yusuke1997/dblp-id-title huggingface dataset:
Conserved and divergent signals in 5' splice site sequences across fungi, metazoa and plants
Reciprocal interaction between IK1 and If in biological pacemakers: A simulation study
Enhancing reproducibility of gene expression analysis with known protein functional relationships: The concept of well-associated protein
Model of Fission Yeast Cell Shape Driven by Membrane-Bound Growth Factors and the Cytoskeleton
Ten quick tips for effective dimensionality reduction
Synaptic Plasticity Enables Adaptive Self-Tuning Critical Networks
Selection for Replicases in Protocells
Social behavioural adaptation in Autism
Novel methods for estimating the instantaneous and overall COVID-19 case fatality risk among care home residents in England
Modelling pathogen spread in a healthcare network: Indirect patient movements
Spike-Based Reinforcement Learning in Continuous State and Action Space: When Policy Gradient Methods Fail
The critical balance between dopamine D2 receptor and RGS for the sensitive detection of a transient decay in dopamine signal
Correction: Reading wild minds: A computational assay of Theory of Mind sophistication across seven primate species
Analogous computations in working memory input, output and motor gating: Electrophysiological and computational modeling evidence
Model-based analysis of influenza A virus replication in genetically engineered cell lines elucidates the impact of host cell factors on key kinetic parameters of virus growth
Quantitative modeling identifies critical cell mechanics driving bile duct lumen formation
Dynamics of morphogen source formation in a growing tissue
Short-term and long-term epidemiological impacts of sustained vector control in various dengue endemic settings: A modelling study
Cortical feedback and gating in odor discrimination and generalization
Priors Engaged in Long-Latency Responses to Mechanical Perturbations Suggest a Rapid Update in State Estimation
Just-in-time: Gaze guidance in natural behavior
Translating Clinical Findings into Knowledge in Drug Safety Evaluation - Drug Induced Liver Injury Prediction System (DILIps)
The MAGMA pipeline for comprehensive genomic analyses of clinical Mycobacterium tuberculosis samples
The feasibility of equilibria in large ecosystems: A primary but neglected concept in the complexity-stability debate
Socioeconomic bias in influenza surveillance
Modelling thalamocortical circuitry shows that visually induced LTP changes laminar connectivity in human visual cortex
Ten Simple Rules for Doing Your Best Research, According to Hamming
Comment on "Using genomic data and machine learning to predict antibiotic resistance: A tutorial paper"
Assessing the performance of real-time epidemic forecasts: A case study of Ebola in the Western Area region of Sierra Leone, 2014-15
Representation learning of genomic sequence motifs with convolutional neural networks
Ten simple rules for drawing scientific comics
MetaLP: An integrative linear programming method for protein inference in metaproteomics
Interacting cells driving the evolution of multicellular life cycles
Profiling cellular morphodynamics by spatiotemporal spectrum decomposition
An entropic barriers diffusion theory of decision-making in multiple alternative tasks
Global dynamics of microbial communities emerge from local interaction rules
A novel kinetic model to demonstrate the independent effects of ATP and ADP/Pi concentrations on sarcomere function
Bayesian calibration, process modeling and uncertainty quantification in biotechnology
Functional parcellation of mouse visual cortex using statistical techniques reveals response-dependent clustering of cortical processing areas
Modeling Networks of Coupled Enzymatic Reactions Using the Total Quasi-Steady State Approximation
Determining Physical Mechanisms of Gene Expression Regulation from Single Cell Gene Expression Data
Reduction of multiscale stochastic biochemical reaction networks using exact moment derivation
Pathway-Based Genomics Prediction using Generalized Elastic Net
Motoneuron-driven computational muscle modelling with motor unit resolution and subject-specific musculoskeletal anatomy
On the optimal design of metabolic RNA labeling experiments
Balanced state of networks of winner-take-all units
Unraveling ChR2-driven stochastic Ca2+ dynamics in astrocytes: A call for new interventional paradigms
A generalized Flory-Stockmayer kinetic theory of connectivity percolation and rigidity percolation of cytoskeletal networks
Integrating unsupervised language model with triplet neural networks for protein gene ontology prediction
Computational investigation of sphingosine kinase 1 (SphK1) and calcium dependent ERK1/2 activation downstream of VEGFR2 in endothelial cells
