yusuke1997/dblp-id-title huggingface dataset:
Insights into the evolutionary forces that shape the codon usage in the viral genome segments encoding intrinsically disordered protein regions
Advancing drug-response prediction using multi-modal and -omics machine learning integration (MOMLIN): a case study on breast cancer clinical data
eQTLHap: a tool for comprehensive eQTL analysis considering haplotypic and genotypic effects
Community effort endorsing multiscale modelling, multiscale data science and multiscale computing for systems medicine
Deep learning in structural bioinformatics: current applications and future perspectives
The prediction approach of drug-induced liver injury: response to the issues of reproducible science of artificial intelligence in real-world applications
Sequence Alignment/Map format: a comprehensive review of approaches and applications
TrimNet: learning molecular representation from triplet messages for biomedicine
A novel pathway mutation perturbation score predicts the clinical outcomes of immunotherapy
Comparative epigenome analysis using Infinium DNA methylation BeadChips
Analysis of insertion-deletion from deep-sequencing data: software evaluation for optimal detection
NASMDR: a framework for miRNA-drug resistance prediction using efficient neural architecture search and graph isomorphism networks
BayesKAT: bayesian optimal kernel-based test for genetic association studies reveals joint genetic effects in complex diseases
QSAR-assisted-MMPA to expand chemical transformation space for lead optimization
Comparative analysis of integrative classification methods for multi-omics data
xQTLbiolinks: a comprehensive and scalable tool for integrative analysis of molecular QTLs
Correction to: Molecular persistent spectral image (Mol-PSI) representation for machine learning models in drug design
Correction to: CRAFT a bioinformatics software for custom prediction of circular RNA functions
Correction to: Enhancing discoveries of molecular QTL studies with small sample size using summary statistic imputation
LRcell : detecting the source of differential expression at the sub-cell-type level from bulk RNA-seq data
deepGraphh : AI-driven web service for graph-based quantitative structure-activity relationship analysis
Comprehensive evaluation of the MM-GBSA method on bromodomain-inhibitor sets
spaLLM: enhancing spatial domain analysis in multi-omics data through large language model integration
A comprehensive overview of lncRNA annotation resources
Accelerating the discovery of antifungal peptides using deep temporal convolutional networks
A deep learning method for predicting metabolite-disease associations via graph neural network
Assessing Random Forest self-reproducibility for optimal short biomarker signature discovery
Computational modeling of brain pathologies: the case of multiple sclerosis
MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization
Beware the Jaccard: the choice of similarity measure is important and non-trivial in genomic colocalisation analysis
MIMESIS: minimal DNA-methylation signatures to quantify and classify tumor signals in tissue and cell-free DNA samples
Discovering novel cancer bio-markers in acquired lapatinib resistance using Bayesian methods
The Edinburgh Mouse Atlas: Using the CD
ChemGenerator: a web server for generating potential ligands for specific targets
MiRLoc: predicting miRNA subcellular localization by incorporating miRNA-mRNA interactions and mRNA subcellular localization
Circadian systems biology in Metazoa
Current trends in computational inference from mass spectrometry-based proteomics
An end-to-end heterogeneous graph attention network for Mycobacterium tuberculosis drug-resistance prediction
Decoding herbal combination models through systematic strategies: insights from target information and traditional Chinese medicine clinical theory
Machine learning methods for predictive proteomics
FR-Match: robust matching of cell type clusters from single cell RNA sequencing data using the Friedman-Rafsky non-parametric test
MultiPep-DLCL: recognition of multifunctional therapeutic peptides through deep learning with label-sequence contrastive learning
Clustering and variable selection evaluation of 13 unsupervised methods for multi-omics data integration
Translational informatics for human microbiota: data resources, models and applications
MLysPRED: graph-based multi-view clustering and multi-dimensional normal distribution resampling techniques to predict multiple lysine sites
3D based generative PROTAC linker design with reinforcement learning
Probe mapping across multiple microarray platforms
Will solid-state drives accelerate your bioinformatics? In-depth profiling, performance analysis and beyond
