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 2022-01-01 to 2026-01-01.)

Article	Citations
The role of admixture in the rare variant contribution to inflammatory bowel disease	648
Single-cell transcriptome analysis defines novel molecular subtypes and reveals therapeutic implications of T/myeloid mixed-phenotype acute leukemia	266
Loss of p53-DREAM-mediated repression of cell cycle genes as a driver of lymph node metastasis in head and neck cancer	220
Correction: Intricate interplay of CRISPR-Cas systems, anti-CRISPR proteins, and antimicrobial resistance genes in a globally successful multi-drug resistant Klebsiella pneumoniae clone	213
Genome-aware annotation of CRISPR guides validates targets in variant cell lines and enhances discovery in screens	206
Single-molecule methylation profiles of cell-free DNA in cancer with nanopore sequencing	205
Curating genomic disease-gene relationships with Gene2Phenotype (G2P)	204
Leveraging new methods for comprehensive characterization of mitochondrial DNA in esophageal squamous cell carcinoma	198
Pervasiveness of HLA allele-specific expression loss across tumor types	149
Beyond the exome: utility of long-read whole genome sequencing in exome-negative autosomal recessive diseases	144
Neutrophil extracellular traps have auto-catabolic activity and produce mononucleosome-associated circulating DNA	130
Publisher Correction: Analysis of transcriptomic features reveals molecular endotypes of SLE with clinical implications	122
Shared genetic architecture between irritable bowel syndrome and psychiatric disorders reveals molecular pathways of the gut-brain axis	118
DNA demethylation triggers cell free DNA release in colorectal cancer cells	109
The landcape of Helicobacter pylori-mediated DNA breaks links bacterial genotoxicity to its oncogenic potential	103
Large-scale discovery of novel neurodevelopmental disorder-related genes through a unified analysis of single-nucleotide and copy number variants	93
Adult genomic medicine: lessons from a multisite study of 2700 patients	85
Replication-associated mechanisms contribute to an increased CpG > TpG mutation burden in mismatch repair-deficient cancers	85
Clinical characteristics and molecular heterogeneity in Follicular lymphoma with extranodal involvement	82
The lung microbiome, peripheral gene expression, and recurrence-free survival after resection of stage II non-small cell lung cancer	82
Investigating the interplay between prematurity and genetic variation in the context of rare developmental disorders	81
Contribution of rare coding variants to microcephaly in individuals with neurodevelopmental disorders	77
Whole-genome sequencing reveals individual and cohort level insights into chromosome 9p syndromes	76
INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance	72
De novo identification of expressed cancer somatic mutations from single-cell RNA sequencing data	71

Spatial intra-tumour heterogeneity and treatment-induced genomic evolution in oesophageal adenocarcinoma: implications for prognosis and therapy	70
Universal clinical Parkinson’s disease axes identify a major influence of neuroinflammation	70
Ethnic variations in metabolic syndrome components and their associations with the gut microbiota: the HELIUS study	69
Glioblastoma-instructed microglia transition to heterogeneous phenotypic states with phagocytic and dendritic cell-like features in patient tumors and patient-derived orthotopic xenografts	69
Correction: Genome Med 15, 115 & Genome Med 16, 3	68
The multiple de novo copy number variant (MdnCNV) phenomenon presents with peri-zygotic DNA mutational signatures and multilocus pathogenic variation	68
Neutralization sensitivity, fusogenicity, and infectivity of Omicron subvariants	63
A human YEATS4 variant confers resistance to TST and IGRA conversion despite Mycobacterium tuberculosis exposure	62
MicroRNA gene dynamics in immune cell subpopulations during aging and atherosclerosis disease development at single-cell resolution	62
Skeletal muscle regeneration failure in ischemic-damaged limbs is associated with pro-inflammatory macrophages and premature differentiation of satellite cells	60
Biological basis of extensive pleiotropy between blood traits and cancer risk	59
Tracing carriage, acquisition, and transmission of ESBL-producing Escherichia coli over two years in a tertiary care hospital	57
Metabolome-wide Mendelian randomization for age at menarche and age at natural menopause	57
Rapid whole genome sequencing of critically ill pediatric patients from genetically underrepresented populations	57
Full-spectral genome analysis of natural killer/T cell lymphoma highlights impacts of genome instability in driving its progression	57
Diversity in EWAS: current state, challenges, and solutions	55
Integrated genomic analyses of acral and mucosal melanomas nominate novel driver genes	54
Transcriptome-wide association study revealed novel causal genes of renal-biopsy proven diabetic nephropathy	54
Single-nucleus RNA sequencing of human pancreatic islets identifies novel gene sets and distinguishes β-cell subpopulations with dynamic transcriptome profiles	54
Genomic and transcriptomic features between primary and paired metastatic fumarate hydratase–deficient renal cell carcinoma	54
Comprehensive pathogen identification and antimicrobial resistance prediction from positive blood cultures using nanopore sequencing technology	53
