yusuke1997/dblp-id-title huggingface dataset:
Biodiversity informatics: the challenge of linking data and the role of shared identifiers
Models, algorithms and programs for phylogeny reconciliation
TG-CDDPM: text-guided antimicrobial peptides generation based on conditional denoising diffusion probabilistic model
Predicting circRNA-drug sensitivity associations by learning multimodal networks using graph auto-encoders and attention mechanism
Towards pharmacogenomics knowledge discovery with the semantic web
Self-supervised deep learning of gene-gene interactions for improved gene expression recovery
The Cellular basis of loss of smell in 2019-nCoV-infected individuals
Comprehensive characterization of alternative splicing in renal cell carcinoma
Somatic variant analysis suite: copy number variation clonal visualization online platform for large-scale single-cell genomics
Towards multi-omics synthetic data integration
PhenoDriver: interpretable framework for studying personalized phenotype-associated driver genes in breast cancer
CHERRY: a Computational metHod for accuratE pRediction of virus-pRokarYotic interactions using a graph encoder-decoder model
DLRAPom: a hybrid pipeline of Optimized XGBoost-guided integrative multiomics analysis for identifying targetable disease-related lncRNA-miRNA-mRNA regulatory axes
From intuition to AI: evolution of small molecule representations in drug discovery
PHR-search: a search framework for protein remote homology detection based on the predicted protein hierarchical relationships
Coronavirus GenBrowser for monitoring the transmission and evolution of SARS-CoV-2
From single- to multi-omics: future research trends in medicinal plants
scINRB: single-cell gene expression imputation with network regularization and bulk RNA-seq data
Improve consensus partitioning via a hierarchical procedure
Trust me if you can: a survey on reliability and interpretability of machine learning approaches for drug sensitivity prediction in cancer
HetDDI: a pre-trained heterogeneous graph neural network model for drug-drug interaction prediction
Landscape of cancer diagnostic biomarkers from specifically expressed genes
AMHMDA: attention aware multi-view similarity networks and hypergraph learning for miRNA-disease associations identification
MetaLogo: a heterogeneity-aware sequence logo generator and aligner
HybridKla: a hybrid deep learning framework for lactylation site prediction
ctGAN: combined transformation of gene expression and survival data with generative adversarial network
Literature mining, ontologies and information visualization for drug repurposing
COIMMR: a computational framework to reveal the contribution of herbal ingredients against human cancer via immune microenvironment and metabolic reprogramming
Deep-joint-learning analysis model of single cell transcriptome and open chromatin accessibility data
Optimized phenotyping of complex morphological traits: enhancing discovery of common and rare genetic variants
Exploring and visualizing multidimensional data in translational research platforms
A novel fast multiple nucleotide sequence alignment method based on FM-index
Current approaches and outstanding challenges of functional annotation of metabolites: a comprehensive review
Predicting potential interactions between lncRNAs and proteins via combined graph auto-encoder methods
Flux balance analysis in the era of metabolomics
Prediction and collection of protein-metabolite interactions
ggmsa: a visual exploration tool for multiple sequence alignment and associated data
BPP: a platform for automatic biochemical pathway prediction
VirulentHunter: deep learning-based virulence factor predictor illuminates pathogenicity in diverse microbial contexts
Simultaneous Enrichment Analysis of all Possible Gene-sets: Unifying Self-Contained and Competitive Methods
Current progress in bioinformatics 2007
Steering veridical large language model analyses by correcting and enriching generated database queries: first steps toward ChatGPT bioinformatics
ESM-BBB-Pred: a fine-tuned ESM 2.0 and deep neural networks for the identification of blood-brain barrier peptides
SpatialCells: automated profiling of tumor microenvironments with spatially resolved multiplexed single-cell data
Using off-target data from whole-exome sequencing to improve genotyping accuracy, association analysis and polygenic risk prediction
Functional meta-omics provide critical insights into long- and short-read assemblies
iProbiotics: a machine learning platform for rapid identification of probiotic properties from whole-genome primary sequences
Bioinformatics helping to mitigate the impact of COVID-19 - Editorial
Inpactor2: a software based on deep learning to identify and classify LTR-retrotransposons in plant genomes
Correction to: ScInfeR: an efficient method for annotating cell types and sub-types in single-cell RNA-seq, ATAC-seq, and spatial omics
Improving structure-based virtual screening performance via learning from scoring function components
