Genome Medicine

Article	Citations
Neutrophil extracellular traps have auto-catabolic activity and produce mononucleosome-associated circulating DNA	733
Genome-aware annotation of CRISPR guides validates targets in variant cell lines and enhances discovery in screens	282
African ancestry-enriched variants in the GATM gene are associated with elevated serum creatinine levels	255
Single-molecule methylation profiles of cell-free DNA in cancer with nanopore sequencing	253
Beyond the exome: utility of long-read whole genome sequencing in exome-negative autosomal recessive diseases	242
Single-cell transcriptome analysis defines novel molecular subtypes and reveals therapeutic implications of T/myeloid mixed-phenotype acute leukemia	235
The role of admixture in the rare variant contribution to inflammatory bowel disease	167
Correction: Intricate interplay of CRISPR-Cas systems, anti-CRISPR proteins, and antimicrobial resistance genes in a globally successful multi-drug resistant Klebsiella pneumoniae clone	154
Loss of p53-DREAM-mediated repression of cell cycle genes as a driver of lymph node metastasis in head and neck cancer	132
Pervasiveness of HLA allele-specific expression loss across tumor types	122
Curating genomic disease-gene relationships with Gene2Phenotype (G2P)	103
Genome-wide methylation detection and episignature analysis using PacBio long-read sequencing	101
Leveraging new methods for comprehensive characterization of mitochondrial DNA in esophageal squamous cell carcinoma	99
The lung microbiome, peripheral gene expression, and recurrence-free survival after resection of stage II non-small cell lung cancer	94
De novo identification of expressed cancer somatic mutations from single-cell RNA sequencing data	89
Adult genomic medicine: lessons from a multisite study of 2700 patients	89
Investigating the interplay between prematurity and genetic variation in the context of rare developmental disorders	87
Publisher Correction: Analysis of transcriptomic features reveals molecular endotypes of SLE with clinical implications	83
The multiple de novo copy number variant (MdnCNV) phenomenon presents with peri-zygotic DNA mutational signatures and multilocus pathogenic variation	81
Replication-associated mechanisms contribute to an increased CpG > TpG mutation burden in mismatch repair-deficient cancers	80
INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance	80
Glioblastoma-instructed microglia transition to heterogeneous phenotypic states with phagocytic and dendritic cell-like features in patient tumors and patient-derived orthotopic xenografts	77
DNA demethylation triggers cell free DNA release in colorectal cancer cells	77
Whole-genome sequencing reveals individual and cohort level insights into chromosome 9p syndromes	75
Clinical characteristics and molecular heterogeneity in Follicular lymphoma with extranodal involvement	73

Contribution of rare coding variants to microcephaly in individuals with neurodevelopmental disorders	72
Shared genetic architecture between irritable bowel syndrome and psychiatric disorders reveals molecular pathways of the gut-brain axis	72
Spatial intra-tumour heterogeneity and treatment-induced genomic evolution in oesophageal adenocarcinoma: implications for prognosis and therapy	71
Ethnic variations in metabolic syndrome components and their associations with the gut microbiota: the HELIUS study	67
Universal clinical Parkinson’s disease axes identify a major influence of neuroinflammation	66
The landcape of Helicobacter pylori-mediated DNA breaks links bacterial genotoxicity to its oncogenic potential	66
The impact of the COVID-19 pandemic and associated lifestyle changes on early-life microbiome development	64
Rapid whole genome sequencing of critically ill pediatric patients from genetically underrepresented populations	64
Tracing carriage, acquisition, and transmission of ESBL-producing Escherichia coli over two years in a tertiary care hospital	64
MicroRNA gene dynamics in immune cell subpopulations during aging and atherosclerosis disease development at single-cell resolution	63
Transcriptome-wide association study revealed novel causal genes of renal-biopsy proven diabetic nephropathy	62
Diversity in EWAS: current state, challenges, and solutions	61
Genomic and transcriptomic features between primary and paired metastatic fumarate hydratase–deficient renal cell carcinoma	59
