yusuke1997/dblp-id-title huggingface dataset:
Single-cell mosaic integration and cell state transfer with auto-scaling self-attention mechanism
xSiGra: explainable model for single-cell spatial data elucidation
iDVIP: identification and characterization of viral integrase inhibitory peptides
LncAS2Cancer: a comprehensive database for alternative splicing of lncRNAs across human cancers
Cofea: correlation-based feature selection for single-cell chromatin accessibility data
RiboReport - benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria
scHiCStackL: a stacking ensemble learning-based method for single-cell Hi-C classification using cell embedding
Long noncoding RNA: a crosslink in biological regulatory network
A practical assembly guideline for genomes with various levels of heterozygosity
Bioinformatics in the Netherlands: the value of a nationwide community
DeepRMSF: a deep learning-based automated approach for predicting atomic-level flexibility in RNA structure
scAdapt: virtual adversarial domain adaptation network for single cell RNA-seq data classification across platforms and species
MSIpixel: a fully automated pipeline for compound annotation and quantitation in mass spectrometry imaging experiments
Navigating the HapMap
DeepAlgPro: an interpretable deep neural network model for predicting allergenic proteins
A versatile and scalable single-cell data integration algorithm based on domain-adversarial and variational approximation
Parameter estimation methods for gene circuit modeling from time-series mRNA data: a comparative study
A systematic evaluation of cell-type-specific differential methylation analysis in bulk tissue
ICBcomb: a comprehensive expression database for immune checkpoint blockade combination therapy
Refinement of computational identification of somatic copy number alterations using DNA methylation microarrays illustrated in cancers of unknown primary
Response to Letter to Editor by A. Derbalah et al.: the role of automation in enhancing reproducibility and interoperability of PBPK models
A comparison of random forest variable selection methods for regression modeling of continuous outcomes
CAT: a conditional association test for microbiome data using a permutation approach
DECEPTICON: a correlation-based strategy for RNA-seq deconvolution inspired by a variation of the Anna Karenina principle
NASTRA: accurate analysis of short tandem repeat markers by nanopore sequencing with repeat-structure-aware algorithm
Phen2Disease: a phenotype-driven model for disease and gene prioritization by bidirectional maximum matching semantic similarities
Prediction of protein-protein interactions between fungus (Magnaporthe grisea) and rice (Oryza sativa L.)
Integrative approaches for predicting protein function and prioritizing genes for complex phenotypes using protein interaction networks
CoRegNet: unraveling gene co-regulation networks from public RNA-Seq repositories using a beta-binomial statistical model
Matching single cells across modalities with contrastive learning and optimal transport
Decoding cancer heterogeneity through super-enhancer landscapes: from subtype discovery to therapeutic opportunity
Bioinformatics mentorship in a resource limited setting
Structural database resources for biological macromolecules
Three lectures on case-control genetic association analysis
Deep learning-driven survival prediction in pan-cancer studies by integrating multimodal histology-genomic data
Unlocking cross-modal interplay of single-cell joint profiling with CellMATE
ORI-Deep: improving the accuracy for predicting origin of replication sites by using a blend of features and long short-term memory network
Evaluating template-based and template-free protein-protein complex structure prediction
Comprehensive evaluation of noise reduction methods for single-cell RNA sequencing data
AgingBank: a manually curated knowledgebase and high-throughput analysis platform that provides experimentally supported multi-omics data relevant to aging in multiple species
Modeling genotype-protein interaction and correlation for Alzheimer's disease: a multi-omics imaging genetics study
Incomplete time-series gene expression in integrative study for islet autoimmunity prediction
An integrative approach to understanding mechanosensation
Alignment-free phylogenetics and population genetics
BICEP: Bayesian inference for rare genomic variant causality evaluation in pedigrees
Broader incorporation of bioinformatics in education: opportunities and challenges
A genome-scale deep learning model to predict gene expression changes of genetic perturbations from multiplex biological networks
Learning single-cell chromatin accessibility profiles using meta-analytic marker genes
The Role of Pattern Databases in Sequence Analysis
