yusuke1997/dblp-id-title huggingface dataset:
MorbidGCN: prediction of multimorbidity with a graph convolutional network based on integration of population phenotypes and disease network
CasANGCL: pre-training and fine-tuning model based on cascaded attention network and graph contrastive learning for molecular property prediction
Systematic analysis and prediction of type IV secreted effector proteins by machine learning approaches
Spatiotemporal constrained RNA-protein heterogeneous network for protein complex identification
Detecting horizontal gene transfer with T-REX and RHOM programs
Correction to: An automatic immunofluorescence pattern classification framework for HEp-2 image based on supervised learning
The genomic and functional characteristics of disease genes
Big-data-based edge biomarkers: study on dynamical drug sensitivity and resistance in individuals
Spatially aware self-representation learning for tissue structure characterization and spatial functional genes identification
RNAactDrug: a comprehensive database of RNAs associated with drug sensitivity from multi-omics data
PHPGAT: predicting phage hosts based on multimodal heterogeneous knowledge graph with graph attention network
Identifying local associations in biological time series: algorithms, statistical significance, and applications
Application of next generation sequencing to human gene fusion detection: computational tools, features and perspectives
Delivering blended bioinformatics training in resource-limited settings: a case study on the University of Khartoum H3ABioNet node
Correlated substitution analysis and the prediction of amino acid structural contacts
Bioinformatics and system biology approaches to identify the diseasome and comorbidities complexities of SARS-CoV-2 infection with the digestive tract disorders
Data mining the human gut microbiota for therapeutic targets
A comprehensive assessment and comparison of tools for HLA class I peptide-binding prediction
ProDom: Automated Clustering of Homologous Domains
Network pharmacology: towards the artificial intelligence-based precision traditional Chinese medicine
scATD: a high-throughput and interpretable framework for single-cell cancer drug resistance prediction and biomarker identification
XOmiVAE: an interpretable deep learning model for cancer classification using high-dimensional omics data
Incorporating higher order network structures to improve miRNA-disease association prediction based on functional modularity
scDCA: deciphering the dominant cell communication assembly of downstream functional events from single-cell RNA-seq data
TAD boundary and strength prediction by integrating sequence and epigenetic profile information
DrugMetric: quantitative drug-likeness scoring based on chemical space distance
Correction to: siGCD: a web server to explore survival interaction of genes, cells and drugs in human cancers
Feature aggregation graph convolutional network based on imaging genetic data for diagnosis and pathogeny identification of Alzheimer's disease
Landscape of SNPs-mediated lncRNA structural variations and their implication in human complex diseases
PharmKG: a dedicated knowledge graph benchmark for bomedical data mining
Adapting bioinformatics curricula for big data
A review of connectivity map and computational approaches in pharmacogenomics
KinomeMETA: meta-learning enhanced kinome-wide polypharmacology profiling
Polyadenylation-related isoform switching in human evolution revealed by full-length transcript structure
RadSigBench: a framework for benchmarking functional genomics signatures of cancer cell radiosensitivity
NmRF: identification of multispecies RNA 2'-O-methylation modification sites from RNA sequences
RNCE: network integration with reciprocal neighbors contextual encoding for multi-modal drug community study on cancer targets
GraphLncLoc: long non-coding RNA subcellular localization prediction using graph convolutional networks based on sequence to graph transformation
VPTMdb: a viral posttranslational modification database
MFPred: prediction of ncRNA families based on multi-feature fusion
IDMIR: identification of dysregulated miRNAs associated with disease based on a miRNA-miRNA interaction network constructed through gene expression data
Complexity of enhancer networks predicts cell identity and disease genes revealed by single-cell multi-omics analysis
A review of Bioinformatics training applied to research in Molecular Medicine, Agriculture and Biodiversity in Costa Rica and Central America
Minimal cut sets in metabolic networks: from conceptual foundations to applications in metabolic engineering and biomedicine
LncReader: identification of dual functional long noncoding RNAs using a multi-head self-attention mechanism
Comprehensive and critical evaluation of individualized pathway activity measurement tools on pan-cancer data
