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 2021-09-01 to 2025-09-01.)

Article	Citations
CondiS web app: imputation of censored lifetimes for machine learning-based survival analysis	1517
ATLIGATOR: editing protein interactions with an atlas-based approach	1079
Detecting spatially co-expressed gene clusters with functional coherence by graph-regularized convolutional neural network	856
LPTD: a novel linear programming-based topology determination method for cryo-EM maps	742
Mocafe: a comprehensive Python library for simulating cancer development with Phase Field Models	617
Integrated Genome Browser App Store	613
PANPROVA: pangenomic prokaryotic evolution of full assemblies	335
MuWU: Mutant-seq library analysis and annotation	302
Icolos: a workflow manager for structure-based post-processing of de novo generated small molecules	291
Idéfix: identifying accidental sample mix-ups in biobanks using polygenic scores	232
Accurate assembly of multiple RNA-seq samples with Aletsch	204
Deep Subspace Mutual Learning for cancer subtypes prediction	203
Completing gene trees without species trees in sub-quadratic time	182
EvoAug-TF: extending evolution-inspired data augmentations for genomic deep learning to TensorFlow	177
HelixGAN a deep-learning methodology for conditional de novo design of α-helix structures	144
Statistical framework to determine indel-length distribution	135
Correction to: GTExVisualizer: a web platform for supporting ageing studies	126
deTELpy: Python package for high-throughput detection of amino acid substitutions in mass spectrometry datasets	120
The 2025 ISCB Accomplishments by a Senior Scientist Award—Dr Amos Bairoch	118
DivPro: diverse protein sequence design with direct structure recovery guidance	114
RVINN: a flexible modeling for inferring dynamic transcriptional and post-transcriptional regulation using physics-informed neural networks	112
MAFFIN: metabolomics sample normalization using maximal density fold change with high-quality metabolic features and corrected signal intensities	108
Increasing confidence in proteomic spectral deconvolution through mass defect	107
SimPlot++: a Python application for representing sequence similarity and detecting recombination	99
TRANSDIRE: data-driven direct reprogramming by a pioneer factor-guided trans-omics approach	90

monaLisa: an R/Bioconductor package for identifying regulatory motifs	90
Reconstructing tumor clonal lineage trees incorporating single-nucleotide variants, copy number alterations and structural variations	88
PsiNorm: a scalable normalization for single-cell RNA-seq data	88
MRDagent: Iterative and Adaptive Parameter Optimisation for stable ctDNA-Based MRD Detection in Heterogeneous Samples	87
DeepPerVar: a multi-modal deep learning framework for functional interpretation of genetic variants in personal genome	84
Prediction of whole-cell transcriptional response with machine learning	83
VeloViz: RNA velocity-informed embeddings for visualizing cellular trajectories	82
Cross-species prediction of essential genes in insects	81
bollito: a flexible pipeline for comprehensive single-cell RNA-seq analyses	81
DeepSVP: integration of genotype and phenotype for structural variant prioritization using deep learning	81
Estimation of cancer cell fractions and clone trees from multi-region sequencing of tumors	81
ADViSELipidomics: a workflow for analyzing lipidomics data	80
The FASTQ+ format and PISA	80
MICER: a pre-trained encoder–decoder architecture for molecular image captioning	78
Deep Local Analysis deconstructs protein–protein interfaces and accurately estimates binding affinity changes upon mutation	78
skandiver: a divergence-based analysis tool for identifying intercellular mobile genetic elements	76
ProSynAR: a reference aware read merger	73
Exploring automatic inconsistency detection for literature-based gene ontology annotation	71
MAGUS+eHMMs: improved multiple sequence alignment accuracy for fragmentary sequences	71
Erratum to: GADGETS: a genetic algorithm for detecting epistasis using nuclear families	70
Aclust2.0: a revamped unsupervised R tool for Infinium methylation beadchips data analyses	69
Random field modeling of multi-trait multi-locus association for detecting methylation quantitative trait loci	69
MetBP: a software tool for detection of interaction between metal ion–RNA base pairs	67
Response to the letter to the editor: On the feasibility of dynamical analysis of network models of biochemical regulation	66
trfermikit: a tool to discover VNTR-associated deletions	66
Continual knowledge infusion into pre-trained biomedical language models	65
RNAglib: a python package for RNA 2.5 D graphs	65
Group-walk: a rigorous approach to group-wise false discovery rate analysis by target-decoy competition	64
PyLiger: scalable single-cell multi-omic data integration in Python	63
GMNN2CD: identification of circRNA–disease associations based on variational inference and graph Markov neural networks	61
CANTATA—prediction of missing links in Boolean networks using genetic programming	61
From high-throughput evaluation to wet-lab studies: advancing mutation effect prediction with a retrieval-enhanced model	60
`Oarfish`: enhanced probabilistic modeling leads to improved accuracy in long read transcriptome quantification	60
Harnessing deep learning for proteome-scale detection of amyloid signaling motifs	59