OOIR: Observatory of International Research

Papers

(The TQCC of Genome Medicine is 25. 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 2020-03-01 to 2024-03-01.)

Article	Citations
Polygenic risk scores: from research tools to clinical instruments	616
CADD-Splice—improving genome-wide variant effect prediction using deep learning-derived splice scores	359
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	352
dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs	284
Deep learning in cancer diagnosis, prognosis and treatment selection	261
Tracking cancer progression: from circulating tumor cells to metastasis	194
Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients	178
An introduction to spatial transcriptomics for biomedical research	177
Best practices for variant calling in clinical sequencing	166
Understanding the impact of antibiotic perturbation on the human microbiome	144
Single-cell transcriptome analysis of tumor and stromal compartments of pancreatic ductal adenocarcinoma primary tumors and metastatic lesions	127
IFN-γ and TNF-α drive a CXCL10+ CCL2+ macrophage phenotype expanded in severe COVID-19 lungs and inflammatory diseases with tissue inflammation	111
Integration of whole genome sequencing into a healthcare setting: high diagnostic rates across multiple clinical entities in 3219 rare disease patients	107
FOXC1-mediated LINC00301 facilitates tumor progression and triggers an immune-suppressing microenvironment in non-small cell lung cancer by regulating the HIF1α pathway	104
Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression	102
Single-cell RNA sequencing reveals the tumor microenvironment and facilitates strategic choices to circumvent treatment failure in a chemorefractory bladder cancer patient	101
Human breast microbiome correlates with prognostic features and immunological signatures in breast cancer	97
A guide for the diagnosis of rare and undiagnosed disease: beyond the exome	97
Multiple approaches for massively parallel sequencing of SARS-CoV-2 genomes directly from clinical samples	96
CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes	88
Microglial PGC-1α protects against ischemic brain injury by suppressing neuroinflammation	85
Integrated analysis of microbiome and host transcriptome reveals correlations between gut microbiota and clinical outcomes in HBV-related hepatocellular carcinoma	84
DeepProg: an ensemble of deep-learning and machine-learning models for prognosis prediction using multi-omics data	84
Intra-host variation and evolutionary dynamics of SARS-CoV-2 populations in COVID-19 patients	82
Guild-based analysis for understanding gut microbiome in human health and diseases	80

