OOIR: Observatory of International Research

Papers

(The H4-Index of Bioinformatics is 57. 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 2021-08-01 to 2025-08-01.)

Article	Citations
CondiS web app: imputation of censored lifetimes for machine learning-based survival analysis	1456
ATLIGATOR: editing protein interactions with an atlas-based approach	1013
LPTD: a novel linear programming-based topology determination method for cryo-EM maps	822
Mocafe: a comprehensive Python library for simulating cancer development with Phase Field Models	716
Integrated Genome Browser App Store	583
PANPROVA: pangenomic prokaryotic evolution of full assemblies	562
MuWU: Mutant-seq library analysis and annotation	307
TRANSDIRE: data-driven direct reprogramming by a pioneer factor-guided trans-omics approach	288
Deep Subspace Mutual Learning for cancer subtypes prediction	287
OpenPhi: an interface to access Philips iSyntax whole slide images for computational pathology	222
RVINN: a flexible modeling for inferring dynamic transcriptional and post-transcriptional regulation using physics-informed neural networks	194
DivPro: diverse protein sequence design with direct structure recovery guidance	190
The 2025 ISCB Accomplishments by a Senior Scientist Award—Dr Amos Bairoch	170
Increasing confidence in proteomic spectral deconvolution through mass defect	168
Accurate assembly of multiple RNA-seq samples with Aletsch	139
Icolos: a workflow manager for structure-based post-processing of de novo generated small molecules	135
Idéfix: identifying accidental sample mix-ups in biobanks using polygenic scores	123
Reconstructing tumor clonal lineage trees incorporating single-nucleotide variants, copy number alterations and structural variations	117
PsiNorm: a scalable normalization for single-cell RNA-seq data	116
Detecting spatially co-expressed gene clusters with functional coherence by graph-regularized convolutional neural network	112
Completing gene trees without species trees in sub-quadratic time	109
SimPlot++: a Python application for representing sequence similarity and detecting recombination	106
MAFFIN: metabolomics sample normalization using maximal density fold change with high-quality metabolic features and corrected signal intensities	104
HelixGAN a deep-learning methodology for conditional de novo design of α-helix structures	99
deTELpy: Python package for high-throughput detection of amino acid substitutions in mass spectrometry datasets	89

Correction to: GTExVisualizer: a web platform for supporting ageing studies	88
EvoAug-TF: extending evolution-inspired data augmentations for genomic deep learning to TensorFlow	85
Statistical framework to determine indel-length distribution	85
monaLisa: an R/Bioconductor package for identifying regulatory motifs	84
DeepSVP: integration of genotype and phenotype for structural variant prioritization using deep learning	83
DeepPerVar: a multi-modal deep learning framework for functional interpretation of genetic variants in personal genome	81
Prediction of whole-cell transcriptional response with machine learning	80
Cross-species prediction of essential genes in insects	76
VeloViz: RNA velocity-informed embeddings for visualizing cellular trajectories	76
bollito: a flexible pipeline for comprehensive single-cell RNA-seq analyses	75
Deconvolution of expression for nascent RNA-sequencing data (DENR) highlights pre-RNA isoform diversity in human cells	75
ProSynAR: a reference aware read merger	74
Exploring automatic inconsistency detection for literature-based gene ontology annotation	73
MAGUS+eHMMs: improved multiple sequence alignment accuracy for fragmentary sequences	73
Erratum to: GADGETS: a genetic algorithm for detecting epistasis using nuclear families	71
Random field modeling of multi-trait multi-locus association for detecting methylation quantitative trait loci	71
Aclust2.0: a revamped unsupervised R tool for Infinium methylation beadchips data analyses	71
skandiver: a divergence-based analysis tool for identifying intercellular mobile genetic elements	69
MetBP: a software tool for detection of interaction between metal ion–RNA base pairs	68
trfermikit: a tool to discover VNTR-associated deletions	67
Response to the letter to the editor: On the feasibility of dynamical analysis of network models of biochemical regulation	66
Group-walk: a rigorous approach to group-wise false discovery rate analysis by target-decoy competition	65
RNAglib: a python package for RNA 2.5 D graphs	65
PyLiger: scalable single-cell multi-omic data integration in Python	65
Continual knowledge infusion into pre-trained biomedical language models	65
The phers R package: using phenotype risk scores based on electronic health records to study Mendelian disease and rare genetic variants	64
CANTATA—prediction of missing links in Boolean networks using genetic programming	64
Estimation of cancer cell fractions and clone trees from multi-region sequencing of tumors	64
The ENDS of assumptions: an online tool for the epistemic non-parametric drug–response scoring	61
ADViSELipidomics: a workflow for analyzing lipidomics data	60
hapCon: estimating contamination of ancient genomes by copying from reference haplotypes	60
DRUMMER—rapid detection of RNA modifications through comparative nanopore sequencing	59
Perceiver CPI: a nested cross-attention network for compound–protein interaction prediction	57
From high-throughput evaluation to wet-lab studies: advancing mutation effect prediction with a retrieval-enhanced model	57
`Oarfish`: enhanced probabilistic modeling leads to improved accuracy in long read transcriptome quantification	57
Harnessing deep learning for proteome-scale detection of amyloid signaling motifs	57