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 2021-12-01 to 2025-12-01.)

Article	Citations
Genome-aware annotation of CRISPR guides validates targets in variant cell lines and enhances discovery in screens	622
Correction: Intricate interplay of CRISPR-Cas systems, anti-CRISPR proteins, and antimicrobial resistance genes in a globally successful multi-drug resistant Klebsiella pneumoniae clone	260
Loss of p53-DREAM-mediated repression of cell cycle genes as a driver of lymph node metastasis in head and neck cancer	217
Pervasiveness of HLA allele-specific expression loss across tumor types	207
Leveraging new methods for comprehensive characterization of mitochondrial DNA in esophageal squamous cell carcinoma	199
Beyond the exome: utility of long-read whole genome sequencing in exome-negative autosomal recessive diseases	198
The role of admixture in the rare variant contribution to inflammatory bowel disease	187
Single-molecule methylation profiles of cell-free DNA in cancer with nanopore sequencing	186
Curating genomic disease-gene relationships with Gene2Phenotype (G2P)	146
Single-cell transcriptome analysis defines novel molecular subtypes and reveals therapeutic implications of T/myeloid mixed-phenotype acute leukemia	137
Neutrophil extracellular traps have auto-catabolic activity and produce mononucleosome-associated circulating DNA	127
Publisher Correction: Analysis of transcriptomic features reveals molecular endotypes of SLE with clinical implications	122
Large-scale discovery of novel neurodevelopmental disorder-related genes through a unified analysis of single-nucleotide and copy number variants	115
Adult genomic medicine: lessons from a multisite study of 2700 patients	107
The multiple de novo copy number variant (MdnCNV) phenomenon presents with peri-zygotic DNA mutational signatures and multilocus pathogenic variation	101
Whole-genome sequencing reveals individual and cohort level insights into chromosome 9p syndromes	89
Clinical characteristics and molecular heterogeneity in Follicular lymphoma with extranodal involvement	83
Spatial intra-tumour heterogeneity and treatment-induced genomic evolution in oesophageal adenocarcinoma: implications for prognosis and therapy	82
Replication-associated mechanisms contribute to an increased CpG > TpG mutation burden in mismatch repair-deficient cancers	82
The lung microbiome, peripheral gene expression, and recurrence-free survival after resection of stage II non-small cell lung cancer	81
The landcape of Helicobacter pylori-mediated DNA breaks links bacterial genotoxicity to its oncogenic potential	79
De novo identification of expressed cancer somatic mutations from single-cell RNA sequencing data	76
Glioblastoma-instructed microglia transition to heterogeneous phenotypic states with phagocytic and dendritic cell-like features in patient tumors and patient-derived orthotopic xenografts	75
Ethnic variations in metabolic syndrome components and their associations with the gut microbiota: the HELIUS study	72
Universal clinical Parkinson’s disease axes identify a major influence of neuroinflammation	70

Contribution of rare coding variants to microcephaly in individuals with neurodevelopmental disorders	70
Shared genetic architecture between irritable bowel syndrome and psychiatric disorders reveals molecular pathways of the gut-brain axis	69
Investigating the interplay between prematurity and genetic variation in the context of rare developmental disorders	69
DNA demethylation triggers cell free DNA release in colorectal cancer cells	69
INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance	68
Neutralization sensitivity, fusogenicity, and infectivity of Omicron subvariants	67
Correction: Genome Med 15, 115 & Genome Med 16, 3	67
Integrated genomic analyses of acral and mucosal melanomas nominate novel driver genes	63
A human YEATS4 variant confers resistance to TST and IGRA conversion despite Mycobacterium tuberculosis exposure	60
Biological basis of extensive pleiotropy between blood traits and cancer risk	58
Tracing carriage, acquisition, and transmission of ESBL-producing Escherichia coli over two years in a tertiary care hospital	57
Diversity in EWAS: current state, challenges, and solutions	56
Single-nucleus RNA sequencing of human pancreatic islets identifies novel gene sets and distinguishes β-cell subpopulations with dynamic transcriptome profiles	56
Full-spectral genome analysis of natural killer/T cell lymphoma highlights impacts of genome instability in driving its progression	56
MicroRNA gene dynamics in immune cell subpopulations during aging and atherosclerosis disease development at single-cell resolution	55
Skeletal muscle regeneration failure in ischemic-damaged limbs is associated with pro-inflammatory macrophages and premature differentiation of satellite cells	55
Single-cell transcriptomics reveals a mechanosensitive injury signaling pathway in early diabetic nephropathy	53
Rapid whole genome sequencing of critically ill pediatric patients from genetically underrepresented populations	53
Longitudinal analysis of genetic and environmental interplay in human metabolic profiles and the implication for metabolic health	53
Comprehensive pathogen identification and antimicrobial resistance prediction from positive blood cultures using nanopore sequencing technology	52
Metabolome-wide Mendelian randomization for age at menarche and age at natural menopause	51
