yusuke1997/dblp-id-title huggingface dataset:
iSoMAs: Finding isoform expression and somatic mutation associations in human cancers
Bayesian inference of transmission chains using timing of symptoms, pathogen genomes and contact data
The two kinds of free energy and the Bayesian revolution
Up-down biphasic volume response of human red blood cells to PIEZO1 activation during capillary transits
Phenotypic delay in the evolution of bacterial antibiotic resistance: Mechanistic models and their implications
CNEr: A toolkit for exploring extreme noncoding conservation
Antibody accessibility determines location of spike surface mutations in SARS-CoV-2 variants
Computational Optogenetics: Empirically-Derived Voltage- and Light-Sensitive Channelrhodopsin-2 Model
Mathematical model predicts response to chemotherapy in advanced non-resectable non-small cell lung cancer patients treated with platinum-based doublet
A system-wide network reconstruction of gene regulation and metabolism in Escherichia coli
Optimal transport analysis reveals trajectories in steady-state systems
Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations
Universal Count Correction for High-Throughput Sequencing
Machine learning assisted intraoperative assessment of brain tumor margins using HRMAS NMR spectroscopy
Top-Down Beta Rhythms Support Selective Attention via Interlaminar Interaction: A Model
Unknotting RNA: A method to resolve computational artifacts
An Integrated Disease/Pharmacokinetic/Pharmacodynamic Model Suggests Improved Interleukin-21 Regimens Validated Prospectively for Mouse Solid Cancers
Evolutionary Dynamics of Strategic Behavior in a Collective-Risk Dilemma
Neural Computation via Neural Geometry: A Place Code for Inter-whisker Timing in the Barrel Cortex?
Virus Capsid Dissolution Studied by Microsecond Molecular Dynamics Simulations
CpG Island Mapping by Epigenome Prediction
SteadyCom: Predicting microbial abundances while ensuring community stability
CytoPy: An autonomous cytometry analysis framework
A comparative computational analysis of IFN-alpha pharmacokinetics and its induced cellular response in mice and humans
Co-localization and confinement of ecto-nucleotidases modulate extracellular adenosine nucleotide distributions
A pipeline for the reconstruction and evaluation of context-specific human metabolic models at a large-scale
Correlation Structure in Micro-ECoG Recordings is Described by Spatially Coherent Components
Modulation of Elementary Calcium Release Mediates a Transition from Puffs to Waves in an IP 3 R Cluster Model
Aberrant DNA methylation defines isoform usage in cancer, with functional implications
tvsfglasso: Time-varying scale-free graphical lasso for network estimation from time-series data
Virtual Patients and Sensitivity Analysis of the Guyton Model of Blood Pressure Regulation: Towards Individualized Models of Whole-Body Physiology
Quantifying the Length and Variance of the Eukaryotic Cell Cycle Phases by a Stochastic Model and Dual Nucleoside Pulse Labelling
Information dynamics of in silico EEG Brain Waves: Insights into oscillations and functions
Spikebench: An open benchmark for spike train time-series classification
Practical considerations for measuring the effective reproductive number, Rt
Time Scale Hierarchies in the Functional Organization of Complex Behaviors
The N-terminal domain of RfaH plays an active role in protein fold-switching
Ankyrin repeats in context with human population variation
Short-term depression and long-term plasticity together tune sensitive range of synaptic plasticity
Understanding disease-associated metabolic changes in human colonic epithelial cells using the iColonEpithelium metabolic reconstruction
Autistic traits foster effective curiosity-driven exploration
A biophysically detailed computational model of urinary bladder small DRG neuron soma
A dynamic calcium-force relationship model for sag behavior in fast skeletal muscle
Microsimulation based quantitative analysis of COVID-19 management strategies
Eurekometrics: Analyzing the Nature of Discovery
Classification of estrogenic compounds by coupling high content analysis and machine learning algorithms
A Bayesian framework for the analysis of systems biology models of the brain
Machine learning-based microarray analyses indicate low-expression genes might collectively influence PAH disease
A mechanistic model of the BLADE platform predicts performance characteristics of 256 different synthetic DNA recombination circuits
A burst-dependent thalamocortical substrate for perceptual awareness
Profile-Wise Analysis: A profile likelihood-based workflow for identifiability analysis, estimation, and prediction with mechanistic mathematical models
