yusuke1997/dblp-id-title huggingface dataset:
Effects of imputation on correlation: implications for analysis of mass spectrometry data from multiple biological matrices
Learning spatial structures of proteins improves protein-protein interaction prediction
slORFfinder: a tool to detect open reading frames resulting from trans -splicing of spliced leader sequences
Multi-layer matrix factorization for cancer subtyping using full and partial multi-omics dataset
Evaluation of consensus strategies for haplotype phasing
MicroRNAs and nervous system diseases: network insights and computational challenges
Saccharomyces genome database: Underlying principles and organisation
A framework of multi-view machine learning for biological spectral unmixing of fluorophores with overlapping excitation and emission spectra
MetaHMEI: meta-learning for prediction of few-shot histone modifying enzyme inhibitors
Correction to: A comprehensive benchmarking of WGS-based deletion structural variant callers
NeuroFANN: identification of neuropathological subtypes in dementia with plasma proteins by using functionally annotated neural network
DeepMobilome: predicting mobile genetic elements using sequencing reads of microbiomes
A unifying framework for bivalent multilocus linkage analysis of allotetraploids
Semi-supervised learning with pseudo-labeling compares favorably with large language models for regulatory sequence prediction
Comprehensive assessment and performance improvement of effector protein predictors for bacterial secretion systems III, IV and VI
Bioinformatics, multiscale modeling and the IUPS Physiome Project
iGRLCDA: identifying circRNA-disease association based on graph representation learning
A novel integrative multimodal classifier to enhance the diagnosis of Parkinson's disease
Evaluating performance of existing computational models in predicting CD8+ T cell pathogenic epitopes and cancer neoantigens
HimGNN: a novel hierarchical molecular graph representation learning framework for property prediction
NIGMS Sandbox: a learning platform toward democratizing cloud computing for biomedical research
Drug repositioning based on multi-view learning with matrix completion
BioModels.net Web Services, a free and integrated toolkit for computational modelling software
Systematic benchmarking of statistical methods to assess differential expression of circular RNAs
The HUPO proteomics standards initiative - easing communication and minimizing data loss in a changing world
Cardioinformatics: the nexus of bioinformatics and precision cardiology
A review on machine learning principles for multi-view biological data integration
Elevated incidence of somatic mutations at prevalent genetic sites
Improved prediction of protein-protein interaction using a hybrid of functional-link Siamese neural network and gradient boosting machines
ULDNA: integrating unsupervised multi-source language models with LSTM-attention network for high-accuracy protein-DNA binding site prediction
RLBind: a deep learning method to predict RNA-ligand binding sites
The shape of chromatin: insights from computational recognition of geometric patterns in Hi-C data
DeepVF: a deep learning-based hybrid framework for identifying virulence factors using the stacking strategy
The dilemma of choosing the ideal permutation strategy while estimating statistical significance of genome-wide enrichment
Zero-shot-capable identification of phage-host relationships with whole-genome sequence representation by contrastive learning
Therapeutic targets and signaling mechanisms of vitamin C activity against sepsis: a bioinformatics study
HNetGO: protein function prediction via heterogeneous network transformer
Software engineering the mixed model for genome-wide association studies on large samples
SIFLoc: a self-supervised pre-training method for enhancing the recognition of protein subcellular localization in immunofluorescence microscopic images
AlgPred 2.0: an improved method for predicting allergenic proteins and mapping of IgE epitopes
TMBstable: a variant caller controls performance variation across heterogeneous sequencing samples
Conjoint analysis of succinylome and phosphorylome reveals imbalanced HDAC phosphorylation-driven succinylayion dynamic contibutes to lung cancer
PLM_Sol: predicting protein solubility by benchmarking multiple protein language models with the updated Escherichia coli protein solubility dataset
MITNet: a fusion transformer and convolutional neural network architecture approach for T-cell epitope prediction
Setting the basis of best practices and standards for curation and annotation of logical models in biology - highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop
From multi-omics data to the cancer druggable gene discovery: a novel machine learning-based approach
Computational drug repositioning based on the relationships between substructure-indication
Machine learning application identifies novel gene signatures from transcriptomic data of spontaneous canine hemangiosarcoma
DECO: a framework for jointly analyzing de novo and rare case/control variants, and biological pathways
