yusuke1997/dblp-id-title huggingface dataset:
Transferring entropy to the realm of GxG interactions
Application of Atlas of Cancer Signalling Network in preclinical studies
ProFAB - open protein functional annotation benchmark
emPDBA: protein-DNA binding affinity prediction by combining features from binding partners and interface learned with ensemble regression model
Prediction of potential miRNA-disease associations based on stacked autoencoder
Survey and comparative assessments of computational multi-omics integrative methods with multiple regulatory networks identifying distinct tumor compositions across pan-cancer data sets
Single-cell causal network inferred by cross-mapping entropy
GLDADec: marker-gene guided LDA modeling for bulk gene expression deconvolution
Identifying protein complexes and functional modules - from static PPI networks to dynamic PPI networks
R5hmCFDV: computational identification of RNA 5-hydroxymethylcytosine based on deep feature fusion and deep voting
It is time to apply biclustering: a comprehensive review of biclustering applications in biological and biomedical data
Multi-Cover Persistence (MCP)-based machine learning for polymer property prediction
DBGRU-SE: predicting drug-drug interactions based on double BiGRU and squeeze-and-excitation attention mechanism
Can molecular dynamics simulations improve predictions of protein-ligand binding affinity with machine learning?
Generic framework for high-dimensional fixed-effects ANOVA
Individualized network-based drug repositioning infrastructure for precision oncology in the panomics era
A prediction model for blood-brain barrier penetrating peptides based on masked peptide transformers with dynamic routing
A comprehensive comparative review of sequence-based predictors of DNA- and RNA-binding residues
The framework for population epigenetic study
The microRNA target site landscape is a novel molecular feature associating alternative polyadenylation with immune evasion activity in breast cancer
Large-scale benchmark study of survival prediction methods using multi-omics data
STNGS: a deep scaffold learning-driven generation and screening framework for discovering potential novel psychoactive substances
A diagnostic genomic signal processing (GSP)-based system for automatic feature analysis and detection of COVID-19
Recent developments of software and database in microbial genomics and functional genomics
Single-cell RNA-seq data analysis reveals functionally relevant biomarkers of early brain development and their regulatory footprints in human embryonic stem cells (hESCs)
Novel multi-omics deconfounding variational autoencoders can obtain meaningful disease subtyping
XGSEA: CROSS-species gene set enrichment analysis via domain adaptation
preMLI: a pre-trained method to uncover microRNA-lncRNA potential interactions
Computational modeling of single-cell dynamics data
Cancerous time estimation for interpreting the evolution of lung adenocarcinoma
FG-BERT: a generalized and self-supervised functional group-based molecular representation learning framework for properties prediction
BioMOBY: An Open Source Biological Web Services Proposal
P-CSN: single-cell RNA sequencing data analysis by partial cell-specific network
GPU-powered tools boost molecular visualization
The global dissemination of bacterial infections necessitates the study of reverse genomic epidemiology
Interpretation of deep learning in genomics and epigenomics
Self-supervised learning with chemistry-aware fragmentation for effective molecular property prediction
TIMER is a Siamese neural network-based framework for identifying both general and species-specific bacterial promoters
CSM-carbohydrate: protein-carbohydrate binding affinity prediction and docking scoring function
Topological network measures for drug repositioning
Cell-type deconvolution for bulk RNA-seq data using single-cell reference: a comparative analysis and recommendation guideline
InterPro: An Integrated Documentation Resource for Protein Families, Domains and Functional Sites
Comparative analysis of molecular fingerprints in prediction of drug combination effects
Integrating genetic algorithms and language models for enhanced enzyme design
Extensible open source content management systems and frameworks: a solution for many needs of a bioinformatics group
Bioinformatic analysis of SMN1-ACE/ACE2 interactions hinted at a potential protective effect of spinal muscular atrophy against COVID-19-induced lung injury
Adverse events associated with potential drugs for COVID-19: a case study from real-world data
Shared-weight graph framework for comprehensive protein stability prediction across diverse mutation types
On the limits of active module identification
Finding sequence motifs in prokaryotic genomes - a brief practical guide for a microbiologist
Characteristics of plant circular RNAs
