yusuke1997/dblp-id-title huggingface dataset:
RNA methylation and diseases: experimental results, databases, Web servers and computational models
The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation
Principals about principal components in statistical genetics
A high-dimensional linkage analysis model for characterizing crossover interference
methylClass : an R package to construct DNA methylation-based classification models
Alpha_Mesh_Swc : automatic and robust surface mesh generation from the skeleton description of brain cells
A penalized linear mixed model with generalized method of moments for prediction analysis on high-dimensional multi-omics data
MMRFBiolinks: an R-package for integrating and analyzing MMRF-CoMMpass data
Mass spectrometry-based protein identification in proteomics - a review
To pack or not to pack: revisiting protein side-chain packing in the post-AlphaFold era
Critical technologies for bioinformatics
circRNA-binding protein site prediction based on multi-view deep learning, subspace learning and multi-view classifier
Review of statistical methodologies for the detection of parent-of-origin effects in family trio genome-wide association data with binary disease traits
CRISPRlnc: a machine learning method for lncRNA-specific single-guide RNA design of CRISPR/Cas9 system
A comprehensive overview of oncogenic pathways in human cancer
KinaseFusionDB: an integrative knowledge of kinase fusion proteins in multi-scales
Features that define the best ChIP-seq peak calling algorithms
Exploring effectiveness of ab-initio protein-protein docking methods on a novel antibacterial protein complex dataset
A systematic evaluation of data processing and problem formulation of CRISPR off-target site prediction
Fast and automated protein-DNA/RNA macromolecular complex modeling from cryo-EM maps
DeepPhosPPI: a deep learning framework with attention-CNN and transformer for predicting phosphorylation effects on protein-protein interactions
DeepSCP: utilizing deep learning to boost single-cell proteome coverage
Enhancing TFEA.ChIP with ENCODE regulatory maps for generalizable transcription factor enrichment
BatchDTA: implicit batch alignment enhances deep learning-based drug-target affinity estimation
Multi-omics analysis of Helicobacter pylori -associated gastric cancer identifies hub genes as a novel therapeutic biomarker
Discovering trends and hotspots of biosafety and biosecurity research via machine learning
SNRMPACDC: computational model focused on Siamese network and random matrix projection for anticancer synergistic drug combination prediction
GREAP: a comprehensive enrichment analysis software for human genomic regions
BioGPT: generative pre-trained transformer for biomedical text generation and mining
Algorithms and tools for analysis and management of mass spectrometry data
Retraction and replacement of: FGeneBERT: function-driven pre-trained gene language model for metagenomics
BLAST and Go?
Rare variant association tests for ancestry-matched case-control data based on conditional logistic regression
Ferroptosis-related lncRNA pairs to predict the clinical outcome and molecular characteristics of pancreatic ductal adenocarcinoma
SnapHiC-D: a computational pipeline to identify differential chromatin contacts from single-cell Hi-C data
Unsupervised and self-supervised deep learning approaches for biomedical text mining
Bioinformatic approaches for functional annotation and pathway inference in metagenomics data
GutBalance: a server for the human gut microbiome-based disease prediction and biomarker discovery with compositionality addressed
Machine learning on protein-protein interaction prediction: models, challenges and trends
Clustering and classification methods for single-cell RNA-sequencing data
Correction to: ProtGraph: a tool for the quick and comprehensive exploration and exploitation of the peptide search space derived from protein sequence databases using graphs
CDHu40: a novel marker gene set of neuroendocrine prostate cancer
MG-RAST version 4 - lessons learned from a decade of low-budget ultra-high-throughput metagenome analysis
Exploration of cellular reaction systems
stImage: a versatile framework for optimizing spatial transcriptomic analysis through customizable deep histology and location informed integration
Erratum to: Analysis, identification and visualization of subgroups in genomics
Eravacycline, an antibacterial drug, repurposed for pancreatic cancer therapy: insights from a molecular-based deep learning model
Comment on 'rigorous benchmarking of T cell receptor repertoire profiling methods for cancer RNA sequencing'
Review and comparative assessment of sequence-based predictors of protein-binding residues
Predicting chromosomal compartments directly from the nucleotide sequence with DNA-DDA