AI-guided discovery and optimization of antimicrobial peptides through species-aware language model
Discovery of host-directed modulators of virus infection by probing the SARS-CoV-2-host protein-protein interaction network
Knowledge sharing and collaboration in translational research, and the DC-THERA Directory
Improved drug response prediction by drug target data integration via network-based profiling
Auto-Kla: a novel web server to discriminate lysine lactylation sites using automated machine learning
MyoV: a deep learning-based tool for the automated quantification of muscle fibers
Meta-DHGNN: method for CRS-related cytokines analysis in CAR-T therapy based on meta-learning directed heterogeneous graph neural network
RNAdegformer: accurate prediction of mRNA degradation at nucleotide resolution with deep learning
Accurate and interpretable gene expression imputation on scRNA-seq data using IGSimpute
Affymetrix GeneChip microarray preprocessing for multivariate analyses
PanomiR: a systems biology framework for analysis of multi-pathway targeting by miRNAs
Multi-modality attribute learning-based method for drug-protein interaction prediction based on deep neural network
STW-MD: a novel spatio-temporal weighting and multi-step decision tree method for considering spatial heterogeneity in brain gene expression data
Survey of miRNA-miRNA cooperative regulation principles across cancer types
Computational recognition of lncRNA signature of tumor-infiltrating B lymphocytes with potential implications in prognosis and immunotherapy of bladder cancer
Prediction of protein-ligand binding affinity via deep learning models
FusionNW, a potential clinical impact assessment of kinases in pan-cancer fusion gene network
MolEM: a unified generative framework for molecular graphs and sequential orders
Advances in the field of phage-based therapy with special emphasis on computational resources
A multi-step and multi-scale bioinformatic protocol to investigate potential SARS-CoV-2 vaccine targets
MGCNSS: miRNA-disease association prediction with multi-layer graph convolution and distance-based negative sample selection strategy
CRISP: a deep learning architecture for GC × GC-TOFMS contour ROI identification, simulation and analysis in imaging metabolomics
Inferring gene networks from time series microarray data using dynamic Bayesian networks
VirGrapher: a graph-based viral identifier for long sequences from metagenomes
BETA: a comprehensive benchmark for computational drug-target prediction
scPAS: single-cell phenotype-associated subpopulation identifier
DDK-Linker: a network-based strategy identifies disease signals by linking high-throughput omics datasets to disease knowledge
Delineation of modular proteins: Domain boundary prediction from sequence information
mi-IsoNet: systems-scale microRNA landscape reveals rampant isoform-mediated gain of target interaction diversity and signaling specificity
Fast and efficient searching of biological data resources - using EB-eye
Benchmarking transcription factor binding site prediction models: a comparative analysis on synthetic and biological data
Integrating spatial transcriptomics and bulk RNA-seq: predicting gene expression with enhanced resolution through graph attention networks
A consensus-based classification workflow to determine genetically inferred ancestry from comprehensive genomic profiling of patients with solid tumors
Metric learning for comparing genomic data with triplet network
Tracking the pipeline: immunoinformatics and the COVID-19 vaccine design
APPTEST is a novel protocol for the automatic prediction of peptide tertiary structures
Graph contrastive learning of subcellular-resolution spatial transcriptomics improves cell type annotation and reveals critical molecular pathways
Improving life sciences information retrieval using semantic web technology
RAMP: response-aware multi-task learning with contrastive regularization for cancer drug response prediction
Identification of alternative splicing-derived cancer neoantigens for mRNA vaccine development
RmsdXNA: RMSD prediction of nucleic acid-ligand docking poses using machine-learning method
MODEC: an unsupervised clustering method integrating omics data for identifying cancer subtypes
Bioinformatics of alternative splicing and its regulation
Complex hierarchical structures analysis in single-cell data with Poincaré deep manifold transformation
A comprehensive review and evaluation of computational methods for identifying protein complexes from protein-protein interaction networks
Genotypic-phenotypic landscape computation based on first principle and deep learning
scDFN: enhancing single-cell RNA-seq clustering with deep fusion networks
KCRR: a nonlinear machine learning with a modified genomic similarity matrix improved the genomic prediction efficiency
Parallel computing for genome sequence processing
NeuroPpred-Fuse: an interpretable stacking model for prediction of neuropeptides by fusing sequence information and feature selection methods
Tracing the evolution of aneuploid cancers by multiregional sequencing with CRUST
