yusuke1997/dblp-id-title huggingface dataset:
Predicting drug-induced hepatotoxicity based on biological feature maps and diverse classification strategies
Precision probiotics supplement strategy in aging population based on gut microbiome composition
DEKP: a deep learning model for enzyme kinetic parameter prediction based on pretrained models and graph neural networks
Proteomic analysis and prediction of amino acid variations that influence protein posttranslational modifications
iLearn : an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data
DeePhafier: a phage lifestyle classifier using a multilayer self-attention neural network combining protein information
CSGDN: contrastive signed graph diffusion network for predicting crop gene-phenotype associations
High-throughput modeling and analysis of protein structural dynamics
Rare variant association on unrelated individuals in case-control studies using aggregation tests: existing methods and current limitations
Viewing and Annotating Sequence Data with Artemis
Noninvasive fetal genotyping using deep neural networks
Dimensionality reduction approach for many-objective epistasis analysis
Recognizing binding sites of poorly characterized RNA-binding proteins on circular RNAs using attention Siamese network
Comparative analysis of machine learning-based approaches for identifying therapeutic peptides targeting SARS-CoV-2
A cloud-based training module for efficient de novo transcriptome assembly using Nextflow and Google cloud
Deciphering signatures of natural selection via deep learning
A universal model of RNA.DNA: DNA triplex formation accurately predicts genome-wide RNA-DNA interactions
Cell fate conversion prediction by group sparse optimization method utilizing single-cell and bulk OMICs data
RLEAAI: improving antibody-antigen interaction prediction using protein language model and sequence order information
CysModDB: a comprehensive platform with the integration of manually curated resources and analysis tools for cysteine posttranslational modifications
iDMer: an integrative and mechanism-driven response system for identifying compound interventions for sudden virus outbreak
A new publisher for Briefings in Bioinformatics
Differential RNA methylation using multivariate statistical methods
Letter to the Editor: On the stability and ranking of predictors from random forest variable importance measures
MkcDBGAS: a reference-free approach to identify comprehensive alternative splicing events in a transcriptome
Quantitative model for genome-wide cyclic AMP receptor protein binding site identification and characteristic analysis
Coupled matrix-matrix and coupled tensor-matrix completion methods for predicting drug-target interactions
Architecture, function and prediction of long signal peptides
Predicting protein stability changes upon mutations with dual-view ensemble learning from single sequence
Correction to: Introducing π-HelixNovo for practical large-scale de novo peptide sequencing
A similarity-based deep learning approach for determining the frequencies of drug side effects
Homeolog expression quantification methods for allopolyploids
Comparison of imputation and imputation-free methods for statistical analysis of mass spectrometry data with missing data
DROEG: a method for cancer drug response prediction based on omics and essential genes integration
Kled: an ultra-fast and sensitive structural variant detection tool for long-read sequencing data
Comparative genomics approach to detecting split-coding regions in a low-coverage genome: lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes)
Data-driven rational biosynthesis design: from molecules to cell factories
Reasoning over genetic variance information in cause-and-effect models of neurodegenerative diseases
Exploring the potential of large language model-based chatbots in challenges of ribosome profiling data analysis: a review
DDID: a comprehensive resource for visualization and analysis of diet-drug interactions
Teaching the ABCs of bioinformatics: a brief introduction to the Applied Bioinformatics Course
Ontology-based Knowledge Representation for Bioinformatics
Toward completion of the Earth's proteome: an update a decade later
Estimation and control of multiple testing error rates for microarray studies
Towards molecular structure discovery from cryo-ET density volumes via modelling auxiliary semantic prototypes
From contigs towards chromosomes: automatic improvement of long read assemblies (ILRA)
Deep reinforcement learning identifies personalized intermittent androgen deprivation therapy for prostate cancer
Making Sense of Score Statistics for Sequence Alignments
TP53_PROF: a machine learning model to predict impact of missense mutations in TP53
The iPhylo suite: an interactive platform for building and annotating biological and chemical taxonomic trees
