Director, Machine Learning

Phillipe Loher

Director, Machine Learning

Short Bio

Phillipe specializes in Big Data processing for biological discovery. Phillipe has worked for the Computational Medicine Center at Thomas Jefferson University for over 9 years where he has designed many algorithms and software systems needed to efficiently analyze thousands of large datasets. His involvement in advanced software engineering algorithms and programs spans more than 18 years. During that time, he has been involved in a large number of applied computer science and computer engineering activities including: machine learning, data analytics, high performance computing, digital signal processing, low level device drivers, mobile phone platform development, security and security encryption algorithms, and cloud-development. Before joining Thomas Jefferson University (TJU), Phillipe worked at IBM Lotus Software for 8.5 years in various Software Engineering roles within the feature development teams. For several years prior to leaving IBM, he served as manager of software engineers and teams located around the globe.

Publications

2023

  • Akins, RB, Ostberg, K, Cherlin, T, Tsiouplis, NJ, Loher, P, Rigoutsos, I. The Typical tRNA Co-Expresses Multiple 5' tRNA Halves Whose Sequences and Abundances Depend on Isodecoder and Isoacceptor and Change with Tissue Type, Cell Type, and Disease. Noncoding RNA. 2023;9 (6):. doi: 10.3390/ncrna9060069. PubMed PMID:37987365 PubMed Central PMC10660753.
  • Pliatsika, V, Cherlin, T, Loher, P, Vlantis, P, Nagarkar, P, Nersisyan, S, Rigoutsos, I. MINRbase: a comprehensive database of nuclear- and mitochondrial-ribosomal-RNA-derived fragments (rRFs). Nucleic Acids Res. 2023; :. doi: 10.1093/nar/gkad833. PubMed PMID:37843123.
  • Nersisyan, S, Montenont, E, Loher, P, Middleton, EA, Campbell, R, Bray, P, Rigoutsos, I. Characterization of all small RNAs in and comparisons across cultured megakaryocytes and platelets of healthy individuals and COVID-19 patients. J Thromb Haemost. 2023;21 (11):3252-3267. doi: 10.1016/j.jtha.2023.07.028. PubMed PMID:37558133 .
  • Zebrowski, AM, Loher, P, Buckler, DG, Rigoutsos, I, Carr, BG, Wiebe, DJ. Using medicare claims to estimate risk-adjusted performance of Pennsylvania trauma centers. PLOS Digit Health. 2023;2 (6):e0000263. doi: 10.1371/journal.pdig.0000263. PubMed PMID:37267229 PubMed Central PMC10237397.

2022

  • Bhatlekar S, Jacob S, Tugolukova E, Manne BK, Kosaka Y, Loher P, O'Connell RM, Planelles V, Rondina MT, Rigoutsos I, Bray PF. Interferon α-induced SAMHD1 regulates human cultured megakaryocyte apoptosis and proplatelet formation. Haematologica. 2022 Feb 1;107(2):558-561. doi: 10.3324/haematol.2021.279864. PubMed PMID:34758609 PubMed Central PMCID:PMC8804568.

2021

  • Zingone A, Sinha S, Ante M, Nguyen C, Daujotyte D, Bowman ED, Sinha N, Mitchell KA, Chen Q, Yan C, Loher P, Meerzaman D, Ruppin E, Ryan BM. A comprehensive map of alternative polyadenylation in African American and European American lung cancer patients. Nat Commun. 2021 Sep 23;12(1):5605. doi: 10.1038/s41467-021-25763-5. PubMed PMID:34556645.
  • Kaufman EJ, Zebrowski AM, Holena DN, Loher P, Wiebe DJ, Carr BG. The Short and the Long of it: Timing of Mortality for Older Adults in a State Trauma System. J Surg Res. 2021 Jul 16;268:17-24. doi: 10.1016/j.jss.2021.06.042. Epub ahead of print. PubMed PMID:34280661.
  • Dika E, Broseghini E, Porcellini E, Lambertini M, Riefolo M, Durante G, Loher P, Roncarati R, Bassi C, Misciali C, Negrini M, Rigoutsos I, Londin E, Patrizi A, Ferracin M. Unraveling the role of microRNA/isomiR network in multiple primary melanoma pathogenesis. Cell Death Dis. 2021 May 12;12(5):473. doi: 10.1038/s41419-021-03764-y. PubMed PMID:33980826.
  • 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.
  • Cherlin, T, Magee, R, Jing, Y, Pliatsika, V, Loher, P, Rigoutsos, I. Ribosomal RNA fragmentation into short RNAs (rRFs) is modulated in a sex- and population of origin-specific manner. BMC Biol 18, 38 (2020). doi: 10.1186/s12915-020-0763-0. PubMed PMID:32279660.
  • Salcedo, A, Tarabichi, M, Espiritu, SMG, Deshwar, AG, David, M, Wilson, NM, Dentro, S, Wintersinger, JA, Liu, LY, Ko, M, Sivanandan, S, Zhang, H, Zhu, K, Ou Yang, TH, Chilton, JM, Buchanan, A, Lalansingh, CM, P'ng, C, Anghel, CV, Umar, I, Lo, B, Zou, W; DREAM SMC-Het Participants, Simpson, JT, Stuart, JM, Anastassiou, D, Guan, Y, Ewing, AD, Ellrott, K, Wedge, DC, Morris, Q, Van Loo, P, Boutros, PC. A community effort to create standards for evaluating tumor subclonal reconstruction. Nat Biotechnol. 2020;38(1):97–107. doi: 10.1038/s41587-019-0364-z. PubMed PMID: 31919445.