VirusCircBase: a database of virus circular RNAs
A tool for feature extraction from biological sequences
Transcriptomic studies revealed pathophysiological impact of COVID-19 to predominant health conditions
Review of tandem repeat search tools: a systematic approach to evaluating algorithmic performance
PSSP-MVIRT: peptide secondary structure prediction based on a multi-view deep learning architecture
Biomedical named entity recognition and linking datasets: survey and our recent development
Network analysis of multivariate time series data in biological systems: methods and applications
Defining the functional divergence of orthologous genes between human and mouse in the context of miRNA regulation
Constructing the dynamic transcriptional regulatory networks to identify phenotype-specific transcription regulators
scMUG: deep clustering analysis of single-cell RNA-seq data on multiple gene functional modules
Comprehensive benchmarking of large language models for RNA secondary structure prediction
Sequence pre-training-based graph neural network for predicting lncRNA-miRNA associations
DRAG: design RNAs as hierarchical graphs with reinforcement learning
Multi-omic analysis tools for microbial metabolites prediction
Matrix reconstruction with reliable neighbors for predicting potential MiRNA-disease associations
Using deep neural networks and biological subwords to detect protein S-sulfenylation sites
Dynamics of ubiquitin-mediated signalling: insights from mathematical modelling and experimental studies
Making Decisions for Structural Genomics
Melanoma 2.0. Skin cancer as a paradigm for emerging diagnostic technologies, computational modelling and artificial intelligence
Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations
scCorrector: a robust method for integrating multi-study single-cell data
OTTM: an automated classification tool for translational drug discovery from omics data
MetaPredictor: in silico prediction of drug metabolites based on deep language models with prompt engineering
Using conceptual modeling to improve genome data management
Deciphering cell states and the cellular ecosystem to improve risk stratification in acute myeloid leukemia
Dual balanced augmented topological noncoding RNA disease triplet association in heterogeneous graphs
Elucidating transcriptomic profiles from single-cell RNA sequencing data using nature-inspired compressed sensing
A denoised multi-omics integration framework for cancer subtype classification and survival prediction
CyclicPepedia: a knowledge base of natural and synthetic cyclic peptides
Robust variable selection methods with Cox model - a selective practical benchmark study
A guide to in silico vaccine discovery for eukaryotic pathogens
Advances in phage-host interaction prediction: in silico method enhances the development of phage therapies
Shape mapping: genetic mapping meets geometric morphometrics
Principal component analysis of binary genomics data
Global characterization of B cell receptor repertoire in COVID-19 patients by single-cell V(D)J sequencing
MCCS: a novel recognition pattern-based method for fast track discovery of anti-SARS-CoV-2 drugs
PATRIC as a unique resource for studying antimicrobial resistance
Automatic recognition of protein subcellular location patterns in single cells from immunofluorescence images based on deep learning
Do we need different machine learning algorithms for QSAR modeling? A comprehensive assessment of 16 machine learning algorithms on 14 QSAR data sets
Converting single nucleotide variants between genome builds: from cautionary tale to solution
SynOmics: integrating multi-omics data through feature interaction networks
Multicancer analyses of short tandem repeat variations reveal shared gene regulatory mechanisms
Network-guided identification of cancer-selective combinatorial therapies in ovarian cancer
Computational profiling of the gut-brain axis: microflora dysbiosis insights to neurological disorders
DisBalance: a platform to automatically build balance-based disease prediction models and discover microbial biomarkers from microbiome data
Understanding the disease genome: gene essentiality and the interplay of selection, recombination and mutation
DiffPROTACs is a deep learning-based generator for proteolysis targeting chimeras
Improving drug response prediction by integrating multiple data sources: matrix factorization, kernel and network-based approaches
Diff-AMP: tailored designed antimicrobial peptide framework with all-in-one generation, identification, prediction and optimization
Computational methods for discovering gene networks from expression data
