OOIR: Observatory of International Research

Papers

(The H4-Index of Genome Medicine is 55. 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 2020-03-01 to 2024-03-01.)

Article	Citations
Polygenic risk scores: from research tools to clinical instruments	616
CADD-Splice—improving genome-wide variant effect prediction using deep learning-derived splice scores	359
Characterisation of the transcriptome and proteome of SARS-CoV-2 reveals a cell passage induced in-frame deletion of the furin-like cleavage site from the spike glycoprotein	352
dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs	284
Deep learning in cancer diagnosis, prognosis and treatment selection	261
Tracking cancer progression: from circulating tumor cells to metastasis	194
Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients	178
An introduction to spatial transcriptomics for biomedical research	177
Best practices for variant calling in clinical sequencing	166
Understanding the impact of antibiotic perturbation on the human microbiome	144
Single-cell transcriptome analysis of tumor and stromal compartments of pancreatic ductal adenocarcinoma primary tumors and metastatic lesions	127
IFN-γ and TNF-α drive a CXCL10+ CCL2+ macrophage phenotype expanded in severe COVID-19 lungs and inflammatory diseases with tissue inflammation	111
Integration of whole genome sequencing into a healthcare setting: high diagnostic rates across multiple clinical entities in 3219 rare disease patients	107
FOXC1-mediated LINC00301 facilitates tumor progression and triggers an immune-suppressing microenvironment in non-small cell lung cancer by regulating the HIF1α pathway	104
Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression	102
Single-cell RNA sequencing reveals the tumor microenvironment and facilitates strategic choices to circumvent treatment failure in a chemorefractory bladder cancer patient	101
A guide for the diagnosis of rare and undiagnosed disease: beyond the exome	97
Human breast microbiome correlates with prognostic features and immunological signatures in breast cancer	97
Multiple approaches for massively parallel sequencing of SARS-CoV-2 genomes directly from clinical samples	96
CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes	88
Microglial PGC-1α protects against ischemic brain injury by suppressing neuroinflammation	85
DeepProg: an ensemble of deep-learning and machine-learning models for prognosis prediction using multi-omics data	84
Integrated analysis of microbiome and host transcriptome reveals correlations between gut microbiota and clinical outcomes in HBV-related hepatocellular carcinoma	84
Intra-host variation and evolutionary dynamics of SARS-CoV-2 populations in COVID-19 patients	82
Guild-based analysis for understanding gut microbiome in human health and diseases	80

A Klebsiella pneumoniae ST307 outbreak clone from Germany demonstrates features of extensive drug resistance, hypermucoviscosity, and enhanced iron acquisition	80
Epigenome-wide meta-analysis of blood DNA methylation in newborns and children identifies numerous loci related to gestational age	80
Single-nucleus transcriptome analysis of human brain immune response in patients with severe COVID-19	79
Small-molecule MMP2/MMP9 inhibitor SB-3CT modulates tumor immune surveillance by regulating PD-L1	77
Polygenic risk scores in the clinic: new perspectives needed on familiar ethical issues	77
Robust barcoding and identification of Mycobacterium tuberculosis lineages for epidemiological and clinical studies	76
Strain-level epidemiology of microbial communities and the human microbiome	72
Role of the intestinal microbiome and microbial-derived metabolites in immune checkpoint blockade immunotherapy of cancer	72
Clinical implementation of RNA sequencing for Mendelian disease diagnostics	71
High-grade serous tubo-ovarian cancer refined with single-cell RNA sequencing: specific cell subtypes influence survival and determine molecular subtype classification	68
Clinical and molecular characterization of virus-positive and virus-negative Merkel cell carcinoma	68
Sequence-based prediction of SARS-CoV-2 vaccine targets using a mass spectrometry-based bioinformatics predictor identifies immunogenic T cell epitopes	67
Integrated analysis of single-cell and bulk RNA sequencing data reveals a pan-cancer stemness signature predicting immunotherapy response	67
Clinical trial design in the era of precision medicine	65
MHC-I genotype and tumor mutational burden predict response to immunotherapy	64
Mitochondrial DNA copy number can influence mortality and cardiovascular disease via methylation of nuclear DNA CpGs	63
The murine Microenvironment Cell Population counter method to estimate abundance of tissue-infiltrating immune and stromal cell populations in murine samples using gene expression	62
Hepatocellular carcinoma patients with high circulating cytotoxic T cells and intra-tumoral immune signature benefit from pembrolizumab: results from a single-arm phase 2 trial	60
Dietary fiber intake, the gut microbiome, and chronic systemic inflammation in a cohort of adult men	60
Burden of tumor mutations, neoepitopes, and other variants are weak predictors of cancer immunotherapy response and overall survival	59
Recommendations for clinical interpretation of variants found in non-coding regions of the genome	59
PRMT1-mediated H4R3me2a recruits SMARCA4 to promote colorectal cancer progression by enhancing EGFR signaling	59
A community-driven resource for genomic epidemiology and antimicrobial resistance prediction of Neisseria gonorrhoeae at Pathogenwatch	58
Mobilization of the nonconjugative virulence plasmid from hypervirulent Klebsiella pneumoniae	58
5′-tRF-GlyGCC: a tRNA-derived small RNA as a novel biomarker for colorectal cancer diagnosis	58
Transcriptome analysis and functional characterization of cerebral organoids in bipolar disorder	58
A comparison of epigenetic mitotic-like clocks for cancer risk prediction	57
Improved analysis of CRISPR fitness screens and reduced off-target effects with the BAGEL2 gene essentiality classifier	57
The complexities of the diet-microbiome relationship: advances and perspectives	57
Discovery of CD80 and CD86 as recent activation markers on regulatory T cells by protein-RNA single-cell analysis	55
Single-cell characterization of macrophages in glioblastoma reveals MARCO as a mesenchymal pro-tumor marker	55
The landscape of host genetic factors involved in immune response to common viral infections	55
The neuroimmune axis of Alzheimer’s disease	55
Microbial signature in IgE-mediated food allergies	55