Attention is all you need: utilizing attention in AI-enabled drug discovery
Benchmarking knowledge graph embedding models for the prediction of oligogenic combinations
PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact
MS-BACL: enhancing metabolic stability prediction through bond graph augmentation and contrastive learning
CpGFuse: a holistic approach for accurate identification of methylation states of DNA CpG sites
ChemMORT: an automatic ADMET optimization platform using deep learning and multi-objective particle swarm optimization
A generally applicable lightweight method for calculating a value structure for tools and services in bioinformatics infrastructure projects
Bubble: a fast single-cell RNA-seq imputation using an autoencoder constrained by bulk RNA-seq data
Managing batch effects in microbiome data
cropCSM: designing safe and potent herbicides with graph-based signatures
Translational bioinformatics in the era of real-time biomedical, health care and wellness data streams
Using cross-validation to evaluate predictive accuracy of survival risk classifiers based on high-dimensional data
Clustering malignant cell states using universally variable genes
Error modelled gene expression analysis (EMOGEA) provides a superior overview of time course RNA-seq measurements and low count gene expression
Validation of gene regulatory networks: scientific and inferential
RepurposeDrugs: an interactive web-portal and predictive platform for repurposing mono- and combination therapies
Bioinformatics tools for the structural elucidation of multi-subunit protein complexes by mass spectrometric analysis of protein-protein cross-links
Computational analysis of protein interaction networks for infectious diseases
miRPreM and tiRPreM: Improved methodologies for the prediction of miRNAs and tRNA-induced small non-coding RNAs for model and non-model organisms
The landscape of different molecular modules in an immune microenvironment during tuberculosis infection
Problems, challenges and promises: perspectives on precision medicine
A robust statistical approach for finding informative spatially associated pathways
Comprehensive evaluation of methods for differential expression analysis of metatranscriptomics data
Deep autoregressive generative models capture the intrinsics embedded in T-cell receptor repertoires
Connectome verification: inter-rater and connection reliability of tract-tracing-based intrinsic hypothalamic connectivity
Network-based drug discovery by integrating systems biology and computational technologies
MultiWaverX : modeling latent sex-biased admixture history
Using Tablet for visual exploration of second-generation sequencing data
Knowledge bases and software support for variant interpretation in precision oncology
Advancing promiscuous aggregating inhibitor analysis with intelligent machine learning classification
Two-stage-vote ensemble framework based on integration of mutation data and gene interaction network for uncovering driver genes
Expression of Concern to: OPUS-Rota4: a gradient-based protein side-chain modeling framework assisted by deep learning-based predictors
An in silico approach to identification, categorization and prediction of nucleic acid binding proteins
Genome-wide characterization of lncRNAs in acute myeloid leukemia
Accurate flexible refinement for atomic-level protein structure using cryo-EM density maps and deep learning
Testing cell-type-specific mediation effects in genome-wide epigenetic studies
Generating pregnant patient biological profiles by deconvoluting clinical records with electronic health record foundation models
Specific network information gain for detecting the critical state of colorectal cancer based on gut microbiome
Problems and Solutions in Biological Sequence Analysis, Mark Borodovsky, Svetlana Ekisheva
Validation of transcriptome signature reversion for drug repurposing in oncology
Collaborative science in the next-generation sequencing era: a viewpoint on how to combine exome sequencing data across sites to identify novel disease susceptibility genes
Enhanced compound-protein binding affinity prediction by representing protein multimodal information via a coevolutionary strategy
Systematic analysis of supervised machine learning as an effective approach to predicate β-lactam resistance phenotype in Streptococcus pneumoniae
The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling
A deep learning feature importance test framework for integrating informative high-dimensional biomarkers to improve disease outcome prediction
100 Years of evolving gene-disease complexities and scientific debutants
Dockey: a modern integrated tool for large-scale molecular docking and virtual screening
