Genome Medicine

(The TQCC of Genome Medicine is 26. 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 2020-06-01 to 2024-06-01.)
CADD-Splice—improving genome-wide variant effect prediction using deep learning-derived splice scores386
Characterisation of the transcriptome and proteome of SARS-CoV-2 reveals a cell passage induced in-frame deletion of the furin-like cleavage site from the spike glycoprotein363
dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs320
Deep learning in cancer diagnosis, prognosis and treatment selection295
An introduction to spatial transcriptomics for biomedical research236
Best practices for variant calling in clinical sequencing194
Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients188
Understanding the impact of antibiotic perturbation on the human microbiome162
Single-cell transcriptome analysis of tumor and stromal compartments of pancreatic ductal adenocarcinoma primary tumors and metastatic lesions137
Integration of whole genome sequencing into a healthcare setting: high diagnostic rates across multiple clinical entities in 3219 rare disease patients123
IFN-γ and TNF-α drive a CXCL10+ CCL2+ macrophage phenotype expanded in severe COVID-19 lungs and inflammatory diseases with tissue inflammation121
A guide for the diagnosis of rare and undiagnosed disease: beyond the exome120
Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression113
Human breast microbiome correlates with prognostic features and immunological signatures in breast cancer109
FOXC1-mediated LINC00301 facilitates tumor progression and triggers an immune-suppressing microenvironment in non-small cell lung cancer by regulating the HIF1α pathway107
Multiple approaches for massively parallel sequencing of SARS-CoV-2 genomes directly from clinical samples104
DeepProg: an ensemble of deep-learning and machine-learning models for prognosis prediction using multi-omics data99
Microglial PGC-1α protects against ischemic brain injury by suppressing neuroinflammation94
Integrated analysis of microbiome and host transcriptome reveals correlations between gut microbiota and clinical outcomes in HBV-related hepatocellular carcinoma91
A Klebsiella pneumoniae ST307 outbreak clone from Germany demonstrates features of extensive drug resistance, hypermucoviscosity, and enhanced iron acquisition90
CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes90
Integrated analysis of single-cell and bulk RNA sequencing data reveals a pan-cancer stemness signature predicting immunotherapy response88
Intra-host variation and evolutionary dynamics of SARS-CoV-2 populations in COVID-19 patients87
Clinical implementation of RNA sequencing for Mendelian disease diagnostics87
Clinical trial design in the era of precision medicine86
Robust barcoding and identification of Mycobacterium tuberculosis lineages for epidemiological and clinical studies85
Polygenic risk scores in the clinic: new perspectives needed on familiar ethical issues84
Guild-based analysis for understanding gut microbiome in human health and diseases84
Single-nucleus transcriptome analysis of human brain immune response in patients with severe COVID-1983
Small-molecule MMP2/MMP9 inhibitor SB-3CT modulates tumor immune surveillance by regulating PD-L182
Role of the intestinal microbiome and microbial-derived metabolites in immune checkpoint blockade immunotherapy of cancer82
High-grade serous tubo-ovarian cancer refined with single-cell RNA sequencing: specific cell subtypes influence survival and determine molecular subtype classification81
Strain-level epidemiology of microbial communities and the human microbiome76
The neuroimmune axis of Alzheimer’s disease73
Recommendations for clinical interpretation of variants found in non-coding regions of the genome72
A comparison of epigenetic mitotic-like clocks for cancer risk prediction71
Dietary fiber intake, the gut microbiome, and chronic systemic inflammation in a cohort of adult men70
Sequence-based prediction of SARS-CoV-2 vaccine targets using a mass spectrometry-based bioinformatics predictor identifies immunogenic T cell epitopes69
A community-driven resource for genomic epidemiology and antimicrobial resistance prediction of Neisseria gonorrhoeae at Pathogenwatch68
Mitochondrial DNA copy number can influence mortality and cardiovascular disease via methylation of nuclear DNA CpGs68
The murine Microenvironment Cell Population counter method to estimate abundance of tissue-infiltrating immune and stromal cell populations in murine samples using gene expression68
Single-cell characterization of macrophages in glioblastoma reveals MARCO as a mesenchymal pro-tumor marker65
Microbial signature in IgE-mediated food allergies65
PRMT1-mediated H4R3me2a recruits SMARCA4 to promote colorectal cancer progression by enhancing EGFR signaling64
Mobilization of the nonconjugative virulence plasmid from hypervirulent Klebsiella pneumoniae64
Improved analysis of CRISPR fitness screens and reduced off-target effects with the BAGEL2 gene essentiality classifier63
Hepatocellular carcinoma patients with high circulating cytotoxic T cells and intra-tumoral immune signature benefit from pembrolizumab: results from a single-arm phase 2 trial63
5′-tRF-GlyGCC: a tRNA-derived small RNA as a novel biomarker for colorectal cancer diagnosis61
The complexities of the diet-microbiome relationship: advances and perspectives61
The landscape of host genetic factors involved in immune response to common viral infections60
Artificial intelligence enables comprehensive genome interpretation and nomination of candidate diagnoses for rare genetic diseases59