The GR2D2 estimator for the precision matrices
Deep learning approaches for non-coding genetic variant effect prediction: current progress and future prospects
Genomic hallmarks and therapeutic targets of ribosome biogenesis in cancer
Domain mobility in proteins: functional and evolutionary implications
Integrating Reinforcement Learning and Monte Carlo Tree Search for enhanced neoantigen vaccine design
Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research
Deep generative modeling and clustering of single cell Hi-C data
High-performance deep learning pipeline predicts individuals in mixtures of DNA using sequencing data
ScCAEs: deep clustering of single-cell RNA-seq via convolutional autoencoder embedding and soft K-means
UniDL4BioPep: a universal deep learning architecture for binary classification in peptide bioactivity
Classification of mass-spectrometric data in clinical proteomics using learning vector quantization methods
Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models
Biological knowledge graph-guided investigation of immune therapy response in cancer with graph neural network
A review of methods for predicting DNA N6-methyladenine sites
A survey on the algorithm and development of multiple sequence alignment
Quantum computing in bioinformatics: a systematic review mapping
GRAFT: a graph-aware fusion transformer for cancer driver gene prediction
A novel heterophilic graph diffusion convolutional network for identifying cancer driver genes
A multiple network-based bioinformatics pipeline for the study of molecular mechanisms in oncological diseases for personalized medicine
Vertical integration methods for gene expression data analysis
From G1 to M: a comparative study of methods for identifying cell cycle phases
WMSA 2: a multiple DNA/RNA sequence alignment tool implemented with accurate progressive mode and a fast win-win mode combining the center star and progressive strategies
Combining experiments with multi-cell agent-based modeling to study biological tissue patterning
Identification of viral-mediated pathogenic mechanisms in neurodegenerative diseases using network-based approaches
scDOT: enhancing single-cell RNA-Seq data annotation and uncovering novel cell types through multi-reference integration
Impacts of somatic mutations on gene expression: an association perspective
Editorial: Omics research and bioinformatics - joined-up thinking or anarchy?
Issues in Predicting Protein Function From Sequence
A universal approach for integrating super large-scale single-cell transcriptomes by exploring gene rankings
DeTox: a pipeline for the detection of toxins in venomous organisms
TransMA: an explainable multi-modal deep learning model for predicting properties of ionizable lipid nanoparticles in mRNA delivery
Simulation-guided pan-cancer analysis identifies a novel regulator of CpG island hypermethylation heterogeneity
DeepTTA: a transformer-based model for predicting cancer drug response
DeepHomo2.0: improved protein-protein contact prediction of homodimers by transformer-enhanced deep learning
DS-MVP: identifying disease-specific pathogenicity of missense variants by pre-training representation
Benchmarking recent computational tools for DNA-binding protein identification
Data imbalance in drug response prediction: multi-objective optimization approach in deep learning setting
Liquidhope: methylome and genomic profiling from very limited quantities of plasma-derived DNA
multiMiAT: an optimal microbiome-based association test for multicategory phenotypes
Experimental evidence validating the computational inference of functional associations from gene fusion events: a critical survey
Conceptual and computational framework for logical modelling of biological networks deregulated in diseases
GenoPheno: cataloging large-scale phenotypic and next-generation sequencing data within human datasets
State-of-the-art technology in modern computer-aided drug design
Big data management challenges in health research - a literature review
Response to the letter 'testing the effectiveness of MyPROSLE in classifying patients with lupus nephritis'
Progress in single-access information systems for wheat and rice crop improvement
A tale of solving two computational challenges in protein science: neoantigen prediction and protein structure prediction
Timely need for navigating the potential and downsides of LLMs in healthcare and biomedicine
Application of learning to rank in bioinformatics tasks
Systematic investigation of the homology sequences around the human fusion gene breakpoints in pan-cancer - bioinformatics study for a potential link to MMEJ
CaliBayes and BASIS: integrated tools for the calibration, simulation and storage of biological simulation models
MRAgent: an LLM-based automated agent for causal knowledge discovery in disease via Mendelian randomization
DNA copy number profiling using single-cell sequencing
Addressing data imbalance problems in ligand-binding site prediction using a variational autoencoder and a convolutional neural network
Local ancestry inference in heterogeneous populations - Are recent recombination events more relevant?
