OOIR: Observatory of International Research

Papers

(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 2020-07-01 to 2024-07-01.)

Article	Citations
CADD-Splice—improving genome-wide variant effect prediction using deep learning-derived splice scores	392
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 glycoprotein	366
dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs	328
Deep learning in cancer diagnosis, prognosis and treatment selection	314
An introduction to spatial transcriptomics for biomedical research	251
Best practices for variant calling in clinical sequencing	195
Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients	191
Understanding the impact of antibiotic perturbation on the human microbiome	167
Single-cell transcriptome analysis of tumor and stromal compartments of pancreatic ductal adenocarcinoma primary tumors and metastatic lesions	141
Integration of whole genome sequencing into a healthcare setting: high diagnostic rates across multiple clinical entities in 3219 rare disease patients	130
IFN-γ and TNF-α drive a CXCL10+ CCL2+ macrophage phenotype expanded in severe COVID-19 lungs and inflammatory diseases with tissue inflammation	128
A guide for the diagnosis of rare and undiagnosed disease: beyond the exome	126
Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression	116
Human breast microbiome correlates with prognostic features and immunological signatures in breast cancer	112
FOXC1-mediated LINC00301 facilitates tumor progression and triggers an immune-suppressing microenvironment in non-small cell lung cancer by regulating the HIF1α pathway	110
DeepProg: an ensemble of deep-learning and machine-learning models for prognosis prediction using multi-omics data	107
Microglial PGC-1α protects against ischemic brain injury by suppressing neuroinflammation	98
Integrated analysis of microbiome and host transcriptome reveals correlations between gut microbiota and clinical outcomes in HBV-related hepatocellular carcinoma	97
A Klebsiella pneumoniae ST307 outbreak clone from Germany demonstrates features of extensive drug resistance, hypermucoviscosity, and enhanced iron acquisition	94
Integrated analysis of single-cell and bulk RNA sequencing data reveals a pan-cancer stemness signature predicting immunotherapy response	94
Clinical trial design in the era of precision medicine	92
CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes	91
Clinical implementation of RNA sequencing for Mendelian disease diagnostics	91
Intra-host variation and evolutionary dynamics of SARS-CoV-2 populations in COVID-19 patients	89
Robust barcoding and identification of Mycobacterium tuberculosis lineages for epidemiological and clinical studies	88

