Publications

  • Max O Meneveau, Rick D Vavolizza, Anwaruddin Mohammad, Pankaj Kumar, Joseph T Manderfield, Colleen Callahan, Kevin T Lynch, Tarek Abbas, Craig L Slingluff Jr, Stefan Bekiranov. A Step Toward Personalized Surgical Decision Making: Machine Learning Predicts One Versus Numerous Melanoma Lymph Node Metastases Using RNA-Sequencing. Annals of Surgery, 2022.
  • Yu Zhang, Caroline P Riedstra, Sarah Wang, Sonia Patel, Tobias Bald, Pankaj Kumar, Ali Rohani, David F Kashatus, Stergios J Moschos, Andrew C Dudley. Melanoma cells appropriate pericyte: endothelial cell crosstalk during perivascular invasion in the brain. bioRxiv, 2022.
  • Jamie L Null, Dae Joong Kim, James V McCann, Pankaj Kumar, Lincy Edatt, Chad V Pecot, Andrew C Dudley. Periostin+ stromal cells guide lymphovascular invasion by cancer cells. bioRxiv, 2022.
  • Parikh R*, Wilson B*, Marah L, Su Z, Saha S, Kumar P, Huang Fenix, Dutta A. tRForest: a novel random forest-based algorithm for tRNA-derived fragment target prediction. NAR Genomics and Bioinformatics, 2022 Volume 4, Issue 2, June 2022, lqac037.
  • Simpson M, Frisbee A, Kumar P, Schwan C, Aktories K, Petri WA. Clostridioides difficile Binary Toxin Is Recognized by the Toll-Like Receptor 2/6 Heterodimer to Induce a Nuclear Factor-κB Response. J Infect Dis. 2022 Apr 1;225(7):1296-1300. doi: 10.1093/infdis/jiaa620. PubMed PMID: 33011801; PubMed Central PMCID: PMC8974845. Cited 3 times, IF = 5.226, Rank 56 of 162 in IMMUNOLOGY journals.
  • Meneveau MO, Kumar P, Lynch KT, Patel SP, Slingluff CL. The vaccine-site microenvironment: impacts of antigen, adjuvant, and same-site vaccination on antigen presentation and immune signaling. J Immunother Cancer. 2022 Mar;10(3). doi: 10.1136/jitc-2021-003533. PubMed PMID: 35277457; PubMed Central PMCID: PMC8919469. Cited 0 times, IF = 13.751, Rank 8 of 162 in IMMUNOLOGY journals.
  • Uddin MJ, Leslie JL, Burgess SL, Oakland N, Thompson B, Abhyankar M, Revilla J, Frisbee A, Donlan AN, Kumar P, Petri WA Jr. The IL-33-ILC2 pathway protects from amebic colitis. Mucosal Immunol. 2022 Jan;15(1):165-175. doi: 10.1038/s41385-021-00442-2. Epub 2021 Aug 16. PubMed PMID: 34400793; PubMed Central PMCID: PMC8732277. Cited 3 times, IF = 7.313, Rank 30 of 162 in IMMUNOLOGY journals.
  • Seegren, P. V., Harper, L. R., Downs, T. K., Zhao, X. -Y., Viswanathan, S. B., Stremska, M. E., . . . Desai, B. N. (2023). Reduced mitochondrial calcium uptake in macrophages is a major driver of inflammaging. NATURE AGING, 3(7), 796-+. doi:10.1038/s43587-023-00436-8
  • Null, J. L., Kim, D. J., McCann, V. J., Pramoonjago, P., Fox, J. W., Zeng, J., . . . Dudley, A. C. (2023). Periostin thorn Stromal Cells Guide Lymphovascular Invasion by Cancer Cells. CANCER RESEARCH, 83(13), 2105-2122. doi:10.1158/0008-5472.CAN-22-2412
  • Kim, D. J., Anandh, S., Null, J. L., Przanowski, P., Bhatnagar, S., Kumar, P., . . . Dudley, A. C. (2023). Priming a vascular-selective cytokine response permits CD8+ T-cell entry into tumors. NATURE COMMUNICATIONS, 14(1). doi:10.1038/s41467-023-37807-z
  • Parikh, R., Wilson, B., Marrah, L., Su, Z., Saha, S., Kumar, P., . . . Dutta, A. (2022). tRForest: a novel random forest-based algorithm for tRNA-derived fragment target prediction. NAR GENOMICS AND BIOINFORMATICS, 4(2). doi:10.1093/nargab/lqac037
  • Meneveau, M. O., Kumar, P., Lynch, K. T., Patel, S. P., & Slingluff, C. L. (2022). The vaccine-site microenvironment: impacts of antigen, adjuvant, and same-site vaccination on antigen presentation and immune signaling. JOURNAL FOR IMMUNOTHERAPY OF CANCER, 10(3). doi:10.1136/jitc-2021-003533
  • Jan, N., Hays, R. A., Oakland, D. N., Kumar, P., Ramakrishnan, G., Behm, B. W., . . . Marie, C. (2021). Fecal Microbiota Transplantation Increases Colonic IL-25 and Dampens Tissue Inflammation in Patients with Recurrent Clostridioides difficile. MSPHERE, 6(5). doi:10.1128/mSphere.00669-21
  • Eki, R., She, J., Parlak, M., Benamar, M., Du, K. -P., Kumar, P., & Abbas, T. (2020). A robust CRISPR-Cas9-based fluorescent reporter assay for the detection and quantification of DNA double-strand break repair. NUCLEIC ACIDS RESEARCH, 48(21). doi:10.1093/nar/gkaa897