Reconstructing feedback representations in the ventral visual pathway with a generative adversarial autoencoder
Communication and Common Interest
Determinants of the Spatiotemporal Dynamics of the 2009 H1N1 Pandemic in Europe: Implications for Real-Time Modelling
Accurate Encoding and Decoding by Single Cells: Amplitude Versus Frequency Modulation
In Search of the Biological Significance of Modular Structures in Protein Networks
Systems Pharmacology and Rational Polypharmacy: Nitric Oxide-Cyclic GMP Signaling Pathway as an Illustrative Example and Derivation of the General Case
Number and Size Distribution of Colorectal Adenomas under the Multistage Clonal Expansion Model of Cancer
A Multiscale Approach to Characterize the Early Aggregation Steps of the Amyloid-Forming Peptide GNNQQNY from the Yeast Prion Sup-35
SuperEdgeGO: Edge-supervised graph representation learning for enhanced protein function prediction
Red Queen Dynamics with Non-Standard Fitness Interactions
Dynamic Nucleosome Movement Provides Structural Information of Topological Chromatin Domains in Living Human Cells
Stimulus-dependent Maximum Entropy Models of Neural Population Codes
mixOmics: An R package for 'omics feature selection and multiple data integration
Toward a theory of coactivation patterns in excitable neural networks
Correction: Persistent Activity in Neural Networks with Dynamic Synapses
Correction: AI-Assisted chemical probe discovery for the understudied Calcium-Calmodulin Dependent Kinase, PNCK
International Society for Computational Biology Honors Dana Pe'er with Top Bioinformatics/Computational Biology Award for 2014
A mutation-level covariate model for mutational signatures
Quantifying the roles of host movement and vector dispersal in the transmission of vector-borne diseases of livestock
Genome-Wide Localization of Protein-DNA Binding and Histone Modification by a Bayesian Change-Point Method with ChIP-seq Data
Eleven quick tips for architecting biomedical informatics workflows with cloud computing
Multivariable association discovery in population-scale meta-omics studies
Estimating error rates for single molecule protein sequencing experiments
Computer Simulations Suggest a Key Role of Membranous Nanodomains in Biliary Lipid Secretion
Modeling and prediction of clinical symptom trajectories in Alzheimer's disease using longitudinal data
Medusa: Software to build and analyze ensembles of genome-scale metabolic network reconstructions
Inferring interaction partners from protein sequences using mutual information
Tight basis cycle representatives for persistent homology of large biological data sets
Nonlinear Gap Junctions Enable Long-Distance Propagation of Pulsating Calcium Waves in Astrocyte Networks
Quantification of transplant-derived circulating cell-free DNA in absence of a donor genotype
Phase-lags in large scale brain synchronization: Methodological considerations and in-silico analysis
Disentangling choice value and choice conflict in sequential decisions under risk
Contextual influence on confidence judgments in human reinforcement learning
Differential allelic representation (DAR) identifies candidate eQTLs and improves transcriptome analysis
Dissecting the regulatory roles of ORM proteins in the sphingolipid pathway of plants
RIDDLE: Race and ethnicity Imputation from Disease history with Deep LEarning
Comparative Analysis of the Macroscale Structural Connectivity in the Macaque and Human Brain
MCAM: Multiple Clustering Analysis Methodology for Deriving Hypotheses and Insights from High-Throughput Proteomic Datasets
Protein Complex Evolution Does Not Involve Extensive Network Rewiring
An efficient coding theory for a dynamic trajectory predicts non-uniform allocation of entorhinal grid cells to modules
Getting Started in Computational Immunology
Regulatory properties of transcription factors with diverse mechanistic function
Coiled-Coil Proteins Facilitated the Functional Expansion of the Centrosome
Rhythmicity is linked to expression cost at the protein level but to expression precision at the mRNA level
Evaluating the effectiveness of ensemble voting in improving the accuracy of consensus signals produced by various DTWA algorithms from step-current signals generated during nanopore sequencing
Ten simple rules for initial data analysis
Analyzing and Quantifying the Gain-of-Function Enhancement of IP 3 Receptor Gating by Familial Alzheimer's Disease-Causing Mutants in Presenilins
Optimisation strategies for directed evolution without sequencing
Novel Models of Visual Topographic Map Alignment in the Superior Colliculus