NP-TCMtarget: a network pharmacology platform for exploring mechanisms of action of traditional Chinese medicine
Benchmark of embedding-based methods for accurate and transferable prediction of drug response
Comprehensive human respiratory genome catalogue underlies the high resolution and precision of the respiratory microbiome
Multiple errors correction for position-limited DNA sequences with GC balance and no homopolymer for DNA-based data storage
Data-driven selection of analysis decisions in single-cell RNA-seq trajectory inference
Computational Models of Cells and Tissues: Machines, Agents and Fungal Infection
Lipid network and moiety analysis for revealing enzymatic dysregulation and mechanistic alterations from lipidomics data
The virtual cell - a candidate co-ordinator for 'middle-out' modelling of biological systems
Bioinformatics resources facilitate understanding and harnessing clinical research of SARS-CoV-2
DD-PRiSM: a deep learning framework for decomposition and prediction of synergistic drug combinations
GRANet: a graph residual attention network for gene regulatory network inference
Web repositories of natural agents promote pests and pathogenic microbes management
MINE: a new way to design genetics experiments for discovery
Computational approaches to therapeutic antibody design: established methods and emerging trends
What (not) to expect when classifying rare events
Structural dynamics and allostery of Rab proteins: strategies for drug discovery and design
Data curation + process curation=data integration + science
An interpretable block-attention network for identifying regulatory feature interactions
GcDUO: an open-source software for GC × GC-MS data analysis
Computational Systems Biomedicine
Ion entropy and accurate entropy-based FDR estimation in metabolomics
Assessing protein conformational sampling methods based on bivariate lag-distributions of backbone angles
HSSPPI: hierarchical and spatial-sequential modeling for PPIs prediction
A multivariable cis -Mendelian randomization method robust to weak instrument bias and horizontal pleiotropy bias
Circling in on plasmids: benchmarking plasmid detection and reconstruction tools for short-read data from diverse species
Optimizing in silico drug discovery: simulation of connected differential expression signatures and applications to benchmarking
Representing, storing and accessing molecular interaction data: a review of models and tools
Study of transcription factor druggabilty for prostate cancer using structure information, gene regulatory networks and protein moonlighting
DNA Bloom Filter enables anti-contamination and file version control for DNA-based data storage
MLCDForest: multi-label classification with deep forest in disease prediction for long non-coding RNAs
Deep-AFPpred: identifying novel antifungal peptides using pretrained embeddings from seq2vec with 1DCNN-BiLSTM
Human host status inference from temporal microbiome changes via recurrent neural networks
Performance evaluation of transcriptomics data normalization for survival risk prediction
Next-generation sequencing data analysis
How much can deep learning improve prediction of the responses to drugs in cancer cell lines?
The rise of taxon-specific epitope predictors
Simultaneous test and estimation of total genetic effect in eQTL integrative analysis through mixed models
Can machine learning consistently improve the scoring power of classical scoring functions? Insights into the role of machine learning in scoring functions
High-throughput sequencing of the T-cell receptor repertoire: pitfalls and opportunities
DNA-MP: a generalized DNA modifications predictor for multiple species based on powerful sequence encoding method
Generative models for protein sequence modeling: recent advances and future directions
Deep learning in single-cell and spatial transcriptomics data analysis: advances and challenges from a data science perspective
DeepFormer: a hybrid network based on convolutional neural network and flow-attention mechanism for identifying the function of DNA sequences
Deep learning methods for biomedical named entity recognition: a survey and qualitative comparison
A practical guide to the art of RNA gene prediction
Leveraging the attention mechanism to improve the identification of DNA N6-methyladenine sites
Utilizing profile hidden Markov model databases for discovering viruses from metagenomic data: a comprehensive review
Evaluation of biomedical text-mining systems: Lessons learned from information retrieval
Enhancing cryo-EM structure prediction with DeepTracer and AlphaFold2 integration
Progress and challenges in predicting protein interfaces
STRsensor: a computationally efficient method for STR allele-typing from massively parallel sequencing data
A comprehensive review and comparison of existing computational methods for protein function prediction
