yusuke1997/dblp-id-title huggingface dataset:
Pep2Path: Automated Mass Spectrometry-Guided Genome Mining of Peptidic Natural Products
Cross-species functional modules link proteostasis to human normal aging
Population dynamics and entrainment of basal ganglia pacemakers are shaped by their dendritic arbors
Thermodynamic Stability of Histone H3 Is a Necessary but not Sufficient Driving Force for its Evolutionary Conservation
Estimating ectopic beat probability with simplified statistical models that account for experimental uncertainty
Inferring RNA-binding protein target preferences using adversarial domain adaptation
Reliable estimation of tree branch lengths using deep neural networks
A Compact Statistical Model of the Song Syntax in Bengalese Finch
Evaluating the impact of test-trace-isolate for COVID-19 management and alternative strategies
Correction: Practical considerations for measuring the effective reproductive number, Rt
Role of Hsp70 ATPase Domain Intrinsic Dynamics and Sequence Evolution in Enabling its Functional Interactions with NEFs
Bayesian estimation of community size and overlap from random subsamples
Optimizing spatial allocation of seasonal influenza vaccine under temporal constraints
Nash Equilibria in Multi-Agent Motor Interactions
Eleven quick tips to unlock the power of in vivo data science
Dialogue mechanisms between astrocytic and neuronal networks: A whole-brain modelling approach
Striatal network modeling in Huntington's Disease
Module-Based Analysis of Robustness Tradeoffs in the Heat Shock Response System
A Biophysical Model of the Mitochondrial Respiratory System and Oxidative Phosphorylation
Large-Scale Trends in the Evolution of Gene Structures within 11 Animal Genomes
Autocrine signaling can explain the emergence of Allee effects in cancer cell populations
The Molecular Mechanism of Ion-Dependent Gating in Secondary Transporters
Fast Synchronization of Ultradian Oscillators Controlled by Delta-Notch Signaling with Cis-Inhibition
A Self-Organizing Algorithm for Modeling Protein Loops
Meta-Reinforcement Learning reconciles surprise, value, and control in the anterior cingulate cortex
Inferring Metabolic States in Uncharacterized Environments Using Gene-Expression Measurements
Insights into substrate recognition and specificity for IgG by Endoglycosidase S2
AimSeg: A machine-learning-aided tool for axon, inner tongue and myelin segmentation
Tuft dendrites of pyramidal neurons operate as feedback-modulated functional subunits
Deep template-based protein structure prediction
Integrative Genomics-Based Discovery of Novel Regulators of the Innate Antiviral Response
Using an Insect Mushroom Body Circuit to Encode Route Memory in Complex Natural Environments
Modeling Systems-Level Regulation of Host Immune Responses
Scar shape analysis and simulated electrical instabilities in a non-ischemic dilated cardiomyopathy patient cohort
Convolutional neural networks improve species distribution modelling by capturing the spatial structure of the environment
An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1
Ohno-miRNAs: miRNA pairs derived from whole-genome duplication
Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks
Functional conservation of sequence determinants at rapidly evolving regulatory regions across mammals
Electrical coupling controls dimensionality and chaotic firing of inferior olive neurons
Drug Discovery Using Chemical Systems Biology: Identification of the Protein-Ligand Binding Network To Explain the Side Effects of CETP Inhibitors
Dynamical compensation and structural identifiability of biological models: Analysis, implications, and reconciliation
Intermittent Motion in Desert Locusts: Behavioural Complexity in Simple Environments
Cooperative Gating and Spatial Organization of Membrane Proteins through Elastic Interactions
The What and Where of Adding Channel Noise to the Hodgkin-Huxley Equations
Regulation of Signal Duration and the Statistical Dynamics of Kinase Activation by Scaffold Proteins
A Genome-Scale Metabolic Reconstruction of Mycoplasma genitalium , i PS189
Mechanics of lung cancer: A finite element model shows strain amplification during early tumorigenesis
GCNCDA: A new method for predicting circRNA-disease associations based on Graph Convolutional Network Algorithm
An explainable covariate compartmental model for predicting the spatio-temporal patterns of dengue in Sri Lanka
eVIP2: Expression-based variant impact phenotyping to predict the function of gene variants
Steady-State Kinetic Modeling Constrains Cellular Resting States and Dynamic Behavior
Neutral competition explains the clonal composition of neural organoids
Robustness of neuronal tuning to binaural sound localization cues against age-related loss of inhibitory synaptic inputs
