yusuke1997/dblp-id-title huggingface dataset:
BertTCR: a Bert-based deep learning framework for predicting cancer-related immune status based on T cell receptor repertoire
A hybrid positive unlabeled learning framework for uncovering scaffolds across human proteome by measuring the propensity to drive phase separation
Gene expression profiling of SARS-CoV-2 infections reveal distinct primary lung cell and systemic immune infection responses that identify pathways relevant in COVID-19 disease
Erratum to: LARMD: integration of bioinformatic resources to profile ligand-driven protein dynamics with a case on the activation of estrogen receptor
Dissection of human MiRNA regulatory influence to subpathway
Multi-variable AUC for sifting complementary features and its biomedical application
ProjectSVR: mapping single-cell RNA-seq data to reference atlases by supported vector regression
Toward more accurate pan-specific MHC-peptide binding prediction: a review of current methods and tools
Application of deep learning in cancer epigenetics through DNA methylation analysis
Model parameters of molecular evolution explain genomic correlations
MlyPredCSED: based on extreme point deviation compensated clustering combined with cross-scale convolutional neural networks to predict multiple lysine sites in human
PolyAtailor: measuring poly(A) tail length from short-read and long-read sequencing data
Deleterious synonymous mutation identification based on selective ensemble strategy
Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases
Few-shot classification of Cryo-ET subvolumes with deep Brownian distance covariance
Rapid innovation in ChIP-seq peak-calling algorithms is outdistancing benchmarking efforts
SSI-DDI: substructure-substructure interactions for drug-drug interaction prediction
MoDAFold: a strategy for predicting the structure of missense mutant protein based on AlphaFold2 and molecular dynamics
Transcriptional landscape of cholangiocarcinoma revealed by weighted gene coexpression network analysis
The BREW workshop series: a stimulating experience in PhD education
Deep learning models for disease-associated circRNA prediction: a review
Corrigendum to: gm RAD: an integrated SNP calling pipeline for genetic mapping with RADseq across a hybrid population
SynergyX: a multi-modality mutual attention network for interpretable drug synergy prediction
Mapping cancer heterogeneity: a consensus network approach to subtypes and pathways
A fully differentiable ligand pose optimization framework guided by deep learning and a traditional scoring function
ConSpaS: a contrastive learning framework for identifying spatial domains by integrating local and global similarities
An overview of image-processing methods for Affymetrix GeneChips
Challenges and opportunities in network-based solutions for biological questions
iGTP: learning interpretable cellular embedding for inferring biological mechanisms underlying single-cell transcriptomics
MOAI: a multi-outcome interaction identification approach reveals an interaction between vaspin and carcinoembryonic antigen on colorectal cancer prognosis
Studying statistical properties of regulatory DNA sequences, and their use in predicting regulatory regions in the eukaryotic genomes
PB-LKS: a python package for predicting phage-bacteria interaction through local K-mer strategy
Statistical modeling and significance estimation of multi-way chromatin contacts with HyperloopFinder
Multi-omics approaches for revealing the complexity of cardiovascular disease
Inflated false discovery rate due to volcano plots: problem and solutions
DMRU: generative deep learning to unravel condition-specific cytosine methylation in plants
DCiPatho: deep cross-fusion networks for genome scale identification of pathogens
Learning directed acyclic graphs for ligands and receptors based on spatially resolved transcriptomic data of ovarian cancer
Opportunities and challenges for ChatGPT and large language models in biomedicine and health
TPD: a web tool for tipping-point detection based on dynamic network biomarker
Identification of miRNA-disease associations via deep forest ensemble learning based on autoencoder
scGIR: deciphering cellular heterogeneity via gene ranking in single-cell weighted gene correlation networks
Cell-specific priors rescue differential gene expression in spatial spot-based technologies
BERT-TFBS: a novel BERT-based model for predicting transcription factor binding sites by transfer learning
Letter to the Editor: On Reviews and Papers on New Methods
Serverless computing in omics data analysis and integration
Artificial intelligence in the prediction of protein-ligand interactions: recent advances and future directions
ReadCurrent: a VDCNN-based tool for fast and accurate nanopore selective sequencing
AI for predicting chemical-effect associations at the chemical universe level - <tt>deepFPlearn</tt>