Feasibility of sample size calculation for RNA-seq studies
Probes containing runs of guanines provide insights into the biophysics and bioinformatics of Affymetrix GeneChips
An approach to gene-based testing accounting for dependence of tests among nearby genes
Deep learning model for protein multi-label subcellular localization and function prediction based on multi-task collaborative training
PTTM: dissecting the profile of tumor tissue microbiome to reveal microbiota features and associations with host transcriptome
Software Review HOBACGEN: Homologous Bacterial Genes Database
AITeQ: a machine learning framework for Alzheimer's prediction using a distinctive five-gene signature
Heterogeneous data integration methods for patient similarity networks
An overview on nucleic-acid G-quadruplex prediction: from rule-based methods to deep neural networks
Comprehensive assessment of flexible-ligand docking algorithms: current effectiveness and challenges
A comparative analysis of cell-type adjustment methods for epigenome-wide association studies based on simulated and real data sets
Circular RNA: an emerging key player in RNA world
Correction to: Unveiling cross-reactivity: implications for immune response modulation in cancer
MRSL: a causal network pruning algorithm based on GWAS summary data
A comparative analysis of biclustering algorithms for gene expression data
Deepening the knowledge of rare diseases dependent on angiogenesis through semantic similarity clustering and network analysis
Efficient prediction of peptide self-assembly through sequential and graphical encoding
Transfer learning of clinical outcomes from preclinical molecular data, principles and perspectives
Negative Binomial mixed models estimated with the maximum likelihood method can be used for longitudinal RNAseq data
ACP-CapsPred: an explainable computational framework for identification and functional prediction of anticancer peptides based on capsule network
Sequencing era methods for identifying signatures of selection in the genome
Toward more realistic drug-target interaction predictions
Controlling for confounding variables in MS-omics protocol: why modularity matters
Pise: Software for Building Bioinformatics Webs
Comprehensive review and assessment of computational methods for predicting RNA post-transcriptional modification sites from RNA sequences
Degrees of freedom analysis in educational research and decision-making: leveraging qualitative data to promote excellence in bioinformatics training and education
Network medicine in ovarian cancer: topological properties to drug discovery
PScL-HDeep: image-based prediction of protein subcellular location in human tissue using ensemble learning of handcrafted and deep learned features with two-layer feature selection
A Hitchhiker's guide to RNA-RNA structure and interaction prediction tools
BioDSNN: a dual-stream neural network with hybrid biological knowledge integration for multi-gene perturbation response prediction
Structure-based prediction of post-translational modification cross-talk within proteins using complementary residue- and residue pair-based features
Robustness and resilience of computational deconvolution methods for bulk RNA sequencing data
Next generation sequencing in functional genomics
Hyperbolic relational graph convolution networks plus: a simple but highly efficient QSAR-modeling method
A strategy for multimodal data integration: application to biomarkers identification in spinocerebellar ataxia
The stacking strategy-based hybrid framework for identifying non-coding RNAs
Correction to: Bioinformatics in Russia: history and present-day landscape
Integrating regulatory features data for prediction of functional disease-associated SNPs
Protein structure databases with new web services for structural biology and biomedical research
Propagating uncertainty in microarray data analysis
SWEET: a single-sample network inference method for deciphering individual features in disease
NCBI-compliant genome submissions: tips and tricks to save time and money
Modelling protein functional domains in signal transduction using Maude
MSI-DTI: predicting drug-target interaction based on multi-source information and multi-head self-attention
The challenges of delivering bioinformatics training in the analysis of high-throughput data
An integrated deep learning framework for the interpretation of untargeted metabolomics data
Homoeologous gene expression and co-expression network analyses and evolutionary inference in allopolyploids
Benchmarking multi-omics integration algorithms across single-cell RNA and ATAC data
scBOL: a universal cell type identification framework for single-cell and spatial transcriptomics data
Deep learning for drug-drug interaction extraction from the literature: a review
