yusuke1997/dblp-id-title huggingface dataset:
Quality Assessment of Protein Docking Models Based on Graph Neural Network
Towards rational computational peptide design
Reliable machine learning models in genomic medicine using conformal prediction
Efficient semi-supervised semantic segmentation of electron microscopy cancer images with sparse annotations
MIntO: A Modular and Scalable Pipeline For Microbiome Metagenomic and Metatranscriptomic Data Integration
Improving fluorescence lifetime imaging microscopy phasor accuracy using convolutional neural networks
Corrigendum: Machine Learning for Causal Inference in Biological Networks: Perspectives of This Challenge
Integrative In Silico Investigation Reveals the Host-Virus Interactions in Repurposed Drugs Against SARS-CoV-2
A Tool for Segmentation of Secondary Structures in 3D Cryo-EM Density Map Components Using Deep Convolutional Neural Networks
Identification of novel drug targets for Helicobacter pylori: structure-based virtual screening of potential inhibitors against DAH7PS protein involved in the shikimate pathway
Meeting in the Middle: Towards Successful Multidisciplinary Bioimage Analysis Collaboration
Current successes and remaining challenges in protein function prediction
Comprehensive structural and functional analyses of RAD50 nsSNPs: from prediction to impact assessment
An End-To-End Pipeline for Fully Automatic Morphological Quantification of Mouse Brain Structures From MRI Imagery
Structure-based neural network protein-carbohydrate interaction predictions at the residue level
Harnessing computational immunology to design targeted subunit vaccines for infectious bursal disease in poultry
A computer vision framework for quantification of feather growth patterns
Joint visualization of seasonal influenza serology and phylogeny to inform vaccine composition
Investigating the molecular mechanism of iguratimod act on SLE using network pharmacology and molecular docking analysis
Predicting the Effects of Drug Combinations Using Probabilistic Matrix Factorization
GeneCloudOmics: A Data Analytic Cloud Platform for High-Throughput Gene Expression Analysis
A systematic evaluation of state-of-the-art deconvolution methods in spatial transcriptomics: insights from cardiovascular disease and chronic kidney disease
MetaWin 3: open-source software for meta-analysis
Visualizing Phytochemical-Protein Interaction Networks: Momordica charantia and Cancer
Towards Human in the Loop Analysis of Complex Point Clouds: Advanced Visualizations, Quantifications, and Communication Features in Virtual Reality
PASS: Protein Annotation Surveillance Site for Protein Annotation Using Homologous Clusters, NLP, and Sequence Similarity Networks
Applications and Comparison of Dimensionality Reduction Methods for Microbiome Data
The origin of eukaryotes and rise in complexity were synchronous with the rise in oxygen
Editorial: Inference of Biological Networks
Where are we in the implementation of tissue-specific epigenetic clocks?
Propedia v2.3: A novel representation approach for the peptide-protein interaction database using graph-based structural signatures
Sequencing technologies and hardware-accelerated parallel computing transform computational genomics research
Immersive and interactive visualization of 3D spatio-temporal data using a space time hypercube: Application to cell division and morphogenesis analysis
PanViTa: Pan Virulence and resisTance analysis
DJExpress: An Integrated Application for Differential Splicing Analysis and Visualization
Orthogonal outlier detection and dimension estimation for improved MDS embedding of biological datasets
Opportunities and challenges in interpretable deep learning for drug sensitivity prediction of cancer cells
K-Neighbourhood Analysis: A Method for Understanding SMLM Images as Compositions of Local Neighbourhoods
Editorial: Big data and artificial intelligence for genomics and therapeutics - Proceedings of the 19th Annual Meeting of the MidSouth Computational Biology and Bioinformatics Society (MCBIOS)
Genomic analysis of Listeria monocytogenes strains from dairy products in Ethiopia
A Review of Feature Selection Methods for Machine Learning-Based Disease Risk Prediction
Singularity Containers Improve Reproducibility and Ease of Use in Computational Image Analysis Workflows
The Effect of Model Directionality on Cell-Type-Specific Differential DNA Methylation Analysis
A graph-based machine learning framework identifies critical properties of FVIII that lead to hemophilia A
A Molecular Docking Study of Human STEAP2 for the Discovery of New Potential Anti-Prostate Cancer Chemotherapeutic Candidates
