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 2021-04-01 to 2025-04-01.)

Article	Citations
STModule: identifying tissue modules to uncover spatial components and characteristics of transcriptomic landscapes	512
The genetics and epidemiology of N- and O-immunoglobulin A glycomics	434
Neoantigen DNA vaccines are safe, feasible, and induce neoantigen-specific immune responses in triple-negative breast cancer patients	195
Multi-omics uncovers immune-modulatory molecules in plasma contributing to resistance exercise-ameliorated locomotor disability after incomplete spinal cord injury	162
Integrating pharmacogenomics and cheminformatics with diverse disease phenotypes for cell type-guided drug discovery	157
Destination shapes antibiotic resistance gene acquisitions, abundance increases, and diversity changes in Dutch travelers	154
Inter-species geographic signatures for tracing horizontal gene transfer and long-term persistence of carbapenem resistance	152
Comprehensive genomic and tumour immune profiling reveals potential therapeutic targets in malignant pleural mesothelioma	149
Spatial transcriptome profiling identifies DTX3L and BST2 as key biomarkers in esophageal squamous cell carcinoma tumorigenesis	143
Demonstrating trustworthiness when collecting and sharing genomic data: public views across 22 countries	131
Circulating bacterial signature is linked to metabolic disease and shifts with metabolic alleviation after bariatric surgery	117
An atlas connecting shared genetic architecture of human diseases and molecular phenotypes provides insight into COVID-19 susceptibility	114
Systems pharmacogenomics identifies novel targets and clinically actionable therapeutics for medulloblastoma	114
Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants	108
Non-cancer-related pathogenic germline variants and expression consequences in ten-thousand cancer genomes	101
Whole genome sequencing-based classification of human-related Haemophilus species and detection of antimicrobial resistance genes	98
Single-cell exome sequencing reveals multiple subclones in metastatic colorectal carcinoma	96
Landscape and selection of vaccine epitopes in SARS-CoV-2	92
Identification of a cytokine-dominated immunosuppressive class in squamous cell lung carcinoma with implications for immunotherapy resistance	92
Single-nucleus transcriptome analysis of human brain immune response in patients with severe COVID-19	91
A mixture model for signature discovery from sparse mutation data	89
Transcriptomic perspectives of memory-like NK cells and aging	88
African-specific alleles modify risk for asthma at the 17q12-q21 locus in African Americans	87
The role of genetic testing in diagnosis and care of inherited cardiac conditions in a specialised multidisciplinary clinic	85
Loss of Y in leukocytes as a risk factor for critical COVID-19 in men	79

Pervasiveness of HLA allele-specific expression loss across tumor types	79
Clinical utility of periodic reinterpretation of CNVs of uncertain significance: an 8-year retrospective study	79
ReporTree: a surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data	74
A machine learning classifier using 33 host immune response mRNAs accurately distinguishes viral and non-viral acute respiratory illnesses in nasal swab samples	72
Combining optical genome mapping and RNA-seq for structural variants detection and interpretation in unsolved neurodevelopmental disorders	70
Curating genomic disease-gene relationships with Gene2Phenotype (G2P)	66
Circular RNA landscape in extracellular vesicles from human biofluids	66
In vivo genome editing in mouse restores dystrophin expression in Duchenne muscular dystrophy patient muscle fibers	63
Germline HLA-B evolutionary divergence influences the efficacy of immune checkpoint blockade therapy in gastrointestinal cancer	60
Untargeted metabolomic profiling reveals molecular signatures associated with type 2 diabetes in Nigerians	60
The exceptions that prove the rule—a historical view of bedaquiline susceptibility	57
Leveraging new methods for comprehensive characterization of mitochondrial DNA in esophageal squamous cell carcinoma	57
Genome sequencing as a generic diagnostic strategy for rare disease	56
Meta-analysis identifies common gut microbiota associated with multiple sclerosis	55
Rare subclonal sequencing of breast cancers indicates putative metastatic driver mutations are predominately acquired after dissemination	55
ENU-based dominant genetic screen identifies contractile and neuronal gene mutations in congenital heart disease	54
A validated heart-specific model for splice-disrupting variants in childhood heart disease	54
Variability of polygenic prediction for body mass index in Africa	54
PheSeq, a Bayesian deep learning model to enhance and interpret the gene-disease association studies	53
Using multiplexed functional data to reduce variant classification inequities in underrepresented populations	53
Analysis of admixed Greenlandic siblings shows that the mean genotypic values for metabolic phenotypes differ between Inuit and Europeans	52
Knockout mice with pituitary malformations help identify human cases of hypopituitarism	52
Leveraging genomic diversity for discovery in an electronic health record linked biobank: the UCLA ATLAS Community Health Initiative	51
Epigenetic age and long-term cancer risk following a stroke	51
Long-read sequencing identifies a common transposition haplotype predisposing for CLCNKB deletions	50
ClinPrior: an algorithm for diagnosis and novel gene discovery by network-based prioritization	50