Guild-based analysis for understanding gut microbiome in human health and diseases	88
Polygenic risk scores in the clinic: new perspectives needed on familiar ethical issues	85
The neuroimmune axis of Alzheimer’s disease	84
Role of the intestinal microbiome and microbial-derived metabolites in immune checkpoint blockade immunotherapy of cancer	84
High-grade serous tubo-ovarian cancer refined with single-cell RNA sequencing: specific cell subtypes influence survival and determine molecular subtype classification	84
Single-nucleus transcriptome analysis of human brain immune response in patients with severe COVID-19	84
Small-molecule MMP2/MMP9 inhibitor SB-3CT modulates tumor immune surveillance by regulating PD-L1	82
Strain-level epidemiology of microbial communities and the human microbiome	78
Recommendations for clinical interpretation of variants found in non-coding regions of the genome	77
Dietary fiber intake, the gut microbiome, and chronic systemic inflammation in a cohort of adult men	72
The murine Microenvironment Cell Population counter method to estimate abundance of tissue-infiltrating immune and stromal cell populations in murine samples using gene expression	71
Sequence-based prediction of SARS-CoV-2 vaccine targets using a mass spectrometry-based bioinformatics predictor identifies immunogenic T cell epitopes	70
A community-driven resource for genomic epidemiology and antimicrobial resistance prediction of Neisseria gonorrhoeae at Pathogenwatch	69
Mitochondrial DNA copy number can influence mortality and cardiovascular disease via methylation of nuclear DNA CpGs	68
Mobilization of the nonconjugative virulence plasmid from hypervirulent Klebsiella pneumoniae	68
Hepatocellular carcinoma patients with high circulating cytotoxic T cells and intra-tumoral immune signature benefit from pembrolizumab: results from a single-arm phase 2 trial	67
Single-cell characterization of macrophages in glioblastoma reveals MARCO as a mesenchymal pro-tumor marker	67
PRMT1-mediated H4R3me2a recruits SMARCA4 to promote colorectal cancer progression by enhancing EGFR signaling	66
Microbial signature in IgE-mediated food allergies	66
Improved analysis of CRISPR fitness screens and reduced off-target effects with the BAGEL2 gene essentiality classifier	64
The complexities of the diet-microbiome relationship: advances and perspectives	62
5′-tRF-GlyGCC: a tRNA-derived small RNA as a novel biomarker for colorectal cancer diagnosis	62
The landscape of host genetic factors involved in immune response to common viral infections	62
Clinical laboratory test-wide association scan of polygenic scores identifies biomarkers of complex disease	61
Artificial intelligence enables comprehensive genome interpretation and nomination of candidate diagnoses for rare genetic diseases	60
Somalier: rapid relatedness estimation for cancer and germline studies using efficient genome sketches	57
Population genomics and antimicrobial resistance in Corynebacterium diphtheriae	57
Distinct transcriptional programs stratify ovarian cancer cell lines into the five major histological subtypes	56
Rare deleterious mutations of HNRNP genes result in shared neurodevelopmental disorders	55
Development and validation of a trans-ancestry polygenic risk score for type 2 diabetes in diverse populations	55
Human reference gut microbiome catalog including newly assembled genomes from under-represented Asian metagenomes	55
Explaining decisions of graph convolutional neural networks: patient-specific molecular subnetworks responsible for metastasis prediction in breast cancer	54
The effects of the Green-Mediterranean diet on cardiometabolic health are linked to gut microbiome modifications: a randomized controlled trial	53
Pervasive generation of non-canonical subgenomic RNAs by SARS-CoV-2	53
MDR M. tuberculosis outbreak clone in Eswatini missed by Xpert has elevated bedaquiline resistance dated to the pre-treatment era	53
Microbiota restoration reduces antibiotic-resistant bacteria gut colonization in patients with recurrent Clostridioides difficile infection from the open-label PUNCH CD study	52
Molecular profiling of advanced malignancies guides first-line N-of-1 treatments in the I-PREDICT treatment-naïve study	51
Cord blood DNA methylome in newborns later diagnosed with autism spectrum disorder reflects early dysregulation of neurodevelopmental and X-linked genes	48
Epigenetic signatures in cancer: proper controls, current challenges and the potential for clinical translation	47
Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants	46
Gut microbial determinants of clinically important improvement in patients with rheumatoid arthritis	46
Genetic diversity and characteristics of high-level tigecycline resistance Tet(X) in Acinetobacter species	46
Whole-genome sequencing with long reads reveals complex structure and origin of structural variation in human genetic variations and somatic mutations in cancer	45
Deconvolution of cell type-specific drug responses in human tumor tissue with single-cell RNA-seq	44
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 transcription	43
DNA methylation and body mass index from birth to adolescence: meta-analyses of epigenome-wide association studies	42
Single-cell genomic and transcriptomic landscapes of primary and metastatic colorectal cancer tumors	42
Ten-year longitudinal molecular epidemiology study of Escherichia coli and Klebsiella species bloodstream infections in Oxfordshire, UK	41
Single-cell profiling of human dura and meningioma reveals cellular meningeal landscape and insights into meningioma immune response	40
Identification of new driver and passenger mutations within APOBEC-induced hotspot mutations in bladder cancer	40

