yusuke1997/dblp-id-title huggingface dataset:
Correction to: kTWAS: integrating kernel machine with transcriptome-wide association studies improves statistical power and reveals novel genes
Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks
DNA sequence symmetries from randomness: the origin of the Chargaff's second parity rule
scHiMe: predicting single-cell DNA methylation levels based on single-cell Hi-C data
The WWWH of remote homolog detection: The state of the art
Advances in network-based metabolic pathway analysis and gene expression data integration
Improving Single-Cell RNA-seq Clustering by Integrating Pathways
DeepFGRN: inference of gene regulatory network with regulation type based on directed graph embedding
netANOVA: novel graph clustering technique with significance assessment via hierarchical ANOVA
BML: a versatile web server for bipartite motif discovery
Literature-based discovery of new candidates for drug repurposing
Boosting signals in gene-based association studies via efficient SNP selection
Dynamic modeling and network approaches for omics time course data: overview of computational approaches and applications
MambaPhase: deep learning for liquid-liquid phase separation protein classification
Scanning window analysis of non-coding regions within normal-tumor whole-genome sequence samples
Predicting potential microbe-disease associations based on multi-source features and deep learning
A feature extraction free approach for protein interactome inference from co-elution data
SVDF: enhancing structural variation detect from long-read sequencing via automatic filtering strategies
Serial co-expression analysis of host factors from SARS-CoV viruses highly converges with former high-throughput screenings and proposes key regulators
GFSeeker: a splicing-graph-based approach for accurate gene fusion detection from long-read RNA sequencing data
Knowledge-based expert systems and a proof-of-concept case study for multiple sequence alignment construction and analysis
Tutorial section: Designing microarray oligonucleotide probes
Similarity of markers identified from cancer gene expression studies: observations from GEO
Improving data workflow systems with cloud services and use of open data for bioinformatics research
PreHom-PCLM: protein remote homology detection by combing motifs and protein cubic language model
Integrating network pharmacology and in silico analysis deciphers Withaferin-A's anti-breast cancer potential via hedgehog pathway and target network interplay
DeepEnzyme: a robust deep learning model for improved enzyme turnover number prediction by utilizing features of protein 3D-structures
Benchmarking orthology methods using phylogenetic patterns defined at the base of Eukaryotes
Computational methods for the integrative analysis of single-cell data
stHGC: a self-supervised graph representation learning for spatial domain recognition with hybrid graph and spatial regularization
scHiClassifier: a deep learning framework for cell type prediction by fusing multiple feature sets from single-cell Hi-C data
Computational methods and biomarker discovery strategies for spatial proteomics: a review in immuno-oncology
A critical assessment of the feature selection methods used for biomarker discovery in current metaproteomics studies
Heterogeneous graph attention network based on meta-paths for lncRNA-disease association prediction
MHTAN-DTI: Metapath-based hierarchical transformer and attention network for drug-target interaction prediction
TIGER: technical variation elimination for metabolomics data using ensemble learning architecture
TRIAGE: an R package for regulatory gene analysis
Secondary structure prediction of long noncoding RNA: review and experimental comparison of existing approaches
RFPR-IDP: reduce the false positive rates for intrinsically disordered protein and region prediction by incorporating both fully ordered proteins and disordered proteins
Entropy-based inference of transition states and cellular trajectory for single-cell transcriptomics
A novel graph attention model for predicting frequencies of drug-side effects from multi-view data
PROSITE: A Documented Database Using Patterns and Profiles as Motif Descriptors
Precision DNA methylation typing via hierarchical clustering of Nanopore current signals and attention-based neural network
Bioinformatics for precision oncology
Erratum to: Identification of multiple RNAs using feature fusion
DSNetax: a deep learning species annotation method based on a deep-shallow parallel framework
Deciphering clonal dynamics and metastatic routines in a rare patient of synchronous triple-primary tumors and multiple metastases with MPTevol
Corrigendum to 'OPUS-Rota4: a gradient-based protein side-chain modeling framework assisted by deep learning-based predictors'
A computing platform to map ecological metabolism by integrating functional mapping and the metabolic theory of ecology
Rossmann-toolbox: a deep learning-based protocol for the prediction and design of cofactor specificity in Rossmann fold proteins
