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 2021-05-01 to 2025-05-01.)

Article	Citations
Correction to: GTExVisualizer: a web platform for supporting ageing studies	1248
Predicting anti-cancer drug response by finding optimal subset of drugs	812
Accurate assembly of multiple RNA-seq samples with Aletsch	715
Statistical framework to determine indel-length distribution	618
OpenPhi: an interface to access Philips iSyntax whole slide images for computational pathology	579
Detecting spatially co-expressed gene clusters with functional coherence by graph-regularized convolutional neural network	488
CondiS web app: imputation of censored lifetimes for machine learning-based survival analysis	431
Completing gene trees without species trees in sub-quadratic time	271
ATLIGATOR: editing protein interactions with an atlas-based approach	267
PsiNorm: a scalable normalization for single-cell RNA-seq data	243
Practical selection of representative sets of RNA-seq samples using a hierarchical approach	239
deTELpy: Python package for high-throughput detection of amino acid substitutions in mass spectrometry datasets	194
LPTD: a novel linear programming-based topology determination method for cryo-EM maps	177
Mocafe: a comprehensive Python library for simulating cancer development with Phase Field Models	165
EvoAug-TF: extending evolution-inspired data augmentations for genomic deep learning to TensorFlow	158
Integrated Genome Browser App Store	142
PANPROVA: pangenomic prokaryotic evolution of full assemblies	131
MuWU: Mutant-seq library analysis and annotation	127
Clustering single-cell RNA-seq data by rank constrained similarity learning	120
Haplotype-based membership inference from summary genomic data	117
TRANSDIRE: data-driven direct reprogramming by a pioneer factor-guided trans-omics approach	116
Deep Subspace Mutual Learning for cancer subtypes prediction	111
pKPDB: a protein data bank extension database of pKa and pI theoretical values	107
Reconstructing tumor clonal lineage trees incorporating single-nucleotide variants, copy number alterations and structural variations	103
Icolos: a workflow manager for structure-based post-processing of de novo generated small molecules	100

MAFFIN: metabolomics sample normalization using maximal density fold change with high-quality metabolic features and corrected signal intensities	99
3Cnet: pathogenicity prediction of human variants using multitask learning with evolutionary constraints	97
HelixGAN a deep-learning methodology for conditional de novo design of α-helix structures	95
CrossTalkeR: analysis and visualization of ligand–receptorne tworks	94
monaLisa: an R/Bioconductor package for identifying regulatory motifs	93
ELIXIR: providing a sustainable infrastructure for life science data at European scale	88
Non-parametric modelling of temporal and spatial counts data from RNA-seq experiments	86
DTI-Voodoo: machine learning over interaction networks and ontology-based background knowledge predicts drug–target interactions	82
Increasing confidence in proteomic spectral deconvolution through mass defect	81
SimPlot++: a Python application for representing sequence similarity and detecting recombination	78
Idéfix: identifying accidental sample mix-ups in biobanks using polygenic scores	77
DeepSVP: integration of genotype and phenotype for structural variant prioritization using deep learning	76
Refget: standardized access to reference sequences	76
The ENDS of assumptions: an online tool for the epistemic non-parametric drug–response scoring	75
VeloViz: RNA velocity-informed embeddings for visualizing cellular trajectories	75
DRUMMER—rapid detection of RNA modifications through comparative nanopore sequencing	75
DeepPerVar: a multi-modal deep learning framework for functional interpretation of genetic variants in personal genome	74
Prediction of whole-cell transcriptional response with machine learning	74
GMNN2CD: identification of circRNA–disease associations based on variational inference and graph Markov neural networks	69
Inference of 3D genome architecture by modeling overdispersion of Hi-C data	69
Accurate spliced alignment of long RNA sequencing reads	67
Decomposing mosaic tandem repeats accurately from long reads	66
RNAsolo: a repository of cleaned PDB-derived RNA 3D structures	66
WMDS.net: a network control framework for identifying key players in transcriptome programs	64
Cross-species prediction of essential genes in insects	64
Deep Local Analysis deconstructs protein–protein interfaces and accurately estimates binding affinity changes upon mutation	63
Hardware acceleration of genomics data analysis: challenges and opportunities	61
CANTATA—prediction of missing links in Boolean networks using genetic programming	61
ProSynAR: a reference aware read merger	60
PyLiger: scalable single-cell multi-omic data integration in Python	60
Estimation of cancer cell fractions and clone trees from multi-region sequencing of tumors	59
MAGUS+eHMMs: improved multiple sequence alignment accuracy for fragmentary sequences	58
bollito: a flexible pipeline for comprehensive single-cell RNA-seq analyses	58