Adding context to the pneumococcal core genes using bioinformatic analysis of the intergenic pangenome of Streptococcus pneumoniae
A cost and community perspective on the barriers to microbiome data reuse
Cryo-EM Analyses Permit Visualization of Structural Polymorphism of Biological Macromolecules
Editorial: Expert opinions in protein bioinformatics: 2022
Screening of Potent Phytochemical Inhibitors Against SARS-CoV-2 Main Protease: An Integrative Computational Approach
Extending Association Rule Mining to Microbiome Pattern Analysis: Tools and Guidelines to Support Real Applications
DNA methylation biomarker analysis from low-survival-rate cancers based on genetic functional approaches
PhIP-Seq: methods, applications and challenges
Editorial: Graph representation learning in biological network
Caveats to Deep Learning Approaches to RNA Secondary Structure Prediction
Metascan: METabolic Analysis, SCreening and ANnotation of Metagenomes
NCMW: A Python Package to Analyze Metabolic Interactions in the Nasal Microbiome
DNA Methylation, Aging, and Cancer Risk: A Mini-Review
Protein structure prediction in the era of AI: Challenges and limitations when applying to in silico force spectroscopy
An assessment of bioinformatics tools for the detection of human endogenous retroviral insertions in short-read genome sequencing data
Machine Learning for Causal Inference in Biological Networks: Perspectives of This Challenge
Molecular docking and molecular dynamic simulation studies to identify potential terpenes against Internalin A protein of Listeria monocytogenes
Circr, a Computational Tool to Identify miRNA: circRNA Associations
QSPRmodeler - An open source application for molecular predictive analytics
The quantum hypercube as a k-mer graph
ApE, A Plasmid Editor: A Freely Available DNA Manipulation and Visualization Program
Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at Scale
Developing a ceRNA-based lncRNA-miRNA-mRNA regulatory network to uncover roles in skeletal muscle development
Bioinformatics proficiency among African students
Editorial: Multi-omics approaches in the study of human disease mechanisms
Prediction of Adverse Drug Reaction Linked to Protein Targets Using Network-Based Information and Machine Learning
Digital staining facilitates biomedical microscopy
Geometric deep learning as a potential tool for antimicrobial peptide prediction
No-boundary thinking for artificial intelligence in bioinformatics and education
Application of network pharmacology in the study of mechanism of Chinese medicine in the treatment of ulcerative colitis: A review
BrcaDx: precise identification of breast cancer from expression data using a minimal set of features
CAEM-GBDT: a cancer subtype identifying method using multi-omics data and convolutional autoencoder network
A standards perspective on genomic data reusability and reproducibility
Divergent evolution of low-complexity regions in the vertebrate CPEB protein family
BioViz Connect: Web Application Linking CyVerse Cloud Resources to Genomic Visualization in the Integrated Genome Browser
Recent Advances in the Prediction of Subcellular Localization of Proteins and Related Topics
Identification of Biomarkers Controlling Cell Fate In Blood Cell Development
OC_Finder: Osteoclast Segmentation, Counting, and Classification Using Watershed and Deep Learning
Development of an antimicrobial resistance plasmid transfer gene database for enteric bacteria
Bootstrap confidence for molecular evolutionary estimates from tumor bulk sequencing data
Predictive identification and design of potent inhibitors targeting resistance-inducing candidate genes from E. coli whole-genome sequences
SPLACE: A tool to automatically SPLit, Align, and ConcatenatE genes for phylogenomic inference of several organisms
Editorial: Phasor analysis for fluorescence lifetime data
CIRCprimerXL: Convenient and High-Throughput PCR Primer Design for Circular RNA Quantification
End-to-end 3D instance segmentation of synthetic data and embryo microscopy images with a 3D Mask R-CNN
Bioinformatic and Experimental Analysis of T Cell Immune Reactivity to SARS-CoV-2 and its Variants
RecruitPlotEasy: An Advanced Read Recruitment Plot Tool for Assessing Metagenomic Population Abundance and Genetic Diversity
Protein Complex Organization Imposes Constraints on Proteome Dysregulation in Cancer
Targeting aldose reductase using natural African compounds as promising agents for managing diabetic complications
Molecular timetrees using relaxed clocks and uncertain phylogenies
Deep learning for MYC binding site recognition
Perspective on the challenges and opportunities of accelerating drug discovery with artificial intelligence
Grand Challenges in Bioinformatics Data Visualization
