yusuke1997/dblp-id-title huggingface dataset:
scGMAAE: Gaussian mixture adversarial autoencoders for diversification analysis of scRNA-seq data
Gene set enrichment analysis: performance evaluation and usage guidelines
MetaGeno: a chromosome-wise multi-task genomic framework for ischaemic stroke risk prediction
Reconciling multiple connectivity-based systems biology methods for drug repurposing
binny : an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets
SELF-Former: multi-scale gene filtration transformer for single-cell spatial reconstruction
Bridging semantics and syntax with graph algorithms - state-of-the-art of extracting biomedical relations
Functional annotation of proteomic sequences based on consensus of sequence and structural analysis
Fuzzy Petri nets for modelling of uncertain biological systems
Embracing an integromic approach to tissue biomarker research in cancer: Perspectives and lessons learned
A comprehensive analysis of the IEDB MHC class-I automated benchmark
Regulatory variants: from detection to predicting impact
Unraveling viral drug targets: a deep learning-based approach for the identification of potential binding sites
DECA: harnessing interpretable transformer model for cellular deconvolution of chromatin accessibility profile
Strand Orientation Bias Detector to determine the probability of FFPE sequencing artifacts
A hybrid demultiplexing strategy that improves performance and robustness of cell hashing
PSnoD: identifying potential snoRNA-disease associations based on bounded nuclear norm regularization
A large-scale assessment of sequence database search tools for homology-based protein function prediction
Phylogenetic-evolutionary Approaches to Bioinformatics
Do protein language models learn phylogeny?
Methods for Pattern Discovery in Unaligned Biological Sequences
Adjustment of scRNA-seq data to improve cell-type decomposition of spatial transcriptomics
Optimizing drug development in oncology by clinical trial simulation: Why and how?
A parameter-free deep embedded clustering method for single-cell RNA-seq data
Computational model for ncRNA research
Multi-modality artificial intelligence in digital pathology
Prediction of biomarker-disease associations based on graph attention network and text representation
A new approach to decode DNA methylome and genomic variants simultaneously from double strand bisulfite sequencing
Seeing the wood for the trees: a forest of methods for optimization and omic-network integration in metabolic modelling
epitope3D: a machine learning method for conformational B-cell epitope prediction
Utilizing graph machine learning within drug discovery and development
IgIDivA: immunoglobulin intraclonal diversification analysis
A comprehensive review and benchmark of differential analysis tools for Hi-C data
Epigenetically regulated gene expression profiles reveal four molecular subtypes with prognostic and therapeutic implications in colorectal cancer
Choosing appropriate models for protein-protein interaction networks: a comparison study
GADIFF: a transferable graph attention diffusion model for generating molecular conformations
Evaluating hierarchical machine learning approaches to classify biological databases
DGHNE: network enhancement-based method in identifying disease-causing genes through a heterogeneous biomedical network
The improved de Bruijn graph for multitask learning: predicting functions, subcellular localization, and interactions of noncoding RNAs
A roadmap of clustering algorithms: finding a match for a biomedical application
ReCIDE: robust estimation of cell type proportions by integrating single-reference-based deconvolutions
GOPhage: protein function annotation for bacteriophages by integrating the genomic context
NetCoMi: network construction and comparison for microbiome data in R
MicroRNAs and their variants in an RNA world: implications for complex interactions and diverse roles in an RNA regulatory network
Wrapping and Interoperating Bioinformatics Resources Using CORBA
CRISPR-DIPOFF: an interpretable deep learning approach for CRISPR Cas-9 off-target prediction
EGFI: drug-drug interaction extraction and generation with fusion of enriched entity and sentence information
Co-mutation modules capture the evolution and transmission patterns of SARS-CoV-2
Meta-Prism: Ultra-fast and highly accurate microbial community structure search utilizing dual indexing and parallel computation
Experimental design and data analysis of Ago-RIP-Seq experiments for the identification of microRNA targets
Versatile interactions and bioinformatics analysis of noncoding RNAs
Guidelines for reproducible analysis of adaptive immune receptor repertoire sequencing data
Consensus statement on the credibility assessment of machine learning predictors
A technical review of multi-omics data integration methods: from classical statistical to deep generative approaches
scMMAE: masked cross-attention network for single-cell multimodal omics fusion to enhance unimodal omics
scGGAN: single-cell RNA-seq imputation by graph-based generative adversarial network
The accurate prediction and characterization of cancerlectin by a combined machine learning and GO analysis
De novo generation of dual-target ligands using adversarial training and reinforcement learning
Are all of the human exons alternatively spliced?
