OOIR: Observatory of International Research

Papers

(The H4-Index of Bioinformatics is 56. 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 2021-04-01 to 2025-04-01.)

Article	Citations
Corrigendum to: HRIBO: high-throughput analysis of bacterial ribosome profiling data	1179
2023 ISCB innovator award: Dana Pe’er	773
qTeller: a tool for comparative multi-genomic gene expression analysis	686
EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts	587
webSCST: an interactive web application for single-cell RNA-sequencing data and spatial transcriptomic data integration	554
The 2024 Outstanding Contributions to ISCB Award—Dr Scott Markel	463
Disease gene prediction with privileged information and heteroscedastic dropout	389
SPDE: a multi-functional software for sequence processing and data extraction	265
Embeddings of genomic region sets capture rich biological associations in lower dimensions	252
SD2: spatially resolved transcriptomics deconvolution through integration of dropout and spatial information	229
Characterizing domain-specific open educational resources by linking ISCB Communities of Special Interest to Wikipedia	222
HAMdetector: a Bayesian regression model that integrates information to detect HLA-associated mutations	180
Biomedical evidence engineering for data-driven discovery	175
Correction to: GTExVisualizer: a web platform for supporting ageing studies	156
Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs	147
ISMB 2022 proceedings	135
Current structure predictors are not learning the physics of protein folding	134
Improved allele-specific single-cell copy number estimation in low-coverage DNA-sequencing	127
MitoVisualize: a resource for analysis of variants in human mitochondrial RNAs and DNA	125
Deep structure integrative representation of multi-omics data for cancer subtyping	117
CLIN-X: pre-trained language models and a study on cross-task transfer for concept extraction in the clinical domain	116
Predicting spatially resolved gene expression via tissue morphology using adaptive spatial GNNs	113
Computing optimal factories in metabolic networks with negative regulation	106
Calib-RT: an open source python package for peptide retention time calibration in DIA mass spectrometry data	100
ExplorATE: a new pipeline to explore active transposable elements from RNA-seq data	100

Looking at the BiG picture: incorporating bipartite graphs in drug response prediction	95
MultiBaC: an R package to remove batch effects in multi-omic experiments	94
Effective knowledge graph embeddings based on multidirectional semantics relations for polypharmacy side effects prediction	93
RiboGraph: an interactive visualization system for ribosome profiling data at read length resolution	93
SPARSE: a sparse hypergraph neural network for learning multiple types of latent combinations to accurately predict drug–drug interactions	91
Fine-tuning protein embeddings for functional similarity evaluation	89
DiffChIPL: a differential peak analysis method for high-throughput sequencing data with biological replicates based on limma	84
Biological Random Walks: multi-omics integration for disease gene prioritization	82
On the feasibility of dynamical analysis of network models of biochemical regulation	80
Clustering single-cell RNA-seq data by rank constrained similarity learning	79
HPOFiller: identifying missing protein–phenotype associations by graph convolutional network	74
REALGAR: a web app of integrated respiratory omics data	74
DrugCVar: a platform for evidence-based drug annotation for genetic variants in cancer	74
Gene Tracer: a smart, interactive, voice-controlled Alexa skill For gene information retrieval and browsing, mutation annotation and network visualization	74
I2b2-etl: Python application for importing electronic health data into the informatics for integrating biology and the bedside platform	73
SimBu: bias-aware simulation of bulk RNA-seq data with variable cell-type composition	73
MMGraph: a multiple motif predictor based on graph neural network and coexisting probability for ATAC-seq data	72
massDatabase: utilities for the operation of the public compound and pathway database	71
ASURAT: functional annotation-driven unsupervised clustering of single-cell transcriptomes	70
GLIDER: function prediction from GLIDE-based neighborhoods	70
teff: estimation of Treatment EFFects on transcriptomic data using causal random forest	68
Deep statistical modelling of nanopore sequencing translocation times reveals latent non-B DNA structures	67
medna-metadata: an open-source data management system for tracking environmental DNA samples and metadata	65
Overcoming selection bias in synthetic lethality prediction	64
A weighted distance-based approach for deriving consensus tumor evolutionary trees	63
GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data	63
Phylogenetic diversity statistics for all clades in a phylogeny	63
Reconstructing tumor clonal lineage trees incorporating single-nucleotide variants, copy number alterations and structural variations	61
Haplotype-based membership inference from summary genomic data	60
GraphLoc: a graph neural network model for predicting protein subcellular localization from immunohistochemistry images	59
Practical selection of representative sets of RNA-seq samples using a hierarchical approach	57
tSFM 1.0: tRNA Structure–Function Mapper	56
PrISM: precision for integrative structural models	56
SNIKT: sequence-independent adapter identification and removal in long-read shotgun sequencing data	56