yusuke1997/dblp-id-title huggingface dataset:
Deciphering HLA-I motifs across HLA peptidomes improves neo-antigen predictions and identifies allostery regulating HLA specificity
Confidence Sharing: An Economic Strategy for Efficient Information Flows in Animal Groups
Temporal Dynamics and Developmental Maturation of Salience, Default and Central-Executive Network Interactions Revealed by Variational Bayes Hidden Markov Modeling
Mechanism of Arrhythmogenesis Driven by Early After Depolarizations in Cardiac Tissue
Filter inference: A scalable nonlinear mixed effects inference approach for snapshot time series data
Theoretical Analysis of Competing Conformational Transitions in Superhelical DNA
Correction: A computational modeling approach for predicting multicell spheroid patterns based on signaling-induced differential adhesion
dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design
Does the Potential for Chaos Constrain the Embryonic Cell-Cycle Oscillator?
Atypically larger variability of resource allocation accounts for visual working memory deficits in schizophrenia
Multi-study inference of regulatory networks for more accurate models of gene regulation
SARS-CoV-2 infection perturbs enhancer mediated transcriptional regulation of key pathways
Association test using Copy Number Profile Curves (CONCUR) enhances power in rare copy number variant analysis
Widespread position-specific conservation of synonymous rare codons within coding sequences
Axonal Velocity Distributions in Neural Field Equations
A First-Principles Model of Early Evolution: Emergence of Gene Families, Species, and Preferred Protein Folds
A Mixture of Delta-Rules Approximation to Bayesian Inference in Change-Point Problems
Spatial separation of two different pathways accounting for the generation of calcium signals in astrocytes
Identification of Key Processes that Control Tumor Necrosis Factor Availability in a Tuberculosis Granuloma
An Integrative Approach to Computational Modelling of the Gene Regulatory Network Controlling Clostridium botulinum Type A1 Toxin Production
MitoTracer facilitates the identification of informative mitochondrial mutations for precise lineage reconstruction
Two-Dimensionality of Yeast Colony Expansion Accompanied by Pattern Formation
A Compact Representation of Drawing Movements with Sequences of Parabolic Primitives
A Boolean Function for Neural Induction Reveals a Critical Role of Direct Intercellular Interactions in Patterning the Ectoderm of the Ascidian Embryo
Machine Learning Estimates of Natural Product Conformational Energies
A Mathematical Model of CR3/TLR2 Crosstalk in the Context of Francisella tularensis Infection
SCRaPL: A Bayesian hierarchical framework for detecting technical associates in single cell multiomics data
Ten quick tips for computational analysis of medical images
Cell-type annotation with accurate unseen cell-type identification using multiple references
Consistent pattern of epidemic slowing across many geographies led to longer, flatter initial waves of the COVID-19 pandemic
scaDA: A novel statistical method for differential analysis of single-cell chromatin accessibility sequencing data
Differences in Visual-Spatial Input May Underlie Different Compression Properties of Firing Fields for Grid Cell Modules in Medial Entorhinal Cortex
Stochastic Modeling of Expression Kinetics Identifies Messenger Half-Lives and Reveals Sequential Waves of Co-ordinated Transcription and Decay
Compounds without borders: A mechanism for quantifying complex odors and responses to scent-pollution in bumblebees
Predictive network modeling in human induced pluripotent stem cells identifies key driver genes for insulin responsiveness
The influence of saccades on yaw gaze stabilization in fly flight
Cortical ignition dynamics is tightly linked to the core organisation of the human connectome
Computational Prediction and Experimental Verification of New MAP Kinase Docking Sites and Substrates Including Gli Transcription Factors
Protein Surface Softness Is the Origin of Enzyme Cold-Adaptation of Trypsin
The Molecular Clock of Neutral Evolution Can Be Accelerated or Slowed by Asymmetric Spatial Structure
Fast Spatiotemporal Smoothing of Calcium Measurements in Dendritic Trees
The Impact of Contact Tracing in Clustered Populations
Correction: The role of the encapsulated cargo in microcompartment assembly
Plasticity-Driven Self-Organization under Topological Constraints Accounts for Non-random Features of Cortical Synaptic Wiring
Reconstructing tumor evolutionary histories and clone trees in polynomial-time with SubMARine
Functional Representation of Enzymes by Specific Peptides
4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments
Ten Simple Rules for Selecting a Bio-ontology
