Nestoras Karathanasis

Dr. Nestoras Karathanasis is a teaching assistant professor at the College of Life Science at Thomas Jefferson University (TJU) in Philadelphia. He received his PhD from the University of Crete, Greece in the field of "miRNA-mRNA interactions related with cancer" in 2013 and in 2015 was appointed Lead Bioinformatician at Miroculus company in San Francisco before joining TJU.

He has an active interest in precision medicine and his work focuses on the statistical integration of different omics data, the development of miRNA mapping tools and apply machine learning algorithms to address biological questions in key areas such as cancer. As a teaching assistant professor, he has developed three graduate-level courses on computational skill acquisition, (i.e. R programming, data visualization, and transcriptomics data analysis). In 2018, he created and led a machine learning team from the Computational Medicine Center of TJU in participating in the DREAM Single Cell Transcriptomics challenge. His team ranked 6th place among 49 participating teams. As of 2019, he is co-recipient of the TJU Data Science Award for his work as a member of the Computational Medicine Center team.

2021

• Planell N, Lagani V, Sebastian-Leon P, van der Kloet F, Ewing E, Karathanasis N, Urdangarin A, Arozarena I, Jagodic M, Tsamardinos I, Tarazona S, Conesa A, Tegner J, Gomez-Cabrero D. STATegra: Multi-Omics Data Integration - A Conceptual Scheme With a Bioinformatics Pipeline. Front Genet. 2021 Mar 4;12:620453. doi: 10.3389/fgene.2021.620453. PubMed PMID:33747045 PubMed Central PMCID:PMC7970106.
• Loher P, Karathanasis N. Machine Learning Approaches Identify Genes Containing Spatial Information From Single-Cell Transcriptomics Data. Front Genet. 2021 Feb 1;11:612840. doi: 10.3389/fgene.2020.612840. PubMed PMID:33633771 PubMed Central PMCID:PMC7902049.
• Loher P, Karathanasis N, Londin E, Bray P, Pliatsika V, Telonis AG, Rigoutsos I. IsoMiRmap-fast, deterministic, and exhaustive mining of isomiRs from short RNA-seq datasets. Bioinformatics. 2021 Jan 20:btab016. doi: 10.1093/bioinformatics/btab016. Epub ahead of print. PubMed PMID:33471076.

2020

• Tanevski, J, Nguyen, T, Truong, B, Karaiskos, N, Ahsen, ME, Zhang, X, Shu, C, Xu, K, Liang, X, Hu, Y, Pham, HV, Xiaomei, L, Le, TD, Tarca, AL, Bhatti, G, Romero, R, Karathanasis, N, Loher, P, Chen, Y, Ouyang, Z, Mao, D, Zhang, Y, Zand, M, Ruan, J, Hafemeister, C, Qiu, P, Tran, D, Nguyen, T, Gabor, A, Yu, T, Guinney, J, Glaab, E, Krause, R, Banda, P; DREAM SCTC Consortium, Stolovitzky, G, Rajewsky, N, Saez-Rodriguez, J, Meyer, P. Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data. Life Sci Alliance. 2020 Sep 24;3(11):e202000867. doi: 10.26508/lsa.202000867. PubMed PMID:32972997.

2019

• Fernandes, SJ, Morikawa, H, Ewing, E, Ruhrmann, S, Joshi, RN, Lagani, V, Karathanasis, N, Khademi, M, Planell, N, Schmidt, A, Tsamardinos, I, Olsson, T, Piehl, F, Kockum, I, Jagodic, M, Tegnér, J, Gomez-Cabrero, D. Non-parametric combination analysis of multiple data types enables detection of novel regulatory mechanisms in T cells of multiple sclerosis patients. Sci Rep. 2019 Aug 19;9(1):11996. doi: 10.1038/s41598-019-48493-7. PubMed PMID:31427643.
• Ewing, E, Kular, L, Fernandes, SJ, Karathanasis, N, Lagani, V, Ruhrmann, S, Tsamardinos, I, Tegner, J, Piehl, F, Gomez-Cabrero, D, Maja Jagodic, M. Combining evidence from four immune cell types identifies DNA methylation patterns that implicate functionally distinct pathways during Multiple Sclerosis progression. EBioMedicine 2019 Apr. doi: 10.1016/j.ebiom.2019.04.042. PubMed PMID:31053557.

2016

• Karathanasis, N, Tsamardinos, I, Lagani, V. omicsNPC: Applying the Non-Parametric Combination Methodology to the Integrative Analysis of Heterogeneous Omics Data. PLoS ONE. 2016;11 (11):e0165545. doi: 10.1371/journal.pone.0165545. PubMed PMID:27812137 PubMed Central PMC5094732.

2015

• Karathanasis, N, Tsamardinos, I, Poirazi, P. MiRduplexSVM: A High-Performing MiRNA-Duplex Prediction and Evaluation Methodology. PLoS ONE. 2015;10 (5):e0126151. doi: 10.1371/journal.pone.0126151. PubMed PMID:25961860 PubMed Central PMC4427487.
• Oulas, A, Karathanasis, N, Louloupi, A, Pavlopoulos, GA, Poirazi, P, Kalantidis, K, Iliopoulos, I. Prediction of miRNA targets. Methods Mol. Biol. 2015;1269 :207-29. doi: 10.1007/978-1-4939-2291-8_13. PubMed PMID:25577381.

2014

• Ho, VM, Dallalzadeh, LO, Karathanasis, N, Keles, MF, Vangala, S, Grogan, T, Poirazi, P, Martin, KC. GluA2 mRNA distribution and regulation by miR-124 in hippocampal neurons. Mol. Cell. Neurosci. 2014;61 :1-12. doi: 10.1016/j.mcn.2014.04.006. PubMed PMID:24784359 PubMed Central PMC4134974.
• Karathanasis, N, Tsamardinos, I, Poirazi, P. Don"t use a cannon to kill the. miRNA mosquito. Bioinformatics. 2014;30 (7):1047-8. doi: 10.1093/bioinformatics/btu100. PubMed PMID:24618472.

2012

• Oulas, A, Karathanasis, N, Louloupi, A, Iliopoulos, I, Kalantidis, K, Poirazi, P. A new microRNA target prediction tool identifies a novel interaction of a putative miRNA with CCND2. RNA Biol. 2012;9 (9):1196-207. doi: 10.4161/rna.21725. PubMed PMID:22954617 PubMed Central PMC3579887.

2011

• Oulas, A, Karathanasis, N, Louloupi, A, Poirazi, P. Finding cancer-associated miRNAs: methods and tools. Mol. Biotechnol. 2011;49 (1):97-107. doi: 10.1007/s12033-011-9416-4. PubMed PMID:21607762.
• Oulas, A, Karathanasis, N, Poirazi, P. Computational identification of miRNAs involved in cancer. Methods Mol. Biol. 2011;676 :23-41. doi: 10.1007/978-1-60761-863-8_2. PubMed PMID:20931387.

1. "Detection of RNA using ligation actuated loop mediated amplification methods and digital microfluidics" U.S. Provisional Patent Application No.: 62/352,503 June 20, 2016

Email: nestoras.karathanasis@jefferson.edu