Genome Medicine

Papers
(The TQCC of Genome Medicine is 24. 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 2020-12-01 to 2024-12-01.)
ArticleCitations
CADD-Splice—improving genome-wide variant effect prediction using deep learning-derived splice scores443
Deep learning in cancer diagnosis, prognosis and treatment selection404
dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs389
An introduction to spatial transcriptomics for biomedical research344
Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients203
A guide for the diagnosis of rare and undiagnosed disease: beyond the exome160
Integration of whole genome sequencing into a healthcare setting: high diagnostic rates across multiple clinical entities in 3219 rare disease patients139
Human breast microbiome correlates with prognostic features and immunological signatures in breast cancer135
IFN-γ and TNF-α drive a CXCL10+ CCL2+ macrophage phenotype expanded in severe COVID-19 lungs and inflammatory diseases with tissue inflammation132
Integrated analysis of single-cell and bulk RNA sequencing data reveals a pan-cancer stemness signature predicting immunotherapy response125
Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression120
Clinical trial design in the era of precision medicine120
DeepProg: an ensemble of deep-learning and machine-learning models for prognosis prediction using multi-omics data120
The neuroimmune axis of Alzheimer’s disease118
Microglial PGC-1α protects against ischemic brain injury by suppressing neuroinflammation110
Recommendations for clinical interpretation of variants found in non-coding regions of the genome110
A Klebsiella pneumoniae ST307 outbreak clone from Germany demonstrates features of extensive drug resistance, hypermucoviscosity, and enhanced iron acquisition100
High-grade serous tubo-ovarian cancer refined with single-cell RNA sequencing: specific cell subtypes influence survival and determine molecular subtype classification99
Clinical implementation of RNA sequencing for Mendelian disease diagnostics99
Robust barcoding and identification of Mycobacterium tuberculosis lineages for epidemiological and clinical studies99
Guild-based analysis for understanding gut microbiome in human health and diseases98
Intra-host variation and evolutionary dynamics of SARS-CoV-2 populations in COVID-19 patients95
CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes93
Polygenic risk scores in the clinic: new perspectives needed on familiar ethical issues92
Dietary fiber intake, the gut microbiome, and chronic systemic inflammation in a cohort of adult men90
Role of the intestinal microbiome and microbial-derived metabolites in immune checkpoint blockade immunotherapy of cancer90
Single-nucleus transcriptome analysis of human brain immune response in patients with severe COVID-1984
Mobilization of the nonconjugative virulence plasmid from hypervirulent Klebsiella pneumoniae79
Hepatocellular carcinoma patients with high circulating cytotoxic T cells and intra-tumoral immune signature benefit from pembrolizumab: results from a single-arm phase 2 trial78
Improved analysis of CRISPR fitness screens and reduced off-target effects with the BAGEL2 gene essentiality classifier76
A community-driven resource for genomic epidemiology and antimicrobial resistance prediction of Neisseria gonorrhoeae at Pathogenwatch76
Clinical laboratory test-wide association scan of polygenic scores identifies biomarkers of complex disease75
Single-cell characterization of macrophages in glioblastoma reveals MARCO as a mesenchymal pro-tumor marker72
PRMT1-mediated H4R3me2a recruits SMARCA4 to promote colorectal cancer progression by enhancing EGFR signaling71
5′-tRF-GlyGCC: a tRNA-derived small RNA as a novel biomarker for colorectal cancer diagnosis65
Artificial intelligence enables comprehensive genome interpretation and nomination of candidate diagnoses for rare genetic diseases65
Distinct transcriptional programs stratify ovarian cancer cell lines into the five major histological subtypes64
The complexities of the diet-microbiome relationship: advances and perspectives63
Development and validation of a trans-ancestry polygenic risk score for type 2 diabetes in diverse populations60
Rare deleterious mutations of HNRNP genes result in shared neurodevelopmental disorders60
Human reference gut microbiome catalog including newly assembled genomes from under-represented Asian metagenomes59
Epigenetic signatures in cancer: proper controls, current challenges and the potential for clinical translation59
Microbiota restoration reduces antibiotic-resistant bacteria gut colonization in patients with recurrent Clostridioides difficile infection from the open-label PUNCH CD study58
Explaining decisions of graph convolutional neural networks: patient-specific molecular subnetworks responsible for metastasis prediction in breast cancer58
Single-cell genomic and transcriptomic landscapes of primary and metastatic colorectal cancer tumors58
Pervasive generation of non-canonical subgenomic RNAs by SARS-CoV-256
The effects of the Green-Mediterranean diet on cardiometabolic health are linked to gut microbiome modifications: a randomized controlled trial55
Molecular profiling of advanced malignancies guides first-line N-of-1 treatments in the I-PREDICT treatment-naïve study55
Genetic diversity and characteristics of high-level tigecycline resistance Tet(X) in Acinetobacter species55
Identification of novel protein biomarkers and drug targets for colorectal cancer by integrating human plasma proteome with genome53
MetaRNN: differentiating rare pathogenic and rare benign missense SNVs and InDels using deep learning53
Tumor microenvironment remodeling after neoadjuvant immunotherapy in non-small cell lung cancer revealed by single-cell RNA sequencing53
