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 2020-11-01 to 2024-11-01.)

Article	Citations
CADD-Splice—improving genome-wide variant effect prediction using deep learning-derived splice scores	443
Deep learning in cancer diagnosis, prognosis and treatment selection	404
dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs	389
An introduction to spatial transcriptomics for biomedical research	344
Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients	203
A guide for the diagnosis of rare and undiagnosed disease: beyond the exome	160
Integration of whole genome sequencing into a healthcare setting: high diagnostic rates across multiple clinical entities in 3219 rare disease patients	139
Human breast microbiome correlates with prognostic features and immunological signatures in breast cancer	135
IFN-γ and TNF-α drive a CXCL10+ CCL2+ macrophage phenotype expanded in severe COVID-19 lungs and inflammatory diseases with tissue inflammation	132
Integrated analysis of single-cell and bulk RNA sequencing data reveals a pan-cancer stemness signature predicting immunotherapy response	125
Clinical trial design in the era of precision medicine	120
DeepProg: an ensemble of deep-learning and machine-learning models for prognosis prediction using multi-omics data	120
Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression	120
The neuroimmune axis of Alzheimer’s disease	118
Recommendations for clinical interpretation of variants found in non-coding regions of the genome	110
Microglial PGC-1α protects against ischemic brain injury by suppressing neuroinflammation	110
Integrated analysis of microbiome and host transcriptome reveals correlations between gut microbiota and clinical outcomes in HBV-related hepatocellular carcinoma	105
A Klebsiella pneumoniae ST307 outbreak clone from Germany demonstrates features of extensive drug resistance, hypermucoviscosity, and enhanced iron acquisition	100
Robust barcoding and identification of Mycobacterium tuberculosis lineages for epidemiological and clinical studies	99
High-grade serous tubo-ovarian cancer refined with single-cell RNA sequencing: specific cell subtypes influence survival and determine molecular subtype classification	99
Clinical implementation of RNA sequencing for Mendelian disease diagnostics	99
Guild-based analysis for understanding gut microbiome in human health and diseases	98
Intra-host variation and evolutionary dynamics of SARS-CoV-2 populations in COVID-19 patients	95
CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes	93
Polygenic risk scores in the clinic: new perspectives needed on familiar ethical issues	92

Dietary fiber intake, the gut microbiome, and chronic systemic inflammation in a cohort of adult men	90
Role of the intestinal microbiome and microbial-derived metabolites in immune checkpoint blockade immunotherapy of cancer	90
Single-nucleus transcriptome analysis of human brain immune response in patients with severe COVID-19	84
Mobilization of the nonconjugative virulence plasmid from hypervirulent Klebsiella pneumoniae	79
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	78
A community-driven resource for genomic epidemiology and antimicrobial resistance prediction of Neisseria gonorrhoeae at Pathogenwatch	76
Improved analysis of CRISPR fitness screens and reduced off-target effects with the BAGEL2 gene essentiality classifier	76
Clinical laboratory test-wide association scan of polygenic scores identifies biomarkers of complex disease	75
Single-cell characterization of macrophages in glioblastoma reveals MARCO as a mesenchymal pro-tumor marker	72
PRMT1-mediated H4R3me2a recruits SMARCA4 to promote colorectal cancer progression by enhancing EGFR signaling	71
Artificial intelligence enables comprehensive genome interpretation and nomination of candidate diagnoses for rare genetic diseases	65
5′-tRF-GlyGCC: a tRNA-derived small RNA as a novel biomarker for colorectal cancer diagnosis	65
Distinct transcriptional programs stratify ovarian cancer cell lines into the five major histological subtypes	64
The complexities of the diet-microbiome relationship: advances and perspectives	63
Population genomics and antimicrobial resistance in Corynebacterium diphtheriae	63
Development and validation of a trans-ancestry polygenic risk score for type 2 diabetes in diverse populations	60
Rare deleterious mutations of HNRNP genes result in shared neurodevelopmental disorders	60
Human reference gut microbiome catalog including newly assembled genomes from under-represented Asian metagenomes	59
Epigenetic signatures in cancer: proper controls, current challenges and the potential for clinical translation	59
Microbiota restoration reduces antibiotic-resistant bacteria gut colonization in patients with recurrent Clostridioides difficile infection from the open-label PUNCH CD study	58
Single-cell genomic and transcriptomic landscapes of primary and metastatic colorectal cancer tumors	58
Explaining decisions of graph convolutional neural networks: patient-specific molecular subnetworks responsible for metastasis prediction in breast cancer	58
MDR M. tuberculosis outbreak clone in Eswatini missed by Xpert has elevated bedaquiline resistance dated to the pre-treatment era	58
Pervasive generation of non-canonical subgenomic RNAs by SARS-CoV-2	56
Molecular profiling of advanced malignancies guides first-line N-of-1 treatments in the I-PREDICT treatment-naïve study	55
The effects of the Green-Mediterranean diet on cardiometabolic health are linked to gut microbiome modifications: a randomized controlled trial	55