Sample-specific perturbation of gene interactions identifies breast cancer subtypes
PhosPiR: an automated phosphoproteomic pipeline in R
Erratum to: Machine learning-based analysis of multi-omics data on the cloud for investigating gene regulations
Visualising Gene Expression in Its Metabolic Context
Identification of species-specific RNA N6-methyladinosine modification sites from RNA sequences
Multi-modal optimization to identify personalized biomarkers for disease prediction of individual patients with cancer
Genome-resolved metagenomics using environmental and clinical samples
Accurately identifying nucleic-acid-binding sites through geometric graph learning on language model predicted structures
Robust knowledge-guided biclustering for multi-omics data
Integrating CORUM and co-fractionation mass spectrometry to create enhanced benchmarks for protein complex predictions
Bioinformatics in Germany: toward a national-level infrastructure
A proteogenomic approach to understand splice isoform functions through sequence and expression-based computational modeling
Dynamics of transcriptional and post-transcriptional regulation
Web-based drug repurposing tools: a survey
Modeling and analyzing single-cell multimodal data with deep parametric inference
Accurate multistage prediction of protein crystallization propensity using deep-cascade forest with sequence-based features
m 6 Aexpress-BHM : predicting m6A regulation of gene expression in multiple-groups context by a Bayesian hierarchical mixture model
Adaptive multi-source multi-view latent feature learning for inferring potential disease-associated miRNAs
MutateX: an automated pipeline for in silico saturation mutagenesis of protein structures and structural ensembles
HiC4D-SPOT: a spatiotemporal outlier detection tool for Hi-C data
A deep learning method for repurposing antiviral drugs against new viruses via multi-view nonnegative matrix factorization and its application to SARS-CoV-2
Data integration for plant genomics - exemplars from the integration of Arabidopsis thaliana databases
A global initiative on addressing bioinformatics' grand challenges
StereoMM: a graph fusion model for integrating spatial transcriptomic data and pathological images
The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability
Systematic review of computational methods for identifying miRNA-mediated RNA-RNA crosstalk
High-throughput single-cell RNA-seq data imputation and characterization with surrogate-assisted automated deep learning
S2Snet: deep learning for low molecular weight RNA identification with nanopore
Correction to: Toward molecular diagnosis of major depressive disorder by plasma peptides using a deep learning approach
Cancer Target Gene Screening: a web application for breast cancer target gene screening using multi-omics data analysis
An evaluation of noncoding genome annotation tools through enrichment analysis of 15 genome-wide association studies
Identifying miRNAs, targets and functions
Integrated hybrid de novo assembly technologies to obtain high-quality pig genome using short and long reads
Computational methods for identifying miRNA sponge interactions
Toward microRNA-mediated gene regulatory networks in plants
CAP-RNAseq: an integrated pipeline for functional annotation and prioritization of co-expression clusters
tcrBLOSUM: an amino acid substitution matrix for sensitive alignment of distant epitope-specific TCRs
scRGCL: a cell type annotation method for single-cell RNA-seq data using residual graph convolutional neural network with contrastive learning
Similarity-based machine learning methods for predicting drug-target interactions: a brief review
ScInfeR: an efficient method for annotating cell types and sub-types in single-cell RNA-seq, ATAC-seq, and spatial omics
A gentle introduction to pangenomics
Visualizing and comparing results of different peptide identification methods
A comprehensive review of computational prediction of genome-wide features
MLSNet: a deep learning model for predicting transcription factor binding sites
MCCS, a novel characterization method for protein-ligand complex
sc-REnF: An entropy guided robust feature selection for single-cell RNA-seq data
ATAC-pipe: general analysis of genome-wide chromatin accessibility
Integrating multi-network topology for gene function prediction using deep neural networks
Sequence-based prediction of pH-dependent protein solubility using CamSol
Dual-channel hypergraph convolutional network for predicting herb-disease associations
Optimization of cell lines as tumour models by integrating multi-omics data
Complementary multi-modality molecular self-supervised learning via non-overlapping masking for property prediction