A comparison of scRNA-seq annotation methods based on experimentally labeled immune cell subtype dataset
Image-based molecular representation learning for drug development: a survey
Mitigating cold-start problems in drug-target affinity prediction with interaction knowledge transferring
DSTG: deconvoluting spatial transcriptomics data through graph-based artificial intelligence
Evaluation of machine learning models on protein level inference from prioritized RNA features
Exon array data analysis using Affymetrix power tools and R statistical software
SPIN: sex-specific and pathway-based interpretable neural network for sexual dimorphism analysis
ClusterX: a novel representation learning-based deep clustering framework for accurate visual inspection in virtual screening
Generative prediction of real-world prevalent SARS-CoV-2 mutation with in silico virus evolution
Decoding CRISPR-Cas PAM recognition with UniDesign
Public services from the European Bioinformatics Institute
Biclustering data analysis: a comprehensive survey
SARITA: a large language model for generating the S1 subunit of the SARS-CoV-2 spike protein
Deep contrastive learning for predicting cancer prognosis using gene expression values
GPS-Palm: a deep learning-based graphic presentation system for the prediction of S-palmitoylation sites in proteins
Predicting microRNA-disease associations from lncRNA-microRNA interactions via Multiview Multitask Learning
Critical limitations of prognostic signatures based on risk scores summarized from gene expression levels: a case study for resected stage I non-small-cell lung cancer
Identifying pleiotropic genes via the composite test amidst the complexity of polygenic traits
Taxonomic binning of metagenome samples generated by next-generation sequencing technologies
Predicting drug-target binding affinity with cross-scale graph contrastive learning
scDeepInsight: a supervised cell-type identification method for scRNA-seq data with deep learning
An artificial intelligence-based approach for identifying the proteins regulating liquid-liquid phase separation
Multiomics integration-based molecular characterizations of COVID-19
The relative value of operon predictions
Correction to: A benchmark study on current GWAS models in admixed populations
2HiGWAS: a unifying high-dimensional platform to infer the global genetic architecture of trait development
CMTT-JTracker: a fully test-time adaptive framework serving automated cell lineage construction
Metabolic networks of the Nicotiana genus in the spotlight: content, progress and outlook
Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond
Modular arrangements of sequence motifs determine the functional diversity of KDM proteins
Generative Adversarial Matrix Completion Network based on Multi-Source Data Fusion for miRNA-Disease Associations Prediction
Data construction for phosphorylation site prediction
RVFScan predicts virulence factor genes and hypervirulence of the clinical metagenome
Improving protein fold recognition using triplet network and ensemble deep learning
CPPred-FL: a sequence-based predictor for large-scale identification of cell-penetrating peptides by feature representation learning
FCCCSR_Glu: a semi-supervised learning model based on FCCCSR algorithm for prediction of glutarylation sites
A hitchhiker's guide to expressed sequence tag (EST) analysis
LBCEPred: a machine learning model to predict linear B-cell epitopes
SMURF: embedding single-cell RNA-seq data with matrix factorization preserving self-consistency
Identifying psychiatric disorder-associated gut microbiota using microbiota-related gene set enrichment analysis
A comparison of deep learning-based pre-processing and clustering approaches for single-cell RNA sequencing data
DrugRepV: a compendium of repurposed drugs and chemicals targeting epidemic and pandemic viruses
When orthologs diverge between human and mouse
MSlocPRED: deep transfer learning-based identification of multi-label mRNA subcellular localization
Next generation tools for the annotation of human SNPs
Predicting drug-disease associations through layer attention graph convolutional network
A pan-cancer interrogation of intronic polyadenylation and its association with cancer characteristics
PCA-based GRS analysis enhances the effectiveness for genetic correlation detection
An algorithmic perspective of de novo cis-regulatory motif finding based on ChIP-seq data
CyanoPATH: a knowledgebase of genome-scale functional repertoire for toxic cyanobacterial blooms
Proteome Bioinformatics. Edited by Simon J. Hubbard and Andrew R. Jones,
A network-based method for brain disease gene prediction by integrating brain connectome and molecular network
Towards more accurate prediction of ubiquitination sites: a comprehensive review of current methods, tools and features
Gene co-expression analysis for functional classification and gene-disease predictions
