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 2021-09-01 to 2025-09-01.)

Article	Citations
Genome-aware annotation of CRISPR guides validates targets in variant cell lines and enhances discovery in screens	603
Non-cancer-related pathogenic germline variants and expression consequences in ten-thousand cancer genomes	547
The role of admixture in the rare variant contribution to inflammatory bowel disease	230
Loss of p53-DREAM-mediated repression of cell cycle genes as a driver of lymph node metastasis in head and neck cancer	193
Pervasiveness of HLA allele-specific expression loss across tumor types	189
Correction: Intricate interplay of CRISPR-Cas systems, anti-CRISPR proteins, and antimicrobial resistance genes in a globally successful multi-drug resistant Klebsiella pneumoniae clone	178
Beyond the exome: utility of long-read whole genome sequencing in exome-negative autosomal recessive diseases	168
Neutrophil extracellular traps have auto-catabolic activity and produce mononucleosome-associated circulating DNA	156
Curating genomic disease-gene relationships with Gene2Phenotype (G2P)	152
Single-molecule methylation profiles of cell-free DNA in cancer with nanopore sequencing	137
Leveraging new methods for comprehensive characterization of mitochondrial DNA in esophageal squamous cell carcinoma	117
Universal clinical Parkinson’s disease axes identify a major influence of neuroinflammation	111
Shared genetic architecture between irritable bowel syndrome and psychiatric disorders reveals molecular pathways of the gut-brain axis	111
The landcape of Helicobacter pylori-mediated DNA breaks links bacterial genotoxicity to its oncogenic potential	111
De novo identification of expressed cancer somatic mutations from single-cell RNA sequencing data	101
Publisher Correction: Analysis of transcriptomic features reveals molecular endotypes of SLE with clinical implications	96
Integrative epigenomic and high-throughput functional enhancer profiling reveals determinants of enhancer heterogeneity in gastric cancer	94
Large-scale discovery of novel neurodevelopmental disorder-related genes through a unified analysis of single-nucleotide and copy number variants	86
Spatial intra-tumour heterogeneity and treatment-induced genomic evolution in oesophageal adenocarcinoma: implications for prognosis and therapy	78
Contribution of rare coding variants to microcephaly in individuals with neurodevelopmental disorders	78
INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance	75
Ethnic variations in metabolic syndrome components and their associations with the gut microbiota: the HELIUS study	75
The lung microbiome, peripheral gene expression, and recurrence-free survival after resection of stage II non-small cell lung cancer	73
DNA demethylation triggers cell free DNA release in colorectal cancer cells	70
The vaginal microbiota and innate immunity after local excisional treatment for cervical intraepithelial neoplasia	69

Replication-associated mechanisms contribute to an increased CpG > TpG mutation burden in mismatch repair-deficient cancers	65
Glioblastoma-instructed microglia transition to heterogeneous phenotypic states with phagocytic and dendritic cell-like features in patient tumors and patient-derived orthotopic xenografts	65
The multiple de novo copy number variant (MdnCNV) phenomenon presents with peri-zygotic DNA mutational signatures and multilocus pathogenic variation	65
Tracing carriage, acquisition, and transmission of ESBL-producing Escherichia coli over two years in a tertiary care hospital	64
Biological basis of extensive pleiotropy between blood traits and cancer risk	63
Correction: Genome Med 15, 115 & Genome Med 16, 3	63
Single-cell transcriptomics reveals a mechanosensitive injury signaling pathway in early diabetic nephropathy	63
Full-spectral genome analysis of natural killer/T cell lymphoma highlights impacts of genome instability in driving its progression	63
Comprehensive pathogen identification and antimicrobial resistance prediction from positive blood cultures using nanopore sequencing technology	62
Single-nucleus RNA sequencing of human pancreatic islets identifies novel gene sets and distinguishes β-cell subpopulations with dynamic transcriptome profiles	60
Neutralization sensitivity, fusogenicity, and infectivity of Omicron subvariants	60
ClinVar and HGMD genomic variant classification accuracy has improved over time, as measured by implied disease burden	60
Integrated genomic analyses of acral and mucosal melanomas nominate novel driver genes	59
Comprehensive multi-omics integration identifies differentially active enhancers during human brain development with clinical relevance	58
Genomic and transcriptomic features between primary and paired metastatic fumarate hydratase–deficient renal cell carcinoma	57
Skeletal muscle regeneration failure in ischemic-damaged limbs is associated with pro-inflammatory macrophages and premature differentiation of satellite cells	54
Longitudinal analysis of genetic and environmental interplay in human metabolic profiles and the implication for metabolic health	53
Rapid whole genome sequencing of critically ill pediatric patients from genetically underrepresented populations	53
Metabolome-wide Mendelian randomization for age at menarche and age at natural menopause	51
The effects of the Green-Mediterranean diet on cardiometabolic health are linked to gut microbiome modifications: a randomized controlled trial	51
Diversity in EWAS: current state, challenges, and solutions	50