Pfam 10 years on: 10 000 families and still growing
SC-VAR: a computational tool for interpreting polygenic disease risks using single-cell epigenomic data
Bioinformatics, Genomics, and Proteomics: Getting the Big Picture (Biotechnology in the 21st Century): Ann Finney Batiza
miWords: transformer-based composite deep learning for highly accurate discovery of pre-miRNA regions across plant genomes
PREDAC-CNN: predicting antigenic clusters of seasonal influenza A viruses with convolutional neural network
Ensemble learning methods and heterogeneous graph network fusion: building drug-gene-disease triple association prediction models
Identifying pleiotropic genes for complex phenotypes with summary statistics from a perspective of composite null hypothesis testing
Propagation, detection and correction of errors using the sequence database network
Large-scale information retrieval and correction of noisy pharmacogenomic datasets through residual thresholded deep matrix factorization
A comparative benchmarking and evaluation framework for heterogeneous network-based drug repositioning methods
Editorial: The informatics of post-translational modification and its implications for systems biology
Consensus-based clustering of single cells by reconstructing cell-to-cell dissimilarity
HTINet2: herb-target prediction via knowledge graph embedding and residual-like graph neural network
MITGARD: an automated pipeline for mitochondrial genome assembly in eukaryotic species using RNA-seq data
PLSDA-batch: a multivariate framework to correct for batch effects in microbiome data
Deep forest ensemble learning for classification of alignments of non-coding RNA sequences based on multi-view structure representations
A machine learning-based method to optimize the immunogenicity of human leukocyte antigen class I-restricted neoantigens
BiTSC 2: Bayesian inference of tumor clonal tree by joint analysis of single-cell SNV and CNA data
Multi-view learning framework for predicting unknown types of cancer markers via directed graph neural networks fitting regulatory networks
Computational modelling folate metabolism and DNA methylation: implications for understanding health and ageing
A gentle introduction to understanding preclinical data for cancer pharmaco-omic modeling
IndGOterm: a qualitative method for the identification of individually dysregulated GO terms in cancer
Energy entropy vector: a novel approach for efficient microbial genomic sequence analysis and classification
Graph-pMHC: graph neural network approach to MHC class II peptide presentation and antibody immunogenicity
MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment
Ori-Finder 3: a web server for genome-wide prediction of replication origins in Saccharomyces cerevisiae
Deciphering lineage-relevant gene regulatory networks during endoderm formation by InPheRNo-ChIP
Adversarial regularized autoencoder graph neural network for microbe-disease associations prediction
A survey on deep learning in DNA/RNA motif mining
Translational bioinformatics in mental health: open access data sources and computational biomarker discovery
Selecting gene features for unsupervised analysis of single-cell gene expression data
KDGene: knowledge graph completion for disease gene prediction using interactional tensor decomposition
GAABind: a geometry-aware attention-based network for accurate protein-ligand binding pose and binding affinity prediction
Bioinformatics tools for the identification of gene clusters that biosynthesize specialized metabolites
PCAO2: an ontology for integration of prostate cancer associated genotypic, phenotypic and lifestyle data
Resolving the problem of multiple accessions of the same transcript deposited across various public databases
Disease category-specific annotation of variants using an ensemble learning framework
Identification and function annotation of long intervening noncoding RNAs
HBV-infected hepatocellular carcinoma can be robustly classified into three clinically relevant subgroups by a novel analytical protocol
UNMF: a unified nonnegative matrix factorization for multi-dimensional omics data
Reconstruction of gene regulatory networks for Caenorhabditis elegans using tree-shaped gene expression data
A survey of experimental and computational identification of small proteins
Immune cell infiltration-based signature for prognosis and immunogenomic analysis in breast cancer
Approaching the holistic transcriptome - convolution and deconvolution in transcriptomics
Bridging-BPs: a novel approach to predict potential drug-target interactions based on a bridging heterogeneous graph and BPs2vec
Introduction into the analysis of high-throughput-sequencing based epigenome data
