yusuke1997/dblp-id-title huggingface dataset:
A scalable unsupervised learning of scRNAseq data detects rare cells through integration of structure-preserving embedding, clustering and outlier detection
Ovarian cancer is detectable from peripheral blood using machine learning over T-cell receptor repertoires
Multiple Testing of Gene Sets from Gene Ontology: Possibilities and Pitfalls
ADCNet: a unified framework for predicting the activity of antibody-drug conjugates
MTD: a unique pipeline for host and meta-transcriptome joint and integrative analyses of RNA-seq data
Hierarchical mixed-model expedites genome-wide longitudinal association analysis
Network control principles for identifying personalized driver genes in cancer
Meta-i6mA: an interspecies predictor for identifying DNA N6-methyladenine sites of plant genomes by exploiting informative features in an integrative machine-learning framework
HHOMR: a hybrid high-order moment residual model for miRNA-disease association prediction
DTI-CDF: a cascade deep forest model towards the prediction of drug-target interactions based on hybrid features
Linked data and provenance in biological data webs
Iteratively reweighted LASSO for mapping multiple quantitative trait loci
Leveraging developmental landscapes for model selection in Boolean gene regulatory networks
Improving artificial intelligence pipeline for liver malignancy diagnosis using ultrasound images and video frames
Recent advances in sequence-based protein structure prediction
Genetic determinants of obesity in Korean populations: exploring genome-wide associations and polygenic risk scores
myMIR: a genome-wide microRNA targets identification and annotation tool
Leveraging multi-omics data to empower quantitative systems pharmacology in immuno-oncology
Text mining approaches for dealing with the rapidly expanding literature on COVID-19
Open-source chemogenomic data-driven algorithms for predicting drug-target interactions
Ranking prognosis markers in cancer genomic studies
Integrated bulk and single-cell transcriptomes reveal pyroptotic signature in prognosis and therapeutic options of hepatocellular carcinoma by combining deep learning
ICSDA: a multi-modal deep learning model to predict breast cancer recurrence and metastasis risk by integrating pathological, clinical and gene expression data
Gene expression prediction from histology images via hypergraph neural networks
Challenges of sequencing human genomes
Molecular substructure tree generative model for de novo drug design
Hairpins in bookstacks: Information retrieval from biomedical text
Cross-population enhancement of PrediXcan predictions with a gnomAD-based east Asian reference framework
Systematic assessment of imputation performance using the 1000 Genomes reference panels
M6A2Target: a comprehensive database for targets of m6A writers, erasers and readers
Robust logistic regression to narrow down the winner's curse for rare and recessive susceptibility variants
Sincast: a computational framework to predict cell identities in single-cell transcriptomes using bulk atlases as references
Combining evolution and protein language models for an interpretable cancer driver mutation prediction with D2Deep
Buying in to bioinformatics: an introduction to commercial sequence analysis software
A strategy combining denoising and cryo-EM single particle analysis
scRDAN: a robust domain adaptation network for cell type annotation across single-cell RNA sequencing data
Reproducible probe-level analysis of the Affymetrix Exon 1.0 ST array with R/Bioconductor
Artificial intelligence in bioinformatics: a survey
Class-imbalanced classifiers for high-dimensional data
Collaborative deep learning improves disease-related circRNA prediction based on multi-source functional information
Exome sequence read depth methods for identifying copy number changes
Toward a next-generation atlas of RNA secondary structure
Open Source Software Meets Gene Expression
A cofunctional grouping-based approach for non-redundant feature gene selection in unannotated single-cell RNA-seq analysis
Unveiling human origins of replication using deep learning: accurate prediction and comprehensive analysis
MDICC: novel method for multi-omics data integration and cancer subtype identification
iDeepSubMito: identification of protein submitochondrial localization with deep learning
HpQTL: a geometric morphometric platform to compute the genetic architecture of heterophylly
CCSynergy: an integrative deep-learning framework enabling context-aware prediction of anti-cancer drug synergy
ConvNTC: convolutional neural tensor completion for detecting "A-A-B" type biological triplets
VEGA, the genome browser with a difference
Dual-Network Collaborative Matrix Factorization for predicting small molecule-miRNA associations
scAGCI: an anchor graph-based method for cell clustering from integrated scRNA-seq and scATAC-seq data
AI identifies potent inducers of breast cancer stem cell differentiation based on adversarial learning from gene expression data
Linkage disequilibrium for different scales and applications
Identification and characterization of circRNAs encoded by MERS-CoV, SARS-CoV-1 and SARS-CoV-2
