OOIR: Observatory of International Research

Papers

(The H4-Index of Briefings in Bioinformatics is 70. 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 2022-06-01 to 2026-06-01.)

Article	Citations
Dynamic changes of synergy relationship between lncRNA and immune checkpoint in cancer progression	933
Phage quest: a beginner’s guide to explore viral diversity in the prokaryotic world	568
Deep learning reveals determinants of transcriptional infidelity at nucleotide resolution in the allopolyploid line by goldfish and common carp hybrids	556
Computational model for ncRNA research	473
COWID: an efficient cloud-based genomics workflow for scalable identification of SARS-COV-2	349
QOT: Quantized Optimal Transport for sample-level distance matrix in single-cell omics	296
CpGFuse: a holistic approach for accurate identification of methylation states of DNA CpG sites	243
ETLD: an encoder-transformation layer-decoder architecture for protein contact and mutation effects prediction	241
Ensemble classification based feature selection: a case of identification on plant pentatricopeptide repeat proteins	231
Correction to: Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology	218
SCSMD: Single Cell Consistent Clustering based on Spectral Matrix Decomposition	215
Addressing scalability and managing sparsity and dropout events in single-cell representation identification with ZIGACL	203
Machine learning–augmented m6A-Seq analysis without a reference genome	186
Attribute-guided prototype network for few-shot molecular property prediction	182
Hi-C3: a statistical inference-based model for reconstructing higher-order cell–cell communication networks	159
Systematic evaluation of de novo mutation calling tools using whole genome sequencing data	152
QTFPred: robust high-performance quantum machine learning modeling that predicts main and cooperative transcription factor bindings with base resolution	137
Stoichiometry-preserving and stochasticity-aware identification of m6A from direct RNA sequencing	131
FGeneBERT: function-driven pre-trained gene language model for metagenomics	129
Assessing protein model quality based on deep graph coupled networks using protein language model	127
Learning discriminative and structural samples for rare cell types with deep generative model	124
Predicting microbe–drug associations with structure-enhanced contrastive learning and self-paced negative sampling strategy	120
Towards comprehensive benchmarking of medical vision language models	115
A novel prognostic framework for HBV-infected hepatocellular carcinoma: insights from ferroptosis and iron metabolism proteomics	112
Predicting protein–carbohydrate binding sites: a deep learning approach integrating protein language model embeddings and structural features	110

Improving the performance of single-cell RNA-seq data mining based on relative expression orderings	110
MicroHDF: predicting host phenotypes with metagenomic data using a deep forest-based framework	109
Ensemble learning based on matrix completion improves microbe-disease association prediction	108
Benchmarking of computational methods for m6A profiling with Nanopore direct RNA sequencing	105
Genome assembly and gene identification of biosurfactant-producing bacteria for environmental bioremediation	105
dHICA: a deep transformer-based model enables accurate histone imputation from chromatin accessibility	103
Melanoma 2.0. Skin cancer as a paradigm for emerging diagnostic technologies, computational modelling and artificial intelligence	101
Evaluating large language models for annotating proteins	100
Protein–DNA binding sites prediction based on pre-trained protein language model and contrastive learning	98
AICellType: a large language model-based platform for accurate cell type annotation	95
Computational refinement and multivalent engineering of complementarity-determining region-grafted nanobodies on a humanized scaffold for retaining antiviral efficacy	95
Building multiscale models with PhysiBoSS, an agent-based modeling tool	95
A chronotherapeutics-applicable multi-target therapeutics based on AI: Example of therapeutic hypothermia	92
Self-supervised learning with chemistry-aware fragmentation for effective molecular property prediction	91
Multi-marker testing based on accelerated failure time models under possible left truncation and competing risks	91
A social theory-enhanced graph representation learning framework for multitask prediction of drug–drug interactions	90
Cox-Sage: enhancing Cox proportional hazards model with interpretable graph neural networks for cancer prognosis	89
Graph-RPI: predicting RNA–protein interactions via graph autoencoder and self-supervised learning strategies	88
Machine learning modeling of RNA structures: methods, challenges and future perspectives	88
Large-scale predicting protein functions through heterogeneous feature fusion	87
IGCNSDA: unraveling disease-associated snoRNAs with an interpretable graph convolutional network	86
scAnno: a deconvolution strategy-based automatic cell type annotation tool for single-cell RNA-sequencing data sets	85
Directed evolution of antimicrobial peptides using multi-objective zeroth-order optimization	85
Inferring disease-associated circRNAs by multi-source aggregation based on heterogeneous graph neural network	84
GeNePi: a graphics processing unit enhanced next-generation bioinformatics pipeline for whole-genome sequencing analysis	83
Clustering scRNA-seq data with the cross-view collaborative information fusion strategy	83
Blood-based transcriptomic signature panel identification for cancer diagnosis: benchmarking of feature extraction methods	80
A comprehensive benchmark of tools for efficient genomic interval querying	78
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
DeepCheck: multitask learning aids in assessing microbial genome quality	77
PRIEST: predicting viral mutations with immune escape capability of SARS-CoV-2 using temporal evolutionary information	77
BayesKAT: bayesian optimal kernel-based test for genetic association studies reveals joint genetic effects in complex diseases	77
A robust statistical approach for finding informative spatially associated pathways	75
Multi-modal domain adaptation for revealing spatial functional landscape from spatially resolved transcriptomics	74
DriverOmicsNet: an integrated graph convolutional network for multi-omics exploration of cancer driver genes	74
Improving drug response prediction via integrating gene relationships with deep learning	73
Making PBPK models more reproducible in practice	73
ULDNA: integrating unsupervised multi-source language models with LSTM-attention network for high-accuracy protein–DNA binding site prediction	72
A multichannel graph neural network based on multisimilarity modality hypergraph contrastive learning for predicting unknown types of cancer biomarkers	72
PLMFit: benchmarking transfer learning with protein language models for protein engineering	72
Deep learning in integrating spatial transcriptomics with other modalities	71
Subtype-DCC: decoupled contrastive clustering method for cancer subtype identification based on multi-omics data	71
Clover: tree structure-based efficient DNA clustering for DNA-based data storage	71
STEAM: Spatial Transcriptomics Evaluation Algorithm and Metric for clustering performance	71
HighFold: accurately predicting structures of cyclic peptides and complexes with head-to-tail and disulfide bridge constraints	70