Comethyl: a network-based methylome approach to investigate the multivariate nature of health and disease
sciCNV: high-throughput paired profiling of transcriptomes and DNA copy number variations at single-cell resolution
ARIC: accurate and robust inference of cell type proportions from bulk gene expression or DNA methylation data
Identification of drug-target interactions via multiple kernel-based triple collaborative matrix factorization
Machine learning meets genome assembly
MolAICal: a soft tool for 3D drug design of protein targets by artificial intelligence and classical algorithm
ChIP-GPT: a managed large language model for robust data extraction from biomedical database records
DeepDRK: a deep learning framework for drug repurposing through kernel-based multi-omics integration
Moby and Moby 2: Creatures of the Deep (Web)
cSurvival: a web resource for biomarker interactions in cancer outcomes and in cell lines
Drug-drug interaction prediction: databases, web servers and computational models
Reconstruction of human protein-coding gene functional association network based on machine learning
CARTAR: a comprehensive web tool for identifying potential targets in chimeric antigen receptor therapies using TCGA and GTEx data
Significantly enhancing human antibody affinity via deep learning and computational biology-guided single-point mutations
Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction
Kinase impact assessment in the landscape of fusion genes that retain kinase domains: a pan-cancer study
Molecular persistent spectral image (Mol-PSI) representation for machine learning models in drug design
SpaDiT: diffusion transformer for spatial gene expression prediction using scRNA-seq
Heterogeneous biomedical entity representation learning for gene-disease association prediction
Model ensembling as a tool to form interpretable multi-omic predictors of cancer pharmacosensitivity
CWAS-Plus: estimating category-wide association of rare noncoding variation from whole-genome sequencing data with cell-type-specific functional data
McAN: a novel computational algorithm and platform for constructing and visualizing haplotype networks
Comprehensive single-cell RNA-seq analysis using deep interpretable generative modeling guided by biological hierarchy knowledge
Advances in the Exon-Intron Database (EID)
Prototype-based contrastive substructure identification for molecular property prediction
BACT: nonparametric Bayesian cell typing for single-cell spatial transcriptomics data
Network-based integrative analysis of single-cell transcriptomic and epigenomic data for cell types
miRNA-miRNA crosstalk: from genomics to phenomics
Effect of lossy compression of quality scores on variant calling
Correction to: JCcirc: circRNA full-length sequence assembly through integrated junction contigs
BLAST output visualization in the new sequencing era
Novel in silico tools for designing peptide-based subunit vaccines and immunotherapeutics
Advancing edge-based clustering and graph embedding for biological network analysis: a case study in RASopathies
WheatGP, a genomic prediction method based on CNN and LSTM
STEEL enables high-resolution delineation of spatiotemporal transcriptomic data
HLAB: learning the BiLSTM features from the ProtBert-encoded proteins for the class I HLA-peptide binding prediction
An evolution-based machine learning to identify cancer type-specific driver mutations
Deep learning in GPCR drug discovery: benchmarking the path to accurate peptide binding
The impact of taxon sampling on phylogenetic inference: a review of two decades of controversy
HiFun: homology independent protein function prediction by a novel protein-language self-attention model
A case-control design for testing and estimating epigenetic effects on complex diseases
FunlncModel: integrating multi-omic features from upstream and downstream regulatory networks into a machine learning framework to identify functional lncRNAs
Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity
Generalized reporter score-based enrichment analysis for omics data
The CUT&RUN greenlist: genomic regions of consistent noise are effective normalizing factors for quantitative epigenome mapping
PHAST, PHASTER and PHASTEST: Tools for finding prophage in bacterial genomes
Unsupervised construction of gene regulatory network based on single-cell multi-omics data of colorectal cancer
Protein design via deep learning
AFSE: towards improving model generalization of deep graph learning of ligand bioactivities targeting GPCR proteins
oncoPredict: an R package for predicting in vivo or cancer patient drug response and biomarkers from cell line screening data
A novel two-sample Mendelian randomization framework integrating common and rare variants: application to assess the effect of HDL-C on preeclampsia risk