Depiction of tumor stemlike features and underlying relationships with hazard immune infiltrations based on large prostate cancer cohorts
Editorial: Pathways of bioinformatics - from data to diseases
Linking research of biomedical datasets
Evaluating the consistency of large-scale pharmacogenomic studies
Correction to: Accurate prediction of antibody function and structure using bio-inspired antibody language model
The what, where, how and why of gene ontology - a primer for bioinformaticians
Metabolic models predict fotemustine and the combination of eflornithine/rifamycin and adapalene/cannabidiol for the treatment of gliomas
Machine learning-assisted substrate binding pocket engineering based on structural information
ProTCR: a protein language model-driven framework for decoding TCR-antigen recognition toward precision immunotherapies
iSMNN: batch effect correction for single-cell RNA-seq data via iterative supervised mutual nearest neighbor refinement
Letter to the Editor: Methods for mapping quantitative trait loci in autotetraploid species
List mania: interpreting microarray results with the L2L server
Multi-level multi-view network based on structural contrastive learning for scRNA-seq data clustering
Attention-aware differential learning for predicting peptide-MHC class I binding and T cell receptor recognition
Breaking free from references: a consensus-based approach for community profiling with long amplicon nanopore data
Database identifies FDA-approved drugs with potential to be repurposed for treatment of orphan diseases
Network Pharmacology and bioinformatics analyses identify intersection genes of niacin and COVID-19 as potential therapeutic targets
DenvInD: dengue virus inhibitors database for clinical and molecular research
EnGens: a computational framework for generation and analysis of representative protein conformational ensembles
Cardiac Gene Expression: Methods and Protocols.: Edited by Jun Zhang and Gregg Rokosh
SG-LSTM-FRAME: a computational frame using sequence and geometrical information via LSTM to predict miRNA-gene associations
DeepR2cov: deep representation learning on heterogeneous drug networks to discover anti-inflammatory agents for COVID-19
Bioinformatical approaches to characterize intrinsically disordered/unstructured proteins
CReSIL: accurate identification of extrachromosomal circular DNA from long-read sequences
DeepKEGG: a multi-omics data integration framework with biological insights for cancer recurrence prediction and biomarker discovery
Phylogenetic profiling, an untapped resource for the prediction of secreted proteins and its complementation with sequence-based classifiers in bacterial type III, IV and VI secretion systems
Erratum to: Molecular dynamics simulations for genetic interpretation in protein coding regions: where we are, where to go and when
Deep learning tackles single-cell analysis - a survey of deep learning for scRNA-seq analysis
Logic programming to infer complex RNA expression patterns from RNA-seq data
mbDriver: identifying driver microbes in microbial communities based on time-series microbiome data
Transformer-based anti-noise models for CRISPR-Cas9 off-target activities prediction
irGSEA: the integration of single-cell rank-based gene set enrichment analysis
Integrative machine learning framework for the identification of cell-specific enhancers from the human genome
A bi-Poisson model for clustering gene expression profiles by RNA-seq
scDCCA: deep contrastive clustering for single-cell RNA-seq data based on auto-encoder network
SCREE: a comprehensive pipeline for single-cell multi-modal CRISPR screen data processing and analysis
A multi-label learning framework for predicting antibiotic resistance genes via dual-view modeling
VITALdb: to select the best viroinformatics tools for a desired virus or application
Inference of dynamic networks using time-course data
Deep learning for brain disorders: from data processing to disease treatment
A general optimization protocol for molecular property prediction using a deep learning network
Current progress in patient-specific modeling
Data Warehousing in Molecular Biology
Correction to: VPatho: a deep learning-based two-stage approach for accurate prediction of gain-of-function and loss-of-function variants
BindingSite-AugmentedDTA: enabling a next-generation pipeline for interpretable prediction models in drug repurposing
Polygenic prediction for underrepresented populations through transfer learning by utilizing genetic similarity shared with European populations
Multiple and Optimal Screening Subset: a method selecting global characteristic congeners for robust foodomics analysis
Anc2vec: embedding gene ontology terms by preserving ancestors relationships
IMGT/RobustpMHC: robust training for class-I MHC peptide binding prediction
Detecting miRNAs in deep-sequencing data: a software performance comparison and evaluation
Human body-fluid proteome: quantitative profiling and computational prediction
Graph-based methods for analysing networks in cell biology
A novel computational framework for genome-scale alternative transcription units prediction
HCC subtypes based on the activity changes of immunologic and hallmark gene sets in tumor and nontumor tissues
Bioinformatics for Venom and Toxin Sciences
