OOIR: Observatory of International Research

Papers

(The H4-Index of Briefings in Bioinformatics is 71. 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 2021-10-01 to 2025-10-01.)

Article	Citations
PLMFit: benchmarking transfer learning with protein language models for protein engineering	624
A comprehensive benchmark of tools for efficient genomic interval querying	409
Dynamic changes of synergy relationship between lncRNA and immune checkpoint in cancer progression	343
Melanoma 2.0. Skin cancer as a paradigm for emerging diagnostic technologies, computational modelling and artificial intelligence	328
Protein–DNA binding sites prediction based on pre-trained protein language model and contrastive learning	308
Phage quest: a beginner’s guide to explore viral diversity in the prokaryotic world	300
Cox-Sage: enhancing Cox proportional hazards model with interpretable graph neural networks for cancer prognosis	251
Benchmarking of computational methods for m6A profiling with Nanopore direct RNA sequencing	227
Distant metastasis identification based on optimized graph representation of gene interaction patterns	219
Directed evolution of antimicrobial peptides using multi-objective zeroth-order optimization	215
Computational refinement and multivalent engineering of complementarity-determining region-grafted nanobodies on a humanized scaffold for retaining antiviral efficacy	211
Blood-based transcriptomic signature panel identification for cancer diagnosis: benchmarking of feature extraction methods	206
scGAD: a new task and end-to-end framework for generalized cell type annotation and discovery	192
A novel prognostic framework for HBV-infected hepatocellular carcinoma: insights from ferroptosis and iron metabolism proteomics	171
Computational analyses of bacterial strains from shotgun reads	169
Deep learning reveals determinants of transcriptional infidelity at nucleotide resolution in the allopolyploid line by goldfish and common carp hybrids	161
Computational model for ncRNA research	152
COWID: an efficient cloud-based genomics workflow for scalable identification of SARS-COV-2	140
Clustered tree regression to learn protein energy change with mutated amino acid	138
Machine learning–augmented m6A-Seq analysis without a reference genome	136
Evaluating large language models for annotating proteins	129
dHICA: a deep transformer-based model enables accurate histone imputation from chromatin accessibility	124
Improving the performance of single-cell RNA-seq data mining based on relative expression orderings	122
CharID: a two-step model for universal prediction of interactions between chromatin accessible regions	121
QOT: Quantized Optimal Transport for sample-level distance matrix in single-cell omics	119

Balancing the transcriptome: leveraging sample similarity to improve measures of gene specificity	115
SGNNMD: signed graph neural network for predicting deregulation types of miRNA-disease associations	114
CpGFuse: a holistic approach for accurate identification of methylation states of DNA CpG sites	113
BayesKAT: bayesian optimal kernel-based test for genetic association studies reveals joint genetic effects in complex diseases	112
mbDecoda: a debiased approach to compositional data analysis for microbiome surveys	111
Graph-RPI: predicting RNA–protein interactions via graph autoencoder and self-supervised learning strategies	108
Combining power of different methods to detect associations in large data sets	102
Detection of transcription factors binding to methylated DNA by deep recurrent neural network	100
PMiSLocMF: predicting miRNA subcellular localizations by incorporating multi-source features of miRNAs	100
DeepCheck: multitask learning aids in assessing microbial genome quality	99
CLT-seq as a universal homopolymer-sequencing concept reveals poly(A)-tail-tuned ncRNA regulation	99
scAnno: a deconvolution strategy-based automatic cell type annotation tool for single-cell RNA-sequencing data sets	99
ETLD: an encoder-transformation layer-decoder architecture for protein contact and mutation effects prediction	99
Ensemble classification based feature selection: a case of identification on plant pentatricopeptide repeat proteins	98
A robust statistical approach for finding informative spatially associated pathways	98
Correction to: Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology	97
Letter regarding article named ‘Is acupuncture effective in the treatment of COVID-19 related symptoms? Based on bioinformatics/network topology strategy’	95
Ensemble learning based on matrix completion improves microbe-disease association prediction	95
SCSMD: Single Cell Consistent Clustering based on Spectral Matrix Decomposition	95
Addressing scalability and managing sparsity and dropout events in single-cell representation identification with ZIGACL	91
Inferring disease-associated circRNAs by multi-source aggregation based on heterogeneous graph neural network	89
HighFold: accurately predicting structures of cyclic peptides and complexes with head-to-tail and disulfide bridge constraints	89
A multichannel graph neural network based on multisimilarity modality hypergraph contrastive learning for predicting unknown types of cancer biomarkers	87
Learning discriminative and structural samples for rare cell types with deep generative model	87
Making PBPK models more reproducible in practice	86
Clustering scRNA-seq data with the cross-view collaborative information fusion strategy	85
Protein phosphorylation database and prediction tools	85
ADENet: a novel network-based inference method for prediction of drug adverse events	84
ULDNA: integrating unsupervised multi-source language models with LSTM-attention network for high-accuracy protein–DNA binding site prediction	84
Novel multi-omics deconfounding variational autoencoders can obtain meaningful disease subtyping	81
Deep learning in integrating spatial transcriptomics with other modalities	80
Detecting tipping points of complex diseases by network information entropy	80
MicroHDF: predicting host phenotypes with metagenomic data using a deep forest-based framework	79
From intuition to AI: evolution of small molecule representations in drug discovery	79
Assessing protein model quality based on deep graph coupled networks using protein language model	78
Subtype-DCC: decoupled contrastive clustering method for cancer subtype identification based on multi-omics data	78
Attribute-guided prototype network for few-shot molecular property prediction	77
Multi-modal domain adaptation for revealing spatial functional landscape from spatially resolved transcriptomics	75
Machine learning modeling of RNA structures: methods, challenges and future perspectives	74
A chronotherapeutics-applicable multi-target therapeutics based on AI: Example of therapeutic hypothermia	74
Identification of vital chemical information via visualization of graph neural networks	73
Self-supervised learning with chemistry-aware fragmentation for effective molecular property prediction	73
Building multiscale models with PhysiBoSS, an agent-based modeling tool	73
PRIEST: predicting viral mutations with immune escape capability of SARS-CoV-2 using temporal evolutionary information	72
Integrating AlphaFold and deep learning for atomistic interpretation of cryo-EM maps	71
AptaDiff: de novo design and optimization of aptamers based on diffusion models	71