Understanding structural malleability of the SARS-CoV-2 proteins and relation to the comorbidities
Bioinformatics and Systems Biology: bridging the gap between heterogeneous student backgrounds
DNA methylation analysis in plants: review of computational tools and future perspectives
Sars-escape network for escape prediction of SARS-COV-2
ML-PLIC: a web platform for characterizing protein-ligand interactions and developing machine learning-based scoring functions
Therapeutic peptides identification via kernel risk sensitive loss-based k-nearest neighbor model and multi-Laplacian regularization
A computational toolset for rapid identification of SARS-CoV-2, other viruses and microorganisms from sequencing data
Toward a high-quality pan-genome landscape of Bacillus subtilis by removal of confounding strains
ARAMIS: From systematic errors of NGS long reads to accurate assemblies
Correction to: Adjustment of scRNA-seq data to improve cell-type decomposition of spatial transcriptomics
A review of biomedical datasets relating to drug discovery: a knowledge graph perspective
MACFIV: a novel framework for nonlinear causal inference in the body mass index-hypertension relationship with many weak and pleiotropic genetic instruments
Emboss opens up sequence analysis
Deep learning in retrosynthesis planning: datasets, models and tools
Semantic Web meets Integrative Biology: a survey
Self-supervised deep clustering of single-cell RNA-seq data to hierarchically detect rare cell populations
Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment
SLGCA: spatial cross-level graph contrastive autoencoder for multislice spatial domain identification and microenvironment exploration
PhyImpute and UniFracImpute: two imputation approaches incorporating phylogeny information for microbial count data
Dissecting genetic regulation of metabolic coordination
Protein-DNA binding sites prediction based on pre-trained protein language model and contrastive learning
Reconstructing complex admixture history using a hierarchical model
Bridging artificial intelligence and biological sciences: a comprehensive review of large language models in bioinformatics
Structure-preserved integration of scRNA-seq data using heterogeneous graph neural network
A multichannel graph neural network based on multisimilarity modality hypergraph contrastive learning for predicting unknown types of cancer biomarkers
Systems pharmacology in drug discovery and therapeutic insight for herbal medicines
Analysis of affinity purification-related proteomic data for studying protein-protein interaction networks in cells
Reliable method for predicting the binding affinity of RNA-small molecule interactions using machine learning
Intelligent Batch Epitope Identification and Partitioning: an intelligent tool for the identification of B cell dominant epitopes
DeepAtomicCharge: a new graph convolutional network-based architecture for accurate prediction of atomic charges
VCF-Miner: GUI-based application for mining variants and annotations stored in VCF files
A robust and scalable graph neural network for accurate single-cell classification
Accurate prediction of antibody function and structure using bio-inspired antibody language model
scTsI: an effective two-stage imputation method for single-cell RNA-seq data
Semisynthetic simulation for microbiome data analysis
POSREG: proteomic signature discovered by simultaneously optimizing its reproducibility and generalizability
A biomedical knowledge graph-based method for drug-drug interactions prediction through combining local and global features with deep neural networks
PCLSurv: a prototypical contrastive learning-based multi-omics data integration model for cancer survival prediction
A comprehensive assessment of hurdle and zero-inflated models for single cell RNA-sequencing analysis
GSCA: an integrated platform for gene set cancer analysis at genomic, pharmacogenomic and immunogenomic levels
dbCPM: a manually curated database for exploring the cancer passenger mutations
FireProt 2.0: web-based platform for the fully automated design of thermostable proteins
In silico prediction of host-pathogen protein interactions in melioidosis pathogen Burkholderia pseudomallei and human reveals novel virulence factors and their targets
A comprehensive comparison of residue-level methylation levels with the regression-based gene-level methylation estimations by ReGear
NiPTUNE: an automated pipeline for noninvasive prenatal testing in an accurate, integrative and flexible framework
Exploring diverse approaches for predicting interferon-gamma release: utilizing MHC class II and peptide sequences
Contribution of structural accessibility to the cooperative relationship of TF-lncRNA in myopia