Integrating single-cell datasets with ambiguous batch information by incorporating molecular network features
Fusion of spatiotemporal and network models to prioritize multiscale effects in single-cell perturbations
Virtual screening web servers: designing chemical probes and drug candidates in the cyberspace
Updated review of advances in microRNAs and complex diseases: experimental results, databases, webservers and data fusion
Sensitivity and specificity of information criteria
Clustered tree regression to learn protein energy change with mutated amino acid
rcCAE: a convolutional autoencoder method for detecting intra-tumor heterogeneity and single-cell copy number alterations
Evaluation of in silico tools for the prediction of protein and peptide aggregation on diverse datasets
Multi-view clustering for single-cell RNA-seq data based on graph fusion
Attribute-guided prototype network for few-shot molecular property prediction
Principles of Computational Modeling in NeuroscienceDavid Sterratt, Bruce Graham, Andrew Gillies and David Willshaw
The bioinformatics of the finding that the hepatitis delta virus RNA editing mechanism by a conformational switch exists in genotype 7 in addition to genotype 3
SRDFM: Siamese Response Deep Factorization Machine to improve anti-cancer drug recommendation
MIRACN: a residual convolutional neural network for predicting cell line specific functional regulatory variants
Balancing Clinical Applicability and Scientific Depth in ML Models for MDA5-DM Prognosis
TransBic: bucket trend-preserving biclustering for finding local and interpretable expression patterns
Interpretable artificial intelligence model for accurate identification of medical conditions using immune repertoire
An empirical assessment of validation practices for molecular classifiers
ReHoGCNES-MDA: prediction of miRNA-disease associations using homogenous graph convolutional networks based on regular graph with random edge sampler
eNODAL: an experimentally guided nutriomics data clustering method to unravel complex drug-diet interactions
Identifying cell types by lasso-constraint regularized Gaussian graphical model based on weighted distance penalty
Benchmarking of analytical combinations for COVID-19 outcome prediction using single-cell RNA sequencing data
CellTalkDB: a manually curated database of ligand-receptor interactions in humans and mice
Semantic similarity and machine learning with ontologies
Identification and analysis of the human sex-biased genes
Deep learning in template-free de novo biosynthetic pathway design of natural products
Model-based evaluation of spatiotemporal data reduction methods with unknown ground truth through optimal visualization and interpretability metrics
Path-MGCN: a pathway activity-based multi-view graph convolutional network for determining spatial domains
Mapping morphological shape as a high-dimensional functional curve
A free energy perturbation-assisted machine learning strategy for mimotope screening in neoantigen-based vaccine design
Attention-wise masked graph contrastive learning for predicting molecular property
SDTNBI: an integrated network and chemoinformatics tool for systematic prediction of drug-target interactions and drug repositioning
A Bayesian method for analysing spotted microarray data
Multi-marker linkage disequilibrium mapping of quantitative trait loci
Privacy-aware estimation of relatedness in admixed populations
Categorization of services for seeking information in biomedical literature: a typology for improvement of practice
Introducing π-HelixNovo for practical large-scale de novo peptide sequencing
Toward the functional interpretation of somatic structural variations: bulk- and single-cell approaches
Clustering scRNA-seq data with the cross-view collaborative information fusion strategy
How to cluster gene expression dynamics in response to environmental signals
Characteristics and evolution of the ecosystem of software tools supporting research in molecular biology
Inference of gene coexpression networks from single-cell transcriptome data based on variance decomposition analysis
A comprehensive computational benchmark for evaluating deep learning-based protein function prediction approaches
Metabolism-associated protein network constructing and host-directed anti-influenza drug repurposing
Bayesian unsupervised clustering identifies clinically relevant osteosarcoma subtypes
Identification of drug-side effect association via restricted Boltzmann machines with penalized term
Association score testing for rare variants and binary traits in family data with shared controls
A survey on prediction of specificity-determining sites in proteins
Computational approaches for detecting disease-associated alternative splicing events
Validation strategies for target prediction methods
Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure
Next-generation sequencing: a challenge to meet the increasing demand for training workshops in Australia
ConSIG: consistent discovery of molecular signature from OMIC data
Circular RNAs and complex diseases: from experimental results to computational models
Open source tools and toolkits for bioinformatics: significance, and where are we?