Genomic and transcriptomic features between primary and paired metastatic fumarate hydratase–deficient renal cell carcinoma	51
ClinVar and HGMD genomic variant classification accuracy has improved over time, as measured by implied disease burden	51
The effects of the Green-Mediterranean diet on cardiometabolic health are linked to gut microbiome modifications: a randomized controlled trial	50
Optimized high-throughput whole-genome sequencing workflow for surveillance of influenza A virus	49
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	48
A novel molecular signature identifies mixed subtypes in renal cell carcinoma with poor prognosis and independent response to immunotherapy	48
The WID-CIN test identifies women with, and at risk of, cervical intraepithelial neoplasia grade 3 and invasive cervical cancer	48
DNA methylation memory of pancreatic acinar-ductal metaplasia transition state altering Kras-downstream PI3K and Rho GTPase signaling in the absence of Kras mutation	47
Epigenomic preconditioning of peripheral monocytes determines their transcriptional response to the tumor microenvironment	47
Single-cell multimodal analysis identifies common regulatory programs in synovial fibroblasts of rheumatoid arthritis patients and modeled TNF-driven arthritis	47
Multi-label transcriptional classification of colorectal cancer reflects tumor cell population heterogeneity	47
High fluoroquinolone resistance proportions among multidrug-resistant tuberculosis driven by dominant L2 Mycobacterium tuberculosis clones in the Mumbai Metropolitan Region	46
Refining epigenetic prediction of chronological and biological age	46
Acetyl-CoA metabolism drives epigenome change and contributes to carcinogenesis risk in fatty liver disease	46
The telomere maintenance mechanism spectrum and its dynamics in gliomas	45
Applications of long-read sequencing to Mendelian genetics	45
Single-cell transcriptomic analysis reveals tumor cell heterogeneity and immune microenvironment features of pituitary neuroendocrine tumors	44
TP53 germline testing and hereditary cancer: how somatic events and clinical criteria affect variant detection rate	44
Large-scale copy number alterations are enriched for synthetic viability in BRCA1/BRCA2 tumors	43
Neutralising reactivity against SARS-CoV-2 Delta and Omicron variants by vaccination and infection history	43
Genome sequencing for the diagnosis of intellectual disability as a paradigm for rare diseases in the French healthcare setting: the prospective DEFIDIAG study	43
Correction: Acetyl-CoA metabolism drives epigenome change and contributes to carcinogenesis risk in fatty liver disease	43
T cell receptor beta germline variability is revealed by inference from repertoire data	42
Transcriptional immunogenomic analysis reveals distinct immunological clusters in paediatric nervous system tumours	42
Applicability of epigenetic age models to next-generation methylation arrays	41
Influence network model uncovers relations between biological processes and mutational signatures	41
Cell type-specific changes identified by single-cell transcriptomics in Alzheimer’s disease	40
A robust deep learning workflow to predict CD8 + T-cell epitopes	40
Clonal evolution in primary breast cancers under sequential epirubicin and docetaxel monotherapy	40

Integrated study of systemic and local airway transcriptomes in asthma reveals causal mediation of systemic effects by airway key drivers	40
Prematurity and genetic liability for autism spectrum disorder	40
Identification of diagnostic candidates in Mendelian disorders using an RNA sequencing-centric approach	39
The TyphiNET data visualisation dashboard: unlocking Salmonella Typhi genomics data to support public health	39
Clinical and bacterial determinants of unfavorable tuberculosis treatment outcomes: an observational study in Georgia	39
Identification of novel protein biomarkers and drug targets for colorectal cancer by integrating human plasma proteome with genome	39
Plasma microRNA signatures of aging and their links to health outcomes and mortality: findings from a population-based cohort study	39
EMB is essential for enteric nervous system development mediated by PI3K signaling	38
Prioritizing genes associated with brain disorders by leveraging enhancer-promoter interactions in diverse neural cells and tissues	38
NODAL variants are associated with a continuum of laterality defects from simple D-transposition of the great arteries to heterotaxy	38
Addressing the routine failure to clinically identify monogenic cases of common disease	38
Integrating metabolomics and proteomics to identify novel drug targets for heart failure and atrial fibrillation	37
SARS-CoV-2 infection induces a long-lived pro-inflammatory transcriptional profile	37
PLCG2 is associated with the inflammatory response and is induced by amyloid plaques in Alzheimer’s disease	37
MorphoITH: a framework for deconvolving intra-tumor heterogeneity using tissue morphology	37
imply: improving cell-type deconvolution accuracy using personalized reference profiles	37
Microglial heterogeneity in the ischemic stroke mouse brain of both sexes	37
Knockout mice with pituitary malformations help identify human cases of hypopituitarism	36
Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent Salmonella Typhi	36
Identification of specific susceptibility loci for the early-onset colorectal cancer	36
STModule: identifying tissue modules to uncover spatial components and characteristics of transcriptomic landscapes	36
