yusuke1997/dblp-id-title huggingface dataset:
TransAC4C - a novel interpretable architecture for multi-species identification of N4-acetylcytidine sites in RNA with single-base resolution
Online-adjusted evolutionary biclustering algorithm to identify significant modules in gene expression data
A bioinformatician's guide to the forefront of suffix array construction algorithms
HMPA: a pioneering framework for the noncanonical peptidome from discovery to functional insights
mmGEBLUP: an advanced genomic prediction scheme for genetic improvement of complex traits in crops through integrative analysis of major genes, polygenes, and genotype-environment interactions
Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly
BrowseVCF: a web-based application and workflow to quickly prioritize disease-causative variants in VCF files
Spatial molecular profiling: platforms, applications and analysis tools
Integrative biomarker detection on high-dimensional gene expression data sets: a survey on prior knowledge approaches
Sensitive, reliable and robust circRNA detection from RNA-seq with CirComPara2
Large-scale predicting protein functions through heterogeneous feature fusion
Development of innovative multi-epitope mRNA vaccine against Pseudomonas aeruginosa using in silico approaches
C-C Chemokine receptor-like 2 (CCRL2) acts as coreceptor for human immunodeficiency virus-2
Deep learning-based real-time detection of novel pathogens during sequencing
Toward accurate diagnosis and surveillance of bacterial infections using enhanced strain-level metagenomic next-generation sequencing of infected body fluids
Comprehensive assessment of protein loop modeling programs on large-scale datasets: prediction accuracy and efficiency
Enriching contextualized language model from knowledge graph for biomedical information extraction
CATAD: exploring topologically associating domains from an insight of core-attachment structure
Simulation of DNA sequence evolution under models of recent directional selection
MPCLCDA: predicting circRNA-disease associations by using automatically selected meta-path and contrastive learning
A comprehensive benchmark study of methods for identifying significantly perturbed subnetworks in cancer
A review of bioinformatics education in Germany
Effective multi-modal clustering method via skip aggregation network for parallel scRNA-seq and scATAC-seq data
Chromosome structure modeling tools and their evaluation in bacteria
Benchmark of filter methods for feature selection in high-dimensional gene expression survival data
Metapath-aggregated heterogeneous graph neural network for drug-target interaction prediction
Correcting Illumina data
Prediction of RBP binding sites on circRNAs using an LSTM-based deep sequence learning architecture
Advancing genome-based precision medicine: a review on machine learning applications for rare genetic disorders
HiConfidence: a novel approach uncovering the biological signal in Hi-C data affected by technical biases
Analysis of Emerging Variants of Turkey Reovirus using Machine Learning
Community challenges in biomedical text mining over 10 years: success, failure and the future
FINDSITE: a combined evolution/structure-based approach to protein function prediction
DEWNA: dynamic entropy weight network analysis and its application to the DNA-binding proteome in A549 cells with cisplatin-induced damage
Deep learning for mining protein data
deepHPI: a comprehensive deep learning platform for accurate prediction and visualization of host-pathogen protein-protein interactions
Protein-protein interaction and site prediction using transfer learning
Missing value imputation for gene expression data: computational techniques to recover missing data from available information
Dimension reduction techniques for the integrative analysis of multi-omics data
STAVER: a standardized benchmark dataset-based algorithm for effective variation reduction in large-scale DIA-MS data
An automatic immunofluorescence pattern classification framework for HEp-2 image based on supervised learning
Integrating specific and common topologies of heterogeneous graphs and pairwise attributes for drug-related side effect prediction
Potential inhibitors for the novel coronavirus (SARS-CoV-2)
Highly accurate classification and discovery of microbial protein-coding gene functions using FunGeneTyper: an extensible deep learning framework
Structured sparsity regularization for analyzing high-dimensional omics data
Computational analysis and prediction of lysine malonylation sites by exploiting informative features in an integrative machine-learning framework
Explorer: efficient DNA coding by De Bruijn graph toward arbitrary local and global biochemical constraints
