yusuke1997/dblp-id-title huggingface dataset:
Deep learning based on biologically interpretable genome representation predicts two types of human adaptation of SARS-CoV-2 variants
Exploring the kinase-inhibitor fragment interaction space facilitates the discovery of kinase inhibitor overcoming resistance by mutations
Bioinformatics.Charlie Hodgman, Andrew French and David Westhead Instant
Interpretable modeling of time-resolved single-cell gene-protein expression with CrossmodalNet
AESurv: autoencoder survival analysis for accurate early prediction of coronary heart disease
Hybrid modelling of biological systems using fuzzy continuous Petri nets
Compositional Features of Eukaryotic Genomes for Checking Predicted Genes
Alternative applications for distinct RNA sequencing strategies
NSCGRN: a network structure control method for gene regulatory network inference
Genetic control of RNA editing in neurodegenerative disease
Accurate prediction of inter-protein residue-residue contacts for homo-oligomeric protein complexes
Nonunique UPGMA clusterings of microsatellite markers
Software review: Shopping in the genome market with EnsMart
Literature mining in support of drug discovery
Gene Ontology semantic similarity tools: survey on features and challenges for biological knowledge discovery
Correction to: CReSIL: accurate identification of extrachromosomal circular DNA from long-read sequences
High-quality Protein Knowledge Resource: SWISS-PROT and TrEMBL
Web-based applications for building, managing and analysing kinetic models of biological systems
Bioinformatics on a national scale: an example from Switzerland
To assemble or not to assemble: metagenomic profiling of microbially mediated biogeochemical pathways in complex communities
An effective self-supervised framework for learning expressive molecular global representations to drug discovery
scDFC: A deep fusion clustering method for single-cell RNA-seq data
LARMD: integration of bioinformatic resources to profile ligand-driven protein dynamics with a case on the activation of estrogen receptor
Prediction of driver variants in the cancer genome via machine learning methodologies
Progress and challenges in bioinformatics approaches for enhancer identification
Digital annealing optimization for natural product structure elucidation
High-accuracy protein model quality assessment using attention graph neural networks
Computational identification of mutator-derived lncRNA signatures of genome instability for improving the clinical outcome of cancers: a case study in breast cancer
Measuring the diversity of the human microbiota with targeted next-generation sequencing
scMNMF: a novel method for single-cell multi-omics clustering based on matrix factorization
Compressive biological sequence analysis and archival in the era of high-throughput sequencing technologies
KNIndex: a comprehensive database of physicochemical properties for k-tuple nucleotides
Software agents in molecular computational biology
PANCDR: precise medicine prediction using an adversarial network for cancer drug response
A multi-modal fusion model with enhanced feature representation for chronic kidney disease progression prediction
Evaluating de novo sequencing in proteomics: already an accurate alternative to database-driven peptide identification?
