yusuke1997/dblp-id-title huggingface dataset:
Architecture for interoperable software in biology
Structural coverage of the human interactome
CAPE: a deep learning framework with Chaos-Attention net for Promoter Evolution
Characterizing the stabilization effects of stabilizers in protein-protein systems with end-point binding free energy calculations
Decoding competing endogenous RNA networks for cancer biomarker discovery
CRAFT: a bioinformatics software for custom prediction of circular RNA functions
LargeMetabo: an out-of-the-box tool for processing and analyzing large-scale metabolomic data
Attentional multi-level representation encoding based on convolutional and variance autoencoders for lncRNA-disease association prediction
Diffusion model assisted designing self-assembling collagen mimetic peptides as biocompatible materials
Evaluating long-read assemblers to assemble several aphididae genomes
Quick approximation of threshold values for genome-wide association studies
Computer-aided biomarker discovery for precision medicine: data resources, models and applications
Differentially expressed genes prediction by multiple self-attention on epigenetics data
Integrative-omics for discovery of network-level disease biomarkers: a case study in Alzheimer's disease
Multi-modal features-based human-herpesvirus protein-protein interaction prediction by using LightGBM
CBLRR: a cauchy-based bounded constraint low-rank representation method to cluster single-cell RNA-seq data
Correct machine learning on protein sequences: a peer-reviewing perspective
Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium
Inferring gene regulatory networks from time-series scRNA-seq data via GRANGER causal recurrent autoencoders
A review of methods and databases for metagenomic classification and assembly
MulNet: a scalable framework for reconstructing intra- and intercellular signaling networks from bulk and single-cell RNA-seq data
Gut microbiota: methodological aspects to describe taxonomy and functionality
SAGE-prot: scoring-assisted generative exploration for multi-objective protein design
KGANSynergy: knowledge graph attention network for drug synergy prediction
Detection call algorithms for high-throughput gene expression microarray data
Biological applications of knowledge graph embedding models
Recording negative results of protein-protein interaction assays: an easy way to deal with the biases and errors of interactomic data sets
Systems pharmacology: a combination strategy for improving efficacy of PD-1/PD-L1 blockade
Attention-based generative adversarial networks improve prognostic outcome prediction of cancer from multimodal data
Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation
Pharmacometabonomics: data processing and statistical analysis
Bioinformatics training: selecting an appropriate learning content management system - an example from the European Bioinformatics Institute
eSCAN: scan regulatory regions for aggregate association testing using whole-genome sequencing data
Computational methods to assist in the discovery of pharmacological chaperones for rare diseases
iceDP: identifying inter-chromatin engagement via density peaks clustering algorithm
Comparison of software packages for detecting differential expression in RNA-seq studies
Distinct effect of prenatal and postnatal brain expression across 20 brain disorders and anthropometric social traits: a systematic study of spatiotemporal modularity
Decoding heart failure subtypes with neural networks via differential explanation analysis
Synthetic plasma pool cohort correction for affinity-based proteomics datasets allows multiple study comparison
REDInet: a temporal convolutional network-based classifier for A-to-I RNA editing detection harnessing million known events
The mechanistic, diagnostic and therapeutic novel nucleic acids for hepatocellular carcinoma emerging in past score years
DSN-DDI: an accurate and generalized framework for drug-drug interaction prediction by dual-view representation learning
Exploiting Big Biology: Integrating Large-scale Biological Data for Function Inference
Facilitating prediction of adverse drug reactions by using knowledge graphs and multi-label learning models
Bioinformatics approaches for studying molecular sex differences in complex diseases
Predicting bacterial virulence factors - evaluation of machine learning and negative data strategies
FS-GBDT: identification multicancer-risk module via a feature selection algorithm by integrating Fisher score and GBDT
CeRNASeek: an R package for identification and analysis of ceRNA regulation
BlockPolish: accurate polishing of long-read assembly via block divide-and-conquer
The automatic annotation of bacterial genomes
A novel bioinformatics approach to identify the consistently well-performing normalization strategy for current metabolomic studies