ISAnalytics enables longitudinal and high-throughput clonal tracking studies in hematopoietic stem cell gene therapy applications
NSRGRN: a network structure refinement method for gene regulatory network inference
New insights on human essential genes based on integrated analysis and the construction of the HEGIAP web-based platform
Machine learning on ligand-residue interaction profiles to significantly improve binding affinity prediction
Robust detection of infectious disease, autoimmunity, and cancer from the paratope networks of adaptive immune receptors
BIB's first impact factor is 24.37
DRONet: effectiveness-driven drug repositioning framework using network embedding and ranking learning
Artificial intelligence-driven circRNA vaccine development: multimodal collaborative optimization and a new paradigm for biomedical applications
Swiss-Prot: Juggling between evolution and stability
Systematic identification of Class I HDAC substrates
Computational methods to identify metabolic sub-networks based on metabolomic profiles
An empirical likelihood ratio test robust to individual heterogeneity for differential expression analysis of RNA-seq
Comprehensive evaluation of computational methods for predicting cancer driver genes
MG-BERT: leveraging unsupervised atomic representation learning for molecular property prediction
Biofilm marker discovery with cloud-based dockerized metagenomics analysis of microbial communities
Evaluation of preprocessing, mapping and postprocessing algorithms for analyzing whole genome bisulfite sequencing data
Comparative analysis of methods for identifying somatic copy number alterations from deep sequencing data
A comparative evaluation on prediction methods of nucleosome positioning
Decoding multilevel relationships with the human tissue-cell-molecule network
A microbial knowledge graph-based deep learning model for predicting candidate microbes for target hosts
Benchmarking copy number aberrations inference tools using single-cell multi-omics datasets
Comprehensive evaluation of non-hybrid genome assembly tools for third-generation PacBio long-read sequence data
Predicting differentially methylated cytosines in TET and DNMT3 knockout mutants via a large language model
Contrastively generative self-expression model for single-cell and spatial multimodal data
PrimeNet: rational design of Prime editing pegRNAs by deep learning
Epitope Scanning Using Virtual Matrix-based Algorithms
Decoupled GNNs based on multi-view contrastive learning for scRNA-seq data clustering
Revolutionizing GPCR-ligand predictions: DeepGPCR with experimental validation for high-precision drug discovery
HGCMLDA: predicting lncRNA-disease associations using hypergraph contrastive learning and multi-scale attentional feature fusion
De novo molecular design with deep molecular generative models for PPI inhibitors
A biology-driven deep generative model for cell-type annotation in cytometry
AlphaFold2-aware protein-DNA binding site prediction using graph transformer
Research on RNA modification in disease diagnosis and prognostic biomarkers: current status and challenges
From data to diagnosis: how machine learning is revolutionizing biomarker discovery in idiopathic inflammatory myopathies
Machine-learning scoring functions trained on complexes dissimilar to the test set already outperform classical counterparts on a blind benchmark
Text mining and ontologies in biomedicine: Making sense of raw text
Chemical structure-aware molecular image representation learning
A novel splicing graph allows a direct comparison between exon-based and splice junction-based approaches to alternative splicing detection
Evaluation of ontology structural metrics based on public repository data
Optimized combination methods for exploring and verifying disease-resistant transcription factors in melon
Reconciliation of metabolites and biochemical reactions for metabolic networks
Tutorial Section: Entrez: Making Use of Its Power
Integrated network analysis reveals new genes suggesting COVID-19 chronic effects and treatment
On the classification of microarray gene-expression data
Mining of Assembled Expressed Sequence Tag (EST) Data for Protein Families: Application to the G Protein-coupled Receptor Superfamily
Gram matrix: an efficient representation of molecular conformation and learning objective for molecular pretraining
Semantic Web for Health Care and Life Sciences: a review of the state of the art
Beyond rigid docking: deep learning approaches for fully flexible protein-ligand interactions
Tutorial videos of bioinformatics resources: online distribution trial in Japan named TogoTV
StackTADB: a stacking-based ensemble learning model for predicting the boundaries of topologically associating domains (TADs) accurately in fruit flies