An Evolutionary-Network Model Reveals Stratified Interactions in the V3 Loop of the HIV-1 Envelope
Visual Nonclassical Receptive Field Effects Emerge from Sparse Coding in a Dynamical System
Neural field models for latent state inference: Application to large-scale neuronal recordings
A Biophysical Systems Approach to Identifying the Pathways of Acute and Chronic Doxorubicin Mitochondrial Cardiotoxicity
Causal inference regulates audiovisual spatial recalibration via its influence on audiovisual perception
Exploring Volatile General Anesthetic Binding to a Closed Membrane-Bound Bacterial Voltage-Gated Sodium Channel via Computation
From Structure Prediction to Genomic Screens for Novel Non-Coding RNAs
Fidelity of hyperbolic space for Bayesian phylogenetic inference
Towards mouse genetic-specific RNA-sequencing read mapping
Segmentation of dense and multi-species bacterial colonies using models trained on synthetic microscopy images
Epidemiological and evolutionary consequences of different types of CRISPR-Cas systems
Adolescent and adult mice use both incremental reinforcement learning and short term memory when learning concurrent stimulus-action associations
Evolutionary Game Theory and Social Learning Can Determine How Vaccine Scares Unfold
Dynamic metabolic adaptation can promote species coexistence in competitive microbial communities
Minimizing the number of optimizations for efficient community dynamic flux balance analysis
On the Effect of Thermodynamic Equilibrium on the Assembly Efficiency of Complex Multi-Layered Virus-Like Particles (VLP): the Case of Rotavirus VLP
Impact of Sarcoplasmic Reticulum Calcium Release on Calcium Dynamics and Action Potential Morphology in Human Atrial Myocytes: A Computational Study
MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data
Modeling Inter-trial Variability of Saccade Trajectories: Effects of Lesions of the Oculomotor Part of the Fastigial Nucleus
Identification of animal behavioral strategies by inverse reinforcement learning
Models of Neocortical Layer 5b Pyramidal Cells Capturing a Wide Range of Dendritic and Perisomatic Active Properties
A computational model of postprandial adipose tissue lipid metabolism derived using human arteriovenous stable isotope tracer data
Random-effects meta-analysis of effect sizes as a unified framework for gene set analysis
Flux balance analysis-based metabolic modeling of microbial secondary metabolism: Current status and outlook
A Data-Driven Mathematical Model of CA-MRSA Transmission among Age Groups: Evaluating the Effect of Control Interventions
Does Zipf's law of abbreviation shape birdsong?
Computational modelling identifies primary mediators of crosstalk between DNA damage and oxidative stress responses
PandoGen: Generating complete instances of future SARS-CoV-2 sequences using Deep Learning
On Genetic Specificity in Symbiont-Mediated Host-Parasite Coevolution
Unmet needs for analyzing biological big data: A survey of 704 NSF principal investigators
Formation and Maintenance of Robust Long-Term Information Storage in the Presence of Synaptic Turnover
The More the Tubular: Dynamic Bundling of Actin Filaments for Membrane Tube Formation
Erratic Flu Vaccination Emerges from Short-Sighted Behavior in Contact Networks
The Origin of Behavioral Bursts in Decision-Making Circuitry
MAGICAL: A multi-class classifier to predict synthetic lethal and viable interactions using protein-protein interaction network
Geometric Theory Predicts Bifurcations in Minimal Wiring Cost Trees in Biology Are Flat
The Free Energy Landscape of Dimerization of a Membrane Protein, NanC
Quality of Computationally Inferred Gene Ontology Annotations
Prediction of Protein-Protein Interaction Sites in Sequences and 3D Structures by Random Forests
High-order functional redundancy in ageing explained via alterations in the connectome in a whole-brain model
Interpretable metric learning in comparative metagenomics: The adaptive Haar-like distance
Adaptation in structured populations and fuzzy boundaries between hard and soft sweeps
High-Degree Neurons Feed Cortical Computations
Molecular sampling at logarithmic rates for next-generation sequencing
Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease
The ISCB Student Council Internship Program: Expanding computational biology capacity worldwide
A Physics-Informed Neural Network approach for compartmental epidemiological models
The hourglass organization of the Caenorhabditis elegans connectome
Analysis of Sequence Conservation at Nucleotide Resolution
Geometric De-noising of Protein-Protein Interaction Networks
A Novel Scoring Approach for Protein Co-Purification Data Reveals High Interaction Specificity
Joint representation of molecular networks from multiple species improves gene classification
BARcode DEmixing through Non-negative Spatial Regression (BarDensr)