Corrigendum to: Computational design of ultrashort peptide inhibitors of the receptor-binding domain of the SARS-CoV-2 S protein
Progress and challenge for computational quantification of tissue immune cells
Integrated mRNA sequence optimization using deep learning
DeepIDA-GRU: a deep learning pipeline for integrative discriminant analysis of cross-sectional and longitudinal multiview data with applications to inflammatory bowel disease classification
Long-range alternative splicing contributes to neoantigen specificity in glioblastoma
MetaFluAD: meta-learning for predicting antigenic distances among influenza viruses
Artifacts in spatial transcriptomics data: their detection, importance, prevalence, and prevention
PSTP: accurate residue-level phase separation prediction using protein conformational and language model embeddings
Calling small variants using universality with Bayes-factor-adjusted odds ratios
Phanto-IDP: compact model for precise intrinsically disordered protein backbone generation and enhanced sampling
Computational deconvolution of DNA methylation data from mixed DNA samples
Drug repositioning by prediction of drug's anatomical therapeutic chemical code via network-based inference approaches
On the Parallelisation of Bioinformatics Applications
Phylogenetic inference of inter-population transmission rates for infectious diseases
miRactDB characterizes miRNA-gene relation switch between normal and cancer tissues across pan-cancer
Sequence repetitiveness quantification and de novo repeat detection by weighted k-mer coverage
A comprehensive comparison on cell-type composition inference for spatial transcriptomics data
A data-intelligence-intensive bioinformatics copilot system for large-scale omics research and scientific insights
Species-agnostic transfer learning for cross-species transcriptomics data integration without gene orthology
Disease characterization using a partial correlation-based sample-specific network
Predicting the structures of cyclic peptides containing unnatural amino acids by HighFold2
Dealing with missing values in large-scale studies: microarray data imputation and beyond
MetaAll: integrative bioinformatics workflow for analysing clinical metagenomic data
GAPS: a geometric attention-based network for peptide binding site identification by the transfer learning approach
Hierarchical cell-type identifier accurately distinguishes immune-cell subtypes enabling precise profiling of tissue microenvironment with single-cell RNA-sequencing
CodAn: predictive models for precise identification of coding regions in eukaryotic transcripts
Caveats and pitfalls of ROC analysis in clinical microarray research (and how to avoid them)
Drug repositioning based on weighted local information augmented graph neural network
Multi-objective computational optimization of human 5′ UTR sequences
iDRNA-ITF: identifying DNA- and RNA-binding residues in proteins based on induction and transfer framework
Estimation of non-equilibrium transition rate from gene expression data
Integrative approaches based on genomic techniques in the functional studies on enhancers
Corrigendum to: Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences
Exploration of natural compounds with anti-SARS-CoV-2 activity via inhibition of SARS-CoV-2 Mpro
Spatial transcriptomics prediction from histology jointly through Transformer and graph neural networks
Genotype imputation accuracy and the quality metrics of the minor ancestry in multi-ancestry reference panels
Phase4: Automatic Evaluation of Database Search Methods
Searching for repetitions in biological networks: methods, resources and tools
A comprehensive benchmarking of differential splicing tools for RNA-seq analysis at the event level
Prostate cancer early diagnosis: circulating microRNA pairs potentially beyond single microRNAs upon 1231 serum samples
Plant Genome Databases: From References to Inference Tools
scCancer: a package for automated processing of single-cell RNA-seq data in cancer
PERHAPS: Paired-End short Reads-based HAPlotyping from next-generation Sequencing data
Surveying biomedical relation extraction: a critical examination of current datasets and the proposal of a new resource
DaDL-SChlo: protein subchloroplast localization prediction based on generative adversarial networks and pre-trained protein language model
In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor
Identifying multi-functional bioactive peptide functions using multi-label deep learning
MCAMEF-BERT: an efficient deep learning method for RNA N7-methylguanosine site prediction via multi-branch feature integration
Benchmarking variant callers in next-generation and third-generation sequencing analysis
Kolmogorov-Arnold networks for genomic tasks
A fast and accurate method for SARS-CoV-2 genomic tracing