A comprehensive benchmark of tools for efficient genomic interval querying
Gene-set analysis and reduction
multi-type neighbors enhanced global topology and pairwise attribute learning for drug-protein interaction prediction
Bioinformatics approaches for functional annotation of membrane proteins
Comparative host-pathogen protein-protein interaction analysis of recent coronavirus outbreaks and important host targets identification
THItoGene: a deep learning method for predicting spatial transcriptomics from histological images
Application of non-negative matrix factorization in oncology: one approach for establishing precision medicine
Dimensionality reduction and visualization of single-cell RNA-seq data with an improved deep variational autoencoder
PLP_FS: prediction of lysine phosphoglycerylation sites in protein using support vector machine and fusion of multiple F_Score feature selection
Development and application of an efficient genomic mating method to maximize the production performances of three-way crossbred pigs
CRMSS: predicting circRNA-RBP binding sites based on multi-scale characterizing sequence and structure features
Bioinformatic analysis of bacteria and host cell dual RNA-sequencing experiments
Extended application of genomic selection to screen multiomics data for prognostic signatures of prostate cancer
Public data and open source tools for multi-assay genomic investigation of disease
vsRNAfinder: a novel method for identifying high-confidence viral small RNAs from small RNA-Seq data
HPV-KITE: sequence analysis software for rapid HPV genotype detection
Application of deep learning methods in biological networks
A review of validation strategies for computational drug repositioning
Machine learning application for patient stratification and phenotype/genotype investigation in a rare disease
Multimodal deep learning approaches for single-cell multi-omics data integration
Erratum to: Machine learning approaches and databases for prediction of drug-target interaction: a survey paper
Developing intuitive and explainable algorithms through inspiration from human physiology and computational biology
Demographic confounders distort inference of gene regulatory and gene co-expression networks in cancer
Application of second-generation sequencing to cancer genomics
Critical evaluation of web-based prediction tools for human protein subcellular localization
TERL: classification of transposable elements by convolutional neural networks
Deciphering the etiology and role in oncogenic transformation of the CpG island methylator phenotype: a pan-cancer analysis
Integrated multimodal hierarchical fusion and meta-learning for enhanced molecular property prediction
Mol2Context-vec: learning molecular representation from context awareness for drug discovery
The substitution spectra of coronavirus genomes
scIAE: an integrative autoencoder-based ensemble classification framework for single-cell RNA-seq data
Universal concept signature analysis: genome-wide quantification of new biological and pathological functions of genes and pathways
AFEI: adaptive optimized vertical federated learning for heterogeneous multi-omics data integration
Cooperation of structural motifs controls drug selectivity in cyclin-dependent kinases: an advanced theoretical analysis
Classification of metagenomic sequences: methods and challenges
A statistical framework for predicting critical regions of p53-dependent enhancers
Developing computational model-based diagnostics to analyse clinical chemistry data
Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities
PathSynergy: a deep learning model for predicting drug synergy in liver cancer
Multigene editing: current approaches and beyond
Evaluating approaches to find exon chains based on long reads
CHAI: consensus clustering through similarity matrix integration for cell-type identification
2OM-Pred: prediction of 2- O -methylation sites in ribonucleic acid using diverse classifiers
Identifying the natural polyphenol catechin as a multi-targeted agent against SARS-CoV-2 for the plausible therapy of COVID-19: an integrated computational approach
MinE-RFE: determine the optimal subset from RFE by minimizing the subset-accuracy-defined energy
Adaptive multi-view information bottleneck for multi-omics data clustering
BioWorkflow: Retrieving comprehensive bioinformatics workflows from publications
Positive-unlabeled learning in bioinformatics and computational biology: a brief review
Identification of biomarkers and pathways for the SARS-CoV-2 infections that make complexities in pulmonary arterial hypertension patients
Deep-ABPpred: identifying antibacterial peptides in protein sequences using bidirectional LSTM with word2vec
Assessing deep learning methods in cis-regulatory motif finding based on genomic sequencing data
CanDriS: posterior profiling of cancer-driving sites based on two-component evolutionary model
