PhD Student/Postdoctoral Researcher

Aristeidis Telonis

PhD Student/Postdoctoral Researcher

Short Bio

Aristeidis (Aris) is currently a post-doctoral researcher in the Computational Medicine Center. His scientific work focuses on the biology of small non-coding RNAs, including miRNA isoforms (isomiRs) and tRNA fragments (tRFs), and how they are wired with long transcripts in different biological contexts. He is using bioinformatics, statistical tools and inter-disciplinary approaches to address issues on sex and race disparities in disease as well as integrating information from multiple high-throughput analytical platforms and databases towards understanding complex cellular/molecular phenotypes (systems biology). Aris graduated with a PhD degree from the Biochemistry and Molecular Pharmacology Program at Jefferson. His PhD research was on elucidating the molecular events behind race disparities in triple-negative breast cancer. He holds a Bachelor’s degree in Biology from the University of Patras (Patras, Greece) and a Master’s Degree in Biological Technology from the same University. During his Master’s research he worked on the use of metabolomic analysis as a tool in clinical prognosis.

Publications

2019

  • Desvignes, T, Loher, P, Eilbeck, K, Ma, J, Urgese, G, Fromm, B, Sydes, J, Aparicio-Puerta, E, Barrera, V, Espín, R, Thibord, F, Ros, XB, Londin, E, Telonis, AG, Ficarra, E, Friedländer, MR, Postlethwait, JH, Rigoutsos, I, Hackenberg, M, Vlachos, IS, Halushka, MK, Pantano, L. Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API. Bioinformatics. 2019 Aug 29. doi: 10.1093/bioinformatics/btz675. PubMed PMID:31504201.
  • Telonis, AG, Loher, P, Magee, R, Pliatsika, V, Londin, E, Kirino, Y, Rigoutsos, I. tRNA Fragments Show Intertwining with mRNAs of Specific Repeat Content and Have Links to Disparities. Cancer Res. 2019 Apr 17. doi: 10.1158/0008-5472.CAN-19-0789. PubMed PMID:30996049.

2018

  • Magee, RG, Telonis, AG, Loher, P, Londin, E, Rigoutsos, I. Profiles of miRNA Isoforms and tRNA Fragments in Prostate Cancer. Sci Rep. 2018;8 (1):5314. doi: 10.1038/s41598-018-22488-2. PubMed PMID:29593348 PubMed Central PMC5871839.
  • Telonis, AG, Rigoutsos, I. Race Disparities in the Contribution of miRNA Isoforms and tRNA-Derived Fragments to Triple-Negative Breast Cancer. Cancer Res. 2018;78 (5):1140-1154. doi: 10.1158/0008-5472.CAN-17-1947. PubMed PMID:29229607 PubMed Central PMC5935570.
  • Pliatsika, V, Loher, P, Magee, R, Telonis, AG, Londin, E, Shigematsu, M, Kirino, Y, Rigoutsos, I. MINTbase v2.0: a comprehensive database for tRNA-derived fragments that includes nuclear and mitochondrial fragments from all The Cancer Genome Atlas projects. Nucleic Acids Res. 2018;46 (D1):D152-D159. doi: 10.1093/nar/gkx1075. PubMed PMID:29186503 PubMed Central PMC5753276.
  • Loher, P, Telonis, AG, Rigoutsos, I. Accurate Profiling and Quantification of tRNA Fragments from RNA-Seq Data: A Vade Mecum for MINTmap. Methods Mol. Biol. 2018;1680 :237-255. doi: 10.1007/978-1-4939-7339-2_16. PubMed PMID:29030853.