Current development of integrated web servers for preclinical safety and pharmacokinetics assessments in drug development
Building multiscale models with PhysiBoSS, an agent-based modeling tool
Context-based retrieval of functional modules in protein-protein interaction networks
iWhale: a computational pipeline based on Docker and SCons for detection and annotation of somatic variants in cancer WES data
Correction to: STMGraph: spatial-context-aware of transcriptomes via a dual-remasked dynamic graph attention model
GraphGPSM: a global scoring model for protein structure using graph neural networks
Current status and prospects of computational resources for natural product dereplication: a review
Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives
CIForm as a Transformer-based model for cell-type annotation of large-scale single-cell RNA-seq data
Mitochondria sequence mapping strategies and practicability of mitochondria variant detection from exome and RNA sequencing data
Protein-protein interactions: detection, reliability assessment and applications
Bioinformatics - From Genomes to Therapies: Edited by Thomas Lengauer
Large-scale comparative review and assessment of computational methods for anti-cancer peptide identification
Discovering cooperative biomarkers for heterogeneous complex disease diagnoses
SiameseCPP: a sequence-based Siamese network to predict cell-penetrating peptides by contrastive learning
Correction to: Recent application of artificial intelligence on histopathologic image-based prediction of gene mutation in solid cancers
Line graph attention networks for predicting disease-associated Piwi-interacting RNAs
SPLDExtraTrees: robust machine learning approach for predicting kinase inhibitor resistance
A genome-wide association study to identify candidate genes for erectile dysfunction
Correction to: labelSeg: segment annotation for tumor copy number alteration profiles
Integrated unsupervised-supervised modeling and prediction of protein-peptide affinities at structural level
FastBiCmrMLM: a fast and powerful compressed variance component mixed logistic model for big genomic case-control genome-wide association study
GLDM: hit molecule generation with constrained graph latent diffusion model
Artificial intelligence in drug combination therapy
Alignment-free estimation of sequence conservation for identifying functional sites using protein sequence embeddings
Improving cancer driver gene identification using multi-task learning on graph convolutional network
An efficient curriculum learning-based strategy for molecular graph learning
Predicting potential small molecule-miRNA associations based on bounded nuclear norm regularization
Antibody design using deep learning: from sequence and structure design to affinity maturation
ColorCells: a database of expression, classification and functions of lncRNAs in single cells
An extensive review of tools for manual annotation of documents
scValue: value-based subsampling of large-scale single-cell transcriptomic data for machine and deep learning tasks
WinPop 2.5: Software for representing population genetics phenomena
Large-scale analysis of gene expression profiles
A quantitative model of transcriptional differentiation driving host-pathogen interactions
Evaluating the efficacy of MEANGS for mitochondrial genome assembly of cartilaginous and ray-finned fish species
High-throughput prediction of enzyme promiscuity based on substrate-product pairs
bulkAnalyseR: an accessible, interactive pipeline for analysing and sharing bulk multi-modal sequencing data
Detection algorithms and attentive points of safety signal using spontaneous reporting systems as a clinical data source
e-TSN: an interactive visual exploration platform for target-disease knowledge mapping from literature
Network models in bioinformatics: modeling and analysis for complex diseases
Computational pan-genomics: status, promises and challenges
ngsComposer: an automated pipeline for empirically based NGS data quality filtering
Implications of topological imbalance for representation learning on biomedical knowledge graphs
MORE: a multi-omics data-driven hypergraph integration network for biomedical data classification and biomarker identification
Poincaré maps for visualization of large protein families
Genome-wide circadian rhythm detection methods: systematic evaluations and practical guidelines
Editorial: Stable funding for open source software?