Automated protein function prediction - the genomic challenge
Disease classification: from phenotypic similarity to integrative genomics and beyond
stAA: adversarial graph autoencoder for spatial clustering task of spatially resolved transcriptomics
Machine learning-augmented m6A-Seq analysis without a reference genome
MicroRNAs and complex diseases: from experimental results to computational models
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
TLimmuno2: predicting MHC class II antigen immunogenicity through transfer learning
Benchmarking of viral haplotype reconstruction programmes: an overview of the capacities and limitations of currently available programmes
MST2-RASSF protein-protein interactions through SARAH domains
SGPPI: structure-aware prediction of protein-protein interactions in rigorous conditions with graph convolutional network
Analyzing master regulators and scRNA-seq of COVID-19 patients reveals an underlying anti-SARS-CoV-2 mechanism of ZNF proteins
Reference databases for taxonomic assignment in metagenomics
Cox-Sage: enhancing Cox proportional hazards model with interpretable graph neural networks for cancer prognosis
Predicting RNA polymerase II transcriptional elongation pausing and associated histone code
DITHER: an algorithm for Defining IntraTumor Heterogeneity based on EntRopy
Accurate identification of bacteriophages from metagenomic data using Transformer
ACE configurator for ELISpot: optimizing combinatorial design of pooled ELISpot assays with an epitope similarity model
Grain protein function prediction based on self-attention mechanism and bidirectional LSTM
Interdisciplinary approach towards a systems medicine toolbox using the example of inflammatory diseases
How trees allocate carbon for optimal growth: insight from a game-theoretic model
A feature-based approach to predict hot spots in protein-DNA binding interfaces
iBT-Net: an incremental broad transformer network for cancer drug response prediction
Different molecular enumeration influences in deep learning: an example using aqueous solubility
A systematic evaluation of Hi-C data enhancement methods for enhancing PLAC-seq and HiChIP data
Rag2Mol: structure-based drug design based on retrieval augmented generation
Identification of potential driver mutations in glioblastoma using machine learning
Incorporating network diffusion and peak location information for better single-cell ATAC-seq data analysis
Tools for time-course simulation in systems biology: a brief overview
A literature mining-based approach for identification of cellular pathways associated with chemoresistance in cancer
Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning
Multimodal deep learning for biomedical data fusion: a review
Correction to: HHOMR: a hybrid high-order moment residual model for miRNA-disease association prediction
Methodologies and experimental platforms for generating and analysing microarray and mass spectrometry-based omics data to support P4 medicine
From miRNA regulation to miRNA-TF co-regulation: computational approaches and challenges
Ensembles of knowledge graph embedding models improve predictions for drug discovery
Functional mapping of seasonal transition in perennial plants
RPSubAlign: a novel sequence-based molecular representation method for retrosynthesis prediction with improved validity and robustness
The many faces of sequence alignment
Corrigendum to: Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity
Clair3-trio: high-performance Nanopore long-read variant calling in family trios with trio-to-trio deep neural networks
A systematic analysis of miRNA markers and classification algorithms for forensic body fluid identification
Interpretable feature extraction and dimensionality reduction in ESM2 for protein localization prediction
Reviewing and assessing existing meta-analysis models and tools
Health informatics and EHR to support clinical research in the COVID-19 pandemic: an overview
CPPLS-MLP: a method for constructing cell-cell communication networks and identifying related highly variable genes based on single-cell sequencing and spatial transcriptomics data
MCAM abnormal expression and clinical outcome associations are highly cancer dependent as revealed through pan-cancer analysis
Integration and interplay of machine learning and bioinformatics approach to identify genetic interaction related to ovarian cancer chemoresistance
Orchestrating information across tissues via a novel multitask GAT framework to improve quantitative gene regulation relation modeling for survival analysis
High-dimensional genomic feature selection with the ordered stereotype logit model
A Bayesian model for identifying cancer subtypes from paired methylation profiles