2017

  • Cancer Genome Atlas Research Network. Electronic address: andrew_aguirre@dfci.harvard.edu, Cancer Genome Atlas Research Network. Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma. Cancer Cell. 2017;32 (2):185-203.e13. doi: 10.1016/j.ccell.2017.07.007. PubMed PMID:28810144 PubMed Central PMC5964983.
  • Magee, R, Telonis, AG, Cherlin, T, Rigoutsos, I, Londin, E. Assessment of isomiR Discrimination Using Commercial qPCR Methods. Noncoding RNA. 2017;3 (2):. doi: 10.3390/ncrna3020018. PubMed PMID:28730153 PubMed Central PMC5514785.
  • Rigoutsos, I, Lee, SK, Nam, SY, Anfossi, S, Pasculli, B, Pichler, M, Jing, Y, Rodriguez-Aguayo, C, Telonis, AG, Rossi, S, Ivan, C, Catela Ivkovic, T, Fabris, L, Clark, PM, Ling, H, Shimizu, M, Redis, RS, Shah, MY, Zhang, X, Okugawa, Y, Jung, EJ, Tsirigos, A, Huang, L, Ferdin, J, Gafà, R, Spizzo, R, Nicoloso, MS, Paranjape, AN, Shariati, M, Tiron, A, Yeh, JJ, Teruel-Montoya, R, Xiao, L, Melo, SA, Menter, D, Jiang, ZQ, Flores, ER, Negrini, M, Goel, A, Bar-Eli, M, Mani, SA, Liu, CG, Lopez-Berestein, G, Berindan-Neagoe, I, Esteller, M, Kopetz, S, Lanza, G, Calin, GA. N-BLR, a primate-specific non-coding transcript leads to colorectal cancer invasion and migration. Genome Biol. 2017;18 (1):98. doi: 10.1186/s13059-017-1224-0. PubMed PMID:28535802 PubMed Central PMC5442648.
  • Loher, P, Telonis, AG, Rigoutsos, I. MINTmap: fast and exhaustive profiling of nuclear and mitochondrial tRNA fragments from short RNA-seq data. Sci Rep. 2017;7 :41184. doi: 10.1038/srep41184. PubMed PMID:28220888 PubMed Central PMC5318995.
  • Telonis, AG, Magee, R, Loher, P, Chervoneva, I, Londin, E, Rigoutsos, I. Knowledge about the presence or absence of miRNA isoforms (isomiRs) can successfully discriminate amongst 32 TCGA cancer types. Nucleic Acids Res. 2017;45 (6):2973-2985. doi: 10.1093/nar/gkx082. PubMed PMID:28206648 PubMed Central PMC5389567.
  • Shigematsu, M, Honda, S, Loher, P, Telonis, AG, Rigoutsos, I, Kirino, Y. YAMAT-seq: an efficient method for high-throughput sequencing of mature transfer RNAs. Nucleic Acids Res. 2017;45 (9):e70. doi: 10.1093/nar/gkx005. PubMed PMID:28108659 PubMed Central PMC5605243.

2016

  • Zhou, H, Telonis, AG, Jing, Y, Xia, NL, Biederman, L, Jimbo, M, Blanco, F, Londin, E, Brody, JR, Rigoutsos, I. GPRC5A is a potential oncogene in pancreatic ductal adenocarcinoma cells that is upregulated by gemcitabine with help from HuR. Cell Death Dis. 2016;7 :e2294. doi: 10.1038/cddis.2016.169. PubMed PMID:27415424 PubMed Central PMC4973341.
  • Pliatsika, V, Loher, P, Telonis, AG, Rigoutsos, I. MINTbase: a framework for the interactive exploration of mitochondrial and nuclear tRNA fragments. Bioinformatics. 2016;32 (16):2481-9. doi: 10.1093/bioinformatics/btw194. PubMed PMID:27153631 PubMed Central PMC4978933.
  • Telonis, AG, Loher, P, Kirino, Y, Rigoutsos, I. Consequential considerations when mapping tRNA fragments. BMC Bioinformatics. 2016;17 :123. doi: 10.1186/s12859-016-0921-0. PubMed PMID:26961774 PubMed Central PMC4785646.

