yusuke1997/dblp-id-title huggingface dataset:
Choice of assemblers has a critical impact on de novo assembly of SARS-CoV-2 genome and characterizing variants
Deep learning in bioinformatics
A comprehensive review of cancer survival prediction using multi-omics integration and clinical variables
Predicting ion mobility collision cross sections using projection approximation with ROSIE-PARCS webserver
Exploring functional conservation in silico : a new machine learning approach to RNA-editing
scFed: federated learning for cell type classification with scRNA-seq
Modelling the dynamics of biosystems
Predicting protein interface residues using easily accessible on-line resources
Analysis of evolution of exon-intron structure of eukaryotic genes
Highly accurate diagnosis of papillary thyroid carcinomas based on personalized pathways coupled with machine learning
Virtual screening and molecular dynamics simulation study of plant-derived compounds to identify potential inhibitors of main protease from SARS-CoV-2
Artificial intelligence-enabled microbiome-based diagnosis models for a broad spectrum of cancer types
Spatial-MGCN: a novel multi-view graph convolutional network for identifying spatial domains with attention mechanism
Copy number aberrations from Affymetrix SNP 6.0 genotyping data - how accurate are commonly used prediction approaches?
Dynamic and modular gene regulatory networks drive the development of gametogenesis
Letter to the editor: testing the effectiveness of MyPROSLE in classifying patients with lupus nephritis
Succinylated lysine residue prediction revisited
Understanding proteome quantification in an interactive learning module on Google Cloud Platform
Deqformer: high-definition and scalable deep learning probe design method
Graph-RPI: predicting RNA-protein interactions via graph autoencoder and self-supervised learning strategies
DURIAN: an integrative deconvolution and imputation method for robust signaling analysis of single-cell transcriptomics data
Multiscale topology in interactomic network: from transcriptome to antiaddiction drug repurposing
Robust genetic interaction analysis
Multilevel prioritization of gene regulators associated with consensus molecular subtypes of colorectal cancer
A spatial-temporal gated attention module for molecular property prediction based on molecular geometry
Structure-based pathogenicity relationship identifier for predicting effects of single missense variants and discovery of higher-order cancer susceptibility clusters of mutations
Quantitative annotations of T-Cell repertoire specificity
A predictive paradigm for COVID-19 prognosis based on the longitudinal measure of biomarkers
UBD: incorporating uncertainty in cell type proportion estimates from bulk samples to infer cell-type-specific profiles
Predicting bacterial transcription factor binding sites through machine learning and structural characterization based on DNA duplex stability
A survey on identification and quantification of alternative polyadenylation sites from RNA-seq data
High-performance analysis of biological systems dynamics with the DiVinE model checker
CapHLA: a comprehensive tool to predict peptide presentation and binding to HLA class I and class II
A new framework for drug-disease association prediction combing light-gated message passing neural network and gated fusion mechanism
Deep fusion learning facilitates anatomical therapeutic chemical recognition in drug repurposing and discovery
Adaptive risk-aware sharable and individual subspace learning for cancer survival analysis with multi-modality data
Decoding the similarities and specific differences between latent and active tuberculosis infections based on consistently differential expression networks
DeepDTAF: a deep learning method to predict protein-ligand binding affinity
scMultiGAN: cell-specific imputation for single-cell transcriptomes with multiple deep generative adversarial networks
Knowledge-Based Bioinformatics - From analysis to interpretation.Edited by Gil Alterovitz and Marco Ramoni
Improving the performance of single-cell RNA-seq data mining based on relative expression orderings
CELA-MFP: a contrast-enhanced and label-adaptive framework for multi-functional therapeutic peptides prediction
The Bio* toolkits - A Brief Preview
FedSPL: federated self-paced learning for privacy-preserving disease diagnosis
SC-MEB: spatial clustering with hidden Markov random field using empirical Bayes
SEGreg: a database for human specifically expressed genes and their regulations in cancer and normal tissue
The impact of compound library size on the performance of scoring functions for structure-based virtual screening
Integration of proteomics profiling data to facilitate discovery of cancer neoantigens: a survey
DeepICSH: a complex deep learning framework for identifying cell-specific silencers and their strength from the human genome