A Klebsiella pneumoniae ST307 outbreak clone from Germany demonstrates features of extensive drug resistance, hypermucoviscosity, and enhanced iron acquisition	80
Epigenome-wide meta-analysis of blood DNA methylation in newborns and children identifies numerous loci related to gestational age	80
Single-nucleus transcriptome analysis of human brain immune response in patients with severe COVID-19	79
Small-molecule MMP2/MMP9 inhibitor SB-3CT modulates tumor immune surveillance by regulating PD-L1	77
Polygenic risk scores in the clinic: new perspectives needed on familiar ethical issues	77
Robust barcoding and identification of Mycobacterium tuberculosis lineages for epidemiological and clinical studies	76
Strain-level epidemiology of microbial communities and the human microbiome	72
Role of the intestinal microbiome and microbial-derived metabolites in immune checkpoint blockade immunotherapy of cancer	72
Clinical implementation of RNA sequencing for Mendelian disease diagnostics	71
High-grade serous tubo-ovarian cancer refined with single-cell RNA sequencing: specific cell subtypes influence survival and determine molecular subtype classification	68
Clinical and molecular characterization of virus-positive and virus-negative Merkel cell carcinoma	68
Sequence-based prediction of SARS-CoV-2 vaccine targets using a mass spectrometry-based bioinformatics predictor identifies immunogenic T cell epitopes	67
Integrated analysis of single-cell and bulk RNA sequencing data reveals a pan-cancer stemness signature predicting immunotherapy response	67
Clinical trial design in the era of precision medicine	65
MHC-I genotype and tumor mutational burden predict response to immunotherapy	64
Mitochondrial DNA copy number can influence mortality and cardiovascular disease via methylation of nuclear DNA CpGs	63
The murine Microenvironment Cell Population counter method to estimate abundance of tissue-infiltrating immune and stromal cell populations in murine samples using gene expression	62
Dietary fiber intake, the gut microbiome, and chronic systemic inflammation in a cohort of adult men	60
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	60
Recommendations for clinical interpretation of variants found in non-coding regions of the genome	59
PRMT1-mediated H4R3me2a recruits SMARCA4 to promote colorectal cancer progression by enhancing EGFR signaling	59
Burden of tumor mutations, neoepitopes, and other variants are weak predictors of cancer immunotherapy response and overall survival	59
Mobilization of the nonconjugative virulence plasmid from hypervirulent Klebsiella pneumoniae	58
5′-tRF-GlyGCC: a tRNA-derived small RNA as a novel biomarker for colorectal cancer diagnosis	58
Transcriptome analysis and functional characterization of cerebral organoids in bipolar disorder	58
A community-driven resource for genomic epidemiology and antimicrobial resistance prediction of Neisseria gonorrhoeae at Pathogenwatch	58
Improved analysis of CRISPR fitness screens and reduced off-target effects with the BAGEL2 gene essentiality classifier	57
The complexities of the diet-microbiome relationship: advances and perspectives	57
A comparison of epigenetic mitotic-like clocks for cancer risk prediction	57
Single-cell characterization of macrophages in glioblastoma reveals MARCO as a mesenchymal pro-tumor marker	55
The landscape of host genetic factors involved in immune response to common viral infections	55
The neuroimmune axis of Alzheimer’s disease	55
Microbial signature in IgE-mediated food allergies	55
Discovery of CD80 and CD86 as recent activation markers on regulatory T cells by protein-RNA single-cell analysis	55
Phylogenetically informative mutations in genes implicated in antibiotic resistance in Mycobacterium tuberculosis complex	54
Translating insights from neuropsychiatric genetics and genomics for precision psychiatry	52
Pervasive generation of non-canonical subgenomic RNAs by SARS-CoV-2	51
Rare deleterious mutations of HNRNP genes result in shared neurodevelopmental disorders	49
MDR M. tuberculosis outbreak clone in Eswatini missed by Xpert has elevated bedaquiline resistance dated to the pre-treatment era	49
Artificial intelligence enables comprehensive genome interpretation and nomination of candidate diagnoses for rare genetic diseases	48
Distinct transcriptional programs stratify ovarian cancer cell lines into the five major histological subtypes	48
Microbiota restoration reduces antibiotic-resistant bacteria gut colonization in patients with recurrent Clostridioides difficile infection from the open-label PUNCH CD study	48
Cord blood DNA methylome in newborns later diagnosed with autism spectrum disorder reflects early dysregulation of neurodevelopmental and X-linked genes	46
Explaining decisions of graph convolutional neural networks: patient-specific molecular subnetworks responsible for metastasis prediction in breast cancer	45
The effects of the Green-Mediterranean diet on cardiometabolic health are linked to gut microbiome modifications: a randomized controlled trial	45
Human reference gut microbiome catalog including newly assembled genomes from under-represented Asian metagenomes	45
Clinical laboratory test-wide association scan of polygenic scores identifies biomarkers of complex disease	44
Genetic diversity and characteristics of high-level tigecycline resistance Tet(X) in Acinetobacter species	44
Somalier: rapid relatedness estimation for cancer and germline studies using efficient genome sketches	44
Population genomics and antimicrobial resistance in Corynebacterium diphtheriae	44

