yusuke1997/dblp-id-title huggingface dataset:
SLRanger: an integrated approach for spliced leader detection and operon prediction using long RNA reads
DLTKcat: deep learning-based prediction of temperature-dependent enzyme turnover rates
Nucleosome positioning: resources and tools online
Improving multi-population genomic prediction accuracy using multi-trait GBLUP models which incorporate global or local genetic correlation information
RNA-ModX: a multilabel prediction and interpretation framework for RNA modifications
A study of bias and increasing organismal complexity from their post-translational modifications and reaction site interplays
Minimal information for chemosensitivity assays (MICHA): a next-generation pipeline to enable the FAIRification of drug screening experiments
A versatile pipeline to identify convergently lost ancestral conserved fragments associated with convergent evolution of vocal learning
Algorithms for modeling global and context-specific functional relationship networks
Evaluation of imputation and imputation-free strategies for differential abundance analysis in metaproteomics data
I-SVVS: integrative stochastic variational variable selection to explore joint patterns of multi-omics microbiome data
metaProbiotics: a tool for mining probiotic from metagenomic binning data based on a language model
The role of automation in enhancing reproducibility and interoperability of PBPK models
BatmanNet: bi-branch masked graph transformer autoencoder for molecular representation
MiRNA-disease association prediction based on meta-paths
Parallel stochastic systems biology in the cloud
Comparison and integration of computational methods for deleterious synonymous mutation prediction
SEGCECO: Subgraph Embedding of Gene expression matrix for prediction of CEll-cell COmmunication
Multi-omics integration for both single-cell and spatially resolved data based on dual-path graph attention auto-encoder
gutMEGA: a database of the human gut MEtaGenome Atlas
3t-seq: automatic gene expression analysis of single-copy genes, transposable elements, and tRNAs from RNA-seq data
SGANRDA: semi-supervised generative adversarial networks for predicting circRNA-disease associations
MHCpLogics: an interactive machine learning-based tool for unsupervised data visualization and cluster analysis of immunopeptidomes
Subcellular locations of potential cell wall proteins in plants: predictors, databases and cross-referencing
Mediation analysis in longitudinal study with high-dimensional methylation mediators
Computational knowledge integration in biopharmaceutical research
Deep multi-view contrastive learning for cancer subtype identification
Boca: an open-source RDF store for building Semantic Web applications
Revealing protein-lncRNA interaction
An order-preserving batch-effect correction method based on a monotonic deep learning framework
Prediction of Exact Boundaries of Exons
GEMF: a novel geometry-enhanced mid-fusion network for PLA prediction
THOR: a TMB heterogeneity-adaptive optimization model predicts immunotherapy response using clonal genomic features in group-structured data
Closing the gap between formats for storing layout information in systems biology
Critical downstream analysis steps for single-cell RNA sequencing data
Tools for fundamental analysis functions of TCR repertoires: a systematic comparison
Modelling and simulation techniques for membrane biology
Microbe-bridged disease-metabolite associations identification by heterogeneous graph fusion
Active disease-related compound identification based on capsule network
Correction to: Breaking the barriers of data scarcity in drug-target affinity prediction
Ultrafast clustering algorithms for metagenomic sequence analysis
Docking small peptides remains a great challenge: an assessment using AutoDock Vina
Semiparametric prognosis models in genomic studies
Multimodal data fusion based on IGERNNC algorithm for detecting pathogenic brain regions and genes in Alzheimer's disease
PepLand: a large-scale pre-trained peptide representation model for a comprehensive landscape of both canonical and non-canonical amino acids
TOD-CUP: a gene expression rank-based majority vote algorithm for tissue origin diagnosis of cancers of unknown primary
HLA3D: an integrated structure-based computational toolkit for immunotherapy
Computational resources associating diseases with genotypes, phenotypes and exposures
A workflow to study mechanistic indicators for driver gene prediction with Moonlight
An assessment of computational methods for estimating purity and clonality using genomic data derived from heterogeneous tumor tissue samples
Unveiling hidden connections in omics data via pyPARAGON: an integrative hybrid approach for disease network construction
TSomVar: a tumor-only somatic and germline variant identification method with random forest
A novel antibacterial peptide recognition algorithm based on BERT
GC-balanced polar codes correcting insertions, deletions and substitutions for DNA storage
MKMR: a multi-kernel machine regression model to predict health outcomes using human microbiome data
Reducing false positive rate of docking-based virtual screening by active learning