Demystifying emerging bulk RNA-Seq applications: the application and utility of bioinformatic methodology
A comprehensive overview and critical evaluation of gene regulatory network inference technologies
Proteomic Databases and Software on the Web
Revealing the contribution of somatic gene mutations to shaping tumor immune microenvironment
Building a virtual ligand screening pipeline using free software: a survey
Hound: a novel tool for automated mapping of genotype to phenotype in bacterial genomes assembled de novo
Ortholog identification in the presence of domain architecture rearrangement
Why can deep convolutional neural networks improve protein fold recognition? A visual explanation by interpretation
On the influence of several factors on pathway enrichment analysis
AdaPPI: identification of novel protein functional modules via adaptive graph convolution networks in a protein-protein interaction network
MicroHDF: predicting host phenotypes with metagenomic data using a deep forest-based framework
Learning to SMILES: BAN-based strategies to improve latent representation learning from molecules
Bibliometric review of ATAC-Seq and its application in gene expression
GP4: an integrated Gram-Positive Protein Prediction Pipeline for subcellular localization mimicking bacterial sorting
Transcription factors-DNA interactions in rice: identification and verification
Short EMBOSS User Guide
Denoising DNA deep sequencing data - high-throughput sequencing errors and their correction
Corrigendum to: Dating admixture events is unsolved problem in multi-way admixed populations
Obituary: In memory of Jack Leunissen
Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6
AttenRNA: multi-scale deep attentive model with RNA feature variability analysis
Evolving research trends in bioinformatics
Systematic review regulatory principles of non-coding RNAs in cardiovascular diseases
Resolving complex structures at oncovirus integration loci with conjugate graph
cyclicpeptide : a Python package for cyclic peptide drug design
Computational proteomics: management and analysis of proteomics data
Positional orthology: putting genomic evolutionary relationships into context
BAMBI integrates biostatistical and artificial intelligence methods to improve RNA biomarker discovery
Genome assembly reborn: recent computational challenges
Identification of aberrant pathways and network activities from high-throughput data
Knowledge-based classification of fine-grained immune cell types in single-cell RNA-Seq data
Software review: Analysis for free: Comparing programs for sequence analysis
DeepLncLoc: a deep learning framework for long non-coding RNA subcellular localization prediction based on subsequence embedding
Assessing the consistency of public human tissue RNA-seq data sets
Privacy-preserving techniques of genomic data - a survey
Hiplot: a comprehensive and easy-to-use web service for boosting publication-ready biomedical data visualization
MDNN: memetic deep neural network for genomic prediction
CAIM: coverage-based analysis for identification of microbiome
CMFHMDA: a prediction framework for human disease-microbe associations based on cross-domain matrix factorization
A comprehensive overview of Infinium HumanMethylation450 data processing
Prediction of RNA-binding protein and alternative splicing event associations during epithelial-mesenchymal transition based on inductive matrix completion
bayesynergy: flexible Bayesian modelling of synergistic interaction effects in in vitro drug combination experiments
Recent advances in biomedical literature mining
Mathematics of Evolution and Phylogeny, Edited by Olivier Gascuel
sOCP: a framework predicting smORF coding potential based on TIS and in-frame features and effectively applied in the human genome
Long non-coding RNAs and complex diseases: from experimental results to computational models
COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker data model
An account of in silico identification tools of secreted effector proteins in bacteria and future challenges
The landscape of miRNA-related ceRNA networks for marking different renal cell carcinoma subtypes
Ensemble modeling with machine learning and deep learning to provide interpretable generalized rules for classifying CNS drugs with high prediction power
A benchmark of gene expression tissue-specificity metrics
A deep transfer learning-based protocol accelerates full quantum mechanics calculation of protein
A review on drug repurposing applicable to COVID-19
MCANet: shared-weight-based MultiheadCrossAttention network for drug-target interaction prediction
Revealing the antimicrobial potential of traditional Chinese medicine through text mining and molecular computation
iACVP: markedly enhanced identification of anti-coronavirus peptides using a dataset-specific word2vec model
Protein side-chain packing problem: is there still room for improvement?