Deriving and Using Descriptors of Elementary Functions in Rational Protein Design
Editorial: Computational methods for analysis of DNA methylation data, volume II
Insight to Gene Expression From Promoter Libraries With the Machine Learning Workflow Exp2Ipynb
CRISPR genome editing using computational approaches: A survey
In silico studies of benzothiazole derivatives as potential inhibitors of Anopheles funestus and Anopheles gambiae trehalase
RxNorm for drug name normalization: a case study of prescription opioids in the FDA adverse events reporting system
Blob-B-Gone: a lightweight framework for removing blob artifacts from 2D/3D MINFLUX single-particle tracking data
A Mechanistic Site-Of-Action Model: A Tool for Informing Right Target, Right Compound, And Right Dose for Therapeutic Antagonistic Antibody Programs
Design principles for molecular animation
Spatiotemporal Clustering of Repeated Super-Resolution Localizations via Linear Assignment Problem
Systematic computational hunting for small RNAs derived from ncRNAs during dengue virus infection in endothelial HMEC-1 cells
Detecting subtle transcriptomic perturbations induced by lncRNAs knock-down in single-cell CRISPRi screening using a new sparse supervised autoencoder neural network
XMR: an explainable multimodal neural network for drug response prediction
Bayesian networks and imaging-derived phenotypes highlight the role of fat deposition in COVID-19 hospitalisation risk
Comprehensive genome-scale metabolic model of the human pathogen Cryptococcus neoformans: A platform for understanding pathogen metabolism and identifying new drug targets
Chromatin Network Analyses: Towards Structure-Function Relationships in Epigenomics
Benchmarking software tools for trimming adapters and merging next-generation sequencing data for ancient DNA
Omics data integration in computational biology viewed through the prism of machine learning paradigms
Classification of collagen remodeling in asthma using second-harmonic generation imaging, supervised machine learning and texture-based analysis
Editorial: Transparent machine learning in bio-medicine
Rvisdiff: An R package for interactive visualization of differential expression
DivCom: A Tool for Systematic Partition of Groups of Microbial Profiles Into Intrinsic Subclusters and Distance-Based Subgroup Comparisons
Early Requirement for Bioinformatics in Undergraduate Biology Curricula
TRAL 2.0: Tandem Repeat Detection With Circular Profile Hidden Markov Models and Evolutionary Aligner
Darwinian Evolution of Intelligence
Editorial: Protein recognition and associated diseases
Scoring Functions for Protein-Ligand Binding Affinity Prediction Using Structure-based Deep Learning: A Review
hsa-miR-548d-3p: a potential microRNA to target nucleocapsid and/or capsid genes in multiple members of the Flaviviridae family
A refined pH-dependent coarse-grained model for peptide structure prediction in aqueous solution
Nearest neighbor search on embeddings rapidly identifies distant protein relations
Identifying epigenetic aging moderators using the epigenetic pacemaker
3D Structure From 2D Microscopy Images Using Deep Learning
Short Tandem Repeats as a High-Resolution Marker for Capturing Recent Orangutan Population Evolution
Visualising disease trajectories from population-wide data
Editorial: Bioinformatics in the age of data science: algorithms, methods, and tools applied from Omics to structural data
DNA structural features and variability of complete MHC locus sequences
Exploring the Microbiome Analysis and Visualization Landscape
N-Glycosylation Network Construction and Analysis to Modify Glycans on the Spike (S) Glycoprotein of SARS-CoV-2
Computational Literature-based Discovery for Natural Products Research: Current State and Future Prospects
The HRA Organ Gallery affords immersive superpowers for building and exploring the Human Reference Atlas with virtual reality
A perspective on FAIR quality control in multiplexed imaging data processing
Peptimetric: Quantifying and Visualizing Differences in Peptidomic Data
RIPS (rapid intuitive pathogen surveillance): a tool for surveillance of genome sequence data from foodborne bacterial pathogens
Quantification of muscle fiber malformations using edge detection to investigate chronic muscle pressure ulcers
NOBIAS: Analyzing Anomalous Diffusion in Single-Molecule Tracks With Nonparametric Bayesian Inference
Virulence network of interacting domains of influenza a and mouse proteins
Identification of key hub genes in pancreatic ductal adenocarcinoma: an integrative bioinformatics study
Taxonomy Informed Clustering, an Optimized Method for Purer and More Informative Clusters in Diversity Analysis and Microbiome Profiling
