yusuke1997/dblp-id-title huggingface dataset:
LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on variant call format files
Inferring gene regulatory networks from single-cell gene expression data via deep multi-view contrastive learning
Inter-view contrastive learning and miRNA fusion for lncRNA-protein interaction prediction in heterogeneous graphs
Reinforcement learning-driven exploration of peptide space: accelerating generation of drug-like peptides
Topological ranks reveal functional knowledge encoded in biological networks: a comparative analysis
In-silico discovery of type-2 diabetes-causing host key genes that are associated with the complexity of monkeypox and repurposing common drugs
MiRACLe: an individual-specific approach to improve microRNA-target prediction based on a random contact model
MARPPI: boosting prediction of protein-protein interactions with multi-scale architecture residual network
Deep latent space fusion for adaptive representation of heterogeneous multi-omics data
A knowledge-driven network for fine-grained relationship detection between miRNA and disease
Erratum to: Comprehensive benchmarking of software for mapping whole genome bisulfite data: from read alignment to DNA methylation analysis
Tumor immune microenvironment lncRNAs
Mathematics and evolutionary biology make bioinformatics education comprehensible
The Untranslated Regions of Eukaryotic MRNAs: Structure, Function, Evolution and Bioinformatic Tools for Their Analysis
Gene regulatory network integration with multi-omics data enhances survival predictions in cancer
BioMedR: an R/CRAN package for integrated data analysis pipeline in biomedical study
A comparative benchmark of classic DNA motif discovery tools on synthetic data
Quantum annealing-based clustering of single cell RNA-seq data
Deepro-Glu: combination of convolutional neural network and Bi-LSTM models using ProtBert and handcrafted features to identify lysine glutarylation sites
Detecting tipping points of complex diseases by network information entropy
Analysis of long noncoding RNAs highlights region-specific altered expression patterns and diagnostic roles in Alzheimer's disease
Fast and accurate protein function prediction from sequence through pretrained language model and homology-based label diffusion
Alpha shape and Delaunay triangulation in studies of protein-related interactions
Explainability in transformer models for functional genomics
Recognition of cyanobacteria promoters via Siamese network-based contrastive learning under novel non-promoter generation
Data-driven patient stratification of UK Biobank cohort suggests five endotypes of multimorbidity
AUPRC: a metric for evaluating the performance of in-silico perturbation methods in identifying differentially expressed genes
SIGNET: single-cell RNA-seq-based gene regulatory network prediction using multiple-layer perceptron bagging
NMCMDA: neural multicategory MiRNA-disease association prediction
Bioinformatics for personal genome interpretation
R3Design: deep tertiary structure-based RNA sequence design and beyond
In silico drug repositioning based on drug-miRNA associations
Microbial genome analysis: the COG approach
FEED: a feature selection method based on gene expression decomposition for single cell clustering
Mutational analysis in RNAs: comparing programs for RNA deleterious mutation prediction
Literature-aided interpretation of gene expression data with the weighted global test
Deep learning-based identification of genetic variants: application to Alzheimer's disease classification
Statistical challenges in longitudinal microbiome data analysis
Deeply integrating latent consistent representations in high-noise multi-omics data for cancer subtyping
PPIxGPN: plasma proteomic profiling of neurodegenerative biomarkers with protein-protein interaction-based eXplainable graph propagational network
FungiExpresZ: an intuitive package for fungal gene expression data analysis, visualization and discovery
A primer to frequent itemset mining for bioinformatics
ChIP-AP: an integrated analysis pipeline for unbiased ChIP-seq analysis
Modern bioinformatics meets traditional Chinese medicine
Transfer learning for clustering single-cell RNA-seq data crossing-species and batch, case on uterine fibroids
Bioinformatics Training in the USA
PTMdyna: exploring the influence of post-translation modifications on protein conformational dynamics
Privacy preserving validation for multiomic prediction models
A survey on annotation tools for the biomedical literature
Genome-wide identification and analysis of the eQTL lncRNAs in multiple sclerosis based on RNA-seq data
TriCLFF: a multi-modal feature fusion framework using contrastive learning for spatial domain identification
ILGBMSH: an interpretable classification model for the shRNA target prediction with ensemble learning algorithm
Analysis of sex-biased gene expression in a Eurasian admixed population
MMFGRN: a multi-source multi-model fusion method for gene regulatory network reconstruction
Comparative analysis of algorithms for whole-genome assembly of pyrosequencing data
FLAN: feature-wise latent additive neural models for biological applications
Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis
JSNMF enables effective and accurate integrative analysis of single-cell multiomics data
