Genome Medicine

Article	Citations
Correction: Intricate interplay of CRISPR-Cas systems, anti-CRISPR proteins, and antimicrobial resistance genes in a globally successful multi-drug resistant Klebsiella pneumoniae clone	757
Loss of p53-DREAM-mediated repression of cell cycle genes as a driver of lymph node metastasis in head and neck cancer	297
Genome-aware annotation of CRISPR guides validates targets in variant cell lines and enhances discovery in screens	268
Genome-wide methylation detection and episignature analysis using PacBio long-read sequencing	259
Beyond the exome: utility of long-read whole genome sequencing in exome-negative autosomal recessive diseases	251
The role of admixture in the rare variant contribution to inflammatory bowel disease	238
Leveraging new methods for comprehensive characterization of mitochondrial DNA in esophageal squamous cell carcinoma	174
African ancestry-enriched variants in the GATM gene are associated with elevated serum creatinine levels	159
Curating genomic disease-gene relationships with Gene2Phenotype (G2P)	133
Pervasiveness of HLA allele-specific expression loss across tumor types	125
Neutrophil extracellular traps have auto-catabolic activity and produce mononucleosome-associated circulating DNA	105
Single-cell transcriptome analysis defines novel molecular subtypes and reveals therapeutic implications of T/myeloid mixed-phenotype acute leukemia	105
Single-molecule methylation profiles of cell-free DNA in cancer with nanopore sequencing	101
The multiple de novo copy number variant (MdnCNV) phenomenon presents with peri-zygotic DNA mutational signatures and multilocus pathogenic variation	97
Clinical characteristics and molecular heterogeneity in Follicular lymphoma with extranodal involvement	95
Contribution of rare coding variants to microcephaly in individuals with neurodevelopmental disorders	92
Spatial intra-tumour heterogeneity and treatment-induced genomic evolution in oesophageal adenocarcinoma: implications for prognosis and therapy	92
Whole-genome sequencing reveals individual and cohort level insights into chromosome 9p syndromes	84
Ethnic variations in metabolic syndrome components and their associations with the gut microbiota: the HELIUS study	84
Glioblastoma-instructed microglia transition to heterogeneous phenotypic states with phagocytic and dendritic cell-like features in patient tumors and patient-derived orthotopic xenografts	81
INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance	79
GWAS-by-subtraction reveals new genetic architecture and health implications of type 2 diabetes-independent gestational diabetes mellitus	75
Investigating the interplay between prematurity and genetic variation in the context of rare developmental disorders	75
Replication-associated mechanisms contribute to an increased CpG > TpG mutation burden in mismatch repair-deficient cancers	75
Universal clinical Parkinson’s disease axes identify a major influence of neuroinflammation	74