Simulation-based inference for efficient identification of generative models in computational connectomics
The Edge of Stability: Response Times and Delta Oscillations in Balanced Networks
Correction: Geospatial characteristics of measles transmission in China during 2005-2014
Towards self-describing and FAIR bulk formats for biomedical data
On the Inverse Problem of Binocular 3D Motion Perception
Pathway analysis in metabolomics: Recommendations for the use of over-representation analysis
Faster Adaptation in Smaller Populations: Counterintuitive Evolution of HIV during Childhood Infection
miRNA normalization enables joint analysis of several datasets to increase sensitivity and to reveal novel miRNAs differentially expressed in breast cancer
Oscillatory Regulation of Hes1: Discrete Stochastic Delay Modelling and Simulation
Quantitative and Kinetic Proteomics Reveal ApoE Isoform-dependent Proteostasis Adaptations in Mouse Brain
A Developmental Switch for Hebbian Plasticity
Stochastic modelling of a three-dimensional glycogen granule synthesis and impact of the branching enzyme
A machine learning model trained on a high-throughput antibacterial screen increases the hit rate of drug discovery
BootCellNet, a resampling-based procedure, promotes unsupervised identification of cell populations via robust inference of gene regulatory networks
Evidence for a multi-level trophic organization of the human gut microbiome
Both Ligand- and Cell-Specific Parameters Control Ligand Agonism in a Kinetic Model of G Protein-Coupled Receptor Signaling
Probabilistic models for neural populations that naturally capture global coupling and criticality
RNA3DCNN: Local and global quality assessments of RNA 3D structures using 3D deep convolutional neural networks
Synaptic Plasticity and Connectivity Requirements to Produce Stimulus-Pair Specific Responses in Recurrent Networks of Spiking Neurons
Biobeam - Multiplexed wave-optical simulations of light-sheet microscopy
A Bayesian Approach to Analyse Genetic Variation within RNA Viral Populations
Distinct prediction errors in mesostriatal circuits of the human brain mediate learning about the values of both states and actions: evidence from high-resolution fMRI
Quantitative evaluation of DNA damage repair dynamics to elucidate predictors of autism vs. cancer in individuals with germline PTEN variants
Heterogeneous susceptibility to rotavirus infection and gastroenteritis in two birth cohort studies: Parameter estimation and epidemiological implications
Knowledge-aware contrastive heterogeneous molecular graph learning
Elastohydrodynamics and Kinetics of Protein Patterning in the Immunological Synapse
Tipping points emerge from weak mutualism in metacommunities
Ten simple rules for interpreting and evaluating a meta-analysis
Redox poise in R. rubrum phototrophic growth drives large-scale changes in macromolecular pathways
CovCopCan: An efficient tool to detect Copy Number Variation from amplicon sequencing data in inherited diseases and cancer
Tracking conformational transitions of the gonadotropin hormone receptors in a bilayer of (SDPC) poly-unsaturated lipids from all-atom molecular dynamics simulations
Dynamical model of the CLC-2 ion channel reveals conformational changes associated with selectivity-filter gating
A general hypergraph learning algorithm for drug multi-task predictions in micro-to-macro biomedical networks
A Gene Gravity Model for the Evolution of Cancer Genomes: A Study of 3, 000 Cancer Genomes across 9 Cancer Types
Increased comparability between RNA-Seq and microarray data by utilization of gene sets
Multi-state Modeling of Biomolecules
Fluctuations in auxin levels depend upon synchronicity of cell divisions in a one-dimensional model of auxin transport
Src Kinase Conformational Activation: Thermodynamics, Pathways, and Mechanisms
Learning brain dynamics for decoding and predicting individual differences
Cox-nnet: An artificial neural network method for prognosis prediction of high-throughput omics data
HyperACP: A cutting-edge hybrid framework for anticancer peptide classification via scalable feature extraction and adaptive neighbor-based synthesis
Epidemiological and ecological consequences of virus manipulation of host and vector in plant virus transmission
Bivalent chromatin as a therapeutic target in cancer: An in silico predictive approach for combining epigenetic drugs
Predictive coding networks for temporal prediction
Elastic network modeling of cellular networks unveils sensor and effector genes that control information flow
Calibrating agent-based models to tumor images using representation learning
Modeling the Effects of Cell Cycle M-phase Transcriptional Inhibition on Circadian Oscillation
Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis (MUFFIN)
