OOIR: Observatory of International Research

Papers

(The TQCC of Genome Medicine is 25. 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 2021-06-01 to 2025-06-01.)

Article	Citations
The role of admixture in the rare variant contribution to inflammatory bowel disease	537
Leveraging new methods for comprehensive characterization of mitochondrial DNA in esophageal squamous cell carcinoma	473
Genome-aware annotation of CRISPR guides validates targets in variant cell lines and enhances discovery in screens	216
Correction: Intricate interplay of CRISPR-Cas systems, anti-CRISPR proteins, and antimicrobial resistance genes in a globally successful multi-drug resistant Klebsiella pneumoniae clone	169
Non-cancer-related pathogenic germline variants and expression consequences in ten-thousand cancer genomes	168
Beyond the exome: utility of long-read whole genome sequencing in exome-negative autosomal recessive diseases	165
Curating genomic disease-gene relationships with Gene2Phenotype (G2P)	153
Neutrophil extracellular traps have auto-catabolic activity and produce mononucleosome-associated circulating DNA	143
Loss of p53-DREAM-mediated repression of cell cycle genes as a driver of lymph node metastasis in head and neck cancer	129
Single-molecule methylation profiles of cell-free DNA in cancer with nanopore sequencing	126
Pervasiveness of HLA allele-specific expression loss across tumor types	123
Ethnic variations in metabolic syndrome components and their associations with the gut microbiota: the HELIUS study	120
DNA demethylation triggers cell free DNA release in colorectal cancer cells	118
Integrative epigenomic and high-throughput functional enhancer profiling reveals determinants of enhancer heterogeneity in gastric cancer	105
The multiple de novo copy number variant (MdnCNV) phenomenon presents with peri-zygotic DNA mutational signatures and multilocus pathogenic variation	103
Publisher Correction: Analysis of transcriptomic features reveals molecular endotypes of SLE with clinical implications	102
The landcape of Helicobacter pylori-mediated DNA breaks links bacterial genotoxicity to its oncogenic potential	100
De novo identification of expressed cancer somatic mutations from single-cell RNA sequencing data	99
Glioblastoma-instructed microglia transition to heterogeneous phenotypic states with phagocytic and dendritic cell-like features in patient tumors and patient-derived orthotopic xenografts	99
Spatial intra-tumour heterogeneity and treatment-induced genomic evolution in oesophageal adenocarcinoma: implications for prognosis and therapy	95
Role of the intestinal microbiome and microbial-derived metabolites in immune checkpoint blockade immunotherapy of cancer	89
The lung microbiome, peripheral gene expression, and recurrence-free survival after resection of stage II non-small cell lung cancer	85
INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance	83
Shared genetic architecture between irritable bowel syndrome and psychiatric disorders reveals molecular pathways of the gut-brain axis	79
Large-scale discovery of novel neurodevelopmental disorder-related genes through a unified analysis of single-nucleotide and copy number variants	73