Elucidation of dynamic microRNA regulations in cancer progression using integrative machine learning
VirusRecom: an information-theory-based method for recombination detection of viral lineages and its application on SARS-CoV-2
Graph contrastive learning as a versatile foundation for advanced scRNA-seq data analysis
Machine learning builds full-QM precision protein force fields in seconds
FAMetA: a mass isotopologue-based tool for the comprehensive analysis of fatty acid metabolism
Strategies for calibrating models of biology
Development of interactive biological web applications with R/Shiny
Epigenome signature as an immunophenotype indicator prompts durable clinical immunotherapy benefits in lung adenocarcinoma
Biomedical data, computational methods and tools for evaluating disease-disease associations
Current computational tools for protein lysine acylation site prediction
Evaluation of gene-drug common module identification methods using pharmacogenomics data
Predicting phage-host interactions via feature augmentation and regional graph convolution
Multi-view spectral clustering with latent representation learning for applications on multi-omics cancer subtyping
ADM: adaptive graph diffusion for meta-dimension reduction
Revealing cell-cell communication pathways with their spatially coupled gene programs
DNA barcoding: a six-question tour to improve users' awareness about the method
Enhancer-MDLF: a novel deep learning framework for identifying cell-specific enhancers
Transcriptomic and metabolomic data integration
Measuring the microbiome: perspectives on advances in DNA-based techniques for exploring microbial life
GT-GRN : a graph transformer framework for enhanced gene regulatory network inference via multimodal embedding of expression data and existing network knowledge
Representation of molecules for drug response prediction
Single-cell RNA-sequencing data clustering using variational graph attention auto-encoder with self-supervised leaning
Next Generation Microarray Bioinformatics: Methods and Protocols. Edited by Junbai Wang, Aik Choon Tan and Tianhai Tian
IPFMC: an iterative pathway fusion approach for enhanced multi-omics clustering in cancer research
Mechanistically derived patient-level framework for precision medicine identifies a personalized immune prognostic signature in high-grade serous ovarian cancer
Towards a calculus of biomolecular complexes at equilibrium
Post-transcriptional regulation supports the homeostatic expression of mature RNA
Subtype-DCC: decoupled contrastive clustering method for cancer subtype identification based on multi-omics data
Gene-set approach for expression pattern analysis
Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology
NG-SEM: an effective non-Gaussian structural equation modeling framework for gene regulatory network inference from single-cell RNA-seq data
nMAGMA: a network-enhanced method for inferring risk genes from GWAS summary statistics and its application to schizophrenia
Genomes, genomes everywhere - but where to browse?
RMTLysPTM: recognizing multiple types of lysine PTM sites by deep analysis on sequences
scDecouple: decoupling cellular response from infected proportion bias in scCRISPR-seq
Petri net modelling of biological networks
Mutational signatures of colorectal cancers according to distinct computational workflows
Individualized analysis of differentially expressed miRNAs with application to the identification of miRNAs deregulated commonly in lung cancer tissues
Scoring functions for drug-effect similarity
Correction: Insights from analyses of low complexity regions with canonical methods for protein sequence comparison
ABCModeller: an automatic data mining tool based on a consistent voting method with a user-friendly graphical interface
Correction to: From data to diagnosis: how machine learning is revolutionizing biomarker discovery in idiopathic inflammatory myopathies
idenMD-NRF: a ranking framework for miRNA-disease association identification
Exploiting next-generation sequencing to solve the haplotyping puzzle in polyploids: a simulation study
In silico polypharmacology of natural products
Biolinguistic graph fusion model for circRNA-miRNA association prediction
Benchmarking 13 tools for mutational signature attribution, including a new and improved algorithm
CellGO: a novel deep learning-based framework and webserver for cell-type-specific gene function interpretation
Virus-CKB: an integrated bioinformatics platform and analysis resource for COVID-19 research
Resilience function uncovers the critical transitions in cancer initiation
Detecting coevolving positions in a molecule: why and how to account for phylogeny
Genome annotation of disease-causing microorganisms
A review of neural networks for metagenomic binning
AVPIden: a new scheme for identification and functional prediction of antiviral peptides based on machine learning approaches
Persistent spectral based ensemble learning (PerSpect-EL) for protein-protein binding affinity prediction
Prior knowledge-guided multilevel graph neural network for tumor risk prediction and interpretation via multi-omics data integration
SnapHiC-G: identifying long-range enhancer-promoter interactions from single-cell Hi-C data via a global background model
The identification and characterization of novel transcripts from RNA-seq data
Visualization, benchmarking and characterization of nested single-cell heterogeneity as dynamic forest mixtures
Clinical bioinformatics desiderata for molecular tumor boards
SPNE: sample-perturbed network entropy for revealing critical states of complex biological systems