Efficacy difference of antipsychotics in Alzheimer's disease and schizophrenia: explained with network efficiency and pathway analysis methods
PKSPS: a novel method for predicting kinase of specific phosphorylation sites based on maximum weighted bipartite matching algorithm and phosphorylation sequence enrichment analysis
Probabilistic natural mapping of gene-level tests for genome-wide association studies
Using fold recognition to search for useful proteins: Bayesian approach to fold recognition
Comparative analysis of differential gene expression tools for RNA sequencing time course data
Genome sequencing data analysis for rare disease gene discovery
Genetic association studies: Design, analysis and interpretation
An analysis of human microbe-disease associations
A perspective on genetic and polygenic risk scores - advances and limitations and overview of associated tools
Standigm ASK™: knowledge graph and artificial intelligence platform applied to target discovery in idiopathic pulmonary fibrosis
A model for family-based case-control studies of genetic imprinting and epistasis
Rigorous benchmarking of T-cell receptor repertoire profiling methods for cancer RNA sequencing
Learning representation for multiple biological networks via a robust graph regularized integration approach
MuSERA: Multiple Sample Enriched Region Assessment
Irinotecan and vandetanib create synergies for treatment of pancreatic cancer patients with concomitant TP53 and KRAS mutations
MAPTrans: mutual attention transformer with dynamic meta-path pruning for drug repositioning
Supervised application of internal validation measures to benchmark dimensionality reduction methods in scRNA-seq data
SARS-CoV-2 3D database: understanding the coronavirus proteome and evaluating possible drug targets
Strategies for dealing with incomplete information in the modeling of molecular interaction networks
LPAD: using network construction and label propagation to detect topologically associating domains from Hi-C data
VirGenA: a reference-based assembler for variable viral genomes
Quantitative estimation of intracellular oxidative stress in human tissues
Adapt-Kcr: a novel deep learning framework for accurate prediction of lysine crotonylation sites based on learning embedding features and attention architecture
Capturing large genomic contexts for accurately predicting enhancer-promoter interactions
Updated review of advances in microRNAs and complex diseases: towards systematic evaluation of computational models
Bio-inspired chemical space exploration of terpenoids
Transcriptomics and epigenetic data integration learning module on Google Cloud
A quality control portal for sequencing data deposited at the European genome-phenome archive
Machine learning approaches to decipher hormone and HER2 receptor status phenotypes in breast cancer
A granularity-level information fusion strategy on hypergraph transformer for predicting synergistic effects of anticancer drugs
Reconstructing tumor clonal heterogeneity and evolutionary relationships based on tumor DNA sequencing data
Analysis of metabolomic data: tools, current strategies and future challenges for omics data integration
Protein language models are performant in structure-free virtual screening
Exploring autonomy through computational biomodelling
Recent advances in cancer fusion transcript detection
High-dimensional generalized propensity score with application to omics data
Graph representation learning in bioinformatics: trends, methods and applications
Discovering gene regulatory networks of multiple phenotypic groups using dynamic Bayesian networks
TP-LMMSG: a peptide prediction graph neural network incorporating flexible amino acid property representation
Added predictive value of high-throughput molecular data to clinical data and its validation
A global perspective on evolving bioinformatics and data science training needs
TransIntegrator: capture nearly full protein-coding transcript variants via integrating Illumina and PacBio transcriptomes
HiFreSP: A novel high-frequency sub-pathway mining approach to identify robust prognostic gene signatures
CRISPRCasStack: a stacking strategy-based ensemble learning framework for accurate identification of Cas proteins
BANMF-S: a blockwise accelerated non-negative matrix factorization framework with structural network constraints for single cell imputation
Systems medicine of inflammaging
toxCSM: comprehensive prediction of small molecule toxicity profiles
mCNN-ETC: identifying electron transporters and their functional families by using multiple windows scanning techniques in convolutional neural networks with evolutionary information of protein sequences
Interoperability with Moby 1.0 - It's better than sharing your toothbrush!