Benchmarking of computational demultiplexing methods for single-nucleus RNA sequencing data
Deciphering the genetic code of DNA methylation
Comprehensive assessment of nine docking programs on type II kinase inhibitors: prediction accuracy of sampling power, scoring power and screening power
Performance of gene expression-based single sample predictors for assessment of clinicopathological subgroups and molecular subtypes in cancers: a case comparison study in non-small cell lung cancer
Detection of human interchromosomal trans -splicing in sequence databanks
Understanding the unimodal distributions of cancer occurrence rates: it takes two factors for a cancer to occur
PROSE: phenotype-specific network signatures from individual proteomic samples
RNADiffFold: generative RNA secondary structure prediction using discrete diffusion models
Predicting drug-drug interactions by graph convolutional network with multi-kernel
Transcription factor and microRNA co-regulatory loops: important regulatory motifs in biological processes and diseases
P l DBPred: a novel computational model for discovery of DNA binding proteins in plants
Translational medicine in the Age of Big Data
SpatialcoGCN: deconvolution and spatial information-aware simulation of spatial transcriptomics data via deep graph co-embedding
Rank normalization empowers a t-test for microbiome differential abundance analysis while controlling for false discoveries
Iterative error correction of long sequencing reads maximizes accuracy and improves contig assembly
Monovalent and divalent salt correction algorithms for T m prediction - recommendations for Primer3 usage
GexMolGen: cross-modal generation of hit-like molecules via large language model encoding of gene expression signatures
TransPTM: a transformer-based model for non-histone acetylation site prediction
An Approach to Modelling in Immunology
Analysis of Large-scale Gene Expression Data
Reducing healthcare disparities using multiple multiethnic data distributions with fine-tuning of transfer learning
OPUS-Rota4: a gradient-based protein side-chain modeling framework assisted by deep learning-based predictors
Learning deep features and topological structure of cells for clustering of scRNA-sequencing data
Predicting the function of rice proteins through Multi-instance Multi-label Learning based on multiple features fusion
Persistent Tor-algebra for protein-protein interaction analysis
A survey of current trends in computational drug repositioning
Transcriptome analysis of cepharanthine against a SARS-CoV-2-related coronavirus
VGAE-CCI: variational graph autoencoder-based construction of 3D spatial cell-cell communication network
Evolution of web services in bioinformatics
The small peptide world in long noncoding RNAs
scMHNN: a novel hypergraph neural network for integrative analysis of single-cell epigenomic, transcriptomic and proteomic data
Annual Progress in Bioinformatics 2006
Community curation of bioinformatics software and data resources
Deep learning meets metabolomics: a methodological perspective
Comprehensive characterization genetic regulation and chromatin landscape of enhancer-associated long non-coding RNAs and their implication in human cancer
Supervised analysis of alternative polyadenylation from single-cell and spatial transcriptomics data with spvAPA
A survey on computational strategies for genome-resolved gut metagenomics
DeepPBI-KG: a deep learning method for the prediction of phage-bacteria interactions based on key genes
A reversed framework for the identification of microRNA-target pairs in plants
Closing the circle: current state and perspectives of circular RNA databases
Protein complex structure prediction powered by multiple sequence alignments of interologs from multiple taxonomic ranks and AlphaFold2
3DGT-DDI: 3D graph and text based neural network for drug-drug interaction prediction
Forecasting dominance of SARS-CoV-2 lineages by anomaly detection using deep AutoEncoders
Scaling the walls of discovery: using semantic metadata for integrative problem solving
MicroRNA annotation in plants: current status and challenges
Computational prediction and interpretation of cell-specific replication origin sites from multiple eukaryotes by exploiting stacking framework
Detection of pan-cancer surface protein biomarkers via a network-based approach on transcriptomics data
FluReassort: a database for the study of genomic reassortments among influenza viruses
Editorial: Modelling Cell Systems - The Post-genomic Challenge
Computational systems biology and in silico modeling of the human microbiome
Learning genotype-phenotype associations from gaps in multi-species sequence alignments
A guide to web tools to prioritize candidate genes
DSEATM: drug set enrichment analysis uncovering disease mechanisms by biomedical text mining
DRISEE overestimates errors in metagenomic sequencing data
