yusuke1997/dblp-id-title huggingface dataset:
Soft disorder modulates the assembly path of protein complexes
Identifying COVID-19 peaks using early warning signals
Realistic retinal modeling unravels the differential role of excitation and inhibition to starburst amacrine cells in direction selectivity
Elucidating the complex membrane binding of a protein with multiple anchoring domains using extHMMM
Estimating direct and spill-over impacts of political elections on COVID-19 transmission using synthetic control methods
Modelling the effects of ephaptic coupling on selectivity and response patterns during artificial stimulation of peripheral nerves
Wrangling distributed computing for high-throughput environmental science: An introduction to HTCondor
Computational analysis of the oscillatory behavior at the translation level induced by mRNA levels oscillations due to finite intracellular resources
Dependency Map of Proteins in the Small Ribosomal Subunit
A complete statistical model for calibration of RNA-seq counts using external spike-ins and maximum likelihood theory
A gap-filling algorithm for prediction of metabolic interactions in microbial communities
Practical identifiability analysis of a mechanistic model for the time to distant metastatic relapse and its application to renal cell carcinoma
Thalamocortical control of propofol phase-amplitude coupling
Design of immunogens for eliciting antibody responses that may protect against SARS-CoV-2 variants
Unveiling inter-embryo variability in spindle length over time: Towards quantitative phenotype analysis
Ten Simple Rules for Starting a Regional Student Group
Transcript assembly and annotations: Bias and adjustment
Classification of red blood cell shapes in flow using outlier tolerant machine learning
Deep Supervised, but Not Unsupervised, Models May Explain IT Cortical Representation
Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes
Modeling the Effects of Morphine on Simian Immunodeficiency Virus Dynamics
Effect of mutation mechanisms on variant composition and distribution in Caenorhabditis elegans
PHENSIM: Phenotype Simulator
Selectivity by Small-Molecule Inhibitors of Protein Interactions Can Be Driven by Protein Surface Fluctuations
Integration of unpaired single cell omics data by deep transfer graph convolutional network
Phosphorelays Provide Tunable Signal Processing Capabilities for the Cell
Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data
Ten simple rules for developing a training program
Laminar Neural Field Model of Laterally Propagating Waves of Orientation Selectivity
Conformational Control of the Binding of the Transactivation Domain of the MLL Protein and c-Myb to the KIX Domain of CREB
Significance of Input Correlations in Striatal Function
Modeling drug response using network-based personalized treatment prediction (NetPTP) with applications to inflammatory bowel disease
Computational Account of Spontaneous Activity as a Signature of Predictive Coding
Interdomain Contacts Control Native State Switching of RfaH on a Dual-Funneled Landscape
An Evolution-Based Approach to De Novo Protein Design and Case Study on Mycobacterium tuberculosis
Noise-precision tradeoff in predicting combinations of mutations and drugs
A Platform-Independent Method for Detecting Errors in Metagenomic Sequencing Data: DRISEE
Phylodynamic Inference and Model Assessment with Approximate Bayesian Computation: Influenza as a Case Study
Macro-level Modeling of the Response of C. elegans Reproduction to Chronic Heat Stress
Computational modeling of the gut microbiota reveals putative metabolic mechanisms of recurrent Clostridioides difficile infection
Spatial Configurations of 3D Extracellular Matrix Collagen Density and Anisotropy Simultaneously Guide Angiogenesis
Computationally efficient mechanism discovery for cell invasion with uncertainty quantification
A Geometrically-Constrained Mathematical Model of Mammary Gland Ductal Elongation Reveals Novel Cellular Dynamics within the Terminal End Bud
Outlier Responses Reflect Sensitivity to Statistical Structure in the Human Brain
SCMarker: Ab initio marker selection for single cell transcriptome profiling
Comparing a computational model of visual problem solving with human vision on a difficult vision task