TMBquant: an explainable AI-powered caller advancing tumor mutation burden quantification across heterogeneous samples
A comprehensive benchmarking for evaluating TCR embeddings in modeling TCR-epitope interactions
CloudATAC: a cloud-based framework for ATAC-Seq data analysis
Gene expression inference based on graph neural networks using L1000 data
Circular RNA identification based on multiple seed matching
Predicting microbe-drug associations with structure-enhanced contrastive learning and self-paced negative sampling strategy
The Made-In-Israel Bioinformatics Portal
Benchmarking digital PCR partition classification methods with empirical and simulated duplex data
Alignment-free inference of hierarchical and reticulate phylogenomic relationships
GAE-LGA: integration of multi-omics data with graph autoencoders to identify lncRNA-PCG associations
Gene set analysis methods for the functional interpretation of non-mRNA data - Genomic range and ncRNA data
A critical examination of stoichiometric and path-finding approaches to metabolic pathways
Porpoise: a new approach for accurate prediction of RNA pseudouridine sites
Data imbalance in CRISPR off-target prediction
MSGCL: inferring miRNA-disease associations based on multi-view self-supervised graph structure contrastive learning
Multi-modal chemical information reconstruction from images and texts for exploring the near-drug space
De novo sequencing of plant genomes using second-generation technologies
Toward molecular diagnosis of major depressive disorder by plasma peptides using a deep learning approach
Quantification of biases in predictions of protein-protein binding affinity changes upon mutations
Approaches to neuroscience data integration
A survey of available tools and web servers for analysis of protein-protein interactions and interfaces
Computational approaches and software tools for genetic linkage map estimation in plants
SAM-TB: a whole genome sequencing data analysis website for detection of Mycobacterium tuberculosis drug resistance and transmission
Resolving single-cell copy number profiling for large datasets
Structural and functional analyses of microbial metabolic networks reveal novel insights into genome-scale metabolic fluxes
PGS-server: accuracy, robustness and transferability of polygenic score methods for biobank scale studies
IHP-PING - generating integrated human protein-protein interaction networks on-the-fly
Analysis and Comparison of Metabolic Pathway Databases
SCEBE: an efficient and scalable algorithm for genome-wide association studies on longitudinal outcomes with mixed-effects modeling
Vir2Drug: a drug repurposing framework based on protein similarities between pathogens
Network integration and protein structural binding analysis of neurodegeneration-related interactome
AMDE: a novel attention-mechanism-based multidimensional feature encoder for drug-drug interaction prediction
Bioinformatics approaches for improved recombinant protein production in Escherichia coli: protein solubility prediction
DMFDDI: deep multimodal fusion for drug-drug interaction prediction
Molecular dynamics simulations for genetic interpretation in protein coding regions: where we are, where to go and when
Critical assessment of genome-scale metabolic networks: the need for a unified standard
Vec2image: an explainable artificial intelligence model for the feature representation and classification of high-dimensional biological data by vector-to-image conversion
RaacLogo: a new sequence logo generator by using reduced amino acid clusters
mRNA folding algorithms for structure and codon optimization
Computational resources and strategies to construct single-molecule metabolic models of microbial cells
Contrastive learning for enhancing feature extraction in anticancer peptides
From machine learning to clinical practice: phenotypic clusters of anti-MDA5 antibody-positive dermatomyositis
A review of databases predicting the effects of SNPs in miRNA genes or miRNA-binding sites
FRANC: a unified framework for multi-way local ancestry deconvolution with high density SNP data
Precision oncology: a review to assess interpretability in several explainable methods
Genome Sequence Comparisons: Hurdles in the Fast Lane to Functional Genomics
Computational methods for the detection of cis -regulatory modules
Advancing single-cell RNA-seq data analysis through the fusion of multi-layer perceptron and graph neural network
Mouse-human Comparative Map Resources on the Web
MoCoLo: a testing framework for motif co-localization
The hitchhikers' guide to RNA sequencing and functional analysis
iCRISEE: an integrative analysis of CRISPR screen by reducing false positive hits
Distinct telomere length and molecular signatures in seminoma and non-seminoma of testicular germ cell tumor
B-Lightning: using bait genes for marker gene hunting in single-cell data with complex heterogeneity