2019

  • Pawar, K, Shigematsu, M, Loher, P, Honda, S, Rigoutsos, I, Kirino, Y. Exploration of CCA-added RNAs revealed the expression of mitochondrial non-coding RNAs regulated by CCA-adding enzyme. RNA Biol. 2019 Sep 12:1-9. doi: 10.1080/15476286.2019.1664885. PubMed PMID:31512554.
  • 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.
  • 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.
  • Honda, S, Loher, P, Morichika, K, Shigematsu, M, Kawamura, T, Kirino, Y, Rigoutsos, I, Kirino, Y. Increasing cell density globally enhances the biogenesis of Piwi-interacting RNAs in Bombyx mori germ cells. Sci Rep. 2017;7 (1):4110. doi: 10.1038/s41598-017-04429-7. PubMed PMID:28646211 PubMed Central PMC5482885.
  • Honda, S, Kawamura, T, Loher, P, Morichika, K, Rigoutsos, I, Kirino, Y. The biogenesis pathway of tRNA-derived piRNAs in Bombyx germ cells. Nucleic Acids Res. 2017;45 (15):9108-9120. doi: 10.1093/nar/gkx537. PubMed PMID:28645172 PubMed Central PMC5587776.
  • 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.
  • Magee, R, Loher, P, Londin, E, Rigoutsos, I. Threshold-seq: a tool for determining the threshold in short RNA-seq datasets. Bioinformatics. 2017;33 (13):2034-2036. doi: 10.1093/bioinformatics/btx073. PubMed PMID:28203700 PubMed Central PMC5870860.
  • 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

  • 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.
  • 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.

2015

  • 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.
  • Honda, S, Loher, P, Shigematsu, M, Palazzo, JP, Suzuki, R, Imoto, I, Rigoutsos, I, Kirino, Y. Sex hormone-dependent tRNA halves enhance cell proliferation in breast and prostate cancers. Proc. Natl. Acad. Sci. U.S.A. 2015;112 (29):E3816-25. doi: 10.1073/pnas.1510077112. PubMed PMID:26124144 PubMed Central PMC4517238.
  • Londin, E, Loher, P, Rigoutsos, I. Reply to Backes and Keller: Identification of novel tissue-specific and primate-specific human microRNAs. Proc. Natl. Acad. Sci. U.S.A. 2015;112 (22):E2851. doi: 10.1073/pnas.1505397112. PubMed PMID:25979943 PubMed Central PMC4460515.
  • 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.
  • Loher, P, Londin, ER, Rigoutsos, I. IsomiR expression profiles in human lymphoblastoid cell lines exhibit population and gender dependencies. Oncotarget. 2014;5 (18):8790-802. doi: 10.18632/oncotarget.2405. PubMed PMID:25229428 PubMed Central PMC4226722.
  • Clark, PM, Loher, P, Quann, K, Brody, J, Londin, ER, Rigoutsos, I. Argonaute CLIP-Seq reveals miRNA targetome diversity across tissue types. Sci Rep. 2014;4 :5947. doi: 10.1038/srep05947. PubMed PMID:25103560 PubMed Central PMC4894423.
  • Londin, ER, Hatzimichael, E, Loher, P, Edelstein, L, Shaw, C, Delgrosso, K, Fortina, P, Bray, PF, McKenzie, SE, Rigoutsos, I. The human platelet: strong transcriptome correlations among individuals associate weakly with the platelet proteome. Biol. Direct. 2014;9 :3. doi: 10.1186/1745-6150-9-3. PubMed PMID:24524654 PubMed Central PMC3937023.

2013

  • Bray, PF, McKenzie, SE, Edelstein, LC, Nagalla, S, Delgrosso, K, Ertel, A, Kupper, J, Jing, Y, Londin, E, Loher, P, Chen, HW, Fortina, P, Rigoutsos, I. The complex transcriptional landscape of the anucleate human platelet. BMC Genomics. 2013;14 :1. doi: 10.1186/1471-2164-14-1. PubMed PMID:23323973 PubMed Central PMC3722126.
  • Benetatos, L, Hatzimichael, E, Londin, E, Vartholomatos, G, Loher, P, Rigoutsos, I, Briasoulis, E. The microRNAs within the DLK1-DIO3 genomic region: involvement in disease pathogenesis. Cell. Mol. Life Sci. 2013;70 (5):795-814. doi: 10.1007/s00018-012-1080-8. PubMed PMID:22825660.
  • Loher, P, Vasilakis, N, Malamon, J, Chen, HW and Rigoutsos, I (2013) "HandsFree - Next Generation Sequence Processing, Mapping and Analysis Made Easy" Proceedings DILS2013 doi: DILS-SYS-EC-paper4

2012

  • Loher, P, Rigoutsos, I. Interactive exploration of RNA22 microRNA target predictions. Bioinformatics. 2012;28 (24):3322-3. doi: 10.1093/bioinformatics/bts615. PubMed PMID:23074262.
  • Xia, Z, Clark, P, Huynh, T, Loher, P, Zhao, Y, Chen, HW, Ren, P, Rigoutsos, I, Zhou, R. Molecular dynamics simulations of Ago silencing complexes reveal a large repertoire of admissible "seed-less" targets. Sci Rep. 2012;2 :569. doi: 10.1038/srep00569. PubMed PMID:22888400 PubMed Central PMC3415692.

Contact Info

Email: Phillipe.Loher@jefferson.edu