Evaluating genome sequencing strategies: trio, singleton, and standard testing in rare disease diagnosis	35
Multi-omics uncovers immune-modulatory molecules in plasma contributing to resistance exercise-ameliorated locomotor disability after incomplete spinal cord injury	34
ENU-based dominant genetic screen identifies contractile and neuronal gene mutations in congenital heart disease	34
Antiprogestins reduce epigenetic field cancerization in breast tissue of young healthy women	34
Post-vaccine epidemiology of serotype 3 pneumococci identifies transformation inhibition through prophage-driven alteration of a non-coding RNA	33
The role of genetic testing in diagnosis and care of inherited cardiac conditions in a specialised multidisciplinary clinic	33
The impact of damaging epilepsy and cardiac genetic variant burden in sudden death in the young	33
Return of non-ACMG recommended incidental genetic findings to pediatric patients: considerations and opportunities from experiences in genomic sequencing	32
Genome sequencing as a generic diagnostic strategy for rare disease	32
Polygenic risk for Alzheimer’s disease in healthy aging: age-related and APOE-driven effects on brain structures and cognition	32
Meta-analysis identifies common gut microbiota associated with multiple sclerosis	32
Identification of a cytokine-dominated immunosuppressive class in squamous cell lung carcinoma with implications for immunotherapy resistance	31
A new method for detecting mixed Mycobacterium tuberculosis infection and reconstructing constituent strains provides insights into transmission	31
Evaluating the use of paralogous protein domains to increase data availability for missense variant classification	31
A dynamic single cell-based framework for digital twins to prioritize disease genes and drug targets	31
Smoking-associated gene expression alterations in nasal epithelium reveal immune impairment linked to lung cancer risk	31
The case for including proteomics in routine diagnostic practice for rare disease	30
ACT-Discover: identifying karyotype heterogeneity in pancreatic cancer evolution using ctDNA	30
Intratumor heterogeneity and T cell exhaustion in primary CNS lymphoma	29
The emergence of highly resistant and hypervirulent Klebsiella pneumoniae CC14 clone in a tertiary hospital over 8 years	29
Spatiotemporal single-cell analysis elucidates the cellular and molecular dynamics of human cornea aging	29
Meiotic and mitotic aneuploidies drive arrest of in vitro fertilized human preimplantation embryos	29
Long-term persistence of diverse clones shapes the transmission landscape of invasive Listeria monocytogenes	29
Distinct pathways for genetic and epigenetic predisposition in familial and bilateral Wilms tumor	29
Personalized transcriptional network analysis links age-related loss of gene coordination to individual biological aging	29
Metronidazole response profiles of Gardnerella species are congruent with phylogenetic and comparative genomic analyses	29
Interaction of bacterial genera associated with therapeutic response to immune checkpoint PD-1 blockade in a United States cohort	29
Using multi-scale genomics to associate poorly annotated genes with rare diseases	28
A proteomics analysis of 5xFAD mouse brain regions reveals the lysosome-associated protein Arl8b as a candidate biomarker for Alzheimer’s disease	28
Identification of a PRDM1-regulated T cell network to regulate atherosclerotic plaque inflammation	28
Disease-specific epigenetic deregulation of enhancers, transposons, and polycomb targets in acute promyelocytic leukemia	28
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
spSeudoMap: cell type mapping of spatial transcriptomics using unmatched single-cell RNA-seq data	27
Accumulation of copy number alterations and clinical progression across advanced prostate cancer	27
Spatial transcriptomics analysis of neoadjuvant cabozantinib and nivolumab in advanced hepatocellular carcinoma identifies independent mechanisms of resistance and recurrence	27
Ganciclovir-induced mutations are present in a diverse spectrum of post-transplant malignancies	27
Gut microbiota predicts body fat change following a low-energy diet: a PREVIEW intervention study	27
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
Location and condition based reconstruction of colon cancer microbiome from human RNA sequencing data	27
varCADD: large sets of standing genetic variation enable genome-wide pathogenicity prediction	26
Cardiomyopathies in 100,000 genomes project: interval evaluation improves diagnostic yield and informs strategies for ongoing gene discovery	26
Therapy sculpts the complex interplay between cancer and the immune system during tumour evolution	26
A genome-based survey of invasive pneumococci in Norway over four decades reveals lineage-specific responses to vaccination	26
Building digital histology models of transcriptional tumor programs with generative deep learning for pathology-based precision medicine	26
Integrative analysis of spatial and single-cell transcriptome data from human pancreatic cancer reveals an intermediate cancer cell population associated with poor prognosis	26
Genomic landscape of endometrial polyps	25
Molecular characteristics of breast tumors in patients screened for germline predisposition from a population-based observational study	25
Non-coding cis-regulatory variants in HK1 cause congenital hyperinsulinism with variable disease severity	25