Pankaj Kumar
  • Faculty, University of Virginia
Research focus
  • Systems biology
  • 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.
  • 0 Author merit

Education

PhD

Lab information

Pankaj Kumar Lab
https://bmg.med.virginia.edu/faculty/faculty-research-interests/?facbio=1&id=28747

Publications

https://www.ncbi.nlm.nih.gov/myncbi/pankaj.kumar.2/bibliography/public/
Eki R, She J, Parlak M, Benamar M, Du KP, Kumar P, Abbas T. A robust CRISPR-Cas9-based fluorescent reporter assay for the detection and quantification of DNA double-strand break repair. Nucleic Acids Res. 2020 Dec 2;48(21):e126. doi: 10.1093/nar/gkaa897. PubMed PMID: 33068408; PubMed Central PMCID: PMC7708081.

Su Z, Wilson B, Kumar P, Dutta A. Noncanonical Roles of tRNAs: tRNA Fragments and Beyond. Annu Rev Genet. 2020 Nov 23;54:47-69. doi: 10.1146/annurev-genet-022620-101840. Epub 2020 Aug 25. PubMed PMID: 32841070; PubMed Central PMCID: PMC7686126.

Simpson M, Frisbee A, Kumar P, Schwan C, Aktories K, Petri WA. Clostridioides difficile binary toxin (CDT) is recognized by the TLR2/6 heterodimer to induce an NF-κB response. J Infect Dis. 2020 Oct 3;. doi: 10.1093/infdis/jiaa620. [Epub ahead of print] PubMed PMID: 33011801.

Kumar P, Kiran S, Saha S, Su Z, Paulsen T, Chatrath A, Shibata Y, Shibata E, Dutta A. ATAC-seq identifies thousands of extrachromosomal circular DNA in cancer and cell lines. Sci Adv. 2020 May;6(20):eaba2489. doi: 10.1126/sciadv.aba2489. eCollection 2020 May. PubMed PMID: 32440553; PubMed Central PMCID: PMC7228742.

Pollack KE, Meneveau MO, Melssen MM, Lynch KT, Koeppel AF, Young SJ, Turner S, Kumar P, Sol-Church K, Mauldin IS, Slingluff CL Jr. Incomplete Freund's adjuvant reduces arginase and enhances Th1 dominance, TLR signaling and CD40 ligand expression in the vaccine site microenvironment. J Immunother Cancer. 2020 Apr;8(1). doi: 10.1136/jitc-2020-000544. PubMed PMID: 32350119; PubMed Central PMCID: PMC7213888.

Chatrath A, Przanowska R, Kiran S, Su Z, Saha S, Wilson B, Tsunematsu T, Ahn JH, Lee KY, Paulsen T, Sobierajska E, Kiran M, Tang X, Li T, Kumar P, Ratan A, Dutta A. The pan-cancer landscape of prognostic germline variants in 10,582 patients. Genome Med. 2020 Feb 17;12(1):15. doi: 10.1186/s13073-020-0718-7. PubMed PMID: 32066500; PubMed Central PMCID: PMC7027124.

Paulsen T, Shibata Y, Kumar P, Dillon L, Dutta A. Small extrachromosomal circular DNAs, microDNA, produce short regulatory RNAs that suppress gene expression independent of canonical promoters. Nucleic Acids Res. 2019 May 21;47(9):4586-4596. doi: 10.1093/nar/gkz155. PubMed PMID: 30828735; PubMed Central PMCID: PMC6511871.

Chatrath A, Kiran M, Kumar P, Ratan A, Dutta A. The Germline Variants rs61757955 and rs34988193 Are Predictive of Survival in Lower Grade Glioma Patients. Mol Cancer Res. 2019 May;17(5):1075-1086. doi: 10.1158/1541-7786.MCR-18-0996. Epub 2019 Jan 16. PubMed PMID: 30651372; PubMed Central PMCID: PMC6497557.

Kuscu C, Kumar P, Kiran M, Su Z, Malik A, Dutta A. tRNA fragments (tRFs) guide Ago to regulate gene expression post-transcriptionally in a Dicer-independent manner. RNA. 2018 Aug;24(8):1093-1105. doi: 10.1261/rna.066126.118. Epub 2018 May 29. PubMed PMID: 29844106; PubMed Central PMCID: PMC6049499.

Paulsen T, Kumar P, Koseoglu MM, Dutta A. Discoveries of Extrachromosomal Circles of DNA in Normal and Tumor Cells. Trends Genet. 2018 Apr;34(4):270-278. doi: 10.1016/j.tig.2017.12.010. Epub 2018 Jan 9. Review. PubMed PMID: 29329720; PubMed Central PMCID: PMC5881399.