Navigating the changing learning landscape: perspective from bioinformatics.ca
A powerful framework for an integrative study with heterogeneous omics data: from univariate statistics to multi-block analysis
BamView: visualizing and interpretation of next-generation sequencing read alignments
Tutorial section: Hydropathy - A window on the evasion of water
Unveiling promising drug targets for autism spectrum disorder: insights from genetics, transcriptomics, and proteomics
Correction to: BANMF-S: a blockwise accelerated non-negative matrix factorization framework with structural network constraints for single cell imputation
Machine learning meets omics: applications and perspectives
Assessing polygenic risk score models for applications in populations with under-represented genomics data: an example of Vietnam
Identifying and characterizing drug sensitivity-related lncRNA-TF-gene regulatory triplets
Key residues influencing binding affinities of 2019-nCoV with ACE2 in different species
Ontology-aware neural network: a general framework for pattern mining from microbiome data
Breast cancer prognosis signature: linking risk stratification to disease subtypes
Bayesian Inference for Gene Expression and Proteomics
Correction to: PhosPiR: an automated phosphoproteomic pipeline in R
DMGAT: predicting ncRNA-drug resistance associations based on diffusion map and heterogeneous graph attention network
Tools for the functional interpretation of metabolomic experiments
Individualized metagenomic network model for colorectal cancer diagnosis: insights into viral regulation of gut microecology
scGO: interpretable deep neural network for cell status annotation and disease diagnosis
Correction to: PHR-search: a search framework for protein remote homology detection based on the predicted protein hierarchical relationships
Network analyses in microbiome based on high-throughput multi-omics data
Graphics processing units in bioinformatics, computational biology and systems biology
Defining the single base importance of human mRNAs and lncRNAs
Bioinformatics opportunities for identification and study of medicinal plants
The State of the Art of Mammalian Promoter Recognition
Developing an online programme in computational biology
A comprehensive survey for human transcription factors on expression, regulation, interaction, phenotype and cancer survival
A comprehensive comparison of supervised and unsupervised methods for cell type identification in single-cell RNA-seq
Correction to: Prediction of protein-ligand binding affinity via deep learning models
Computational resources and strategies to assess single-molecule dynamics of the translation process in S. cerevisiae
ToxGIN: an In silico prediction model for peptide toxicity via graph isomorphism networks integrating peptide sequence and structure information
Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences
Mendelian randomization under the omnigenic architecture
PlantBind: an attention-based multi-label neural network for predicting plant transcription factor binding sites
FERREG: ferroptosis-based regulation of disease occurrence, progression and therapeutic response
A dual-modal graph learning framework for identifying interaction events among chemical and biotech drugs
A comprehensive review and evaluation of species richness estimation
ComABAN: refining molecular representation with the graph attention mechanism to accelerate drug discovery
Prognosis and personalized treatment prediction in TP53-mutant hepatocellular carcinoma: an in silico strategy towards precision oncology
Forensic DNA and bioinformatics
Practical analysis of specificity-determining residues in protein families
BioAutoML: automated feature engineering and metalearning to predict noncoding RNAs in bacteria
Systematic evaluation of machine learning methods for identifying human-pathogen protein-protein interactions
MulinforCPI: enhancing precision of compound-protein interaction prediction through novel perspectives on multi-level information integration
COMO: a pipeline for multi-omics data integration in metabolic modeling and drug discovery
Drug-target prediction utilizing heterogeneous bio-linked network embeddings
Cell subpopulation deconvolution reveals breast cancer heterogeneity based on DNA methylation signature
SynBioSS designer: a web-based tool for the automated generation of kinetic models for synthetic biological constructs
Bioinformatics methodologies for coeliac disease and its comorbidities
Bioinformatics strategies for studying the molecular mechanisms of fungal extracellular vesicles with a focus on infection and immune responses
DeepFeature: feature selection in nonimage data using convolutional neural network
Understanding the computational methodologies of systems biology
FEOpti-ACVP: identification of novel anti-coronavirus peptide sequences based on feature engineering and optimization
Computational model for drug research
The anatomy of phenotype ontologies: principles, properties and applications
Tutorial section: Domains and motifs - proteins in bite-sized chunks
Deep generative model for protein subcellular localization prediction
TripletCell: a deep metric learning framework for accurate annotation of cell types at the single-cell level
MloDisDB: a manually curated database of the relations between membraneless organelles and diseases
COWID: an efficient cloud-based genomics workflow for scalable identification of SARS-COV-2
Should we really use graph neural networks for transcriptomic prediction?