Identification of specific susceptibility loci for the early-onset colorectal cancer	50
Systematic genomic analysis of SARS-CoV-2 co-infections throughout the pandemic and segregation of the strains involved	50
Towards elucidating disease-relevant states of neurons and glia by CRISPR-based functional genomics	50
Polygenic risk scores for disease risk prediction in Africa: current challenges and future directions	49
The role of admixture in the rare variant contribution to inflammatory bowel disease	48
Loss of p53-DREAM-mediated repression of cell cycle genes as a driver of lymph node metastasis in head and neck cancer	48
Systematic analysis of Mendelian disease-associated gene variants reveals new classes of cancer-predisposing genes	47
The impact of damaging epilepsy and cardiac genetic variant burden in sudden death in the young	47
Author Correction: Leveraging genomic diversity for discovery in an electronic health record linked biobank: the UCLA ATLAS Community Health Initiative	46
Correction: Applicability of epigenetic age models to next-generation methylation arrays	45
Long-read sequencing reveals the landscape of aberrant alternative splicing and novel therapeutic target in colorectal cancer	45
Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections	45
Beyond the exome: utility of long-read whole genome sequencing in exome-negative autosomal recessive diseases	44
Return of non-ACMG recommended incidental genetic findings to pediatric patients: considerations and opportunities from experiences in genomic sequencing	44
Targeting CDC7 potentiates ATR-CHK1 signaling inhibition through induction of DNA replication stress in liver cancer	43
Early detection of hepatocellular carcinoma via no end-repair enzymatic methylation sequencing of cell-free DNA and pre-trained neural network	42
Annotation of cell types (ACT): a convenient web server for cell type annotation	42
Diversity of CFTR variants across ancestries characterized using 454,727 UK biobank whole exome sequences	41
A dynamic single cell-based framework for digital twins to prioritize disease genes and drug targets	41
Optimizing Nanopore sequencing-based detection of structural variants enables individualized circulating tumor DNA-based disease monitoring in cancer patients	40
Automated prioritization of sick newborns for whole genome sequencing using clinical natural language processing and machine learning	40
Metabolic control by the microbiome	40
GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning	40
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	40

Genome-aware annotation of CRISPR guides validates targets in variant cell lines and enhances discovery in screens	40
Single-molecule methylation profiles of cell-free DNA in cancer with nanopore sequencing	39
Intricate interplay of CRISPR-Cas systems, anti-CRISPR proteins, and antimicrobial resistance genes in a globally successful multi-drug resistant Klebsiella pneumoniae clone	39
Antiprogestins reduce epigenetic field cancerization in breast tissue of young healthy women	39
Acute ischemia induces spatially and transcriptionally distinct microglial subclusters	39
Correction: Intricate interplay of CRISPR-Cas systems, anti-CRISPR proteins, and antimicrobial resistance genes in a globally successful multi-drug resistant Klebsiella pneumoniae clone	39
A guide for the diagnosis of rare and undiagnosed disease: beyond the exome	38
Epigenome-wide association study of kidney function identifies trans-ethnic and ethnic-specific loci	38
The gut microbiota in multiple sclerosis varies with disease activity	37
The genomic landscape of rare disorders in the Middle East	37
Machine learning integrative approaches to advance computational immunology	36
Post-vaccine epidemiology of serotype 3 pneumococci identifies transformation inhibition through prophage-driven alteration of a non-coding RNA	36
Neutrophil extracellular traps have auto-catabolic activity and produce mononucleosome-associated circulating DNA	36
Deep learning in cancer genomics and histopathology	36
Prospective high-throughput genome profiling of advanced cancers: results of the PERMED-01 clinical trial	35
An introduction to spatial transcriptomics for biomedical research	35
Single-cell transcriptomics reveals common epithelial response patterns in human acute kidney injury	35
Multi-site tumor sampling highlights molecular intra-tumor heterogeneity in malignant pleural mesothelioma	35
Metatranscriptomic profiling reveals pathogen and host response signatures of pediatric acute sinusitis and upper respiratory infection	35
IFN-γ and TNF-α drive a CXCL10+ CCL2+ macrophage phenotype expanded in severe COVID-19 lungs and inflammatory diseases with tissue inflammation	35
DNA demethylation triggers cell free DNA release in colorectal cancer cells	35
Clinical evaluation of long-read sequencing-based episignature detection in developmental disorders	34
The landcape of Helicobacter pylori-mediated DNA breaks links bacterial genotoxicity to its oncogenic potential	34
A polygenic score for height identifies an unmeasured genetic predisposition among pediatric patients with idiopathic short stature	34
Mapping in silico genetic networks of the KMT2D tumour suppressor gene to uncover novel functional associations and cancer cell vulnerabilities	34
Whole genome sequencing across clinical trials identifies rare coding variants in GPR68 associated with chemotherapy-induced peripheral neuropathy	34