Robust Huber-LASSO for improved prediction of protein, metabolite and gene expression levels relying on individual genotype data
Dynamic changes of synergy relationship between lncRNA and immune checkpoint in cancer progression
Improving feature selection performance for classification of gene expression data using Harris Hawks optimizer with variable neighborhood learning
Accuracy of protein-level disorder predictions
Improving bulk RNA-seq classification by transferring gene signature from single cells in acute myeloid leukemia
scGGC: a two-stage strategy for single-cell clustering through cellular gene pathway construction
Analysis of sequencing data for probing RNA secondary structures and protein-RNA binding in studying posttranscriptional regulations
Addressing noise in co-expression network construction
VISTA: an integrated framework for structural variant discovery
Exploring TEAD2 as a drug target for therapeutic intervention of cancer: A multi-computational case study
Evaluation of research in biomedical ontologies
A multi-dimensional computational framework of drug-induced hepatotoxicity: integrating molecular structure features with disease pathogenesis
Computational prediction and analysis of species-specific fungi phosphorylation via feature optimization strategy
Integrated analysis of the genome and the transcriptome by FANTOM
DeepDRIM: a deep neural network to reconstruct cell-type-specific gene regulatory network using single-cell RNA-seq data
Corrigendum to: FunRes: resolving tissue-specific functional cell states based on a cell-cell communication network model
IMperm: a fast and comprehensive IMmune Paired-End Reads Merger for sequencing data
FitDevo: accurate inference of single-cell developmental potential using sample-specific gene weight
G-DIRT: a web server for identification and removal of duplicate germplasms based on identity-by-state analysis using single nucleotide polymorphism genotyping data
Drug-drug interaction prediction with Wasserstein Adversarial Autoencoder-based knowledge graph embeddings
Information theory applications for biological sequence analysis
Digital PCR threshold robustness analysis and optimization using dipcensR
Design of an epitope-based peptide vaccine against the SARS-CoV-2: a vaccine-informatics approach
New classifications for quantum bioinformatics: Q-bioinformatics, QCt-bioinformatics, QCg-bioinformatics, and QCr-bioinformatics
SC-AIR-BERT: a pre-trained single-cell model for predicting the antigen-binding specificity of the adaptive immune receptor
Machine learning-based tumor-infiltrating immune cell-associated lncRNAs for predicting prognosis and immunotherapy response in patients with glioblastoma
LDAformer: predicting lncRNA-disease associations based on topological feature extraction and Transformer encoder
Advancing the accuracy of SARS-CoV-2 phosphorylation site detection via meta-learning approach
Assessing the heterogeneity of in silico plasmid predictions based on whole-genome-sequenced clinical isolates
Combining clinical and molecular data in regression prediction models: insights from a simulation study
SenseLab: new developments in disseminating neuroscience information
Corrigendum to: Machine learning approach to gene essentiality prediction: a review
Globally distributed object identification for biological knowledgebases
STForte: tissue context-specific encoding and consistency-aware spatial imputation for spatially resolved transcriptomics
Deep learning-based advances and applications for single-cell RNA-sequencing data analysis
DeepGpgs: a novel deep learning framework for predicting arginine methylation sites combined with Gaussian prior and gated self-attention mechanism
GKNnet: an relational graph convolutional network-based method with knowledge-augmented activation layer for microbial structural variation detection
A computational framework of routine test data for the cost-effective chronic disease prediction
SARS-CoV-2 transmissibility compared between variants of concern and vaccination status
Portable sequencing of Mycobacterium tuberculosis for clinical and epidemiological applications
Assessment of human microbiota stability across longitudinal samples using iteratively growing-partitioned clustering
Ligand-based approach for predicting drug targets and for virtual screening against COVID-19
Automated and reproducible cell identification in mass cytometry using neural networks
Characterization and comparison of gene-centered human interactomes
Evaluating methylation of human ribosomal DNA at each CpG site reveals its utility for cancer detection using cell-free DNA
Informatics challenges in structured RNA
Language model enables end-to-end accurate detection of cancer from cell-free DNA
Perspectives on presentation and pedagogy in aid of bioinformatics education
Ensemble learning based on matrix completion improves microbe-disease association prediction