Multiple Sequence Alignment - The Gateway to Further Analysis
A critical assessment of clustering algorithms to improve cell clustering and identification in single-cell transcriptome study
GCNMF-SDA: predicting snoRNA-disease associations based on graph convolution and non-negative matrix factorization
Advanced bioinformatics methods for practical applications in proteomics
Towards simplified graph neural networks for identifying cancer driver genes in heterophilic networks
GED: a manually curated comprehensive resource for epigenetic modification of gametogenesis
The rise and potential opportunities of large language model agents in bioinformatics and biomedicine
SYSMut: decoding the functional significance of rare somatic mutations in cancer
Response to Letter to Editor 'Timely need for navigating the potential and downsides of LLMs in healthcare and biomedicine'
CapsNet-LDA: predicting lncRNA-disease associations using attention mechanism and capsule network based on multi-view data
Genetic regulation of lncRNA expression in whole human brain and their contribution to CNS disorders
Microbial genomic island discovery, visualization and analysis
Community cohesion looseness in gene networks reveals individualized drug targets and resistance
Visualizing and comparing circular genomes using the CGView family of tools
Tools and collaborative environments for bioinformatics research
LncR2metasta: a manually curated database for experimentally supported lncRNAs during various cancer metastatic events
Continually adapting pre-trained language model to universal annotation of single-cell RNA-seq data
A computational approach for the identification of distant homologs of bacterial riboswitches based on inverse RNA folding
Microbiome Metabolome Integration Platform (MMIP): a web-based platform for microbiome and metabolome data integration and feature identification
ACPred-Fuse: fusing multi-view information improves the prediction of anticancer peptides
AMDBNorm: an approach based on distribution adjustment to eliminate batch effects of gene expression data
HEAP: a task adaptive-based explainable deep learning framework for enhancer activity prediction
Venn diagrams in bioinformatics
ONDSA: a testing framework based on Gaussian graphical models for differential and similarity analysis of multiple omics networks
Screening and validation of lncRNAs and circRNAs as miRNA sponges
A comparison and assessment of computational method for identifying recombination hotspots in Saccharomyces cerevisiae
Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology
A review of bioinformatics degrees in Australia
GASS-Metal: identifying metal-binding sites on protein structures using genetic algorithms
Comparing full variation profile analysis with the conventional consensus method in SARS-CoV-2 phylogeny
PEcnv: accurate and efficient detection of copy number variations of various lengths
C-RCPred: a multi-objective algorithm for interactive secondary structure prediction of RNA complexes integrating user knowledge and SHAPE data
Predicting gene regulatory links from single-cell RNA-seq data using graph neural networks
TRlnc: a comprehensive database for human transcriptional regulatory information of lncRNAs
FitDock: protein-ligand docking by template fitting
Regulatory feedback loops bridge the human gene regulatory network and regulate carcinogenesis
Deep learning radiomics under multimodality explore association between muscle/fat and metastasis and survival in breast cancer patients
IMGT, a system and an ontology that bridge biological and computational spheres in bioinformatics
Correction to: Prediction of transcript structure and concentration using RNA-Seq data
IPPF-FE: an integrated peptide and protein function prediction framework based on fused features and ensemble models
The peripheral and core regions of virus-host network of COVID-19
GPSD: a hybrid learning framework for the prediction of phosphatase-specific dephosphorylation sites
Correction to: m CNN-ETC: identifying electron transporters and their functional families by using multiple windows scanning techniques in convolutional neural networks with evolutionary information of protein sequences
Correction to: Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology
Towards a bioinformatics analysis of anti-Alzheimer's herbal medicines from a target network perspective
Recover then aggregate: unified cross-modal deep clustering with global structural information for single-cell data
Knowledge representation in metabolic pathway databases
MicroRNA-small molecule association identification: from experimental results to computational models
MNMDCDA: prediction of circRNA-disease associations by learning mixed neighborhood information from multiple distances
Drug-pathway association prediction: from experimental results to computational models
A comprehensive study of RNA secondary structure alignment algorithms
GPCR-IPL score: multilevel featurization of GPCR-ligand interaction patterns and prediction of ligand functions from selectivity to biased activation