Deep-DRM: a computational method for identifying disease-related metabolites based on graph deep learning approaches
Current challenges for unseen-epitope TCR interaction prediction and a new perspective derived from image classification
AtCircDB: a tissue-specific database for Arabidopsis circular RNAs
CDCM: a correlation-dependent connectivity map approach to rapidly screen drugs during outbreaks of infectious diseases
Current trends in the bioinformatic sequence analysis of metabolic pathways in prokaryotes
Life sciences on the Semantic Web: the Neurocommons and beyond
Evaluation of single-cell classifiers for single-cell RNA sequencing data sets
Publishing reproducible dynamic kinetic models
Uncertainty-aware genomic classification of Alzheimer's disease: a transformer-based ensemble approach with Monte Carlo dropout
A beginner's guide for FMDV quasispecies analysis: sub-consensus variant detection and haplotype reconstruction using next-generation sequencing
Roles of host small RNAs in the evolution and host tropism of coronaviruses
Metabolomics Standards Workshop and the development of international standards for reporting metabolomics experimental results
Joint similarity nonnegative matrix factorization model for identification of recurrence-related association patterns in tumor
Chrom-Lasso: a lasso regression-based model to detect functional interactions using Hi-C data
A machine learning framework to predict antibiotic resistance traits and yet unknown genes underlying resistance to specific antibiotics in bacterial strains
ImmunoGrid, an integrative environment for large-scale simulation of the immune system for vaccine discovery, design and optimization
Should LLMs be over empowered for high-stake regulatory research?
Bioinformatics Basics: Applications in Biological Science and Medicine.: Edited by Lukas K. Buehler and Hooman H. Rashidi
Using prior knowledge from cellular pathways and molecular networks for diagnostic specimen classification
Comparative study of the mechanism of natural compounds with similar structures using docking and transcriptome data for improving in silico herbal medicine experimentations
The effect of tissue composition on gene co-expression
Genome-wide association neural networks identify genes linked to family history of Alzheimer's disease
Virus classification for viral genomic fragments using PhaGCN2
A review of bioinformatic pipeline frameworks
scCODE: an R package for data-specific differentially expressed gene detection on single-cell RNA-sequencing data
Predicting novel microRNA: a comprehensive comparison of machine learning approaches
MCGAE: unraveling tumor invasion through integrated multimodal spatial transcriptomics
Hive plots - rational approach to visualizing networks
Computational prediction of methylation types of covalently modified lysine and arginine residues in proteins
Circumventing the cut-off for enrichment analysis
DMPPred: a tool for identification of antigenic regions responsible for inducing type 1 diabetes mellitus
TCMFP: a novel herbal formula prediction method based on network target's score integrated with semi-supervised learning genetic algorithms
Identification of haploinsufficient genes from epigenomic data using deep forest
A comprehensive review of bioinformatics tools for chromatin loop calling
NASNet-DTI: accurate drug-target interaction prediction using heterogeneous graphs and node adaptation
Prospects and challenges of cancer systems medicine: from genes to disease networks
Predicting miRNA-disease associations via learning multimodal networks and fusing mixed neighborhood information
DrugDoctor: enhancing drug recommendation in cold-start scenario via visit-level representation learning and training
GLOBE: a contrastive learning-based framework for integrating single-cell transcriptome datasets
Assessing next-generation sequencing-based computational methods for predicting transcriptional regulators with query gene sets
Deciphering optimal molecular determinants of non-hemolytic, cell-penetrating antimicrobial peptides through bioinformatics and Random Forest
SurvivalMeth: a web server to investigate the effect of DNA methylation-related functional elements on prognosis
PhosF3C: a feature fusion architecture with fine-tuned protein language model and conformer for prediction of general phosphorylation site
Paradigms, innovations, and biological applications of RNA velocity: a comprehensive review
Fine-grained selective similarity integration for drug-target interaction prediction
Optimal selection of genetic variants for adjustment of population stratification in European association studies
AI-based IsAb2.0 for antibody design