Full-spectral genome analysis of natural killer/T cell lymphoma highlights impacts of genome instability in driving its progression	58
Integrated genomic analyses of acral and mucosal melanomas nominate novel driver genes	58
Correction: Genome Med 15, 115 & Genome Med 16, 3	58
Biological basis of extensive pleiotropy between blood traits and cancer risk	57
Metabolome-wide Mendelian randomization for age at menarche and age at natural menopause	57
A human YEATS4 variant confers resistance to TST and IGRA conversion despite Mycobacterium tuberculosis exposure	57
Cancer evolution and multi-omic profile of relapsed colorectal liver metastases after treatment	56
Comprehensive pathogen identification and antimicrobial resistance prediction from positive blood cultures using nanopore sequencing technology	55
Neutralization sensitivity, fusogenicity, and infectivity of Omicron subvariants	55
Identifying intra-hospital Norovirus GII transmission using whole-genome sequencing	55
ClinVar and HGMD genomic variant classification accuracy has improved over time, as measured by implied disease burden	53
Single-nucleus RNA sequencing of human pancreatic islets identifies novel gene sets and distinguishes β-cell subpopulations with dynamic transcriptome profiles	52
Single-cell transcriptomics reveals a mechanosensitive injury signaling pathway in early diabetic nephropathy	52
Skeletal muscle regeneration failure in ischemic-damaged limbs is associated with pro-inflammatory macrophages and premature differentiation of satellite cells	51
Longitudinal analysis of genetic and environmental interplay in human metabolic profiles and the implication for metabolic health	50
The telomere maintenance mechanism spectrum and its dynamics in gliomas	50
Single-cell transcriptomic analysis reveals tumor cell heterogeneity and immune microenvironment features of pituitary neuroendocrine tumors	50
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
TP53 germline testing and hereditary cancer: how somatic events and clinical criteria affect variant detection rate	49
A novel molecular signature identifies mixed subtypes in renal cell carcinoma with poor prognosis and independent response to immunotherapy	48
Malaria-MOI: A flexible and scalable tool for predicting multiplicity of infection in malaria parasites	48
Succinate supplementation ameliorates musculoskeletal defects caused by PLOD3 mutations in a BCARD syndrome model	47
NeoGuider: neoepitope prediction using advanced feature engineering	47
Applications of long-read sequencing to Mendelian genetics	47
Single-cell multimodal analysis identifies common regulatory programs in synovial fibroblasts of rheumatoid arthritis patients and modeled TNF-driven arthritis	46
Multi-label transcriptional classification of colorectal cancer reflects tumor cell population heterogeneity	46
Acetyl-CoA metabolism drives epigenome change and contributes to carcinogenesis risk in fatty liver disease	46
The WID-CIN test identifies women with, and at risk of, cervical intraepithelial neoplasia grade 3 and invasive cervical cancer	46
High fluoroquinolone resistance proportions among multidrug-resistant tuberculosis driven by dominant L2 Mycobacterium tuberculosis clones in the Mumbai Metropolitan Region	46
In vivo adenine base editing of mutant Galc gene ameliorates Krabbe disease progression	45
Refining epigenetic prediction of chronological and biological age	45
Empirical evaluation of analytic validity of polygenic scores	44
Optimized high-throughput whole-genome sequencing workflow for surveillance of influenza A virus	44
Epigenomic preconditioning of peripheral monocytes determines their transcriptional response to the tumor microenvironment	44
Tissue-specific gene dosage disruption is a key feature and pathogenic mechanism of structural variants in the human genome	44
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

Influence network model uncovers relations between biological processes and mutational signatures	43
Long-read genome sequencing enhances diagnostics of pediatric neurological disorders	43
Multiomics assessment of lung adenocarcinoma subtypes defined through tumor purity-adjusted DNA methylation	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
The TyphiNET data visualisation dashboard: unlocking Salmonella Typhi genomics data to support public health	41