A comprehensive assessment of cell type-specific differential expression methods in bulk data
Developing a 'personalome' for precision medicine: emerging methods that compute interpretable effect sizes from single-subject transcriptomes
KGETCDA: an efficient representation learning framework based on knowledge graph encoder from transformer for predicting circRNA-disease associations
GAADE: identification spatially variable genes based on adaptive graph attention network
A comparison of deterministic and stochastic approaches for sensitivity analysis in computational systems biology
Elucidating the editome: bioinformatics approaches for RNA editing detection
AFToolkit: a framework for molecular modeling of proteins with AlphaFold-derived representations
Molecular Biology Information Service: an innovative medical library-based bioinformatics support service for biomedical researchers
Biodiversity informatics: organizing and linking information across the spectrum of life
Multi-omics data integration and network-based analysis drives a multiplex drug repurposing approach to a shortlist of candidate drugs against COVID-19
Quantitative model suggests both intrinsic and contextual features contribute to the transcript coding ability determination in cells
Resources for integrative systems biology: from data through databases to networks and dynamic system models
TCR clustering by contrastive learning on antigen specificity
Early cancer detection via multi-omics cfDNA fragmentation using early-late fusion neural network with sample-modality evaluation
Mathematical models of cell cycle regulation
iEssLnc: quantitative estimation of lncRNA gene essentialities with meta-path-guided random walks on the lncRNA-protein interaction network
BERT6mA: prediction of DNA N6-methyladenine site using deep learning-based approaches
PredLLPS_PSSM: a novel predictor for liquid-liquid protein separation identification based on evolutionary information and a deep neural network
scDEA: differential expression analysis in single-cell RNA-sequencing data via ensemble learning
An open-pollinated design for mapping imprinting genes in natural populations
SAResNet: self-attention residual network for predicting DNA-protein binding
Identification of molecular subtypes of dementia by using blood-proteins interaction-aware graph propagational network
iLoc-miRNA: extracellular/intracellular miRNA prediction using deep BiLSTM with attention mechanism
Deciphering gene contributions and etiologies of somatic mutational signatures of cancer
A benchmark study on current GWAS models in admixed populations
Improved drug-target interaction prediction with intermolecular graph transformer
hppRNA - a Snakemake-based handy parameter-free pipeline for RNA-Seq analysis of numerous samples
Benchmarking genome assembly methods on metagenomic sequencing data
Computational principles and practice for decoding immune contexture in the tumor microenvironment
A novel deep learning method for predictive modeling of microbiome data
Comparison of software packages for detecting unannotated translated small open reading frames by Ribo-seq
A systematic assessment of deep learning methods for drug response prediction: from in vitro to clinical applications
A survey on algorithms to characterize transcription factor binding sites
Multi-hierarchical profiling: an emerging and quantitative approach to characterizing diverse biological networks
Systematic bias of correlation coefficient may explain negative accuracy of genomic prediction
Enhancing clinical genomic accuracy with panelGC: a novel metric and tool for quantifying and monitoring GC biases in hybridization capture panel sequencing
Mutations in transmembrane proteins: diseases, evolutionary insights, prediction and comparison with globular proteins
Advances in multi-trait genomic prediction approaches: classification, comparative analysis, and perspectives
Genome-wide DNA methylation analysis identifies candidate epigenetic markers and drivers of hepatocellular carcinoma
PlasmidHunter: accurate and fast prediction of plasmid sequences using gene content profile and machine learning
New approaches for metagenome assembly with short reads
Drug sensitivity prediction from cell line-based pharmacogenomics data: guidelines for developing machine learning models
Studying protein-protein interaction through side-chain modeling method OPUS-Mut
A Comparison of Base-calling Algorithms for Illumina Sequencing Technology
A graph neural network approach for accurate prediction of pathogenicity in multi-type variants
RefTM: reference-guided topic modeling of single-cell chromatin accessibility data
Editorial: Annual progress in bioinformatics
Inferring cell-type-specific gene regulatory network from cellular transcriptomics data with GeneLink+
BloodNet: An attention-based deep network for accurate, efficient, and costless bloodstain time since deposition inference
A novel computational method for inferring competing endogenous interactions
AlloMap6: an R package for genetic linkage analysis in allohexaploids
Integrating AlphaFold and deep learning for atomistic interpretation of cryo-EM maps
Predicting enhancer-promoter interactions by deep learning and matching heuristic
Scaling up drug combination surface prediction
Prediction and identification of the effectors of heterotrimeric G proteins in rice (Oryza sativa L.)