A systematic review of computational methods for designing efficient guides for CRISPR DNA base editor systems
Sensitive Protein Comparisons with Profiles and Hidden Markov Models
Multiple sequence alignment modeling: methods and applications
Canalizing kernel for cell fate determination
Hierarchical multimodal self-attention-based graph neural network for DTI prediction
Removing unwanted variation between samples in Hi-C experiments
VIPpred: a novel model for predicting variant impact on phosphorylation events driving carcinogenesis
LC-MS alignment in theory and practice: a comprehensive algorithmic review
CatLearning: highly accurate gene expression prediction from histone mark
DiMo: discovery of microRNA motifs using deep learning and motif embedding
Tree visualizations of protein sequence embedding space enable improved functional clustering of diverse protein superfamilies
Mutual information stacking method for prediction of the growth traits in pigs
Proteoform characterization based on top-down mass spectrometry
Inferring and analyzing module-specific lncRNA-mRNA causal regulatory networks in human cancer
Cell cycle expression heterogeneity predicts degree of differentiation
The growth of bioinformatics
TIPS: trajectory inference of pathway significance through pseudotime comparison for functional assessment of single-cell RNAseq data
Shedding light on the hidden human proteome expands immunopeptidome in cancer
Biobanking for Europe
ATSE: a peptide toxicity predictor by exploiting structural and evolutionary information based on graph neural network and attention mechanism
PedMiner: a tool for linkage analysis-based identification of disease-associated variants using family based whole-exome sequencing data
Predictive modelling of gene expression from transcriptional regulatory elements
A novel approach to study multi-domain motions in JAK1's activation mechanism based on energy landscape
The genetic algorithm-aided three-stage ensemble learning method identified a robust survival risk score in patients with glioma
Attention-guided variational graph autoencoders reveal heterogeneity in spatial transcriptomics
Robust discovery of gene regulatory networks from single-cell gene expression data by Causal Inference Using Composition of Transactions
A pitfall of wiki solution for biological databases
Image-based modelling of organogenesis
Genome-wide analysis reveals that exon methylation facilitates its selective usage in the human transcriptome
Towards an open, collaborative, reusable framework for sharing hands-on bioinformatics training workshops
Single-cell RNA sequencing data imputation using bi-level feature propagation
VirDetect-AI: a residual and convolutional neural network-based metagenomic tool for eukaryotic viral protein identification
A comprehensive evaluation of popular proteomics software workflows for label-free proteome quantification and imputation
HN-PPISP: a hybrid network based on MLP-Mixer for protein-protein interaction site prediction
Social pathway annotation: extensions of the systems biology metabolic modelling assistant
scHFC: a hybrid fuzzy clustering method for single-cell RNA-seq data optimized by natural computation
Network embedding in biomedical data science
Improving drug response prediction via integrating gene relationships with deep learning
Bioinformatics-assisted, integrated omics studies on medicinal plants
HVIDB: a comprehensive database for human-virus protein-protein interactions
NeuroPred-FRL: an interpretable prediction model for identifying neuropeptide using feature representation learning
GMFGRN: a matrix factorization and graph neural network approach for gene regulatory network inference
An integrated approach for copy number variation discovery in parent-offspring trios
Metagenomic analysis: the challenge of the data bonanza
SMNN: batch effect correction for single-cell RNA-seq data via supervised mutual nearest neighbor detection
Building a knowledge base for systems pathology
Characterization of MinION nanopore data for resequencing analyses
Large-scale data-driven integrative framework for extracting essential targets and processes from disease-associated gene data sets
Statistical method evaluation for differentially methylated CpGs in base resolution next-generation DNA sequencing data
EMNUSS: a deep learning framework for secondary structure annotation in cryo-EM maps
Towards multi-omics characterization of tumor heterogeneity: a comprehensive review of statistical and machine learning approaches
Precise identification of somatic and germline variants in the absence of matched normal samples
From SNP to pathway-based GWAS meta-analysis: do current meta-analysis approaches resolve power and replication in genetic association studies?