Cracking the pattern of tumor evolution based on single-cell copy number alterations
A systematic assessment of cell type deconvolution algorithms for DNA methylation data
Solutions for data integration in functional genomics: a critical assessment and case study
There is no silver bullet - a guide to low-level data transforms and normalisation methods for microarray data
Handbook of Computational Molecular Biology: Edited by Srinivas Aluru
Benchmarking of local genetic correlation estimation methods using summary statistics from genome-wide association studies
Computational insights into the cross-talk between medin and A β : implications for age-related vascular risk factors in Alzheimer's disease
BayeshERG: a robust, reliable and interpretable deep learning model for predicting hERG channel blockers
Gated-GPS: enhancing protein-protein interaction site prediction with scalable learning and imbalance-aware optimization
Computational prediction and interpretation of both general and specific types of promoters in Escherichia coli by exploiting a stacked ensemble-learning framework
Profiling prediction of nuclear receptor modulators with multi-task deep learning methods: toward the virtual screening
Identifying phenotype-associated subpopulations through LP_SGL
Principal microbial groups: compositional alternative to phylogenetic grouping of microbiome data
Predicting protein-membrane interfaces of peripheral membrane proteins using ensemble machine learning
Identifying the kind behind SMILES - anatomical therapeutic chemical classification using structure-only representations
MvMRL: a multi-view molecular representation learning method for molecular property prediction
Large-scale prediction of ADAR-mediated effective human A-to-I RNA editing
Explainable AI for Bioinformatics: Methods, Tools and Applications
Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases
Differential variability analysis of single-cell gene expression data
Systematic evaluation of cell-type deconvolution pipelines for sequencing-based bulk DNA methylomes
MLRDFM: a multi-view Laplacian regularized DeepFM model for predicting miRNA-disease associations
MicroScope - an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data
Challenges in distinguishing functional proteins from polyproteins in databases: implications for drug discovery
Protein.3D Structural Data - Where It Is, and Why We Need It
A multi-modal data harmonisation approach for discovery of COVID-19 drug targets
Analytic approaches to twin data using structural equation models
Multi-stage learning aids applied to hands-on software training
SPRDA: a link prediction approach based on the structural perturbation to infer disease-associated Piwi-interacting RNAs
Computational approaches to amino acid side-chain conformation using combined NMR theoretical and experimental results: leucine-67 in Desulfovibrio vulgaris flavodoxin
TaxSEA: rapid interpretation of microbiome alterations using taxon set enrichment analysis and public databases
Characterization and identification of antimicrobial peptides with different functional activities
JEBIN: analyzing gene co-expressions across multiple datasets by joint network embedding
SADeepcry: a deep learning framework for protein crystallization propensity prediction using self-attention and auto-encoder networks
Emerging bioinformatics for the metabolome
OncoPubMiner: a platform for mining oncology publications
Prediction of drug adverse events using deep learning in pharmaceutical discovery
Tensor decomposition with relational constraints for predicting multiple types of microRNA-disease associations
Database Searching with DNA and Protein Sequences: An Introduction
Links Between Kinetic Data and Sequences in the Alpha/beta-hydrolases Fold Database
MSI-XGNN: an explainable GNN computational framework integrating transcription- and methylation-level biomarkers for microsatellite instability detection
Dating admixture events is unsolved problem in multi-way admixed populations
Inferring tumor purity using multi-omics data based on a uniform machine learning framework MoTP
Metrics for evaluating differentially methylated region sets predicted from BS-seq data
Design and validation issues in RNA-seq experiments
ADH-Enhancer: an attention-based deep hybrid framework for enhancer identification and strength prediction
SLHSD: hybrid scaffolding method based on short and long reads
Comprehensive investigation of pathway enrichment methods for functional interpretation of LC-MS global metabolomics data
A map of mass spectrometry-based in silico fragmentation prediction and compound identification in metabolomics
Signal transduction-related bioinformatics services
SAM-DTA: a sequence-agnostic model for drug-target binding affinity prediction