The spread of a wild plant pathogen is driven by the road network
Regularizing hyperparameters of interacting neural signals in the mouse cortex reflect states of arousal
Methodology for rigorous modeling of protein conformational changes by Rosetta using DEER distance restraints
Systems-level computational modeling demonstrates fuel selection switching in high capacity running and low capacity running rats
The Roots of Bioinformatics in Theoretical Biology
Correction: Frontal cortex tracks surprise separately for different sensory modalities but engages a common inhibitory control mechanism
Biological action at a distance: Correlated pattern formation in adjacent tessellation domains without communication
A Simple Self-Maintaining Metabolic System: Robustness, Autocatalysis, Bistability
Interactions of spatial strategies producing generalization gradient and blocking: A computational approach
Numerical approaches for the rapid analysis of prophylactic efficacy against HIV with arbitrary drug-dosing schemes
Theoretical Insights into the Biophysics of Protein Bi-stability and Evolutionary Switches
Neural surprise in somatosensory Bayesian learning
Does plasmid-based beta-lactam resistance increase E. coli infections: Modelling addition and replacement mechanisms
Structural and practical identifiability of contrast transport models for DCE-MRI
Organization of the core respiratory network: Insights from optogenetic and modeling studies
Inferring the Clonal Structure of Viral Populations from Time Series Sequencing
Computational Model of MicroRNA Control of HIF-VEGF Pathway: Insights into the Pathophysiology of Ischemic Vascular Disease and Cancer
EpiLPS: A fast and flexible Bayesian tool for estimation of the time-varying reproduction number
2018 outstanding contributions to ISCB award: Russ Altman
Integration and multiplexing of positional and contextual information by the hippocampal network
Prediction of PD-L1 inhibition effects for HIV-infected individuals
Diverse task-driven modeling of macaque V4 reveals functional specialization towards semantic tasks
Dynamic Cholesterol-Conditioned Dimerization of the G Protein Coupled Chemokine Receptor Type 4
Topological and statistical analyses of gene regulatory networks reveal unifying yet quantitatively different emergent properties
Metabolic reprogramming dynamics in tumor spheroids: Insights from a multicellular, multiscale model
Contrasting the effects of adaptation and synaptic filtering on the timescales of dynamics in recurrent networks
Close proximity interactions support transmission of ESBL-K. pneumoniae but not ESBL-E. coli in healthcare settings
A regularity index for dendrites - local statistics of a neuron's input space
Dating the Age of the SIV Lineages That Gave Rise to HIV-1 and HIV-2
Neural network models for influenza forecasting with associated uncertainty using Web search activity trends
A Model for Genetic and Epigenetic Regulatory Networks Identifies Rare Pathways for Transcription Factor Induced Pluripotency
Improving reproducibility in computational biology research
Adaptive and optimized COVID-19 vaccination strategies across geographical regions and age groups
A convenient correspondence between k-mer-based metagenomic distances and phylogenetically-informed β-diversity measures
A theoretical framework for analyzing coupled neuronal networks: Application to the olfactory system
Spiking network optimized for word recognition in noise predicts auditory system hierarchy
Correction: Computational Model Explains High Activity and Rapid Cycling of Rho GTPases within Protein Complexes
Variation of mutational burden in healthy human tissues suggests non-random strand segregation and allows measuring somatic mutation rates
On the NF-Y regulome as in ENCODE (2019)
Microarray Analysis of LTR Retrotransposon Silencing Identifies Hdac1 as a Regulator of Retrotransposon Expression in Mouse Embryonic Stem Cells
Mechanochemical Coupling in the Myosin Motor Domain. II. Analysis of Critical Residues
Modeling the interplay of sex hormones in cardiac hypertrophic signaling
Rigid Residue Scan Simulations Systematically Reveal Residue Entropic Roles in Protein Allostery
Identifying determinants of persistent MRSA bacteremia using mathematical modeling
Can Influenza Epidemics Be Prevented by Voluntary Vaccination?
