OOIR: Observatory of International Research

Papers

(The H4-Index of Briefings in Bioinformatics is 69. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2022-01-01 to 2026-01-01.)

Article	Citations
Dynamic changes of synergy relationship between lncRNA and immune checkpoint in cancer progression	734
Clustered tree regression to learn protein energy change with mutated amino acid	485
Improving the performance of single-cell RNA-seq data mining based on relative expression orderings	424
Ensemble learning based on matrix completion improves microbe-disease association prediction	406
STEAM: Spatial Transcriptomics Evaluation Algorithm and Metric for clustering performance	389
Analysis of super-enhancer using machine learning and its application to medical biology	329
Melanoma 2.0. Skin cancer as a paradigm for emerging diagnostic technologies, computational modelling and artificial intelligence	251
Hi-C3: a statistical inference-based model for reconstructing higher-order cell–cell communication networks	247
Phage quest: a beginner’s guide to explore viral diversity in the prokaryotic world	227
Cox-Sage: enhancing Cox proportional hazards model with interpretable graph neural networks for cancer prognosis	217
Computational refinement and multivalent engineering of complementarity-determining region-grafted nanobodies on a humanized scaffold for retaining antiviral efficacy	216
Deep learning reveals determinants of transcriptional infidelity at nucleotide resolution in the allopolyploid line by goldfish and common carp hybrids	212
Computational model for ncRNA research	185
COWID: an efficient cloud-based genomics workflow for scalable identification of SARS-COV-2	177
QOT: Quantized Optimal Transport for sample-level distance matrix in single-cell omics	163
Balancing the transcriptome: leveraging sample similarity to improve measures of gene specificity	152
CpGFuse: a holistic approach for accurate identification of methylation states of DNA CpG sites	147
ETLD: an encoder-transformation layer-decoder architecture for protein contact and mutation effects prediction	145
Ensemble classification based feature selection: a case of identification on plant pentatricopeptide repeat proteins	135
Correction to: Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology	130
Letter regarding article named ‘Is acupuncture effective in the treatment of COVID-19 related symptoms? Based on bioinformatics/network topology strategy’	129
SCSMD: Single Cell Consistent Clustering based on Spectral Matrix Decomposition	120
Addressing scalability and managing sparsity and dropout events in single-cell representation identification with ZIGACL	118
A multichannel graph neural network based on multisimilarity modality hypergraph contrastive learning for predicting unknown types of cancer biomarkers	117
Inferring disease-associated circRNAs by multi-source aggregation based on heterogeneous graph neural network	117

Graph-RPI: predicting RNA–protein interactions via graph autoencoder and self-supervised learning strategies	116
A novel prognostic framework for HBV-infected hepatocellular carcinoma: insights from ferroptosis and iron metabolism proteomics	112
scAnno: a deconvolution strategy-based automatic cell type annotation tool for single-cell RNA-sequencing data sets	112
Building multiscale models with PhysiBoSS, an agent-based modeling tool	108
mbDecoda: a debiased approach to compositional data analysis for microbiome surveys	106
A robust statistical approach for finding informative spatially associated pathways	106
BayesKAT: bayesian optimal kernel-based test for genetic association studies reveals joint genetic effects in complex diseases	105
A comprehensive benchmark of tools for efficient genomic interval querying	102
CLT-seq as a universal homopolymer-sequencing concept reveals poly(A)-tail-tuned ncRNA regulation	101
Blood-based transcriptomic signature panel identification for cancer diagnosis: benchmarking of feature extraction methods	101
A chronotherapeutics-applicable multi-target therapeutics based on AI: Example of therapeutic hypothermia	96
Computational analyses of bacterial strains from shotgun reads	95
dHICA: a deep transformer-based model enables accurate histone imputation from chromatin accessibility	94
Systematic evaluation of de novo mutation calling tools using whole genome sequencing data	94
FGeneBERT: function-driven pre-trained gene language model for metagenomics	92
Self-supervised learning with chemistry-aware fragmentation for effective molecular property prediction	90
DeepCheck: multitask learning aids in assessing microbial genome quality	90
Protein phosphorylation database and prediction tools	88
A social theory-enhanced graph representation learning framework for multitask prediction of drug–drug interactions	86
QTFPred: robust high-performance quantum machine learning modeling that predicts main and cooperative transcription factor bindings with base resolution	86
From intuition to AI: evolution of small molecule representations in drug discovery	85
scGAD: a new task and end-to-end framework for generalized cell type annotation and discovery	85
CharID: a two-step model for universal prediction of interactions between chromatin accessible regions	84
HighFold: accurately predicting structures of cyclic peptides and complexes with head-to-tail and disulfide bridge constraints	84
Beyond metaphor: quantitative reconstruction of Waddington landscape and exploration of cellular behavior	83
Making PBPK models more reproducible in practice	83
Clustering scRNA-seq data with the cross-view collaborative information fusion strategy	81
Predicting microbe–drug associations with structure-enhanced contrastive learning and self-paced negative sampling strategy	81
DriverOmicsNet: an integrated graph convolutional network for multi-omics exploration of cancer driver genes	81
Towards comprehensive benchmarking of medical vision language models	81
MicroHDF: predicting host phenotypes with metagenomic data using a deep forest-based framework	79
Genome assembly and gene identification of biosurfactant-producing bacteria for environmental bioremediation	77
Attribute-guided prototype network for few-shot molecular property prediction	77
A review on the application of bioinformatics tools in food microbiome studies	77
PRIEST: predicting viral mutations with immune escape capability of SARS-CoV-2 using temporal evolutionary information	76
Deep learning in integrating spatial transcriptomics with other modalities	75
Multiple errors correction for position-limited DNA sequences with GC balance and no homopolymer for DNA-based data storage	75
Novel multi-omics deconfounding variational autoencoders can obtain meaningful disease subtyping	75
Benchmarking of computational methods for m6A profiling with Nanopore direct RNA sequencing	73
Detecting tipping points of complex diseases by network information entropy	73
GAABind: a geometry-aware attention-based network for accurate protein–ligand binding pose and binding affinity prediction	72
Improving drug response prediction via integrating gene relationships with deep learning	72
Subtype-DCC: decoupled contrastive clustering method for cancer subtype identification based on multi-omics data	72
Multi-modal domain adaptation for revealing spatial functional landscape from spatially resolved transcriptomics	70