Learning compositional sequences with multiple time scales through a hierarchical network of spiking neurons
Ten simple rules for writing scientific op-ed articles
Evolution of the Multi-Domain Structures of Virulence Genes in the Human Malaria Parasite, Plasmodium falciparum
Large-scale, dynamin-like motions of the human guanylate binding protein 1 revealed by multi-resolution simulations
Geometric and topological characterization of the cytoarchitecture of islets of Langerhans
Genome-wide prediction of topoisomerase IIβ binding by architectural factors and chromatin accessibility
Bursts of Vertex Activation and Epidemics in Evolving Networks
Structure-Based Function Prediction of Uncharacterized Protein Using Binding Sites Comparison
Population Density Modulates Drug Inhibition and Gives Rise to Potential Bistability of Treatment Outcomes for Bacterial Infections
Pervasive, conserved secondary structure in highly charged protein regions
A Primer on Learning in Bayesian Networks for Computational Biology
Molecular Switches at the Synapse Emerge from Receptor and Kinase Traffic
Emergence of Functional Hierarchy in a Multiple Timescale Neural Network Model: A Humanoid Robot Experiment
Decrypting the Sequence of Structural Events during the Gating Transition of Pentameric Ligand-Gated Ion Channels Based on an Interpolated Elastic Network Model
From Bad to Good: Fitness Reversals and the Ascent of Deleterious Mutations
Energetics of optimal undulatory swimming organisms
Estimation of the firing behaviour of a complete motoneuron pool by combining electromyography signal decomposition and realistic motoneuron modelling
Efficiency, Selectivity, and Robustness of Nucleocytoplasmic Transport
LMTRDA: Using logistic model tree to predict MiRNA-disease associations by fusing multi-source information of sequences and similarities
Computation of the electroencephalogram (EEG) from network models of point neurons
Chromatin Loops as Allosteric Modulators of Enhancer-Promoter Interactions
Correction: Representation of foreseeable choice outcomes in orbitofrontal cortex triplet-wise interactions
Cell Cycle Control by a Minimal Cdk Network
Allosteric Communication across the Native and Mutated KIT Receptor Tyrosine Kinase
Dysregulated biodynamics in metabolic attractor systems precede the emergence of amyotrophic lateral sclerosis
Timing and Variability of Galactose Metabolic Gene Activation Depend on the Rate of Environmental Change
Spatial neuronal synchronization and the waveform of oscillations: Implications for EEG and MEG
Principal Component Analysis Characterizes Shared Pathogenetics from Genome-Wide Association Studies
Evolution of phenotypic plasticity leads to tumor heterogeneity with implications for therapy
Ten simple rules for training yourself in an emerging field
The statistics of epidemic transitions
Thalamic bursts modulate cortical synchrony locally to switch between states of global functional connectivity in a cognitive task
Theory and Experimental Validation of a Spatio-temporal Model of Chemotherapy Transport to Enhance Tumor Cell Kill
Attracting Dynamics of Frontal Cortex Ensembles during Memory-Guided Decision-Making
Perturbation Biology: Inferring Signaling Networks in Cellular Systems
A computational method for identifying an optimal combination of existing drugs to repair the action potentials of SQT1 ventricular myocytes
Human representation of multimodal distributions as clusters of samples
Clustering-independent analysis of genomic data using spectral simplicial theory
Linkers of Cell Polarity and Cell Cycle Regulation in the Fission Yeast Protein Interaction Network
Modelling Individual Differences in the Form of Pavlovian Conditioned Approach Responses: A Dual Learning Systems Approach with Factored Representations
Getting Started in Gene Expression Microarray Analysis
Filling-In and Suppression of Visual Perception from Context: A Bayesian Account of Perceptual Biases by Contextual Influences
Critical Slowing Down Governs the Transition to Neuron Spiking
A High-Throughput Screening Approach to Discovering Good Forms of Biologically Inspired Visual Representation
Measuring the unknown: An estimator and simulation study for assessing case reporting during epidemics
Steering Evolution with Sequential Therapy to Prevent the Emergence of Bacterial Antibiotic Resistance
Evolution of Pathogen Specialisation in a Host Metapopulation: Joint Effects of Host and Pathogen Dispersal
When should lockdown be implemented? Devising cost-effective strategies for managing epidemics amid vaccine uncertainty
Mathematical modeling unveils the timeline of CAR-T cell therapy and macrophage-mediated cytokine release syndrome
A Statistical Model to Identify Differentially Expressed Proteins in 2D PAGE Gels
A Survey of Genomic Properties for the Detection of Regulatory Polymorphisms
