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 2021-11-01 to 2025-11-01.)

Article	Citations
The 2025 ISCB Accomplishments by a Senior Scientist Award—Dr Amos Bairoch	1692
DivPro: diverse protein sequence design with direct structure recovery guidance	1228
RVINN: a flexible modeling for inferring dynamic transcriptional and post-transcriptional regulation using physics-informed neural networks	808
LPTD: a novel linear programming-based topology determination method for cryo-EM maps	735
Integrated Genome Browser App Store	706
PANPROVA: pangenomic prokaryotic evolution of full assemblies	395
CondiS web app: imputation of censored lifetimes for machine learning-based survival analysis	329
ATLIGATOR: editing protein interactions with an atlas-based approach	298
TRANSDIRE: data-driven direct reprogramming by a pioneer factor-guided trans-omics approach	247
CompareM2 is a genomes-to-report pipeline for comparing microbial genomes	234
MRDagent: iterative and adaptive parameter optimization for stable ctDNA-based MRD detection in heterogeneous samples	218
getDNB: identifying dynamic network biomarkers of hepatocellular carcinoma from time-varying gene regulations utilizing graph embedding techniques for anomaly detection	199
MAFFIN: metabolomics sample normalization using maximal density fold change with high-quality metabolic features and corrected signal intensities	157
Increasing confidence in proteomic spectral deconvolution through mass defect	128
monaLisa: an R/Bioconductor package for identifying regulatory motifs	127
Mocafe: a comprehensive Python library for simulating cancer development with Phase Field Models	123
EvoAug-TF: extending evolution-inspired data augmentations for genomic deep learning to TensorFlow	120
Statistical framework to determine indel-length distribution	116
Correction to: GTExVisualizer: a web platform for supporting ageing studies	111
Detecting spatially co-expressed gene clusters with functional coherence by graph-regularized convolutional neural network	106
ProteinLIPs: a web server for identifying highly polar and poorly packed interfaces in proteins	100
Icolos: a workflow manager for structure-based post-processing of de novo generated small molecules	99
Accurate assembly of multiple RNA-seq samples with Aletsch	94
HelixGAN a deep-learning methodology for conditional de novo design of α-helix structures	94
deTELpy: Python package for high-throughput detection of amino acid substitutions in mass spectrometry datasets	91

Completing gene trees without species trees in sub-quadratic time	86
Memory-efficient, accelerated protein interaction inference with blocked, multi-GPU D-SCRIPT	86
Scalable inference and identifiability of kinetic parameters for transcriptional bursting from single cell data	86
Reconstructing tumor clonal lineage trees incorporating single-nucleotide variants, copy number alterations and structural variations	85
SimPlot++: a Python application for representing sequence similarity and detecting recombination	84
Idéfix: identifying accidental sample mix-ups in biobanks using polygenic scores	82
The ENDS of assumptions: an online tool for the epistemic non-parametric drug–response scoring	81
Fragmentstein—facilitating data reuse for cell-free DNA fragment analysis	76
Estimation of cancer cell fractions and clone trees from multi-region sequencing of tumors	75
trfermikit: a tool to discover VNTR-associated deletions	74
Inference of 3D genome architecture by modeling overdispersion of Hi-C data	74
Cross-species prediction of essential genes in insects	74
Exploring automatic inconsistency detection for literature-based gene ontology annotation	73
Response to the letter to the editor: On the feasibility of dynamical analysis of network models of biochemical regulation	73
Aclust2.0: a revamped unsupervised R tool for Infinium methylation beadchips data analyses	70
Random field modeling of multi-trait multi-locus association for detecting methylation quantitative trait loci	70
MetBP: a software tool for detection of interaction between metal ion–RNA base pairs	66
skandiver: a divergence-based analysis tool for identifying intercellular mobile genetic elements	66
From high-throughput evaluation to wet-lab studies: advancing mutation effect prediction with a retrieval-enhanced model	65
Harnessing deep learning for proteome-scale detection of amyloid signaling motifs	65
Perceiver CPI: a nested cross-attention network for compound–protein interaction prediction	64
CANTATA—prediction of missing links in Boolean networks using genetic programming	64
hapCon: estimating contamination of ancient genomes by copying from reference haplotypes	64
Floria: fast and accurate strain haplotyping in metagenomes	64
Erratum to: GADGETS: a genetic algorithm for detecting epistasis using nuclear families	63
DeepPerVar: a multi-modal deep learning framework for functional interpretation of genetic variants in personal genome	63
RNAsolo: a repository of cleaned PDB-derived RNA 3D structures	62
DeepSVP: integration of genotype and phenotype for structural variant prioritization using deep learning	61
bollito: a flexible pipeline for comprehensive single-cell RNA-seq analyses	59
ADViSELipidomics: a workflow for analyzing lipidomics data	59
Group-walk: a rigorous approach to group-wise false discovery rate analysis by target-decoy competition	59
MICER: a pre-trained encoder–decoder architecture for molecular image captioning	58
MAGUS+eHMMs: improved multiple sequence alignment accuracy for fragmentary sequences	58
ProSynAR: a reference aware read merger	58
PyLiger: scalable single-cell multi-omic data integration in Python	58