Ensemble of kernel ridge regression-based small molecule-miRNA association prediction in human disease
Predicting the potential human lncRNA-miRNA interactions based on graph convolution network with conditional random field
Data management strategies for multinational large-scale systems biology projects
Inter-kingdom prediction certainty evaluation of protein subcellular localization tools: microbial pathogenesis approach for deciphering host microbe interaction
DiSNEP: a Disease-Specific gene Network Enhancement to improve Prioritizing candidate disease genes
Toward the dynamic interactome: it's about time
Biologically meaningful regulatory logic enhances the convergence rate in Boolean networks and bushiness of their state transition graph
Subgraph extraction and graph representation learning for single cell Hi-C imputation and clustering
A protocol for dynamic model calibration
Comparing the evolutionary conservation between human essential genes, human orthologs of mouse essential genes and human housekeeping genes
GPDOCK: highly accurate docking strategy for metalloproteins based on geometric probability
Single-residue linear and conformational B cell epitopes prediction using random and ESM-2 based projections
Exploring the function of genetic variants in the non-coding genomic regions: approaches for identifying human regulatory variants affecting gene expression
SAMURAI: shallow analysis of copy number alterations using a reproducible and integrated bioinformatics pipeline
A comprehensive overview of computational resources to aid in precision genome editing with engineered nucleases
A critical review of five machine learning-based algorithms for predicting protein stability changes upon mutation
Travelling the world of gene-gene interactions
CancerHubs: a systematic data mining and elaboration approach for identifying novel cancer-related protein interaction hubs
Ensemble learning algorithms for classification of mtDNA into haplogroups
A brief introduction to web-based genome browsers
Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery
WSGMB: weight signed graph neural network for microbial biomarker identification
ProtPhage: a deep learning framework for phage viral protein identification and functional annotation
Introduction to Computational Genomics: A Case Studies Approach Nello Cristianini and Matthew W. Hahn
The next generation of literature analysis: Integration of genomic analysis into text mining
A survey on predicting microbe-disease associations: biological data and computational methods
IDP-EDL: enhancing intrinsically disordered protein prediction by combining protein language model and ensemble deep learning
Phage quest: a beginner's guide to explore viral diversity in the prokaryotic world
TRCirc: a resource for transcriptional regulation information of circRNAs
'We are gathered here today' - EST cluster databases
Progress and challenges in predicting protein-protein interaction sites
The Beta Workbench: a computational tool to study the dynamics of biological systems
FROGS: a powerful tool to analyse the diversity of fungi with special management of internal transcribed spacers
ToxinPred2: an improved method for predicting toxicity of proteins
Current status and future perspectives of computational studies on human-virus protein-protein interactions
Reverse engineering biomolecular systems using -omic data: challenges, progress and opportunities
Self-supervised learning on millions of primary RNA sequences from 72 vertebrates improves sequence-based RNA splicing prediction
SFGAE: a self-feature-based graph autoencoder model for miRNA-disease associations prediction
Comprehensive review and empirical analysis of hallmarks of DNA-, RNA- and protein-binding residues in protein chains
Corrigendum to: Evaluation of machine learning approaches for cell-type identification from single-cell transcriptomics data
Global-local aware Heterogeneous Graph Contrastive Learning for multifaceted association prediction in miRNA-gene-disease networks
ProtFold-DFG: protein fold recognition by combining Directed Fusion Graph and PageRank algorithm
The genetic architecture of heterochrony as a quantitative trait: lessons from a computational model
Addressing the heterogeneity in liver diseases using biological networks
Comprehensive assessment of long-read sequencing platforms and calling algorithms for detection of copy number variation
Network-based analysis revealed significant interactions between risk genes of severe COVID-19 and host genes interacted with SARS-CoV-2 proteins
The bioinformatics toolbox for circRNA discovery and analysis
Lactylation prediction models based on protein sequence and structural feature fusion
A toolbox for developing bioinformatics software
High-resolution shotgun metagenomics: the more data, the better?