PPMS: A framework to Profile Primary MicroRNAs from Single-cell RNA-sequencing datasets
SGNNMD: signed graph neural network for predicting deregulation types of miRNA-disease associations
Leveraging scaffold information to predict protein-ligand binding affinity with an empirical graph neural network
GuidingNet: revealing transcriptional cofactor and predicting binding for DNA methyltransferase by network regularization
A survey and evaluation of Web-based tools/databases for variant analysis of TCGA data
ConvNeXt-MHC: improving MHC-peptide affinity prediction by structure-derived degenerate coding and the ConvNeXt model
The functional determinants in the organization of bacterial genomes
Multi-task prediction-based graph contrastive learning for inferring the relationship among lncRNAs, miRNAs and diseases
sRNAfrag: a pipeline and suite of tools to analyze fragmentation in small RNA sequencing data
Rare variant association test in family-based sequencing studies
A high-throughput single cell-based antibody discovery approach against the full-length SARS-CoV-2 spike protein suggests a lack of neutralizing antibodies targeting the highly conserved S2 domain
SimCH: simulation of single-cell RNA sequencing data by modeling cellular heterogeneity at gene expression level
Deciphering gene expression patterns using large-scale transcriptomic data and its applications
Comparative analyses of gene networks mediating cancer metastatic potentials across lineage types
Machine learning for RNA 2D structure prediction benchmarked on experimental data
An absolute human stemness index associated with oncogenic dedifferentiation
ATTIC is an integrated approach for predicting A-to-I RNA editing sites in three species
Predicting miRNA-disease associations using an ensemble learning framework with resampling method
Improved protein contact prediction using dimensional hybrid residual networks and singularity enhanced loss function
Exact mapping of prokaryotic gene starts
Building an HIV data mashup using Bio2RDF
Inferring single-cell gene regulatory network by non-redundant mutual information
Subtype-WESLR: identifying cancer subtype with weighted ensemble sparse latent representation of multi-view data
Genome-wide functional association networks: background, data & state-of-the-art resources
Proteome-scale analysis of phase-separated proteins in immunofluorescence images
Expression profiling of microRNAs by deep sequencing
Detection of transcription factors binding to methylated DNA by deep recurrent neural network
Filtering out the noise: metagenomic classifiers optimize ancient DNA mapping
Biological applications of support vector machines
Kernel methods for large-scale genomic data analysis
A model for pH coupling of the SARS-CoV-2 spike protein open/closed equilibrium
DeepRNA-Twist: language-model-guided RNA torsion angle prediction with attention-inception network
Systems mapping: how to map genes for biomass allocation toward an ideotype
Pf-Phospho: a machine learning-based phosphorylation sites prediction tool for Plasmodium proteins
A comprehensive comparative assessment of 3D molecular similarity tools in ligand-based virtual screening
HCOP: a searchable database of human orthology predictions
VPatho: a deep learning-based two-stage approach for accurate prediction of gain-of-function and loss-of-function variants
A geometric deep learning framework for drug repositioning over heterogeneous information networks
Disentangling the complexity of low complexity proteins
An initial game-theoretic assessment of enhanced tissue preparation and imaging protocols for improved deep learning inference of spatial transcriptomics from tissue morphology
Combining power of different methods to detect associations in large data sets
A novel computational model ITHCS for enhanced prognostic risk stratification in ESCC by correcting for intratumor heterogeneity
Inference of gene regulatory networks based on directed graph convolutional networks
Robust self-supervised learning strategy to tackle the inherent sparsity in single-cell RNA-seq data
Heterogeneous cryo-EM projection image classification using a two-stage spectral clustering based on novel distance measures
Optimal fusion of genotype and drug embeddings in predicting cancer drug response
RNA-mediated translation regulation in viral genomes: computational advances in the recognition of sequences and structures
A comprehensive drug repurposing study for COVID19 treatment: novel putative dihydroorotate dehydrogenase inhibitors show association to serotonin-dopamine receptors
Bioinformatics for Biologists. Edited by Pavel Pevzner and Ron Shamir
Recent computational developments on CLIP-seq data analysis and microRNA targeting implications
BloodProST: prediction of blood-secretory proteins through self-training
A merged molecular representation deep learning method for blood-brain barrier permeability prediction