From heterogeneous healthcare data to disease-specific biomarker networks: A hierarchical Bayesian network approach
Quantifying cell transitions in C. elegans with data-fitted landscape models
Microtubule instability driven by longitudinal and lateral strain propagation
Universal scale-free representations in human visual cortex
GAGA: A New Algorithm for Genomic Inference of Geographic Ancestry Reveals Fine Level Population Substructure in Europeans
A powerful and versatile colocalization test
Reinforcement learning of altruistic punishment differs between cultures and across the lifespan
Validity conditions of approximations for a target-mediated drug disposition model: A novel first-order approximation and its comparison to other approximations
Competing Mechanistic Hypotheses of Acetaminophen-Induced Hepatotoxicity Challenged by Virtual Experiments
Mitigating COVID-19 outbreaks in workplaces and schools by hybrid telecommuting
Ten simple rules for designing graphical abstracts
The Evolution of Word Composition in Metazoan Promoter Sequence
Ten simple rules for a mom-friendly Academia
Visuoinertial and visual feedback in online steering control
Computational Biology in Colombia
Context-explorer: Analysis of spatially organized protein expression in high-throughput screens
Learning and forgetting using reinforced Bayesian change detection
Gene variants of coagulation related proteins that interact with SARS-CoV-2
A greedy classifier optimization strategy to assess ion channel blocking activity and pro-arrhythmia in hiPSC-cardiomyocytes
Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs
Improving cell-type composition inference in spatial transcriptomics with SpaDAMA
Noradrenergic and Dopaminergic modulation of meta-cognition and meta-control
Noise Reduction by Diffusional Dissipation in a Minimal Quorum Sensing Motif
International Society for Computational Biology Honors Michael Ashburner and Olga Troyanskaya with Top Bioinformatics/Computational Biology Awards for 2011
Graph neural fields: A framework for spatiotemporal dynamical models on the human connectome
Spatial dynamics of feedback and feedforward regulation in cell lineages
A Critical Quantity for Noise Attenuation in Feedback Systems
Compression-enabled interpretability of voxelwise encoding models
On identifying collective displacements in apo-proteins that reveal eventual binding pathways
Chain organization of human interphase chromosome determines the spatiotemporal dynamics of chromatin loci
Allele-Specific Amplification in Cancer Revealed by SNP Array Analysis
What Do I Want from the Publisher of the Future?
Graph of graphs analysis for multiplexed data with application to imaging mass cytometry
Dynamic Electrode-to-Image (DETI) mapping reveals the human brain's spatiotemporal code of visual information
A Scalable Algorithm to Explore the Gibbs Energy Landscape of Genome-Scale Metabolic Networks
Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment
The Next Generation of Transcription Factor Binding Site Prediction
Optimizing crop varietal mixtures for viral disease management: A case study on cassava virus epidemics
Inferring the Forces Controlling Metaphase Kinetochore Oscillations by Reverse Engineering System Dynamics
Sequential infection experiments for quantifying innate and adaptive immunity during influenza infection
Functional Brain Networks Develop from a "Local to Distributed" Organization
The Loss and Gain of Functional Amino Acid Residues Is a Common Mechanism Causing Human Inherited Disease
The Development of Audio-Visual Integration for Temporal Judgements
Biomedical Text Mining and Its Applications
Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals
Compressive instabilities enable cell-induced extreme densification patterns in the fibrous extracellular matrix: Discrete model predictions
Missense variants in human ACE2 strongly affect binding to SARS-CoV-2 Spike providing a mechanism for ACE2 mediated genetic risk in Covid-19: A case study in affinity predictions of interface variants
Developmental shifts in computations used to detect environmental controllability
A New Approach to Model Pitch Perception Using Sparse Coding
Neural network models for sequence-based TCR and HLA association prediction
An individualized causal framework for learning intercellular communication networks that define microenvironments of individual tumors
Scalable phylogenetic profiling using MinHash uncovers likely eukaryotic sexual reproduction genes
Individual-based model highlights the importance of trade-offs for virus-host population dynamics and long-term co-existence
BuDDI: Bulk Deconvolution with Domain Invariance to predict cell-type-specific perturbations from bulk
Phosphorylation by PINK1 Releases the UBL Domain and Initializes the Conformational Opening of the E3 Ubiquitin Ligase Parkin
Hierarchical motor adaptations negotiate failures during force field learning
The importance of non-pharmaceutical interventions during the COVID-19 vaccine rollout
The Inactivation Principle: Mathematical Solutions Minimizing the Absolute Work and Biological Implications for the Planning of Arm Movements