Epigenomic preconditioning of peripheral monocytes determines their transcriptional response to the tumor microenvironment	49
TP53 germline testing and hereditary cancer: how somatic events and clinical criteria affect variant detection rate	49
DNA methylation memory of pancreatic acinar-ductal metaplasia transition state altering Kras-downstream PI3K and Rho GTPase signaling in the absence of Kras mutation	49
Applications of long-read sequencing to Mendelian genetics	48
The telomere maintenance mechanism spectrum and its dynamics in gliomas	48
Single-cell transcriptomic analysis reveals tumor cell heterogeneity and immune microenvironment features of pituitary neuroendocrine tumors	46
A novel molecular signature identifies mixed subtypes in renal cell carcinoma with poor prognosis and independent response to immunotherapy	46
Multi-label transcriptional classification of colorectal cancer reflects tumor cell population heterogeneity	45
Single-cell multimodal analysis identifies common regulatory programs in synovial fibroblasts of rheumatoid arthritis patients and modeled TNF-driven arthritis	45
A small number of early introductions seeded widespread transmission of SARS-CoV-2 in Québec, Canada	45
High fluoroquinolone resistance proportions among multidrug-resistant tuberculosis driven by dominant L2 Mycobacterium tuberculosis clones in the Mumbai Metropolitan Region	44
The WID-CIN test identifies women with, and at risk of, cervical intraepithelial neoplasia grade 3 and invasive cervical cancer	44
Acetyl-CoA metabolism drives epigenome change and contributes to carcinogenesis risk in fatty liver disease	43
Refining epigenetic prediction of chronological and biological age	43
Correction: Acetyl-CoA metabolism drives epigenome change and contributes to carcinogenesis risk in fatty liver disease	43
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	43
Cell type-specific changes identified by single-cell transcriptomics in Alzheimer’s disease	42
Influence network model uncovers relations between biological processes and mutational signatures	42
The TyphiNET data visualisation dashboard: unlocking Salmonella Typhi genomics data to support public health	41
Large-scale copy number alterations are enriched for synthetic viability in BRCA1/BRCA2 tumors	41
Integrated study of systemic and local airway transcriptomes in asthma reveals causal mediation of systemic effects by airway key drivers	41
Neutralising reactivity against SARS-CoV-2 Delta and Omicron variants by vaccination and infection history	41
Clonal evolution in primary breast cancers under sequential epirubicin and docetaxel monotherapy	40
A robust deep learning workflow to predict CD8 + T-cell epitopes	40
Transcriptional immunogenomic analysis reveals distinct immunological clusters in paediatric nervous system tumours	40
T cell receptor beta germline variability is revealed by inference from repertoire data	39
Prioritizing genes associated with brain disorders by leveraging enhancer-promoter interactions in diverse neural cells and tissues	39
Applicability of epigenetic age models to next-generation methylation arrays	39
Multiscale heterogeneity in gastric adenocarcinoma evolution is an obstacle to precision medicine	39

Integrating metabolomics and proteomics to identify novel drug targets for heart failure and atrial fibrillation	39
Identification of novel protein biomarkers and drug targets for colorectal cancer by integrating human plasma proteome with genome	39
PLCG2 is associated with the inflammatory response and is induced by amyloid plaques in Alzheimer’s disease	39
imply: improving cell-type deconvolution accuracy using personalized reference profiles	37
Plasma microRNA signatures of aging and their links to health outcomes and mortality: findings from a population-based cohort study	37
NODAL variants are associated with a continuum of laterality defects from simple D-transposition of the great arteries to heterotaxy	37
Identification of specific susceptibility loci for the early-onset colorectal cancer	36
Microglial heterogeneity in the ischemic stroke mouse brain of both sexes	36
STModule: identifying tissue modules to uncover spatial components and characteristics of transcriptomic landscapes	36
SARS-CoV-2 infection induces a long-lived pro-inflammatory transcriptional profile	36
Addressing the routine failure to clinically identify monogenic cases of common disease	36
Identification of diagnostic candidates in Mendelian disorders using an RNA sequencing-centric approach	36
Identification of a cytokine-dominated immunosuppressive class in squamous cell lung carcinoma with implications for immunotherapy resistance	35
Multi-omics uncovers immune-modulatory molecules in plasma contributing to resistance exercise-ameliorated locomotor disability after incomplete spinal cord injury	35
Targeting CDC7 potentiates ATR-CHK1 signaling inhibition through induction of DNA replication stress in liver cancer	35
Knockout mice with pituitary malformations help identify human cases of hypopituitarism	34
Germline HLA-B evolutionary divergence influences the efficacy of immune checkpoint blockade therapy in gastrointestinal cancer	34
Antiprogestins reduce epigenetic field cancerization in breast tissue of young healthy women	34
The role of genetic testing in diagnosis and care of inherited cardiac conditions in a specialised multidisciplinary clinic	34
Meta-analysis identifies common gut microbiota associated with multiple sclerosis	33
