OOIR: Observatory of International Research

Papers

(The TQCC of Genome Medicine is 27. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 500 papers]. The publications cover those that have been published in the past four years, i.e., from 2019-09-01 to 2023-09-01.)

Article	Citations
Polygenic risk scores: from research tools to clinical instruments	509
Large-scale public data reuse to model immunotherapy response and resistance	377
Molecular profiling for precision cancer therapies	335
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	329
CADD-Splice—improving genome-wide variant effect prediction using deep learning-derived splice scores	268
Genomics of circadian rhythms in health and disease	245
dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs	232
Recommendations for application of the functional evidence PS3/BS3 criterion using the ACMG/AMP sequence variant interpretation framework	228
Deep learning in cancer diagnosis, prognosis and treatment selection	174
Artificial intelligence in clinical and genomic diagnostics	161
Tracking cancer progression: from circulating tumor cells to metastasis	160
Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients	158
Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from South and Southeast Asia	143
Understanding the impact of antibiotic perturbation on the human microbiome	124
Best practices for variant calling in clinical sequencing	123
Digital twins to personalize medicine	117
Relating the gut metagenome and metatranscriptome to immunotherapy responses in melanoma patients	109
Single-cell transcriptome analysis of tumor and stromal compartments of pancreatic ductal adenocarcinoma primary tumors and metastatic lesions	106
IFN-γ and TNF-α drive a CXCL10+ CCL2+ macrophage phenotype expanded in severe COVID-19 lungs and inflammatory diseases with tissue inflammation	93
An introduction to spatial transcriptomics for biomedical research	92
Multiple approaches for massively parallel sequencing of SARS-CoV-2 genomes directly from clinical samples	91
Single-cell RNA sequencing reveals the tumor microenvironment and facilitates strategic choices to circumvent treatment failure in a chemorefractory bladder cancer patient	86
FOXC1-mediated LINC00301 facilitates tumor progression and triggers an immune-suppressing microenvironment in non-small cell lung cancer by regulating the HIF1α pathway	86
Integration of whole genome sequencing into a healthcare setting: high diagnostic rates across multiple clinical entities in 3219 rare disease patients	82
Single-cell transcriptome analysis reveals TOX as a promoting factor for T cell exhaustion and a predictor for anti-PD-1 responses in human cancer	80

CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes	80
Human breast microbiome correlates with prognostic features and immunological signatures in breast cancer	79
Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression	78
Intra-host variation and evolutionary dynamics of SARS-CoV-2 populations in COVID-19 patients	74
From cytogenetics to cytogenomics: whole-genome sequencing as a first-line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability	72
Epigenome-wide meta-analysis of blood DNA methylation in newborns and children identifies numerous loci related to gestational age	72
Guild-based analysis for understanding gut microbiome in human health and diseases	68
Novel risk genes and mechanisms implicated by exome sequencing of 2572 individuals with pulmonary arterial hypertension	68
Is ‘likely pathogenic’ really 90% likely? Reclassification data in ClinVar	67
Integrated analysis of microbiome and host transcriptome reveals correlations between gut microbiota and clinical outcomes in HBV-related hepatocellular carcinoma	65
Neoantigens and genome instability: impact on immunogenomic phenotypes and immunotherapy response	64
Sequence-based prediction of SARS-CoV-2 vaccine targets using a mass spectrometry-based bioinformatics predictor identifies immunogenic T cell epitopes	64
DeepProg: an ensemble of deep-learning and machine-learning models for prognosis prediction using multi-omics data	63
Interactions between the gut microbiome and host gene regulation in cystic fibrosis	63
A Klebsiella pneumoniae ST307 outbreak clone from Germany demonstrates features of extensive drug resistance, hypermucoviscosity, and enhanced iron acquisition	63
Strain-level epidemiology of microbial communities and the human microbiome	63
Polygenic risk scores in the clinic: new perspectives needed on familiar ethical issues	62
Single-nucleus transcriptome analysis of human brain immune response in patients with severe COVID-19	61
Microglial PGC-1α protects against ischemic brain injury by suppressing neuroinflammation	61
Low coverage whole genome sequencing enables accurate assessment of common variants and calculation of genome-wide polygenic scores	60
Role of the intestinal microbiome and microbial-derived metabolites in immune checkpoint blockade immunotherapy of cancer	60
Small-molecule MMP2/MMP9 inhibitor SB-3CT modulates tumor immune surveillance by regulating PD-L1	59
Robust barcoding and identification of Mycobacterium tuberculosis lineages for epidemiological and clinical studies	58
Comprehensive characterization of cell-free tumor DNA in plasma and urine of patients with renal tumors	58
A guide for the diagnosis of rare and undiagnosed disease: beyond the exome	58
Clinical and molecular characterization of virus-positive and virus-negative Merkel cell carcinoma	58
Exome sequencing reveals a high prevalence of BRCA1 and BRCA2 founder variants in a diverse population-based biobank	55
Burden of tumor mutations, neoepitopes, and other variants are weak predictors of cancer immunotherapy response and overall survival	53
MHC-I genotype and tumor mutational burden predict response to immunotherapy	52
Transcriptome analysis and functional characterization of cerebral organoids in bipolar disorder	51
The landscape of host genetic factors involved in immune response to common viral infections	50
The complexities of the diet-microbiome relationship: advances and perspectives	50
A community-driven resource for genomic epidemiology and antimicrobial resistance prediction of Neisseria gonorrhoeae at Pathogenwatch	50
Mitochondrial DNA copy number can influence mortality and cardiovascular disease via methylation of nuclear DNA CpGs	48
Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential	48
An epigenome-wide association study of sex-specific chronological ageing	48
Phylogenetically informative mutations in genes implicated in antibiotic resistance in Mycobacterium tuberculosis complex	47
Clinical implementation of RNA sequencing for Mendelian disease diagnostics	47
Improved analysis of CRISPR fitness screens and reduced off-target effects with the BAGEL2 gene essentiality classifier	47
Inflammatory cytokines and organ dysfunction associate with the aberrant DNA methylome of monocytes in sepsis	47
High-grade serous tubo-ovarian cancer refined with single-cell RNA sequencing: specific cell subtypes influence survival and determine molecular subtype classification	46
Advances in omics-based methods to identify novel targets for malaria and other parasitic protozoan infections	46
Translating insights from neuropsychiatric genetics and genomics for precision psychiatry	46
The murine Microenvironment Cell Population counter method to estimate abundance of tissue-infiltrating immune and stromal cell populations in murine samples using gene expression	46
Re-analysis of whole-exome sequencing data uncovers novel diagnostic variants and improves molecular diagnostic yields for sudden death and idiopathic diseases	46
5′-tRF-GlyGCC: a tRNA-derived small RNA as a novel biomarker for colorectal cancer diagnosis	45
Pervasive generation of non-canonical subgenomic RNAs by SARS-CoV-2	45
Dietary fiber intake, the gut microbiome, and chronic systemic inflammation in a cohort of adult men	44
Discovery of CD80 and CD86 as recent activation markers on regulatory T cells by protein-RNA single-cell analysis	43
Single-cell characterization of macrophages in glioblastoma reveals MARCO as a mesenchymal pro-tumor marker	41