Unsupervised Clustering of Subcellular Protein Expression Patterns in High-Throughput Microscopy Images Reveals Protein Complexes and Functional Relationships between Proteins
ftmsRanalysis: An R package for exploratory data analysis and interactive visualization of FT-MS data
Integration of the Transcriptome and Glycome for Identification of Glycan Cell Signatures
Feasibility of functional magnetic resonance imaging of ocular dominance and orientation preference in primary visual cortex
Diversity of synaptic protein complexes as a function of the abundance of their constituent proteins: A modeling approach
Reservoir computing model of prefrontal cortex creates novel combinations of previous navigation sequences from hippocampal place-cell replay with spatial reward propagation
A Computational, Tissue-Realistic Model of Pressure Ulcer Formation in Individuals with Spinal Cord Injury
Human-environment feedback and the consistency of proenvironmental behavior
Chapter 4: Protein Interactions and Disease
On the influence of prior information evaluated by fully Bayesian criteria in a personalized whole-brain model of epilepsy spread
Parameterized syncmer schemes improve long-read mapping
Tinnitus-like "hallucinations" elicited by sensory deprivation in an entropy maximization recurrent neural network
Recurrent predictive coding models for associative memory employing covariance learning
Predictive representations can link model-based reinforcement learning to model-free mechanisms
A Diffusive Homeostatic Signal Maintains Neural Heterogeneity and Responsiveness in Cortical Networks
The role of the Hes1 crosstalk hub in Notch-Wnt interactions of the intestinal crypt
Using B cell receptor lineage structures to predict affinity
Ten quick tips for biomarker discovery and validation analyses using machine learning
The Generation of Phase Differences and Frequency Changes in a Network Model of Inferior Olive Subthreshold Oscillations
Co-expression Profiling of Autism Genes in the Mouse Brain
Substrate-Driven Mapping of the Degradome by Comparison of Sequence Logos
Quantitative analysis reveals crosstalk mechanisms of heat shock-induced attenuation of NF-κB signaling at the single cell level
tRNA Signatures Reveal a Polyphyletic Origin of SAR11 Strains among Alphaproteobacteria
Binding Free Energy Landscape of Domain-Peptide Interactions
Reconstructing the Genomic Content of Microbiome Taxa through Shotgun Metagenomic Deconvolution
Systems Model of T Cell Receptor Proximal Signaling Reveals Emergent Ultrasensitivity
From Principal Component to Direct Coupling Analysis of Coevolution in Proteins: Low-Eigenvalue Modes are Needed for Structure Prediction
Ten simple rules for an inclusive summer coding program for non-computer-science undergraduates
Quantitative Comparison of Catalytic Mechanisms and Overall Reactions in Convergently Evolved Enzymes: Implications for Classification of Enzyme Function
A Biocurator Perspective: Annotation at the Research Collaboratory for Structural Bioinformatics Protein Data Bank
Combinatorial mathematical modelling approaches to interrogate rear retraction dynamics in 3D cell migration
Incomplete information about the partner affects the development of collaborative strategies in joint action
Paxillin phosphorylation at serine 273 and its effects on Rac, Rho and adhesion dynamics
Testing structural identifiability by a simple scaling method
The impact of news exposure on collective attention in the United States during the 2016 Zika epidemic
Modeling Mitochondrial Bioenergetics with Integrated Volume Dynamics
Bow-tie signaling in c-di-GMP: Machine learning in a simple biochemical network
Bayesian structural time series for biomedical sensor data: A flexible modeling framework for evaluating interventions
An Introduction to Bioinformatics for Glycomics Research
Hidden Markov Modeling with HMMTeacher
Inferring evolutionary trajectories from cross-sectional transcriptomic data to mirror lung adenocarcinoma progression
DigChem: Identification of disease-gene-chemical relationships from Medline abstracts
The Encoding of Decision Difficulty and Movement Time in the Primate Premotor Cortex
Noise Propagation and Signaling Sensitivity in Biological Networks: A Role for Positive Feedback
Leveraging genetic interactions for adverse drug-drug interaction prediction
Adaptive dating and fast proposals: Revisiting the phylogenetic relaxed clock model
The Ascent of the Abundant: How Mutational Networks Constrain Evolution
Semi-automated Curation of Metabolic Models via Flux Balance Analysis: A Case Study with Mycoplasma gallisepticum
Clonal hematopoiesis of indeterminate potential and its impact on patient trajectories after stem cell transplantation
Task-relevant representational spaces in human memory traces
Relating dynamic brain states to dynamic machine states: Human and machine solutions to the speech recognition problem