Detection of primary cancer types via fragment size selection in circulating cell-free extrachromosomal circular DNA	39
Cell type-specific changes identified by single-cell transcriptomics in Alzheimer’s disease	39
Transcriptional immunogenomic analysis reveals distinct immunological clusters in paediatric nervous system tumours	39
Large-scale copy number alterations are enriched for synthetic viability in BRCA1/BRCA2 tumors	38
Neutralising reactivity against SARS-CoV-2 Delta and Omicron variants by vaccination and infection history	37
Integrated study of systemic and local airway transcriptomes in asthma reveals causal mediation of systemic effects by airway key drivers	37
A robust deep learning workflow to predict CD8 + T-cell epitopes	37
Applicability of epigenetic age models to next-generation methylation arrays	37
Clonal evolution in primary breast cancers under sequential epirubicin and docetaxel monotherapy	37
Identification of novel protein biomarkers and drug targets for colorectal cancer by integrating human plasma proteome with genome	36
Prematurity and genetic liability for autism spectrum disorder	36
Clinical and bacterial determinants of unfavorable tuberculosis treatment outcomes: an observational study in Georgia	35
NODAL variants are associated with a continuum of laterality defects from simple D-transposition of the great arteries to heterotaxy	35
Prioritizing genes associated with brain disorders by leveraging enhancer-promoter interactions in diverse neural cells and tissues	35
imply: improving cell-type deconvolution accuracy using personalized reference profiles	34
Plasma microRNA signatures of aging and their links to health outcomes and mortality: findings from a population-based cohort study	34
EMB is essential for enteric nervous system development mediated by PI3K signaling	34
Integrating metabolomics and proteomics to identify novel drug targets for heart failure and atrial fibrillation	33
Identification of diagnostic candidates in Mendelian disorders using an RNA sequencing-centric approach	33
Microglial heterogeneity in the ischemic stroke mouse brain of both sexes	33
Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent Salmonella Typhi	33
SARS-CoV-2 infection induces a long-lived pro-inflammatory transcriptional profile	33
MorphoITH: a framework for deconvolving intra-tumor heterogeneity using tissue morphology	33
Knockout mice with pituitary malformations help identify human cases of hypopituitarism	32
Addressing the routine failure to clinically identify monogenic cases of common disease	32
Multimodal-based analysis of single-cell ATAC-seq data enables highly accurate delineation of clinically relevant tumor cell subpopulations	31
Multi-omics reveals cholesterol-driven macrophage metabolic reprogramming and inflammation in chronic obstructive pulmonary disease	30
ENU-based dominant genetic screen identifies contractile and neuronal gene mutations in congenital heart disease	30
Identification of a cytokine-dominated immunosuppressive class in squamous cell lung carcinoma with implications for immunotherapy resistance	30
A bench-to-data analysis workflow for respiratory syncytial virus whole-genome sequencing with short and long-read approaches	30
Post-vaccine epidemiology of serotype 3 pneumococci identifies transformation inhibition through prophage-driven alteration of a non-coding RNA	30
STModule: identifying tissue modules to uncover spatial components and characteristics of transcriptomic landscapes	30
Return of non-ACMG recommended incidental genetic findings to pediatric patients: considerations and opportunities from experiences in genomic sequencing	29
Polygenic risk for Alzheimer’s disease in healthy aging: age-related and APOE-driven effects on brain structures and cognition	29
A dynamic single cell-based framework for digital twins to prioritize disease genes and drug targets	28
Genome sequencing as a generic diagnostic strategy for rare disease	28
Identification of specific susceptibility loci for the early-onset colorectal cancer	28
Meta-analysis identifies common gut microbiota associated with multiple sclerosis	28
Multi-omics uncovers immune-modulatory molecules in plasma contributing to resistance exercise-ameliorated locomotor disability after incomplete spinal cord injury	28
The role of genetic testing in diagnosis and care of inherited cardiac conditions in a specialised multidisciplinary clinic	28