Detection of somatic structural variants from short-read next-generation sequencing data
GWAS summary-based pathway analysis correcting for the genetic confounding impact of environmental exposures
Review and meta-analysis of the genetic Minimal Cut Set approach for gene essentiality prediction in cancer metabolism
Towards accurate human promoter recognition: a review of currently used sequence features and classification methods
A metagene based similarity network fusion approach for multi-omics data integration identified novel subtypes in renal cell carcinoma
Multiview representation learning for identification of novel cancer genes and their causative biological mechanisms
D3AI-CoV: a deep learning platform for predicting drug targets and for virtual screening against COVID-19
In the loop: promoter-enhancer interactions and bioinformatics
Facts from text: can text mining help to scale-up high-quality manual curation of gene products with ontologies?
Deep generative model for therapeutic targets using transcriptomic disease-associated data - USP7 case study
Structure-based drug repurposing against COVID-19 and emerging infectious diseases: methods, resources and discoveries
HMM-based databases in InterPro
In silico tools for signal transduction research
In silico representation and discovery of transcription factor binding sites
TriTan: an efficient triple nonnegative matrix factorization method for integrative analysis of single-cell multiomics data
Sharing sensitive data in life sciences: an overview of centralized and federated approaches
Biological knowledge management: the emerging role of the Semantic Web technologies
SuperCUT, an unsupervised multimodal image registration with deep learning for biomedical microscopy
EGRET: edge aggregated graph attention networks and transfer learning improve protein-protein interaction site prediction
Letter on the results of the BASiNET method in the paper 'A systematic evaluation of computational tools for lncRNA identification'
ifDEEPre: large protein language-based deep learning enables interpretable and fast predictions of enzyme commission numbers
Logistic tensor decomposition with sparse subspace learning for prediction of multiple disease types of human-virus protein-protein interactions
Online tools for understanding rat physiology
Using provenance to manage knowledge of In Silico experiments
CircView: a visualization and exploration tool for circular RNAs
Updates on drug-target network; facilitating polypharmacology and data integration by growth of DrugBank database
Morphological profiling for drug discovery in the era of deep learning
ConsRM: collection and large-scale prediction of the evolutionarily conserved RNA methylation sites, with implications for the functional epitranscriptome
GESLM algorithm for detecting causal SNPs in GWAS with multiple phenotypes
GVDTI: graph convolutional and variational autoencoders with attribute-level attention for drug-protein interaction prediction
Network approaches for modeling the effect of drugs and diseases
Machine learning methods for prediction of cancer driver genes: a survey paper
Visualizing next-generation sequencing data with JBrowse
Integrative analysis of multi-omics and imaging data with incorporation of biological information via structural Bayesian factor analysis
Combinatorial epigenetic regulation of non-coding RNAs has profound effects on oncogenic pathways in breast cancer subtypes
Evolutionary and codon usage preference insights into spike glycoprotein of SARS-CoV-2
Improved structure-related prediction for insufficient homologous proteins using MSA enhancement and pre-trained language model
A comparative study of rank aggregation methods for partial and top ranked lists in genomic applications
Dynamic-BM: multispecies Dynamic BodyMap database from temporal RNA-seq data
SGCAST: symmetric graph convolutional auto-encoder for scalable and accurate study of spatial transcriptomics
Crowdsourcing in biomedicine: challenges and opportunities
PredictONCO: a web tool supporting decision-making in precision oncology by extending the bioinformatics predictions with advanced computing and machine learning
Blood-based transcriptomic signature panel identification for cancer diagnosis: benchmarking of feature extraction methods
Engineering Virtual Cardiac Tissue
3D-SMGE: a pipeline for scaffold-based molecular generation and evaluation
GiGs: graph-based integrated Gaussian kernel similarity for virus-drug association prediction
Spatially contrastive variational autoencoder for deciphering tissue heterogeneity from spatially resolved transcriptomics
A computational framework for the inheritance pattern of genomic imprinting for complex traits
S2DV: converting SMILES to a drug vector for predicting the activity of anti-HBV small molecules