nhKcr: a new bioinformatics tool for predicting crotonylation sites on human nonhistone proteins based on deep learning
Accounting for the impact of rare variants on causal inference with RARE: a novel multivariable Mendelian randomization method
Predicting potential small molecule-miRNA associations utilizing truncated schatten p-norm
Deep enhanced constraint clustering based on contrastive learning for scRNA-seq data
BioGSF: a graph-driven semantic feature integration framework for biomedical relation extraction
Modern Genome Annotation . Edited by Dmitrij Frishman and Alfonso Valencia
PLM-DBPs: enhancing plant DNA-binding protein prediction by integrating sequence-based and structure-aware protein language models
Strategies for processing and quality control of Illumina genotyping arrays
COSMIC Cancer Gene Census 3D database: understanding the impacts of mutations on cancer targets
Cloud 3D-QSAR: a web tool for the development of quantitative structure-activity relationship models in drug discovery
iRice-MS: An integrated XGBoost model for detecting multitype post-translational modification sites in rice
DeepGRNCS: deep learning-based framework for jointly inferring gene regulatory networks across cell subpopulations
iProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites
A two-task predictor for discovering phase separation proteins and their undergoing mechanism
Base-calling for next-generation sequencing platforms
Computational methods for identifying the critical nodes in biological networks
Identifying drug-target interactions based on graph convolutional network and deep neural network
Relational similarity-based graph contrastive learning for DTI prediction
MultiFeatVotPIP: a voting-based ensemble learning framework for predicting proinflammatory peptides
scLEGA: an attention-based deep clustering method with a tendency for low expression of genes on single-cell RNA-seq data
MENDA: a comprehensive curated resource of metabolic characterization in depression
Multilevel heterogeneous omics data integration with kernel fusion
EpiXFormer: a cross-attention neural network for predicting cell type-specific transcription factor binding sites
Fusing 2D and 3D molecular graphs as unambiguous molecular descriptors for conformational and chiral stereoisomers
PANoptosis, an indicator of COVID-19 severity and outcomes
Identifying spatial domain by adapting transcriptomics with histology through contrastive learning
Peptide-based drug discovery through artificial intelligence: towards an autonomous design of therapeutic peptides
A protein network descriptor server and its use in studying protein, disease, metabolic and drug targeted networks
IHGC-GAN: influence hypergraph convolutional generative adversarial network for risk prediction of late mild cognitive impairment based on imaging genetic data
Discovery of fusion circular RNAs in leukemia with KMT2A::AFF1 rearrangements by the new software CircFusion
Plant genome and transcriptome annotations: from misconceptions to simple solutions
Artificial intelligence-driven prediction of multiple drug interactions
Comprehensive analysis of partial methylation domains in colorectal cancer based on single-cell methylation profiles
CEMIG: prediction of the cis-regulatory motif using the de Bruijn graph from ATAC-seq
TCRpower: quantifying the detection power of T-cell receptor sequencing with a novel computational pipeline calibrated by spike-in sequences
GloEC: a hierarchical-aware global model for predicting enzyme function
Inferring microenvironmental regulation of gene expression from single-cell RNA sequencing data using scMLnet with an application to COVID-19
Machine learning modeling of RNA structures: methods, challenges and future perspectives
A survey of tools for analysing DNA fingerprints
labelSeg: segment annotation for tumor copy number alteration profiles
An inductive transfer learning force field (ITLFF) protocol builds protein force fields in seconds
Comparative study of computational methods to detect the correlated reaction sets in biochemical networks
Artificial intelligence in cryo-EM protein particle picking: recent advances and remaining challenges
ceRNAs in plants: computational approaches and associated challenges for target mimic research
Identification of vital chemical information via visualization of graph neural networks
ANPELA: analysis and performance assessment of the label-free quantification workflow for metaproteomic studies
GCFMCL: predicting miRNA-drug sensitivity using graph collaborative filtering and multi-view contrastive learning
KinScan: AI-based rapid profiling of activity across the kinome
Translational research platforms integrating clinical and omics data: a review of publicly available solutions
Systems biological approaches to the cardiac signaling network