Revealing evolutionary constraints on proteins through sequence analysis
The Mass-Longevity Triangle: Pareto Optimality and the Geometry of Life-History Trait Space
The Evolution of Cell-to-Cell Communication in a Sporulating Bacterium
A hybrid of light-field and light-sheet imaging to study myocardial function and intracardiac blood flow during zebrafish development
On the incongruence of genotype-phenotype and fitness landscapes
Multimeric structure enables the acceleration of KaiB-KaiC complex formation induced by ADP/ATP exchange inhibition
A Unifying Probabilistic View of Associative Learning
Multi-state design of flexible proteins predicts sequences optimal for conformational change
Transient Cognitive Dynamics, Metastability, and Decision Making
Image2Flow: A proof-of-concept hybrid image and graph convolutional neural network for rapid patient-specific pulmonary artery segmentation and CFD flow field calculation from 3D cardiac MRI data
LsrR Quorum Sensing "Switch" Is Revealed by a Bottom-Up Approach
Physics-based simulations of aerial attacks by peregrine falcons reveal that stooping at high speed maximizes catch success against agile prey
Transcriptome Sequencing Reveals Potential Mechanism of Cryptic 3' Splice Site Selection in SF3B1 -mutated Cancers
Erosion of Conserved Binding Sites in Personal Genomes Points to Medical Histories
Bioinformatics in Malaysia: Hope, Initiative, Effort, Reality, and Challenges
Self-crowding of AMPA receptors in the excitatory postsynaptic density can effectuate anomalous receptor sub-diffusion
Adaptive Contact Networks Change Effective Disease Infectiousness and Dynamics
Efficient Reconstruction of Predictive Consensus Metabolic Network Models
Mathematical analysis of left ventricular elastance with respect to afterload change during ejection phase
Learning spatial hearing via innate mechanisms
coupleCoC+: An information-theoretic co-clustering-based transfer learning framework for the integrative analysis of single-cell genomic data
A Structure-Based Approach for Detection of Thiol Oxidoreductases and Their Catalytic Redox-Active Cysteine Residues
Inferring the Source of Transmission with Phylogenetic Data
Every which way? On predicting tumor evolution using cancer progression models
Differential tissue growth and cell adhesion alone drive early tooth morphogenesis: An ex vivo and in silico study
Determinants of Translation Elongation Speed and Ribosomal Profiling Biases in Mouse Embryonic Stem Cells
A real data-driven simulation strategy to select an imputation method for mixed-type trait data
Terminal heterocyst differentiation in the Anabaena patA mutant as a result of post-transcriptional modifications and molecular leakage
A Simple and Accurate Model to Predict Responses to Multi-electrode Stimulation in the Retina
Dynamic modelling of cell cycle arrest through integrated single-cell and mathematical modelling approaches
Two passive mechanical conditions modulate power generation by the outer hair cells
VGsim: Scalable viral genealogy simulator for global pandemic
Evolutionary and Functional Relationships in the Truncated Hemoglobin Family
Latent Factor Analysis to Discover Pathway-Associated Putative Segmental Aneuploidies in Human Cancers
Predicting Affinity Through Homology (PATH): Interpretable binding affinity prediction with persistent homology
Canonical Correlation Analysis for Gene-Based Pleiotropy Discovery
NucleoMap: A computational tool for identifying nucleosomes in ultra-high resolution contact maps
Identification of Key Hinge Residues Important for Nucleotide-Dependent Allostery in E. coli Hsp70/DnaK
Where Have All the Interactions Gone? Estimating the Coverage of Two-Hybrid Protein Interaction Maps
StressME: Unified computing framework of Escherichia coli metabolism, gene expression, and stress responses
Modeling Cellular Noise Underlying Heterogeneous Cell Responses in the Epidermal Growth Factor Signaling Pathway
Estimating the In Vivo Killing Efficacy of Cytotoxic T Lymphocytes across Different Peptide-MHC Complex Densities
DepoScope: Accurate phage depolymerase annotation and domain delineation using large language models
Phenotype-based probabilistic analysis of heterogeneous responses to cancer drugs and their combination efficacy
Role and modulation of various spinal pathways for human upper limb control in different gravity conditions
Species Tree Inference by Minimizing Deep Coalescences
Copper binding leads to increased dynamics in the regulatory N-terminal domain of full-length human copper transporter ATP7B
High Prevalence of Multistability of Rest States and Bursting in a Database of a Model Neuron
The impact of health inequity on spatial variation of COVID-19 transmission in England
Matrigel patterning reflects multicellular contractility
Evolution of Associative Learning in Chemical Networks