Advances and challenges in cell-cell communication inference: a comprehensive review of tools, resources, and future directions
Critical assessment of pan-genomic analysis of metagenome-assembled genomes
Recent trends in RNA informatics: a review of machine learning and deep learning for RNA secondary structure prediction and RNA drug discovery
Impact of similarity metrics on single-cell RNA-seq data clustering
A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing
Unveiling a novel cancer hallmark by evaluation of neural infiltration in cancer
An unbiased comparison of immunoglobulin sequence aligners
Empirical comparison of structure-based pathway methods
Census of exposed aggregation-prone regions in proteomes
Testing and overcoming the limitations of modular response analysis
Deep learning in spatially resolved transcriptomics: a comprehensive technical view
Machine learning methods, databases and tools for drug combination prediction
Letter to the Editor: Current progress in patient-specific modeling by Neal and Kerckhoffs (2010)
Clover: tree structure-based efficient DNA clustering for DNA-based data storage
Protein inference: a review
SICaRiO: short indel call filtering with boosting
Discovery of G-quadruplex-forming sequences in SARS-CoV-2
Evaluation of drug efficacy based on the spatial position comparison of drug-target interaction centers
Decoding Connectivity Map-based drug repurposing for oncotherapy
DeepLncPro: an interpretable convolutional neural network model for identifying long non-coding RNA promoters
Revealing the architecture of genetic and epigenetic regulation: a maximum likelihood model
Deep scSTAR: leveraging deep learning for the extraction and enhancement of phenotype-associated features from single-cell RNA sequencing and spatial transcriptomics data
Evaluation of variable selection methods for random forests and omics data sets
The complexity, challenges and benefits of comparing two transporter classification systems in TCDB and Pfam
Pathogenicity prediction of non-synonymous single nucleotide variants in dilated cardiomyopathy
A review of digital cytometry methods: estimating the relative abundance of cell types in a bulk of cells
CellTICS: an explainable neural network for cell-type identification and interpretation based on single-cell RNA-seq data
Random forest Gini importance favours SNPs with large minor allele frequency: impact, sources and recommendations
Holistic similarity-based prediction of phosphorylation sites for understudied kinases
Information extraction in molecular biology
Personalized immune subtypes based on machine learning predict response to checkpoint blockade in gastric cancer
Towards more accurate prediction of protein folding rates: a review of the existing web-based bioinformatics approaches
DeepYY1: a deep learning approach to identify YY1-mediated chromatin loops
FactVAE: a factorized variational autoencoder for single-cell multi-omics data integration analysis
Unveiling COVID-19-associated organ-specific cell types and cell-specific pathway cascade
Scalable batch-correction approach for integrating large-scale single-cell transcriptomes
AlzRiskMR database: an online database for the impact of exposure factors on Alzheimer's disease
Comparison of the binding characteristics of SARS-CoV and SARS-CoV-2 RBDs to ACE2 at different temperatures by MD simulations
Applications of genome-scale metabolic models to investigate microbial metabolic adaptations in response to genetic or environmental perturbations
idenPC-MIIP: identify protein complexes from weighted PPI networks using mutual important interacting partner relation
EPSD: a well-annotated data resource of protein phosphorylation sites in eukaryotes
Application of wavelet-based tools to study the dynamics of biological processes
Characterizing and explaining the impact of disease-associated mutations in proteins without known structures or structural homologs
'Multi-omic' data analysis using O-miner
CSRefiner: a lightweight framework for fine-tuning cell segmentation models with small datasets
OPUS-Fold3: a gradient-based protein all-atom folding and docking framework on TensorFlow
Exosomal ncRNAs profiling of mycobacterial infection identified miRNA-185-5p as a novel biomarker for tuberculosis
Agents in bioinformatics, computational and systems biology
Identify potential drug candidates within a high-quality compound search space
PySmash: Python package and individual executable program for representative substructure generation and application
ScSmOP: a universal computational pipeline for single-cell single-molecule multiomics data analysis
GeneAnnot: Interfacing GeneCards with high-throughput gene expression compendia
Computational aspects of host-parasite phylogenies
A multi-step completion process model of cell plasticity
Deep structural clustering for single-cell RNA-seq data jointly through autoencoder and graph neural network
Integrating scRNA-seq and scATAC-seq with inter-type attention heterogeneous graph neural networks
stDiff: a diffusion model for imputing spatial transcriptomics through single-cell transcriptomics