Computer programs for eukaryotic gene prediction
Editorial: Accelerating systems biology
CProtMEDIAS: clustering of amino acid sequences encoded by gene families by MErging and DIgitizing Aligned Sequences
Recent developments in the MAFFT multiple sequence alignment program
DeepHost: phage host prediction with convolutional neural network
MetSigDis: a manually curated resource for the metabolic signatures of diseases
Editorial: Current progress in Bioinformatics 2010
Proteoform identification based on top-down tandem mass spectra with peak error corrections
Spatial density of open chromatin: an effective metric for the functional characterization of topologically associated domains
Quercetin for COVID-19 and DENGUE co-infection: a potential therapeutic strategy of targeting critical host signal pathways triggered by SARS-CoV-2 and DENV
Improving drug-target affinity prediction via feature fusion and knowledge distillation
Denoising adaptive deep clustering with self-attention mechanism on single-cell sequencing data
Letter to the Editor: On the term 'interaction' and related phrases in the literature on Random Forests
dbCID: a manually curated resource for exploring the driver indels in human cancer
iCysMod: an integrative database for protein cysteine modifications in eukaryotes
Comparing the Success of Different Prediction Software in Sequence Analysis: A Review
Comprehensive evaluation and practical guideline of gating methods for high-dimensional cytometry data: manual gating, unsupervised clustering, and auto-gating
Exploring transcriptional switches from pairwise, temporal and population RNA-Seq data using deepTS
REBET: a method to determine the number of cell clusters based on batch effect removal
Computational methodologies for modelling, analysis and simulation of signalling networks
Flexible experimentation in the modeling and simulation framework JAMES II - implications for computational systems biology
MetalinksDB: a flexible and contextualizable resource of metabolite-protein interactions
Solving genomic puzzles: computational methods for metagenomic binning
Critical assessment of bioinformatics methods for the characterization of pathological repeat expansions with single-molecule sequencing data
Transcriptome analysis method based on differential distribution evaluation
Correction to: Structure prediction of linear and cyclic peptides using CABS-flex
Mix-Key: graph mixup with key structures for molecular property prediction
Using GBrowse 2.0 to visualize and share next-generation sequence data
mKmer: an unbiased K -mer embedding of microbiomic single-microbe RNA sequencing data
Using the PharmCAT tool for Pharmacogenetic clinical decision support
Editorial: Computational methods for drug repurposing
FORAlign: accelerating gap-affine DNA pairwise sequence alignment using FOR-blocks based on Four Russians approach with linear space complexity
Structural interaction fingerprints and machine learning for predicting and explaining binding of small molecule ligands to RNA
Augmenting small biomedical datasets using generative AI methods based on self-organizing neural networks
A graph auto-encoder model for miRNA-disease associations prediction
An in-depth comparison of linear and non-linear joint embedding methods for bulk and single-cell multi-omics
A heterogeneous network-based method with attentive meta-path extraction for predicting drug-target interactions
iCircRBP-DHN: identification of circRNA-RBP interaction sites using deep hierarchical network
Flexible k-mers with variable-length indels for identifying binding sequences of protein dimers
Combining microarrays and genetic analysis
Accelerating bioactive peptide discovery via mutual information-based meta-learning
Network inference from AP-MS data: computational challenges and solutions
Integrative COVID-19 biological network inference with probabilistic core decomposition
Detecting tissue-specific early warning signals for complex diseases based on dynamical network biomarkers: study of type 2 diabetes by cross-tissue analysis
scATAC-seq preprocessing and imputation evaluation system for visualization, clustering and digital footprinting
Obituary: Walter Fitch and the orthology paradigm
An integrated computational pipeline for designing high-affinity nanobodies with expanded genetic codes
State-of-the-art web services for de novo protein structure prediction
Comparative phylogenetic analysis of SARS-CoV-2 spike protein - possibility effect on virus spillover
A comprehensive review and evaluation of graph neural networks for non-coding RNA and complex disease associations
Deep learning of gene relationships from single cell time-course expression data
SGAE: single-cell gene association entropy for revealing critical states of cell transitions during embryonic development
Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters
Benchmarking deep learning methods for predicting CRISPR/Cas9 sgRNA on- and off-target activities
$\mathcal{S}$ able: bridging the gap in protein structure understanding with an empowering and versatile pre-training paradigm
Comprehensive classification of TP53 somatic missense variants based on their impact on p53 structural stability
Knowledge Integration in Biomedicine: Technology and Community
CoaDTI: multi-modal co-attention based framework for drug-target interaction annotation
Explainable artificial intelligence for omics data: a systematic mapping study
Comprehensive evaluation of deep and graph learning on drug-drug interactions prediction
A comparative study of multi-omics integration tools for cancer driver gene identification and tumour subtyping
CORN - Condition Orientated Regulatory Networks: bridging conditions to gene networks
Mitochondrial DNA enrichment reduced NUMT contamination in porcine NGS analyses
CoPPIs algorithm: a tool to unravel protein cooperative strategies in pathophysiological conditions
Stability and aggregation of ranked gene lists
Protein mass spectra data analysis for clinical biomarker discovery: a global review
Dynamic modelling and analysis of biochemical networks: mechanism-based models and model-based experiments
Current progress in network research: toward reference networks for key model organisms
PCfun: a hybrid computational framework for systematic characterization of protein complex function
Discriminant Analysis and Its Application in DNA Sequence Motif Recognition
Detecting methylation quantitative trait loci using a methylation random field method
Predictive modelling of acute Promyelocytic leukaemia resistance to retinoic acid therapy
Estimation of random effects and identifying heterogeneous genes in meta-analysis of gene expression studies
Predicting the binding of small molecules to nuclear receptors using machine learning
DevOmics: an integrated multi-omics database of human and mouse early embryo
Focused goodness of fit tests for gene set analyses
Artificial intelligence and machine learning approaches using gene expression and variant data for personalized medicine
Discerning novel drug targets for treating Mycobacterium avium ss. paratuberculosis-associated autoimmune disorders: an in silico approach
Sepsis in the era of data-driven medicine: personalizing risks, diagnoses, treatments and prognoses
Indel detection from RNA-seq data: tool evaluation and strategies for accurate detection of actionable mutations
Evaluation of computational programs to predict HLA genotypes from genomic sequencing data
Mutual-assistance learning for trustworthy biomarker discovery and disease prediction
MIMIC: an optimization method to identify cell type-specific marker panel for cell sorting
Consistent semantic representation learning for out-of-distribution molecular property prediction
A structured approach for the engineering of biochemical network models, illustrated for signalling pathways
Functional assignment of metagenomic data: challenges and applications
An Applications-focused Review of Comparative Genomics Tools: Capabilities, Limitations and Future Challenges
Comparative analysis of de novo assemblers for variation discovery in personal genomes
Efficient SARS-CoV-2 variant detection and monitoring with Spike Screen next-generation sequencing
DeNOPA: decoding nucleosome positions sensitively with sparse ATAC-seq data
Computational annotation of miRNA transcription start sites
Integrating multi-omics summary data using a Mendelian randomization framework
Comparative pan-cancer DNA methylation analysis reveals cancer common and specific patterns
ACP_MS: prediction of anticancer peptides based on feature extraction
StaBle-ABPpred: a stacked ensemble predictor based on biLSTM and attention mechanism for accelerated discovery of antibacterial peptides
A rapid bacterial pathogen and antimicrobial resistance diagnosis workflow using Oxford nanopore adaptive sequencing method
Robust and exact structural variation detection with paired-end and soft-clipped alignments: SoftSV compared with eight algorithms
Latent space search based multimodal optimization with personalized edge-network biomarker for multi-purpose early disease prediction
Impact of mutations in SARS-COV-2 spike on viral infectivity and antigenicity
FifBase: a comprehensive fertility-associated indicators factor database for domestic animals
Learning multi-scale heterogenous network topologies and various pairwise attributes for drug-disease association prediction
The relationship between rational drug design and drug side effects
Improving drug-drug interactions prediction with interpretability via meta-path-based information fusion
HyGAnno: hybrid graph neural network-based cell type annotation for single-cell ATAC sequencing data