A computational study on the role of glutamate and NMDA receptors on cortical spreading depression using a multidomain electrodiffusion model
Dynamic Mechanisms of Neocortical Focal Seizure Onset
Evolutionary Optimization of Protein Folding
Efficient modelling of infectious diseases in wildlife: A case study of bovine tuberculosis in wild badgers
Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics
Identifying patterns differing between high-dimensional datasets with generalized contrastive PCA
Emergent Biosynthetic Capacity in Simple Microbial Communities
Comparison of sequence- and structure-based antibody clustering approaches on simulated repertoire sequencing data
Predicting Structure-Function Relations and Survival following Surgical and Bronchoscopic Lung Volume Reduction Treatment of Emphysema
A mathematical model of plasmin-mediated fibrinolysis of single fibrin fibers
Speeded Reaching Movements around Invisible Obstacles
Mutation, drift and selection in single-driver hematologic malignancy: Example of secondary myelodysplastic syndrome following treatment of inherited neutropenia
Criticality in probabilistic models of spreading dynamics in brain networks: Epileptic seizures
Independent Component Analysis in Spiking Neurons
Spike-Based Bayesian-Hebbian Learning of Temporal Sequences
LRSSLMDA: Laplacian Regularized Sparse Subspace Learning for MiRNA-Disease Association prediction
Generalized contrastive PCA is equivalent to generalized eigendecomposition
Linking Proteomic and Transcriptional Data through the Interactome and Epigenome Reveals a Map of Oncogene-induced Signaling
A Comparative Computer Simulation of Dendritic Morphology
Efficient assembly and long-term stability of defensive microbiomes via private resources and community bistability
Synaptic weights that correlate with presynaptic selectivity increase decoding performance
Foldy: An open-source web application for interactive protein structure analysis
FastGGM: An Efficient Algorithm for the Inference of Gaussian Graphical Model in Biological Networks
Approximate planning in spatial search
A Neural Population Model Incorporating Dopaminergic Neurotransmission during Complex Voluntary Behaviors
Recognition of sites of functional specialisation in all known eukaryotic protein kinase families
A Rescorla-Wagner drift-diffusion model of conditioning and timing
Nash equilibrium of attack and defense behaviors between predators and prey
DeepHE: Accurately predicting human essential genes based on deep learning
A Bayesian phylogenetic hidden Markov model for B cell receptor sequence analysis
Maximum-Entropy Models of Sequenced Immune Repertoires Predict Antigen-Antibody Affinity
On the open-source landscape of PLOS Computational Biology
Correction: A Computational Model of the Fetal Circulation to Quantify Blood Redistribution in Intrauterine Growth Restriction
Probing eukaryotic cell mechanics via mesoscopic simulations
Reassessing the modularity of gene co-expression networks using the Stochastic Block Model
Protein-protein interactions in neurodegenerative diseases: A conspiracy theory
A Bayesian non-parametric mixed-effects model of microbial growth curves
Correction: Humans combine value learning and hypothesis testing strategically in multi-dimensional probabilistic reward learning
Network representation of multicellular activity in pancreatic islets: Technical considerations for functional connectivity analysis
Structural and mechanistic diversity in p53-mediated regulation of organismal longevity across taxonomical orders
Correction: Similarities and differences in spatial and non-spatial cognitive maps
Validation framework for epidemiological models with application to COVID-19 models
Correction: An antigenic diversification threshold for falciparum malaria transmission at high endemicity
A Common Mechanism Underlying Food Choice and Social Decisions
Towards reliable quantification of cell state velocities
A quantitative model for the rate-limiting process of UGA alternative assignments to stop and selenocysteine codons
Inferring epidemiological parameters from phylogenies using regression-ABC: A comparative study
Signaling and Adaptation Modulate the Dynamics of the Photosensoric Complex of Natronomonas pharaonis
Noise Contributions in an Inducible Genetic Switch: A Whole-Cell Simulation Study
WormSNAP: A software for fast, accurate, and unbiased detection of fluorescent puncta in C. elegans
MFPred: Rapid and accurate prediction of protein-peptide recognition multispecificity using self-consistent mean field theory
After the honeymoon, the divorce: Unexpected outcomes of disease control measures against endemic infections
Principles that govern competition or co-existence in Rho-GTPase driven polarization
Conformation Regulation of the X Chromosome Inactivation Center: A Model