Improving distance measures between genomic tracks with mutual proximity
Integration of pairwise neighbor topologies and miRNA family and cluster attributes for miRNA-disease association prediction
CircRM: profiling circular RNA modifications from nanopore direct RNA sequencing
SpaNCMG: improving spatial domains identification of spatial transcriptomics using neighborhood-complementary mixed-view graph convolutional network
Deciphering the MHC immunopeptidome of human cancers with Ligand.MHC atlas
How the strengths of Lisp-family languages facilitate building complex and flexible bioinformatics applications
Protein engineering via Bayesian optimization-guided evolutionary algorithm and robotic experiments
Predicting multiple types of miRNA-disease associations using adaptive weighted nonnegative tensor factorization with self-paced learning and hypergraph regularization
Mining small-molecule screens to repurpose drugs
Novel genetic insight for psoriasis: integrative genome-wide analyses in 863 080 individuals and proteome-wide Mendelian randomization
DeepTorrent: a deep learning-based approach for predicting DNA N4-methylcytosine sites
RNA tertiary structure prediction with ModeRNA
Erratum to: Machine learning meets omics applications and perspectives
CosTaL: an accurate and scalable graph-based clustering algorithm for high-dimensional single-cell data analysis
Herb-CMap: a multimodal fusion framework for deciphering the mechanisms of action in traditional Chinese medicine using Suhuang antitussive capsule as a case study
Stratifying TAD boundaries pinpoints focal genomic regions of regulation, damage, and repair
Multi-channel graph attention autoencoders for disease-related lncRNAs prediction
Cracking the black box of deep sequence-based protein-protein interaction prediction
Impact of computational approaches in the fight against COVID-19: an AI guided review of 17 000 studies
AFP-MFL: accurate identification of antifungal peptides using multi-view feature learning
The HLA-I landscape confers prognosis and antitumor immunity in breast cancer
Impact of halogenation on scaffold toxicity assessed using HD-GEM machine learning model
Development and validation of an explainable machine learning model for predicting multidimensional frailty in hospitalized patients with cirrhosis
A GPU-accelerated compute framework for pathogen genomic variant identification to aid genomic epidemiology of infectious disease: a malaria case study
The integration of genome-wide and transcriptome-wide association studies in neurodegenerative diseases: opportunities, challenges, and current methodological innovations
Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses
The RNA world in the 21st century - a systems approach to finding non-coding keys to clinical questions
Genome optimization via virtual simulation to accelerate maize hybrid breeding
Control principles for complex biological networks
Machine learning in bioinformatics
Recent application of artificial intelligence on histopathologic image-based prediction of gene mutation in solid cancers
Letter regarding article named 'Is acupuncture effective in the treatment of COVID-19 related symptoms? Based on bioinformatics/network topology strategy'
MVML-MPI: Multi-View Multi-Label Learning for Metabolic Pathway Inference
Drug-target interaction predication via multi-channel graph neural networks
Whole-genome bisulfite sequencing data analysis learning module on Google Cloud Platform
Comprehensive characterization of tissue-specific circular RNAs in the human and mouse genomes
Unveiling the immune infiltrate modulation in cancer and response to immunotherapy by MIXTURE - an enhanced deconvolution method
Multi-omics regulatory network inference in the presence of missing data
LncRNA-disease association identification using graph auto-encoder and learning to rank
Case study: using sequence homology to identify putative phosphorylation sites in an evolutionarily distant species (honeybee)
Librator: a platform for the optimized analysis, design, and expression of mutable influenza viral antigens
SpaRx: elucidate single-cell spatial heterogeneity of drug responses for personalized treatment
Development of a TMErisk model based on immune infiltration in tumour microenvironment to predict prognosis of immune checkpoint inhibitor treatment in hepatocellular carcinoma
A multi-Poisson dynamic mixture model to cluster developmental patterns of gene expression by RNA-seq
Revealing tumor heterogeneity of breast cancer by utilizing the linkage between somatic and germline mutations
Computationally scalable regression modeling for ultrahigh-dimensional omics data with ParProx
Pathogenicity phenomena in three model systems: from network mining to emerging system-level properties
Intersection of network medicine and machine learning towards investigating the key biomarkers and pathways underlying amyotrophic lateral sclerosis: a systematic review
Iterative clustering algorithm G-DESC-E and pan-cancer key gene analysis based on single-cell sequencing data
Pattern recognition analysis on long noncoding RNAs: a tool for prediction in plants
Exploring phenotype patterns of breast cancer within somatic mutations: a modicum in the intrinsic code
Identification of potential therapeutic targets and mechanisms of COVID-19 through network analysis and screening of chemicals and herbal ingredients
Computational methods for Gene Orthology inference
CellDrift: inferring perturbation responses in temporally sampled single-cell data
Computational aspects of systematic biology
Uni-GBSA: an open-source and web-based automatic workflow to perform MM/GB(PB)SA calculations for virtual screening
Genomic privacy preservation in genome-wide association studies: taxonomy, limitations, challenges, and vision
Interfaces to PeptideAtlas: a case study of standard data access systems
SCPline: An interactive framework for the single-cell proteomics data preprocessing
Can Correlated Mutations in Protein Domain Families Be Used for Protein Design?