The semantic web in translational medicine: current applications and future directions
Diagnostic Prediction of portal vein thrombosis in chronic cirrhosis patients using data-driven precision medicine model
Predicting disease-associated microbes based on similarity fusion and deep learning
CODA: a combo-Seq data analysis workflow
SARS-CoV-2 hot-spot mutations are significantly enriched within inverted repeats and CpG island loci
Benchmarking ensemble machine learning algorithms for multi-class, multi-omics data integration in clinical outcome prediction
Distant metastasis identification based on optimized graph representation of gene interaction patterns
AtacAnnoR: a reference-based annotation tool for single cell ATAC-seq data
Deciphering the genetic interplay between depression and dysmenorrhea: a Mendelian randomization study
Extracting reaction networks from databases-opening Pandora's box
A comprehensive integrated drug similarity resource for in-silico drug repositioning and beyond
CoverageMaster: comprehensive CNV detection and visualization from NGS short reads for genetic medicine applications
PartIES: a disease subtyping framework with Partition-level Integration using diffusion-Enhanced Similarities from multi-omics Data
A comparative study of statistical methods used to identify dependencies between gene expression signals
Diseasome and comorbidities complexities of SARS-CoV-2 infection with common malignant diseases
Regularly updated benchmark sets for statistically correct evaluations of AlphaFold applications
Data and knowledge integration in the life sciences
Graph neural networks for single-cell omics data: a review of approaches and applications
Large language model produces high accurate diagnosis of cancer from end-motif profiles of cell-free DNA
Systematic characterization and prediction of coenzyme A-associated proteins using sequence and network information
A systematic review of molecular representation learning foundation models
Computational recognition for long non-coding RNA (lncRNA): Software and databases
Normalization of RNA-Seq data using adaptive trimmed mean with multi-reference
The BioCyc collection of microbial genomes and metabolic pathways
Distance-guided protein folding based on generalized descent direction
TransRef enables accurate transcriptome assembly by redefining accurate neo-splicing graphs
A comprehensive comparison of tools for differential ChIP-seq analysis
AttABseq: an attention-based deep learning prediction method for antigen-antibody binding affinity changes based on protein sequences
FFMAVP: a new classifier based on feature fusion and multitask learning for identifying antiviral peptides and their subclasses
NAMS webserver: coding potential assessment and functional annotation of plant transcripts
STMGraph: spatial-context-aware of transcriptomes via a dual-remasked dynamic graph attention model
HDIContact: a novel predictor of residue-residue contacts on hetero-dimer interfaces via sequential information and transfer learning strategy
Towards deep phenotyping pregnancy: a systematic review on artificial intelligence and machine learning methods to improve pregnancy outcomes
Multi-kernel feature extraction with dynamic fusion and downsampled residual feature embedding for predicting rice RNA N 6-methyladenine sites
ProSAP: a GUI software tool for statistical analysis and assessment of thermal stability data
Applications and techniques of single-cell RNA sequencing across diverse species
LightCTL: lightweight contrastive TCR-pMHC specificity learning with context-aware prompt
Alignment-free metal ion-binding site prediction from protein sequence through pretrained language model and multi-task learning
Deep learning-based design and experimental validation of a medicine-like human antibody library
Integrative bioinformatics and omics data source interoperability in the next-generation sequencing era - Editorial
Deep4mC: systematic assessment and computational prediction for DNA N4-methylcytosine sites by deep learning
Pan-cancer application of a lung-adenocarcinoma-derived gene-expression-based prognostic predictor
Protein Structure Prediction in Genomics
DAmiRLocGNet: miRNA subcellular localization prediction by combining miRNA-disease associations and graph convolutional networks
Circulating microRNA trafficking and regulation: computational principles and practice
How to establish a bioinformatics postgraduate degree programme - a case study from South Africa
A review of COVID-19 biomarkers and drug targets: resources and tools
TripHLApan: predicting HLA molecules binding peptides based on triple coding matrix and transfer learning
Identifying anti-coronavirus peptides by incorporating different negative datasets and imbalanced learning strategies
A weighted bilinear neural collaborative filtering approach for drug repositioning
ncRNAInter: a novel strategy based on graph neural network to discover interactions between lncRNA and miRNA
Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes
Tracing the footsteps of autophagy in computational biology
kTWAS: integrating kernel machine with transcriptome-wide association studies improves statistical power and reveals novel genes
Systematical identification of cell-specificity of CTCF-gene binding based on epigenetic modifications
Computational Genome Analysis: an Introduction: Richard C. Deonier, Simon Tavaré and Michael S. Waterman
A transformer architecture based on BERT and 2D convolutional neural network to identify DNA enhancers from sequence information
iDHS-Deep: an integrated tool for predicting DNase I hypersensitive sites by deep neural network
Genetic mechanisms of COVID-19 and its association with smoking and alcohol consumption
Recent advances and prospects of computational methods for metabolite identification: a review with emphasis on machine learning approaches
CoT: a transformer-based method for inferring tumor clonal copy number substructure from scDNA-seq data
Correction to: A new paradigm for applying deep learning to protein-ligand interaction prediction
DeepMotifSyn: a deep learning approach to synthesize heterodimeric DNA motifs
miRandb: a resource of online services for miRNA research
Tracing human life trajectory using gut microbial communities by context-aware deep learning
PbsNRs: predict the potential binders and scaffolds for nuclear receptors
A review of enzyme design in catalytic stability by artificial intelligence
Evo-Devo-EpiR: a genome-wide search platform for epistatic control on the evolution of development
Protein turnover models for LC-MS data of heavy water metabolic labeling
Proper joint analysis of summary association statistics requires the adjustment of heterogeneity in SNP coverage pattern
Predicting ncRNA-protein interactions based on dual graph convolutional network and pairwise learning
Digital DNA lifecycle security and privacy: an overview
Software Review
Survey of local and global biological network alignment: the need to reconcile the two sides of the same coin
Systematic evaluation of de novo mutation calling tools using whole genome sequencing data
Efficient test for deviation from Hardy-Weinberg equilibrium with known or ambiguous typing in highly polymorphic loci
GPMeta: a GPU-accelerated method for ultrarapid pathogen identification from metagenomic sequences
Pioneering topological methods for network-based drug-target prediction by exploiting a brain-network self-organization theory
Evaluating assembly and variant calling software for strain-resolved analysis of large DNA viruses
Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes
Recognition of rare antinuclear antibody patterns based on a novel attention-based enhancement framework
Evolution and applications of plant pathway resources and databases
Enhancing RNA-seq analysis by addressing all co-existing biases using a self-benchmarking approach with 2D structural insights
Adapting differential molecular representation with hierarchical prompts for multi-label property prediction
Methodological aspects of whole-genome bisulfite sequencing analysis
scTCA: a hybrid Transformer-CNN architecture for imputation and denoising of scDNA-seq data
Self-awareness of retrosynthesis via chemically inspired contrastive learning for reinforced molecule generation
ENNAVIA is a novel method which employs neural networks for antiviral and anti-coronavirus activity prediction for therapeutic peptides
Computational medicine: quantitative modeling of complex diseases
scEVOLVE: cell-type incremental annotation without forgetting for single-cell RNA-seq data
Guided diffusion for molecular generation with interaction prompt
Building biomedical web communities using a semantically aware content management system
Trends in the development of miRNA bioinformatics tools
Information Resources for the Bioinformatician
Bioinformatics and system biology approach to identify the influences of COVID-19 on cardiovascular and hypertensive comorbidities
ViBE: a hierarchical BERT model to identify eukaryotic viruses using metagenome sequencing data
Online tools to support literature-based discovery in the life sciences
Congruency in the prediction of pathogenic missense mutations: state-of-the-art web-based tools
A systematic evaluation of the computational tools for lncRNA identification
Drug knowledge bases and their applications in biomedical informatics research
Screening single-cell trajectories via continuity assessments for cell transition potential
Multi-view Multichannel Attention Graph Convolutional Network for miRNA-disease association prediction
A survey and systematic assessment of computational methods for drug response prediction
Cancer subtyping with heterogeneous multi-omics data via hierarchical multi-kernel learning
Benchmarking community drug response prediction models: datasets, models, tools, and metrics for cross-dataset generalization analysis
RefRGim: an intelligent reference panel reconstruction method for genotype imputation with convolutional neural networks