H2Opred: a robust and efficient hybrid deep learning model for predicting 2'-O-methylation sites in human RNA
The digital revolution in phenotyping
Understanding relationships between epigenetic marks and their application to robust assignment of chromatin states
Integrating multi-scale neighbouring topologies and cross-modal similarities for drug-protein interaction prediction
PHIAF: prediction of phage-host interactions with GAN-based data augmentation and sequence-based feature fusion
Scoring alignments by embedding vector similarity
sAMP-PFPDeep: Improving accuracy of short antimicrobial peptides prediction using three different sequence encodings and deep neural networks
Knowledge-guided multi-level network modeling with experimental characterization identifies PRKCA as a novel biomarker and tumor suppressor triggering ferroptosis in prostate cancer
DeepCPP: a deep neural network based on nucleotide bias information and minimum distribution similarity feature selection for RNA coding potential prediction
TSNAPred: predicting type-specific nucleic acid binding residues via an ensemble approach
Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology
Beware of the generic machine learning-based scoring functions in structure-based virtual screening
Analysis of selection in protein-coding sequences accounting for common biases
Stratified neural networks in a time-to-event setting
Benchmarking CRISPR on-target sgRNA design
A network medicine approach to build a comprehensive atlas for the prognosis of human cancer
PreDTIs: prediction of drug-target interactions based on multiple feature information using gradient boosting framework with data balancing and feature selection techniques
Bioinformatic approaches to blood and tissue microbiome analyses: challenges and perspectives
RNA trafficking and subcellular localization - a review of mechanisms, experimental and predictive methodologies
Concepts and methods for transcriptome-wide prediction of chemical messenger RNA modifications with machine learning
A deep learning model to identify gene expression level using cobinding transcription factor signals
MathFeature: feature extraction package for DNA, RNA and protein sequences based on mathematical descriptors
MSFT-transformer: a multistage fusion tabular transformer for disease prediction using metagenomic data
MTD: a mammalian transcriptomic database to explore gene expression and regulation
HiC4D: forecasting spatiotemporal Hi-C data with residual ConvLSTM
IMOVNN: incomplete multi-omics data integration variational neural networks for gut microbiome disease prediction and biomarker identification
Multi-view multi-level contrastive graph convolutional network for cancer subtyping on multi-omics data
Bioinformatics/network topology analysis of acupuncture in the treatment of COVID-19: response to methodological issues
Comparative analysis of machine learning algorithms on the microbial strain-specific AMP prediction
Evaluation of graphical models for multi-group metabolomics data
Spatial proximity and gene function: a new dimension in prokaryotic gene association network analysis with 3D-GeneNet
Editorial: Current progress in Bioinformatics 2012
A landscape of synthetic viable interactions in cancer
UPicker: a semi-supervised particle picking transformer method for cryo-EM micrographs
NSL2CD: identifying potential circRNA-disease associations based on network embedding and subspace learning
MOFormer: navigating the antimicrobial peptide design space with Pareto-based multi-objective transformer
Evaluation of propensity score methods for causal inference with high-dimensional covariates
SPCS: a spatial and pattern combined smoothing method for spatial transcriptomic expression
Evaluating discrepancies in dimensionality reduction for time-series single-cell RNA-sequencing data
IMOP-Cancer: identifying mutation order pairs impacting cancer phenotypes
Discriminative pattern mining and its applications in bioinformatics
Next-generation Bioinformatics: connecting bases to genes, networks and disease
Platform-independent approach for cancer detection from gene expression profiles of peripheral blood cells
RNAlight: a machine learning model to identify nucleotide features determining RNA subcellular localization
Arabidopsis Genome Analysis As Exemplified By Analysis of Chromosome 4
Large scale RNA-binding proteins/LncRNAs interaction analysis to uncover lncRNA nuclear localization mechanisms
SSG-LUGIA: Single Sequence based Genome Level Unsupervised Genomic Island Prediction Algorithm
Review: High-performance computing to detect epistasis in genome scale data sets
META-DDIE: predicting drug-drug interaction events with few-shot learning
Evaluation and comparison of methods for recapitulation of 3D spatial chromatin structures