A dynamic single cell-based framework for digital twins to prioritize disease genes and drug targets	33
Post-vaccine epidemiology of serotype 3 pneumococci identifies transformation inhibition through prophage-driven alteration of a non-coding RNA	33
ENU-based dominant genetic screen identifies contractile and neuronal gene mutations in congenital heart disease	33
Return of non-ACMG recommended incidental genetic findings to pediatric patients: considerations and opportunities from experiences in genomic sequencing	33
The impact of damaging epilepsy and cardiac genetic variant burden in sudden death in the young	33
Metronidazole response profiles of Gardnerella species are congruent with phylogenetic and comparative genomic analyses	32
ACT-Discover: identifying karyotype heterogeneity in pancreatic cancer evolution using ctDNA	32
Genome sequencing as a generic diagnostic strategy for rare disease	32
Evaluating the use of paralogous protein domains to increase data availability for missense variant classification	32
The case for including proteomics in routine diagnostic practice for rare disease	31
Smoking-associated gene expression alterations in nasal epithelium reveal immune impairment linked to lung cancer risk	31
The emergence of highly resistant and hypervirulent Klebsiella pneumoniae CC14 clone in a tertiary hospital over 8 years	31
Long-term persistence of diverse clones shapes the transmission landscape of invasive Listeria monocytogenes	31
Distinct pathways for genetic and epigenetic predisposition in familial and bilateral Wilms tumor	31
A new method for detecting mixed Mycobacterium tuberculosis infection and reconstructing constituent strains provides insights into transmission	31
Spatiotemporal single-cell analysis elucidates the cellular and molecular dynamics of human cornea aging	31
Interaction of bacterial genera associated with therapeutic response to immune checkpoint PD-1 blockade in a United States cohort	30
Meiotic and mitotic aneuploidies drive arrest of in vitro fertilized human preimplantation embryos	30
Ganciclovir-induced mutations are present in a diverse spectrum of post-transplant malignancies	30
Functional pre-therapeutic evaluation by genome editing of variants of uncertain significance of essential tumor suppressor genes	30
An 8-gene machine learning model improves clinical prediction of severe dengue progression	30
A proteomics analysis of 5xFAD mouse brain regions reveals the lysosome-associated protein Arl8b as a candidate biomarker for Alzheimer’s disease	29
Integrative analysis of spatial and single-cell transcriptome data from human pancreatic cancer reveals an intermediate cancer cell population associated with poor prognosis	29
Cardiomyopathies in 100,000 genomes project: interval evaluation improves diagnostic yield and informs strategies for ongoing gene discovery	29
Gut microbiota predicts body fat change following a low-energy diet: a PREVIEW intervention study	29
Using multi-scale genomics to associate poorly annotated genes with rare diseases	29
A transcriptome-wide association study of Alzheimer’s disease using prediction models of relevant tissues identifies novel candidate susceptibility genes	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
Accumulation of copy number alterations and clinical progression across advanced prostate cancer	28
spSeudoMap: cell type mapping of spatial transcriptomics using unmatched single-cell RNA-seq data	28
Location and condition based reconstruction of colon cancer microbiome from human RNA sequencing data	28
Distinct pathway-based effects of blood pressure and body mass index on cardiovascular traits: comparison of novel Mendelian randomization approaches	28
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	27
An expedited screening platform for the discovery of anti-ageing compounds in vitro and in vivo	27
Lethal variants in humans: lessons learned from a large molecular autopsy cohort	27
Molecular characteristics of breast tumors in patients screened for germline predisposition from a population-based observational study	27
SvAnna: efficient and accurate pathogenicity prediction of coding and regulatory structural variants in long-read genome sequencing	27
SARS-CoV-2 population dynamics in immunocompetent individuals in a closed transmission chain shows genomic diversity over the course of infection	27
Microbiota of the prostate tumor environment investigated by whole-transcriptome profiling	26
Penetrance estimation of Alzheimer disease in SORL1 loss-of-function variant carriers using a family-based strategy and stratification by APOE genotypes	26
Molecular-guided therapy for the treatment of patients with relapsed and refractory childhood cancers: a Beat Childhood Cancer Research Consortium trial	26
Keeping up with the pathogens: improved antimicrobial resistance detection and prediction from Pseudomonas aeruginosa genomes	26
Non-coding cis-regulatory variants in HK1 cause congenital hyperinsulinism with variable disease severity	25
Building digital histology models of transcriptional tumor programs with generative deep learning for pathology-based precision medicine	25
De novo transcriptomic subtyping of colorectal cancer liver metastases in the context of tumor heterogeneity	25
Genome-wide identification and characterization of circular RNA m6A modification in pancreatic cancer	25
Clinical implementation of RNA sequencing for Mendelian disease diagnostics	25
varCADD: large sets of standing genetic variation enable genome-wide pathogenicity prediction	25