GA-GBLUP: leveraging the genetic algorithm to improve the predictability of genomic selection
TRAmHap: accurate prediction of transcriptional activity from DNA methylation haplotypes in bisulfite-sequencing data
FormulationAI: a novel web-based platform for drug formulation design driven by artificial intelligence
An updated overview of experimental and computational approaches to identify non-canonical DNA/RNA structures with emphasis on G-quadruplexes and R-loops
Ensuring privacy and security of genomic data and functionalities
Cooperative driver pathways discovery by multiplex network embedding
Visualizing time-related data in biology, a review
Computational methods, databases and tools for synthetic lethality prediction
Identification of cancer mini-drivers by deciphering selective landscape in the cancer genome
Consensus clustering with missing labels (ccml): a consensus clustering tool for multi-omics integrative prediction in cohorts with unequal sample coverage
Lysosome activation in peripheral blood mononuclear cells and prognostic significance of circulating LC3B in COVID-19
SingleFrag: a deep learning tool for MS/MS fragment and spectral prediction and metabolite annotation
Application of Bayesian phylogenetic inference modelling for evolutionary genetic analysis and dynamic changes in 2019-nCoV
AniAMPpred: artificial intelligence guided discovery of novel antimicrobial peptides in animal kingdom
Network-based methods for predicting essential genes or proteins: a survey
A deep learning-based method for the prediction of DNA interacting residues in a protein
Inter-domain distance prediction based on deep learning for domain assembly
Knowledge networks in the age of the Semantic Web
Bioinformatics education dissemination with an evolutionary problem solving perspective
NetMIM: network-based multi-omics integration with block missingness for biomarker selection and disease outcome prediction
Detecting expressed genes in cell populations at the single-cell level with scGeneXpress
Computational drug repositioning based on multi-similarities bilinear matrix factorization
Comparison and benchmark of structural variants detected from long read and long-read assembly
Network-based modeling of herb combinations in traditional Chinese medicine
QuantifyPoly(A): reshaping alternative polyadenylation landscapes of eukaryotes with weighted density peak clustering
Balancing the transcriptome: leveraging sample similarity to improve measures of gene specificity
The five pillars of computational reproducibility: bioinformatics and beyond
Multimodal zero-shot learning of previously unseen epitranscriptomes from RNA-seq data
Deep learning joint models for extracting entities and relations in biomedical: a survey and comparison
LDA-VGHB: identifying potential lncRNA-disease associations with singular value decomposition, variational graph auto-encoder and heterogeneous Newton boosting machine
A high-dimensional omnibus test for set-based association analysis
PhaGenus: genus-level classification of bacteriophages using a Transformer model
SGCLDGA: unveiling drug-gene associations through simple graph contrastive learning
Methods and resources to access mutation-dependent effects on cancer drug treatment
LR-GNN: a graph neural network based on link representation for predicting molecular associations
Pan-cancer analyses reveal regulation and clinical outcome association of the shelterin complex in cancer
miRDis: a Web tool for endogenous and exogenous microRNA discovery based on deep-sequencing data analysis
A comprehensive survey on computational methods of non-coding RNA and disease association prediction
Adjusting confounders in ranking biomarkers: a model-based ROC approach
PMiSLocMF: predicting miRNA subcellular localizations by incorporating multi-source features of miRNAs
Optimized detection of differential expression in global profiling experiments: case studies in clinical transcriptomic and quantitative proteomic datasets
Bioinformatics in the orphan crops
A solid quality-control analysis of AB SOLiD short-read sequencing data
Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences
Identify drug repurposing candidates by mining the Protein Data Bank
Integrating bioinformatic strategies in spatial life science research
Joint reconstruction of cis-regulatory interaction networks across multiple tissues using single-cell chromatin accessibility data
ABC-Net: a divide-and-conquer based deep learning architecture for SMILES recognition from molecular images
Novel ChIP-seq simulating program with superior versatility: isChIP
A comprehensive review on knowledge graphs for complex diseases
Detecting microsatellite instability by length comparison of microsatellites in the 3′ untranslated region with RNA-seq
