Anindya Dutta University of Virginia School of Medicine Charlottesville,VA
1 protocol

Teressa Paulsen University of Virginia School of Medicine Charlottesville,VA
1 protocol

Shekhar Saha Shekhar Saha
1 protocol

Zhangli Su University of Virginia School of Medicine Charlottesville,VA
1 protocol

Pankaj Kumar
  • Faculty, University of Virginia School of Medicine Charlottesville,VA
Research focus
  • I use computational methods to make novel biological discoveries about the regulation of gene expression in cancers from genomic and transcriptomic data generated by big consortia like The Cancer Genome Atlas (TCGA), Encyclopedia of DNA elements (ENCODE), The Genotype-Tissue Expression (GTEx), etc. Our unbiased approach to analyzing high-throughput small RNA sequencing data resulted in the discovery of a
    new class of small RNAs called transfer RNA fragments (tRFs) (Kumar et al. BMC Biol. 2014; Kumar et al., Nucleic Acids Res. 2015; Kumar et al., Trends Biochem Sci. 2016; Kuscu et al., RNA 2018, Su et al., Annual
    Review of Genetics 2020). I use techniques like PAR-CLIP, CLASH and Sylamer analysis, CDF plot, etc. to understand the regulation by tRFs. My ongoing aim is to understand the role of tRF in gene regulation. My
    bioinformatics expertise has also been instrumental in the discovery of a new class of extra-chromosomal circular DNA (eccDNA, a.k.a. microDNA). I was the lead author on the paper that reported the use of paired-end
    high-throughput sequencing method to identify circular DNA in the normal mammalian tissue and cell lines (Shibata/Kumar et al., Science 2012; Dillon/Kumar et al., Cell Rep 2015; Paulsen et al., Trends Genet. 2018; Kumar et al., Science Advances 2020). I am also the developer of the Circle_finder algorithm pipeline that has been used by our lab as well as other research labs across the world for detecting the eccDNA from any paired-end high-throughput sequencing data. I have published twenty papers on genomics. I have fifteen years of experience in genomics. I am the Bioinformatics core director at UVA and have handled a diverse array of omics data (genomics, transcriptomics, proteomics, etc.) and have vast experience in analyzing data generated by high-throughput methods.
  • 1 Author merit
1 Protocol published
ATAC-Seq-based Identification of Extrachromosomal Circular DNA in Mammalian Cells and Its Validation Using Inverse PCR and FISH
Authors:  Zhangli Su, Shekhar Saha, Teressa Paulsen, Pankaj Kumar and Anindya Dutta, date: 05/05/2021, view: 686, Q&A: 0

Recent studies from multiple labs including ours have demonstrated the importance of extrachromosomal circular DNA (eccDNA) from yeast to humans (Shibata et al., 2012; Dillon et al., 2015; Møller et al., 2016; Kumar et al., 2017; Turner et

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