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	338
Loss of p53-DREAM-mediated repression of cell cycle genes as a driver of lymph node metastasis in head and neck cancer	291
Genome-aware annotation of CRISPR guides validates targets in variant cell lines and enhances discovery in screens	275
The role of admixture in the rare variant contribution to inflammatory bowel disease	266
Leveraging new methods for comprehensive characterization of mitochondrial DNA in esophageal squamous cell carcinoma	182
Pervasiveness of HLA allele-specific expression loss across tumor types	177
Circulating DNA reveals nucleosome occupancy patterns that are associated with nucleosome-DNA affinity and are affected in cancer	127
Integration of genetic evidence to identify approved drug targets	113
Curating genomic disease-gene relationships with Gene2Phenotype (G2P)	112
Neutrophil extracellular traps have auto-catabolic activity and produce mononucleosome-associated circulating DNA	107
VariantMedium: sensitive and generalizable somatic point mutation calling with 3D DenseNets trained and evaluated on experimental data	104
Single-molecule methylation profiles of cell-free DNA in cancer with nanopore sequencing	103
Beyond the exome: utility of long-read whole genome sequencing in exome-negative autosomal recessive diseases	100
Genome-wide methylation detection and episignature analysis using PacBio long-read sequencing	98
African ancestry-enriched variants in the GATM gene are associated with elevated serum creatinine levels	96
Single-cell transcriptome analysis defines novel molecular subtypes and reveals therapeutic implications of T/myeloid mixed-phenotype acute leukemia	95
The multiple de novo copy number variant (MdnCNV) phenomenon presents with peri-zygotic DNA mutational signatures and multilocus pathogenic variation	88
Clinical characteristics and molecular heterogeneity in Follicular lymphoma with extranodal involvement	86
Ethnic variations in metabolic syndrome components and their associations with the gut microbiota: the HELIUS study	85
Universal clinical Parkinson’s disease axes identify a major influence of neuroinflammation	80
De novo identification of expressed cancer somatic mutations from single-cell RNA sequencing data	79
Publisher Correction: Analysis of transcriptomic features reveals molecular endotypes of SLE with clinical implications	75
Investigating the interplay between prematurity and genetic variation in the context of rare developmental disorders	73
Whole-genome sequencing reveals individual and cohort level insights into chromosome 9p syndromes	71
DNA demethylation triggers cell free DNA release in colorectal cancer cells	70

The impact of the COVID-19 pandemic and associated lifestyle changes on early-life microbiome development	70
Adult genomic medicine: lessons from a multisite study of 2700 patients	69
INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance	69
The lung microbiome, peripheral gene expression, and recurrence-free survival after resection of stage II non-small cell lung cancer	69
Replication-associated mechanisms contribute to an increased CpG > TpG mutation burden in mismatch repair-deficient cancers	66
GWAS-by-subtraction reveals new genetic architecture and health implications of type 2 diabetes-independent gestational diabetes mellitus	66
Shared genetic architecture between irritable bowel syndrome and psychiatric disorders reveals molecular pathways of the gut-brain axis	65
Contribution of rare coding variants to microcephaly in individuals with neurodevelopmental disorders	63
Glioblastoma-instructed microglia transition to heterogeneous phenotypic states with phagocytic and dendritic cell-like features in patient tumors and patient-derived orthotopic xenografts	61
Single-cell transcriptomics reveals a mechanosensitive injury signaling pathway in early diabetic nephropathy	60
Spatial intra-tumour heterogeneity and treatment-induced genomic evolution in oesophageal adenocarcinoma: implications for prognosis and therapy	60
The landcape of Helicobacter pylori-mediated DNA breaks links bacterial genotoxicity to its oncogenic potential	60
Tracing carriage, acquisition, and transmission of ESBL-producing Escherichia coli over two years in a tertiary care hospital	59
Biological basis of extensive pleiotropy between blood traits and cancer risk	59
A human YEATS4 variant confers resistance to TST and IGRA conversion despite Mycobacterium tuberculosis exposure	58
MicroRNA gene dynamics in immune cell subpopulations during aging and atherosclerosis disease development at single-cell resolution	58
