OOIR: Observatory of International Research

Papers

(The H4-Index of Bioinformatics is 60. 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 2022-01-01 to 2026-01-01.)

Article	Citations
The 2025 ISCB Accomplishments by a Senior Scientist Award—Dr Amos Bairoch	1802
DivPro: diverse protein sequence design with direct structure recovery guidance	1404
RVINN: a flexible modeling for inferring dynamic transcriptional and post-transcriptional regulation using physics-informed neural networks	871
LPTD: a novel linear programming-based topology determination method for cryo-EM maps	796
Integrated Genome Browser App Store	768
CondiS web app: imputation of censored lifetimes for machine learning-based survival analysis	477
deTELpy: Python package for high-throughput detection of amino acid substitutions in mass spectrometry datasets	348
Memory-efficient, accelerated protein interaction inference with blocked, multi-GPU D-SCRIPT	281
Statistical framework to determine indel-length distribution	235
CompareM2 is a genomes-to-report pipeline for comparing microbial genomes	219
MRDagent: iterative and adaptive parameter optimization for stable ctDNA-based MRD detection in heterogeneous samples	166
getDNB: identifying dynamic network biomarkers of hepatocellular carcinoma from time-varying gene regulations utilizing graph embedding techniques for anomaly detection	143
Mocafe: a comprehensive Python library for simulating cancer development with Phase Field Models	140
Correction to: GTExVisualizer: a web platform for supporting ageing studies	138
IntegrAlign: a comprehensive tool for multi-immunofluorescence panel integration through image alignment	133
ProteinLIPs: a web server for identifying highly polar and poorly packed interfaces in proteins	133
NOODAI: a webserver for network-oriented multi-omics data analysis and integration pipeline	127
Completing gene trees without species trees in sub-quadratic time	118
MAFFIN: metabolomics sample normalization using maximal density fold change with high-quality metabolic features and corrected signal intensities	111
PANPROVA: pangenomic prokaryotic evolution of full assemblies	111
Viral Diseases Explorer: a webtool to identify viral disease information derived from multiple LLMs	107
ATLIGATOR: editing protein interactions with an atlas-based approach	103
EvoAug-TF: extending evolution-inspired data augmentations for genomic deep learning to TensorFlow	96
Icolos: a workflow manager for structure-based post-processing of de novo generated small molecules	94
TRANSDIRE: data-driven direct reprogramming by a pioneer factor-guided trans-omics approach	92

HelixGAN a deep-learning methodology for conditional de novo design of α-helix structures	90
Reconstructing tumor clonal lineage trees incorporating single-nucleotide variants, copy number alterations and structural variations	90
Increasing confidence in proteomic spectral deconvolution through mass defect	89
SimPlot++: a Python application for representing sequence similarity and detecting recombination	89
Accurate assembly of multiple RNA-seq samples with Aletsch	87
FastDup: a scalable duplicate marking tool using speculation-and-test mechanism	84
monaLisa: an R/Bioconductor package for identifying regulatory motifs	81
Fragmentstein—facilitating data reuse for cell-free DNA fragment analysis	78
Response to the letter to the editor: On the feasibility of dynamical analysis of network models of biochemical regulation	78
Cross-species prediction of essential genes in insects	78
insilicoSV: a flexible grammar-based framework for structural variant simulation and placement	77
Exploring automatic inconsistency detection for literature-based gene ontology annotation	76
Random field modeling of multi-trait multi-locus association for detecting methylation quantitative trait loci	74
MetBP: a software tool for detection of interaction between metal ion–RNA base pairs	73
skandiver: a divergence-based analysis tool for identifying intercellular mobile genetic elements	72
Harnessing deep learning for proteome-scale detection of amyloid signaling motifs	70
CANTATA—prediction of missing links in Boolean networks using genetic programming	69
ProSynAR: a reference aware read merger	69
The phers R package: using phenotype risk scores based on electronic health records to study Mendelian disease and rare genetic variants	68
The ENDS of assumptions: an online tool for the epistemic non-parametric drug–response scoring	68
Decomposing mosaic tandem repeats accurately from long reads	68
Deep Local Analysis deconstructs protein–protein interfaces and accurately estimates binding affinity changes upon mutation	68
MPBind: a multitask protein binding site predictor using protein language models and equivariant GNNs	67
FastSCODE: an accelerated SCODE algorithm for inferring gene regulatory networks on manycore processors	66
Aclust2.0: a revamped unsupervised R tool for Infinium methylation beadchips data analyses	66
WMDS.net: a network control framework for identifying key players in transcriptome programs	65
DRUMMER—rapid detection of RNA modifications through comparative nanopore sequencing	65
PyLiger: scalable single-cell multi-omic data integration in Python	65
Floria: fast and accurate strain haplotyping in metagenomes	63
GMNN2CD: identification of circRNA–disease associations based on variational inference and graph Markov neural networks	62
Inference of 3D genome architecture by modeling overdispersion of Hi-C data	62
From high-throughput evaluation to wet-lab studies: advancing mutation effect prediction with a retrieval-enhanced model	62
Evidential meta-model for molecular property prediction	61
MICER: a pre-trained encoder–decoder architecture for molecular image captioning	60
The FASTQ+ format and PISA	60