MeSHHeading2vec: a new method for representing MeSH headings as vectors based on graph embedding algorithm
Erratum to: Evaluation of in silico tools for the prediction of protein and peptide aggregation on diverse datasets
Deep neural network learning biological condition information refines gene-expression-based cell subtypes
PanDepth, an ultrafast and efficient genomic tool for coverage calculation
LRTCLS: low-rank tensor completion with Laplacian smoothing regularization for unveiling the post-transcriptional machinery of N 6-methylation (m6A)-mediated diseases
PRODeepSyn: predicting anticancer synergistic drug combinations by embedding cell lines with protein-protein interaction network
Benchmarking cell-type clustering methods for spatially resolved transcriptomics data
Systematic optimization of host-directed therapeutic targets and preclinical validation of repositioned antiviral drugs
An overview of data models for the analysis of biochemical pathways
Managing the life cycle of a portfolio of open data resources at the SIB Swiss Institute of Bioinformatics
Federation in genomics pipelines: techniques and challenges
Repun: an accurate small variant representation unification method for multiple sequencing platforms
Detecting differential DNA methylation from sequencing of bisulfite converted DNA of diverse species
Introducing enzymatic cleavage features and transfer learning realizes accurate peptide half-life prediction across species and organs
MiRAGE: mining relationships for advanced generative evaluation in drug repositioning
A systematic comparison of novel and existing differential analysis methods for CyTOF data
Machine learning revealed stemness features and a novel stemness-based classification with appealing implications in discriminating the prognosis, immunotherapy and temozolomide responses of 906 glioblastoma patients
Predicting TCR sequences for unseen antigen epitopes using structural and sequence features
Elemental metabolomics
Ensemble classification based feature selection: a case of identification on plant pentatricopeptide repeat proteins
VisANT: an integrative framework for networks in systems biology
SMAC: identifying DNA N6-methyladenine (6mA) at the single-molecule level using SMRT CCS data
A novel convolution attention model for predicting transcription factor binding sites by combination of sequence and shape
RiceSNP-BST: a deep learning framework for predicting biotic stress-associated SNPs in rice
GE-Impute: graph embedding-based imputation for single-cell RNA-seq data
A dual-scale fused hypergraph convolution-based hyperedge prediction model for predicting missing reactions in genome-scale metabolic networks
A comparison of metabolic labeling and statistical methods to infer genome-wide dynamics of RNA turnover
MHADTI: predicting drug-target interactions via multiview heterogeneous information network embedding with hierarchical attention mechanisms
Application of artificial intelligence and machine learning for COVID-19 drug discovery and vaccine design
Jupytope: computational extraction of structural properties of viral epitopes
A comprehensive review of scaffolding methods in genome assembly
Bringing Web 2.0 to bioinformatics
Dissecting and predicting different types of binding sites in nucleic acids based on structural information
HiCDiff: single-cell Hi-C data denoising with diffusion models
Comparative assessment of long-read error correction software applied to Nanopore RNA-sequencing data
Partial least squares: a versatile tool for the analysis of high-dimensional genomic data
SmProt: a database of small proteins encoded by annotated coding and non-coding RNA loci
Kinase-inhibitor binding affinity prediction with pretrained graph encoder and language model
HINGRL: predicting drug-disease associations with graph representation learning on heterogeneous information networks
FGeneBERT: function-driven pre-trained gene language model for metagenomics
Complex p53 dynamics regulated by miR-125b in cellular responses to reactive oxidative stress and DNA damage
MORE interpretable multi-omic regulatory networks to characterise phenotypes
Row versus column correlations: avoiding the ecological fallacy in RNA/protein expression studies
Software Review Exploring Protein Domain Structure
Benchmarking of long-read sequencing, assemblers and polishers for yeast genome
ELSSI: parallel SNP-SNP interactions detection by ensemble multi-type detectors
HITS-PR-HHblits: protein remote homology detection by combining PageRank and Hyperlink-Induced Topic Search
Splicing defects in rare diseases: transcriptomics and machine learning strategies towards genetic diagnosis
Information retrieval and knowledge discovery utilising a biomedical Semantic Web
MHCLMDA: multihypergraph contrastive learning for miRNA-disease association prediction