A spectral framework to map QTLs affecting joint differential networks of gene co-expression
Estimating the dimensionality of the manifold underlying multi-electrode neural recordings
ProtFus: A Comprehensive Method Characterizing Protein-Protein Interactions of Fusion Proteins
HyperTraPS-CT: Inference and prediction for accumulation pathways with flexible data and model structures
HAYSTAC: A Bayesian framework for robust and rapid species identification in high-throughput sequencing data
Estimation of the breadth of CD4bs targeting HIV antibodies by molecular modeling and machine learning
Polarizable Water Model for the Coarse-Grained MARTINI Force Field
Complete Firing-Rate Response of Neurons with Complex Intrinsic Dynamics
Using real-time data to guide decision-making during an influenza pandemic: A modelling analysis
Coding of object location by heterogeneous neural populations with spatially dependent correlations in weakly electric fish
A computational account of threat-related attentional bias
Data-driven brain network models differentiate variability across language tasks
Target Essentiality and Centrality Characterize Drug Side Effects
Ten simple rules for developing visualization tools in genomics
Modeling Recursive RNA Interference
How growers make decisions impacts plant disease control
Elucidating relationships between P.falciparum prevalence and measures of genetic diversity with a combined genetic-epidemiological model of malaria
COEXIST: Coordinated single-cell integration of serial multiplexed tissue images
SCMFMDA: Predicting microRNA-disease associations based on similarity constrained matrix factorization
Individual differences in the perception of probability
Accurate and Fast Simulation of Channel Noise in Conductance-Based Model Neurons by Diffusion Approximation
Recognition and reconstruction of cell differentiation patterns with deep learning
Combining molecular dynamics simulations and scoring method to computationally model ubiquitylated linker histones in chromatosomes
Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen
Ten Simple Rules to Protect Your Intellectual Property
Kinetically-Defined Component Actions in Gene Repression
A model for cooperative gating of L-type Ca2+ channels and its effects on cardiac alternans dynamics
Time varying methods to infer extremes in dengue transmission dynamics
The evolution of environmentally mediated social interactions and posthumous spite under isolation by distance
Synaptic plasticity onto inhibitory neurons as a mechanism for ocular dominance plasticity
Optimal Control Predicts Human Performance on Objects with Internal Degrees of Freedom
Uncovering the impact of randomness in HIV hotspot formation: A mathematical modeling study
Kinetic Rate Constant Prediction Supports the Conformational Selection Mechanism of Protein Binding
A Granger Causality Measure for Point Process Models of Ensemble Neural Spiking Activity
Linear-nonlinear cascades capture synaptic dynamics
Specificity and Evolvability in Eukaryotic Protein Interaction Networks
Agent-based model provides insight into the mechanisms behind failed regeneration following volumetric muscle loss injury
Numerical Approach to Spatial Deterministic-Stochastic Models Arising in Cell Biology
A quadratically regularized functional canonical correlation analysis for identifying the global structure of pleiotropy with NGS data
A high-frequency mobility big-data reveals how COVID-19 spread across professions, locations and age groups
Limits on reliable information flows through stochastic populations
Genomics and Privacy: Implications of the New Reality of Closed Data for the Field
Designing a course model for distance-based online bioinformatics training in Africa: The H3ABioNet experience
Dynamic modelling of the PI3K/MTOR signalling network uncovers biphasic dependence of mTORC1 activity on the mTORC2 subunit SIN1
Changing Cellular Location of CheZ Predicted by Molecular Simulations
Continuing Education Workshops in Bioinformatics Positively Impact Research and Careers
Bayesian phylodynamics of avian influenza A virus H9N2 in Asia with time-dependent predictors of migration
Ten simple rules for designing analogue science games
Domestic cat nose functions as a highly efficient coiled parallel gas chromatograph
Modulation of Network Excitability by Persistent Activity: How Working Memory Affects the Response to Incoming Stimuli
Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome
Fixation patterns in simple choice reflect optimal information sampling
Correction: Temporal Gillespie algorithm: Fast simulation of contagion processes on time-varying networks
Analysis of the relationship between coexpression domains and chromatin 3D organization
Multi-scale Visualization of Molecular Architecture Using Real-Time Ambient Occlusion in Sculptor