ClinVar and HGMD genomic variant classification accuracy has improved over time, as measured by implied disease burden	53
Longitudinal analysis of genetic and environmental interplay in human metabolic profiles and the implication for metabolic health	52
Optimized high-throughput whole-genome sequencing workflow for surveillance of influenza A virus	52
The effects of the Green-Mediterranean diet on cardiometabolic health are linked to gut microbiome modifications: a randomized controlled trial	52
Single-cell transcriptomics reveals a mechanosensitive injury signaling pathway in early diabetic nephropathy	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
Multi-label transcriptional classification of colorectal cancer reflects tumor cell population heterogeneity	51
DNA methylation memory of pancreatic acinar-ductal metaplasia transition state altering Kras-downstream PI3K and Rho GTPase signaling in the absence of Kras mutation	51
Epigenomic preconditioning of peripheral monocytes determines their transcriptional response to the tumor microenvironment	49
Single-cell transcriptomic analysis reveals tumor cell heterogeneity and immune microenvironment features of pituitary neuroendocrine tumors	48
Single-cell multimodal analysis identifies common regulatory programs in synovial fibroblasts of rheumatoid arthritis patients and modeled TNF-driven arthritis	48
The WID-CIN test identifies women with, and at risk of, cervical intraepithelial neoplasia grade 3 and invasive cervical cancer	48
Applications of long-read sequencing to Mendelian genetics	47
Acetyl-CoA metabolism drives epigenome change and contributes to carcinogenesis risk in fatty liver disease	46
NeoGuider: neoepitope prediction using advanced feature engineering	45
TP53 germline testing and hereditary cancer: how somatic events and clinical criteria affect variant detection rate	45
A novel molecular signature identifies mixed subtypes in renal cell carcinoma with poor prognosis and independent response to immunotherapy	44
The telomere maintenance mechanism spectrum and its dynamics in gliomas	44
High fluoroquinolone resistance proportions among multidrug-resistant tuberculosis driven by dominant L2 Mycobacterium tuberculosis clones in the Mumbai Metropolitan Region	44
Refining epigenetic prediction of chronological and biological age	44
Correction: Acetyl-CoA metabolism drives epigenome change and contributes to carcinogenesis risk in fatty liver disease	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
Neutralising reactivity against SARS-CoV-2 Delta and Omicron variants by vaccination and infection history	43
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	42
A robust deep learning workflow to predict CD8 + T-cell epitopes	42
Prematurity and genetic liability for autism spectrum disorder	42
Cell type-specific changes identified by single-cell transcriptomics in Alzheimer’s disease	42
Integrated study of systemic and local airway transcriptomes in asthma reveals causal mediation of systemic effects by airway key drivers	41

Large-scale copy number alterations are enriched for synthetic viability in BRCA1/BRCA2 tumors	41
Applicability of epigenetic age models to next-generation methylation arrays	40
EMB is essential for enteric nervous system development mediated by PI3K signaling	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	40
Identification of novel protein biomarkers and drug targets for colorectal cancer by integrating human plasma proteome with genome	40
Clonal evolution in primary breast cancers under sequential epirubicin and docetaxel monotherapy	40
Clinical and bacterial determinants of unfavorable tuberculosis treatment outcomes: an observational study in Georgia	40
Plasma microRNA signatures of aging and their links to health outcomes and mortality: findings from a population-based cohort study	39
Prioritizing genes associated with brain disorders by leveraging enhancer-promoter interactions in diverse neural cells and tissues	39
MorphoITH: a framework for deconvolving intra-tumor heterogeneity using tissue morphology	39
SARS-CoV-2 infection induces a long-lived pro-inflammatory transcriptional profile	39
imply: improving cell-type deconvolution accuracy using personalized reference profiles	39
Identification of diagnostic candidates in Mendelian disorders using an RNA sequencing-centric approach	38
Integrating metabolomics and proteomics to identify novel drug targets for heart failure and atrial fibrillation	38
Microglial heterogeneity in the ischemic stroke mouse brain of both sexes	38
Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent Salmonella Typhi	38
NODAL variants are associated with a continuum of laterality defects from simple D-transposition of the great arteries to heterotaxy	37
PLCG2 is associated with the inflammatory response and is induced by amyloid plaques in Alzheimer’s disease	37
Addressing the routine failure to clinically identify monogenic cases of common disease	37
A dynamic single cell-based framework for digital twins to prioritize disease genes and drug targets	36
STModule: identifying tissue modules to uncover spatial components and characteristics of transcriptomic landscapes	36
The role of genetic testing in diagnosis and care of inherited cardiac conditions in a specialised multidisciplinary clinic	36