Bioinformatics Approaches to Predict Mutation Effects in the Binding Site of the Proangiogenic Molecule CD93
Machine learning methods for protein-protein binding affinity prediction in protein design
A Unified Computational Framework for a Robust, Reliable, and Reproducible Identification of Novel miRNAs From the RNA Sequencing Data
Integrated Cells and Collagen Fibers Spatial Image Analysis
Scalable Microbial Strain Inference in Metagenomic Data Using StrainFacts
The META tool optimizes metagenomic analyses across sequencing platforms and classifiers
Assessing equivalent and inverse change in genes between diverse experiments
COVID-19 Multi-Targeted Drug Repurposing Using Few-Shot Learning
Improving acne severity detection: a GAN framework with contour accentuation for image deblurring
MARTin - an open-source platform for microarray analysis
VirHunter: A Deep Learning-Based Method for Detection of Novel RNA Viruses in Plant Sequencing Data
Multi-Dimensional Spectral Single Molecule Localization Microscopy
Moving beyond the desktop: prospects for practical bioimage analysis via the web
RNAStat: An Integrated Tool for Statistical Analysis of RNA 3D Structures
ASPM May be Related to the Malignant Progression of Hepatitis B and is Associated With a Poor Prognosis of Hepatocellular Carcinoma
Reliable and Scalable Identification and Prioritization of Putative Cellulolytic Anaerobes With Large Genome Data
CardIAP: calcium transients confocal image analysis tool
Effects of highly active antiretroviral therapy initiation on epigenomic DNA methylation in persons living with HIV
Time-calibrated phylogeny of neotropical freshwater fishes
RCSB Protein Data Bank: visualizing groups of experimentally determined PDB structures alongside computed structure models of proteins
BSImp: Imputing Partially Observed Methylation Patterns for Evaluating Methylation Heterogeneity
Exploring microbial functional biodiversity at the protein family level - From metagenomic sequence reads to annotated protein clusters
Completing a molecular timetree of apes and monkeys
Dynamic Solution Space Division-Based Methods for Calculating Reaction Deletion Strategies for Constraint-Based Metabolic Networks for Substance Production: DynCubeProd
Leveraging primate-specific genomic information for genetic studies of complex diseases
A General Framework to Learn Tertiary Structure for Protein Sequence Characterization
Efficient Cross-Correlation Filtering of One- and Two-Color Single Molecule Localization Microscopy Data
Interactive extraction of diverse vocal units from a planar embedding without the need for prior sound segmentation
PRONAME: a user-friendly pipeline to process long-read nanopore metabarcoding data by generating high-quality consensus sequences
Metagenomic Analysis Using Phylogenetic Placement - A Review of the First Decade
Construction and Comprehensive Analysis of ceRNA Networks and Tumor-Infiltrating Immune Cells in Hepatocellular Carcinoma With Vascular Invasion
Editorial: Women in bioinformatics
Predicting genetic interactions, cell line dependencies and drug sensitivities with variational graph auto-encoder
Connecting the dots: A practical evaluation of web-tools for describing protein dynamics as networks
A systematic overview of single-cell transcriptomics databases, their use cases, and limitations
VTR: A Web Tool for Identifying Analogous Contacts on Protein Structures and Their Complexes
EPIphany - A Platform for Analysis and Visualization of Peptide Immunoarray Data
A review of model evaluation metrics for machine learning in genetics and genomics
Choosing the most suitable NGS technology to combine with a standardized viral enrichment protocol for obtaining complete avian orthoreovirus genomes from metagenomic samples
Optimizing Voronoi-based quantifications for reaching interactive analysis of 3D localizations in the million range
Gene length is a pivotal feature to explain disparities in transcript capture between single transcriptome techniques
Data Driven Cell Cycle Model to Quantify the Efficacy of Cancer Therapeutics Targeting Specific Cell-Cycle Phases From Flow Cytometry Results
Optimal ranking and directional signature classification using the integral strategy of multi-objective optimization-based association rule mining of multi-omics data
Visualizing RNA Structures by SAXS-Driven MD Simulations
VariBench, new variation benchmark categories and data sets
Uncertainty Visualization: Concepts, Methods, and Applications in Biological Data Visualization
Assessing 2D visual encoding of 3D spatial connectivity
A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance
Bioinformatics and the Metaverse: Are We Ready?