Epigenetic signatures in cancer: proper controls, current challenges and the potential for clinical translation	43
Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants	42
Gut microbial determinants of clinically important improvement in patients with rheumatoid arthritis	41
Molecular profiling of advanced malignancies guides first-line N-of-1 treatments in the I-PREDICT treatment-naïve study	41
Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale	41
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	40
Deconvolution of cell type-specific drug responses in human tumor tissue with single-cell RNA-seq	40
Epigenetic deregulation of lamina-associated domains in Hutchinson-Gilford progeria syndrome	39
Whole-genome sequencing with long reads reveals complex structure and origin of structural variation in human genetic variations and somatic mutations in cancer	39
The Medical Genome Initiative: moving whole-genome sequencing for rare disease diagnosis to the clinic	39
DNA methylation and body mass index from birth to adolescence: meta-analyses of epigenome-wide association studies	38
Development and validation of a trans-ancestry polygenic risk score for type 2 diabetes in diverse populations	38
Rare variant analysis of 4241 pulmonary arterial hypertension cases from an international consortium implicates FBLN2, PDGFD, and rare de novo variants in PAH	37
cfNOMe — A single assay for comprehensive epigenetic analyses of cell-free DNA	37
Gene family information facilitates variant interpretation and identification of disease-associated genes in neurodevelopmental disorders	37
Implementing genomic screening in diverse populations	36
Highly elevated polygenic risk scores are better predictors of myocardial infarction risk early in life than later	35
Single-cell profiling of human dura and meningioma reveals cellular meningeal landscape and insights into meningioma immune response	35
ClinSV: clinical grade structural and copy number variant detection from whole genome sequencing data	35
Phylogroup stability contrasts with high within sequence type complex dynamics of Escherichia coli bloodstream infection isolates over a 12-year period	35
Identification of new driver and passenger mutations within APOBEC-induced hotspot mutations in bladder cancer	35
PLCG2 is associated with the inflammatory response and is induced by amyloid plaques in Alzheimer’s disease	34
An atlas connecting shared genetic architecture of human diseases and molecular phenotypes provides insight into COVID-19 susceptibility	34
Ten-year longitudinal molecular epidemiology study of Escherichia coli and Klebsiella species bloodstream infections in Oxfordshire, UK	34
Improved prediction of fracture risk leveraging a genome-wide polygenic risk score	34
Maintenance of the human memory T cell repertoire by subset and tissue site	33
Evaluating the potential for respiratory metagenomics to improve treatment of secondary infection and detection of nosocomial transmission on expanded COVID-19 intensive care units	33
Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India	33
Detection of ctDNA in plasma of patients with clinically localised prostate cancer is associated with rapid disease progression	33
The global dissemination of hospital clones of Enterococcus faecium	33
ASXL3 bridges BRD4 to BAP1 complex and governs enhancer activity in small cell lung cancer	33
Demonstrating trustworthiness when collecting and sharing genomic data: public views across 22 countries	33
Optimized polyepitope neoantigen DNA vaccines elicit neoantigen-specific immune responses in preclinical models and in clinical translation	32
Ancestry-specific predisposing germline variants in cancer	32
ClinGen Variant Curation Interface: a variant classification platform for the application of evidence criteria from ACMG/AMP guidelines	32
Gut microbiota predicts body fat change following a low-energy diet: a PREVIEW intervention study	31
Angiosarcoma heterogeneity and potential therapeutic vulnerability to immune checkpoint blockade: insights from genomic sequencing	31
Widespread and tissue-specific expression of endogenous retroelements in human somatic tissues	31
A population-based gene expression signature of molecular clock phase from a single epidermal sample	31
Trans-ethnic gut microbial signatures of prediabetic subjects from India and Denmark	31
Characterization of the dual functional effects of heat shock proteins (HSPs) in cancer hallmarks to aid development of HSP inhibitors	31
Fecal microbiota transplantation in gastrointestinal disorders: time for precision medicine	31
A single early-in-life antibiotic course increases susceptibility to DSS-induced colitis	31
Drivers of methicillin-resistant Staphylococcus aureus (MRSA) lineage replacement in China	30
Editing GWAS: experimental approaches to dissect and exploit disease-associated genetic variation	30
Multi-site tumor sampling highlights molecular intra-tumor heterogeneity in malignant pleural mesothelioma	30
Maternal and early life exposures and their potential to influence development of the microbiome	30
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	29
A global overview of genetically interpretable multimorbidities among common diseases in the UK Biobank	29
CAPICE: a computational method for Consequence-Agnostic Pathogenicity Interpretation of Clinical Exome variations	29
Integrative -omics and HLA-ligandomics analysis to identify novel drug targets for ccRCC immunotherapy	28
Interaction of bacterial genera associated with therapeutic response to immune checkpoint PD-1 blockade in a United States cohort	28
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	28
Exploiting genomics to mitigate the public health impact of antimicrobial resistance	28
An international policy on returning genomic research results	28
Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults	28
Single-cell genomic and transcriptomic landscapes of primary and metastatic colorectal cancer tumors	28
The aging mouse microbiome has obesogenic characteristics	28
Metabolic control by the microbiome	28
Shallow whole-genome sequencing of plasma cell-free DNA accurately differentiates small from non-small cell lung carcinoma	27
Genotype imputation and variability in polygenic risk score estimation	27
Clinical implications of host genetic variation and susceptibility to severe or critical COVID-19	27
Exploratory analysis of age and sex dependent DNA methylation patterns on the X-chromosome in whole blood samples	26
Genetic variation in the Middle East—an opportunity to advance the human genetics field	26
Crosstalk between microRNA expression and DNA methylation drives the hormone-dependent phenotype of breast cancer	26
Epigenomics and transcriptomics of systemic sclerosis CD4+ T cells reveal long-range dysregulation of key inflammatory pathways mediated by disease-associated susceptibility loci	26
MetaRNN: differentiating rare pathogenic and rare benign missense SNVs and InDels using deep learning	26
DNA methylation signature in blood mirrors successful weight-loss during lifestyle interventions: the CENTRAL trial	26
Mendelian randomization analysis of 37 clinical factors and coronary artery disease in East Asian and European populations	26
Genome-scale CRISPR screens identify host factors that promote human coronavirus infection	25
Bacteroides vulgatus and Bacteroides dorei predict immune-related adverse events in immune checkpoint blockade treatment of metastatic melanoma	25
A mutation-based gene set predicts survival benefit after immunotherapy across multiple cancers and reveals the immune response landscape	25
The colorectal cancer-associated faecal microbiome of developing countries resembles that of developed countries	25
Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections	25
Evaluating the transcriptional fidelity of cancer models	25