Whole-genome sequencing with long reads reveals complex structure and origin of structural variation in human genetic variations and somatic mutations in cancer52
Gut microbial determinants of clinically important improvement in patients with rheumatoid arthritis51
Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants50
Deconvolution of cell type-specific drug responses in human tumor tissue with single-cell RNA-seq49
Unsupervised spatially embedded deep representation of spatial transcriptomics48
Single-cell profiling of human dura and meningioma reveals cellular meningeal landscape and insights into meningioma immune response47
PLCG2 is associated with the inflammatory response and is induced by amyloid plaques in Alzheimer’s disease45
Exploiting genomics to mitigate the public health impact of antimicrobial resistance44
Rare variant analysis of 4241 pulmonary arterial hypertension cases from an international consortium implicates FBLN2, PDGFD, and rare de novo variants in PAH44
Ten-year longitudinal molecular epidemiology study of Escherichia coli and Klebsiella species bloodstream infections in Oxfordshire, UK44
Metabolic control by the microbiome44
Maternal and early life exposures and their potential to influence development of the microbiome44
ClinGen Variant Curation Interface: a variant classification platform for the application of evidence criteria from ACMG/AMP guidelines43
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
ClinSV: clinical grade structural and copy number variant detection from whole genome sequencing data43
Improved prediction of fracture risk leveraging a genome-wide polygenic risk score42
Maintenance of the human memory T cell repertoire by subset and tissue site42
Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India41
Evaluating the potential for respiratory metagenomics to improve treatment of secondary infection and detection of nosocomial transmission on expanded COVID-19 intensive care units41
Gut microbiota predicts body fat change following a low-energy diet: a PREVIEW intervention study41
Interaction of bacterial genera associated with therapeutic response to immune checkpoint PD-1 blockade in a United States cohort41
Optimized polyepitope neoantigen DNA vaccines elicit neoantigen-specific immune responses in preclinical models and in clinical translation40
An atlas connecting shared genetic architecture of human diseases and molecular phenotypes provides insight into COVID-19 susceptibility40
Editing GWAS: experimental approaches to dissect and exploit disease-associated genetic variation40
The gut microbiota in multiple sclerosis varies with disease activity40
Clinical implications of host genetic variation and susceptibility to severe or critical COVID-1939
Implementing genomic screening in diverse populations39
Multi-site tumor sampling highlights molecular intra-tumor heterogeneity in malignant pleural mesothelioma39
The global dissemination of hospital clones of Enterococcus faecium39
Highly elevated polygenic risk scores are better predictors of myocardial infarction risk early in life than later39
Integrating single-cell sequencing data with GWAS summary statistics reveals CD16+monocytes and memory CD8+T cells involved in severe COVID-1939
Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-1938
Demonstrating trustworthiness when collecting and sharing genomic data: public views across 22 countries38
Single-cell multimodal analysis identifies common regulatory programs in synovial fibroblasts of rheumatoid arthritis patients and modeled TNF-driven arthritis38
Phylogroup stability contrasts with high within sequence type complex dynamics of Escherichia coli bloodstream infection isolates over a 12-year period38
Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq data37
Mendelian randomization analysis of 37 clinical factors and coronary artery disease in East Asian and European populations37
Single-cell transcriptomics reveals common epithelial response patterns in human acute kidney injury37
A global overview of genetically interpretable multimorbidities among common diseases in the UK Biobank37
Human liver single nucleus and single cell RNA sequencing identify a hepatocellular carcinoma-associated cell-type affecting survival37
Drivers of methicillin-resistant Staphylococcus aureus (MRSA) lineage replacement in China36
Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections36
Refining epigenetic prediction of chronological and biological age36
GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning36
Genome-scale CRISPR screens identify host factors that promote human coronavirus infection36
A transcriptome-wide association study of Alzheimer’s disease using prediction models of relevant tissues identifies novel candidate susceptibility genes36
Identification of epigenome-wide DNA methylation differences between carriers of APOE ε4 and APOE ε2 alleles35
Whole-genome sequencing as an investigational device for return of hereditary disease risk and pharmacogenomic results as part of the All of Us Research Program35
Phenome-wide investigation of the causal associations between childhood BMI and adult trait outcomes: a two-sample Mendelian randomization study34
Congruent microbiome signatures in fibrosis-prone autoimmune diseases: IgG4-related disease and systemic sclerosis34
Single-cell transcriptomics reveal a unique memory-like NK cell subset that accumulates with ageing and correlates with disease severity in COVID-1933
Tumor fraction-guided cell-free DNA profiling in metastatic solid tumor patients33
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 study33