MAGERI: Computational pipeline for molecular-barcoded targeted resequencing
Spatial dynamics of synthetic microbial mutualists and their parasites
Internality and the internalisation of failure: Evidence from a novel task
Establishing a Statistical Link between Network Oscillations and Neural Synchrony
Modeling scenarios for mitigating outbreaks in congregate settings
Discovering functional sequences with RELICS, an analysis method for CRISPR screens
Bayesian polynomial neural networks and polynomial neural ordinary differential equations
Effect of Regulatory Architecture on Broad versus Narrow Sense Heritability
Impact of variability in cell cycle periodicity on cell population dynamics
Identification of Conserved Moieties in Metabolic Networks by Graph Theoretical Analysis of Atom Transition Networks
Mechanism for Collective Cell Alignment in Myxococcus xanthus Bacteria
Improving the Modeling of Disease Data from the Government Surveillance System: A Case Study on Malaria in the Brazilian Amazon
Modeling Cancer Progression via Pathway Dependencies
Learning Reward Uncertainty in the Basal Ganglia
Differential effects of propofol and ketamine on critical brain dynamics
A novel hypergraph model for identifying and prioritizing personalized drivers in cancer
A Feedback Model of Attention Explains the Diverse Effects of Attention on Neural Firing Rates and Receptive Field Structure
Sarcomeric Pattern Formation by Actin Cluster Coalescence
Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP)
Similarities and differences in spatial and non-spatial cognitive maps
Rapid prediction of crucial hotspot interactions for icosahedral viral capsid self-assembly by energy landscape atlasing validated by mutagenesis
Impact of Heterogeneity in Sexual Behavior on Effectiveness in Reducing HIV Transmission with Test-and-Treat Strategy
Molecular Infectious Disease Epidemiology: Survival Analysis and Algorithms Linking Phylogenies to Transmission Trees
ToMExO: A probabilistic tree-structured model for cancer progression
Live Coverage of Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB) 2009
Overcoming CRISPR-Cas9 off-target prediction hurdles: A novel approach with ESB rebalancing strategy and CRISPR-MCA model
Detecting and quantifying heterogeneity in susceptibility using contact tracing data
Regulation of the Nucleosome Repeat Length In Vivo by the DNA Sequence, Protein Concentrations and Long-Range Interactions
Why Are Computational Neuroscience and Systems Biology So Separate?
Perspectives for the reconstruction of 3D chromatin conformation using single cell Hi-C data
Bayesian parameter estimation for automatic annotation of gene functions using observational data and phylogenetic trees
Learning and interpreting the gene regulatory grammar in a deep learning framework
Monkeys and Humans Share a Common Computation for Face/Voice Integration
A Boolean Model of the Gene Regulatory Network Underlying Mammalian Cortical Area Development
A comprehensive ensemble model for comparing the allosteric effect of ordered and disordered proteins
Bang-Bang Control of Feeding: Role of Hypothalamic and Satiety Signals
Short Conduction Delays Cause Inhibition Rather than Excitation to Favor Synchrony in Hybrid Neuronal Networks of the Entorhinal Cortex
Kinetics of Rhodopsin Deactivation and Its Role in Regulating Recovery and Reproducibility of Rod Photoresponse
Modeling Somatic Evolution in Tumorigenesis
The Sign Rule and Beyond: Boundary Effects, Flexibility, and Noise Correlations in Neural Population Codes
Inferring Dynamic Signatures of Microbes in Complex Host Ecosystems
Sparse deep predictive coding captures contour integration capabilities of the early visual system
Phylogenetic analysis of migration, differentiation, and class switching in B cells
Flexible neural connectivity under constraints on total connection strength
FunSpace: A functional and spatial analytic approach to cell imaging data using entropy measures
Computational Methods for Protein Identification from Mass Spectrometry Data
A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination
Impact of ligand binding on VEGFR1, VEGFR2, and NRP1 localization in human endothelial cells
An automated interface for sedimentation velocity analysis in SEDFIT
Proteins with Complex Architecture as Potential Targets for Drug Design: A Case Study of Mycobacterium tuberculosi s
Eleven quick tips to build a usable REST API for life sciences
Persistent Chaos of Measles Epidemics in the Prevaccination United States Caused by a Small Change in Seasonal Transmission Patterns
Timescales of motor memory formation in dual-adaptation