Upstream analysis of alternative splicing: a review of computational approaches to predict context-dependent splicing factors
Letter to the Editor: on the stability and internal consistency of component-wise sparse mixture regression-based clustering
Algebraic shortcuts for leave-one-out cross-validation in supervised network inference
DeepHapNet: a haplotype assembly method based on RetNet and deep spectral clustering
Prognostic outcome prediction by semi-supervised least squares classification
Bioinformatics and machine learning approach identifies potential drug targets and pathways in COVID-19
Unveiling cross-reactivity: implications for immune response modulation in cancer
Deep-belief network for predicting potential miRNA-disease associations
The role of ncRNA regulatory mechanisms in diseases - case on gestational diabetes
Individualized identification of disease-associated pathways with disrupted coordination of gene expression
Genome-wide identification and predictive modeling of polyadenylation sites in eukaryotes
Single-cell Hi-C data analysis: safety in numbers
Toward a gold standard for benchmarking gene set enrichment analysis
A comprehensive benchmarking of machine learning algorithms and dimensionality reduction methods for drug sensitivity prediction
Use of Elasticsearch-based business intelligence tools for integration and visualization of biological data
Mut-Map: Comprehensive Computational Pipeline for Structural Mapping and Analysis of Cancer-Associated Mutations
Heterogeneous graph contrastive learning with gradient balance for drug repositioning
Computational resources for ribosome profiling: from database to Web server and software
A large-scale investigation and identification of methicillin-resistant Staphylococcus aureus based on peaks binning of matrix-assisted laser desorption ionization-time of flight MS spectra
Advances of computational methods enhance the development of multi-epitope vaccines
Anthem: a user customised tool for fast and accurate prediction of binding between peptides and HLA class I molecules
Estimating cell type-specific differential expression using deconvolution
Classification-based pathway analysis using GPNet with novel P -value computation
A systematic comparison of normalization methods for eQTL analysis
Statistical significance in biological sequence analysis
Detection of drug-drug interactions through data mining studies using clinical sources, scientific literature and social media
RNA2HLA: HLA-based quality control of RNA-seq datasets
A roadmap for T cell receptor-peptide-bound major histocompatibility complex binding prediction by machine learning: glimpse and foresight
SCSMD: Single Cell Consistent Clustering based on Spectral Matrix Decomposition
KPRR: a novel machine learning approach for effectively capturing nonadditive effects in genomic prediction
Normal Mode Analysis Theoretical and Applications to Biological and Chemical Systems
HCovDock: an efficient docking method for modeling covalent protein-ligand interactions
BioFNet: biological functional network database for analysis and synthesis of biological systems
A roadmap for multi-omics data integration using deep learning
Discovering and detecting transposable elements in genome sequences
BioManager: the use of a bioinformatics web application as a teaching tool in undergraduate bioinformatics training
Bioinformatics education in India
Assessing the impact of batch effect associated missing values on downstream analysis in high-throughput biomedical data
Insights from analyses of low complexity regions with canonical methods for protein sequence comparison
Exploring associations of non-coding RNAs in human diseases via three-matrix factorization with hypergraph-regular terms on center kernel alignment
Unraveling chloroplast transcriptomes with ChloroSeq, an organelle RNA-Seq bioinformatics pipeline
PepTCR-Net: prediction of multi-class antigen peptides by T-cell receptor sequences with deep learning
CrossICC: iterative consensus clustering of cross-platform gene expression data without adjusting batch effect
FL-DTD: an integrated pipeline to predict the drug interacting targets by feedback loop-based network analysis
GGN-GO: geometric graph networks for predicting protein function by multi-scale structure features
Reference genome and annotation updates lead to contradictory prognostic predictions in gene expression signatures: a case study of resected stage I lung adenocarcinoma
Incremental modelling and analysis of biological systems with fuzzy hybrid Petri nets
Notions of similarity for systems biology models
STALLION: a stacking-based ensemble learning framework for prokaryotic lysine acetylation site prediction
CPADS: a web tool for comprehensive pancancer analysis of drug sensitivity
LEPSCAN - a web server for searching latent periodicity in DNA sequences
GPU computing for systems biology