Advancing microbial diagnostics: a universal phylogeny guided computational algorithm to find unique sequences for precise microorganism detection
The landscape of the methodology in drug repurposing using human genomic data: a systematic review
Improving comparative analyses of Hi-C data via contrastive self-supervised learning
TUnA: an uncertainty-aware transformer model for sequence-based protein-protein interaction prediction
Incorporating local ancestry information to predict genetically associated DNA methylation in admixed populations
Artificial intelligence and machine learning methods in predicting anti-cancer drug combination effects
MUSCLE: multi-view and multi-scale attentional feature fusion for microRNA-disease associations prediction
Genome-wide discovery of viral microRNAs based on phylogenetic analysis and structural evolution of various human papillomavirus subtypes
High-dimensional mediation analysis for longitudinal mediators and survival outcomes
mUSP: a high-accuracy map of the in situ crosstalk of ubiquitylation and SUMOylation proteome predicted via the feature enhancement approach
STNN-DDI: a Substructure-aware Tensor Neural Network to predict Drug-Drug Interactions
InstaDock: A single-click graphical user interface for molecular docking-based virtual high-throughput screening
PREDAC-FluB: predicting antigenic clusters of seasonal influenza B viruses with protein language model embedding based convolutional neural network
Gene set analysis methods: statistical models and methodological differences
Synthetic data sets for the identification of key ingredients for RNA-seq differential analysis
The BRaliBase dent - a tale of benchmark design and interpretation
How computer science can help in understanding the 3D genome architecture
Recent advances of automated methods for searching and extracting genomic variant information from biomedical literature
MutEx: a multifaceted gateway for exploring integrative pan-cancer genomic data
How do we share data in COVID-19 research? A systematic review of COVID-19 datasets in PubMed Central Articles
Computational approaches for circRNAs prediction and in silico characterization
Artificial intelligence-aided protein engineering: from topological data analysis to deep protein language models
A fast and globally optimal solution for RNA-seq quantification
2D molecular graphics: a flattened world of chemistry and biology
Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods
Correction to: Inflated false discovery rate due to volcano plots: problem and solutions
Quantum computing algorithms: getting closer to critical problems in computational biology
deepNEC: a novel alignment-free tool for the identification and classification of nitrogen biochemical network-related enzymes using deep learning
Vector NTI, a balanced all-in-one sequence analysis suite
A survey on computational methods in discovering protein inhibitors of SARS-CoV-2
Molecular networks for the study of TCM Pharmacology
Are dropout imputation methods for scRNA-seq effective for scATAC-seq data?