Characterizing efficient feature selection for single-cell expression analysis
Searching similar local 3D micro-environments in protein structure databases with MicroMiner
Prediction of drug-disease associations by integrating common topologies of heterogeneous networks and specific topologies of subnets
Protein Function From the Perspective of Molecular Interactions and Genetic Networks
Integration of Boolean models exemplified on hepatocyte signal transduction
A review on viral data sources and search systems for perspective mitigation of COVID-19
Web scraping technologies in an API world
cfDiffusion: diffusion-based efficient generation of high quality scRNA-seq data with classifier-free guidance
Subgenome phasing for complex allopolyploidy: case-based benchmarking and recommendations
Learning discriminative and structural samples for rare cell types with deep generative model
Reusability and composability in process description maps: RAS-RAF-MEK-ERK signalling
Response to 'comment on rigorous benchmarking of T cell receptor repertoire profiling methods for cancer RNA sequencing' by Davydov A.N.; Bolotin D.A.; Poslavsky S. V. and Chudakov D.M
Deletion variants calling in third-generation sequencing data based on a dual-attention mechanism
Towards a comprehensive picture of the genetic landscape of complex traits
Topoly: Python package to analyze topology of polymers
Network biology methods integrating biological data for translational science
GEMDiff: a diffusion workflow bridges between normal and tumor gene expression states: a breast cancer case study
On the validity of time-dependent AUC estimators
Integrative biology - the way forward
ComplexQA: a deep graph learning approach for protein complex structure assessment
Techniques for learning and transferring knowledge for microbiome-based classification and prediction: review and assessment
Microsatellite instability status differentially associates with intratumoral immune microenvironment in human cancers
RiceSNP-ABST: a deep learning approach to identify abiotic stress-associated single nucleotide polymorphisms in rice
A comprehensive review of the imbalance classification of protein post-translational modifications
Accurate protein function prediction via graph attention networks with predicted structure information
The miRNA: a small but powerful RNA for COVID-19
Annotating publicly-available samples and studies using interpretable modeling of unstructured metadata
Untangling the complexity of blood coagulation network: use of computational modelling in pharmacology and diagnostics
Automation of in-silico data analysis processes through workflow management systems
Semantic web for integrated network analysis in biomedicine
Likelihood-based tests for detecting circadian rhythmicity and differential circadian patterns in transcriptomic applications
High dimensionality reduction by matrix factorization for systems pharmacology
TSSFinder - fast and accurate ab initio prediction of the core promoter in eukaryotic genomes
A feature extraction method based on noise reduction for circRNA-miRNA interaction prediction combining multi-structure features in the association networks
Computational tools for plant small RNA detection and categorization
Computational approaches for discovery of mutational signatures in cancer
KGDiff: towards explainable target-aware molecule generation with knowledge guidance
StackIL6: a stacking ensemble model for improving the prediction of IL-6 inducing peptides
Comparison of sparse biclustering algorithms for gene expression datasets
Differentiable rotamer sampling with molecular force fields
Biological network analysis with deep learning
Personalized cancer immunotherapy using Systems Medicine approaches
Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies
EMcnv: enhancing CNV detection performance through ensemble strategies with heterogeneous meta-graph neural networks
ROC analysis: applications to the classification of biological sequences and 3D structures
A survey of gene expression meta-analysis: methods and applications
Current innovations and future challenges of network motif detection
Nmix: a hybrid deep learning model for precise prediction of 2'-O-methylation sites based on multi-feature fusion and ensemble learning
SCDD: a novel single-cell RNA-seq imputation method with diffusion and denoising
Computational prediction of drug-target interactions using chemogenomic approaches: an empirical survey
A very simple and fast way to access and validate algorithms in reproducible research
RegScan: a GWAS tool for quick estimation of allele effects on continuous traits and their combinations
DrugAssist: a large language model for molecule optimization
MHCBI: a pipeline for calculating peptide-MHC binding energy using semi-empirical quantum mechanical methods with explicit/implicit solvent models
Comparison of the general co-expression landscapes between human and mouse
Systematic identification of cancer-type-specific drugs based on essential genes and validations in lung adenocarcinoma
A comprehensive survey of regulatory network inference methods using single cell RNA sequencing data