Ten simple rules for starting (and sustaining) an academic data science initiative
The Self-Limiting Dynamics of TGF-β Signaling In Silico and In Vitro , with Negative Feedback through PPM1A Upregulation
EGFR Signal-Network Reconstruction Demonstrates Metabolic Crosstalk in EMT
Model-Based Characterization of Inflammatory Gene Expression Patterns of Activated Macrophages
The Interplay between Wnt Mediated Expansion and Negative Regulation of Growth Promotes Robust Intestinal Crypt Structure and Homeostasis
Neuronal Spike Timing Adaptation Described with a Fractional Leaky Integrate-and-Fire Model
Complex interactions can create persistent fluctuations in high-diversity ecosystems
Receptor recharge time drastically reduces the number of captured particles
Optimizing testing for COVID-19 in India
ASCENT (Automated Simulations to Characterize Electrical Nerve Thresholds): A pipeline for sample-specific computational modeling of electrical stimulation of peripheral nerves
The hierarchical organization of autocatalytic reaction networks and its relevance to the origin of life
Fast and robust deconvolution of tumor infiltrating lymphocyte from expression profiles using least trimmed squares
ALKBH7 Variant Related to Prostate Cancer Exhibits Altered Substrate Binding
Recurrent neural networks as neuro-computational models of human speech recognition
Dynamic Prestress in a Globular Protein
Novel Approach to Meta-Analysis of Microarray Datasets Reveals Muscle Remodeling-related Drug Targets and Biomarkers in Duchenne Muscular Dystrophy
Evidence of Functional Protein Dynamics from X-Ray Crystallographic Ensembles
4Cin: A computational pipeline for 3D genome modeling and virtual Hi-C analyses from 4C data
Interspecies chimeric conditions affect the developmental rate of human pluripotent stem cells
Neural network features distinguish chemosensory stimuli in Caenorhabditis elegans
Ten simple rules for scientists getting started in science education
Expanding and improving analyses of nucleotide recoding RNA-seq experiments with the EZbakR suite
Identification of Potential Pathway Mediation Targets in Toll-like Receptor Signaling
Tensorpac: An open-source Python toolbox for tensor-based phase-amplitude coupling measurement in electrophysiological brain signals
Autistic traits influence the strategic diversity of information sampling: Insights from two-stage decision models
Integrating Transgenic Vector Manipulation with Clinical Interventions to Manage Vector-Borne Diseases
Perturbations in dynamical models of whole-brain activity dissociate between the level and stability of consciousness
OpenCASA: A new open-source and scalable tool for sperm quality analysis
Lipid Tail Protrusion in Simulations Predicts Fusogenic Activity of Influenza Fusion Peptide Mutants and Conformational Models
Coding Conspecific Identity and Motion in the Electric Sense
Systematic comparison of differential expression networks in MTB mono-, HIV mono- and MTB/HIV co-infections for drug repurposing
Convergence, sampling and total order estimator effects on parameter orthogonality in global sensitivity analysis
Second Order Dimensionality Reduction Using Minimum and Maximum Mutual Information Models
Assessing intra-lab precision and inter-lab repeatability of outgrowth assays of HIV-1 latent reservoir size
Statistical Resolution of Ambiguous HLA Typing Data
Within-Host Bacterial Diversity Hinders Accurate Reconstruction of Transmission Networks from Genomic Distance Data
Sampling Realistic Protein Conformations Using Local Structural Bias
Reverse Engineering the Gap Gene Network of Drosophila melanogaster
Ten simple rules for unbiased teaching
A method for the inference of cytokine interaction networks
The ISCB: Growing and Evolving in Step with Science
Reverse-engineered models reveal differential membrane properties of autonomic and cutaneous unmyelinated fibers
Differential effect of supercoiling on bacterial transcription in topological domains
Quantifying Stochastic Noise in Cultured Circadian Reporter Cells
Computational analysis of 5-fluorouracil anti-tumor activity in colon cancer using a mechanistic pharmacokinetic/pharmacodynamic model
Modeling habitat connectivity in support of multiobjective species movement: An application to amphibian habitat systems
Slowness and Sparseness Have Diverging Effects on Complex Cell Learning
SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis
Query-Dependent Banding (QDB) for Faster RNA Similarity Searches
Disease-driven reduction in human mobility influences human-mosquito contacts and dengue transmission dynamics
phyC: Clustering cancer evolutionary trees
Investigating the Conformational Stability of Prion Strains through a Kinetic Replication Model
Predicting the Receptive Range of Olfactory Receptors
Association Rate Constants of Ras-Effector Interactions Are Evolutionarily Conserved
Stochastic Modeling of Mouse Motor Activity under Deep Brain Stimulation: The Extraction of Arousal Information
An Analysis of Enzyme Kinetics Data for Mitochondrial DNA Strand Termination by Nucleoside Reverse Transcription Inhibitors
Genetic Redundancies Enhance Information Transfer in Noisy Regulatory Circuits
