yusuke1997/dblp-id-title huggingface dataset:
Endemicity and prevalence of multipartite viruses under heterogeneous between-host transmission
seekCRIT: Detecting and characterizing differentially expressed circular RNAs using high-throughput sequencing data
Learning structured population models from data with WSINDy
Poly(A)-DG: A deep-learning-based domain generalization method to identify cross-species Poly(A) signal without prior knowledge from target species
Control of neurite growth and guidance by an inhibitory cell-body signal
Markov state modelling reveals heterogeneous drug-inhibition mechanism of Calmodulin
A deep learning approach for time-consistent cell cycle phase prediction from microscopy data
Processing of Multi-dimensional Sensorimotor Information in the Spinal and Cerebellar Neuronal Circuitry: A New Hypothesis
Navigable maps of structural brain networks across species
Top-down control of cortical gamma-band communication via pulvinar induced phase shifts in the alpha rhythm
Confidence intervals by constrained optimization - An algorithm and software package for practical identifiability analysis in systems biology
MicroRNA-Gene Association As a Prognostic Biomarker in Cancer Exposes Disease Mechanisms
iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections
Estimating the time-varying effective reproduction number via Cycle Threshold-based Transformer
Network mechanisms underlying the role of oscillations in cognitive tasks
Myopic control of neural dynamics
How neuronal morphology impacts the synchronisation state of neuronal networks
Inferring effective networks of spiking neurons using a continuous-time estimator of transfer entropy
Transmembrane helical interactions in the CFTR channel pore
A Quick Guide to Software Licensing for the Scientist-Programmer
A Novel Model to Combine Clinical and Pathway-Based Transcriptomic Information for the Prognosis Prediction of Breast Cancer
Location-Dependent Excitatory Synaptic Interactions in Pyramidal Neuron Dendrites
Fluctuating environments select for short-term phenotypic variation leading to long-term exploration
Mitigation Strategies for Pandemic Influenza A: Balancing Conflicting Policy Objectives
Propagating annotations of molecular networks using in silico fragmentation
Optimal learning with excitatory and inhibitory synapses
DeepConv-DTI: Prediction of drug-target interactions via deep learning with convolution on protein sequences
RNA folding using quantum computers
Comparative analyses of parasites with a comprehensive database of genome-scale metabolic models
GenoVi, an open-source automated circular genome visualizer for bacteria and archaea
Human Germline Antibody Gene Segments Encode Polyspecific Antibodies
A musculoskeletal finite element model of rat knee joint for evaluating cartilage biomechanics during gait
Network propagation in the cytoscape cyberinfrastructure
Real-time estimation of disease activity in emerging outbreaks using internet search information
A Boolean network model of hypoxia, mechanosensing and TGF-β signaling captures the role of phenotypic plasticity and mutations in tumor metastasis
Chromatin structures from integrated AI and polymer physics model
Modeling of Oxygen Transport and Cellular Energetics Explains Observations on In Vivo Cardiac Energy Metabolism
Metabolic Regulation in Progression to Autoimmune Diabetes
First Principles Modeling of Nonlinear Incidence Rates in Seasonal Epidemics
Mechanical stress and anionic lipids synergistically stabilize an atypical structure of the angiotensin II type 1 receptor (AT1)
A mathematical model of calcium dynamics: Obesity and mitochondria-associated ER membranes
Quantifying the distribution of feature values over data represented in arbitrary dimensional spaces
Reconstructing Mammalian Sleep Dynamics with Data Assimilation
scMoMtF: An interpretable multitask learning framework for single-cell multi-omics data analysis
Towards an Evolutionary Model of Transcription Networks
Quantitative Modeling of Escherichia coli Chemotactic Motion in Environments Varying in Space and Time
Perturbation-based Markovian Transmission Model for Probing Allosteric Dynamics of Large Macromolecular Assembling: A Study of GroEL-GroES
Prediction of Transcriptional Terminators in Bacillus subtilis and Related Species
A computational model of spatio-temporal cardiac intracellular calcium handling with realistic structure and spatial flux distribution from sarcoplasmic reticulum and t-tubule reconstructions
The Limitations of Model-Based Experimental Design and Parameter Estimation in Sloppy Systems
Mechanistic modeling suggests stroma-targeting antibody-drug conjugates as an alternative to cancer-targeting in cases of heterogeneous target exspression
