adhesion elongation under an actin fiber
Analysis of Slow (Theta) Oscillations as a Potential Temporal Reference Frame for Information Coding in Sensory Cortices
Epigenetic Landscapes Explain Partially Reprogrammed Cells and Identify Key Reprogramming Genes
Projecting contact matrices in 177 geographical regions: An update and comparison with empirical data for the COVID-19 era
The Effect of Incentives and Meta-incentives on the Evolution of Cooperation
Model-Based Deconvolution of Cell Cycle Time-Series Data Reveals Gene Expression Details at High Resolution
Probabilistic Inference in General Graphical Models through Sampling in Stochastic Networks of Spiking Neurons
Fixation probabilities in graph-structured populations under weak selection
Distinct Types of Disorder in the Human Proteome: Functional Implications for Alternative Splicing
BIO-LGCA: A cellular automaton modelling class for analysing collective cell migration
Boltzmann Energy-based Image Analysis Demonstrates that Extracellular Domain Size Differences Explain Protein Segregation at Immune Synapses
The missing link: Predicting connectomes from noisy and partially observed tract tracing data
Cell-Based Multi-Parametric Model of Cleft Progression during Submandibular Salivary Gland Branching Morphogenesis
Optimal forgetting: Semantic compression of episodic memories
Regression Analysis of Combined Gene Expression Regulation in Acute Myeloid Leukemia
A Hierarchy of Time-Scales and the Brain
Design of a Trichromatic Cone Array
Bursts and Heavy Tails in Temporal and Sequential Dynamics of Foraging Decisions
Stochastic Drift in Mitochondrial DNA Point Mutations: A Novel Perspective Ex Silico
Mixotrophy for carbon-conserving waste upcycling
Identifying a developmental transition in honey bees using gene expression data
Estimating the distribution of parameters in differential equations with repeated cross-sectional data
On the Estimation of Intron Evolution
Inferring Neuronal Dynamics from Calcium Imaging Data Using Biophysical Models and Bayesian Inference
Cracking the neural code for word recognition in convolutional neural networks
Tuning collective behaviour in zebrafish with genetic modification
An electrodiffusive neuron-extracellular-glia model for exploring the genesis of slow potentials in the brain
Emergent order in epithelial sheets by interplay of cell divisions and cell fate regulation
Ten simple rules for making biomedical data resources accessible
A new Graph Gaussian embedding method for analyzing the effects of cognitive training
Molecular Mechanisms in the Activation of Abscisic Acid Receptor PYR1
Automatically tracking neurons in a moving and deforming brain
A Reaction-Diffusion Model of Human Brain Development
Exploring chromatin hierarchical organization via Markov State Modelling
Personalized logical models to investigate cancer response to BRAF treatments in melanomas and colorectal cancers
A Hidden Markov Model for Single Particle Tracks Quantifies Dynamic Interactions between LFA-1 and the Actin Cytoskeleton
Nine quick tips for open meta-analyses
How Synchronization Protects from Noise
Better tired than lost: Turtle ant trail networks favor coherence over short edges
MASCOT-Skyline integrates population and migration dynamics to enhance phylogeographic reconstructions
beachmat: A Bioconductor C++ API for accessing high-throughput biological data from a variety of R matrix types
In silico Experimentation of Glioma Microenvironment Development and Anti-tumor Therapy
Persistent Activity in Neural Networks with Dynamic Synapses
Ten Simple Rules for Developing a Short Bioinformatics Training Course
Mathematical modeling of the molecular switch of TNFR1-mediated signaling pathways applying Petri net formalism and in silico knockout analysis
Retraction: Measures of Clade Confidence Do Not Correlate with Accuracy of Phylogenetic Trees
Automated Discovery of Functional Generality of Human Gene Expression Programs
iDrug: Integration of drug repositioning and drug-target prediction via cross-network embedding
Fast Pairwise Structural RNA Alignments by Pruning of the Dynamical Programming Matrix
Ten simple rules for tackling your first mathematical models: A guide for graduate students by graduate students
Validation of Skeletal Muscle cis -Regulatory Module Predictions Reveals Nucleotide Composition Bias in Functional Enhancers
Chemotherapy-induced cachexia and model-informed dosing to preserve lean mass in cancer treatment
FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants
A Multi-scale Analysis of Influenza A Virus Fitness Trade-offs due to Temperature-dependent Virus Persistence
Evolutionary dynamics on sequential temporal networks
Calcium imaging and dynamic causal modelling reveal brain-wide changes in effective connectivity and synaptic dynamics during epileptic seizures
Do we advise as one likes? The alignment bias in social advice giving
A structured model and likelihood approach to estimate yeast prion propagon replication rates and their asymmetric transmission
A simplified modelling framework facilitates more complex representations of plant circadian clocks
Quantifying Type-Specific Reproduction Numbers for Nosocomial Pathogens: Evidence for Heightened Transmission of an Asian Sequence Type 239 MRSA Clone
ResMiCo: Increasing the quality of metagenome-assembled genomes with deep learning
Memory Maintenance in Synapses with Calcium-Based Plasticity in the Presence of Background Activity
Tradeoff Between Stability and Multispecificity in the Design of Promiscuous Proteins