Software Review: Protein Family Alignment Annotation
Dr AFC: drug repositioning through anti-fibrosis characteristic
Inferring kinase-phosphosite regulation from phosphoproteome-enriched cancer multi-omics datasets
MuSiC2: cell-type deconvolution for multi-condition bulk RNA-seq data
Boosting predictabilities of agronomic traits in rice using bivariate genomic selection
A comparison between similarity matrices for principal component analysis to assess population stratification in sequenced genetic data sets
Allelic Association and Disease Mapping
MEANGS: an efficient seed-free tool for de novo assembling animal mitochondrial genome using whole genome NGS data
Sequencing dropout-and-batch effect normalization for single-cell mRNA profiles: a survey and comparative analysis
JCcirc: circRNA full-length sequence assembly through integrated junction contigs
Integration of network models and evolutionary analysis into high-throughput modeling of protein dynamics and allosteric regulation: theory, tools and applications
MANOCCA: a robust and computationally efficient test of covariance in high-dimension multivariate omics data
An integrated approach to determine the abundance, mutation rate and phylogeny of the SARS-CoV-2 genome
DOOR: a prokaryotic operon database for genome analyses and functional inference
EvANI benchmarking workflow for evolutionary distance estimation
A comprehensive survey of the approaches for pathway analysis using multi-omics data integration
Protein-protein interaction and pathway databases, a graphical review
Lesion Shedding Model: unraveling site-specific contributions to ctDNA
An efficient multi-locus mixed model framework for the detection of small and linked QTLs in F2
DeepIRES: a hybrid deep learning model for accurate identification of internal ribosome entry sites in cellular and viral mRNAs
Predicting the stability of mutant proteins by computational approaches: an overview
Heterogeneous molecular processes among the causes of how sequence similarity scores can fail to recapitulate phylogeny
A review of SNP heritability estimation methods
Systematic analysis of the Plk-mediated phosphoregulation in eukaryotes
DiMA: sequence diversity dynamics analyser for viruses
Concept drift detection in toxicology datasets using discriminative subgraph-based drift detector
Multi-task bioassay pre-training for protein-ligand binding affinity prediction
Corrigendum to: Genetic mechanisms of COVID-19 and its association with smoking and alcohol consumption
Best practice and reproducible science are required to advance artificial intelligence in real-world applications
Gene association analysis: a survey of frequent pattern mining from gene expression data
AMGDTI: drug-target interaction prediction based on adaptive meta-graph learning in heterogeneous network
A practical guide for DNase-seq data analysis: from data management to common applications
Comparing genome versus proteome-based identification of clinical bacterial isolates
A dynamic framework for quantifying the genetic architecture of phenotypic plasticity
Breaking the barriers of data scarcity in drug-target affinity prediction
Atomistic simulations reveal impacts of missense mutations on the structure and function of SynGAP1
Network-based identification of key master regulators associated with an immune-silent cancer phenotype
Coloured Petri nets for multilevel, multiscale and multidimensional modelling of biological systems
Template-based protein-protein docking exploiting pairwise interfacial residue restraints
DAESTB: inferring associations of small molecule-miRNA via a scalable tree boosting model based on deep autoencoder
Alzforum and SWAN: the present and future of scientific web communities
Molecular characterization, biological function, tumor microenvironment association and clinical significance of m6A regulators in lung adenocarcinoma
Learning representations for gene ontology terms by jointly encoding graph structure and textual node descriptors
A benchmarking of workflows for detecting differential splicing and differential expression at isoform level in human RNA-seq studies
MHCRoBERTa: pan-specific peptide-MHC class I binding prediction through transfer learning with label-agnostic protein sequences
D3EGFR: a webserver for deep learning-guided drug sensitivity prediction and drug response information retrieval for EGFR mutation-driven lung cancer
Sequence-based prediction model of protein crystallization propensity using machine learning and two-level feature selection
FAIR Header Reference genome: a TRUSTworthy standard
AD-Syn-Net: systematic identification of Alzheimer's disease-associated mutation and co-mutation vulnerabilities via deep learning
Understanding tissue expression evolution: from expression phylogeny to phylogenetic network
Analysis, identification and visualization of subgroups in genomics
Deep learning-based clustering approaches for bioinformatics
In silico prediction of the structure of membrane proteins: Is it feasible?