Hybridized distance- and contact-based hierarchical structure modeling for folding soluble and membrane proteins
Asymmetric Switching in a Homodimeric ABC Transporter: A Simulation Study
Computational identification of the selenocysteine tRNA (tRNASec) in genomes
From cells to tissue: How cell scale heterogeneity impacts glioblastoma growth and treatment response
Hypergraphs and Cellular Networks
AIME: Autoencoder-based integrative multi-omics data embedding that allows for confounder adjustments
Identification of Cell Type-Specific Differences in Erythropoietin Receptor Signaling in Primary Erythroid and Lung Cancer Cells
Using birth-death processes to infer tumor subpopulation structure from live-cell imaging drug screening data
Defining an Essence of Structure Determining Residue Contacts in Proteins
Molecular insights on the mechanism of α1-antitrypsin condensate formation and maturation
coTRaCTE predicts co-occurring transcription factors within cell-type specific enhancers
Self Containment, a Property of Modular RNA Structures, Distinguishes microRNAs
Attenuation of HIV severity by slightly deleterious mutations can explain the long-term trajectory of virulence evolution
Success-efficient/failure-safe strategy for hierarchical reinforcement motor learning
Independent regulation of gene expression level and noise by histone modifications
Removal of AU Bias from Microarray mRNA Expression Data Enhances Computational Identification of Active MicroRNAs
Learning to Predict miRNA-mRNA Interactions from AGO CLIP Sequencing and CLASH Data
Learning spatio-temporal patterns with Neural Cellular Automata
BlueRecording: A pipeline for the efficient calculation of extracellular recordings in large-scale neural circuit models
Flux-based hierarchical organization of Escherichia coli's metabolic network
"Gate-keeper" Residues and Active-Site Rearrangements in DNA Polymerase μ Help Discriminate Non-cognate Nucleotides
Mechanical Network in Titin Immunoglobulin from Force Distribution Analysis
AncesTree: An interactive immunoglobulin lineage tree visualizer
Chapter 3: Small Molecules and Disease
New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx
Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks
Modeling the assembly order of multimeric heteroprotein complexes
Development of an experiment-split method for benchmarking the generalization of a PTM site predictor: Lysine methylome as an example
Questioning the Ubiquity of Neofunctionalization
Vesicular Stomatitis Virus Polymerase's Strong Affinity to Its Template Suggests Exotic Transcription Models
Vigilance, arousal, and acetylcholine: Optimal control of attention in a simple detection task
Predicting seasonal influenza using supermarket retail records
Utargetome: A targetome prediction tool for modified U1-snRNAs to identify distal-target positions with improved selectivity
How to Write a Presubmission Inquiry
Biophysical Fitness Landscapes for Transcription Factor Binding Sites
Molecular Mechanism for the Dual Alcohol Modulation of Cys-loop Receptors
Mechanisms of Firing Patterns in Fast-Spiking Cortical Interneurons
Correction: Bayesian inference and comparison of stochastic transcription elongation models
Coupling Mechanical Deformations and Planar Cell Polarity to Create Regular Patterns in the Zebrafish Retina
Inferring a network from dynamical signals at its nodes
An in-silico human cell model reveals the influence of spatial organization on RNA splicing
Balanced networks under spike-time dependent plasticity
Consensus-Phenotype Integration of Transcriptomic and Metabolomic Data Implies a Role for Metabolism in the Chemosensitivity of Tumour Cells
The Role of Exposure History on HIV Acquisition: Insights from Repeated Low-dose Challenge Studies
Similar sensorimotor transformations control balance during standing and walking
ScITree: Scalable Bayesian inference of transmission tree from epidemiological and genomic data
Effect of 1918 PB1-F2 Expression on Influenza A Virus Infection Kinetics
A spatially resolved stochastic model reveals the role of supercoiling in transcription regulation
How peak knee loads are affected by changing the mass of lower-limb body segments during walking
Ten simple rules for improving communication among scientists
Correction: From Dynamic Expression Patterns to Boundary Formation in the Presomitic Mesoderm
Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data
Modelling novelty detection in the thalamocortical loop
Plasticity of growth laws tunes resource allocation strategies in bacteria
Regulation of Spatiotemporal Patterns by Biological Variability: General Principles and Applications to Dictyostelium discoideum
Ten Simple Rules for Approaching a New Job
Mitochondrial network structure controls cell-to-cell mtDNA variability generated by cell divisions
Quantitative profiling of protease specificity
ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation
The lexical categorization model: A computational model of left ventral occipito-temporal cortex activation in visual word recognition
Epidemic Reconstruction in a Phylogenetics Framework: Transmission Trees as Partitions of the Node Set
Uncovering the subtype-specific temporal order of cancer pathway dysregulation
Coordinate Dependence of Variability Analysis
A Universal Mechanism Ties Genotype to Phenotype in Trinucleotide Diseases
Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure
Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes
Patterns of Mesenchymal Condensation in a Multiscale, Discrete Stochastic Model
Pupillary response is associated with the reset and switching of functional brain networks during salience processing
Hydrodynamics of transient cell-cell contact: The role of membrane permeability and active protrusion length
The biophysical basis underlying the maintenance of early phase long-term potentiation
Evaluation of residue-residue contact prediction methods: From retrospective to prospective
A novel virtual screening procedure identifies Pralatrexate as inhibitor of SARS-CoV-2 RdRp and it reduces viral replication in vitro
The genetic basis for adaptation of model-designed syntrophic co-cultures
Viral Proteins Originated De Novo by Overprinting Can Be Identified by Codon Usage: Application to the "Gene Nursery" of Deltaretroviruses
Knotted artifacts in predicted 3D RNA structures
Divergence of Mammalian Higher Order Chromatin Structure Is Associated with Developmental Loci
Using genomic data and machine learning to predict antibiotic resistance: A tutorial paper
Gene name errors: Lessons not learned
Correction: Projecting contact matrices in 177 geographical regions: An update and comparison with empirical data for the COVID-19 era
Understanding the transmission of bacterial agents of sapronotic diseases using an ecosystem-based approach: A first spatially realistic metacommunity model
Quantifying cooperative multisite binding in the hub protein LC8 through Bayesian inference
Highly accessible AU-rich regions in 3' untranslated regions are hotspots for binding of regulatory factors
Utilizing longitudinal microbiome taxonomic profiles to predict food allergy via Long Short-Term Memory networks
Dynamic bistable switches enhance robustness and accuracy of cell cycle transitions
Analyzing nested experimental designs - A user-friendly resampling method to determine experimental significance
Novel mutation in hexokinase 2 confers resistance to 2-deoxyglucose by altering protein dynamics
"Getting Started In...": A Series Not to Miss
Directional Summation in Non-direction Selective Retinal Ganglion Cells
Collaborative nowcasting of COVID-19 hospitalization incidences in Germany
Computational Biology in Costa Rica: The Role of a Small Country in the Global Context of Bioinformatics
Moving Education Forward, Again!
The impact of the spatial heterogeneity of resistant cells and fibroblasts on treatment response
Longitudinally monitored immune biomarkers predict the timing of COVID-19 outcomes
MVST: Identifying spatial domains of spatial transcriptomes from multiple views using multi-view graph convolutional networks
Modeling the Violation of Reward Maximization and Invariance in Reinforcement Schedules
Noise, multisensory integration, and previous response in perceptual disambiguation
Activated Membrane Patches Guide Chemotactic Cell Motility
Transient crosslinking kinetics optimize gene cluster interactions
Nucleus accumbens dopamine release reflects Bayesian inference during instrumental learning
Identification of Mechanosensitive Genes during Embryonic Bone Formation
Identification of immune signatures predictive of clinical protection from malaria
Encoding time in neural dynamic regimes with distinct computational tradeoffs
G2Φnet: Relating genotype and biomechanical phenotype of tissues with deep learning
Transformations of sensory information in the brain suggest changing criteria for optimality
Long-term dynamics of measles in London: Titrating the impact of wars, the 1918 pandemic, and vaccination
Systematic Search for Recipes to Generate Induced Pluripotent Stem Cells
How Obstacles Perturb Population Fronts and Alter Their Genetic Structure
A multi-objective based clustering for inferring BCR clonal lineages from high-throughput B cell repertoire data
Folding Free Energies of 5′-UTRs Impact Post-Transcriptional Regulation on a Genomic Scale in Yeast
FiCoS: A fine-grained and coarse-grained GPU-powered deterministic simulator for biochemical networks
Oscillatory dynamics of Rac1 activity in Dictyostelium discoideum amoebae
Postinhibitory excitation in motoneurons can be facilitated by hyperpolarization-activated inward currents: A simulation study