Genomic and transcriptomic features between primary and paired metastatic fumarate hydratase–deficient renal cell carcinoma	57
Transcriptome-wide association study revealed novel causal genes of renal-biopsy proven diabetic nephropathy	57
Correction: Genome Med 15, 115 & Genome Med 16, 3	56
Neutralization sensitivity, fusogenicity, and infectivity of Omicron subvariants	55
Identifying intra-hospital Norovirus GII transmission using whole-genome sequencing	55
Metabolome-wide Mendelian randomization for age at menarche and age at natural menopause	53
Full-spectral genome analysis of natural killer/T cell lymphoma highlights impacts of genome instability in driving its progression	52
Cancer evolution and multi-omic profile of relapsed colorectal liver metastases after treatment	52
Skeletal muscle regeneration failure in ischemic-damaged limbs is associated with pro-inflammatory macrophages and premature differentiation of satellite cells	51
Single-nucleus RNA sequencing of human pancreatic islets identifies novel gene sets and distinguishes β-cell subpopulations with dynamic transcriptome profiles	51
ClinVar and HGMD genomic variant classification accuracy has improved over time, as measured by implied disease burden	50
The WID-CIN test identifies women with, and at risk of, cervical intraepithelial neoplasia grade 3 and invasive cervical cancer	49
Comprehensive pathogen identification and antimicrobial resistance prediction from positive blood cultures using nanopore sequencing technology	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
Longitudinal analysis of genetic and environmental interplay in human metabolic profiles and the implication for metabolic health	49
In vivo adenine base editing of mutant Galc gene ameliorates Krabbe disease progression	48
NeoGuider: neoepitope prediction using advanced feature engineering	48
Malaria-MOI: A flexible and scalable tool for predicting multiplicity of infection in malaria parasites	48
Tissue-specific gene dosage disruption is a key feature and pathogenic mechanism of structural variants in the human genome	47
Empirical evaluation of analytic validity of polygenic scores	47
TP53 germline testing and hereditary cancer: how somatic events and clinical criteria affect variant detection rate	46
Succinate supplementation ameliorates musculoskeletal defects caused by PLOD3 mutations in a BCARD syndrome model	46
Multi-label transcriptional classification of colorectal cancer reflects tumor cell population heterogeneity	45
The telomere maintenance mechanism spectrum and its dynamics in gliomas	45
High fluoroquinolone resistance proportions among multidrug-resistant tuberculosis driven by dominant L2 Mycobacterium tuberculosis clones in the Mumbai Metropolitan Region	44
Applications of long-read sequencing to Mendelian genetics	43
A novel molecular signature identifies mixed subtypes in renal cell carcinoma with poor prognosis and independent response to immunotherapy	42
Epigenomic preconditioning of peripheral monocytes determines their transcriptional response to the tumor microenvironment	42
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	41
Single-cell transcriptomic analysis reveals tumor cell heterogeneity and immune microenvironment features of pituitary neuroendocrine tumors	41
Psychiatric genetic liability is associated with the severity of COVID-19 and other acute respiratory infections: an observational study across five Northern European countries	40
Refining epigenetic prediction of chronological and biological age	39
Optimized high-throughput whole-genome sequencing workflow for surveillance of influenza A virus	39
Long-read genome sequencing enhances diagnostics of pediatric neurological disorders	39

Transcriptional immunogenomic analysis reveals distinct immunological clusters in paediatric nervous system tumours	38
Influence network model uncovers relations between biological processes and mutational signatures	38
Correction: Acetyl-CoA metabolism drives epigenome change and contributes to carcinogenesis risk in fatty liver disease	38
Genome sequencing for the diagnosis of intellectual disability as a paradigm for rare diseases in the French healthcare setting: the prospective DEFIDIAG study	37
A robust deep learning workflow to predict CD8 + T-cell epitopes	37
Large-scale copy number alterations are enriched for synthetic viability in BRCA1/BRCA2 tumors	37
Integrated study of systemic and local airway transcriptomes in asthma reveals causal mediation of systemic effects by airway key drivers	37
Applicability of epigenetic age models to next-generation methylation arrays	36
Multiomics assessment of lung adenocarcinoma subtypes defined through tumor purity-adjusted DNA methylation	36