Machine learning for synergistic network pharmacology: a comprehensive overview
Drug resistance prediction and resistance genes identification in Mycobacterium tuberculosis based on a hierarchical attentive neural network utilizing genome-wide variants
The network structural entropy for single-cell RNA sequencing data during skin aging
ImmuneMirror: A machine learning-based integrative pipeline and web server for neoantigen prediction
scEGG: an exogenous gene-guided clustering method for single-cell transcriptomic data
Biological feature validation of estimated gene interaction networks from microarray data: a case study on MYC in lymphomas
A molecular modelling approach for identifying antiviral selenium-containing heterocyclic compounds that inhibit the main protease of SARS-CoV-2: an in silico investigation
Predicting MHC class I binder: existing approaches and a novel recurrent neural network solution
DOMSCNet: a deep learning model for the classification of stomach cancer using multi-layer omics data
Consistency and overfitting of multi-omics methods on experimental data
Prediction of anticancer peptides based on an ensemble model of deep learning and machine learning using ordinal positional encoding
Fuse feeds as one: cross-modal framework for general identification of AMPs
'Bingo' - a large language model- and graph neural network-based workflow for the prediction of essential genes from protein data
Models of coding sequence evolution
Landscape of the long non-coding RNA transcriptome in human heart
Bioinformatics training: a review of challenges, actions and support requirements
Shaping the nebulous enhancer in the era of high-throughput assays and genome editing
Flux balance analysis of biological systems: applications and challenges
Cooperative driver pathway discovery via fusion of multi-relational data of genes, miRNAs and pathways
A Markov random field model-based approach for differentially expressed gene detection from single-cell RNA-seq data
PathMethy: an interpretable AI framework for cancer origin tracing based on DNA methylation
Accurate feature selection improves single-cell RNA-seq cell clustering
Combining literature text mining with microarray data: advances for system biology modeling
scSorterDL: a deep neural network-enhanced ensemble LDAs for single cell classifications
Applications of alignment-free methods in epigenomics
Power and sample size calculations for high-throughput sequencing-based experiments
Recent development of Ori-Finder system and DoriC database for microbial replication origins
Identification of differentially expressed peptides in high-throughput proteomics data
Representing bioinformatics causality
A chronotherapeutics-applicable multi-target therapeutics based on AI: Example of therapeutic hypothermia
Deep learning for biological age estimation
Development of biomarker classifiers from high-dimensional data
MetaDegron: multimodal feature-integrated protein language model for predicting E3 ligase targeted degrons
scENCORE: leveraging single-cell epigenetic data to predict chromatin conformation using graph embedding
InferLoop: leveraging single-cell chromatin accessibility for the signal of chromatin loop
GADRP: graph convolutional networks and autoencoders for cancer drug response prediction
CycPeptMP: enhancing membrane permeability prediction of cyclic peptides with multi-level molecular features and data augmentation
A multivalent three-point linkage analysis model of autotetraploids
Spatially aligned graph transfer learning for characterizing spatial regulatory heterogeneity
Comparative studies of AlphaFold, RoseTTAFold and Modeller: a case study involving the use of G-protein-coupled receptors
Feature extraction approaches for biological sequences: a comparative study of mathematical features
Systematic comparison of ligand-based and structure-based virtual screening methods on poly (ADP-ribose) polymerase-1 inhibitors
DeepDISOBind: accurate prediction of RNA-, DNA- and protein-binding intrinsically disordered residues with deep multi-task learning
Predictive approaches for drug combination discovery in cancer
KGE-UNIT: toward the unification of molecular interactions prediction based on knowledge graph and multi-task learning on drug discovery
Tuberculosis Vaccine Design: Influence of the Completed Genome Sequence
SIngle cell level Genotyping Using scRna Data (SIGURD)
ProJect: a powerful mixed-model missing value imputation method