Kumar P, Dillon LW, Shibata Y, Jazaeri AA, Jones DR, Dutta A. Normal and Cancerous Tissues Release Extrachromosomal Circular DNA (eccDNA) into the Circulation. Mol Cancer Res. 2017 Sep;15(9):1197-1205. doi: 10.1158/1541-7786.MCR-17-0095. Epub 2017 May 26. PubMed PMID: 28550083; PubMed Central PMCID: PMC5581709.

Kumar P, Kuscu C, Dutta A. Biogenesis and Function of Transfer RNA-Related Fragments (tRFs). Trends Biochem Sci. 2016 Aug;41(8):679-689. doi: 10.1016/j.tibs.2016.05.004. Epub 2016 Jun 1. Review. PubMed PMID: 27263052; PubMed Central PMCID: PMC5173347.

Dillon LW, Kumar P, Shibata Y, Wang YH, Willcox S, Griffith JD, Pommier Y, Takeda S, Dutta A. Production of Extrachromosomal MicroDNAs Is Linked to Mismatch Repair Pathways and Transcriptional Activity. Cell Rep. 2015 Jun 23;11(11):1749-59. doi: 10.1016/j.celrep.2015.05.020. Epub 2015 Jun 4. PubMed PMID: 26051933; PubMed Central PMCID: PMC4481157.

Kumar P, Mudunuri SB, Anaya J, Dutta A. tRFdb: a database for transfer RNA fragments. Nucleic Acids Res. 2015 Jan;43(Database issue):D141-5. doi: 10.1093/nar/gku1138. Epub 2014 Nov 11. PubMed PMID: 25392422; PubMed Central PMCID: PMC4383946.

Kumar P, Anaya J, Mudunuri SB, Dutta A. Meta-analysis of tRNA derived RNA fragments reveals that they are evolutionarily conserved and associate with AGO proteins to recognize specific RNA targets. BMC Biol. 2014 Oct 1;12:78. doi: 10.1186/s12915-014-0078-0. PubMed PMID: 25270025; PubMed Central PMCID: PMC4203973.

Im JS, Keaton M, Lee KY, Kumar P, Park J, Dutta A. ATR checkpoint kinase and CRL1βTRCP collaborate to degrade ASF1a and thus repress genes overlapping with clusters of stalled replication forks. Genes Dev. 2014 Apr 15;28(8):875-87. doi: 10.1101/gad.239194.114. Epub 2014 Apr 3. PubMed PMID: 24700029; PubMed Central PMCID: PMC4003279.

Shibata Y, Kumar P, Layer R, Willcox S, Gagan JR, Griffith JD, Dutta A. Extrachromosomal microDNAs and chromosomal microdeletions in normal tissues. Science. 2012 Apr 6;336(6077):82-6. doi: 10.1126/science.1213307. Epub 2012 Mar 8. PubMed PMID: 22403181; PubMed Central PMCID: PMC3703515.

Kumar P, Nagarajaram HA. A study on mutational dynamics of simple sequence repeats in relation to mismatch repair system in prokaryotic genomes. J Mol Evol. 2012 Apr;74(3-4):127-39. doi: 10.1007/s00239-012-9491-6. Epub 2012 Mar 14. PubMed PMID: 22415400.

Kumar P, Chaitanya PS, Nagarajaram HA. PSSRdb: a relational database of polymorphic simple sequence repeats extracted from prokaryotic genomes. Nucleic Acids Res. 2011 Jan;39(Database issue):D601-5. doi: 10.1093/nar/gkq1198. Epub 2010 Nov 25. PubMed PMID: 21112874; PubMed Central PMCID: PMC3013739.

Mudunuri SB, Kumar P, Rao AA, Pallamsetty S, Nagarajaram HA. G-IMEx: A comprehensive software tool for detection of microsatellites from genome sequences. Bioinformation. 2010 Nov 1;5(5):221-3. doi: 10.6026/97320630005221. PubMed PMID: 21364802; PubMed Central PMCID: PMC3040503.

Sreenu VB, Kumar P, Nagaraju J, Nagarajam HA. Simple sequence repeats in mycobacterial genomes. J Biosci. 2007 Jan;32(1):3-15. doi: 10.1007/s12038-007-0002-7. PubMed PMID: 17426376.

Sreenu VB, Kumar P, Nagaraju J, Nagarajaram HA. Microsatellite polymorphism across the M. tuberculosis and M. bovis genomes: implications on genome evolution and plasticity. BMC Genomics. 2006 Apr 10;7:78. doi: 10.1186/1471-2164-7-78. PubMed PMID: 16603092; PubMed Central PMCID: PMC1501019.
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