A novel Bayesian framework for harmonizing information across tissues and studies to increase cell type deconvolution accuracy
Comprehensive assessment of cellular senescence in the tumor microenvironment
jSRC: a flexible and accurate joint learning algorithm for clustering of single-cell RNA-sequencing data
Prediction of transcript structure and concentration using RNA-Seq data
Identifying the potential miRNA biomarkers based on multi-view networks and reinforcement learning for diseases
Understanding YTHDF2-mediated mRNA degradation by m6A-BERT-Deg
LiBis: an ultrasensitive alignment augmentation for low-input bisulfite sequencing
Systematic evaluation of computational tools to predict the effects of mutations on protein stability in the absence of experimental structures
Aperture: alignment-free detection of structural variations and viral integrations in circulating tumor DNA
scPanel: a tool for automatic identification of sparse gene panels for generalizable patient classification using scRNA-seq datasets
Multi-level association rule mining and network pharmacology to identify the polypharmacological effects of herbal materials and compounds in traditional medicine
Network propagation for GWAS analysis: a practical guide to leveraging molecular networks for disease gene discovery
Statistical analysis of multiple regions-of-interest in multiplexed spatial proteomics data
Making authentic science accessible - the benefits and challenges of integrating bioinformatics into a high-school science curriculum
Online resources of cancer data: barriers, benefits and lessons
Methods in Microarray Normalization, Edited by Phillip Stafford
DeepMiceTL: a deep transfer learning based prediction of mice cardiac conduction diseases using early electrocardiograms
ChemFLuo: a web-server for structure analysis and identification of fluorescent compounds
SilenceREIN: seeking silencers on anchors of chromatin loops by deep graph neural networks
Improved criteria and comparative genomics tool provide new insights into grass paleogenomics
Evaluating large language models for annotating proteins
Machine learning approaches and databases for prediction of drug-target interaction: a survey paper
Semantic similarity analysis of protein data: assessment with biological features and issues
A roadmap to multifactor dimensionality reduction methods
Improving protein identification from tandem mass spectrometry data by one-step methods and integrating data from other platforms
Extraction of microRNA-target interaction sentences from biomedical literature by deep learning approach
Bio/chemoinformatics in India: an outlook
Predicting Protein Subcellular Localisation From Amino Acid Sequence Information
Mining plant endogenous target mimics from miRNA-lncRNA interactions based on dual-path parallel ensemble pruning method
Proper imputation of missing values in proteomics datasets for differential expression analysis
A hybrid deep learning framework for gene regulatory network inference from single-cell transcriptomic data
Comparability and reproducibility of biomedical data
m6A regulator-mediated methylation modification patterns and characteristics of immunity and stemness in low-grade glioma
TEINet: a deep learning framework for prediction of TCR-epitope binding specificity
Inferring disease-associated circRNAs by multi-source aggregation based on heterogeneous graph neural network
Computational modelling of atherosclerosis
Using molecular embeddings in QSAR modeling: does it make a difference?