Virtual Reference Environments: a simple way to make research reproducible
Current opportunities and challenges in microbial metagenome analysis - a bioinformatic perspective
A model-free approach for detecting interactions in genetic association studies
A transformer-based genomic prediction method fused with knowledge-guided module
Generating and screening de novo compounds against given targets using ultrafast deep learning models as core components
A review of network-based approaches to drug repositioning
PTFSpot: deep co-learning on transcription factors and their binding regions attains impeccable universality in plants
BIOTIC: a Bayesian framework to integrate single-cell multi-omics for transcription factor activity inference and improve identity characterization of cells
Preprocessing and downstream analysis of microarray DNA copy number profiles
RIBOSS detects novel translational events by combining long- and short-read transcriptome and translatome profiling
Normalization of circulating microRNA expression data obtained by quantitative real-time RT-PCR
Stochastic Modelling for Systems Biology: Darren J. Wilkinson
Self-supervised contrastive learning for integrative single cell RNA-seq data analysis
Current challenges and best-practice protocols for microbiome analysis
Comprehensive overview and assessment of computational prediction of microRNA targets in animals
Computational determination of gene age and characterization of evolutionary dynamics in human
A novel molecular representation with BiGRU neural networks for learning atom
Putting microarrays in a context: Integrated analysis of diverse biological data
A genomic data resource for predicting antimicrobial resistance from laboratory-derived antimicrobial susceptibility phenotypes
Software Review Introduction
Designing interpretable deep learning applications for functional genomics: a quantitative analysis
Qmatey: an automated pipeline for fast exact matching-based alignment and strain-level taxonomic binning and profiling of metagenomes
An overview of computational methods in single-cell transcriptomic cell type annotation
A spectral clustering with self-weighted multiple kernel learning method for single-cell RNA-seq data
QOT: Quantized Optimal Transport for sample-level distance matrix in single-cell omics
Cancer gene prioritization by integrative analysis of mRNA expression and DNA copy number data: a comparative review
Protein subcellular localization based on deep image features and criterion learning strategy
Software review: Federating data with Information Integrator
Review of applications of high-throughput sequencing in personalized medicine: barriers and facilitators of future progress in research and clinical application
Comparative evaluation of isoform-level gene expression estimation algorithms for RNA-seq and exon-array platforms
SHINE: protein language model-based pathogenicity prediction for short inframe insertion and deletion variants
Precise uncertain significance prediction using latent space matrix factorization models: genomics variant and heterogeneous clinical data-driven approaches
CrossFuse-XGBoost: accurate prediction of the maximum recommended daily dose through multi-feature fusion, cross-validation screening and extreme gradient boosting
scMMT: a multi-use deep learning approach for cell annotation, protein prediction and embedding in single-cell RNA-seq data
Convolutional neural network-based annotation of bacterial type IV secretion system effectors with enhanced accuracy and reduced false discovery
CpG-island-based annotation and analysis of human housekeeping genes
The challenges of informatics in synthetic biology: from biomolecular networks to artificial organisms
CoBRA: compound binding site prediction using RNA language model
An artificial neural network model based on DNA damage response genes to predict outcomes of lower-grade glioma patients
GTE-PPIS: a protein-protein interaction site predictor based on graph transformer and equivariant graph neural network
Longitudinal urine metabolic profiling and gestational age prediction in human pregnancy
Deep learning for drug response prediction in cancer
Attention-based cross domain graph neural network for prediction of drug-drug interactions
RTCpredictor: identification of read-through chimeric RNAs from RNA sequencing data
The repertoire of copy number alteration signatures in human cancer
Comparative genome assembly