Evaluating genome sequencing strategies: trio, singleton, and standard testing in rare disease diagnosis	28
Antiprogestins reduce epigenetic field cancerization in breast tissue of young healthy women	28
The impact of damaging epilepsy and cardiac genetic variant burden in sudden death in the young	28
Meiotic and mitotic aneuploidies drive arrest of in vitro fertilized human preimplantation embryos	27
Evaluating the use of paralogous protein domains to increase data availability for missense variant classification	27
Proteomic landscape analysis of undifferentiated pleomorphic sarcoma	27
Spatial multi-omics characterization of neuroblastoma reveals ferroptosis-associated metabolic features in high-risk tumors	26
A new method for detecting mixed Mycobacterium tuberculosis infection and reconstructing constituent strains provides insights into transmission	26
Spatiotemporal single-cell analysis elucidates the cellular and molecular dynamics of human cornea aging	26
An integrated platform for concurrent structural and single-nucleotide variants improves copy-number detection and reveals pathogenic alleles in undiagnosed Mendelian families	26
Smoking-associated gene expression alterations in nasal epithelium reveal immune impairment linked to lung cancer risk	25
Distinct pathways for genetic and epigenetic predisposition in familial and bilateral Wilms tumor	25
Personalized transcriptional network analysis links age-related loss of gene coordination to individual biological aging	25
ACT-Discover: identifying karyotype heterogeneity in pancreatic cancer evolution using ctDNA	25
Long-term persistence of diverse clones shapes the transmission landscape of invasive Listeria monocytogenes	25
The emergence of highly resistant and hypervirulent Klebsiella pneumoniae CC14 clone in a tertiary hospital over 8 years	25
Metronidazole response profiles of Gardnerella species are congruent with phylogenetic and comparative genomic analyses	25
The case for including proteomics in routine diagnostic practice for rare disease	25
DNA methylation analysis of NOTCH1 variants reveals the first episignature for non-syndromic congenital heart defects	24
Gut microbiota predicts body fat change following a low-energy diet: a PREVIEW intervention study	24
A proteomics analysis of 5xFAD mouse brain regions reveals the lysosome-associated protein Arl8b as a candidate biomarker for Alzheimer’s disease	24
Accumulation of copy number alterations and clinical progression across advanced prostate cancer	24
Identification of a PRDM1-regulated T cell network to regulate atherosclerotic plaque inflammation	23
Location and condition based reconstruction of colon cancer microbiome from human RNA sequencing data	23
Distinct pathway-based effects of blood pressure and body mass index on cardiovascular traits: comparison of novel Mendelian randomization approaches	23
Co-occurrence of transcriptionally distinct persister cell states underpins neoadjuvant therapy resistance in triple‑negative breast cancer	23
spSeudoMap: cell type mapping of spatial transcriptomics using unmatched single-cell RNA-seq data	23
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	23
Integrative analysis of spatial and single-cell transcriptome data from human pancreatic cancer reveals an intermediate cancer cell population associated with poor prognosis	23
Ganciclovir-induced mutations are present in a diverse spectrum of post-transplant malignancies	23
Spatial transcriptomics analysis of neoadjuvant cabozantinib and nivolumab in advanced hepatocellular carcinoma identifies independent mechanisms of resistance and recurrence	22
Intratumor heterogeneity and T cell exhaustion in primary CNS lymphoma	22
Cardiomyopathies in 100,000 genomes project: interval evaluation improves diagnostic yield and informs strategies for ongoing gene discovery	22
Single base focal hypermutation cooccurs with structural variation as an early event in advanced prostate tumourigenesis with ancestry specific independence: a multi-ancestral observational study	22
Using multi-scale genomics to associate poorly annotated genes with rare diseases	22

Disease-specific epigenetic deregulation of enhancers, transposons, and polycomb targets in acute promyelocytic leukemia	22
Multi-omics reveals key molecular and cellular features of advanced small cell lung cancers associated with distinct therapeutic opportunities	22