Forman persistent Ricci curvature (FPRC)-based machine learning models for protein-ligand binding affinity prediction
Towards routine employment of computational tools for antimicrobial resistance determination via high-throughput sequencing
Molecular group and correlation guided structural learning for multi-phenotype prediction
VRprofile: gene-cluster-detection-based profiling of virulence and antibiotic resistance traits encoded within genome sequences of pathogenic bacteria
A transformer-based deep learning survival prediction model and an explainable XGBoost anti-PD-1/PD-L1 outcome prediction model based on the cGAS-STING-centered pathways in hepatocellular carcinoma
Improving protein-ligand docking and screening accuracies by incorporating a scoring function correction term
Unsupervised and supervised AI on molecular dynamics simulations reveals complex characteristics of HLA-A2-peptide immunogenicity
Advanced computing for systems biology
ALDPI: adaptively learning importance of multi-scale topologies and multi-modality similarities for drug-protein interaction prediction
Is acupuncture effective in the treatment of COVID-19 related symptoms? Based on bioinformatics/network topology strategy
Global Computing for Bioinformatics
Assessing computational predictions of antimicrobial resistance phenotypes from microbial genomes
Persistent spectral simplicial complex-based machine learning for chromosomal structural analysis in cellular differentiation
Multimodal functional deep learning for multiomics data
A statistical procedure to map high-order epistasis for complex traits
Algorithm-agnostic significance testing in supervised learning with multimodal data
Result verification, code verification and computation of support values in phylogenetics
Identification of multiple RNAs using feature fusion
The detection and characterization of pleiotropy: discovery, progress, and promise
New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing
Evidential deep learning for trustworthy prediction of enzyme commission number
ExoBCD: a comprehensive database for exosomal biomarker discovery in breast cancer
Structure-preserved dimension reduction using joint triplets sampling for multi-batch integration of single-cell transcriptomic data
Deep learning-based pseudo-mass spectrometry imaging analysis for precision medicine
New framework for recombination and adaptive evolution analysis with application to the novel coronavirus SARS-CoV-2
FusionDTA: attention-based feature polymerizer and knowledge distillation for drug-target binding affinity prediction
New techniques to identify the tissue of origin for cancer of unknown primary in the era of precision medicine: progress and challenges
scAnno: a deconvolution strategy-based automatic cell type annotation tool for single-cell RNA-sequencing data sets
Multi-modal domain adaptation for revealing spatial functional landscape from spatially resolved transcriptomics
Current RNA-seq methodology reporting limits reproducibility
An omics perspective on drug target discovery platforms
An evaluation of supervised methods for identifying differentially methylated regions in Illumina methylation arrays
Statistical software for gene mapping by admixture linkage disequilibrium
DEMO-EM2: assembling protein complex structures from cryo-EM maps through intertwined chain and domain fitting
Characterization of gastric cancer stem-like molecular features, immune and pharmacogenomic landscapes
Improved the heterodimer protein complex prediction with protein language models
Interpretation of 10 years of Alzheimer's disease genetic findings in the perspective of statistical heterogeneity
Out of distribution learning in bioinformatics: advancements and challenges
Expression profile of immune checkpoint genes and their roles in predicting immunotherapy response
CAKE: a flexible self-supervised framework for enhancing cell visualization, clustering and rare cell identification
Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases
Editorial: The Future of Publishing Microarray Data
TMBclaw: tumor clone-aware graph learning improves immunotherapy response prediction across heterogeneous cohorts
Identifying potential small molecule-miRNA associations via Robust PCA based on γ -norm regularization
Heavy chain sequence-based classifier for the specificity of human antibodies
Locating transcription factor binding sites by fully convolutional neural network
A Review of Bioinformatics Education in the UK
GPS-Uber: a hybrid-learning framework for prediction of general and E3-specific lysine ubiquitination sites
Investigations of sequencing data and sample type on HLA class Ia typing with different computational tools
Improved inter-protein contact prediction using dimensional hybrid residual networks and protein language models