Location deviations of DNA functional elements affected SNP mapping in the published databases and references
Deep embedded clustering with multiple objectives on scRNA-seq data
Computational analysis of mutation spectra
Bioinformatics for glycomics: Status, methods, requirements and perspectives
AGAT-PPIS: a novel protein-protein interaction site predictor based on augmented graph attention network with initial residual and identity mapping
MATTE: a pipeline of transcriptome module alignment for anti-noise phenotype-gene-related analysis
Learning transcriptional regulation on a genome scale: a theoretical analysis based on gene expression data
Predicting functional outcome in ischemic stroke patients using genetic, environmental, and clinical factors: a machine learning analysis of population-based prospective cohort study
HyMM: hybrid method for disease-gene prediction by integrating multiscale module structure
A review on the application of bioinformatics tools in food microbiome studies
A community-supported metaproteomic pipeline for improving peptide identifications in hydrothermal vent microbiota
Deep learning in systems medicine
Are dropout imputation methods for scRNA-seq effective for scHi-C data?
Proteomics and phosphoproteomics in precision medicine: applications and challenges
An allometric model for mapping seed development in plants
Single-cell multi-omics analysis identifies context-specific gene regulatory gates and mechanisms
Pharmacoinformatics and molecular dynamics simulation-based phytochemical screening of neem plant (Azadiractha indica) against human cancer by targeting MCM7 protein
Gene co-expression analyses: an overview from microarray collections in Arabidopsis thaliana
dynDeepDRIM: a dynamic deep learning model to infer direct regulatory interactions using time-course single-cell gene expression data
Prediction of RNA-interacting residues in a protein using CNN and evolutionary profile
AnnoView enables large-scale analysis, comparison, and visualization of microbial gene neighborhoods
A cross-study analysis of drug response prediction in cancer cell lines
Deep learning identifies explainable reasoning paths of mechanism of action for drug repurposing from multilayer biological network
Systematic benchmark of ancient DNA read mapping
BFAST: joint dimension reduction and spatial clustering with Bayesian factor analysis for zero-inflated spatial transcriptomics data
Graph- and rule-based learning algorithms: a comprehensive review of their applications for cancer type classification and prognosis using genomic data
Network approaches to systems biology analysis of complex disease: integrative methods for multi-omics data
Biomedical data and computational models for drug repositioning: a comprehensive review
A brief history of bioinformatics
NIPT-PG: empowering non-invasive prenatal testing to learn from population genomics through an incremental pan-genomic approach
Identification of pan-cancer Ras pathway activation with deep learning
Updated review of advances in microRNAs and complex diseases: taxonomy, trends and challenges of computational models
MRCIP: a robust Mendelian randomization method accounting for correlated and idiosyncratic pleiotropy
CAMOIP: a web server for comprehensive analysis on multi-omics of immunotherapy in pan-cancer
Accounting for differential variability in detecting differentially methylated regions
Clinical significance and immunogenomic landscape analyses of the immune cell signature based prognostic model for patients with breast cancer
MAMnet: detecting and genotyping deletions and insertions based on long reads and a deep learning approach
Improved prediction of DNA and RNA binding proteins with deep learning models
Interactive visual analysis of drug-target interaction networks using Drug Target Profiler, with applications to precision medicine and drug repurposing
Accurate and fast cell marker gene identification with COSG
A novel circRNA-miRNA association prediction model based on structural deep neural network embedding
Multi-omics to characterize the functional relationships of R-loops with epigenetic modifications, RNAPII transcription and gene expression