Transcriptional Regulation: Effects of Promoter Proximal Pausing on Speed, Synchrony and Reliability
Dowker complex based machine learning (DCML) models for protein-ligand binding affinity prediction
Social Interactions in Myxobacterial Swarming
In Silico Single-Molecule Manipulation of DNA with Rigid Body Dynamics
3D Complex: A Structural Classification of Protein Complexes
Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re-arrangement
A disordered encounter complex is central to the yeast Abp1p SH3 domain binding pathway
Emergence of sparse coding, balance and decorrelation from a biologically-grounded spiking neural network model of learning in the primary visual cortex
Biophysical Parameters Modification Could Overcome Essential Hearing Gaps
Mapping Information Flow in Sensorimotor Networks
Aggregation Propensity of the Human Proteome
Four different mechanisms for switching cell polarity
A three-dimensional phase-field model for multiscale modeling of thrombus biomechanics in blood vessels
Automated Identification of Core Regulatory Genes in Human Gene Regulatory Networks
Nonmechanistic forecasts of seasonal influenza with iterative one-week-ahead distributions
Federated epidemic surveillance
Coarse-grained model of serial dilution dynamics in synthetic human gut microbiome
ISMB/ECCB 2007: The Premier Conference on Computational Biology
Molecular Machines in the Synapse: Overlapping Protein Sets Control Distinct Steps in Neurosecretion
OSS-DBS: Open-source simulation platform for deep brain stimulation with a comprehensive automated modeling
A Computational Model for the AMPA Receptor Phosphorylation Master Switch Regulating Cerebellar Long-Term Depression
A Statistical Framework to Identify Deviation from Time Linearity in Epigenetic Aging
Competitive Dynamics in MSTd: A Mechanism for Robust Heading Perception Based on Optic Flow
Ten simple rules to consider regarding preprint submission
Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE)
Synthetic population generation with public health characteristics for spatial agent-based models
Comparison of Filtering Methods for the Modeling and Retrospective Forecasting of Influenza Epidemics
Constructing a full, multiple-layer interactome for SARS-CoV-2 in the context of lung disease: Linking the virus with human genes and microbes
Ensemble inference of unobserved infections in networks using partial observations
Accurate Path Integration in Continuous Attractor Network Models of Grid Cells
Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities
Correction: Structure Modeling of All Identified G Protein-Coupled Receptors in the Human Genome
Average beta burst duration profiles provide a signature of dynamical changes between the ON and OFF medication states in Parkinson's disease
Selective ion permeation involves complexation with carboxylates and lysine in a model human sodium channel
Ab Initio Modeling and Experimental Assessment of Janus Kinase 2 (JAK2) Kinase-Pseudokinase Complex Structure
Tissue specific LRRK2 interactomes reveal a distinct striatal functional unit
Correction: Bayesian hypothesis testing and experimental design for two-photon imaging data
Toxin production spontaneously becomes regulated by local cell density in evolving bacterial populations
Deep Learning for Population Genetic Inference
Identification and Classification of Conserved RNA Secondary Structures in the Human Genome
Bayesian active sound localisation: To what extent do humans perform like an ideal-observer?
Functional Connectivity's Degenerate View of Brain Computation
Applying Super-Resolution and Tomography Concepts to Identify Receptive Field Subunits in the Retina
Decoupling Environment-Dependent and Independent Genetic Robustness across Bacterial Species
Network-neuron interactions underlying sensory responses of layer 5 pyramidal tract neurons in barrel cortex
A dynamic power-law sexual network model of gonorrhoea outbreaks
An agent-based modeling approach for lung fibrosis in response to COVID-19
Simulation of Molecular Data under Diverse Evolutionary Scenarios
Information integration in large brain networks
Explaining the Timing of Natural Scene Understanding with a Computational Model of Perceptual Categorization
Genome Landscapes of Disease: Strategies to Predict the Phenotypic Consequences of Human Germline and Somatic Variation
Coherent Motion of Monolayer Sheets under Confinement and Its Pathological Implications
Raising awareness of uncertain choices in empirical data analysis: A teaching concept toward replicable research practices
Minimal cross-trial generalization in learning the representation of an odor-guided choice task
Mobility can promote the evolution of cooperation via emergent self-assortment dynamics