Multi-model predictive analysis of RNA solvent accessibility based on modified residual attention mechanism
KansformerEPI: a deep learning framework integrating KAN and transformer for predicting enhancer-promoter interactions
BioRED: a rich biomedical relation extraction dataset
Drug-target interactions prediction via deep collaborative filtering with multiembeddings
Comparison and evaluation of integrative methods for the analysis of multilevel omics data: a study based on simulated and experimental cancer data
Identifying the tissues-of-origin of circulating cell-free DNAs is a promising way in noninvasive diagnostics
dSCOPE: a software to detect sequences critical for liquid-liquid phase separation
Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions
Sequence analysis by iterated maps, a review
Spatial histology and gene-expression representation and generative learning via online self-distillation contrastive learning
Decoding functional cell-cell communication events by multi-view graph learning on spatial transcriptomics
Shall genomic correlation structure be considered in copy number variants detection?
DockEM: an enhanced method for atomic-scale protein-ligand docking refinement leveraging low-to-medium resolution cryo-EM density maps
An approach for normalization and quality control for NanoString RNA expression data
Multi-view contrastive heterogeneous graph attention network for lncRNA-disease association prediction
Systematic evaluation of normalization approaches in tandem mass tag and label-free protein quantification data using PRONE
Conceptual data modelling for bioinformatics
DTI-MLCD: predicting drug-target interactions using multi-label learning with community detection method
A survey and evaluations of histogram-based statistics in alignment-free sequence comparison
Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases
Deep learning model reveals potential risk genes for ADHD, especially Ephrin receptor gene EPHA5
CPARI: a novel approach combining cell partitioning with absolute and relative imputation to address dropout in single-cell RNA-seq data
A 3D pocket-aware lead optimization model with knowledge guidance and its application for discovery of new glutaminyl cyclase inhibitors
A conceptual framework for human-AI collaborative genome annotation
Phylogeny-aware linear B-cell epitope predictor detects targets associated with immune response to orthopoxviruses
Integration of protein sequence and protein-protein interaction data by hypergraph learning to identify novel protein complexes
Computational systems biology of the cell cycle
A systematic evaluation of normalization methods in quantitative label-free proteomics
Compositional diversity and evolutionary pattern of coronavirus accessory proteins
Rediscovery rate estimation for assessing the validation of significant findings in high-throughput studies
Interpretable high-order knowledge graph neural network for predicting synthetic lethality in human cancers
Comprehensive assessment of deep generative architectures for de novo drug design
DeepCheck: multitask learning aids in assessing microbial genome quality
COFFEE: consensus single cell-type specific inference for gene regulatory networks
Predicting disease trait with genomic data: a composite kernel approach
TIPS: a novel pathway-guided joint model for transcriptome-wide association studies
Artificial intelligence in clinical research of cancers
Bayesian functional analysis for untargeted metabolomics data with matching uncertainty and small sample sizes
BioSeq-Analysis: a platform for DNA, RNA and protein sequence analysis based on machine learning approaches
Current Approaches to Whole Genome Phylogenetic Analysis
Common introns within orthologous genes: software and application to plants
LSTM-PHV: prediction of human-virus protein-protein interactions by LSTM with word2vec
GAEDGRN: reconstruction of gene regulatory networks based on gravity-inspired graph autoencoders
ST-SCSR: identifying spatial domains in spatial transcriptomics data via structure correlation and self-representation
ExosomePurity: tumour purity deconvolution in serum exosomes based on miRNA signatures
Ontologies of Developmental Anatomy: Their Current and Future Roles
scHyper: reconstructing cell-cell communication through hypergraph neural networks
Response to letter to editor "On 'Bioinformatics in Russia: history and present-day landscape' by M.A. Nawaz, I.E. Pamirsky, and K.S. Golokhvast" by Mikhail Gelfand
Correction to: DOMSCNet: a deep learning model for the classification of stomach cancer using multi-layer omics data
Thinking points for effective batch correction on biomedical data
HISNAPI: a bioinformatic tool for dynamic hot spot analysis in nucleic acid-protein interface with a case study
Machine-designed biotherapeutics: opportunities, feasibility and advantages of deep learning in computational antibody discovery
Formal verification of bioinformatics software using model checking and theorem proving
Detecting sparse microbial association signals adaptively from longitudinal microbiome data based on generalized estimating equations
Molecular dynamics recipes for genome research
Sixty-five years of the long march in protein secondary structure prediction: the final stretch?
