OOIR: Observatory of International Research

Papers

(The H4-Index of Bioinformatics is 44. 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 2022-08-01 to 2026-08-01.)

Article	Citations
RVINN: a flexible modeling for inferring dynamic transcriptional and post-transcriptional regulation using physics-informed neural networks	2387
Correction to: GTExVisualizer: a web platform for supporting ageing studies	1990
ProteinLIPs: a web server for identifying highly polar and poorly packed interfaces in proteins	374
IntegrAlign: a comprehensive tool for multi-immunofluorescence panel integration through image alignment	282
NOODAI: a webserver for network-oriented multi-omics data analysis and integration pipeline	199
Memory-efficient, accelerated protein interaction inference with blocked, multi-GPU D-SCRIPT	151
Mixtum: a graphical tool for two-way admixture analysis in population genetics based on f -statistics	132
FracFixR: a compositional statistical framework for absolute proportion estimation between fractions in RNA sequencing data	116
FastDup: a scalable duplicate marking tool using speculation-and-test mechanism	116
From genes to trajectories: mapping genetic influences on Huntington’s disease progression	111
MDCompress: better, faster compression of molecular dynamics simulation trajectories	110
MCOAN: multimodal contrastive representation learning for cross-omics adaptive disease regulatory network prediction	96
ATLIGATOR: editing protein interactions with an atlas-based approach	93
Icolos: a workflow manager for structure-based post-processing of de novo generated small molecules	85
The 2025 ISCB Accomplishments by a Senior Scientist Award—Dr Amos Bairoch	84
HelixGAN a deep-learning methodology for conditional de novo design of α-helix structures	81
FUSE: data-driven functional segmentation of DNA methylation data	80
deTELpy: Python package for high-throughput detection of amino acid substitutions in mass spectrometry datasets	73
Diagnosing scientific replicability through probabilistic distinguishability	73
NAViFluX: a visualization‑centric platform for interactive analysis, refinement and design of genome‑scale metabolic networks	73
DivPro: diverse protein sequence design with direct structure recovery guidance	72
A-liner: linear alignment visualizer for genome comparisons	70
CodonMoE: DNA language models for codon-dependent mRNA prediction	66
Viral Diseases Explorer: a webtool to identify viral disease information derived from multiple LLMs	66
ChromCall: assigning chromatin status to defined genomic regions using epigenomic profiling data	65

Increasing confidence in proteomic spectral deconvolution through mass defect	60
HKD-CPI: high-order knowledge distillation enhanced inductive compound-protein interaction prediction	60
LoMuS: low-rank adaptation with sequence multi-representation improves protein stability prediction	60
getDNB: identifying dynamic network biomarkers of hepatocellular carcinoma from time-varying gene regulations utilizing graph embedding techniques for anomaly detection	59
MRDagent: iterative and adaptive parameter optimization for stable ctDNA-based MRD detection in heterogeneous samples	59
Statistical framework to determine indel-length distribution	59
Accurate assembly of multiple RNA-seq samples with Aletsch	58
3DICE: interpretable 3D cross-modal learning for drug–target interaction prediction and large-scale drug discovery	55
ProMeta: a meta-learning framework for robust disease diagnosis and prediction from plasma proteomics	54
Likelihood-based optimization enables accurate copy number estimation for paralogous genes using exome data	53
NPBIP: predicting binding preferences of uncharacterized nucleic-acid-binding proteins	53
DirectASRM: uncovering allele-specific post-transcriptional RNA modifications through direct RNA sequencing	50
Refining sequence-to-expression modelling with chromatin accessibility	49
EvoAug-TF: extending evolution-inspired data augmentations for genomic deep learning to TensorFlow	49
Group-walk: a rigorous approach to group-wise false discovery rate analysis by target-decoy competition	46
CompareM2 is a genomes-to-report pipeline for comparing microbial genomes	46
The phers R package: using phenotype risk scores based on electronic health records to study Mendelian disease and rare genetic variants	46
CANTATA—prediction of missing links in Boolean networks using genetic programming	45
Harnessing deep learning for proteome-scale detection of amyloid signaling motifs	45
skandiver: a divergence-based analysis tool for identifying intercellular mobile genetic elements	44
FastSCODE: an accelerated SCODE algorithm for inferring gene regulatory networks on manycore processors	44
ADViSELipidomics: a workflow for analyzing lipidomics data	44