Knockout mice with pituitary malformations help identify human cases of hypopituitarism	35
Polygenic risk for Alzheimer’s disease in healthy aging: age-related and APOE-driven effects on brain structures and cognition	35
The impact of damaging epilepsy and cardiac genetic variant burden in sudden death in the young	35
Post-vaccine epidemiology of serotype 3 pneumococci identifies transformation inhibition through prophage-driven alteration of a non-coding RNA	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	33
Identification of a cytokine-dominated immunosuppressive class in squamous cell lung carcinoma with implications for immunotherapy resistance	33
Multi-omics uncovers immune-modulatory molecules in plasma contributing to resistance exercise-ameliorated locomotor disability after incomplete spinal cord injury	33
Evaluating genome sequencing strategies: trio, singleton, and standard testing in rare disease diagnosis	33
Return of non-ACMG recommended incidental genetic findings to pediatric patients: considerations and opportunities from experiences in genomic sequencing	33
Meta-analysis identifies common gut microbiota associated with multiple sclerosis	32
Identification of specific susceptibility loci for the early-onset colorectal cancer	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	31
ACT-Discover: identifying karyotype heterogeneity in pancreatic cancer evolution using ctDNA	31
The case for including proteomics in routine diagnostic practice for rare disease	31
Interaction of bacterial genera associated with therapeutic response to immune checkpoint PD-1 blockade in a United States cohort	30
Long-term persistence of diverse clones shapes the transmission landscape of invasive Listeria monocytogenes	30
Distinct pathways for genetic and epigenetic predisposition in familial and bilateral Wilms tumor	30
Meiotic and mitotic aneuploidies drive arrest of in vitro fertilized human preimplantation embryos	30
A new method for detecting mixed Mycobacterium tuberculosis infection and reconstructing constituent strains provides insights into transmission	30
Metronidazole response profiles of Gardnerella species are congruent with phylogenetic and comparative genomic analyses	30
Spatiotemporal single-cell analysis elucidates the cellular and molecular dynamics of human cornea aging	29
An 8-gene machine learning model improves clinical prediction of severe dengue progression	29
Personalized transcriptional network analysis links age-related loss of gene coordination to individual biological aging	29
The emergence of highly resistant and hypervirulent Klebsiella pneumoniae CC14 clone in a tertiary hospital over 8 years	29
An integrated platform for concurrent structural and single-nucleotide variants improves copy-number detection and reveals pathogenic alleles in undiagnosed Mendelian families	29
Identification of a PRDM1-regulated T cell network to regulate atherosclerotic plaque inflammation	29
Smoking-associated gene expression alterations in nasal epithelium reveal immune impairment linked to lung cancer risk	29
Disease-specific epigenetic deregulation of enhancers, transposons, and polycomb targets in acute promyelocytic leukemia	29
spSeudoMap: cell type mapping of spatial transcriptomics using unmatched single-cell RNA-seq data	29
A proteomics analysis of 5xFAD mouse brain regions reveals the lysosome-associated protein Arl8b as a candidate biomarker for Alzheimer’s disease	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	28
Using multi-scale genomics to associate poorly annotated genes with rare diseases	28
Ganciclovir-induced mutations are present in a diverse spectrum of post-transplant malignancies	27
Accumulation of copy number alterations and clinical progression across advanced prostate cancer	27
Intratumor heterogeneity and T cell exhaustion in primary CNS lymphoma	27
Location and condition based reconstruction of colon cancer microbiome from human RNA sequencing data	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
Cardiomyopathies in 100,000 genomes project: interval evaluation improves diagnostic yield and informs strategies for ongoing gene discovery	27
Molecular-guided therapy for the treatment of patients with relapsed and refractory childhood cancers: a Beat Childhood Cancer Research Consortium trial	26
Spatial transcriptomics analysis of neoadjuvant cabozantinib and nivolumab in advanced hepatocellular carcinoma identifies independent mechanisms of resistance and recurrence	26
SvAnna: efficient and accurate pathogenicity prediction of coding and regulatory structural variants in long-read genome sequencing	26
Gut microbiota predicts body fat change following a low-energy diet: a PREVIEW intervention study	26
Building digital histology models of transcriptional tumor programs with generative deep learning for pathology-based precision medicine	25
Genomic landscape of endometrial polyps	25
varCADD: large sets of standing genetic variation enable genome-wide pathogenicity prediction	25
RNA profiling of blood platelets noninvasively differentiates colorectal cancer from healthy donors and noncancerous intestinal diseases: a retrospective cohort study	25
Life Identification Number (LIN) codes for the genomic taxonomy of Corynebacterium diphtheriae strains	25
Penetrance estimation of Alzheimer disease in SORL1 loss-of-function variant carriers using a family-based strategy and stratification by APOE genotypes	25