MetaRNN: differentiating rare pathogenic and rare benign missense SNVs and InDels using deep learning	40
Rare variant analysis of 4241 pulmonary arterial hypertension cases from an international consortium implicates FBLN2, PDGFD, and rare de novo variants in PAH	40
Maintenance of the human memory T cell repertoire by subset and tissue site	39
PLCG2 is associated with the inflammatory response and is induced by amyloid plaques in Alzheimer’s disease	39
ClinSV: clinical grade structural and copy number variant detection from whole genome sequencing data	39
Improved prediction of fracture risk leveraging a genome-wide polygenic risk score	39
Optimized polyepitope neoantigen DNA vaccines elicit neoantigen-specific immune responses in preclinical models and in clinical translation	38
An atlas connecting shared genetic architecture of human diseases and molecular phenotypes provides insight into COVID-19 susceptibility	38
The global dissemination of hospital clones of Enterococcus faecium	38
Implementing genomic screening in diverse populations	38
Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India	38
Tumor microenvironment remodeling after neoadjuvant immunotherapy in non-small cell lung cancer revealed by single-cell RNA sequencing	38
Metabolic control by the microbiome	37
Characterization of the dual functional effects of heat shock proteins (HSPs) in cancer hallmarks to aid development of HSP inhibitors	37
Interaction of bacterial genera associated with therapeutic response to immune checkpoint PD-1 blockade in a United States cohort	37
ClinGen Variant Curation Interface: a variant classification platform for the application of evidence criteria from ACMG/AMP guidelines	37
Highly elevated polygenic risk scores are better predictors of myocardial infarction risk early in life than later	37
Detection of ctDNA in plasma of patients with clinically localised prostate cancer is associated with rapid disease progression	37
Maternal and early life exposures and their potential to influence development of the microbiome	37
ASXL3 bridges BRD4 to BAP1 complex and governs enhancer activity in small cell lung cancer	37
Gut microbiota predicts body fat change following a low-energy diet: a PREVIEW intervention study	36
Multi-site tumor sampling highlights molecular intra-tumor heterogeneity in malignant pleural mesothelioma	36
Editing GWAS: experimental approaches to dissect and exploit disease-associated genetic variation	36
Evaluating the potential for respiratory metagenomics to improve treatment of secondary infection and detection of nosocomial transmission on expanded COVID-19 intensive care units	36
Drivers of methicillin-resistant Staphylococcus aureus (MRSA) lineage replacement in China	36
Demonstrating trustworthiness when collecting and sharing genomic data: public views across 22 countries	36
Phylogroup stability contrasts with high within sequence type complex dynamics of Escherichia coli bloodstream infection isolates over a 12-year period	35
The gut microbiota in multiple sclerosis varies with disease activity	35
A population-based gene expression signature of molecular clock phase from a single epidermal sample	35
Exploiting genomics to mitigate the public health impact of antimicrobial resistance	35
Angiosarcoma heterogeneity and potential therapeutic vulnerability to immune checkpoint blockade: insights from genomic sequencing	35
Molecular correlates and therapeutic targets in T cell-inflamed versus non-T cell-inflamed tumors across cancer types	34
Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq data	33
GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning	33
A global overview of genetically interpretable multimorbidities among common diseases in the UK Biobank	33
Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections	33
A mutation-based gene set predicts survival benefit after immunotherapy across multiple cancers and reveals the immune response landscape	32
The aging mouse microbiome has obesogenic characteristics	32
Genome-scale CRISPR screens identify host factors that promote human coronavirus infection	32
Mendelian randomization analysis of 37 clinical factors and coronary artery disease in East Asian and European populations	32
Human liver single nucleus and single cell RNA sequencing identify a hepatocellular carcinoma-associated cell-type affecting survival	32
CAPICE: a computational method for Consequence-Agnostic Pathogenicity Interpretation of Clinical Exome variations	32
Genotype imputation and variability in polygenic risk score estimation	32
Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults	32
A single early-in-life antibiotic course increases susceptibility to DSS-induced colitis	32
Whole-genome sequencing as an investigational device for return of hereditary disease risk and pharmacogenomic results as part of the All of Us Research Program	31
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 study	31
Trans-ethnic gut microbial signatures of prediabetic subjects from India and Denmark	31
Clinical implications of host genetic variation and susceptibility to severe or critical COVID-19	31
An implementation science approach to evaluating pathogen whole genome sequencing in public health	30
An international policy on returning genomic research results	30
DNA methylation signature in blood mirrors successful weight-loss during lifestyle interventions: the CENTRAL trial	30
Refining epigenetic prediction of chronological and biological age	30
Epigenomics and transcriptomics of systemic sclerosis CD4+ T cells reveal long-range dysregulation of key inflammatory pathways mediated by disease-associated susceptibility loci	30
A transcriptome-wide association study of Alzheimer’s disease using prediction models of relevant tissues identifies novel candidate susceptibility genes	30
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 study	29
Evaluating the transcriptional fidelity of cancer models	29
Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19	29
Variation in targetable genomic alterations in non-small cell lung cancer by genetic ancestry, sex, smoking history, and histology	28
Single-cell transcriptomics reveals common epithelial response patterns in human acute kidney injury	28
Identification of epigenome-wide DNA methylation differences between carriers of APOE ε4 and APOE ε2 alleles	28
Crosstalk between microRNA expression and DNA methylation drives the hormone-dependent phenotype of breast cancer	28
Bacteroides vulgatus and Bacteroides dorei predict immune-related adverse events in immune checkpoint blockade treatment of metastatic melanoma	28
A lepidic gene signature predicts patient prognosis and sensitivity to immunotherapy in lung adenocarcinoma	28
The colorectal cancer-associated faecal microbiome of developing countries resembles that of developed countries	27
Cryopreservation of human cancers conserves tumour heterogeneity for single-cell multi-omics analysis	27
Comprehensive genomic and tumour immune profiling reveals potential therapeutic targets in malignant pleural mesothelioma	27
Population study of the gut microbiome: associations with diet, lifestyle, and cardiometabolic disease	27
Tumor fraction-guided cell-free DNA profiling in metastatic solid tumor patients	27
Integrating single-cell sequencing data with GWAS summary statistics reveals CD16+monocytes and memory CD8+T cells involved in severe COVID-19	27
Single-cell multimodal analysis identifies common regulatory programs in synovial fibroblasts of rheumatoid arthritis patients and modeled TNF-driven arthritis	27
The vaginal microbiota and innate immunity after local excisional treatment for cervical intraepithelial neoplasia	27
X-CNV: genome-wide prediction of the pathogenicity of copy number variations	26
Emergence and evolution of antimicrobial resistance genes and mutations in Neisseria gonorrhoeae	26
Molecular profiling of human non-small cell lung cancer by single-cell RNA-seq	26
Genetic variation in the Middle East—an opportunity to advance the human genetics field	26