Matrix factorization for biomedical link prediction and scRNA-seq data imputation: an empirical survey
Benchmarking methods for detecting differential states between conditions from multi-subject single-cell RNA-seq data
Functional Information in SWISS-PROT: the Basis for Large-scale Characterisation of Protein Sequences
iAMP-Attenpred: a novel antimicrobial peptide predictor based on BERT feature extraction method and CNN-BiLSTM-Attention combination model
Identifying and training deep learning neural networks on biomedical-related datasets
miniSNV: accurate and fast single nucleotide variant calling from nanopore sequencing data
Current efforts in the analysis of RNAi and RNAi target genes
microT-CNN: an avant-garde deep convolutional neural network unravels functional miRNA targets beyond canonical sites
MambaCpG: an accurate model for single-cell DNA methylation status imputation using mamba
MAResNet: predicting transcription factor binding sites by combining multi-scale bottom-up and top-down attention and residual network
Revisiting genome-wide association studies from statistical modelling to machine learning
GCdiscrimination: identification of gastric cancer based on a milliliter of blood
MMiKG: a knowledge graph-based platform for path mining of microbiota-mental diseases interactions
Deep-learning optimized DEOCSU suite provides an iterable pipeline for accurate ChIP-exo peak calling
Hypergraph-based persistent cohomology (HPC) for molecular representations in drug design
In silico tools for accurate HLA and KIR inference from clinical sequencing data empower immunogenetics on individual-patient and population scales
Application of in silico positional cloning and bioinformatic mutation analysis to the study of eye diseases
Identifying mutual exclusivity across cancer genomes: computational approaches to discover genetic interaction and reveal tumor vulnerability
Experience using web services for biological sequence analysis
Pragmatic soft-decision data readout of encoded large DNA
Robots as intelligent assistants to face COVID-19 pandemic
Essentiality-specific pathogenicity prioritization gene score to improve filtering of disease sequence data
Directed evolution of antimicrobial peptides using multi-objective zeroth-order optimization
A reproducibility analysis-based statistical framework for residue-residue evolutionary coupling detection
RSVdb: a comprehensive database of transcriptome RNA structure
Statistical methods for detecting differentially methylated regions based on MethylCap-seq data
Integrative pharmacological mechanism of vitamin C combined with glycyrrhizic acid against COVID-19: findings of bioinformatics analyses
Data mining in the Life Sciences with Random Forest: a walk in the park or lost in the jungle?
HCRNet: high-throughput circRNA-binding event identification from CLIP-seq data using deep temporal convolutional network
A selective review of robust variable selection with applications in bioinformatics
MOSim: bulk and single-cell multilayer regulatory network simulator
Quantifying Waddington's epigenetic landscape: a comparison of single-cell potency measures
Statistically designing microarrays and microarray experiments to enhance sensitivity and specificity
Integrated omics analysis reveals the alteration of gut microbe-metabolites in obese adults
What's the target: understanding two decades of in silico microRNA-target prediction
IGCNSDA: unraveling disease-associated snoRNAs with an interpretable graph convolutional network
Using traditional machine learning and deep learning methods for on- and off-target prediction in CRISPR/Cas9: a review
Measures for the degree of overlap of gene signatures and applications to TCGA
A large language model framework for literature-based disease-gene association prediction
A survey on adverse drug reaction studies: data, tasks and machine learning methods
FoldRec-C2C: protein fold recognition by combining cluster-to-cluster model and protein similarity network
Feature selection with vector-symbolic architectures: a case study on microbial profiles of shotgun metagenomic samples of colorectal cancer
An efficient approach to large-scale genotype-phenotype association analyses
Current Progress in computational metabolomics
Fuzzy kernel evidence Random Forest for identifying pseudouridine sites
A survey on computational models for predicting protein-protein interactions
Landscape of drug-resistance mutations in kinase regulatory hotspots
Investigating microRNA-mediated regulation of the nascent nuclear transcripts in plants: a bioinformatics workflow
BATMat: Bioinformatics Autodiscovery of Training Materials
A network-based algorithm for the identification of moonlighting noncoding RNAs and its application in sepsis
Pattern recognition and probabilistic measures in alignment-free sequence analysis
Pattern recognition in bioinformatics