Seasonal variation in SARS-CoV-2 transmission in temperate climates: A Bayesian modelling study in 143 European regions
An agent-based model to simulate the transmission dynamics of bloodborne pathogens within hospitals
Rapid runtime learning by curating small datasets of high-quality items obtained from memory
ATRPred: A machine learning based tool for clinical decision making of anti-TNF treatment in rheumatoid arthritis patients
Identification of Allelic Imbalance with a Statistical Model for Subtle Genomic Mosaicism
Mechanisms of hemoglobin cycling in anemia patients treated with erythropoiesis-stimulating agents
Retroviral Integration Process in the Human Genome: Is It Really Non-Random? A New Statistical Approach
Structure-Function Network Mapping and Its Assessment via Persistent Homology
Phosphorylation of the Arp2 Subunit Relieves Auto-inhibitory Interactions for Arp2/3 Complex Activation
Leveraging functional annotation to identify genes associated with complex diseases
Investigating the Structure and Dynamics of the PIK3CA Wild-Type and H1047R Oncogenic Mutant
Interacting particle models on the impact of spatially heterogeneous human behavioral factors on dynamics of infectious diseases
Viral Proteins Acquired from a Host Converge to Simplified Domain Architectures
On the identification of differentially-active transcription factors from ATAC-seq data
Integrated pan-cancer analysis of RNA binding protein HuR investigates its biomarker potential in prognosis, immunotherapy, and drug sensitivity
Bistable Forespore Engulfment in Bacillus subtilis by a Zipper Mechanism in Absence of the Cell Wall
Think: Theory for Africa
Top-Down Inputs Enhance Orientation Selectivity in Neurons of the Primary Visual Cortex during Perceptual Learning
4D nucleome equation predicts gene expression controlled by long-range enhancer-promoter interaction
The Significance of the 2013 Nobel Prize in Chemistry and the Challenges Ahead
Conflict Resolution as Near-Threshold Decision-Making: A Spiking Neural Circuit Model with Two-Stage Competition for Antisaccadic Task
Game Theory of Social Distancing in Response to an Epidemic
Modelling to explore the potential impact of asymptomatic human infections on transmission and dynamics of African sleeping sickness
Chemically Based Mathematical Model for Development of Cerebral Cortical Folding Patterns
Revisiting Date and Party Hubs: Novel Approaches to Role Assignment in Protein Interaction Networks
Ambiguity drives higher-order Pavlovian learning
Evolution of Networks for Body Plan Patterning; Interplay of Modularity, Robustness and Evolvability
Probing instructions for expression regulation in gene nucleotide compositions
ST-CellSeg: Cell segmentation for imaging-based spatial transcriptomics using multi-scale manifold learning
A Common Cortical Circuit Mechanism for Perceptual Categorical Discrimination and Veridical Judgment
Correction: CTD: An information-theoretic algorithm to interpret sets of metabolomic and transcriptomic perturbations in the context of graphical models
Coordinate Regulation of G Protein Signaling via Dynamic Interactions of Receptor and GAP
PlasClass improves plasmid sequence classification
AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses
Inference of weak-form partial differential equations describing migration and proliferation mechanisms in wound healing experiments on cancer cells
A plausible accelerating function of intermediate states in cancer metastasis
Cell Groups Reveal Structure of Stimulus Space
Modelling the spread and mitigation of an emerging vector-borne pathogen: Citrus greening in the U.S
Spontaneous Local Gamma Oscillation Selectively Enhances Neural Network Responsiveness
Nanometer scale difference in myofilament lattice structure of muscle alters muscle function in a spatially explicit model
What lies underneath: Precise classification of brain states using time-dependent topological structure of dynamics
H- and m-channel overexpression promotes seizure-like events by impairing the ability of inhibitory neurons to process correlated inputs
Analysis and Computational Dissection of Molecular Signature Multiplicity
Early detection of disease outbreaks and non-outbreaks using incidence data: A framework using feature-based time series classification and machine learning
A Computational Model of Liver Iron Metabolism
Analysis of Graph Invariants in Functional Neocortical Circuitry Reveals Generalized Features Common to Three Areas of Sensory Cortex
Recentrifuge: Robust comparative analysis and contamination removal for metagenomics
Hindcasts and forecasts of suicide mortality in US: A modeling study
Search Algorithms as a Framework for the Optimization of Drug Combinations
Identification of key somatic oncogenic mutation based on a confounder-free causal inference model
From Dynamic Expression Patterns to Boundary Formation in the Presomitic Mesoderm