A network-based matrix factorization framework for ceRNA co-modules recognition of cancer genomic data
Molecular design in drug discovery: a comprehensive review of deep generative models
Corrigendum to: Comprehensive and critical evaluation of individualized pathway activity measurement tools on pan-cancer data
Revisiting benchmark study for response to methodological critiques of 'Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases'
Development of a cloud-based Bioinformatics Training Platform
Comparison of haplotype-based tests for detecting gene-environment interactions with rare variants
Identifying complex motifs in massive omics data with a variable-convolutional layer in deep neural network
Applications of InterPro in Protein Annotation and Genome Analysis
Ontology-based annotations and semantic relations in large-scale (epi)genomics data
DGCL: dual-graph neural networks contrastive learning for molecular property prediction
Predicting binding affinities of emerging variants of SARS-CoV-2 using spike protein sequencing data: observations, caveats and recommendations
Predicting protein stability changes upon single-point mutation: a thorough comparison of the available tools on a new dataset
Assessment of the functionality and usability of open-source rare variant analysis pipelines
The computational challenges of applying comparative-based computational methods to whole genomes
Graph domain adaptation-based framework for gene expression enhancement and cell type identification in large-scale spatially resolved transcriptomics
Deciphering principles of nucleosome interactions and impact of cancer-associated mutations from comprehensive interaction network analysis
Systematic evaluation of differential splicing tools for RNA-seq studies
ADENet: a novel network-based inference method for prediction of drug adverse events
ASPIRER: a new computational approach for identifying non-classical secreted proteins based on deep learning
epitope1D: accurate taxonomy-aware B-cell linear epitope prediction
Accuracy or novelty: what can we gain from target-specific machine-learning-based scoring functions in virtual screening?
Review: On the analysis and interpretation of correlations in metabolomic data
PGBind: pocket-guided explicit attention learning for protein-ligand docking
IsAb: a computational protocol for antibody design
Editorial: Alignment-free methods in computational biology
Pathogenetic profiling of COVID-19 and SARS-like viruses
Estimating the divisibility of complex biological networks by sparseness indices
Principal component analysis based methods in bioinformatics studies
Letter to the Editor: Stability of Random Forest importance measures
Harnessing large language models' zero-shot and few-shot learning capabilities for regulatory research
CCLA: an accurate method and web server for cancer cell line authentication using gene expression profiles
GTAD: a graph-based approach for cell spatial composition inference from integrated scRNA-seq and ST-seq data
TMKit: a Python interface for computational analysis of transmembrane proteins
Benchmarking computational tools for polymorphic transposable element detection
Predicting molecular properties based on the interpretable graph neural network with multistep focus mechanism
MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences
Biological applications of the theory of birth-and-death processes
Computational design of ultrashort peptide inhibitors of the receptor-binding domain of the SARS-CoV-2 S protein
scMLC: an accurate and robust multiplex community detection method for single-cell multi-omics data
HTCL-DDI: a hierarchical triple-view contrastive learning framework for drug-drug interaction prediction
TaxaGO: a novel, phylogenetically informed gene ontology enrichment analysis tool
Recent advances in computer-aided drug design
Bioinformatics analysis of alternative splicing
From masking repeats to identifying functional repeats in the mouse transcriptome
PIPET: predicting relevant subpopulations in single-cell data using phenotypic information from bulk data
A systematic comparison of data- and knowledge-driven approaches to disease subtype discovery
Integrative systems biology approaches for analyzing microbiome dysbiosis and species interactions
Corrigendum to: Bioinformatics: scalability, capabilities and training in the data-driven era
Benchmarking association analyses of continuous exposures with RNA-seq in observational studies
Tools for managing and analyzing microarray data
Prediction of protein-carbohydrate complex binding affinity using structural features
Drug repositioning for orphan diseases
The PRINTS Database: A Resource for Identification of Protein Families
Data science in unveiling COVID-19 pathogenesis and diagnosis: evolutionary origin to drug repurposing