Correction: Rapid molecular diagnostics of tuberculosis resistance by targeted stool sequencing	33
Emerging genetic complexity and rare genetic variants in neurodegenerative brain diseases	33
Efficacy and safety of novel multiple-chain DAP-CAR-T cells targeting mesothelin in ovarian cancer and mesothelioma: a single-arm, open-label and first-in-human study	33
Correction to: Whole genome sequencing-based classifcation of human-related Haemophilus species and detection of antimicrobial resistance genes	33
Mendelian randomization and genetic colocalization infer the effects of the multi-tissue proteome on 211 complex disease-related phenotypes	32
pVACview: an interactive visualization tool for efficient neoantigen prioritization and selection	32
Long-term persistence of diverse clones shapes the transmission landscape of invasive Listeria monocytogenes	32
Somatic mutational profiles and germline polygenic risk scores in human cancer	32
Analysis of 3760 hematologic malignancies reveals rare transcriptomic aberrations of driver genes	32
Integrative epigenomic and high-throughput functional enhancer profiling reveals determinants of enhancer heterogeneity in gastric cancer	31
Genomic surveillance of multidrug-resistant organisms based on long-read sequencing	31
Patient-derived xenograft models capture genomic heterogeneity in endometrial cancer	31
Novel temporal and spatial patterns of metastatic colonization from breast cancer rapid-autopsy tumor biopsies	31
Rare deleterious mutations of HNRNP genes result in shared neurodevelopmental disorders	31
A global cancer data integrator reveals principles of synthetic lethality, sex disparity and immunotherapy	30
Human liver single nucleus and single cell RNA sequencing identify a hepatocellular carcinoma-associated cell-type affecting survival	30
Genome-wide analyses of multiple obesity-related cytokines and hormones informs biology of cardiometabolic traits	30
An epigenetic and transcriptomic signature of immune tolerance in human monocytes through multi-omics integration	30
The vaginal microbiota and innate immunity after local excisional treatment for cervical intraepithelial neoplasia	30
Evaluating the potential for respiratory metagenomics to improve treatment of secondary infection and detection of nosocomial transmission on expanded COVID-19 intensive care units	30
A pan-cancer landscape of telomeric content shows that RAD21 and HGF alterations are associated with longer telomeres	29
Evaluating the use of paralogous protein domains to increase data availability for missense variant classification	29
Constructing germline research cohorts from the discarded reads of clinical tumor sequences	29
Publisher Correction: Analysis of transcriptomic features reveals molecular endotypes of SLE with clinical implications	29
Genomic architecture of autism spectrum disorder in Qatar: The BARAKA-Qatar Study	29
CTpathway: a CrossTalk-based pathway enrichment analysis method for cancer research	28
SRT-Server: powering the analysis of spatial transcriptomic data	28
Mendelian gene identification through mouse embryo viability screening	28
Non-canonical antigens are the largest fraction of peptides presented by MHC class I in mismatch repair deficient murine colorectal cancer	28
The emergence of highly resistant and hypervirulent Klebsiella pneumoniae CC14 clone in a tertiary hospital over 8 years	28
De novo identification of expressed cancer somatic mutations from single-cell RNA sequencing data	28
The multiple de novo copy number variant (MdnCNV) phenomenon presents with peri-zygotic DNA mutational signatures and multilocus pathogenic variation	27
Ancestry-driven metabolite variation provides insights into disease states in admixed populations	27
Novel genetic markers for chronic kidney disease in a geographically isolated population of Indigenous Australians: Individual and multiple phenotype genome-wide association study	27
ACT-Discover: identifying karyotype heterogeneity in pancreatic cancer evolution using ctDNA	27
Universal clinical Parkinson’s disease axes identify a major influence of neuroinflammation	27
Prostate cancers with distinct transcriptional programs in Black and White men	27
Mechanistic insights into the interactions between cancer drivers and the tumour immune microenvironment	27
Intra-prostatic tumour evolution, steps in metastatic spread and histogenomic associations revealed by integration of multi-region whole-genome sequencing with histopathological features	27
An atlas of cell-type-specific interactome networks across 44 human tumor types	27
Smoking-associated gene expression alterations in nasal epithelium reveal immune impairment linked to lung cancer risk	26
Nanopore-based random genomic sampling for intraoperative molecular diagnosis	26
Interaction of bacterial genera associated with therapeutic response to immune checkpoint PD-1 blockade in a United States cohort	26
Spatial intra-tumour heterogeneity and treatment-induced genomic evolution in oesophageal adenocarcinoma: implications for prognosis and therapy	26
SenPred: a single-cell RNA sequencing-based machine learning pipeline to classify deeply senescent dermal fibroblast cells for the detection of an in vivo senescent cell burden	26
Combined exome and transcriptome sequencing of non-muscle-invasive bladder cancer: associations between genomic changes, expression subtypes, and clinical outcomes	26
INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance	26
Spatial multi-omics: novel tools to study the complexity of cardiovascular diseases	26