How does the structure of data impact cell-cell similarity? Evaluating how structural properties influence the performance of proximity metrics in single cell RNA-seq data
CMGN: a conditional molecular generation net to design target-specific molecules with desired properties
RBP-TSTL is a two-stage transfer learning framework for genome-scale prediction of RNA-binding proteins
MDGF-MCEC: a multi-view dual attention embedding model with cooperative ensemble learning for CircRNA-disease association prediction
LOGOWheat: deep learning-based prediction of regulatory effects for noncoding variants in wheats
AIGen: an artificial intelligence software for complex genetic data analysis
MPTherm: database for membrane protein thermodynamics for understanding folding and stability
Evaluation of different computational methods for DNA methylation-based biological age
DSGAT: predicting frequencies of drug side effects by graph attention networks
MDBuilder: a PyMOL plugin for the preparation of molecular dynamics simulations
Classification and gene selection of triple-negative breast cancer subtype embedding gene connectivity matrix in deep neural network
Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources
Graph convolutional networks for computational drug development and discovery
Variable calling of m6A and associated features in databases: a guide for end-users
Investigating biocomplexity through the agent-based paradigm
Approaches to dimensionality reduction in proteomic biomarker studies
Detection of germline CNVs from gene panel data: benchmarking the state of the art
Causes, consequences and solutions of phylogenetic incongruence
Comprehensive analysis reveals distinct mutational signature and its mechanistic insights of alcohol consumption in human cancers
Transfer learning in proteins: evaluating novel protein learned representations for bioinformatics tasks
Editorial: International, interdisciplinary, multi-level bioinformatics training and education
Integrating multiple traits for improving polygenic risk prediction in disease and pharmacogenomics GWAS
HMMPolish: a coding region polishing tool for TGS-sequenced RNA viruses
iCircDA-MF: identification of circRNA-disease associations based on matrix factorization
A transferable deep learning approach to fast screen potential antiviral drugs against SARS-CoV-2
Comparative analysis of models in predicting the effects of SNPs on TF-DNA binding using large-scale in vitro and in vivo data
Applying polygenic risk score methods to pharmacogenomics GWAS: challenges and opportunities
Predicting the structure of unexplored novel fentanyl analogues by deep learning model
WDNE: an integrative graphical model for inferring differential networks from multi-platform gene expression data with missing values
Advances in computational approaches in identifying synergistic drug combinations
SPRoBERTa: protein embedding learning with local fragment modeling
A cloud-based learning module for biomarker discovery
SEAOP: a statistical ensemble approach for outlier detection in quantitative proteomics data
epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation
SSNMDI: a novel joint learning model of semi-supervised non-negative matrix factorization and data imputation for clustering of single-cell RNA-seq data
Tutorial section: Biological Sequence Databases
Current status and future challenges in T-cell receptor/peptide/MHC molecular dynamics simulations
Knowledge Graphs for drug repurposing: a review of databases and methods
Integrative approaches for predicting microRNA function and prioritizing disease-related microRNA using biological interaction networks
Cell-cell communication inference and analysis in the tumour microenvironments from single-cell transcriptomics: data resources and computational strategies
Biomedical ontologies: a functional perspective
EVAtool: an optimized reads assignment tool for small ncRNA quantification and its application in extracellular vesicle datasets
Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing
Functional mapping of ontogeny in flowering plants
On "Bioinformatics in Russia: history and present-day landscape" by M.A. Nawaz, I.E. Pamirsky, and K.S. Golokhvast
Computational intelligence approaches for pattern discovery in biological systems
Consistent gene signature of schizophrenia identified by a novel feature selection strategy from comprehensive sets of transcriptomic data
DeepSVM-fold: protein fold recognition by combining support vector machines and pairwise sequence similarity scores generated by deep learning networks
Out-of-the-box deep learning prediction of quantum-mechanical partial charges by graph representation and transfer learning
A novel framework for phage-host prediction via logical probability theory and network sparsification
Comparison of methods to detect differentially expressed genes between single-cell populations
Nonlinear embedding and integration of omics data: a fast and tuning-free approach
Systems Biology: the Reincarnation of Systems Theory Applied in Biology?