Machine learning alternative to systems biology should not solely depend on data
PUTransGCN: identification of piRNA-disease associations based on attention encoding graph convolutional network and positive unlabelled learning
Cross-ancestry information transfer framework improves protein abundance prediction and protein-trait association identification
A microarray analysis for differential gene expression in the soybean genome using Bioconductor and R
Editorial: Bioinformatics and Economics
Enhancing protein dynamics analysis with hydrophilic polyethylene glycol cross-linkers
Comparison of microbiome samples: methods and computational challenges
miR+Pathway: the integration and visualization of miRNA and KEGG pathways
Integrated multi-omics with machine learning to uncover the intricacies of kidney disease
ETLD: an encoder-transformation layer-decoder architecture for protein contact and mutation effects prediction
kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes
ProtGraph: a tool for the quick and comprehensive exploration and exploitation of the peptide search space derived from protein sequence databases using graphs
Prediction of allosteric druggable pockets of cyclin-dependent kinases
Federated transfer learning with differential privacy for multi-omics survival analysis
Best practices in bioinformatics training for life scientists
CAFU: a Galaxy framework for exploring unmapped RNA-Seq data
ADEIP: an integrated platform of age-dependent expression and immune profiles across human tissues
Comprehensive review and evaluation of computational methods for identifying FLT3-internal tandem duplication in acute myeloid leukaemia
Computational analysis of miRNA targets in plants: current status and challenges
Deep transfer learning for clinical decision-making based on high-throughput data: comprehensive survey with benchmark results
Optimized patient-specific immune checkpoint inhibitor therapies for cancer treatment based on tumor immune microenvironment modeling
Network analytics for drug repurposing in COVID-19
Response to 'Letter to the Editor: on the stability and internal consistency of component-wise sparse mixture regression based clustering', Zhang et al.
miCGR: interpretable deep neural network for predicting both site-level and gene-level functional targets of microRNA
Deconvolution of spatial transcriptomics data via graph contrastive learning and partial least square regression
The role of quantitative structure-activity relationships (QSAR) in biomolecular discovery
Methods and protocols for prediction of immunogenic epitopes
A comprehensive review of protein-centric predictors for biomolecular interactions: from proteins to nucleic acids and beyond
Survey of MapReduce frame operation in bioinformatics
Assessing the performance of computational predictors for estimating protein stability changes upon missense mutations
A review of statistical methods for prediction of proteolytic cleavage
Clinical trials, progression-speed differentiating features and swiftness rule of the innovative targets of first-in-class drugs
A comprehensive method protocol for annotation and integrated functional understanding of lncRNAs
Enhancing LncRNA-miRNA interaction prediction with multimodal contrastive representation learning
Effect of normalization methods on the performance of supervised learning algorithms applied to HTSeq-FPKM-UQ data sets: 7SK RNA expression as a predictor of survival in patients with colon adenocarcinoma
Polygenic approaches to detect gene-environment interactions when external information is unavailable
Enhanced polygenic risk score incorporating gene-environment interaction suggests the association of major depressive disorder with cardiac and lung function
AntiCP 2.0: an updated model for predicting anticancer peptides
Deep learning in integrating spatial transcriptomics with other modalities
DeepCNV: a deep learning approach for authenticating copy number variations
ACLNDA: an asymmetric graph contrastive learning framework for predicting noncoding RNA-disease associations in heterogeneous graphs
'Artificial intelligence and machine learning in RNA biology'
A comprehensive review and comparison of existing computational methods for intrinsically disordered protein and region prediction
Multimodal contrastive learning for spatial gene expression prediction using histology images
A novel framework integrating AI model and enzymological experiments promotes identification of SARS-CoV-2 3CL protease inhibitors and activity-based probe
A comprehensive review of online resources for microRNA-diseases associations: the state of the art
RiboChat: a chat-style web interface for analysis and annotation of ribosome profiling data
Predicting miRNA-disease associations based on lncRNA-miRNA interactions and graph convolution networks
Performance evaluation of DNA copy number segmentation methods