The representational hierarchy in human and artificial visual systems in the presence of object-scene regularities
Connection between Oligomeric State and Gating Characteristics of Mechanosensitive Ion Channels
Bayesian inference of multi-point macromolecular architecture mixtures at nanometre resolution
Combinations of Protein-Chemical Complex Structures Reveal New Targets for Established Drugs
e MatchSite: Sequence Order-Independent Structure Alignments of Ligand Binding Pockets in Protein Models
Mean-Fields and Neural Masses
GINOM: A statistical framework for assessing interval overlap of multiple genomic features
A model of resource partitioning between foraging bees based on learning
Multi-context modeling of driver pathways reveals common and specific mechanisms across 23 cancer types
Agent-based modeling of morphogenetic systems: Advantages and challenges
Balanced Synaptic Input Shapes the Correlation between Neural Spike Trains
A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations
Machine learning to design integral membrane channelrhodopsins for efficient eukaryotic expression and plasma membrane localization
Structural Insights into Separase Architecture and Substrate Recognition through Computational Modelling of Caspase-Like and Death Domains
Optima TB: A tool to help optimally allocate tuberculosis spending
MRDtarget: A heuristic Gaussian approach for optimizing targeted capture regions to enhance Minimal Residual Disease detection
Predicting host taxonomic information from viral genomes: A comparison of feature representations
Using deep learning to decipher the impact of telomerase promoter mutations on the dynamic metastatic morpholome
A multi-scale model of gas transport in the lung to study heterogeneous lung ventilation during the multiple-breath washout test
Systematic analysis of noise reduction properties of coupled and isolated feed-forward loops
Chapter 12: Human Microbiome Analysis
Survival Kinetics of Starving Bacteria Is Biphasic and Density-Dependent
Multiscale effects of excitatory-inhibitory homeostasis in lesioned cortical networks: A computational study
Evaluating the use of social contact data to produce age-specific short-term forecasts of SARS-CoV-2 incidence in England
Non-Bulk-Like Solvent Behavior in the Ribosome Exit Tunnel
An analysis of tissue-specific alternative splicing at the protein level
Horizontal transfer between loose compartments stabilizes replication of fragmented ribozymes
End-to-end neural system identification with neural information flow
Genomic data integration systematically biases interactome mapping
Quantifying the impact of ecological memory on the dynamics of interacting communities
Rate-dependent effects of lidocaine on cardiac dynamics: Development and analysis of a low-dimensional drug-channel interaction model
A beta-Poisson model for infectious disease transmission
Regulatory Control and the Costs and Benefits of Biochemical Noise
Correction: StanDep: Capturing transcriptomic variability improves context-specific metabolic models
Changes in Postural Syntax Characterize Sensory Modulation and Natural Variation of C . elegans Locomotion
The importance of urgency in decision making based on dynamic information
A loop-counting method for covariate-corrected low-rank biclustering of gene-expression and genome-wide association study data
Dynamics and Potential Impact of the Immune Response to Chronic Myelogenous Leukemia
Multiscale Embedded Gene Co-expression Network Analysis
MiDAS - Meaningful Immunogenetic Data at Scale
Model Cortical Association Fields Account for the Time Course and Dependence on Target Complexity of Human Contour Perception
Using the antibody-antigen binding interface to train image-based deep neural networks for antibody-epitope classification
A three-dimensional multiscale model for the prediction of thrombus growth under flow with single-platelet resolution
A multi-objective genetic algorithm to find active modules in multiplex biological networks
Demonstrating the utility of flexible sequence queries against indexed short reads with FlexTyper
Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways
Only a topological method can identify all possible network structures capable of Robust Perfect Adaptation
Optimal Dynamics for Quality Control in Spatially Distributed Mitochondrial Networks
Differentiation of Cytopathic Effects (CPE) induced by influenza virus infection using deep Convolutional Neural Networks (CNN)
Analysis of Physicochemical and Structural Properties Determining HIV-1 Coreceptor Usage
Temporal novelty detection and multiple timescale integration drive Drosophila orientation dynamics in temporally diverse olfactory environments