Computational resources for identifying and describing proteins driving liquid-liquid phase separation
Docking of peptides to GPCRs using a combination of CABS-dock with FlexPepDock refinement
NeuroPred-CLQ: incorporating deep temporal convolutional networks and multi-head attention mechanism to predict neuropeptides
Simulation of P systems with active membranes on CUDA
PLMFit: benchmarking transfer learning with protein language models for protein engineering
Complex genome assembly based on long-read sequencing
Advances in translational bioinformatics: computational approaches for the hunting of disease genes
Virus finding tools: current solutions and limitations
Genome variation discovery with high-throughput sequencing data
Propensity score matching enables batch-effect-corrected imputation in single-cell RNA-seq analysis
Multi-source biological knowledge-guided hypergraph spatiotemporal subnetwork embedding for protein complex identification
The winning methods for predicting cellular position in the DREAM single-cell transcriptomics challenge
Making PBPK models more reproducible in practice
Microbial bioinformatics for food safety and production
eccDNA Atlas: a comprehensive resource of eccDNA catalog
An overview of machine learning methods for monotherapy drug response prediction
MAEST: accurately spatial domain detection in spatial transcriptomics with graph masked autoencoder
SMMPPI: a machine learning-based approach for prediction of modulators of protein-protein interactions and its application for identification of novel inhibitors for RBD: hACE2 interactions in SARS-CoV-2
Bioinformatics methods in drug repurposing for Alzheimer's disease
A rank-based algorithm of differential expression analysis for small cell line data with statistical control
Seq2Topt: a sequence-based deep learning predictor of enzyme optimal temperature
Protein interactions and disease: computational approaches to uncover the etiology of diseases
GraphATC: advancing multilevel and multi-label anatomical therapeutic chemical classification via atom-level graph learning
Comprehensive analysis of Helicobacter pylori infection-associated diseases based on miRNA-mRNA interaction network
Novel systems biology experimental pipeline reveals matairesinol's antimetastatic potential in prostate cancer: an integrated approach of network pharmacology, bioinformatics, and experimental validation
Evaluation of single-cell RNAseq labelling algorithms using cancer datasets
From tradition to innovation: conventional and deep learning frameworks in genome annotation
A universal framework for single-cell multi-omics data integration with graph convolutional networks
A machine learning framework based on multi-source feature fusion for circRNA-disease association prediction
Computational biology for cardiovascular biomarker discovery
Analysis of CDNA Microarray Images
Letter to the editor: evaluating computational tools for lncRNA identification on independent datasets
ProsmORF-pred: a machine learning-based method for the identification of small ORFs in prokaryotic genomes
Computational methods to explore chromatin state dynamics
Reusable tutorials for using cloud-based computing environments for the analysis of bacterial gene expression data from bulk RNA sequencing
AntiFormer: graph enhanced large language model for binding affinity prediction
Editor's Note on 'Bioinformatics in Russia: history and present-day landscape'
Real-time classification of datasets with hardware embedded neuromorphic neural networks
VirNucPro: an identifier for the identification of viral short sequences using six-frame translation and large language models
A simple guide to de novo transcriptome assembly and annotation
Probabilistic methods of identifying genes in prokaryotic genomes: Connections to the HMM theory
Lessons from a decade of integrating cancer copy number alterations with gene expression profiles
Evotuning protocols for Transformer-based variant effect prediction on multi-domain proteins
Teaching the bioinformatics of signaling networks: an integrated approach to facilitate multi-disciplinary learning
csORF-finder: an effective ensemble learning framework for accurate identification of multi-species coding short open reading frames
Drug-target interaction prediction: databases, web servers and computational models
Deciphering the genetic architecture of human brain structure and function: a brief survey on recent advances of neuroimaging genomics