RNAEditor: easy detection of RNA editing events and the introduction of editing islands
scGAD: a new task and end-to-end framework for generalized cell type annotation and discovery
CCPA: cloud-based, self-learning modules for consensus pathway analysis using GO, KEGG and Reactome
Systematic assessment of pathway databases, based on a diverse collection of user-submitted experiments
Informatics in neuroscience
IECata: interpretable bilinear attention network and evidential deep learning improve the catalytic efficiency prediction of enzymes
OrthoDisease: tracking disease gene orthologs across 100 species
Graph deep learning enabled spatial domains identification for spatial transcriptomics
Clarion is a multi-label problem transformation method for identifying mRNA subcellular localizations
SC-Track: a robust cell-tracking algorithm for generating accurate single-cell lineages from diverse cell segmentations
Accounting for noise when clustering biological data
iDRPro-SC: identifying DNA-binding proteins and RNA-binding proteins based on subfunction classifiers
Correction to: Revolutionizing GPCR-ligand predictions: DeepGPCR with experimental validation for high-precision drug discovery
scESI: evolutionary sparse imputation for single-cell transcriptomes from nearest neighbor cells
Correction to: Quantum computing algorithms: getting closer to critical problems in computational biology
Multiscale modelling in immunology: a review
cfMethylPre: deep transfer learning enhances cancer detection based on circulating cell-free DNA methylation profiling
Introducing TEC-LncMir for prediction of lncRNA-miRNA interactions through deep learning of RNA sequences
A computational approach to developing a multi-epitope vaccine for combating Pseudomonas aeruginosa -induced pneumonia and sepsis
Interaction-based transcriptome analysis via differential network inference
Evolution of gene regulation - on the road towards computational inferences
RNet: a network strategy to predict RNA binding preferences
Bayesian inference for genomic imprinting underlying developmental characteristics
Elucidating the interactions between Kinesin-5/BimC and the microtubule: insights from TIRF microscopy and molecular dynamics simulations
A single-cell multimodal view on gene regulatory network inference from transcriptomics and chromatin accessibility data
Chinese medical dialogue information extraction via contrastive multi-utterance inference
Tensor factorization toward precision medicine
Benchmarking of computational methods for predicting circRNA-disease associations
Methodological implementation of mixed linear models in multi-locus genome-wide association studies
Jemboss reloaded
M3Site: multiclass multimodal learning for protein active site identification and classification
LIMO-GCN: a linear model-integrated graph convolutional network for predicting Alzheimer disease genes
Rich annotation of DNA sequencing variants by leveraging the Ensembl Variant Effect Predictor with plugins
Prediction of lncRNAs and their interactions with nucleic acids: benchmarking bioinformatics tools
scAMAC: self-supervised clustering of scRNA-seq data based on adaptive multi-scale autoencoder
HNSPPI: a hybrid computational model combing network and sequence information for predicting protein-protein interaction
MMsurv: a multimodal multi-instance multi-cancer survival prediction model integrating pathological images, clinical information, and sequencing data
Multilevel superposition for deciphering the conformational variability of protein ensembles
Multimodal multiobjective optimization with structural network control principles to optimize personalized drug targets for drug discovery of individual patients
SpaGIC: graph-informed clustering in spatial transcriptomics via self-supervised contrastive learning