Systematic comparative study of computational methods for T-cell receptor sequencing data analysis
ACR: metagenome-assembled prokaryotic and eukaryotic genome refinement tool
Improving therapeutic synergy score predictions with adverse effects using multi-task heterogeneous network learning
DrugReSC: targeting disease-critical cell subpopulations with single-cell transcriptomic data for drug repurposing in cancer
VISN: virus instance segmentation network for TEM images using deep attention transformer
Snipe: highly sensitive pathogen detection from metagenomic sequencing data
Systematic evaluation of transcriptomics-based deconvolution methods and references using thousands of clinical samples
AttentionGRN: a functional and directed graph transformer for gene regulatory network reconstruction from scRNA-seq data
High performance cellular level agent-based simulation with FLAME for the GPU
Case studies in reproducibility
Challenges and prospects in the analysis of large-scale gene expression data
Progress and opportunities of foundation models in bioinformatics
A new paradigm for applying deep learning to protein-ligand interaction prediction
MESPool: Molecular Edge Shrinkage Pooling for hierarchical molecular representation learning and property prediction
Motif discovery and transcription factor binding sites before and after the next-generation sequencing era
Advances and critical aspects in cancer treatment development using digital twins
HIP: a method for high-dimensional multi-view data integration and prediction accounting for subgroup heterogeneity
Integrative open workflow for confident annotation and molecular networking of metabolomics MSE/DIA data
A review of metrics measuring dissimilarity for rooted phylogenetic networks
PredCID: prediction of driver frameshift indels in human cancer
Online in silico validation of disease and gene sets, clusterings or subnetworks with DIGEST
A comparison of mechanistic signaling pathway activity analysis methods
A review of deep learning models for the prediction of chromatin interactions with DNA and epigenomic profiles
Matrix factorization-based data fusion for the prediction of RNA-binding proteins and alternative splicing event associations during epithelial-mesenchymal transition
RNA-RNA interactions between SARS-CoV-2 and host benefit viral development and evolution during COVID-19 infection
DeepSS2GO: protein function prediction from secondary structure
Predicting nucleic acid binding sites by attention map-guided graph convolutional network with protein language embeddings and physicochemical information
Structural landscapes of PPI interfaces
Computational anti-COVID-19 drug design: progress and challenges
A survey of software tools for microRNA discovery and characterization using RNA-seq
IMPRINTS.CETSA and IMPRINTS.CETSA.app: an R package and a Shiny application for the analysis and interpretation of IMPRINTS-CETSA data
Locus-specific expression analysis of transposable elements
A compressed variance component mixed model framework for detecting small and linked QTL-by-environment interactions
CryoSegNet: accurate cryo-EM protein particle picking by integrating the foundational AI image segmentation model and attention-gated U-Net
Beyond the base pairs: comparative genome-wide DNA methylation profiling across sequencing technologies
Protein-RNA interaction prediction with deep learning: structure matters
Integrated use of bioinformatic resources reveals that co-targeting of histone deacetylases, IKBK and SRC inhibits epithelial-mesenchymal transition in cancer
Knowledge-based BERT: a method to extract molecular features like computational chemists
GraphTGI: an attention-based graph embedding model for predicting TF-target gene interactions
Comparative study of joint analysis of microarray gene expression data in survival prediction and risk assessment of breast cancer patients
Three-nucleotide periodicity of nucleotide diversity in a population enables the identification of open reading frames
From Molecular Activities and Processes to Biological Function
DPADM: a novel algorithm for detecting drug-pathway associations based on high-throughput transcriptional response to compounds
sTPLS: identifying common and specific correlated patterns under multiple biological conditions
Spectral clustering of single cells using Siamese nerual network combined with improved affinity matrix
Distance-based phylogenetic inference from typing data: a unifying view
The Rat Genome Database 2013 - data, tools and users
SatXplor - a comprehensive pipeline for satellite DNA analyses in complex genome assemblies
Critical assessment of high-throughput standalone methods for secondary structure prediction
Fold-LTR-TCP: protein fold recognition based on triadic closure principle
Link synthetic lethality to drug sensitivity of cancer cells
iEnhance: a multi-scale spatial projection encoding network for enhancing chromatin interaction data resolution