Identification of novel protein biomarkers and drug targets for colorectal cancer by integrating human plasma proteome with genome	35
Clonal evolution in primary breast cancers under sequential epirubicin and docetaxel monotherapy	35
The TyphiNET data visualisation dashboard: unlocking Salmonella Typhi genomics data to support public health	35
Cell type-specific changes identified by single-cell transcriptomics in Alzheimer’s disease	34
Prematurity and genetic liability for autism spectrum disorder	34
Single-cell analysis of the progeria arterial wall reveals progerin-induced progressive, cell type-specific dysfunction and somatic mutation accumulation	33
Circulating tumor DNA precision oncology enables effective and sensitive molecular diagnostics and actionable target detection in pediatric solid tumors - the INFORM experience	33
SARS-CoV-2 infection induces a long-lived pro-inflammatory transcriptional profile	32
Clinical and bacterial determinants of unfavorable tuberculosis treatment outcomes: an observational study in Georgia	32
Plasma microRNA signatures of aging and their links to health outcomes and mortality: findings from a population-based cohort study	32
Detection of primary cancer types via fragment size selection in circulating cell-free extrachromosomal circular DNA	32
MGCL-ST: multi-view graph contrastive learning for spatial transcriptomics imputation	32
imply: improving cell-type deconvolution accuracy using personalized reference profiles	31
Prioritizing genes associated with brain disorders by leveraging enhancer-promoter interactions in diverse neural cells and tissues	31
NODAL variants are associated with a continuum of laterality defects from simple D-transposition of the great arteries to heterotaxy	31
EMB is essential for enteric nervous system development mediated by PI3K signaling	31
MorphoITH: a framework for deconvolving intra-tumor heterogeneity using tissue morphology	31
Microglial heterogeneity in the ischemic stroke mouse brain of both sexes	30
Survival Genie 2: a next-generation web server for targeted and single-cell-based survival analyses	30
Return of non-ACMG recommended incidental genetic findings to pediatric patients: considerations and opportunities from experiences in genomic sequencing	30
Identification of diagnostic candidates in Mendelian disorders using an RNA sequencing-centric approach	30
Integrating metabolomics and proteomics to identify novel drug targets for heart failure and atrial fibrillation	30
Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent Salmonella Typhi	30
Multi-omics reveals cholesterol-driven macrophage metabolic reprogramming and inflammation in chronic obstructive pulmonary disease	30
Multimodal-based analysis of single-cell ATAC-seq data enables highly accurate delineation of clinically relevant tumor cell subpopulations	29
Knockout mice with pituitary malformations help identify human cases of hypopituitarism	29
Multi-omics uncovers immune-modulatory molecules in plasma contributing to resistance exercise-ameliorated locomotor disability after incomplete spinal cord injury	29
STModule: identifying tissue modules to uncover spatial components and characteristics of transcriptomic landscapes	29
ENU-based dominant genetic screen identifies contractile and neuronal gene mutations in congenital heart disease	29
Proteomic landscape analysis of undifferentiated pleomorphic sarcoma	29
Post-vaccine epidemiology of serotype 3 pneumococci identifies transformation inhibition through prophage-driven alteration of a non-coding RNA	29
A bench-to-data analysis workflow for respiratory syncytial virus whole-genome sequencing with short and long-read approaches	29
Polygenic risk for Alzheimer’s disease in healthy aging: age-related and APOE-driven effects on brain structures and cognition	28
Genome sequencing as a generic diagnostic strategy for rare disease	28
Spatial ecology of breast cancer reveals co-evolution of proliferative and dormant niches	28
Correction: Patient induced pluripotent stem cells identify specificities of a reticular pseudodrusen phenotype in age-related macular degeneration	28
The role of genetic testing in diagnosis and care of inherited cardiac conditions in a specialised multidisciplinary clinic	28
Identification of specific susceptibility loci for the early-onset colorectal cancer	28
Meta-analysis identifies common gut microbiota associated with multiple sclerosis	28
Evaluating genome sequencing strategies: trio, singleton, and standard testing in rare disease diagnosis	28
Long-term persistence of diverse clones shapes the transmission landscape of invasive Listeria monocytogenes	27