Tracking and predicting U.S. influenza activity with a real-time surveillance network
Quantifying Intramolecular Binding in Multivalent Interactions: A Structure-Based Synergistic Study on Grb2-Sos1 Complex
Contributions of mechanical loading and hormonal changes to eccentric hypertrophy during volume overload: A Bayesian analysis using logic-based network models
Ten simple rules for making research software more robust
The Impact of Imitation on Vaccination Behavior in Social Contact Networks
Construction and Validation of a Regulatory Network for Pluripotency and Self-Renewal of Mouse Embryonic Stem Cells
Building a continuous benchmarking ecosystem in bioinformatics
Assessing the performance of methods for cell clustering from single-cell DNA sequencing data
Cerebellar Nuclear Neurons Use Time and Rate Coding to Transmit Purkinje Neuron Pauses
Determining Effects of Non-synonymous SNPs on Protein-Protein Interactions using Supervised and Semi-supervised Learning
Effects of spatial heterogeneity on bacterial genetic circuits
Response nonlinearities in networks of spiking neurons
Epidemiological modeling of Trypanosoma cruzi: Low stercorarian transmission and failure of host adaptive immunity explain the frequency of mixed infections in humans
Structure Learning in Bayesian Sensorimotor Integration
phastSim: Efficient simulation of sequence evolution for pandemic-scale datasets
Membrane Binding of MinE Allows for a Comprehensive Description of Min-Protein Pattern Formation
Inferring evolutionary pathways and directed genotype networks of foodborne pathogens
Mechano-chemical Interactions in Cardiac Sarcomere Contraction: A Computational Modeling Study
Genome-Wide Survey for Biologically Functional Pseudogenes
The Landscape of the Prion Protein's Structural Response to Mutation Revealed by Principal Component Analysis of Multiple NMR Ensembles
Multi-scale computational study of the mechanical regulation of cell mitotic rounding in epithelia
Evolution to alternative levels of stable diversity leaves areas of niche space unexplored
Fast and Accurate Resonance Assignment of Small-to-Large Proteins by Combining Automated and Manual Approaches
OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations
Genome Scale-Differential Flux Analysis reveals deregulation of lung cell metabolism on SARS-CoV-2 infection
Using Chemical Reaction Kinetics to Predict Optimal Antibiotic Treatment Strategies
Ten quick tips for getting the most scientific value out of numerical data
Mechanistic insights into ligand dissociation from the SARS-CoV-2 spike glycoprotein
Phylogeny-corrected identification of microbial gene families relevant to human gut colonization
Intrinsic Noise Induces Critical Behavior in Leaky Markovian Networks Leading to Avalanching
Emergence of a Small-World Functional Network in Cultured Neurons
Cortical networks with multiple interneuron types generate oscillatory patterns during predictive coding
Ten simple rules to bridge ecology and palaeoecology by publishing outside palaeoecological journals
G4mismatch: Deep neural networks to predict G-quadruplex propensity based on G4-seq data
Radio-frequency exposure of the yellow fever mosquito (A. aegypti) from 2 to 240 GHz
Correction: Modeling and MEG evidence of early consonance processing in auditory cortex
DNA spontaneously wrapping around a histone core prefers negative supercoiling: A Brownian dynamics study
A computational model of stereoscopic prey capture in praying mantises
Optimal Compensation for Temporal Uncertainty in Movement Planning
Segmentation and genome annotation algorithms for identifying chromatin state and other genomic patterns
Indirect Reciprocity under Incomplete Observation
Robustness of Learning That Is Based on Covariance-Driven Synaptic Plasticity
Deep reinforcement learning for optimal experimental design in biology
Pathway-specific protein domains are predictive for human diseases
Recombination Rate and Selection Strength in HIV Intra-patient Evolution
The NOSTRA model: Coherent estimation of infection sources in the case of possible nosocomial transmission
Shedding light on blue-green photosynthesis: A wavelength-dependent mathematical model of photosynthesis in Synechocystis sp. PCC 6803
Spatial Analysis of Expression Patterns Predicts Genetic Interactions at the Mid-Hindbrain Boundary
Network resonance can be generated independently at distinct levels of neuronal organization
Bayes-optimal estimation of overlap between populations of fixed size
Mutual influence between language and perception in multi-agent communication games
Indirect reciprocity with Bayesian reasoning and biases
Is Protein Folding Sub-Diffusive?