TACOS: a novel approach for accurate prediction of cell-specific long noncoding RNAs subcellular localization
Machine learning and statistical methods for clustering single-cell RNA-sequencing data
OPATs: Omnibus P-value association tests
Benchmarking of computational methods for m6A profiling with Nanopore direct RNA sequencing
Network-based identification genetic effect of SARS-CoV-2 infections to Idiopathic pulmonary fibrosis (IPF) patients
GSScore: a novel Graphormer-based shell-like scoring method for protein-ligand docking
TG468: a text graph convolutional network for predicting clinical response to immune checkpoint inhibitor therapy
A multi-view graph contrastive learning framework for deciphering spatially resolved transcriptomics data
BioM2 : biologically informed multi-stage machine learning for phenotype prediction using omics data
DeepHisCoM: deep learning pathway analysis using hierarchical structural component models
Bridging heterogeneous mutation data to enhance disease gene discovery
TARGET-SL: precision essential gene prediction using driver prioritisation and synthetic lethality
A social theory-enhanced graph representation learning framework for multitask prediction of drug-drug interactions
InDEP: an interpretable machine learning approach to predict cancer driver genes from multi-omics data
Scopy: an integrated negative design python library for desirable HTS/VS database design
Structure prediction of linear and cyclic peptides using CABS-flex
Synthetic observations from deep generative models and binary omics data with limited sample size
Reconstruction of plasmids by shotgun sequencing from environmental DNA: which bioinformatic workflow?
Pairwise sequence alignment - it's all about us!
scMGATGRN: a multiview graph attention network-based method for inferring gene regulatory networks from single-cell transcriptomic data
Metabolomics and the challenges ahead
m6ATM: a deep learning framework for demystifying the m6A epitranscriptome with Nanopore long-read RNA-seq data
Long non-coding RNA transcriptome of uncharacterized samples can be accurately imputed using protein-coding genes
An Ariadne's thread to the identification and annotation of noncoding RNAs in eukaryotes
DSCC: disease subtyping using spectral clustering and community detection from consensus networks
High-resolution transcription factor binding sites prediction improved performance and interpretability by deep learning method
circRIP: an accurate tool for identifying circRNA-RBP interactions
Normalization and quantification of differential expression in gene expression microarrays
Viral informatics: bioinformatics-based solution for managing viral infections
Correction to: sciCNV: high-throughput paired profiling of transcriptomes and DNA copy number variations at single-cell resolution
NetTDP: permutation-based true discovery proportions for differential co-expression network analysis
Identifying drug-target interactions via heterogeneous graph attention networks combined with cross-modal similarities
deepTAD: an approach for identifying topologically associated domains based on convolutional neural network and transformer model
DRdriver: identifying drug resistance driver genes using individual-specific gene regulatory network
A primer on precision medicine informatics
Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees
siGCD: a web server to explore survival interaction of genes, cells and drugs in human cancers
FP-GNN: a versatile deep learning architecture for enhanced molecular property prediction
Oxford nanopore sequencing in clinical microbiology and infection diagnostics
Identifying spatial domains of spatially resolved transcriptomics via multi-view graph convolutional networks
Short human eccDNAs are predictable from sequences
Targeted metabolic reconstruction: a novel approach for the characterization of plant-pathogen interactions
Evaluation of epitranscriptome-wide N6-methyladenosine differential analysis methods
A deep learning-based approach to model anomalous diffusion of membrane proteins: the case of the nicotinic acetylcholine receptor
EcTracker: Tracking and elucidating ectopic expression leveraging large-scale scRNA-seq studies
The role of ontologies in biological and biomedical research: a functional perspective
Signaling repurposable drug combinations against COVID-19 by developing the heterogeneous deep herb-graph method
Corrigendum to: Comprehensive review and empirical analysis of hallmarks of DNA-, RNA- and protein-binding residues in protein chains
iAMP-CA2L: a new CNN-BiLSTM-SVM classifier based on cellular automata image for identifying antimicrobial peptides and their functional types
NNKcat: deep neural network to predict catalytic constants (Kcat) by integrating protein sequence and substrate structure with enhanced data imbalance handling