MGF6mARice: prediction of DNA N6-methyladenine sites in rice by exploiting molecular graph feature and residual block
Computational techniques for elucidating plant-pathogen interactions from large-scale experiments on fungi and oomycetes
ToxCodAn: a new toxin annotator and guide to venom gland transcriptomics
A review on longitudinal data analysis with random forest
Meta learning for mutant HLA class I epitope immunogenicity prediction to accelerate cancer clinical immunotherapy
Detecting SARS-CoV-2 and its variant strains with a full genome tiling array
Context-dependent gene regulatory network reveals regulation dynamics and cell trajectories using unspliced transcripts
Corrigendum to: How trees allocate carbon for optimal growth: insight from a game-theoretic model
Phenotypic Data in FlyBase
A simple way to detect disease-associated cellular molecular alterations from mixed-cell blood samples
GTE: a graph learning framework for prediction of T-cell receptors and epitopes binding specificity
Adaptive sequencing using nanopores and deep learning of mitochondrial DNA
scCRT: a contrastive-based dimensionality reduction model for scRNA-seq trajectory inference
Drug-drug interaction prediction with learnable size-adaptive molecular substructures
A review of genomic data warehousing systems
Prediction of disease-free survival for precision medicine using cooperative learning on multi-omic data
A survey of tools for variant analysis of next-generation genome sequencing data
Designing antimicrobial peptides using deep learning and molecular dynamic simulations
High-quality pan-genome of Escherichia coli generated by excluding confounding and highly similar strains reveals an association between unique gene clusters and genomic islands
Benchmarking differential abundance analysis methods for correlated microbiome sequencing data
Predicting human microbe-disease associations via graph attention networks with inductive matrix completion
Knowledge-based data analysis comes of age
The Life Sciences Semantic Web is Full of Creeps!
Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline
Themis: advancing precision oncology through comprehensive molecular subtyping and optimization
Three-stage quality control strategies for DNA re-sequencing data
Diagnostics of viral infections using high-throughput genome sequencing data
Improving the identification of miRNA-disease associations with multi-task learning on gene-disease networks
Exploration of whole genome amplification generated chimeric sequences in long-read sequencing data
Differential performance of RoseTTAFold in antibody modeling
EMLI-ICC: an ensemble machine learning-based integration algorithm for metastasis prediction and risk stratification in intrahepatic cholangiocarcinoma
Predicting protein phosphorylation sites in soybean using interpretable deep tabular learning network
Correction: Comparison and benchmark of structural variants detected from long read and long-read assembly
Establishing a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia
Human-like layout algorithms for signalling hypergraphs: outlining requirements
Extraction of biological interaction networks from scientific literature
Erratum: usDSM: a novel method for deleterious synonymous mutation prediction using undersampling scheme
RNAdvisor: a comprehensive benchmarking tool for the measure and prediction of RNA structural model quality
Predictability of antigen binding based on short motifs in the antibody CDRH3
A comprehensive investigation of statistical and machine learning approaches for predicting complex human diseases on genomic variants
DeepSSV: detecting somatic small variants in paired tumor and normal sequencing data with convolutional neural network
The recent progress in proteochemometric modelling: focusing on target descriptors, cross-term descriptors and application scope
Addressing scalability and managing sparsity and dropout events in single-cell representation identification with ZIGACL
Farm Animal Genome Databases
TransFoxMol: predicting molecular property with focused attention
Linear: a framework to enable existing software to resolve structural variants in long reads with flexible and efficient alignment-free statistical models
Erratum to: Evotuning protocols for Transformer-based variant effect prediction on multi-domain proteins
Unsupervised pattern recognition: An introduction to the whys and wherefores of clustering microarray data
Meta-GDBP: a high-level stacked regression model to improve anticancer drug response prediction
Software applications for flux balance analysis
PYF: a multi-functional algorithm for predicting production and optimizing metabolic engineering strategy in Escherichia coli microbial consortia
Mutational signatures and mutable motifs in cancer genomes
Chromatin loop anchors predict transcript and exon usage