The vaginal microbiota and innate immunity after local excisional treatment for cervical intraepithelial neoplasia	69
Universal clinical Parkinson’s disease axes identify a major influence of neuroinflammation	66
Neutralization sensitivity, fusogenicity, and infectivity of Omicron subvariants	66
Rapid whole genome sequencing of critically ill pediatric patients from genetically underrepresented populations	66
Full-spectral genome analysis of natural killer/T cell lymphoma highlights impacts of genome instability in driving its progression	63
Correction: Genome Med 15, 115 & Genome Med 16, 3	62
Biological basis of extensive pleiotropy between blood traits and cancer risk	60
Comprehensive pathogen identification and antimicrobial resistance prediction from positive blood cultures using nanopore sequencing technology	60
Tracing carriage, acquisition, and transmission of ESBL-producing Escherichia coli over two years in a tertiary care hospital	59
Using single-nucleus RNA-sequencing to interrogate transcriptomic profiles of archived human pancreatic islets	58
Genomic and transcriptomic features between primary and paired metastatic fumarate hydratase–deficient renal cell carcinoma	57
ClinVar and HGMD genomic variant classification accuracy has improved over time, as measured by implied disease burden	57
Diversity in EWAS: current state, challenges, and solutions	57
Skeletal muscle regeneration failure in ischemic-damaged limbs is associated with pro-inflammatory macrophages and premature differentiation of satellite cells	57
Single-cell transcriptomics reveals a mechanosensitive injury signaling pathway in early diabetic nephropathy	57
Single-nucleus RNA sequencing of human pancreatic islets identifies novel gene sets and distinguishes β-cell subpopulations with dynamic transcriptome profiles	56
Comprehensive multi-omics integration identifies differentially active enhancers during human brain development with clinical relevance	54
Advancing precision public health using human genomics: examples from the field and future research opportunities	53
Integrated genomic analyses of acral and mucosal melanomas nominate novel driver genes	53
Metabolome-wide Mendelian randomization for age at menarche and age at natural menopause	53
The effects of the Green-Mediterranean diet on cardiometabolic health are linked to gut microbiome modifications: a randomized controlled trial	52
DNA methylation memory of pancreatic acinar-ductal metaplasia transition state altering Kras-downstream PI3K and Rho GTPase signaling in the absence of Kras mutation	52
Longitudinal analysis within one hospital in sub-Saharan Africa over 20 years reveals repeated replacements of dominant clones of Klebsiella pneumoniae and stresses the importance to include temporal	51
TP53 germline testing and hereditary cancer: how somatic events and clinical criteria affect variant detection rate	51
High fluoroquinolone resistance proportions among multidrug-resistant tuberculosis driven by dominant L2 Mycobacterium tuberculosis clones in the Mumbai Metropolitan Region	49
A small number of early introductions seeded widespread transmission of SARS-CoV-2 in Québec, Canada	49
Acetyl-CoA metabolism drives epigenome change and contributes to carcinogenesis risk in fatty liver disease	49
The WID-CIN test identifies women with, and at risk of, cervical intraepithelial neoplasia grade 3 and invasive cervical cancer	49
An implementation science approach to evaluating pathogen whole genome sequencing in public health	48
Refining epigenetic prediction of chronological and biological age	46
Applications of long-read sequencing to Mendelian genetics	46
High-grade serous tubo-ovarian cancer refined with single-cell RNA sequencing: specific cell subtypes influence survival and determine molecular subtype classification	46
Maintenance of the human memory T cell repertoire by subset and tissue site	45
Multi-label transcriptional classification of colorectal cancer reflects tumor cell population heterogeneity	44
Genetic correlation and causal relationships between cardio-metabolic traits and lung function impairment	44
The telomere maintenance mechanism spectrum and its dynamics in gliomas	44
Single-cell multimodal analysis identifies common regulatory programs in synovial fibroblasts of rheumatoid arthritis patients and modeled TNF-driven arthritis	43
Single-cell transcriptomic analysis reveals tumor cell heterogeneity and immune microenvironment features of pituitary neuroendocrine tumors	43
A novel molecular signature identifies mixed subtypes in renal cell carcinoma with poor prognosis and independent response to immunotherapy	43
Applicability of epigenetic age models to next-generation methylation arrays	42
Secondary resistance to anti-EGFR therapy by transcriptional reprogramming in patient-derived colorectal cancer models	42
Correction: Acetyl-CoA metabolism drives epigenome change and contributes to carcinogenesis risk in fatty liver disease	42
Transcriptional immunogenomic analysis reveals distinct immunological clusters in paediatric nervous system tumours	41
Influence network model uncovers relations between biological processes and mutational signatures	41
T cell receptor beta germline variability is revealed by inference from repertoire data	40
Large-scale copy number alterations are enriched for synthetic viability in BRCA1/BRCA2 tumors	40
Integrated study of systemic and local airway transcriptomes in asthma reveals causal mediation of systemic effects by airway key drivers	40
Neutralising reactivity against SARS-CoV-2 Delta and Omicron variants by vaccination and infection history	38
Dietary fiber intake, the gut microbiome, and chronic systemic inflammation in a cohort of adult men	38
The TyphiNET data visualisation dashboard: unlocking Salmonella Typhi genomics data to support public health	38