BISC: accurate inference of transcriptional bursting kinetics from single-cell transcriptomic data
STMHCpan, an accurate Star-Transformer-based extensible framework for predicting MHC I allele binding peptides
Investigating the role of Simpson's paradox in the analysis of top-ranked features in high-dimensional bioinformatics datasets
DeepCap-Kcr: accurate identification and investigation of protein lysine crotonylation sites based on capsule network
hDirect-MAP: projection-free single-cell modeling of response to checkpoint immunotherapy
Evaluation of different computational methods on 5-methylcytosine sites identification
Bioinformatics tools and database resources for systems genetics analysis in mice - a short review and an evaluation of future needs
Identification of miRNA-disease associations via multiple information integration with Bayesian ranking
Editorial: Identity and Interoperability in Bioinformatics
Bioinformatics in Russia: history and present-day landscape
ZSeeker: an optimized algorithm for Z-DNA detection in genomic sequences
CoraL: interpretable contrastive meta-learning for the prediction of cancer-associated ncRNA-encoded small peptides
NPI-GNN: Predicting ncRNA-protein interactions with deep graph neural networks
iFORM/eQTL: an ultrahigh-dimensional platform for inferring the global genetic architecture of gene transcripts
Enhancer-driven gene regulatory networks inference from single-cell RNA-seq and ATAC-seq data
Capacity building for whole genome sequencing of Mycobacterium tuberculosis and bioinformatics in high TB burden countries
Information quality in proteomics
Inferring network interactions within a cell
A computational framework to unify orthogonal information in DNA methylation and copy number aberrations in cell-free DNA for early cancer detection
HLAIImaster: a deep learning method with adaptive domain knowledge predicts HLA II neoepitope immunogenic responses
Correction to: Privacy-aware estimation of relatedness in admixed populations
Predicting cell line-specific synergistic drug combinations through a relational graph convolutional network with attention mechanism
Potential of dissimilarity measure-based computation of protein thermal stability data for determining protein interactions
SCANER: robust and sensitive identification of malignant cells from the scRNA-seq profiled tumor ecosystem
Detecting multi-way epistasis in family-based association studies
An analysis of protein language model embeddings for fold prediction
Exploiting drug-disease relationships for computational drug repositioning
Identify gestational diabetes mellitus by deep learning model from cell-free DNA at the early gestation stage
PhaTYP: predicting the lifestyle for bacteriophages using BERT
Protein functional annotation of simultaneously improved stability, accuracy and false discovery rate achieved by a sequence-based deep learning
MMSMAPlus: a multi-view multi-scale multi-attention embedding model for protein function prediction
Explainable deep neural networks for predicting sample phenotypes from single-cell transcriptomics
MGEGFP: a multi-view graph embedding method for gene function prediction based on adaptive estimation with GCN
A comprehensive evaluation of connectivity methods for L1000 data
Construction of a hierarchical gene regulatory network centered around a transcription factor
Deep graph convolutional network-based multi-omics integration for cancer driver gene identification
A self-attention-driven deep learning framework for inference of transcriptional gene regulatory networks
A practical guide for the functional annotation of genetic variations using SNPnexus
Data-driven identification of SARS-CoV-2 subpopulations using PhenoGraph and binary-coded genomic data
Bioinformatics toolbox for exploring target mutation-induced drug resistance
Computationally prioritized drugs inhibit SARS-CoV-2 infection and syncytia formation
KLFDAPC: a supervised machine learning approach for spatial genetic structure analysis
Network information improves cancer outcome prediction
Iterative feature representation algorithm to improve the predictive performance of N7-methylguanosine sites
Performance evaluation of computational methods for splice-disrupting variants and improving the performance using the machine learning-based framework
MCFF-MTDDI: multi-channel feature fusion for multi-typed drug-drug interaction prediction
ProteinF3S: boosting enzyme function prediction by fusing protein sequence, structure, and surface
T4SEfinder: a bioinformatics tool for genome-scale prediction of bacterial type IV secreted effectors using pre-trained protein language model
NIDM: network impulsive dynamics on multiplex biological network for disease-gene prediction
Prediction of disease-associated nsSNPs by integrating multi-scale ResNet models with deep feature fusion