GraphCDA: a hybrid graph representation learning framework based on GCN and GAT for predicting disease-associated circRNAs
Post genome-wide association analysis: dissecting computational pathway/network-based approaches
Haxe as a Swiss knife for bioinformatic applications: the SeqPHASE case story
PPICT: an integrated deep neural network for predicting inter-protein PTM cross-talk
LION: an integrated R package for effective prediction of ncRNA-protein interaction
Community-driven roadmap for integrated disease maps
Comparison of approaches to transcriptomic analysis in multi-sampled tumors
Machine learning-based analysis of multi-omics data on the cloud for investigating gene regulations
Development and experimental validation of computational methods for human antibody affinity enhancement
Prediction of multi-relational drug-gene interaction via Dynamic hyperGraph Contrastive Learning
A survey of generative AI for de novo drug design: new frontiers in molecule and protein generation
Machine learning approaches for drug combination therapies
Identifying cancer prognosis genes through causal learning
Identification of the RNase-binding site of SARS-CoV-2 RNA for anchor primer-PCR detection of viral loading in 306 COVID-19 patients
Learning global dependencies and multi-semantics within heterogeneous graph for predicting disease-related lncRNAs
Deep learning approaches for neural decoding across architectures and recording modalities
Small noncoding RNA discovery and profiling with sRNAtools based on high-throughput sequencing
CovEpiAb: a comprehensive database and analysis resource for immune epitopes and antibodies of human coronaviruses
Computer-aided prediction and design of IL-6 inducing peptides: IL-6 plays a crucial role in COVID-19
CASH: a constructing comprehensive splice site method for detecting alternative splicing events
Predicting transcriptional changes induced by molecules with MiTCP
Probabilistic graphical models for genetic association studies
The present and future of de novo whole-genome assembly
Sample size calculation in metabolic phenotyping studies
A statistical design for testing apomictic diversification through linkage analysis
Pathway integration and annotation: building a puzzle with non-matching pieces and no reference picture
An inductive graph neural network model for compound-protein interaction prediction based on a homogeneous graph
Accurate identification of structural variations from cancer samples
CHTKC: a robust and efficient k-mer counting algorithm based on a lock-free chaining hash table
Evaluation of tools for highly variable gene discovery from single-cell RNA-seq data
Multi-scale modelling in computational biomedicine
Evaluating the state of the art in missing data imputation for clinical data
Mathematical modeling and computational prediction of cancer drug resistance
Predicting the interaction biomolecule types for lncRNA: an ensemble deep learning approach
Enhancing discoveries of molecular QTL studies with small sample size using summary statistic imputation
SubLocEP: a novel ensemble predictor of subcellular localization of eukaryotic mRNA based on machine learning
scNovel: a scalable deep learning-based network for novel rare cell discovery in single-cell transcriptomics
A new method to accurately identify single nucleotide variants using small FFPE breast samples
Statistical methods in genetics
idenPC-CAP: Identify protein complexes from weighted RNA-protein heterogeneous interaction networks using co-assemble partner relation
Biomedical text mining for research rigor and integrity: tasks, challenges, directions
MrGPS: an m6A-related gene pair signature to predict the prognosis and immunological impact of glioma patients
How to design a single-cell RNA-sequencing experiment: pitfalls, challenges and perspectives
Bioinformatics resources for SARS-CoV-2 discovery and surveillance
DeepTFtyper: an interpretable morphology-aware graph neural network for translating histopathology images into molecular subtypes in small cell lung cancer
Large-scale comparison of machine learning algorithms for target prediction of natural products
CharID: a two-step model for universal prediction of interactions between chromatin accessible regions
A large-scale comparative assessment of methods for residue-residue contact prediction
Disease spreading modeling and analysis: a survey
Normal tissue content impact on the GBM molecular classification
HelPredictor models single-cell transcriptome to predict human embryo lineage allocation
The road towards data integration in human genomics: players, steps and interactions
Directed graph attention networks for predicting asymmetric drug-drug interactions
Evaluation of somatic copy number estimation tools for whole-exome sequencing data
scRECL: representative ensembles with contrastive learning for scRNA-seq data clustering analysis
Dual-stage optimizer for systematic overestimation adjustment applied to multi-objective genetic algorithms for biomarker selection
Optimizing sample size for supervised machine learning with bulk transcriptomic sequencing: a learning curve approach
Attention mechanism models for precision medicine
FIRM: Flexible integration of single-cell RNA-sequencing data for large-scale multi-tissue cell atlas datasets
SoyDNGP: a web-accessible deep learning framework for genomic prediction in soybean breeding
PIWI-interacting RNAs in human diseases: databases and computational models
Benchmarking mapping algorithms for cell-type annotating in mouse brain by integrating single-nucleus RNA-seq and Stereo-seq data