  • Simpson, M., Frisbee, A., Kumar, P., Schwan, C., Aktories, K., & Petri, W. A. J. (2022). Clostridioides difficile Binary Toxin Is Recognized by the Toll-Like Receptor 2/6 Heterodimer to Induce a Nuclear Factor-κB Response. JOURNAL OF INFECTIOUS DISEASES, 225(7), 1296-1300. doi:10.1093/infdis/jiaa620
  • Su, Z., Wilson, B., Kumar, P., & Dutta, A. (2020). Noncanonical Roles of tRNAs: tRNA Fragments and Beyond. ANNUAL REVIEW OF GENETICS, VOL 54, 2020, 54, 47-69. doi:10.1146/annurev-genet-022620-101840
  • Kumar, P., Kiran, S., Saha, S., Su, Z., Paulsen, T., Chatrath, A., . . . Dutta, A. (2020). ATAC-seq identifies thousands of extrachromosomal circular DNA in cancer and cell lines. SCIENCE ADVANCES, 6(20) doi:10.1126/sciadv.aba2489
  • Pollack, K. E., Meneveau, M. O., Melssen, M. M., Lynch, K. T., Koeppel, A. F., Young, S. J., . . . Slingluff, C. L. J. (2020). Incomplete Freund's adjuvant reduces arginase and enhances Th1 dominance, TLR signaling and CD40 ligand expression in the vaccine site microenvironment. JOURNAL FOR IMMUNOTHERAPY OF CANCER, 8(1). doi:10.1136/jitc-2020-000544
  • Chatrath, A., Przanowska, R., Kiran, S., Su, Z., Saha, S., Wilson, B., . . . Dutta, A. (2020). The pan-cancer landscape of prognostic germline variants in 10,582 patients. GENOME MEDICINE, 12(1). doi:10.1186/s13073-020-0718-7
  • Paulsen, T., Shibata, Y., Kumar, P., Dillon, L., & Dutta, A. (2019). Small extrachromosomal circular DNAs, microDNA, produce short regulatory RNAs that suppress gene expression independent of canonical promoters. NUCLEIC ACIDS RESEARCH, 47(9), 4586-4596. doi:10.1093/nar/gkz155
  • Chatrath, A., Kiran, M., Kumar, P., Ratan, A., & Dutta, A. (2019). The Germline Variants rs61757955 and rs34988193 Are Predictive of Survival in Lower Grade Glioma Patients. MOLECULAR CANCER RESEARCH, 17(5), 1075-1086. doi:10.1158/1541-7786.MCR-18-0996
  • Kuscu, C., Kumar, P., Kiran, M., Su, Z., Malik, A., & Dutta, A. (2018). tRNA fragments (tRFs) guide Ago to regulate gene expression post-transcriptionally in a Dicer-independent manner. RNA, 24(8), 1093-1105. doi:10.1261/rna.066126.118
  • Paulsen, T., Kumar, P., Koseoglu, M. M., & Dutta, A. (2018). Discoveries of Extrachromosomal Circles of DNA in Normal and Tumor Cells. TRENDS IN GENETICS, 34(4), 270-278. doi:10.1016/j.tig.2017.12.010
  • Kumar, P., Dillon, L. W., Shibata, Y., Jazaeri, A. A., Jones, D. R., & Dutta, A. (2017). Normal and Cancerous Tissues Release Extrachromosomal Circular DNA (eccDNA) into the Circulation. MOLECULAR CANCER RESEARCH, 15(9), 1197-1205. doi:10.1158/1541-7786.MCR-17-0095
  • Kumar, P., Kuscu, C., & Dutta, A. (2016). Biogenesis and Function of Transfer RNA-Related Fragments (tRFs). TRENDS IN BIOCHEMICAL SCIENCES, 41(8), 679-689. doi:10.1016/j.tibs.2016.05.004
  • Dillon, L. W., Kumar, P., Shibata, Y., Wang, Y. -H., Willcox, S., Griffith, J. D., . . . Dutta, A. (2015). Production of Extrachromosomal MicroDNAs Is Linked to Mismatch Repair Pathways and Transcriptional Activity. CELL REPORTS, 11(11), 1749-1759. doi:10.1016/j.celrep.2015.05.020
  • Kumar, P., Anaya, J., Mudunuri, S. B., & Dutta, A. (2014). Meta-analysis of tRNA derived RNA fragments reveals that they are evolutionarily conserved and associate with AGO proteins to recognize specific RNA targets. BMC BIOLOGY, 12. doi:10.1186/s12915-014-0078-0
  • Im, J. -S., Keaton, M., Lee, K. Y., Kumar, P., Park, J., & Dutta, A. (2014). ATR checkpoint kinase and CRL1βTRCP collaborate to degrade ASF1a and thus repress genes overlapping with clusters of stalled replication forks. GENES & DEVELOPMENT, 28(8), 875-887. doi:10.1101/gad.239194.114
  • Shibata, Y., Kumar, P., Layer, R., Willcox, S., Gagan, J. R., Griffith, J. D., & Dutta, A. (2012). Extrachromosomal MicroDNAs and Chromosomal Microdeletions in Normal Tissues. SCIENCE, 336(6077), 82-86. doi:10.1126/science.1213307
  • Kumar, P., Chaitanya, P. S., & Nagarajaram, H. A. (2011). PSSRdb: a relational database of polymorphic simple sequence repeats extracted from prokaryotic genomes. NUCLEIC ACIDS RESEARCH, 39, D601-D605. doi: 10.1093/nar/gkq1198
  • Mudunuri, S. B., Kumar, P., Rao, A. A., Sanaboina, P. S., & Nagarajaram, H. A. (2010). G-IMEx: A comprehensive software tool for detection of microsatellites from genome sequences. BIOINFORMATION, 5(5), 221-223. doi:10.6026/97320630005221