Approaches to embryonic neurodevelopment: from neural cell to neural tube formation through mathematical models
SVPath: an accurate pipeline for predicting the pathogenicity of human exon structural variants
Dynamical roles of biological regulatory circuits
Editorial: Bioinformatics education in the 21st century
Computational challenges of sequence classification in microbiomic data
End-to-end interpretable disease-gene association prediction
SmartGate is a spatial metabolomics tool for resolving tissue structures
A Bayesian approach to estimate MHC-peptide binding threshold
MpbPPI: a multi-task pre-training-based equivariant approach for the prediction of the effect of amino acid mutations on protein-protein interactions
Corrigendum to: Inferring microenvironmental regulation of gene expression from single-cell RNA sequencing data using scMLnet with an application to COVID-19
Review on predicting pairwise relationships between human microbes, drugs and diseases: from biological data to computational models
CLIP: accurate prediction of disordered linear interacting peptides from protein sequences using co-evolutionary information
usDSM: a novel method for deleterious synonymous mutation prediction using undersampling scheme
Attention-aware contrastive learning for predicting T cell receptor-antigen binding specificity
Dual-stream cross-modal fusion alignment network for survival analysis
Drug repurposing for COVID-19: could vitamin C combined with glycyrrhizic acid be at play by the findings of Li et al.'s database-based network pharmacology analysis?
MTGIpick allows robust identification of genomic islands from a single genome
SEGtool: a specifically expressed gene detection tool and applications in human tissue and single-cell sequencing data
DeFusion: a denoised network regularization framework for multi-omics integration
The mathematical exploration for the mechanism of lung adenocarcinoma formation and progression
A point cloud-based deep learning strategy for protein-ligand binding affinity prediction
Noncoding RNA family classification based on multifeature fusion and convolutional block attention residual network
scSTAR reveals hidden heterogeneity with a real-virtual cell pair structure across conditions in single-cell RNA sequencing data
Detecting associations of rare variants with common diseases: collapsing or haplotyping?
Correction to: Synthetic plasma pool cohort correction for affinity-based proteomics datasets allows multiple study comparison
MPEK: a multitask deep learning framework based on pretrained language models for enzymatic reaction kinetic parameters prediction
Human Sequence Variation and Mutation Databases
Integrating massive RNA-seq data to elucidate transcriptome dynamics in Drosophila melanogaster
On the core segmentation algorithms of copy number variation detection tools
Prediction of tumor purity from gene expression data using machine learning
Bioinformatics tools and challenges in structural analysis of lipidomics MS/MS data
Comparison of high-throughput single-cell RNA sequencing data processing pipelines
Reconsideration of in silico siRNA design from a perspective of heterogeneous data integration: problems and solutions
The UCSC genome browser and associated tools
TopoQA: a topological deep learning-based approach for protein complex structure interface quality assessment
Not all T cell epitopes are equally desired: a review of in silico tools for the prediction of cytokine-inducing potential of T-cell epitopes
Predicting miRNA-disease associations based on graph random propagation network and attention network
A heterogeneous network embedding framework for predicting similarity-based drug-target interactions
Topological and geometric analysis of cell states in single-cell transcriptomic data
Published anti-SARS-CoV-2 in vitro hits share common mechanisms of action that synergize with antivirals
Biological network extraction from scientific literature: state of the art and challenges
AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads
Multiomics dynamic learning enables personalized diagnosis and prognosis for pancancer and cancer subtypes
Opportunities for community awareness platforms in personal genomics and bioinformatics education
Innovative super-resolution in spatial transcriptomics: a transformer model exploiting histology images and spatial gene expression
Frontiers of biomedical text mining: current progress
A generic parallel framework for inferring large-scale gene regulatory networks from expression profiles: application to Alzheimer's disease network
Multi-Manifolds fusing hyperbolic graph network balanced by pareto optimization for identifying spatial domains of spatial transcriptomics
DLpTCR: an ensemble deep learning framework for predicting immunogenic peptide recognized by T cell receptor
Where to search top-K biomedical ontologies?
