OOIR: Observatory of International Research

Papers

(The H4-Index of Bioinformatics is 58. 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 2021-06-01 to 2025-06-01.)

Article	Citations
Correction to: GTExVisualizer: a web platform for supporting ageing studies	1317
Predicting anti-cancer drug response by finding optimal subset of drugs	861
Accurate assembly of multiple RNA-seq samples with Aletsch	751
Statistical framework to determine indel-length distribution	647
OpenPhi: an interface to access Philips iSyntax whole slide images for computational pathology	517
Detecting spatially co-expressed gene clusters with functional coherence by graph-regularized convolutional neural network	473
CondiS web app: imputation of censored lifetimes for machine learning-based survival analysis	278
Completing gene trees without species trees in sub-quadratic time	272
deTELpy: Python package for high-throughput detection of amino acid substitutions in mass spectrometry datasets	260
ATLIGATOR: editing protein interactions with an atlas-based approach	260
LPTD: a novel linear programming-based topology determination method for cryo-EM maps	206
Mocafe: a comprehensive Python library for simulating cancer development with Phase Field Models	184
EvoAug-TF: extending evolution-inspired data augmentations for genomic deep learning to TensorFlow	177
Integrated Genome Browser App Store	167
PANPROVA: pangenomic prokaryotic evolution of full assemblies	148
MuWU: Mutant-seq library analysis and annotation	145
Haplotype-based membership inference from summary genomic data	131
TRANSDIRE: data-driven direct reprogramming by a pioneer factor-guided trans-omics approach	130
pKPDB: a protein data bank extension database of pKa and pI theoretical values	123
Reconstructing tumor clonal lineage trees incorporating single-nucleotide variants, copy number alterations and structural variations	114
Icolos: a workflow manager for structure-based post-processing of de novo generated small molecules	113
Idéfix: identifying accidental sample mix-ups in biobanks using polygenic scores	106
Non-parametric modelling of temporal and spatial counts data from RNA-seq experiments	103
Practical selection of representative sets of RNA-seq samples using a hierarchical approach	102
3Cnet: pathogenicity prediction of human variants using multitask learning with evolutionary constraints	99

DTI-Voodoo: machine learning over interaction networks and ontology-based background knowledge predicts drug–target interactions	97
MAFFIN: metabolomics sample normalization using maximal density fold change with high-quality metabolic features and corrected signal intensities	97
Deep Subspace Mutual Learning for cancer subtypes prediction	95
SimPlot++: a Python application for representing sequence similarity and detecting recombination	94
monaLisa: an R/Bioconductor package for identifying regulatory motifs	89
Increasing confidence in proteomic spectral deconvolution through mass defect	88
PsiNorm: a scalable normalization for single-cell RNA-seq data	83
HelixGAN a deep-learning methodology for conditional de novo design of α-helix structures	81
ELIXIR: providing a sustainable infrastructure for life science data at European scale	80
DeepSVP: integration of genotype and phenotype for structural variant prioritization using deep learning	79
Refget: standardized access to reference sequences	79
DeepPerVar: a multi-modal deep learning framework for functional interpretation of genetic variants in personal genome	78
Prediction of whole-cell transcriptional response with machine learning	76
DRUMMER—rapid detection of RNA modifications through comparative nanopore sequencing	76
Inference of 3D genome architecture by modeling overdispersion of Hi-C data	75
Cross-species prediction of essential genes in insects	73
Deep Local Analysis deconstructs protein–protein interfaces and accurately estimates binding affinity changes upon mutation	70
WMDS.net: a network control framework for identifying key players in transcriptome programs	69
ProSynAR: a reference aware read merger	67
PyLiger: scalable single-cell multi-omic data integration in Python	67
MAGUS+eHMMs: improved multiple sequence alignment accuracy for fragmentary sequences	67
CANTATA—prediction of missing links in Boolean networks using genetic programming	67
Exploring automatic inconsistency detection for literature-based gene ontology annotation	65
Aclust2.0: a revamped unsupervised R tool for Infinium methylation beadchips data analyses	64
Erratum to: GADGETS: a genetic algorithm for detecting epistasis using nuclear families	64
Random field modeling of multi-trait multi-locus association for detecting methylation quantitative trait loci	62
skandiver: a divergence-based analysis tool for identifying intercellular mobile genetic elements	62
MetBP: a software tool for detection of interaction between metal ion–RNA base pairs	61
Tysserand—fast and accurate reconstruction of spatial networks from bioimages	60
Fragmentstein—facilitating data reuse for cell-free DNA fragment analysis	59
Probabilistic identification of bacterial essential genes via insertion density using TraDIS data with Tn5 libraries	59
Deconvolution of expression for nascent RNA-sequencing data (DENR) highlights pre-RNA isoform diversity in human cells	58
trfermikit: a tool to discover VNTR-associated deletions	58
Evidential meta-model for molecular property prediction	58