The impact of the COVID-19 pandemic and associated lifestyle changes on early-life microbiome development	72
De novo identification of expressed cancer somatic mutations from single-cell RNA sequencing data	71
Adult genomic medicine: lessons from a multisite study of 2700 patients	69
The landcape of Helicobacter pylori-mediated DNA breaks links bacterial genotoxicity to its oncogenic potential	67
Publisher Correction: Analysis of transcriptomic features reveals molecular endotypes of SLE with clinical implications	67
The lung microbiome, peripheral gene expression, and recurrence-free survival after resection of stage II non-small cell lung cancer	64
Shared genetic architecture between irritable bowel syndrome and psychiatric disorders reveals molecular pathways of the gut-brain axis	64
DNA demethylation triggers cell free DNA release in colorectal cancer cells	63
Diversity in EWAS: current state, challenges, and solutions	63
Genomic and transcriptomic features between primary and paired metastatic fumarate hydratase–deficient renal cell carcinoma	62
Correction: Genome Med 15, 115 & Genome Med 16, 3	61
MicroRNA gene dynamics in immune cell subpopulations during aging and atherosclerosis disease development at single-cell resolution	61
Transcriptome-wide association study revealed novel causal genes of renal-biopsy proven diabetic nephropathy	61
Metabolome-wide Mendelian randomization for age at menarche and age at natural menopause	59
Cancer evolution and multi-omic profile of relapsed colorectal liver metastases after treatment	58
Biological basis of extensive pleiotropy between blood traits and cancer risk	58
Identifying intra-hospital Norovirus GII transmission using whole-genome sequencing	57
Comprehensive pathogen identification and antimicrobial resistance prediction from positive blood cultures using nanopore sequencing technology	56
Neutralization sensitivity, fusogenicity, and infectivity of Omicron subvariants	55
ClinVar and HGMD genomic variant classification accuracy has improved over time, as measured by implied disease burden	54
Tracing carriage, acquisition, and transmission of ESBL-producing Escherichia coli over two years in a tertiary care hospital	54
Longitudinal analysis of genetic and environmental interplay in human metabolic profiles and the implication for metabolic health	53
A human YEATS4 variant confers resistance to TST and IGRA conversion despite Mycobacterium tuberculosis exposure	53
Single-nucleus RNA sequencing of human pancreatic islets identifies novel gene sets and distinguishes β-cell subpopulations with dynamic transcriptome profiles	53
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	52
Full-spectral genome analysis of natural killer/T cell lymphoma highlights impacts of genome instability in driving its progression	51
Integrated genomic analyses of acral and mucosal melanomas nominate novel driver genes	50
TP53 germline testing and hereditary cancer: how somatic events and clinical criteria affect variant detection rate	49
Single-cell transcriptomic analysis reveals tumor cell heterogeneity and immune microenvironment features of pituitary neuroendocrine tumors	49
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
Multi-label transcriptional classification of colorectal cancer reflects tumor cell population heterogeneity	46
In vivo adenine base editing of mutant Galc gene ameliorates Krabbe disease progression	46
Single-cell multimodal analysis identifies common regulatory programs in synovial fibroblasts of rheumatoid arthritis patients and modeled TNF-driven arthritis	45
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	45
Epigenomic preconditioning of peripheral monocytes determines their transcriptional response to the tumor microenvironment	45
High fluoroquinolone resistance proportions among multidrug-resistant tuberculosis driven by dominant L2 Mycobacterium tuberculosis clones in the Mumbai Metropolitan Region	45
Long-read genome sequencing enhances diagnostics of pediatric neurological disorders	45
Empirical evaluation of analytic validity of polygenic scores	45
Acetyl-CoA metabolism drives epigenome change and contributes to carcinogenesis risk in fatty liver disease	44
Refining epigenetic prediction of chronological and biological age	44
A novel molecular signature identifies mixed subtypes in renal cell carcinoma with poor prognosis and independent response to immunotherapy	44
Optimized high-throughput whole-genome sequencing workflow for surveillance of influenza A virus	44
DNA methylation memory of pancreatic acinar-ductal metaplasia transition state altering Kras-downstream PI3K and Rho GTPase signaling in the absence of Kras mutation	43
The telomere maintenance mechanism spectrum and its dynamics in gliomas	43
Tissue-specific gene dosage disruption is a key feature and pathogenic mechanism of structural variants in the human genome	42
Applications of long-read sequencing to Mendelian genetics	42
Correction: Acetyl-CoA metabolism drives epigenome change and contributes to carcinogenesis risk in fatty liver disease	39

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

Intratumor heterogeneity and T cell exhaustion in primary CNS lymphoma	22
Integrative analysis of spatial and single-cell transcriptome data from human pancreatic cancer reveals an intermediate cancer cell population associated with poor prognosis	22
Rare variation in neurological disease genes and its role in multiple sclerosis mimicry and phenotype	22
Using multi-scale genomics to associate poorly annotated genes with rare diseases	22
Dynamics of tumor ecosystems and microbiome in response to neoadjuvant ABFOLFOX treatment in patients with unresectable colorectal cancer with liver metastasis	22
Life Identification Number (LIN) codes for the genomic taxonomy of Corynebacterium diphtheriae strains	22
varCADD: large sets of standing genetic variation enable genome-wide pathogenicity prediction	22