OOIR: Observatory of International Research

Papers

(The H4-Index of Briefings in Bioinformatics is 63. 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 2021-02-01 to 2025-02-01.)

Article	Citations
Letter regarding article named ‘Is acupuncture effective in the treatment of COVID-19 related symptoms? Based on bioinformatics/network topology strategy’	806
ExsgRNA: reduce off-target efficiency by on-target mismatched sgRNA	346
MCIBox: a toolkit for single-molecule multi-way chromatin interaction visualization and micro-domains identification	233
Incomplete time-series gene expression in integrative study for islet autoimmunity prediction	165
Correction to: Molecular persistent spectral image (Mol-PSI) representation for machine learning models in drug design	161
Towards molecular structure discovery from cryo-ET density volumes via modelling auxiliary semantic prototypes	156
Twenty years of advances in prediction of nucleic acid-binding residues in protein sequences	154
BioGSF: a graph-driven semantic feature integration framework for biomedical relation extraction	140
Complex p53 dynamics regulated by miR-125b in cellular responses to reactive oxidative stress and DNA damage	135
bulkAnalyseR: an accessible, interactive pipeline for analysing and sharing bulk multi-modal sequencing data	122
Fast heritability estimation based on MINQUE and batch training	120
Integrating network pharmacology and in silico analysis deciphers Withaferin-A’s anti-breast cancer potential via hedgehog pathway and target network interplay	117
Knowledge-based classification of fine-grained immune cell types in single-cell RNA-Seq data	117
eSCAN: scan regulatory regions for aggregate association testing using whole-genome sequencing data	116
HIP: a method for high-dimensional multi-view data integration and prediction accounting for subgroup heterogeneity	115
Learning discriminative and structural samples for rare cell types with deep generative model	115
An initial game-theoretic assessment of enhanced tissue preparation and imaging protocols for improved deep learning inference of spatial transcriptomics from tissue morphology	113
CReSIL: accurate identification of extrachromosomal circular DNA from long-read sequences	113
Interpretable modeling of time-resolved single-cell gene–protein expression with CrossmodalNet	109
Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly	108
SGPPI: structure-aware prediction of protein–protein interactions in rigorous conditions with graph convolutional network	108
iDRPro-SC: identifying DNA-binding proteins and RNA-binding proteins based on subfunction classifiers	106
Identification of vital chemical information via visualization of graph neural networks	102
Application of deep learning in cancer epigenetics through DNA methylation analysis	98
EnGens: a computational framework for generation and analysis of representative protein conformational ensembles	97

Assessing protein model quality based on deep graph coupled networks using protein language model	97
Clover: tree structure-based efficient DNA clustering for DNA-based data storage	94
Unsupervised construction of gene regulatory network based on single-cell multi-omics data of colorectal cancer	94
Forman persistent Ricci curvature (FPRC)-based machine learning models for protein–ligand binding affinity prediction	93
preMLI: a pre-trained method to uncover microRNA–lncRNA potential interactions	92
Artificial intelligence in drug discovery: applications and techniques	92
Contexts and contradictions: a roadmap for computational drug repurposing with knowledge inference	87
spaCI: deciphering spatial cellular communications through adaptive graph model	86
Improved model quality assessment using sequence and structural information by enhanced deep neural networks	86
Letter to the editor: testing the effectiveness of MyPROSLE in classifying patients with lupus nephritis	86
ETLD: an encoder-transformation layer-decoder architecture for protein contact and mutation effects prediction	85
Defining the single base importance of human mRNAs and lncRNAs	85
COWID: an efficient cloud-based genomics workflow for scalable identification of SARS-COV-2	83
Genome optimization via virtual simulation to accelerate maize hybrid breeding	81
DeepMiceTL: a deep transfer learning based prediction of mice cardiac conduction diseases using early electrocardiograms	80
Accurate flexible refinement for atomic-level protein structure using cryo-EM density maps and deep learning	77
Representation of molecules for drug response prediction	77
IndGOterm: a qualitative method for the identification of individually dysregulated GO terms in cancer	77
KDGene: knowledge graph completion for disease gene prediction using interactional tensor decomposition	76
SEGCECO: Subgraph Embedding of Gene expression matrix for prediction of CEll-cell COmmunication	75
IGCNSDA: unraveling disease-associated snoRNAs with an interpretable graph convolutional network	74
MGCNSS: miRNA–disease association prediction with multi-layer graph convolution and distance-based negative sample selection strategy	74
Evaluation of propensity score methods for causal inference with high-dimensional covariates	73
Heavy chain sequence-based classifier for the specificity of human antibodies	73
Liquidhope: methylome and genomic profiling from very limited quantities of plasma-derived DNA	73
Correction to: siGCD: a web server to explore survival interaction of genes, cells and drugs in human cancers	73
Knowledge bases and software support for variant interpretation in precision oncology	73
GASS-Metal: identifying metal-binding sites on protein structures using genetic algorithms	73
A strategy combining denoising and cryo-EM single particle analysis	73
Improving drug response prediction via integrating gene relationships with deep learning	69
Quantitative estimation of intracellular oxidative stress in human tissues	69
Potential of dissimilarity measure-based computation of protein thermal stability data for determining protein interactions	68
Corrigendum to: Computational design of ultrashort peptide inhibitors of the receptor-binding domain of the SARS-CoV-2 S protein	68
GPMeta: a GPU-accelerated method for ultrarapid pathogen identification from metagenomic sequences	67
Chrom-Lasso: a lasso regression-based model to detect functional interactions using Hi-C data	66
BindingSite-AugmentedDTA: enabling a next-generation pipeline for interpretable prediction models in drug repurposing	66
Machine learning modeling of RNA structures: methods, challenges and future perspectives	65
Transcriptomic studies revealed pathophysiological impact of COVID-19 to predominant health conditions	64
SuperCUT, an unsupervised multimodal image registration with deep learning for biomedical microscopy	63
ML-PLIC: a web platform for characterizing protein–ligand interactions and developing machine learning-based scoring functions	63
Deep reinforcement learning identifies personalized intermittent androgen deprivation therapy for prostate cancer	63
A genome-scale deep learning model to predict gene expression changes of genetic perturbations from multiplex biological networks	63
Improving drug-target affinity prediction via feature fusion and knowledge distillation	63