Microbiota restoration reduces antibiotic-resistant bacteria gut colonization in patients with recurrent Clostridioides difficile infection from the open-label PUNCH CD study	40
Mobilization of the nonconjugative virulence plasmid from hypervirulent Klebsiella pneumoniae	40
A comparison of epigenetic mitotic-like clocks for cancer risk prediction	40
Microbial signature in IgE-mediated food allergies	40
Rare deleterious mutations of HNRNP genes result in shared neurodevelopmental disorders	40
Genetic diversity and characteristics of high-level tigecycline resistance Tet(X) in Acinetobacter species	39
Cord blood DNA methylome in newborns later diagnosed with autism spectrum disorder reflects early dysregulation of neurodevelopmental and X-linked genes	39
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	38
Recommendations for the collection and use of multiplexed functional data for clinical variant interpretation	38
PRMT1-mediated H4R3me2a recruits SMARCA4 to promote colorectal cancer progression by enhancing EGFR signaling	37
A KHDC3L mutation resulting in recurrent hydatidiform mole causes genome-wide DNA methylation loss in oocytes and persistent imprinting defects post-fertilisation	37
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	37
Epigenetic signatures in cancer: proper controls, current challenges and the potential for clinical translation	36
Integrated analysis of single-cell and bulk RNA sequencing data reveals a pan-cancer stemness signature predicting immunotherapy response	35
Gut microbial determinants of clinically important improvement in patients with rheumatoid arthritis	35
Distinct transcriptional programs stratify ovarian cancer cell lines into the five major histological subtypes	35
A highly sensitive and specific workflow for detecting rare copy-number variants from exome sequencing data	35
Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants	35
Recommendations for clinical interpretation of variants found in non-coding regions of the genome	34
Towards a European health research and innovation cloud (HRIC)	34
Stepwise evolution and convergent recombination underlie the global dissemination of carbapenemase-producing Escherichia coli	34
Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale	34
MDR M. tuberculosis outbreak clone in Eswatini missed by Xpert has elevated bedaquiline resistance dated to the pre-treatment era	34
pTuneos: prioritizing tumor neoantigens from next-generation sequencing data	34
Artificial intelligence enables comprehensive genome interpretation and nomination of candidate diagnoses for rare genetic diseases	33
Somalier: rapid relatedness estimation for cancer and germline studies using efficient genome sketches	33
DNA methylation and body mass index from birth to adolescence: meta-analyses of epigenome-wide association studies	33
Explaining decisions of graph convolutional neural networks: patient-specific molecular subnetworks responsible for metastasis prediction in breast cancer	33
The Medical Genome Initiative: moving whole-genome sequencing for rare disease diagnosis to the clinic	33
Epigenetic deregulation of lamina-associated domains in Hutchinson-Gilford progeria syndrome	33
Clinical laboratory test-wide association scan of polygenic scores identifies biomarkers of complex disease	33
Human reference gut microbiome catalog including newly assembled genomes from under-represented Asian metagenomes	33
Gene family information facilitates variant interpretation and identification of disease-associated genes in neurodevelopmental disorders	33
Neoantigen-specific immunity in low mutation burden colorectal cancers of the consensus molecular subtype 4	33
The effects of the Green-Mediterranean diet on cardiometabolic health are linked to gut microbiome modifications: a randomized controlled trial	33
Population genomics and antimicrobial resistance in Corynebacterium diphtheriae	33
A proactive genotype-to-patient-phenotype map for cystathionine beta-synthase	32
Phylogroup stability contrasts with high within sequence type complex dynamics of Escherichia coli bloodstream infection isolates over a 12-year period	31
Whole-genome sequencing with long reads reveals complex structure and origin of structural variation in human genetic variations and somatic mutations in cancer	31
Long non-coding RNAs identify a subset of luminal muscle-invasive bladder cancer patients with favorable prognosis	31
Text-mining clinically relevant cancer biomarkers for curation into the CIViC database	31
Identification of new driver and passenger mutations within APOBEC-induced hotspot mutations in bladder cancer	31
Comparative analysis of functional assay evidence use by ClinGen Variant Curation Expert Panels	30
De novo variants in exomes of congenital heart disease patients identify risk genes and pathways	30
A single early-in-life antibiotic course increases susceptibility to DSS-induced colitis	30
Detection of ctDNA in plasma of patients with clinically localised prostate cancer is associated with rapid disease progression	30
Rare variant analysis of 4241 pulmonary arterial hypertension cases from an international consortium implicates FBLN2, PDGFD, and rare de novo variants in PAH	29
ASXL3 bridges BRD4 to BAP1 complex and governs enhancer activity in small cell lung cancer	29
Implementing genomic screening in diverse populations	29
Demonstrating trustworthiness when collecting and sharing genomic data: public views across 22 countries	29
Deconvolution of cell type-specific drug responses in human tumor tissue with single-cell RNA-seq	29
ClinSV: clinical grade structural and copy number variant detection from whole genome sequencing data	29
Dissecting the genetic basis of comorbid epilepsy phenotypes in neurodevelopmental disorders	28
Fecal microbiota transplantation in gastrointestinal disorders: time for precision medicine	28
cfNOMe — A single assay for comprehensive epigenetic analyses of cell-free DNA	28
An atlas connecting shared genetic architecture of human diseases and molecular phenotypes provides insight into COVID-19 susceptibility	28
A chromosomal connectome for psychiatric and metabolic risk variants in adult dopaminergic neurons	28
Optimized polyepitope neoantigen DNA vaccines elicit neoantigen-specific immune responses in preclinical models and in clinical translation	28
Improved prediction of fracture risk leveraging a genome-wide polygenic risk score	27
Maintenance of the human memory T cell repertoire by subset and tissue site	27
Trans-ethnic gut microbial signatures of prediabetic subjects from India and Denmark	27
Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India	27