Sara Javadzadeh
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View article: Analysis of targeted and whole genome sequencing of PacBio HiFi reads for a comprehensive genotyping of gene-proximal and phenotype-associated Variable Number Tandem Repeats
Analysis of targeted and whole genome sequencing of PacBio HiFi reads for a comprehensive genotyping of gene-proximal and phenotype-associated Variable Number Tandem Repeats Open
Variable Number Tandem repeats (VNTRs) refer to repeating motifs of size greater than five bp. VNTRs are an important source of genetic variation, and have been associated with multiple Mendelian and complex phenotypes. However, the highly…
View article: Inhibition of human-HPV hybrid ecDNA enhancers reduces oncogene expression and tumor growth in oropharyngeal cancer
Inhibition of human-HPV hybrid ecDNA enhancers reduces oncogene expression and tumor growth in oropharyngeal cancer Open
Extrachromosomal circular DNA (ecDNA) has been found in most types of human cancers, and ecDNA incorporating viral genomes has recently been described, specifically in human papillomavirus (HPV)-mediated oropharyngeal cancer (OPC). However…
View article: Inhibition of novel human-HPV hybrid ecDNA enhancers reduces oncogene expression and tumor growth in oropharyngeal cancer
Inhibition of novel human-HPV hybrid ecDNA enhancers reduces oncogene expression and tumor growth in oropharyngeal cancer Open
View article: LongTR: genome-wide profiling of genetic variation at tandem repeats from long reads
LongTR: genome-wide profiling of genetic variation at tandem repeats from long reads Open
Tandem repeats are frequent across the human genome, and variation in repeat length has been linked to a variety of traits. Recent improvements in long read sequencing technologies have the potential to greatly improve tandem repeat analys…
View article: Genome-wide profiling of genetic variation at tandem repeat from long reads
Genome-wide profiling of genetic variation at tandem repeat from long reads Open
Tandem repeats are frequent across the human genome, and variation in repeat length has been linked to a variety of traits. Recent improvements in long read sequencing technologies have the potential to greatly improve TR analysis, especia…
View article: A deep population reference panel of tandem repeat variation
A deep population reference panel of tandem repeat variation Open
Tandem repeats (TRs) represent one of the largest sources of genetic variation in humans and are implicated in a range of phenotypes. Here we present a deep characterization of TR variation based on high coverage whole genome sequencing fr…
View article: A deep population reference panel of tandem repeat variation
A deep population reference panel of tandem repeat variation Open
Tandem repeats (TRs) represent one of the largest sources of genetic variation in humans and are implicated in a range of phenotypes. Here we present a deep characterization of TR variation based on high coverage whole genome sequencing fr…
View article: DeepViFi
DeepViFi Open
We consider the problem of identifying viral reads in human host genome data. We pose the problem as open-set classification as reads can originate from unknown sources such as bacterial and fungal genomes. Sequence-matching methods have l…
View article: FastViFi: Fast and accurate detection of (Hybrid) Viral DNA and RNA
FastViFi: Fast and accurate detection of (Hybrid) Viral DNA and RNA Open
DNA viruses are important infectious agents known to mediate a large number of human diseases, including cancer. Viral integration into the host genome and the formation of hybrid transcripts are also associated with increased pathogenicit…
View article: Sparse Binary Relation Representations for Genome Graph Annotation
Sparse Binary Relation Representations for Genome Graph Annotation Open
High-throughput DNA sequencing data are accumulating in public repositories, and efficient approaches for storing and indexing such data are in high demand. In recent research, several graph data structures have been proposed to represent …
View article: Sparse Binary Relation Representations for Genome Graph Annotation
Sparse Binary Relation Representations for Genome Graph Annotation Open
High-throughput DNA sequencing data is accumulating in public repositories, and efficient approaches for storing and indexing such data are in high demand. In recent research, several graph data structures have been proposed to represent l…