Effects of subclinical depression on prefrontal-striatal model-based and model-free learning
Generation of Diverse Biological Forms through Combinatorial Interactions between Tissue Polarity and Growth
Perturbation-Response Scanning Reveals Ligand Entry-Exit Mechanisms of Ferric Binding Protein
Probabilistic Phylogenetic Inference with Insertions and Deletions
NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated Ribosomes
Experimental guidance for discovering genetic networks through hypothesis reduction on time series
The multi-dimensional challenges of controlling respiratory virus transmission in indoor spaces: Insights from the linkage of a microscopic pedestrian simulation and SARS-CoV-2 transmission model
Complete hazard ranking to analyze right-censored data: An ALS survival study
Finding New Order in Biological Functions from the Network Structure of Gene Annotations
Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling
Predicting the target landscape of kinase inhibitors using 3D convolutional neural networks
Emergent neutrality in consumer-resource dynamics
Function and energy consumption constrain neuronal biophysics in a canonical computation: Coincidence detection
Correlation between Oncogenic Mutations and Parameter Sensitivity of the Apoptosis Pathway Model
Haptic communication between humans is tuned by the hard or soft mechanics of interaction
Parameter estimation and identifiability in a neural population model for electro-cortical activity
Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets
An Integrated Regulatory Network Reveals Pervasive Cross-Regulation among Transcription and Splicing Factors
Mechanisms of sensorimotor adaptation in a hierarchical state feedback control model of speech
Rats spontaneously perceive global motion direction of drifting plaids
Ten Simple Rules for a successful remote postdoc
Comprehensive characterization of respiratory genes based on a computational framework in pan-cancer to develop stratified treatment strategies
The Role of Cell Volume in the Dynamics of Seizure, Spreading Depression, and Anoxic Depolarization
Influence of the vessel wall geometry on the wall-induced migration of red blood cells
Interactions between all pairs of neighboring trees in 16 forests worldwide reveal details of unique ecological processes in each forest, and provide windows into their evolutionary histories
CLAW: An automated Snakemake workflow for the assembly of chloroplast genomes from long-read data
Improving virtual screening of G protein-coupled receptors via ligand-directed modeling
Correction: A Well-Defined Readily Releasable Pool with Fixed Capacity for Storing Vesicles at Calyx of Held
Standard multiscale entropy reflects neural dynamics at mismatched temporal scales: What's signal irregularity got to do with it?
Prepaid parameter estimation without likelihoods
Optimal sequence-based design for multi-antigen HIV-1 vaccines using minimally distant antigens
Increasing the Power to Detect Causal Associations by Combining Genotypic and Expression Data in Segregating Populations
Time-resolved dynamic computational modeling of human EEG recordings reveals gradients of generative mechanisms for the MMN response
Reconstruction of Tissue-Specific Metabolic Networks Using CORDA
Correction: A method to quantify mechanobiologic forces during zebrafish cardiac development using 4-D light sheet imaging and computational modeling
Designing and running an advanced Bioinformatics and genome analyses course in Tunisia
Analysis of Stochastic Strategies in Bacterial Competence: A Master Equation Approach
Exploiting ecology in drug pulse sequences in favour of population reduction
Chiral evasion and stereospecific antifolate resistance in Staphylococcus aureus
Sensitivity Analysis of Flux Determination in Heart by H 2 18 O -provided Labeling Using a Dynamic Isotopologue Model of Energy Transfer Pathways
Identifying the combinatorial control of signal-dependent transcription factors
Protein Meta-Functional Signatures from Combining Sequence, Structure, Evolution, and Amino Acid Property Information
A phase transition induces chaos in a predator-prey ecosystem with a dynamic fitness landscape
IsRNAcirc: 3D structure prediction of circular RNAs based on coarse-grained molecular dynamics simulation
Environmental and ecological controls of the spatial distribution of microbial populations in aggregates
AvP: A software package for automatic phylogenetic detection of candidate horizontal gene transfers
Computational drug repurposing against SARS-CoV-2 reveals plasma membrane cholesterol depletion as key factor of antiviral drug activity
On the Adjacency Matrix of RyR2 Cluster Structures
Interrupting behaviour: Minimizing decision costs via temporal commitment and low-level interrupts
SpatialKNifeY (SKNY): Extending from spatial domain to surrounding area to identify microenvironment features with single-cell spatial omics data
Identification of dynamic mass-action biochemical reaction networks using sparse Bayesian methods
Coexistence of Lateral and Co-Tuned Inhibitory Configurations in Cortical Networks
The Ortholog Conjecture Is Untestable by the Current Gene Ontology but Is Supported by RNA Sequencing Data