Ryan E. Mills
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View article: A personalized multi‐platform assessment of somatic mosaicism in the human frontal cortex
A personalized multi‐platform assessment of somatic mosaicism in the human frontal cortex Open
Background Somatic mutations in individual cells lead to genomic mosaicism, contributing to the intricate regulatory landscape of genetic disorders and cancers. To evaluate and refine the detection of somatic mosaicism across different tec…
View article: Structural and transduction patterns of human-specific polymorphic SVA insertions
Structural and transduction patterns of human-specific polymorphic SVA insertions Open
Background SINE variable number tandem repeat Alu elements (SVAs) are a unique group of hominid-specific composite retrotransposons with highly variable internal structure. They represent the youngest TE family in humans and contribute to …
View article: Multi-platform framework for mapping somatic retrotransposition in human tissues
Multi-platform framework for mapping somatic retrotransposition in human tissues Open
Mobile element insertions (MEI) shape the human genome in both germline and somatic tissues. While inherited MEIs are well characterized, mapping somatic MEIs (sMEI) in non-cancer tissues remains challenging due to their low allelic fracti…
View article: Genomic Signatures of Poor Prognosis in Merkel Cell Carcinoma: A Single-Institution Prospective Study
Genomic Signatures of Poor Prognosis in Merkel Cell Carcinoma: A Single-Institution Prospective Study Open
Merkel cell carcinoma (MCC) is an aggressive disease with poor survival outcomes and increasing incidence. There is a clear and present need for enhanced understanding of cellular mechanisms of tumorigenesis, validation of robust genetic s…
View article: Domain-specific embeddings uncover latent genetics knowledge
Domain-specific embeddings uncover latent genetics knowledge Open
The inundating rate of scientific publishing means every researcher will miss new discoveries from overwhelming saturation. To address this limitation, we employ natural language processing to overcome human limitations in reading, curatio…
View article: A personalized multi-platform assessment of somatic mosaicism in the human frontal cortex
A personalized multi-platform assessment of somatic mosaicism in the human frontal cortex Open
Somatic mutations in individual cells create genomic mosaicism, influencing genetic disorders and cancers. While clonal mutations in cancers are well-studied, rarer somatic variants in normal tissues remain poorly characterized. This study…
View article: Nuclear mitochondrial DNA insertions are prevalent in the human brain and accumulate over time in fibroblasts
Nuclear mitochondrial DNA insertions are prevalent in the human brain and accumulate over time in fibroblasts Open
Background The transfer of mitochondrial DNA into the nuclear genomes of eukaryotes (Numts) has been linked to lifespan in non‐human species and recently demonstrated to occur in rare instances from one human generation to the next. Method…
View article: Long Noncoding RNAs Expressed in Mouse Pituitary Development and Mature Hormone-Producing Cells
Long Noncoding RNAs Expressed in Mouse Pituitary Development and Mature Hormone-Producing Cells Open
Mammalian genomes contain thousands of genes for long noncoding RNA (lncRNAs), some of which have been shown to affect protein coding gene expression through diverse mechanisms. The lncRNA transcripts are longer than 200 nucleotides and ar…
View article: Complex genetic variation in nearly complete human genomes
Complex genetic variation in nearly complete human genomes Open
Diverse sets of complete human genomes are required to construct a pangenome reference and to understand the extent of complex structural variation. Here, we sequence 65 diverse human genomes and build 130 haplotype-resolved assemblies (13…
View article: Somatic nuclear mitochondrial DNA insertions are prevalent in the human brain and accumulate over time in fibroblasts
Somatic nuclear mitochondrial DNA insertions are prevalent in the human brain and accumulate over time in fibroblasts Open
The transfer of mitochondrial DNA into the nuclear genomes of eukaryotes (Numts) has been linked to lifespan in nonhuman species and recently demonstrated to occur in rare instances from one human generation to the next. Here, we investiga…
View article: Genomic data resources of the Brain Somatic Mosaicism Network for neuropsychiatric diseases
Genomic data resources of the Brain Somatic Mosaicism Network for neuropsychiatric diseases Open
Somatic mosaicism is defined as an occurrence of two or more populations of cells having genomic sequences differing at given loci in an individual who is derived from a single zygote. It is a characteristic of multicellular organisms that…
View article: Candida albicans selection for human commensalism results in substantial within-host diversity without decreasing fitness for invasive disease
Candida albicans selection for human commensalism results in substantial within-host diversity without decreasing fitness for invasive disease Open
Candida albicans is a frequent colonizer of human mucosal surfaces as well as an opportunistic pathogen. C . albicans is remarkably versatile in its ability to colonize diverse host sites with differences in oxygen and nutrient availabilit…
