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
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
Mixtum: a graphical tool for two-way admixture analysis in population genetics based on f -statistics	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
MDCompress: better, faster compression of molecular dynamics simulation trajectories	69
Refining sequence-to-expression modelling with chromatin accessibility	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
RNAsolo: a repository of cleaned PDB-derived RNA 3D structures	57
Decomposing mosaic tandem repeats accurately from long reads	57
Deep Local Analysis deconstructs protein–protein interfaces and accurately estimates binding affinity changes upon mutation	57
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
From high-throughput evaluation to wet-lab studies: advancing mutation effect prediction with a retrieval-enhanced model	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