Computational Biology: Moving into the Future One Click at a Time
Getting Started in Tiling Microarray Analysis
A Primer on Regression Methods for Decoding cis -Regulatory Logic
Comparative Genomics Search for Losses of Long-Established Genes on the Human Lineage
Partitioning variability in animal behavioral videos using semi-supervised variational autoencoders
Characterizing steady states of genome-scale metabolic networks in continuous cell cultures
Optimized Treatment Schedules for Chronic Myeloid Leukemia
Learning unsupervised feature representations for single cell microscopy images with paired cell inpainting
SpaK/SpaR Two-component System Characterized by a Structure-driven Domain-fusion Method and in Vitro Phosphorylation Studies
RNA structure prediction using positive and negative evolutionary information
Computational identification and experimental characterization of preferred downstream positions in human core promoters
Population Decoding in Rat Barrel Cortex: Optimizing the Linear Readout of Correlated Population Responses
The role of leptomeningeal collaterals in redistributing blood flow during stroke
Computational Methods for Exploration and Analysis of Macromolecular Structure and Dynamics
FusionPathway: Prediction of pathways and therapeutic targets associated with gene fusions in cancer
Reinforcement Learning on Slow Features of High-Dimensional Input Streams
Dimensional reduction of emergent spatiotemporal cortical dynamics via a maximum entropy moment closure
Theory of axo-axonic inhibition
Dopamine facilitates the response to glutamatergic inputs in astrocyte cell models
Machine learning-based investigation of the cancer protein secretory pathway
Binding Polymorphism in the DNA Bound State of the Pdx1 Homeodomain
Metastable spiking networks in the replica-mean-field limit
Error-based or target-based? A unified framework for learning in recurrent spiking networks
Local Gene Regulation Details a Recognition Code within the LacI Transcriptional Factor Family
SNPdetector: A Software Tool for Sensitive and Accurate SNP Detection
Constructive connectomics: How neuronal axons get from here to there using gene-expression maps derived from their family trees
Construct prognostic models of multiple myeloma with pathway information incorporated
Optimizing laboratory-based surveillance networks for monitoring multi-genotype or multi-serotype infections
Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture
Inferring reaction network structure from single-cell, multiplex data, using toric systems theory
The covariance perceptron: A new paradigm for classification and processing of time series in recurrent neuronal networks
Barcoding T Cell Calcium Response Diversity with Methods for Automated and Accurate Analysis of Cell Signals (MAAACS)
Kernel Bayesian logistic tensor decomposition with automatic rank determination for predicting multiple types of miRNA-disease associations
A Graph-Centric Approach for Metagenome-Guided Peptide and Protein Identification in Metaproteomics
Synergistic interventions to control COVID-19: Mass testing and isolation mitigates reliance on distancing
HAT: Hypergraph analysis toolbox
Coenzyme Q Biosynthesis: Evidence for a Substrate Access Channel in the FAD-Dependent Monooxygenase Coq6
Precise cortical contributions to sensorimotor feedback control during reactive balance
Separating Timing, Movement Conditions and Individual Differences in the Analysis of Human Movement
Pyfectious: An individual-level simulator to discover optimal containment policies for epidemic diseases
Malleable Machines in Transcription Regulation: The Mediator Complex
Ten quick tips to perform meaningful and reproducible molecular docking calculations
Theoretical efficiency limits and speed-efficiency trade-off in myosin motors
A platform-independent framework for phenotyping of multiplex tissue imaging data
Conformational ensemble of native α-synuclein in solution as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations
Deep learning detection of dynamic exocytosis events in fluorescence TIRF microscopy
Combinatorial Pooling Enables Selective Sequencing of the Barley Gene Space
Generative AI mitigates representation bias and improves model fairness through synthetic health data
Image-based flow simulation of platelet aggregates under different shear rates
Automatic Filtering and Substantiation of Drug Safety Signals
Known allosteric proteins have central roles in genetic disease
A neurocomputational theory of action regulation predicts motor behavior in neurotypical individuals and patients with Parkinson's disease
Correlated receptor transport processes buffer single-cell heterogeneity
Stepwise Catalytic Mechanism via Short-Lived Intermediate Inferred from Combined QM/MM MERP and PES Calculations on Retaining Glycosyltransferase ppGalNAcT2
Sharing and Specificity of Co-expression Networks across 35 Human Tissues
Defect patterns on the curved surface of fish retinae suggest a mechanism of cone mosaic formation
scCaT: An explainable capsulating architecture for sepsis diagnosis transferring from single-cell RNA sequencing
Error Correction and the Structure of Inter-Trial Fluctuations in a Redundant Movement Task
Geospatial characteristics of measles transmission in China during 2005-2014
Place Cell Rate Remapping by CA3 Recurrent Collaterals
Binding Site Graphs: A New Graph Theoretical Framework for Prediction of Transcription Factor Binding Sites
Using text-mined trait data to test for cooperate-and-radiate co-evolution between ants and plants