Machine learning for phytopathology: from the molecular scale towards the network scale
Label-free proteome quantification and evaluation
How bioinformatics resources work with G4 RNAs
TWO-SIGMA-G: a new competitive gene set testing framework for scRNA-seq data accounting for inter-gene and cell-cell correlation
DNAgenie: accurate prediction of DNA-type-specific binding residues in protein sequences
Fast heritability estimation based on MINQUE and batch training
Evaluation of a two-stage framework for prediction using big genomic data
CNA2Subpathway: identification of dysregulated subpathway driven by copy number alterations in cancer
Heterogeneous multi-scale neighbor topologies enhanced drug-disease association prediction
Discovering common pathogenetic processes between COVID-19 and diabetes mellitus by differential gene expression pattern analysis
Pathway enrichment analysis approach based on topological structure and updated annotation of pathway
A comprehensive review and comparison of different computational methods for protein remote homology detection
Improved model quality assessment using sequence and structural information by enhanced deep neural networks
Single-cell multi-omics sequencing: application trends, COVID-19, data analysis issues and prospects
iPiDi-PUL: identifying Piwi-interacting RNA-disease associations based on positive unlabeled learning
DeepDDS: deep graph neural network with attention mechanism to predict synergistic drug combinations
Design powerful predictor for mRNA subcellular location prediction in Homo sapiens
Evaluation of integrative clustering methods for the analysis of multi-omics data
A review and performance evaluation of clustering frameworks for single-cell Hi-C data
Characterizing viral circRNAs and their application in identifying circRNAs in viruses
Exploring miRNA-target gene pair detection in disease with coRmiT
WEVar: a novel statistical learning framework for predicting noncoding regulatory variants
Comparative assessment of differential network analysis methods
Pharmaco-miR: linking microRNAs and drug effects
FunRes: resolving tissue-specific functional cell states based on a cell-cell communication network model
MPI-VGAE: protein-metabolite enzymatic reaction link learning by variational graph autoencoders
Critical review of conformational B-cell epitope prediction methods
A novel statistical method for decontaminating T-cell receptor sequencing data
SVHunter: long-read-based structural variation detection through the transformer model
Structural mapping: how to study the genetic architecture of a phenotypic trait through its formation mechanism
Detecting novel cell type in single-cell chromatin accessibility data via open-set domain adaptation
HNCGAT: a method for predicting plant metabolite-protein interaction using heterogeneous neighbor contrastive graph attention network
Gepasi 3.0
High-dimensional variable selection for ordinal outcomes with error control
P dif -mediated antibiotic resistance genes transfer in bacteria identified by pdifFinder
ProTICS reveals prognostic impact of tumor infiltrating immune cells in different molecular subtypes
A QTL model to map the common genetic basis for correlative phenotypic plasticity
High-dimensional generalized median adaptive lasso with application to omics data
OpenHelix: bioinformatics education outside of a different box
miProBERT: identification of microRNA promoters based on the pre-trained model BERT
Do deep learning models make a difference in the identification of antimicrobial peptides?
Critical assessment and performance improvement of plant-pathogen protein-protein interaction prediction methods
An overview of diffusion models for intracellular dynamics analysis
In silico signaling modeling to understand cancer pathways and treatment responses
Software applications toward quantitative metabolic flux analysis and modeling
Binding site matching in rational drug design: algorithms and applications
VBayesMM: variational Bayesian neural network to prioritize important relationships of high-dimensional microbiome multiomics data
Identifying the critical states of complex diseases by the dynamic change of multivariate distribution
AIMMS suite: a web server dedicated for prediction of drug resistance on protein mutation
Environmental bio-monitoring with high-throughput sequencing
Multimodal analysis of gene expression from postmortem brains and blood identifies synaptic vesicle trafficking genes to be associated with Parkinson's disease
A comparative review of short genetic variant databases across humans and animal species
Protein phosphorylation database and prediction tools
Partial order relation-based gene ontology embedding improves protein function prediction
On the dynamical incompleteness of the Protein Data Bank
Surveying and benchmarking techniques to analyse DNA gel fingerprint images