View article: Supplementary table 6 from Early HPV ctDNA Kinetics and Imaging Biomarkers Predict Therapeutic Response in p16+ Oropharyngeal Squamous Cell Carcinoma
Supplementary table 6 from Early HPV ctDNA Kinetics and Imaging Biomarkers Predict Therapeutic Response in p16+ Oropharyngeal Squamous Cell Carcinoma Open
Detailed summary of HPV16 genome somatic INDELs identified by targeted capture sequencing analysis of FFPE tumor specimens
View article: Data from Early HPV ctDNA Kinetics and Imaging Biomarkers Predict Therapeutic Response in p16+ Oropharyngeal Squamous Cell Carcinoma
Data from Early HPV ctDNA Kinetics and Imaging Biomarkers Predict Therapeutic Response in p16+ Oropharyngeal Squamous Cell Carcinoma Open
Purpose:In locally advanced p16+ oropharyngeal squamous cell carcinoma (OPSCC), (i) to investigate kinetics of human papillomavirus (HPV) circulating tumor DNA (ctDNA) and association with tumor progression after chemoradiation, and (ii) t…
View article: Supplementary figure and table legends from Early HPV ctDNA Kinetics and Imaging Biomarkers Predict Therapeutic Response in p16+ Oropharyngeal Squamous Cell Carcinoma
Supplementary figure and table legends from Early HPV ctDNA Kinetics and Imaging Biomarkers Predict Therapeutic Response in p16+ Oropharyngeal Squamous Cell Carcinoma Open
Legends for supplementary figure and tables
View article: Supplementary table 7 from Early HPV ctDNA Kinetics and Imaging Biomarkers Predict Therapeutic Response in p16+ Oropharyngeal Squamous Cell Carcinoma
Supplementary table 7 from Early HPV ctDNA Kinetics and Imaging Biomarkers Predict Therapeutic Response in p16+ Oropharyngeal Squamous Cell Carcinoma Open
Detailed summary of HPV to host genome integration sites identified by targeted capture sequencing analysis of FFPE tumor specimens
View article: Supplementary table 2 from Early HPV ctDNA Kinetics and Imaging Biomarkers Predict Therapeutic Response in p16+ Oropharyngeal Squamous Cell Carcinoma
Supplementary table 2 from Early HPV ctDNA Kinetics and Imaging Biomarkers Predict Therapeutic Response in p16+ Oropharyngeal Squamous Cell Carcinoma Open
Next generation sequencing quality control data, HPViewer read counts and somatic alteration burden
View article: Supplementary table 7 from Early HPV ctDNA Kinetics and Imaging Biomarkers Predict Therapeutic Response in p16+ Oropharyngeal Squamous Cell Carcinoma
Supplementary table 7 from Early HPV ctDNA Kinetics and Imaging Biomarkers Predict Therapeutic Response in p16+ Oropharyngeal Squamous Cell Carcinoma Open
Detailed summary of HPV to host genome integration sites identified by targeted capture sequencing analysis of FFPE tumor specimens
View article: Supplementary table 4 from Early HPV ctDNA Kinetics and Imaging Biomarkers Predict Therapeutic Response in p16+ Oropharyngeal Squamous Cell Carcinoma
Supplementary table 4 from Early HPV ctDNA Kinetics and Imaging Biomarkers Predict Therapeutic Response in p16+ Oropharyngeal Squamous Cell Carcinoma Open
Detailed summary of host genome somatic INDELs identified by targeted capture sequencing analysis of FFPE tumor specimens
View article: Supplementary table 2 from Early HPV ctDNA Kinetics and Imaging Biomarkers Predict Therapeutic Response in p16+ Oropharyngeal Squamous Cell Carcinoma
Supplementary table 2 from Early HPV ctDNA Kinetics and Imaging Biomarkers Predict Therapeutic Response in p16+ Oropharyngeal Squamous Cell Carcinoma Open
Next generation sequencing quality control data, HPViewer read counts and somatic alteration burden
View article: Supplementary table 6 from Early HPV ctDNA Kinetics and Imaging Biomarkers Predict Therapeutic Response in p16+ Oropharyngeal Squamous Cell Carcinoma
Supplementary table 6 from Early HPV ctDNA Kinetics and Imaging Biomarkers Predict Therapeutic Response in p16+ Oropharyngeal Squamous Cell Carcinoma Open
Detailed summary of HPV16 genome somatic INDELs identified by targeted capture sequencing analysis of FFPE tumor specimens
View article: Data from Early HPV ctDNA Kinetics and Imaging Biomarkers Predict Therapeutic Response in p16+ Oropharyngeal Squamous Cell Carcinoma
Data from Early HPV ctDNA Kinetics and Imaging Biomarkers Predict Therapeutic Response in p16+ Oropharyngeal Squamous Cell Carcinoma Open
Purpose:In locally advanced p16+ oropharyngeal squamous cell carcinoma (OPSCC), (i) to investigate kinetics of human papillomavirus (HPV) circulating tumor DNA (ctDNA) and association with tumor progression after chemoradiation, and (ii) t…
View article: Supplementary table 3 from Early HPV ctDNA Kinetics and Imaging Biomarkers Predict Therapeutic Response in p16+ Oropharyngeal Squamous Cell Carcinoma
Supplementary table 3 from Early HPV ctDNA Kinetics and Imaging Biomarkers Predict Therapeutic Response in p16+ Oropharyngeal Squamous Cell Carcinoma Open
Detailed summary of host genome somatic single nucleotide variations identified by targeted capture sequencing analysis of FFPE tumor specimens
View article: Supplementary table 5 from Early HPV ctDNA Kinetics and Imaging Biomarkers Predict Therapeutic Response in p16+ Oropharyngeal Squamous Cell Carcinoma
Supplementary table 5 from Early HPV ctDNA Kinetics and Imaging Biomarkers Predict Therapeutic Response in p16+ Oropharyngeal Squamous Cell Carcinoma Open
Detailed summary of HPV16 genome somatic single nucleotide variations identified by targeted capture sequencing analysis of FFPE tumor specimens