Interactive and coordinated visualization approaches for biological data analysis
Benchmarking multi-platform sequencing technologies for human genome assembly
Regression on imperfect class labels derived by unsupervised clustering
A comparative analysis of amino acid encoding schemes for the prediction of flexible length linear B-cell epitopes
Ultraliser: a framework for creating multiscale, high-fidelity and geometrically realistic 3D models for in silico neuroscience
Cancer-specific expression quantitative loci are affected by expression dysregulation
Advantages of mixing bioinformatics and visualization approaches for analyzing sRNA-mediated regulatory bacterial networks
ExonSkipAD provides the functional genomic landscape of exon skipping events in Alzheimer's disease
Clustering-based Approaches to Discovering and Visualising Microarray Data Patterns
Function determinants of TET proteins: the arrangements of sequence motifs with specific codes
Prioritizing prognostic-associated subpopulations and individualized recurrence risk signatures from single-cell transcriptomes of colorectal cancer
Drug repositioning based on the heterogeneous information fusion graph convolutional network
scDeconv : an R package to deconvolve bulk DNA methylation data with scRNA-seq data and paired bulk RNA-DNA methylation data
TargetCLP: clathrin proteins prediction combining transformed and evolutionary scale modeling-based multi-view features via weighted feature integration approach
LncFinder: an integrated platform for long non-coding RNA identification utilizing sequence intrinsic composition, structural information and physicochemical property
Filter and Wrapper Stacking Ensemble (FWSE): a robust approach for reliable biomarker discovery in high-dimensional omics data
Predicting miRNA-disease associations based on graph attention networks and dual Laplacian regularized least squares
Immuno-informatics analysis predicts B and T cell consensus epitopes for designing peptide vaccine against SARS-CoV-2 with 99.82% global population coverage
A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis
HighFold: accurately predicting structures of cyclic peptides and complexes with head-to-tail and disulfide bridge constraints
Comparative analysis and prediction of quorum-sensing peptides using feature representation learning and machine learning algorithms
Multiobjective optimization-driven primer design mechanism: towards user-specified parameters of PCR primer
RNA-binding protein recognition based on multi-view deep feature and multi-label learning
False discovery rate: the Achilles' heel of proteogenomics
PL-search: a profile-link-based search method for protein remote homology detection
iAMPCN: a deep-learning approach for identifying antimicrobial peptides and their functional activities
CytoPred: 7-gene pair metric for AML cytogenetic risk prediction
Identification and Functional Modelling of DNA Sequence Elements of Transcription
STCGAN: a novel cycle-consistent generative adversarial network for spatial transcriptomics cellular deconvolution
Review and comparative assessment of similarity-based methods for prediction of drug-protein interactions in the druggable human proteome
Challenges and opportunities of developing bioinformatics platforms in Africa: the case of BurkinaBioinfo at Joseph Ki-Zerbo University, Burkina Faso
PHAST and RPHAST: phylogenetic analysis with space/time models
MotifCNN-fold: protein fold recognition based on fold-specific features extracted by motif-based convolutional neural networks
pMHChat, characterizing the interactions between major histocompatibility complex class II molecules and peptides with large language models and deep hypergraph learning
Comprehensive bioinformatics and machine learning analyses for breast cancer staging using TCGA dataset
A multi-task prediction method based on neighborhood structure embedding and signed graph representation learning to infer the relationship between circRNA, miRNA, and cancer
siRNADiscovery: a graph neural network for siRNA efficacy prediction via deep RNA sequence analysis
Microarray is an efficient tool for circRNA profiling
Bioinformatics approaches and resources for single nucleotide polymorphism functional analysis
Two interactive Bioinformatics courses at the Bielefeld University Bioinformatics Server
Biological database design and implementation
PTBGRP: predicting phage-bacteria interactions with graph representation learning on microbial heterogeneous information network
PAGE-based transfer learning from single-cell to bulk sequencing enhances model generalization for sepsis diagnosis
ZetaDesign: an end-to-end deep learning method for protein sequence design and side-chain packing
Artificial intelligence in drug discovery: applications and techniques
Molecular subtyping of cancer: current status and moving toward clinical applications
Comparative Analysis of Regulatory Patterns in Bacterial Genomes
Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes
Editorial: Building successful biological databases
Multiview network embedding for drug-target Interactions prediction by consistent and complementary information preserving
