OOIR: Observatory of International Research

Papers

(The H4-Index of Bioinformatics is 59. 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 2021-12-01 to 2025-12-01.)

Article	Citations
The 2025 ISCB Accomplishments by a Senior Scientist Award—Dr Amos Bairoch	1764
DivPro: diverse protein sequence design with direct structure recovery guidance	1323
RVINN: a flexible modeling for inferring dynamic transcriptional and post-transcriptional regulation using physics-informed neural networks	840
LPTD: a novel linear programming-based topology determination method for cryo-EM maps	774
Integrated Genome Browser App Store	740
PANPROVA: pangenomic prokaryotic evolution of full assemblies	439
CondiS web app: imputation of censored lifetimes for machine learning-based survival analysis	341
deTELpy: Python package for high-throughput detection of amino acid substitutions in mass spectrometry datasets	304
Memory-efficient, accelerated protein interaction inference with blocked, multi-GPU D-SCRIPT	267
Statistical framework to determine indel-length distribution	254
CompareM2 is a genomes-to-report pipeline for comparing microbial genomes	225
MRDagent: iterative and adaptive parameter optimization for stable ctDNA-based MRD detection in heterogeneous samples	209
getDNB: identifying dynamic network biomarkers of hepatocellular carcinoma from time-varying gene regulations utilizing graph embedding techniques for anomaly detection	163
Mocafe: a comprehensive Python library for simulating cancer development with Phase Field Models	133
Correction to: GTExVisualizer: a web platform for supporting ageing studies	132
Detecting spatially co-expressed gene clusters with functional coherence by graph-regularized convolutional neural network	129
ProteinLIPs: a web server for identifying highly polar and poorly packed interfaces in proteins	129
IntegrAlign: a comprehensive tool for multi-immunofluorescence panel integration through image alignment	127
NOODAI: a webserver for network-oriented multi-omics data analysis and integration pipeline	117
Completing gene trees without species trees in sub-quadratic time	115
Viral Diseases Explorer: a webtool to identify viral disease information derived from multiple LLMs	105
ATLIGATOR: editing protein interactions with an atlas-based approach	104
EvoAug-TF: extending evolution-inspired data augmentations for genomic deep learning to TensorFlow	101
Icolos: a workflow manager for structure-based post-processing of de novo generated small molecules	99
TRANSDIRE: data-driven direct reprogramming by a pioneer factor-guided trans-omics approach	93

HelixGAN a deep-learning methodology for conditional de novo design of α-helix structures	90
Increasing confidence in proteomic spectral deconvolution through mass defect	89
MAFFIN: metabolomics sample normalization using maximal density fold change with high-quality metabolic features and corrected signal intensities	88
Reconstructing tumor clonal lineage trees incorporating single-nucleotide variants, copy number alterations and structural variations	88
SimPlot++: a Python application for representing sequence similarity and detecting recombination	87
Accurate assembly of multiple RNA-seq samples with Aletsch	87
monaLisa: an R/Bioconductor package for identifying regulatory motifs	86
Fragmentstein—facilitating data reuse for cell-free DNA fragment analysis	81
Cross-species prediction of essential genes in insects	79
Response to the letter to the editor: On the feasibility of dynamical analysis of network models of biochemical regulation	76
trfermikit: a tool to discover VNTR-associated deletions	76
WMDS.net: a network control framework for identifying key players in transcriptome programs	75
insilicoSV: a flexible grammar-based framework for structural variant simulation and placement	74
`Oarfish`: enhanced probabilistic modeling leads to improved accuracy in long read transcriptome quantification	74
Exploring automatic inconsistency detection for literature-based gene ontology annotation	74
Random field modeling of multi-trait multi-locus association for detecting methylation quantitative trait loci	72
MetBP: a software tool for detection of interaction between metal ion–RNA base pairs	69
skandiver: a divergence-based analysis tool for identifying intercellular mobile genetic elements	67
Harnessing deep learning for proteome-scale detection of amyloid signaling motifs	67
From high-throughput evaluation to wet-lab studies: advancing mutation effect prediction with a retrieval-enhanced model	67
Erratum to: GADGETS: a genetic algorithm for detecting epistasis using nuclear families	66
CANTATA—prediction of missing links in Boolean networks using genetic programming	66
ProSynAR: a reference aware read merger	65
Decomposing mosaic tandem repeats accurately from long reads	65
RNAglib: a python package for RNA 2.5 D graphs	64
AFragmenter: schema-free, tuneable protein domain segmentation for AlphaFold protein structures	63
ADViSELipidomics: a workflow for analyzing lipidomics data	63
DeepPerVar: a multi-modal deep learning framework for functional interpretation of genetic variants in personal genome	62
Perceiver CPI: a nested cross-attention network for compound–protein interaction prediction	62
The phers R package: using phenotype risk scores based on electronic health records to study Mendelian disease and rare genetic variants	61
Deep Local Analysis deconstructs protein–protein interfaces and accurately estimates binding affinity changes upon mutation	60
Estimation of cancer cell fractions and clone trees from multi-region sequencing of tumors	60
The ENDS of assumptions: an online tool for the epistemic non-parametric drug–response scoring	59
Group-walk: a rigorous approach to group-wise false discovery rate analysis by target-decoy competition	59
Inference of 3D genome architecture by modeling overdispersion of Hi-C data	59