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 2022-05-01 to 2026-05-01.)

Article	Citations
Dynamic changes of synergy relationship between lncRNA and immune checkpoint in cancer progression	897
STEAM: Spatial Transcriptomics Evaluation Algorithm and Metric for clustering performance	535
Analysis of super-enhancer using machine learning and its application to medical biology	534
Hi-C3: a statistical inference-based model for reconstructing higher-order cell–cell communication networks	461
Self-supervised learning with chemistry-aware fragmentation for effective molecular property prediction	347
Protein phosphorylation database and prediction tools	299
Multi-marker testing based on accelerated failure time models under possible left truncation and competing risks	286
A chronotherapeutics-applicable multi-target therapeutics based on AI: Example of therapeutic hypothermia	242
Improving drug response prediction via integrating gene relationships with deep learning	239
Multiple errors correction for position-limited DNA sequences with GC balance and no homopolymer for DNA-based data storage	229
Improving the performance of single-cell RNA-seq data mining based on relative expression orderings	213
FGeneBERT: function-driven pre-trained gene language model for metagenomics	209
Stoichiometry-preserving and stochasticity-aware identification of m6A from direct RNA sequencing	199
Deep learning in integrating spatial transcriptomics with other modalities	178
Learning discriminative and structural samples for rare cell types with deep generative model	176
Phage quest: a beginner’s guide to explore viral diversity in the prokaryotic world	151
Assessing protein model quality based on deep graph coupled networks using protein language model	151
Deep learning reveals determinants of transcriptional infidelity at nucleotide resolution in the allopolyploid line by goldfish and common carp hybrids	136
Computational model for ncRNA research	131
COWID: an efficient cloud-based genomics workflow for scalable identification of SARS-COV-2	127
QOT: Quantized Optimal Transport for sample-level distance matrix in single-cell omics	126
Balancing the transcriptome: leveraging sample similarity to improve measures of gene specificity	123
CpGFuse: a holistic approach for accurate identification of methylation states of DNA CpG sites	121
ETLD: an encoder-transformation layer-decoder architecture for protein contact and mutation effects prediction	117
Ensemble classification based feature selection: a case of identification on plant pentatricopeptide repeat proteins	111

Correction to: Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology	109
SCSMD: Single Cell Consistent Clustering based on Spectral Matrix Decomposition	107
Attribute-guided prototype network for few-shot molecular property prediction	106
Addressing scalability and managing sparsity and dropout events in single-cell representation identification with ZIGACL	106
Large-scale predicting protein functions through heterogeneous feature fusion	103
Evaluating large language models for annotating proteins	102
AICellType: a large language model-based platform for accurate cell type annotation	102
PLMFit: benchmarking transfer learning with protein language models for protein engineering	101
Clustered tree regression to learn protein energy change with mutated amino acid	97
Cox-Sage: enhancing Cox proportional hazards model with interpretable graph neural networks for cancer prognosis	97
From intuition to AI: evolution of small molecule representations in drug discovery	96
Building multiscale models with PhysiBoSS, an agent-based modeling tool	94
PMiSLocMF: predicting miRNA subcellular localizations by incorporating multi-source features of miRNAs	94
Novel multi-omics deconfounding variational autoencoders can obtain meaningful disease subtyping	92
Clover: tree structure-based efficient DNA clustering for DNA-based data storage	91
Computational refinement and multivalent engineering of complementarity-determining region-grafted nanobodies on a humanized scaffold for retaining antiviral efficacy	91
GAABind: a geometry-aware attention-based network for accurate protein–ligand binding pose and binding affinity prediction	90
AptaDiff: de novo design and optimization of aptamers based on diffusion models	89
Protein–DNA binding sites prediction based on pre-trained protein language model and contrastive learning	89
ULDNA: integrating unsupervised multi-source language models with LSTM-attention network for high-accuracy protein–DNA binding site prediction	87
Graph-RPI: predicting RNA–protein interactions via graph autoencoder and self-supervised learning strategies	86
Machine learning modeling of RNA structures: methods, challenges and future perspectives	86
A social theory-enhanced graph representation learning framework for multitask prediction of drug–drug interactions	85
Melanoma 2.0. Skin cancer as a paradigm for emerging diagnostic technologies, computational modelling and artificial intelligence	85
dHICA: a deep transformer-based model enables accurate histone imputation from chromatin accessibility	85
scAnno: a deconvolution strategy-based automatic cell type annotation tool for single-cell RNA-sequencing data sets	83
Subtype-DCC: decoupled contrastive clustering method for cancer subtype identification based on multi-omics data	83
DeepCheck: multitask learning aids in assessing microbial genome quality	81
Blood-based transcriptomic signature panel identification for cancer diagnosis: benchmarking of feature extraction methods	81
mbDecoda: a debiased approach to compositional data analysis for microbiome surveys	78
CLT-seq as a universal homopolymer-sequencing concept reveals poly(A)-tail-tuned ncRNA regulation	78
A comprehensive benchmark of tools for efficient genomic interval querying	78
BayesKAT: bayesian optimal kernel-based test for genetic association studies reveals joint genetic effects in complex diseases	77
PRIEST: predicting viral mutations with immune escape capability of SARS-CoV-2 using temporal evolutionary information	77
Systematic evaluation of de novo mutation calling tools using whole genome sequencing data	76
QTFPred: robust high-performance quantum machine learning modeling that predicts main and cooperative transcription factor bindings with base resolution	75
Machine learning–augmented m6A-Seq analysis without a reference genome	75
Clustering scRNA-seq data with the cross-view collaborative information fusion strategy	73
A multichannel graph neural network based on multisimilarity modality hypergraph contrastive learning for predicting unknown types of cancer biomarkers	72
GeNePi: a graphics processing unit enhanced next-generation bioinformatics pipeline for whole-genome sequencing analysis	72
Predicting protein–carbohydrate binding sites: a deep learning approach integrating protein language model embeddings and structural features	72
Predicting microbe–drug associations with structure-enhanced contrastive learning and self-paced negative sampling strategy	71
Beyond metaphor: quantitative reconstruction of Waddington landscape and exploration of cellular behavior	71
Towards comprehensive benchmarking of medical vision language models	70
A novel prognostic framework for HBV-infected hepatocellular carcinoma: insights from ferroptosis and iron metabolism proteomics	69
scGAD: a new task and end-to-end framework for generalized cell type annotation and discovery	69
IGCNSDA: unraveling disease-associated snoRNAs with an interpretable graph convolutional network	69