OOIR: Observatory of International Research

Papers

(The H4-Index of Bioinformatics is 50. 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
DivPro: diverse protein sequence design with direct structure recovery guidance	2180
RVINN: a flexible modeling for inferring dynamic transcriptional and post-transcriptional regulation using physics-informed neural networks	1807
CondiS web app: imputation of censored lifetimes for machine learning-based survival analysis	1029
Correction to: GTExVisualizer: a web platform for supporting ageing studies	621
ProteinLIPs: a web server for identifying highly polar and poorly packed interfaces in proteins	408
IntegrAlign: a comprehensive tool for multi-immunofluorescence panel integration through image alignment	344
NOODAI: a webserver for network-oriented multi-omics data analysis and integration pipeline	222
deTELpy: Python package for high-throughput detection of amino acid substitutions in mass spectrometry datasets	176
Memory-efficient, accelerated protein interaction inference with blocked, multi-GPU D-SCRIPT	142
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	122
Mixtum: a graphical tool for two-way admixture analysis in population genetics based on f -statistics	103
Accurate assembly of multiple RNA-seq samples with Aletsch	103
Viral Diseases Explorer: a webtool to identify viral disease information derived from multiple LLMs	103
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	93
From genes to trajectories: mapping genetic influences on Huntington’s disease progression	86
getDNB: identifying dynamic network biomarkers of hepatocellular carcinoma from time-varying gene regulations utilizing graph embedding techniques for anomaly detection	85
MCOAN: multimodal contrastive representation learning for cross-omics adaptive disease regulatory network prediction	84
Statistical framework to determine indel-length distribution	79
EvoAug-TF: extending evolution-inspired data augmentations for genomic deep learning to TensorFlow	78
ATLIGATOR: editing protein interactions with an atlas-based approach	78
Icolos: a workflow manager for structure-based post-processing of de novo generated small molecules	77
HelixGAN a deep-learning methodology for conditional de novo design of α-helix structures	76
The 2025 ISCB Accomplishments by a Senior Scientist Award—Dr Amos Bairoch	76

Reconstructing tumor clonal lineage trees incorporating single-nucleotide variants, copy number alterations and structural variations	75
Mocafe: a comprehensive Python library for simulating cancer development with Phase Field Models	74
Increasing confidence in proteomic spectral deconvolution through mass defect	72
Refining sequence-to-expression modelling with chromatin accessibility	69
MDCompress: better, faster compression of molecular dynamics simulation trajectories	69
FUSE: data-driven functional segmentation of DNA methylation data	68
Diagnosing scientific replicability through probabilistic distinguishability	68
NAViFluX: a visualization‑centric platform for interactive analysis, refinement and design of genome‑scale metabolic networks	68
CodonMoE: DNA language models for codon-dependent mRNA prediction	64
HKD-CPI: high-order knowledge distillation enhanced inductive compound-protein interaction prediction	62
Estimation of cancer cell fractions and clone trees from multi-region sequencing of tumors	61
Group-walk: a rigorous approach to group-wise false discovery rate analysis by target-decoy competition	59
The phers R package: using phenotype risk scores based on electronic health records to study Mendelian disease and rare genetic variants	59
Inference of 3D genome architecture by modeling overdispersion of Hi-C data	58
Deep Local Analysis deconstructs protein–protein interfaces and accurately estimates binding affinity changes upon mutation	57
RNAsolo: a repository of cleaned PDB-derived RNA 3D structures	57
Decomposing mosaic tandem repeats accurately from long reads	57
From high-throughput evaluation to wet-lab studies: advancing mutation effect prediction with a retrieval-enhanced model	56
Random field modeling of multi-trait multi-locus association for detecting methylation quantitative trait loci	56
Exploring automatic inconsistency detection for literature-based gene ontology annotation	56
MetBP: a software tool for detection of interaction between metal ion–RNA base pairs	55
CANTATA—prediction of missing links in Boolean networks using genetic programming	54
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	52
Evidential meta-model for molecular property prediction	51