Pioneering bioinformatics with agent-based modelling: an innovative protocol to accurately forecast skin or respiratory allergic reactions to chemical sensitizers
Approximate estimation of cell-type resolution transcriptome in bulk tissue through matrix completion
Algorithmic strategies for the single nucleotide polymorphism haplotype assembly problem
Computational discrete models of tissue growth and regeneration
Critical assessment of structure-based sequence alignment methods at distant relationships
An integrated brain-specific network identifies genes associated with neuropathologic and clinical traits of Alzheimer's disease
Physiological RNA dynamics in RNA-Seq analysis
Advances, challenges and opportunities of phylogenetic and social network analysis using COVID-19 data
Allotetraploid and autotetraploid models of linkage analysis
A model-agnostic framework to enhance knowledge graph-based drug combination prediction with drug-drug interaction data and supervised contrastive learning
A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis
Facilitating the use of large-scale biological data and tools in the era of translational bioinformatics
Research progress of miRNA-disease association prediction and comparison of related algorithms
Federated sharing and processing of genomic datasets for tertiary data analysis
Learning protein subcellular localization multi-view patterns from heterogeneous data of imaging, sequence and networks
Quantile regression for challenging cases of eQTL mapping
GOWDL: gene ontology-driven wide and deep learning model for cell typing of scRNA-seq data
The impact of HGT on phylogenomic reconstruction methods
Pathogenic gene prediction based on network embedding
Protein-peptide docking using CABS-dock and contact information
Analysis of cancer omics data: a selective review of statistical techniques
LmTag: functional-enrichment and imputation-aware tag SNP selection for population-specific genotyping arrays
scaLR: a low-resource deep neural network-based platform for single cell analysis and biomarker discovery
INTREPPPID - an orthologue-informed quintuplet network for cross-species prediction of protein-protein interaction
Breast cancer classification: linking molecular mechanisms to disease prognosis
Integrative, normalization-insusceptible statistical analysis of RNA-Seq data, with improved differential expression and unbiased downstream functional analysis
Systems Bioinformatics: increasing precision of computational diagnostics and therapeutics through network-based approaches
dCCA: detecting differential covariation patterns between two types of high-throughput omics data
Heterogeneous information network and its application to human health and disease
Benchmarking enrichment analysis methods with the disease pathway network
A review of feature selection strategies utilizing graph data structures and Knowledge Graphs
AEPMA: peptide-microbe association prediction based on autoevolutionary heterogeneous graph learning
A survey of current work in biomedical text mining
Higher order interaction analysis quantifies coordination in the epigenome revealing novel biological relationships in Kabuki syndrome
Functional alterations caused by mutations reflect evolutionary trends of SARS-CoV-2
In silico model for miRNA-mediated regulatory network in cancer
Bioinformatics Education - Perspectives and Challenges out of Africa
Identifying complex gene-gene interactions: a mixed kernel omnibus testing approach
GeneRaMeN enables integration, comparison, and meta-analysis of multiple ranked gene lists to identify consensus, unique, and correlated genes
Multi-task adaptive pooling enabled synergetic learning of RNA modification across tissue, type and species from low-resolution epitranscriptomes
Predicting functional UTR variants by integrating region-specific features
Discretization of gene expression data revised