RNAI-FRID: novel feature representation method with information enhancement and dimension reduction for RNA-RNA interaction
Characterization on the oncogenic effect of the missense mutations of p53 via machine learning
DeepHPV: a deep learning model to predict human papillomavirus integration sites
ReProMSig: an integrative platform for development and application of reproducible multivariable models for cancer prognosis supporting guideline-based transparent reporting
BiGATAE: a bipartite graph attention auto-encoder enhancing spatial domain identification from single-slice to multi-slices
A framework for predicting variable-length epitopes of human-adapted viruses using machine learning methods
Comparative analysis of methods for genome-wide nucleosome cartography
IEPAPI: a method for immune epitope prediction by incorporating antigen presentation and immunogenicity
Decoding brain memory formation by single-cell RNA sequencing
Identification of significant gene expression changes in multiple perturbation experiments using knockoffs
Exploring pharmacological active ingredients of traditional Chinese medicine by pharmacotranscriptomic map in ITCM
CosGeneGate selects multi-functional and credible biomarkers for single-cell analysis
A bioimage informatics platform for high-throughput embryo phenotyping
An interpretable single-cell RNA sequencing data clustering method based on latent Dirichlet allocation
An enhanced cascade-based deep forest model for drug combination prediction
Automated glycopeptide analysis - review of current state and future directions
Multiphysical graph neural network (MP-GNN) for COVID-19 drug design
Large-scale Production of Mouse Phenotypes: the Search for Animal Models for Inherited M. Diseases in Humans
EGPDI: identifying protein-DNA binding sites based on multi-view graph embedding fusion
DeepImmuno: deep learning-empowered prediction and generation of immunogenic peptides for T-cell immunity
A fast and powerful linear mixed model approach for genotype-environment interaction tests in large-scale GWAS
BEERS2: RNA-Seq simulation through high fidelity in silico modeling
Advances in metaheuristics for gene selection and classification of microarray data
The GTPB training programme in Portugal
VIPPID: a gene-specific single nucleotide variant pathogenicity prediction tool for primary immunodeficiency diseases
Handbook of Bioinspired Algorithms and Applications: Edited by Stephan Olariu and Albert Y
Implementing the FAIR Data Principles in precision oncology: review of supporting initiatives
MPA-MutPred: a novel strategy for accurately predicting the binding affinity change upon mutation in membrane protein complexes
Data-balanced transformer for accelerated ionizable lipid nanoparticles screening in mRNA delivery
Current Progress in Bioinformatics 2016
Handcrafted versus non-handcrafted (self-supervised) features for the classification of antimicrobial peptides: complementary or redundant?
GAERF: predicting lncRNA-disease associations by graph auto-encoder and random forest
Comparison of methods for estimating genetic correlation between complex traits using GWAS summary statistics
A novel prognostic framework for HBV-infected hepatocellular carcinoma: insights from ferroptosis and iron metabolism proteomics
Disrupted microbial cross-feeding and altered L-phenylalanine consumption in people living with HIV
Deep drug-target binding affinity prediction with multiple attention blocks
Correction to: STCGAN: a novel cycle-consistent generative adversarial network for spatial transcriptomics cellular deconvolution
ExsgRNA: reduce off-target efficiency by on-target mismatched sgRNA
Getting Started with Acedb
Reconciling multiple connectivity scores for drug repurposing
A novel Bayesian hierarchical model for detecting differential circadian pattern in transcriptomic applications
NABP-BERT: NANOBODY®-antigen binding prediction based on bidirectional encoder representations from transformers (BERT) architecture
scPLAN: a hierarchical computational framework for single transcriptomics data annotation, integration and cell-type label refinement
Editorial: Second-generation sequencing
The role of drug profiles as similarity metrics: applications to repurposing, adverse effects detection and drug-drug interactions
DeepHeteroCDA: circRNA-drug sensitivity associations prediction via multi-scale heterogeneous network and graph attention mechanism
Data Analysis and Graphics Using R: An Example-Based Approach, Second Edition.: John Maindonald and John Braun
Comparative Genomics Tools Applied to Bioterrorism Defence
Comprehensive comparative analysis of methods and software for identifying viral integrations
A kinetic model for solving a combination optimization problem in ab-initio Cryo-EM 3D reconstruction
Detecting and overcoming systematic bias in high-throughput screening technologies: a comprehensive review of practical issues and methodological solutions
Evaluation of out-of-distribution detection methods for data shifts in single-cell transcriptomics
Likelihood-based feature representation learning combined with neighborhood information for predicting circRNA-miRNA associations