OOIR: Observatory of International Research

Papers

(The H4-Index of Bioinformatics is 51. 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
DivPro: diverse protein sequence design with direct structure recovery guidance	2121
RVINN: a flexible modeling for inferring dynamic transcriptional and post-transcriptional regulation using physics-informed neural networks	1739
CondiS web app: imputation of censored lifetimes for machine learning-based survival analysis	988
Correction to: GTExVisualizer: a web platform for supporting ageing studies	603
ProteinLIPs: a web server for identifying highly polar and poorly packed interfaces in proteins	400
IntegrAlign: a comprehensive tool for multi-immunofluorescence panel integration through image alignment	336
NOODAI: a webserver for network-oriented multi-omics data analysis and integration pipeline	207
deTELpy: Python package for high-throughput detection of amino acid substitutions in mass spectrometry datasets	171
Memory-efficient, accelerated protein interaction inference with blocked, multi-GPU D-SCRIPT	165
CompareM2 is a genomes-to-report pipeline for comparing microbial genomes	134
MRDagent: iterative and adaptive parameter optimization for stable ctDNA-based MRD detection in heterogeneous samples	129
Viral Diseases Explorer: a webtool to identify viral disease information derived from multiple LLMs	116
Accurate assembly of multiple RNA-seq samples with Aletsch	101
Mixtum: a graphical tool for two-way admixture analysis in population genetics based on f -statistics	100
FastDup: a scalable duplicate marking tool using speculation-and-test mechanism	98
FracFixR: a compositional statistical framework for absolute proportion estimation between fractions in RNA sequencing data	96
From genes to trajectories: mapping genetic influences on Huntington’s disease progression	90
getDNB: identifying dynamic network biomarkers of hepatocellular carcinoma from time-varying gene regulations utilizing graph embedding techniques for anomaly detection	87
MCOAN: multimodal contrastive representation learning for cross-omics adaptive disease regulatory network prediction	85
Statistical framework to determine indel-length distribution	80
MAFFIN: metabolomics sample normalization using maximal density fold change with high-quality metabolic features and corrected signal intensities	79
ATLIGATOR: editing protein interactions with an atlas-based approach	77
EvoAug-TF: extending evolution-inspired data augmentations for genomic deep learning to TensorFlow	76
The 2025 ISCB Accomplishments by a Senior Scientist Award—Dr Amos Bairoch	74
Icolos: a workflow manager for structure-based post-processing of de novo generated small molecules	74

Increasing confidence in proteomic spectral deconvolution through mass defect	74
Mocafe: a comprehensive Python library for simulating cancer development with Phase Field Models	73
HelixGAN a deep-learning methodology for conditional de novo design of α-helix structures	72
MDCompress: better, faster compression of molecular dynamics simulation trajectories	71
Reconstructing tumor clonal lineage trees incorporating single-nucleotide variants, copy number alterations and structural variations	69
ADViSELipidomics: a workflow for analyzing lipidomics data	68
Group-walk: a rigorous approach to group-wise false discovery rate analysis by target-decoy competition	67
Estimation of cancer cell fractions and clone trees from multi-region sequencing of tumors	67
DeepPerVar: a multi-modal deep learning framework for functional interpretation of genetic variants in personal genome	65
The phers R package: using phenotype risk scores based on electronic health records to study Mendelian disease and rare genetic variants	65
Inference of 3D genome architecture by modeling overdispersion of Hi-C data	64
Deep Local Analysis deconstructs protein–protein interfaces and accurately estimates binding affinity changes upon mutation	62
Response to the letter to the editor: On the feasibility of dynamical analysis of network models of biochemical regulation	61
Decomposing mosaic tandem repeats accurately from long reads	60
Fragmentstein—facilitating data reuse for cell-free DNA fragment analysis	58
Exploring automatic inconsistency detection for literature-based gene ontology annotation	57
From high-throughput evaluation to wet-lab studies: advancing mutation effect prediction with a retrieval-enhanced model	57
RNAsolo: a repository of cleaned PDB-derived RNA 3D structures	57
MetBP: a software tool for detection of interaction between metal ion–RNA base pairs	56
Random field modeling of multi-trait multi-locus association for detecting methylation quantitative trait loci	56
Harnessing deep learning for proteome-scale detection of amyloid signaling motifs	54
FastSCODE: an accelerated SCODE algorithm for inferring gene regulatory networks on manycore processors	54
CANTATA—prediction of missing links in Boolean networks using genetic programming	54
Evidential meta-model for molecular property prediction	52
AFragmenter: schema-free, tuneable protein domain segmentation for AlphaFold protein structures	52
TripLexicon: prediction and analysis of gene regulatory RNA–DNA interactions	52
WMDS.net: a network control framework for identifying key players in transcriptome programs	51