Discovery of CD80 and CD86 as recent activation markers on regulatory T cells by protein-RNA single-cell analysis57
Population genomics and antimicrobial resistance in Corynebacterium diphtheriae56
Clinical laboratory test-wide association scan of polygenic scores identifies biomarkers of complex disease55
Somalier: rapid relatedness estimation for cancer and germline studies using efficient genome sketches55
Distinct transcriptional programs stratify ovarian cancer cell lines into the five major histological subtypes53
Pervasive generation of non-canonical subgenomic RNAs by SARS-CoV-253
Human reference gut microbiome catalog including newly assembled genomes from under-represented Asian metagenomes53
Microbiota restoration reduces antibiotic-resistant bacteria gut colonization in patients with recurrent Clostridioides difficile infection from the open-label PUNCH CD study52
Explaining decisions of graph convolutional neural networks: patient-specific molecular subnetworks responsible for metastasis prediction in breast cancer52
MDR M. tuberculosis outbreak clone in Eswatini missed by Xpert has elevated bedaquiline resistance dated to the pre-treatment era52
The effects of the Green-Mediterranean diet on cardiometabolic health are linked to gut microbiome modifications: a randomized controlled trial51
Rare deleterious mutations of HNRNP genes result in shared neurodevelopmental disorders51
Molecular profiling of advanced malignancies guides first-line N-of-1 treatments in the I-PREDICT treatment-naïve study50
Development and validation of a trans-ancestry polygenic risk score for type 2 diabetes in diverse populations50
Cord blood DNA methylome in newborns later diagnosed with autism spectrum disorder reflects early dysregulation of neurodevelopmental and X-linked genes47
Epigenetic signatures in cancer: proper controls, current challenges and the potential for clinical translation47
Genetic diversity and characteristics of high-level tigecycline resistance Tet(X) in Acinetobacter species46
Gut microbial determinants of clinically important improvement in patients with rheumatoid arthritis44
Deconvolution of cell type-specific drug responses in human tumor tissue with single-cell RNA-seq44
Whole-genome sequencing with long reads reveals complex structure and origin of structural variation in human genetic variations and somatic mutations in cancer44
Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants44
SARS-CoV-2 vaccine ChAdOx1 nCoV-19 infection of human cell lines reveals low levels of viral backbone gene transcription alongside very high levels of SARS-CoV-2 S glycoprotein gene transcription43
DNA methylation and body mass index from birth to adolescence: meta-analyses of epigenome-wide association studies42
cfNOMe — A single assay for comprehensive epigenetic analyses of cell-free DNA41
Ten-year longitudinal molecular epidemiology study of Escherichia coli and Klebsiella species bloodstream infections in Oxfordshire, UK39
Improved prediction of fracture risk leveraging a genome-wide polygenic risk score39
Single-cell profiling of human dura and meningioma reveals cellular meningeal landscape and insights into meningioma immune response39
Rare variant analysis of 4241 pulmonary arterial hypertension cases from an international consortium implicates FBLN2, PDGFD, and rare de novo variants in PAH39
Single-cell genomic and transcriptomic landscapes of primary and metastatic colorectal cancer tumors39
Maintenance of the human memory T cell repertoire by subset and tissue site39
Optimized polyepitope neoantigen DNA vaccines elicit neoantigen-specific immune responses in preclinical models and in clinical translation38
Identification of new driver and passenger mutations within APOBEC-induced hotspot mutations in bladder cancer38
The global dissemination of hospital clones of Enterococcus faecium38
Implementing genomic screening in diverse populations38
An atlas connecting shared genetic architecture of human diseases and molecular phenotypes provides insight into COVID-19 susceptibility38
PLCG2 is associated with the inflammatory response and is induced by amyloid plaques in Alzheimer’s disease38
ClinSV: clinical grade structural and copy number variant detection from whole genome sequencing data38
Highly elevated polygenic risk scores are better predictors of myocardial infarction risk early in life than later37
ASXL3 bridges BRD4 to BAP1 complex and governs enhancer activity in small cell lung cancer37
Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India37
Tumor microenvironment remodeling after neoadjuvant immunotherapy in non-small cell lung cancer revealed by single-cell RNA sequencing36
Detection of ctDNA in plasma of patients with clinically localised prostate cancer is associated with rapid disease progression36
MetaRNN: differentiating rare pathogenic and rare benign missense SNVs and InDels using deep learning36
Phylogroup stability contrasts with high within sequence type complex dynamics of Escherichia coli bloodstream infection isolates over a 12-year period35
Gut microbiota predicts body fat change following a low-energy diet: a PREVIEW intervention study35
Demonstrating trustworthiness when collecting and sharing genomic data: public views across 22 countries35
ClinGen Variant Curation Interface: a variant classification platform for the application of evidence criteria from ACMG/AMP guidelines35
Drivers of methicillin-resistant Staphylococcus aureus (MRSA) lineage replacement in China35