Switches, Excitable Responses and Oscillations in the Ring1B/Bmi1 Ubiquitination System
Correction: A mathematical model describing the localization and spread of influenza A virus infection within the human respiratory tract
Exploring the Composition of Protein-Ligand Binding Sites on a Large Scale
A Biologically Plausible Computational Theory for Value Integration and Action Selection in Decisions with Competing Alternatives
Rocky Mountain Conference on Bioinformatics Celebrates 10 Years
Monitoring real-time transmission heterogeneity from incidence data
COVIDomic: A multi-modal cloud-based platform for identification of risk factors associated with COVID-19 severity
A neural field model for color perception unifying assimilation and contrast
Application of Rigidity Theory to the Thermostabilization of Lipase A from Bacillus subtilis
Extending Integrate-and-Fire Model Neurons to Account for the Effects of Weak Electric Fields and Input Filtering Mediated by the Dendrite
Noise Suppression and Surplus Synchrony by Coincidence Detection
Sensing ecosystem dynamics via audio source separation: A case study of marine soundscapes off northeastern Taiwan
Efficient Bayesian inference for mechanistic modelling with high-throughput data
The interplay between somatic and dendritic inhibition promotes the emergence and stabilization of place fields
SAveRUNNER: A network-based algorithm for drug repurposing and its application to COVID-19
Transcriptional Bursting in Gene Expression: Analytical Results for General Stochastic Models
Influence of Sequence Changes and Environment on Intrinsically Disordered Proteins
Making Informed Choices about Microarray Data Analysis
Benchmarking of deep learning algorithms for 3D instance segmentation of confocal image datasets
Computational Aspects of Feedback in Neural Circuits
Tree polynomials identify a link between co-transcriptional R-loops and nascent RNA folding
SANTA: Quantifying the Functional Content of Molecular Networks
A New Principle for Information Storage in an Enzymatic Pathway Model
Transcription Factor Binding Profiles Reveal Cyclic Expression of Human Protein-coding Genes and Non-coding RNAs
Context-specific network modeling identifies new crosstalk in β-adrenergic cardiac hypertrophy
Correction: A circuit model of auditory cortex
A simulation framework to determine optimal strength training and musculoskeletal geometry for sprinting and distance running
Living on Three Time Scales: The Dynamics of Plasma Cell and Antibody Populations Illustrated for Hepatitis A Virus
p13CMFA: Parsimonious 13C metabolic flux analysis
Data-driven contact structures: From homogeneous mixing to multilayer networks
Deep convolutional and conditional neural networks for large-scale genomic data generation
The Neuroglial Potassium Cycle during Neurotransmission: Role of Kir4.1 Channels
Evaluating the utility of brightfield image data for mechanism of action prediction
The Role of Conserved Waters in Conformational Transitions of Q61H K-ras
Disentangling juxtacrine from paracrine signalling in dynamic tissue
Ten simple rules for successfully managing EU research grants
Statistical Modeling of Transcription Factor Binding Affinities Predicts Regulatory Interactions
Fast Simulation of Mechanical Heterogeneity in the Electrically Asynchronous Heart Using the MultiPatch Module
Optimal closed-loop deep brain stimulation using multiple independently controlled contacts
Analyzing ChIP-chip Data Using Bioconductor
Generalism drives abundance: A computational causal discovery approach
Learning predictive signatures of HLA type from T-cell repertoires
Tximeta: Reference sequence checksums for provenance identification in RNA-seq
Design principles for the glycoprotein quality control pathway
Optimal Properties of Analog Perceptrons with Excitatory Weights
Evolution of innate behavioral strategies through competitive population dynamics
Therapeutic dose prediction of α5-GABA receptor modulation from simulated EEG of depression severity
Inhibition of RPS6K reveals context-dependent Akt activity in luminal breast cancer cells
Emergent Dynamics of Thymocyte Development and Lineage Determination
Data-driven multi-scale mathematical modeling of SARS-CoV-2 infection reveals heterogeneity among COVID-19 patients
Climbing Escher's stairs: A way to approximate stability landscapes in multidimensional systems
Subcellular Location of PKA Controls Striatal Plasticity: Stochastic Simulations in Spiny Dendrites
CCAST: A Model-Based Gating Strategy to Isolate Homogeneous Subpopulations in a Heterogeneous Population of Single Cells
Matrix feedback enables diverse higher-order patterning of the extracellular matrix
Neural coding in the visual system of Drosophila melanogaster: How do small neural populations support visually guided behaviours?