Joint analysis of miRNA and mRNA expression data
scMitoMut for calling mitochondrial lineage-related mutations in single cells
PELMI: Realize robust DNA image storage under general errors via parity encoding and local mean iteration
A survey of error-correction methods for next-generation sequencing
ProgCAE: a deep learning-based method that integrates multi-omics data to predict cancer subtypes
ZoomQA: residue-level protein model accuracy estimation with machine learning on sequential and 3D structural features
Biochemical simulations: stochastic, approximate stochastic and hybrid approaches
A survey of sequence alignment algorithms for next-generation sequencing
Forward LASSO analysis for high-order interactions in genome-wide association study
Statistical detection of differentially expressed genes based on RNA-seq: from biological to phylogenetic replicates
Influenza virus reassortment patterns exhibit preference and continuity while uncovering cross-species transmission events
A systematic review of analytical methods used in genetic association analysis of the X-chromosome
The Protein Data Bank and lessons in data management
DeepSTF: predicting transcription factor binding sites by interpretable deep neural networks combining sequence and shape
Corrigendum to: Computational annotation of miRNA transcription start sites
MAK: a machine learning framework improved genomic prediction via multi-target ensemble regressor chains and automatic selection of assistant traits
Web tools to fight pandemics: the COVID-19 experience
NeuroPred-PLM: an interpretable and robust model for neuropeptide prediction by protein language model
TBC2health: a database of experimentally validated health-beneficial effects of tea bioactive compounds
Identification and comprehensive characterization of lncRNAs with copy number variations and their driving transcriptional perturbed subpathways reveal functional significance for cancer
An evidence-based lexical pattern approach for quality assurance of Gene Ontology relations
fastDRH: a webserver to predict and analyze protein-ligand complexes based on molecular docking and MM/PB(GB)SA computation
Computational/in silico methods in drug target and lead prediction
Riboexp: an interpretable reinforcement learning framework for ribosome density modeling
GR-p K a: a message-passing neural network with retention mechanism for p K a prediction
The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies
Metabolomics technology and bioinformatics
DELFMUT: duplex sequencing-oriented depth estimation model for stable detection of low-frequency mutations
Gene-based mediation analysis in epigenetic studies
PCLasso: a protein complex-based, group lasso-Cox model for accurate prognosis and risk protein complex discovery
Precision medicine needs pioneering clinical bioinformaticians
Letter to the Editor: SeqXML and OrthoXML: standards for sequence and orthology information
SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks
Deep learning of pharmacogenomics resources: moving towards precision oncology
Machine learning-based integrative analysis of methylome and transcriptome identifies novel prognostic DNA methylation signature in uveal melanoma
LogicGep: Boolean networks inference using symbolic regression from time-series transcriptomic profiling data
Contrastive learning-based computational histopathology predict differential expression of cancer driver genes
MDF-SA-DDI: predicting drug-drug interaction events based on multi-source drug fusion, multi-source feature fusion and transformer self-attention mechanism
Making the difference: integrating structural variation detection tools
DeepBAM: a high-accuracy single-molecule CpG methylation detection tool for Oxford nanopore sequencing
TEnGExA: an R package based tool for tissue enrichment and gene expression analysis
Identifying correlations driven by influential observations in large datasets
De-motif sampling: an approach to decompose hierarchical motifs with applications in T cell recognition
Get ready to GO! A biologist's guide to the Gene Ontology
Graph databases in systems biology: a systematic review
Genome-wide discovery of pre-miRNAs: comparison of recent approaches based on machine learning
A comparative analysis of RNA-binding proteins binding models learned from RNAcompete, RNA Bind-n-Seq and eCLIP data