Evaluating the use of paralogous protein domains to increase data availability for missense variant classification	27
The impact of damaging epilepsy and cardiac genetic variant burden in sudden death in the young	27
An integrated platform for concurrent structural and single-nucleotide variants improves copy-number detection and reveals pathogenic alleles in undiagnosed Mendelian families	27
Smoking-associated gene expression alterations in nasal epithelium reveal immune impairment linked to lung cancer risk	27
Distinct pathways for genetic and epigenetic predisposition in familial and bilateral Wilms tumor	27
Tumor-naïve ctDNA detection with deep learning-enhanced error suppression for sensitive mutation calling	27
The case for including proteomics in routine diagnostic practice for rare disease	26
Metronidazole response profiles of Gardnerella species are congruent with phylogenetic and comparative genomic analyses	26
ACT-Discover: identifying karyotype heterogeneity in pancreatic cancer evolution using ctDNA	26
The emergence of highly resistant and hypervirulent Klebsiella pneumoniae CC14 clone in a tertiary hospital over 8 years	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
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
Personalized transcriptional network analysis links age-related loss of gene coordination to individual biological aging	24
Using multi-scale genomics to associate poorly annotated genes with rare diseases	24
Multi-omics reveals key molecular and cellular features of advanced small cell lung cancers associated with distinct therapeutic opportunities	24
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	24
Dynamics of tumor ecosystems and microbiome in response to neoadjuvant ABFOLFOX treatment in patients with unresectable colorectal cancer with liver metastasis	24
Distinct pathway-based effects of blood pressure and body mass index on cardiovascular traits: comparison of novel Mendelian randomization approaches	24
Disease-specific epigenetic deregulation of enhancers, transposons, and polycomb targets in acute promyelocytic leukemia	24
Location and condition based reconstruction of colon cancer microbiome from human RNA sequencing data	23
Co-occurrence of transcriptionally distinct persister cell states underpins neoadjuvant therapy resistance in triple‑negative breast cancer	23
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	23
Cardiomyopathies in 100,000 genomes project: interval evaluation improves diagnostic yield and informs strategies for ongoing gene discovery	23
Intratumor heterogeneity and T cell exhaustion in primary CNS lymphoma	23
A proteomics analysis of 5xFAD mouse brain regions reveals the lysosome-associated protein Arl8b as a candidate biomarker for Alzheimer’s disease	23
Tandem repeat polymorphisms are associated with brain structure: results of two large population-based studies	22
Accumulation of copy number alterations and clinical progression across advanced prostate cancer	22
Trimodal, uncertainty-guided whole-slide framework for genome-scale spatial expression and image-only virtual perturbation in cancer cohorts	22

DNA methylation analysis of NOTCH1 variants reveals the first episignature for non-syndromic congenital heart defects	22
Ganciclovir-induced mutations are present in a diverse spectrum of post-transplant malignancies	22
spSeudoMap: cell type mapping of spatial transcriptomics using unmatched single-cell RNA-seq data	22
Multi-omics profiles of sex hormone-binding globulin are associated with subclinical atherosclerosis in men with HIV	22
Integrative analysis of spatial and single-cell transcriptome data from human pancreatic cancer reveals an intermediate cancer cell population associated with poor prognosis	21
SARS-CoV-2 population dynamics in immunocompetent individuals in a closed transmission chain shows genomic diversity over the course of infection	21
Therapy sculpts the complex interplay between cancer and the immune system during tumour evolution	21
Spatial transcriptomics analysis of neoadjuvant cabozantinib and nivolumab in advanced hepatocellular carcinoma identifies independent mechanisms of resistance and recurrence	21
Genetically supported drug target prioritization for rare diseases	21
Identification of a PRDM1-regulated T cell network to regulate atherosclerotic plaque inflammation	21
Combining multiplexed functional data to improve variant classification	21
Molecular-guided therapy for the treatment of patients with relapsed and refractory childhood cancers: a Beat Childhood Cancer Research Consortium trial	21