Solving Navigational Uncertainty Using Grid Cells on Robots
Scalable gradients enable Hamiltonian Monte Carlo sampling for phylodynamic inference under episodic birth-death-sampling models
A phenomenological computational model of the evoked action potential fitted to human cochlear implant responses
Predicting and comparing transcription start sites in single cell populations
Nonlinear expression patterns and multiple shifts in gene network interactions underlie robust phenotypic change in Drosophila melanogaster selected for night sleep duration
The promiscuous enzyme medium-chain 3-keto-acyl-CoA thiolase triggers a vicious cycle in fatty-acid beta-oxidation
Most Undirected Random Graphs Are Amplifiers of Selection for Birth-Death Dynamics, but Suppressors of Selection for Death-Birth Dynamics
A demonstration of modularity, reuse, reproducibility, portability and scalability for modeling and simulation of cardiac electrophysiology using Kepler Workflows
Computational Reconstruction of NFκB Pathway Interaction Mechanisms during Prostate Cancer
An Evolutionary Approach for Identifying Driver Mutations in Colorectal Cancer
ASA3P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates
Resource competition-driven bistability and stochastic switching amplify gene expression noise
An association between prediction errors and risk-seeking: Theory and behavioral evidence
Predicting explorative motor learning using decision-making and motor noise
Integrating Sequencing Technologies in Personal Genomics: Optimal Low Cost Reconstruction of Structural Variants
Collective Animal Behavior from Bayesian Estimation and Probability Matching
Perceptual Learning via Modification of Cortical Top-Down Signals
Using a multi-strain infectious disease model with physical information neural networks to study the time dependence of SARS-CoV-2 variants of concern
Shrinking to bird size with dinosaur-level cancer defences: Evolution of cancer suppression over macroevolutionary time
Optimality of sparse olfactory representations is not affected by network plasticity
Suboptimal community growth mediated through metabolite crossfeeding promotes species diversity in the gut microbiota
DeepPL: A deep-learning-based tool for the prediction of bacteriophage lifecycle
Local epigenomic state cannot discriminate interacting and non-interacting enhancer-promoter pairs with high accuracy
Amyloidogenic Regions and Interaction Surfaces Overlap in Globular Proteins Related to Conformational Diseases
Paradoxical Evidence Integration in Rapid Decision Processes
Teaching deep networks to see shape: Lessons from a simplified visual world
Practical fluorescence reconstruction microscopy for large samples and low-magnification imaging
Disease gene prediction for molecularly uncharacterized diseases
A Pareto approach to resolve the conflict between information gain and experimental costs: Multiple-criteria design of carbon labeling experiments
Deep-learning models reveal how context and listener attention shape electrophysiological correlates of speech-to-language transformation
Emergence and suppression of cooperation by action visibility in transparent games
Multiscale modeling of HBV infection integrating intra- and intercellular viral propagation to analyze extracellular viral markers
Observable variations in human sex ratio at birth
Fixation times on directed graphs
A Novel Cell Traction Force Microscopy to Study Multi-Cellular System
Self-organization of collective escape in pigeon flocks
Network Models of TEM β-Lactamase Mutations Coevolving under Antibiotic Selection Show Modular Structure and Anticipate Evolutionary Trajectories
Single-cell mutational burden distributions in birth-death processes
Constrained brain volume in an efficient coding model explains the fraction of excitatory and inhibitory neurons in sensory cortices
A confirmation bias in perceptual decision-making due to hierarchical approximate inference
Knowledge-guided data mining on the standardized architecture of NRPS: Subtypes, novel motifs, and sequence entanglements
Protein Homology Network Families Reveal Step-Wise Diversification of Type III and Type IV Secretion Systems
Cell-TRACTR: A transformer-based model for end-to-end segmentation and tracking of cells
Structural comparison of homologous protein-RNA interfaces reveals widespread overall conservation contrasted with versatility in polar contacts
TwinCons: Conservation score for uncovering deep sequence similarity and divergence
The Role of Environmental Transmission in Recurrent Avian Influenza Epidemics
Emergent spatiotemporal population dynamics with cell-length control of synthetic microbial consortia
Epithelial competition determines gene therapy potential to suppress Fanconi Anemia oral cancer risk
Modelling locust foraging: How and why food affects group formation
Exon Array Analysis of Head and Neck Cancers Identifies a Hypoxia Related Splice Variant of LAMA3 Associated with a Poor Prognosis