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 2021-02-01 to 2025-02-01.)

Article	Citations
EPS: automated feature selection in case–control studies using extreme pseudo-sampling	961
PAX2GRAPHML: a python library for large-scale regulation network analysis using BioPAX	570
On the stability of log-rank test under labeling errors	552
PaIntDB: network-based omics integration and visualization using protein–protein interactions in Pseudomonas aeruginosa	502
ACES: Analysis of Conservation with an Extensive list of Species	460
ViTAL: Vision TrAnsformer based Low coverage SARS-CoV-2 lineage assignment	451
Selection among site-dependent structurally constrained substitution models of protein evolution by approximate Bayesian computation	376
Utilizing image and caption information for biomedical document classification	325
PrISM: precision for integrative structural models	258
ASES: visualizing evolutionary conservation of alternative splicing in proteins	247
An OMICs-based meta-analysis to support infection state stratification	217
Corrigendum to: HRIBO: high-throughput analysis of bacterial ribosome profiling data	190
Gene Tracer: a smart, interactive, voice-controlled Alexa skill For gene information retrieval and browsing, mutation annotation and network visualization	187
2023 ISCB innovator award: Dana Pe’er	169
Robustly interrogating machine learning-based scoring functions: what are they learning?	153
wenda_gpu: fast domain adaptation for genomic data	149
ATLIGATOR: editing protein interactions with an atlas-based approach	140
A weighted distance-based approach for deriving consensus tumor evolutionary trees	130
XRRpred: accurate predictor of crystal structure quality from protein sequence	122
webSCST: an interactive web application for single-cell RNA-sequencing data and spatial transcriptomic data integration	111
Predicting spatially resolved gene expression via tissue morphology using adaptive spatial GNNs	107
CIBRA identifies genomic alterations with a system-wide impact on tumor biology	105
learnMSA2: deep protein multiple alignments with large language and hidden Markov models	104
StructuralVariantAnnotation: a R/Bioconductor foundation for a caller-agnostic structural variant software ecosystem	104
PsiNorm: a scalable normalization for single-cell RNA-seq data	104

Metagenomic functional profiling: to sketch or not to sketch?	98
Identification of cell-type-specific spatially variable genes accounting for excess zeros	97
Polypharmacy side-effect prediction with enhanced interpretability based on graph feature attention network	96
fastISM: performantin silicosaturation mutagenesis for convolutional neural networks	95
monaLisa: an R/Bioconductor package for identifying regulatory motifs	94
Target–Decoy MineR for determining the biological relevance of variables in noisy datasets	91
GNN-based embedding for clustering scRNA-seq data	87
SOMDE: a scalable method for identifying spatially variable genes with self-organizing map	84
Telogator: a method for reporting chromosome-specific telomere lengths from long reads	84
Non-parametric modelling of temporal and spatial counts data from RNA-seq experiments	82
Clustering single-cell RNA-seq data by rank constrained similarity learning	80
Cooperative sequence clustering and decoding for DNA storage system with fountain codes	78
scWMC: weighted matrix completion-based imputation of scRNA-seq data via prior subspace information	77
On the stability of log-rank test under labeling errors	76
An incrementally updatable and scalable system for large-scale sequence search using the Bentley–Saxe transformation	75
scKINETICS: inference of regulatory velocity with single-cell transcriptomics data	75
DIMPL: a bioinformatics pipeline for the discovery of structured noncoding RNA motifs in bacteria	74
ISMB 2022 proceedings	71
SharePro: an accurate and efficient genetic colocalization method accounting for multiple causal signals	70
Metaball skinning of synthetic astroglial morphologies into realistic mesh models for in silico simulations and visual analytics	69
miRe2e: a full end-to-end deep model based on transformers for prediction of pre-miRNAs	69
SPOT: a web-tool enabling swift profiling of transcriptomes	68
Graph2MDA: a multi-modal variational graph embedding model for predicting microbe–drug associations	66
Tree2GD: a phylogenomic method to detect large-scale gene duplication events	62
Effective knowledge graph embeddings based on multidirectional semantics relations for polypharmacy side effects prediction	62
BSDE: barycenter single-cell differential expression for case–control studies	61
On the feasibility of dynamical analysis of network models of biochemical regulation	61
OpenPhi: an interface to access Philips iSyntax whole slide images for computational pathology	60
A cross-level information transmission network for hierarchical omics data integration and phenotype prediction from a new genotype	60
An integrative pipeline for circular RNA quantitative trait locus discovery with application in human T cells	59
PathwAX II: network-based pathway analysis with interactive visualization of network crosstalk	59
The 2024 Outstanding Contributions to ISCB Award—Dr Scott Markel	58
Reconstructing tumor clonal lineage trees incorporating single-nucleotide variants, copy number alterations and structural variations	58