Dynamic Integration of Value Information into a Common Probability Currency as a Theory for Flexible Decision Making
Stochastic shielding and edge importance for Markov chains with timescale separation
Inferring tumor-specific cancer dependencies through integrating ex vivo drug response assays and drug-protein profiling
Ten Simple Rules for Editing Wikipedia
Membrane contact probability: An essential and predictive character for the structural and functional studies of membrane proteins
Emergent neural dynamics and geometry for generalization in a transitive inference task
Interplay between Constraints, Objectives, and Optimality for Genome-Scale Stoichiometric Models
Quantifying the Turnover of Transcriptional Subclasses of HIV-1-Infected Cells
A Synergism between Adaptive Effects and Evolvability Drives Whole Genome Duplication to Fixation
Use of Long Term Molecular Dynamics Simulation in Predicting Cancer Associated SNPs
A Keller-Segel model for C elegans L1 aggregation
Effective cell membrane tension protects red blood cells against malaria invasion
Enzymatic and non-enzymatic pathways of kynurenines' dimerization: the molecular factors for oxidative stress development
Co-evolution networks of HIV/HCV are modular with direct association to structure and function
Systematic computational assessment of atrial function impairment due to fibrotic remodeling in electromechanical properties
The role of childrens' vaccination for COVID-19 - Pareto-optimal allocations of vaccines
Bacterial clustering amplifies the reshaping of eutrophic plumes around marine particles: A hybrid data-driven model
PEPIS: A Pipeline for Estimating Epistatic Effects in Quantitative Trait Locus Mapping and Genome-Wide Association Studies
Individualization as Driving Force of Clustering Phenomena in Humans
Ten simple rules for serving as an editor
What constrains food webs? A maximum entropy framework for predicting their structure with minimal biases
Spatial structure facilitates evolutionary rescue by drug resistance
Intra-tumor heterogeneity, turnover rate and karyotype space shape susceptibility to missegregation-induced extinction
Explaining the flaws in human random generation as local sampling with momentum
Enhancing the Prioritization of Disease-Causing Genes through Tissue Specific Protein Interaction Networks
Ten Simple Rules for a Computational Biologist's Laboratory Notebook
Are transient protein-protein interactions more dispensable?
Conservation laws by virtue of scale symmetries in neural systems
Quantification of Circadian Rhythms in Single Cells
Identification of Ohnolog Genes Originating from Whole Genome Duplication in Early Vertebrates, Based on Synteny Comparison across Multiple Genomes
Asymmetric PTEN Distribution Regulated by Spatial Heterogeneity in Membrane-Binding State Transitions
Deep neural networks explain spiking activity in auditory cortex
A combined computational and experimental investigation of the filtration function of splenic macrophages in sickle cell disease
Optimising efficacy of antibiotics against systemic infection by varying dosage quantities and times
Improved protein complex prediction with AlphaFold-multimer by denoising the MSA profile
Human impedance modulation to improve visuo-haptic perception
Dynamic distribution decomposition for single-cell snapshot time series identifies subpopulations and trajectories during iPSC reprogramming
Microheterogeneity-induced conduction slowing and wavefront collisions govern macroscopic conduction behavior: A computational and experimental study
Teasing Apart Translational and Transcriptional Components of Stochastic Variations in Eukaryotic Gene Expression
Orchestrated neuronal migration and cortical folding: A computational and experimental study
Coherency of circadian rhythms in the SCN is governed by the interplay of two coupling factors
Large Scale Chromosome Folding Is Stable against Local Changes in Chromatin Structure
Inference of Gene Regulatory Networks with Sparse Structural Equation Models Exploiting Genetic Perturbations
Modeling differentiation-state transitions linked to therapeutic escape in triple-negative breast cancer
Role of DARPP-32 and ARPP-21 in the Emergence of Temporal Constraints on Striatal Calcium and Dopamine Integration
Competitive plasticity to reduce the energetic costs of learning
Noise correlations and neuronal diversity may limit the utility of winner-take-all readout in a pop out visual search task
Sample-efficient identification of high-dimensional antibiotic synergy with a normalized diagonal sampling design
Predicting antimicrobial resistance using conserved genes
What Population Reveals about Individual Cell Identity: Single-Cell Parameter Estimation of Models of Gene Expression in Yeast
Ten simple rules for successfully supporting first-generation/low-income (FLI) students in STEM