Interaction of bacterial genera associated with therapeutic response to immune checkpoint PD-1 blockade in a United States cohort35
Metabolic control by the microbiome35
Exploiting genomics to mitigate the public health impact of antimicrobial resistance35
Characterization of the dual functional effects of heat shock proteins (HSPs) in cancer hallmarks to aid development of HSP inhibitors35
Multi-site tumor sampling highlights molecular intra-tumor heterogeneity in malignant pleural mesothelioma35
Editing GWAS: experimental approaches to dissect and exploit disease-associated genetic variation34
A population-based gene expression signature of molecular clock phase from a single epidermal sample34
Angiosarcoma heterogeneity and potential therapeutic vulnerability to immune checkpoint blockade: insights from genomic sequencing34
Evaluating the potential for respiratory metagenomics to improve treatment of secondary infection and detection of nosocomial transmission on expanded COVID-19 intensive care units34
A global overview of genetically interpretable multimorbidities among common diseases in the UK Biobank33
Maternal and early life exposures and their potential to influence development of the microbiome33
Molecular correlates and therapeutic targets in T cell-inflamed versus non-T cell-inflamed tumors across cancer types33
A single early-in-life antibiotic course increases susceptibility to DSS-induced colitis32
The aging mouse microbiome has obesogenic characteristics32
CAPICE: a computational method for Consequence-Agnostic Pathogenicity Interpretation of Clinical Exome variations32
Fecal microbiota transplantation in gastrointestinal disorders: time for precision medicine32
Genotype imputation and variability in polygenic risk score estimation32
Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq data31
Mendelian randomization analysis of 37 clinical factors and coronary artery disease in East Asian and European populations31
Anti-SARS-CoV-2 IgA and IgG in human milk after vaccination is dependent on vaccine type and previous SARS-CoV-2 exposure: a longitudinal study31
Human liver single nucleus and single cell RNA sequencing identify a hepatocellular carcinoma-associated cell-type affecting survival31
Clinical implications of host genetic variation and susceptibility to severe or critical COVID-1931
Trans-ethnic gut microbial signatures of prediabetic subjects from India and Denmark31
A mutation-based gene set predicts survival benefit after immunotherapy across multiple cancers and reveals the immune response landscape30
Whole-genome sequencing as an investigational device for return of hereditary disease risk and pharmacogenomic results as part of the All of Us Research Program30
DNA methylation signature in blood mirrors successful weight-loss during lifestyle interventions: the CENTRAL trial30
A transcriptome-wide association study of Alzheimer’s disease using prediction models of relevant tissues identifies novel candidate susceptibility genes30
Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults30
Epigenomics and transcriptomics of systemic sclerosis CD4+ T cells reveal long-range dysregulation of key inflammatory pathways mediated by disease-associated susceptibility loci30
An international policy on returning genomic research results30
The gut microbiota in multiple sclerosis varies with disease activity30
Genome-scale CRISPR screens identify host factors that promote human coronavirus infection29
Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections29
An implementation science approach to evaluating pathogen whole genome sequencing in public health29
GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning29
Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-1928
Evaluating the transcriptional fidelity of cancer models28
Single-cell transcriptomics reveals common epithelial response patterns in human acute kidney injury28
Bacteroides vulgatus and Bacteroides dorei predict immune-related adverse events in immune checkpoint blockade treatment of metastatic melanoma28
Effectiveness and safety of Bifidobacterium and berberine in human hyperglycemia and their regulatory effect on the gut microbiota: a multi-center, double-blind, randomized, parallel-controlled study28
Identification of epigenome-wide DNA methylation differences between carriers of APOE ε4 and APOE ε2 alleles27
Crosstalk between microRNA expression and DNA methylation drives the hormone-dependent phenotype of breast cancer27
Population study of the gut microbiome: associations with diet, lifestyle, and cardiometabolic disease27
Single-cell multimodal analysis identifies common regulatory programs in synovial fibroblasts of rheumatoid arthritis patients and modeled TNF-driven arthritis27
The colorectal cancer-associated faecal microbiome of developing countries resembles that of developed countries26
X-CNV: genome-wide prediction of the pathogenicity of copy number variations26
The vaginal microbiota and innate immunity after local excisional treatment for cervical intraepithelial neoplasia26
Genetic variation in the Middle East—an opportunity to advance the human genetics field26
Cryopreservation of human cancers conserves tumour heterogeneity for single-cell multi-omics analysis26
Comprehensive genomic and tumour immune profiling reveals potential therapeutic targets in malignant pleural mesothelioma26
Refining epigenetic prediction of chronological and biological age26
A lepidic gene signature predicts patient prognosis and sensitivity to immunotherapy in lung adenocarcinoma26