Inferring modulators of genetic interactions with epistatic nested effects models
Computational Analysis of Phosphopeptide Binding to the Polo-Box Domain of the Mitotic Kinase PLK1 Using Molecular Dynamics Simulation
Virtual neural network-guided optimization of non-invasive brain stimulation in Alzheimer's disease
Paired fruit flies synchronize behavior: Uncovering social interactions in Drosophila melanogaster
Simulations of blood as a suspension predicts a depth dependent hematocrit in the circulation throughout the cerebral cortex
Accessing a Hidden Conformation of the Maltose Binding Protein Using Accelerated Molecular Dynamics
Exploring E-cadherin-peptidomimetics interaction using NMR and computational studies
Molecular mechanisms of fentanyl mediated β-arrestin biased signaling
CAERUS: Predicting CAncER oUtcomeS Using Relationship between Protein Structural Information, Protein Networks, Gene Expression Data, and Mutation Data
Gene Prioritization by Compressive Data Fusion and Chaining
A framework for modelling desert locust population dynamics and large-scale dispersal
Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types
Metabolic Reconstruction and Modeling of Nitrogen Fixation in Rhizobium etli
Potassium Starvation in Yeast: Mechanisms of Homeostasis Revealed by Mathematical Modeling
Modeling the genetic relatedness of Plasmodium falciparum parasites following meiotic recombination and cotransmission
Intraneuronal binding of amyloid beta with reelin - Implications for the onset of Alzheimer's disease
Attention-based deep clustering method for scRNA-seq cell type identification
Quantum chemistry reveals thermodynamic principles of redox biochemistry
Noise Driven Evolutionary Waves
Emergence of belief-like representations through reinforcement learning
A systematic approach to decipher crosstalk in the p53 signaling pathway using single cell dynamics
Quantitative Live Imaging of Human Embryonic Stem Cell Derived Neural Rosettes Reveals Structure-Function Dynamics Coupled to Cortical Development
Odorant mixtures elicit less variable and faster responses than pure odorants
Coding Locations Relative to One or Many Landmarks in Childhood
Non-canonical Activation of Akt in Serum-Stimulated Fibroblasts, Revealed by Comparative Modeling of Pathway Dynamics
Atomic resolution mechanism of ligand binding to a solvent inaccessible cavity in T4 lysozyme
Parameterization of intraoperative human microelectrode recordings: Linking action potential morphology to brain anatomy
Population FBA predicts metabolic phenotypes in yeast
A continuum-mechanical skeletal muscle model including actin-titin interaction predicts stable contractions on the descending limb of the force-length relation
Foraging as sampling without replacement: A Bayesian statistical model for estimating biases in target selection
Social Feedback and the Emergence of Rank in Animal Society
The super repertoire of type IV effectors in the pangenome of Ehrlichia spp. provides insights into host-specificity and pathogenesis
Quantitative comparison between sub-millisecond time resolution single-molecule FRET measurements and 10-second molecular simulations of a biosensor protein
Inferring hidden structure in multilayered neural circuits
Mechanistic modeling of light-induced chemotactic infiltration of bacteria into leaf stomata
Impact of variants of concern on SARS-CoV-2 viral dynamics in non-human primates
neuroWalknet, a controller for hexapod walking allowing for context dependent behavior
Metrics for Assessing Cytoskeletal Orientational Correlations and Consistency
The Biocurator: Connecting and Enhancing Scientific Data
Conserved Expression Patterns Predict microRNA Targets
Fast yet force-effective mode of supracellular collective cell migration due to extracellular force transmission
H3 Histone Tail Conformation within the Nucleosome and the Impact of K14 Acetylation Studied Using Enhanced Sampling Simulation
Analysis of Nearly One Thousand Mammalian Mirtrons Reveals Novel Features of Dicer Substrates
Mathematical modelling reveals cellular dynamics within tumour spheroids
Dosing time optimization of antihypertensive medications by including the circadian rhythm in pharmacokinetic-pharmacodynamic models
Chaotic dynamics in spatially distributed neuronal networks generate population-wide shared variability
An Automated Phenotype-Driven Approach ( Gene Force) for Refining Metabolic and Regulatory Models
A Unifying Mechanistic Model of Selective Attention in Spiking Neurons
Sparse Gamma Rhythms Arising through Clustering in Adapting Neuronal Networks
Unraveling Protein Networks with Power Graph Analysis
Identification of High-Impact cis -Regulatory Mutations Using Transcription Factor Specific Random Forest Models
bigPint: A Bioconductor visualization package that makes big data pint-sized
Transcription reshapes RNA hairpin folding pathways revealed by all-atom molecular dynamics simulations
Host centric drug repurposing for viral diseases
A local uPAR-plasmin-TGFβ1 positive feedback loop in a qualitative computational model of angiogenic sprouting explains the in vitro effect of fibrinogen variants
Two-variable nullcline analysis of ionic general equilibrium predicts calcium homeostasis in ventricular myocytes
Combinatorial Binding in Human and Mouse Embryonic Stem Cells Identifies Conserved Enhancers Active in Early Embryonic Development
Per-sample immunoglobulin germline inference from B cell receptor deep sequencing data