Accurately deciphering spatial domains for spatially resolved transcriptomics with stCluster
NanoDeep: a deep learning framework for nanopore adaptive sampling on microbial sequencing
NCMCMDA: miRNA-disease association prediction through neighborhood constraint matrix completion
CellMsg: graph convolutional networks for ligand-receptor-mediated cell-cell communication analysis
polyGBLUP: a modified genomic best linear unbiased prediction improved the genomic prediction efficiency for autopolyploid species
Towards dynamic genome-scale models
AutoXAI4Omics: an automated explainable AI tool for omics and tabular data
Computational model for disease research
Anti-bias training for (sc)RNA-seq: experimental and computational approaches to improve precision
Identification of metal ion-binding sites in RNA structures using deep learning method
IK-DDI: a novel framework based on instance position embedding and key external text for DDI extraction
Refining computational inference of gene regulatory networks: integrating knockout data within a multi-task framework
Batch effect removal methods for microarray gene expression data integration: a survey
ProsperousPlus : a one-stop and comprehensive platform for accurate protease-specific substrate cleavage prediction and machine-learning model construction
Structured Sparse Regularized TSK Fuzzy System for predicting therapeutic peptides
dHICA: a deep transformer-based model enables accurate histone imputation from chromatin accessibility
Transformation and model choice for RNA-seq co-expression analysis
Unheeded SARS-CoV-2 proteins? A deep look into negative-sense RNA
Interpretation of differential gene expression results of RNA-seq data: review and integration
Assessment of selection pressure exerted on genes from complete pangenomes helps to improve the accuracy in the prediction of new genes
A deep learning approach for filtering structural variants in short read sequencing data
Identification, characterization and expression analysis of circRNA encoded by SARS-CoV-1 and SARS-CoV-2
Nanopore sequencing data analysis: state of the art, applications and challenges
Benchmarking network-based gene prioritization methods for cerebral small vessel disease
RIOT - Rapid Immunoglobulin Overview Tool - annotation of nucleotide and amino acid immunoglobulin sequences using an open germline database
MSIsensor-ct: microsatellite instability detection using cfDNA sequencing data
Bayesian methods in bioinformatics and computational systems biology
CACIMAR: cross-species analysis of cell identities, markers, regulations, and interactions using single-cell RNA sequencing data
Epidemiological data analysis of viral quasispecies in the next-generation sequencing era
Comparing enrichment analysis and machine learning for identifying gene properties that discriminate between gene classes
EP3: an ensemble predictor that accurately identifies type III secreted effectors
Veterinary systems biology for bridging the phenotype-genotype gap via computational modeling for disease epidemiology and animal welfare
A comprehensive review of the analysis and integration of omics data for SARS-CoV-2 and COVID-19
An evaluation of methods to test predefined genomic regions for differential methylation in bisulfite sequencing data
KGANCDA: predicting circRNA-disease associations based on knowledge graph attention network
iATMEcell: identification of abnormal tumor microenvironment cells to predict the clinical outcomes in cancer based on cell-cell crosstalk network
Domain-specific introduction to machine learning terminology, pitfalls and opportunities in CRISPR-based gene editing
Optimizing genomic control in mixed model associations with binary diseases
SPANN: annotating single-cell resolution spatial transcriptome data with scRNA-seq data
Harmonizing semantic annotations for computational models in biology
A review of genetic variant databases and machine learning tools for predicting the pathogenicity of breast cancer
Towards scaling elementary flux mode computation
Prediction and Phylogenetic Analysis of Mammalian Short Interspersed Elements (SINEs)
Methods of privacy-preserving genomic sequencing data alignments
MethPriorGCN: a deep learning tool for inferring DNA methylation prior knowledge and guiding personalized medicine
Identification of active molecules against Mycobacterium tuberculosis through machine learning
Penalized feature selection and classification in bioinformatics
DISMIR: Deep learning-based noninvasive cancer detection by integrating DNA sequence and methylation information of individual cell-free DNA reads
HGTphyloDetect: facilitating the identification and phylogenetic analysis of horizontal gene transfer
Bioinformatics in Latin America and SoIBio impact, a tale of spin-off and expansion around genomes and protein structures