Variation in targetable genomic alterations in non-small cell lung cancer by genetic ancestry, sex, smoking history, and histology33
An implementation science approach to evaluating pathogen whole genome sequencing in public health33
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 study32
Population study of the gut microbiome: associations with diet, lifestyle, and cardiometabolic disease32
Trans-ethnic gut microbial signatures of prediabetic subjects from India and Denmark32
A mutation-based gene set predicts survival benefit after immunotherapy across multiple cancers and reveals the immune response landscape32
Cryopreservation of human cancers conserves tumour heterogeneity for single-cell multi-omics analysis31
Genetic and functional interaction network analysis reveals global enrichment of regulatory T cell genes influencing basal cell carcinoma susceptibility31
Bacteroides vulgatus and Bacteroides dorei predict immune-related adverse events in immune checkpoint blockade treatment of metastatic melanoma31
Multi-tissue neocortical transcriptome-wide association study implicates 8 genes across 6 genomic loci in Alzheimer’s disease31
Crosstalk between microRNA expression and DNA methylation drives the hormone-dependent phenotype of breast cancer31
Single-cell RNA transcriptome analysis of CNS immune cells reveals CXCL16/CXCR6 as maintenance factors for tissue-resident T cells that drive synapse elimination31
Applications of long-read sequencing to Mendelian genetics31
Prospective high-throughput genome profiling of advanced cancers: results of the PERMED-01 clinical trial31
Evaluating the transcriptional fidelity of cancer models31
ESBL plasmids in Klebsiella pneumoniae: diversity, transmission and contribution to infection burden in the hospital setting31
Emergence and evolution of antimicrobial resistance genes and mutations in Neisseria gonorrhoeae30
An international policy on returning genomic research results30
X-CNV: genome-wide prediction of the pathogenicity of copy number variations29
Molecular profiling of human non-small cell lung cancer by single-cell RNA-seq29
DevKidCC allows for robust classification and direct comparisons of kidney organoid datasets29
A lepidic gene signature predicts patient prognosis and sensitivity to immunotherapy in lung adenocarcinoma29
Extracellular matrix profiles determine risk and prognosis of the squamous cell carcinoma subtype of non-small cell lung carcinoma29
The vaginal microbiota and innate immunity after local excisional treatment for cervical intraepithelial neoplasia29
Comprehensive genomic and tumour immune profiling reveals potential therapeutic targets in malignant pleural mesothelioma29
Predicting heterogeneity in clone-specific therapeutic vulnerabilities using single-cell transcriptomic signatures28
Identification of a cytokine-dominated immunosuppressive class in squamous cell lung carcinoma with implications for immunotherapy resistance28
The colorectal cancer-associated faecal microbiome of developing countries resembles that of developed countries28
Calorie restriction improves metabolic state independently of gut microbiome composition: a randomized dietary intervention trial27
Spatial transcriptomics analysis of neoadjuvant cabozantinib and nivolumab in advanced hepatocellular carcinoma identifies independent mechanisms of resistance and recurrence27
Cell type-specific changes identified by single-cell transcriptomics in Alzheimer’s disease27
Landscape and selection of vaccine epitopes in SARS-CoV-227
Large-scale genomic analysis of global Klebsiella pneumoniae plasmids reveals multiple simultaneous clusters of carbapenem-resistant hypervirulent strains27
Multi-omics colocalization with genome-wide association studies reveals a context-specific genetic mechanism at a childhood onset asthma risk locus26
Integrative statistical analyses of multiple liquid biopsy analytes in metastatic breast cancer26
Breast cancer risks associated with missense variants in breast cancer susceptibility genes26
Constructing germline research cohorts from the discarded reads of clinical tumor sequences26
scGRNom: a computational pipeline of integrative multi-omics analyses for predicting cell-type disease genes and regulatory networks26
Epigenome-wide association study of kidney function identifies trans-ethnic and ethnic-specific loci26
Identification of TBX15 as an adipose master trans regulator of abdominal obesity genes25
Mode and dynamics of vanA-type vancomycin resistance dissemination in Dutch hospitals25
Rapid molecular diagnostics of tuberculosis resistance by targeted stool sequencing25
Genome-wide sequencing as a first-tier screening test for short tandem repeat expansions25
A dynamic single cell-based framework for digital twins to prioritize disease genes and drug targets25
Genetic variation in the Middle East—an opportunity to advance the human genetics field24
Advancing precision public health using human genomics: examples from the field and future research opportunities24
Patient and provider perspectives on polygenic risk scores: implications for clinical reporting and utilization24
The transcriptional landscape and biomarker potential of circular RNAs in prostate cancer24
Targeting CDC7 potentiates ATR-CHK1 signaling inhibition through induction of DNA replication stress in liver cancer24
The genetic case for cardiorespiratory fitness as a clinical vital sign and the routine prescription of physical activity in healthcare24
Reanalysis of exome negative patients with rare disease: a pragmatic workflow for diagnostic applications24
Destination shapes antibiotic resistance gene acquisitions, abundance increases, and diversity changes in Dutch travelers24
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