2015

  • Telonis, AG, Loher, P, Jing, Y, Londin, E, Rigoutsos, I. Beyond the one-locus-one-miRNA paradigm: microRNA isoforms enable deeper insights into breast cancer heterogeneity. Nucleic Acids Res. 2015;43 (19):9158-75. doi: 10.1093/nar/gkv922. PubMed PMID:26400174 PubMed Central PMC4627084.
  • Telonis, AG, Loher, P, Honda, S, Jing, Y, Palazzo, J, Kirino, Y, Rigoutsos, I. Dissecting tRNA-derived fragment complexities using personalized transcriptomes reveals novel fragment classes and unexpected dependencies. Oncotarget. 2015;6 (28):24797-822. doi: 10.18632/oncotarget.4695. PubMed PMID:26325506 PubMed Central PMC4694795.
  • Jimbo, M, Blanco, FF, Huang, YH, Telonis, AG, Screnci, BA, Cosma, GL, Alexeev, V, Gonye, GE, Yeo, CJ, Sawicki, JA, Winter, JM, Brody, JR. Targeting the mRNA-binding protein HuR impairs malignant characteristics of pancreatic ductal adenocarcinoma cells. Oncotarget. 2015;6 (29):27312-31. doi: 10.18632/oncotarget.4743. PubMed PMID:26314962 PubMed Central PMC4694992.
  • Telonis, AG, Margarity, M. Phobos: A novel software for recording rodents" behavior during the thigmotaxis and the elevated plus-maze test. Neurosci. Lett. 2015;599 :81-5. doi: 10.1016/j.neulet.2015.05.045. PubMed PMID:26007702.
  • Telonis, AG, Kirino, Y, Rigoutsos, I. Mitochondrial tRNA-lookalikes in nuclear chromosomes: could they be functional?. RNA Biol. 2015;12 (4):375-80. doi: 10.1080/15476286.2015.1017239. PubMed PMID:25849196 PubMed Central PMC4615777.
  • Honda, S, Shigematsu, M, Morichika, K, Telonis, AG, Kirino, Y. Four-leaf clover qRT-PCR: A convenient method for selective quantification of mature tRNA. RNA Biol. 2015;12 (5):501-8. doi: 10.1080/15476286.2015.1031951. PubMed PMID:25833336 PubMed Central PMC4615770.
  • Londin, E, Loher, P, Telonis, AG, Quann, K, Clark, P, Jing, Y, Hatzimichael, E, Kirino, Y, Honda, S, Lally, M, Ramratnam, B, Comstock, CE, Knudsen, KE, Gomella, L, Spaeth, GL, Hark, L, Katz, LJ, Witkiewicz, A, Rostami, A, Jimenez, SA, Hollingsworth, MA, Yeh, JJ, Shaw, CA, McKenzie, SE, Bray, P, Nelson, PT, Zupo, S, Van Roosbroeck, K, Keating, MJ, Calin, GA, Yeo, C, Jimbo, M, Cozzitorto, J, Brody, JR, Delgrosso, K, Mattick, JS, Fortina, P, Rigoutsos, I. Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs. Proc. Natl. Acad. Sci. U.S.A. 2015;112 (10):E1106-15. doi: 10.1073/pnas.1420955112. PubMed PMID:25713380 PubMed Central PMC4364231.

2014

  • Telonis, AG, Loher, P, Kirino, Y, Rigoutsos, I. Nuclear and mitochondrial tRNA-lookalikes in the human genome. Front Genet. 2014;5 :344. doi: 10.3389/fgene.2014.00344. PubMed PMID:25339973 PubMed Central PMC4189335.
  • Gkourogianni, A, Kosteria, I, Telonis, AG, Margeli, A, Mantzou, E, Konsta, M, Loutradis, D, Mastorakos, G, Papassotiriou, I, Klapa, MI, Kanaka-Gantenbein, C, Chrousos, GP. Plasma metabolomic profiling suggests early indications for predisposition to latent insulin resistance in children conceived by ICSI. PLoS ONE. 2014;9 (4):e94001. doi: 10.1371/journal.pone.0094001. PubMed PMID:24728198 PubMed Central PMC3984097.

Contact Info

Email: Aristeidis.Telonis@jefferson.edu