iCDA-CGR: Identification of circRNA-disease associations based on Chaos Game Representation
Modeling Bi-modality Improves Characterization of Cell Cycle on Gene Expression in Single Cells
A hidden Markov model reliably characterizes ketamine-induced spectral dynamics in macaque local field potentials and human electroencephalograms
A SuperLearner-based pipeline for the development of DNA methylation-derived predictors of phenotypic traits
Diverse processing underlying frequency integration in midbrain neurons of barn owls
The Statistics of Bulk Segregant Analysis Using Next Generation Sequencing
Integrating Bioinformatics Tools to Handle Glycosylation
Parallel Computational Subunits in Dentate Granule Cells Generate Multiple Place Fields
Randomized Spatial PCA (RASP): A computationally efficient method for dimensionality reduction of high-resolution spatial transcriptomics data
A teaching proposal for a short course on biomedical data science
Cellular Interrogation: Exploiting Cell-to-Cell Variability to Discriminate Regulatory Mechanisms in Oscillatory Signalling
Neural modelling of the encoding of fast frequency modulation
Subgraphs of functional brain networks identify dynamical constraints of cognitive control
Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA
Optimality of Human Contour Integration
Intrinsic Gain Modulation and Adaptive Neural Coding
Cluster detection with random neighbourhood covering: Application to invasive Group A Streptococcal disease
Recombinant vector vaccine evolution
An open source tool for automatic spatiotemporal assessment of calcium transients and local 'signal-close-to-noise' activity in calcium imaging data
Hierarchical Modeling of Activation Mechanisms in the ABL and EGFR Kinase Domains: Thermodynamic and Mechanistic Catalysts of Kinase Activation by Cancer Mutations
Model-Based Analysis of HER Activation in Cells Co-Expressing EGFR, HER2 and HER3
Ten Simple Rules for landing on the right job after your PhD or postdoc
Inferring phenomenological models of first passage processes
Multiscale networks in Alzheimer's disease identify brain hypometabolism as central across biological scales
Mechanisms of Zero-Lag Synchronization in Cortical Motifs
Social inequalities in vaccine coverage and their effects on epidemic spreading
A Well-Defined Readily Releasable Pool with Fixed Capacity for Storing Vesicles at Calyx of Held
Network architecture of transcriptomic stress responses in zebrafish embryos
Diverse type 2 diabetes genetic risk factors functionally converge in a phenotype-focused gene network
Simulating Microdosimetry in a Virtual Hepatic Lobule
PopART-IBM, a highly efficient stochastic individual-based simulation model of generalised HIV epidemics developed in the context of the HPTN 071 (PopART) trial
Effective Reduced Diffusion-Models: A Data Driven Approach to the Analysis of Neuronal Dynamics
Protein domain-based prediction of drug/compound-target interactions and experimental validation on LIM kinases
Finding recurrent RNA structural networks with fast maximal common subgraphs of edge-colored graphs
RNAi Development
The structure and robustness of ecological networks with two interaction types
Decentralized control of insect walking: A simple neural network explains a wide range of behavioral and neurophysiological results
Structure-Based Sequence Alignment of the Transmembrane Domains of All Human GPCRs: Phylogenetic, Structural and Functional Implications
Cell-Specific Cardiac Electrophysiology Models
Evolutionary Game Dynamics in Populations with Heterogenous Structures
The topology of genome-scale metabolic reconstructions unravels independent modules and high network flexibility
Robustness and Evolvability of the Human Signaling Network
The pursuit of happiness: A reinforcement learning perspective on habituation and comparisons
Quantifying Cell Fate Decisions for Differentiation and Reprogramming of a Human Stem Cell Network: Landscape and Biological Paths
Haisu: Hierarchically supervised nonlinear dimensionality reduction
Uncertainty quantification in cerebral circulation simulations focusing on the collateral flow: Surrogate model approach with machine learning
Computational Modeling and Analysis of Insulin Induced Eukaryotic Translation Initiation
How Thioredoxin Dissociates Its Mixed Disulfide
State Based Model of Long-Term Potentiation and Synaptic Tagging and Capture
Modelling the transport of fluid through heterogeneous, whole tumours in silico
Identification of Molecular Pathologies Sufficient to Cause Neuropathic Excitability in Primary Somatosensory Afferents Using Dynamical Systems Theory
Ten simple rules for thriving in a post-baccalaureate research program
The Integrated Role of Wnt/β-Catenin, N-Glycosylation, and E-Cadherin-Mediated Adhesion in Network Dynamics