Clonal evolution in primary breast cancers under sequential epirubicin and docetaxel monotherapy	38
Identification of novel protein biomarkers and drug targets for colorectal cancer by integrating human plasma proteome with genome	37
A robust deep learning workflow to predict CD8 + T-cell epitopes	37
imply: improving cell-type deconvolution accuracy using personalized reference profiles	37
Cell type-specific changes identified by single-cell transcriptomics in Alzheimer’s disease	37
Multiscale heterogeneity in gastric adenocarcinoma evolution is an obstacle to precision medicine	36
Recombination and lineage-specific mutations linked to the emergence of SARS-CoV-2	36
Integrating metabolomics and proteomics to identify novel drug targets for heart failure and atrial fibrillation	36
Addressing the routine failure to clinically identify monogenic cases of common disease	36
Microglial heterogeneity in the ischemic stroke mouse brain of both sexes	36
A global overview of genetically interpretable multimorbidities among common diseases in the UK Biobank	35
Return of non-ACMG recommended incidental genetic findings to pediatric patients: considerations and opportunities from experiences in genomic sequencing	35
Identification of a cytokine-dominated immunosuppressive class in squamous cell lung carcinoma with implications for immunotherapy resistance	35
PLCG2 is associated with the inflammatory response and is induced by amyloid plaques in Alzheimer’s disease	35
Prioritizing genes associated with brain disorders by leveraging enhancer-promoter interactions in diverse neural cells and tissues	35
Identification of diagnostic candidates in Mendelian disorders using an RNA sequencing-centric approach	35
NODAL variants are associated with a continuum of laterality defects from simple D-transposition of the great arteries to heterotaxy	35
SARS-CoV-2 infection induces a long-lived pro-inflammatory transcriptional profile	35
Germline HLA-B evolutionary divergence influences the efficacy of immune checkpoint blockade therapy in gastrointestinal cancer	35
STModule: identifying tissue modules to uncover spatial components and characteristics of transcriptomic landscapes	34
Multi-omics uncovers immune-modulatory molecules in plasma contributing to resistance exercise-ameliorated locomotor disability after incomplete spinal cord injury	34
Genome sequencing as a generic diagnostic strategy for rare disease	33
GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning	33
Post-vaccine epidemiology of serotype 3 pneumococci identifies transformation inhibition through prophage-driven alteration of a non-coding RNA	33
Knockout mice with pituitary malformations help identify human cases of hypopituitarism	33
Targeting CDC7 potentiates ATR-CHK1 signaling inhibition through induction of DNA replication stress in liver cancer	33
ENU-based dominant genetic screen identifies contractile and neuronal gene mutations in congenital heart disease	33
The impact of damaging epilepsy and cardiac genetic variant burden in sudden death in the young	32
Identification of specific susceptibility loci for the early-onset colorectal cancer	32
Meta-analysis identifies common gut microbiota associated with multiple sclerosis	31
A dynamic single cell-based framework for digital twins to prioritize disease genes and drug targets	31
The role of genetic testing in diagnosis and care of inherited cardiac conditions in a specialised multidisciplinary clinic	31
Antiprogestins reduce epigenetic field cancerization in breast tissue of young healthy women	31
Single-nucleus transcriptome analysis of human brain immune response in patients with severe COVID-19	31
Evaluating the use of paralogous protein domains to increase data availability for missense variant classification	30
Smoking-associated gene expression alterations in nasal epithelium reveal immune impairment linked to lung cancer risk	30
ACT-Discover: identifying karyotype heterogeneity in pancreatic cancer evolution using ctDNA	30
Spatiotemporal single-cell analysis elucidates the cellular and molecular dynamics of human cornea aging	30
Metronidazole response profiles of Gardnerella species are congruent with phylogenetic and comparative genomic analyses	30
Distinct pathways for genetic and epigenetic predisposition in familial and bilateral Wilms tumor	30
Cardiomyopathies in 100,000 genomes project: interval evaluation improves diagnostic yield and informs strategies for ongoing gene discovery	29
Interaction of bacterial genera associated with therapeutic response to immune checkpoint PD-1 blockade in a United States cohort	29
Long-term persistence of diverse clones shapes the transmission landscape of invasive Listeria monocytogenes	29
Using multi-scale genomics to associate poorly annotated genes with rare diseases	29
Mendelian randomization analyses suggest a causal role for circulating GIP and IL-1RA levels in homeostatic model assessment-derived measures of β-cell function and insulin sensitivity in Africans wit	29
The emergence of highly resistant and hypervirulent Klebsiella pneumoniae CC14 clone in a tertiary hospital over 8 years	29
Meiotic and mitotic aneuploidies drive arrest of in vitro fertilized human preimplantation embryos	29
Ganciclovir-induced mutations are present in a diverse spectrum of post-transplant malignancies	29
Functional pre-therapeutic evaluation by genome editing of variants of uncertain significance of essential tumor suppressor genes	29
The case for including proteomics in routine diagnostic practice for rare disease	29
A new method for detecting mixed Mycobacterium tuberculosis infection and reconstructing constituent strains provides insights into transmission	29
Distinct pathway-based effects of blood pressure and body mass index on cardiovascular traits: comparison of novel Mendelian randomization approaches	28
An 8-gene machine learning model improves clinical prediction of severe dengue progression	28
Intratumor heterogeneity and T cell exhaustion in primary CNS lymphoma	28
Spatial transcriptomics analysis of neoadjuvant cabozantinib and nivolumab in advanced hepatocellular carcinoma identifies independent mechanisms of resistance and recurrence	28
Gut microbiota predicts body fat change following a low-energy diet: a PREVIEW intervention study	28
Accumulation of copy number alterations and clinical progression across advanced prostate cancer	28
Location and condition based reconstruction of colon cancer microbiome from human RNA sequencing data	28
SARS-CoV-2 population dynamics in immunocompetent individuals in a closed transmission chain shows genomic diversity over the course of infection	27
An expedited screening platform for the discovery of anti-ageing compounds in vitro and in vivo	27
Integrative analysis of spatial and single-cell transcriptome data from human pancreatic cancer reveals an intermediate cancer cell population associated with poor prognosis	27
Non-coding cis-regulatory variants in HK1 cause congenital hyperinsulinism with variable disease severity	27
A transcriptome-wide association study of Alzheimer’s disease using prediction models of relevant tissues identifies novel candidate susceptibility genes	27
spSeudoMap: cell type mapping of spatial transcriptomics using unmatched single-cell RNA-seq data	27
Keeping up with the pathogens: improved antimicrobial resistance detection and prediction from Pseudomonas aeruginosa genomes	27
A proteomics analysis of 5xFAD mouse brain regions reveals the lysosome-associated protein Arl8b as a candidate biomarker for Alzheimer’s disease	27
Molecular characteristics of breast tumors in patients screened for germline predisposition from a population-based observational study	25
SvAnna: efficient and accurate pathogenicity prediction of coding and regulatory structural variants in long-read genome sequencing	25
Genome-wide identification and characterization of circular RNA m6A modification in pancreatic cancer	25
A genome-based survey of invasive pneumococci in Norway over four decades reveals lineage-specific responses to vaccination	25