Botanical drugs: a new strategy for structure-based target prediction
Computational identification of eukaryotic promoters based on cascaded deep capsule neural networks
scEWE: high-order element-wise weighted ensemble clustering for heterogeneity analysis of single-cell RNA-sequencing data
A novel deep machine learning algorithm with dimensionality and size reduction approaches for feature elimination: thyroid cancer diagnoses with randomly missing data
A computational platform to identify origins of replication sites in eukaryotes
LncTar: a tool for predicting the RNA targets of long noncoding RNAs
An algorithmic perspective on deciphering cell-cell interactions with spatial omics data
Decoding the role of long noncoding RNAs in the healthy aging of centenarians
SPDesign: protein sequence designer based on structural sequence profile using ultrafast shape recognition
Validation in Genetic Association Studies
Performance assessment of computational tools to detect microsatellite instability
Multi-omics integration - a comparison of unsupervised clustering methodologies
Dimensionality and Dependence Problems in Statistical Genomics
Comprehensive assessment of machine learning-based methods for predicting antimicrobial peptides
A multi-omics study of brain tissue transcription and DNA methylation revealing the genetic pathogenesis of ADHD
Application of individualized differential expression analysis in human cancer proteome
MetaFS: Performance assessment of biomarker discovery in metaproteomics
iDOMO: identification of drug combinations via multi-set operations for treating diseases
Deep learning for healthcare: review, opportunities and challenges
Machine learning approaches for the discovery of gene-gene interactions in disease data
Mechanistic study of acupuncture on the pterygopalatine ganglion to improve allergic rhinitis: analysis of multi-target effects based on bioinformatics/network topology strategie
gmRAD: an integrated SNP calling pipeline for genetic mapping with RADseq across a hybrid population
Molecular portraits: the evolution of the concept of transcriptome-based cancer signatures
RGCN-BA: relational graph convolutional network with batch awareness for single-cell RNA sequencing clustering
Correction to: Diagnostic Prediction of portal vein thrombosis in chronic cirrhosis patients using data-driven precision medicine model
Protein Structure Prediction Methods for Drug Design
Single-cell transcriptome-based multilayer network biomarker for predicting prognosis and therapeutic response of gliomas
A practical guide to mechanistic systems modeling in biology using a logic-based approach
ProtCHOIR: a tool for proteome-scale generation of homo-oligomers
Supervised, semi-supervised and unsupervised inference of gene regulatory networks
Toward more accurate prediction of caspase cleavage sites: a comprehensive review of current methods, tools and features
VirusHound-I: prediction of viral proteins involved in the evasion of host adaptive immune response using the random forest algorithm and generative adversarial network for data augmentation
A statistical model for QTL mapping in polysomic autotetraploids underlying double reduction
VIGA: a one-stop tool for eukaryotic virus identification and genome assembly from next-generation-sequencing data
Combined experimental and computational approaches to study the regulatory elements in eukaryotic genes
RNAi as a bioinformatics consumer
Fast and accurate protein intrinsic disorder prediction by using a pretrained language model
De novo assembly of short sequence reads
Replicability in cancer omics data analysis: measures and empirical explorations
Genomic language models (gLMs) decode bacterial genomes for improved gene prediction and translation initiation site identification
Biomolecular Interaction Network Database
A systematic evaluation of computational methods for cell segmentation
Comparison of long- and short-read metagenomic assembly for low-abundance species and resistance genes
Zisland Explorer: detect genomic islands by combining homogeneity and heterogeneity properties
EDS-Kcr: deep supervision based on large language model for identifying protein lysine crotonylation sites across multiple species
Discovering predisposing genes for hereditary breast cancer using deep learning
Recent advances in network-based methods for disease gene prediction
A snapshot of 3649 Web-based services published between 1994 and 2017 shows a decrease in availability after 2 years
ADeditome provides the genomic landscape of A-to-I RNA editing in Alzheimer's disease
GSTRPCA: irregular tensor singular value decomposition for single-cell multi-omics data clustering