Genetic diversity and characteristics of high-level tigecycline resistance Tet(X) in Acinetobacter species	55
MetaRNN: differentiating rare pathogenic and rare benign missense SNVs and InDels using deep learning	53
Tumor microenvironment remodeling after neoadjuvant immunotherapy in non-small cell lung cancer revealed by single-cell RNA sequencing	53
Identification of novel protein biomarkers and drug targets for colorectal cancer by integrating human plasma proteome with genome	53
Whole-genome sequencing with long reads reveals complex structure and origin of structural variation in human genetic variations and somatic mutations in cancer	52
Gut microbial determinants of clinically important improvement in patients with rheumatoid arthritis	51
Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants	50
Deconvolution of cell type-specific drug responses in human tumor tissue with single-cell RNA-seq	49
Unsupervised spatially embedded deep representation of spatial transcriptomics	48
Single-cell profiling of human dura and meningioma reveals cellular meningeal landscape and insights into meningioma immune response	47
DNA methylation and body mass index from birth to adolescence: meta-analyses of epigenome-wide association studies	46
PLCG2 is associated with the inflammatory response and is induced by amyloid plaques in Alzheimer’s disease	45
Maternal and early life exposures and their potential to influence development of the microbiome	44
Exploiting genomics to mitigate the public health impact of antimicrobial resistance	44
Rare variant analysis of 4241 pulmonary arterial hypertension cases from an international consortium implicates FBLN2, PDGFD, and rare de novo variants in PAH	44
Ten-year longitudinal molecular epidemiology study of Escherichia coli and Klebsiella species bloodstream infections in Oxfordshire, UK	44
Metabolic control by the microbiome	44
ClinSV: clinical grade structural and copy number variant detection from whole genome sequencing data	43
ClinGen Variant Curation Interface: a variant classification platform for the application of evidence criteria from ACMG/AMP guidelines	43
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
Improved prediction of fracture risk leveraging a genome-wide polygenic risk score	42
Maintenance of the human memory T cell repertoire by subset and tissue site	42
Interaction of bacterial genera associated with therapeutic response to immune checkpoint PD-1 blockade in a United States cohort	41
Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India	41

Evaluating the potential for respiratory metagenomics to improve treatment of secondary infection and detection of nosocomial transmission on expanded COVID-19 intensive care units	41
Gut microbiota predicts body fat change following a low-energy diet: a PREVIEW intervention study	41
Editing GWAS: experimental approaches to dissect and exploit disease-associated genetic variation	40
The gut microbiota in multiple sclerosis varies with disease activity	40
Optimized polyepitope neoantigen DNA vaccines elicit neoantigen-specific immune responses in preclinical models and in clinical translation	40
An atlas connecting shared genetic architecture of human diseases and molecular phenotypes provides insight into COVID-19 susceptibility	40
The global dissemination of hospital clones of Enterococcus faecium	39
Highly elevated polygenic risk scores are better predictors of myocardial infarction risk early in life than later	39
Implementing genomic screening in diverse populations	39
Multi-site tumor sampling highlights molecular intra-tumor heterogeneity in malignant pleural mesothelioma	39
Integrating single-cell sequencing data with GWAS summary statistics reveals CD16+monocytes and memory CD8+T cells involved in severe COVID-19	39
Clinical implications of host genetic variation and susceptibility to severe or critical COVID-19	39
Single-cell multimodal analysis identifies common regulatory programs in synovial fibroblasts of rheumatoid arthritis patients and modeled TNF-driven arthritis	38
Phylogroup stability contrasts with high within sequence type complex dynamics of Escherichia coli bloodstream infection isolates over a 12-year period	38
Demonstrating trustworthiness when collecting and sharing genomic data: public views across 22 countries	38
Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19	38
Characterization of the dual functional effects of heat shock proteins (HSPs) in cancer hallmarks to aid development of HSP inhibitors	38
Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq data	37
Human liver single nucleus and single cell RNA sequencing identify a hepatocellular carcinoma-associated cell-type affecting survival	37
A global overview of genetically interpretable multimorbidities among common diseases in the UK Biobank	37
Single-cell transcriptomics reveals common epithelial response patterns in human acute kidney injury	37
Mendelian randomization analysis of 37 clinical factors and coronary artery disease in East Asian and European populations	37
Genome-scale CRISPR screens identify host factors that promote human coronavirus infection	36
A transcriptome-wide association study of Alzheimer’s disease using prediction models of relevant tissues identifies novel candidate susceptibility genes	36
Refining epigenetic prediction of chronological and biological age	36
Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections	36
Drivers of methicillin-resistant Staphylococcus aureus (MRSA) lineage replacement in China	36
GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning	36
Identification of epigenome-wide DNA methylation differences between carriers of APOE ε4 and APOE ε2 alleles	35
Genotype imputation and variability in polygenic risk score estimation	35
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	35
DNA methylation signature in blood mirrors successful weight-loss during lifestyle interventions: the CENTRAL trial	34
Phenome-wide investigation of the causal associations between childhood BMI and adult trait outcomes: a two-sample Mendelian randomization study	34
Congruent microbiome signatures in fibrosis-prone autoimmune diseases: IgG4-related disease and systemic sclerosis	34
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	33
Variation in targetable genomic alterations in non-small cell lung cancer by genetic ancestry, sex, smoking history, and histology	33
An implementation science approach to evaluating pathogen whole genome sequencing in public health	33
Single-cell transcriptomics reveal a unique memory-like NK cell subset that accumulates with ageing and correlates with disease severity in COVID-19	33
Tumor fraction-guided cell-free DNA profiling in metastatic solid tumor patients	33
Trans-ethnic gut microbial signatures of prediabetic subjects from India and Denmark	32
A mutation-based gene set predicts survival benefit after immunotherapy across multiple cancers and reveals the immune response landscape	32
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	32
Population study of the gut microbiome: associations with diet, lifestyle, and cardiometabolic disease	32
ESBL plasmids in Klebsiella pneumoniae: diversity, transmission and contribution to infection burden in the hospital setting	31
Multi-tissue neocortical transcriptome-wide association study implicates 8 genes across 6 genomic loci in Alzheimer’s disease	31
Prospective high-throughput genome profiling of advanced cancers: results of the PERMED-01 clinical trial	31
Evaluating the transcriptional fidelity of cancer models	31
Single-cell RNA transcriptome analysis of CNS immune cells reveals CXCL16/CXCR6 as maintenance factors for tissue-resident T cells that drive synapse elimination	31
Cryopreservation of human cancers conserves tumour heterogeneity for single-cell multi-omics analysis	31
Genetic and functional interaction network analysis reveals global enrichment of regulatory T cell genes influencing basal cell carcinoma susceptibility	31
Bacteroides vulgatus and Bacteroides dorei predict immune-related adverse events in immune checkpoint blockade treatment of metastatic melanoma	31
Applications of long-read sequencing to Mendelian genetics	31
Crosstalk between microRNA expression and DNA methylation drives the hormone-dependent phenotype of breast cancer	31
An international policy on returning genomic research results	30
Emergence and evolution of antimicrobial resistance genes and mutations in Neisseria gonorrhoeae	30
DevKidCC allows for robust classification and direct comparisons of kidney organoid datasets	29
Molecular profiling of human non-small cell lung cancer by single-cell RNA-seq	29
Extracellular matrix profiles determine risk and prognosis of the squamous cell carcinoma subtype of non-small cell lung carcinoma	29
The vaginal microbiota and innate immunity after local excisional treatment for cervical intraepithelial neoplasia	29
Comprehensive genomic and tumour immune profiling reveals potential therapeutic targets in malignant pleural mesothelioma	29
X-CNV: genome-wide prediction of the pathogenicity of copy number variations	29
A lepidic gene signature predicts patient prognosis and sensitivity to immunotherapy in lung adenocarcinoma	29
Identification of a cytokine-dominated immunosuppressive class in squamous cell lung carcinoma with implications for immunotherapy resistance	28
The colorectal cancer-associated faecal microbiome of developing countries resembles that of developed countries	28
Predicting heterogeneity in clone-specific therapeutic vulnerabilities using single-cell transcriptomic signatures	28
Cell type-specific changes identified by single-cell transcriptomics in Alzheimer’s disease	27
Landscape and selection of vaccine epitopes in SARS-CoV-2	27
Large-scale genomic analysis of global Klebsiella pneumoniae plasmids reveals multiple simultaneous clusters of carbapenem-resistant hypervirulent strains	27
Calorie restriction improves metabolic state independently of gut microbiome composition: a randomized dietary intervention trial	27
Spatial transcriptomics analysis of neoadjuvant cabozantinib and nivolumab in advanced hepatocellular carcinoma identifies independent mechanisms of resistance and recurrence	27
Epigenome-wide association study of kidney function identifies trans-ethnic and ethnic-specific loci	26
Multi-omics colocalization with genome-wide association studies reveals a context-specific genetic mechanism at a childhood onset asthma risk locus	26
Integrative statistical analyses of multiple liquid biopsy analytes in metastatic breast cancer	26
Single cell characterization of B-lymphoid differentiation and leukemic cell states during chemotherapy in ETV6-RUNX1-positive pediatric leukemia identifies drug-targetable transcription factor activi	26
Breast cancer risks associated with missense variants in breast cancer susceptibility genes	26
Constructing germline research cohorts from the discarded reads of clinical tumor sequences	26
scGRNom: a computational pipeline of integrative multi-omics analyses for predicting cell-type disease genes and regulatory networks	26