Real or fake? Measuring the impact of protein annotation errors on estimates of domain gain and loss events
Cronos: A Machine Learning Pipeline for Description and Predictive Modeling of Microbial Communities Over Time
Corrigendum: Increased Expression of INHBA Is Correlated With Poor Prognosis and High Immune Infiltrating Level in Breast Cancer
Phytochemical baicalin potentially inhibits Bcl-2 and VEGF: an in silico approach
CellPAINT: Turnkey Illustration of Molecular Cell Biology
Benchmarking of Hi-C tools for scaffolding plant genomes obtained from PacBio HiFi and ONT reads
VariantSurvival: a tool to identify genotype-treatment response
Systematic analysis of cell morphodynamics in C. elegans early embryogenesis
BRANEart: Identify Stability Strength and Weakness Regions in Membrane Proteins
Identification of Master Regulators Driving Disease Progression, Relapse, and Drug Resistance in Lung Adenocarcinoma
Towards OntoClean 2.0: A framework for rigidity
The TAO CI ontology of vases of the Ming and Qing dynasties
Ricardo de Almeida Falbo (1964-2020)
Foundational ontologies in action
The metatheory of ontology reuse
Applied ontology issues
Water features and their parts
OLIVE: Ontology Learning With Integrated Vector Embeddings
MIREOT: The minimum information to reference an external ontology term
Technical artifacts: An integrated perspective
Modeling experts, knowledge providers and expertise in Materials Modeling: MAEO as an application ontology of EMMO's ecosystem
VetiVoc: A modular ontology for the fashion, textile and clothing domain
A hybrid approach to domain-independent taxonomy learning
A formal ontology of artefacts
ONTO-TDM domain ontology population for a specific discipline
Corpus-based terminological evaluation of ontologies
A multi-layered ontology for comparing relationship semantics in conceptual models of databases
Towards a core ontology of organisational transformation
Ontology of language, with applications to demographic data
OI-LLM: A Scalable Framework to Integrate Large Scale Ontologies Using Large Language Model
Benchmarking and Assessing Transformations Between Text and Causal Maps via Large Language Models
An ontology-driven framework for specifying, adapting and implementing educational settings
On the Formal Alignment of Foundational Ontologies: Building Mappings Between Basic Formal Ontology and Descriptive Ontology for Linguistic and Cognitive Engineering
The identity of resources on the Web: An ontology for Web architecture
Engineering use cases for modular development of ontologies in OWL
Towards building knowledge by merging multiple ontologies with CoMerger: A partitioning-based approach
Ontology and its applications in skills matching in job recruitment
Ontology development by domain experts (without using the "O" word)
Towards ABox Modularization of semi-expressive Description Logics
Using ontology visualization to facilitate access to knowledge about human disease genes
On the computational realization of formal ontologies: Formalizing an ontology of instantiation in spacetime using Isabelle/HOL as a case study
Editorial: Special Issue on Ontologies and Large-Language Models
Towards a German labor market ontology: Challenges and applications
OntoPneumo: An ontology of pneumology domain
An ontology for maintenance procedure documentation
Foundational patterns benchmark
The formal REA model at the operational level
An Ontology of Exceptions for Knowledge Representation
DOLCE: A descriptive ontology for linguistic and cognitive engineering
A goal-oriented framework for ontology reuse
Abstract vs. social roles - Towards a general theoretical account of roles
Domain modelling and NLP: Formal ontologies? Lexica? Or a bit of both?
Events, their names, and their synchronic structure
A perdurant ontology for interoperating information systems based on interlocking institutional worlds
Development and construction of an ontology to represent simulation data for a generic enterprise
Ontological foundations for conceptual modelling
Utilizing Chat Generative Pre-trained Transformer (ChatGPT) to Support the Development of a Domain Ontology for World Heritage
The OAEI food task: An analysis of a thesaurus alignment task
Ontology summit 2019 communiqué: Explanations
Engineering ontologies for question answering
Ontology Summit 2016 Communique: Ontologies within semantic interoperability ecosystems
A systematic literature review on semantic models for IoT-enabled smart campus
Flexibility and utility of the cell cycle ontology
Ontological realism: Methodology or misdirection?
An ontology co-design method for the co-creation of a continuous care ontology
Internet of things: Toward smart networked systems and societies
From Human- to LLM-Centered Collaborative Ontology Engineering
A proposal to evaluate ontology content
Roles, players and adaptable organizations
Representing a reference foundational ontology of events in SROIQ
Embodied contextualization: Towards a multistratal ontological treatment
Ontology Summit 2018 Communiqué: Contexts in context
Applied Ontology: A foreword by the new Editors-in-Chief
An ontology of suspicious software behavior
An ontological approach to focusing attention and enhancing machine perception on the Web
An ontology of online user feedback in software engineering
Modeling artificial agents' actions in context - a deontic cognitive event ontology
Formal ontology of space, time, and physical entities in classical mechanics
The MATHESIS meta-knowledge engineering framework: Ontology-driven development of intelligent tutoring systems