Job Description

Must have 1 year of research experience in research with a BS degree. Must have the BS degree in one of the following: engineering, bioengineering, physics, computational biology, and bioinformatics. Must commit to at least 2 years of work at this position. Must commit to 8 hours of in-person work Monday-Friday. Work flexibility can be arranged. Job description: To work on RNA research – the most exciting frontier in the central dogma, acting as the bridge to connect genetic information transfer from DNA to protein. The focus is on developing new technologies for direct sequencing of RNA molecules in the human transcriptomes. The work has direct impact on human health and disease (cancer, neurodegeneration). The techniques in use: Nanopore sequence, illumina sequencing, genome-wide data analysis, denaturing PAGE/urea gels for analysis of RNA, sequencing gels for RNA, SDS/PAGE gels for proteins, molecular biology of gene cloning and plasmid construction, extraction of DNA and RNA. No animal work required. For more information, please see the following publications and our website: Tavakoli, S, Nabizadeh, M, Makhamreh, A, Gamper, H, Rezapour, NK, Hou, YM, Wanunu, M, Rouhanifard, SH. (2023) Semi-quantitative detection of pseudouridine modifications and type I/II hypermodifications in human mRNAs using direct, long-read sequencing. Nat Commun 14(1):334. PMID:36658122; PMCID:PMC9852470 Gamper, H, McCormick, C, Makhamreh, A, Wanunu, M, Rouhanifard, SH, Hou, YM. (2023) Enzymatic synthesis of RNA standards for mapping and quantifying RNA modifications in sequencing analysis. Methods in Enzymology, Academic Press, PMID: 37925177 Hou, YM, Nakano, Y. (2024) Breaking the deadlock in genetic code expansion. Invited for an article in News & Views, commenting on the paper in Nature “Adding a,a-disubstituted and b-linked monomers to the genetic code of an organism. Nature Chem Biology, PMID: 38467845. Avila, YI, Rebolledo, LP, Skelly, E, de Freitas Saito, R, Wei, H, Lilley, D, Stanley RE, Hou, YM, Yang, H, Sztuba-Solinska, J, Chen, SJ, Dokholyan, NV, Tan, C, Li, K, He, X, Zhang, X, Miles, W, Franco, E, Binzel, DW, Guo, P, Afonin, KA (2024) Cracking the code: Enhancing molecular tools for progress in nanotechnology. ACS Applied Bio Materials, PMID: 38833534; PMCID: PMC11190997. Masuda, I, Hou, YM. (2024) A tRNA modification pattern that facilitates interpretation of the genetic code. Submitted to Frontier in Microbiology, PMID: 38933027; PMCID: PMC11199890. Namani, S, Kavetsky, K, Lin, CY, Maharjan, S, Gamper, H, Li, NS, Piccirilli, J, Hou*, YM, Drndic*, M. (2024) Unraveling RNA conformation dynamics in mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episode syndrome with solid-state nanopores. ACS Nano, PMID: 38906834, DOI:10.1021/acsnano.4c04625 Maharjan, S, Gamper, H, Yamaki, Y, Christian, T, Henley, RY, Li, NS, Suzuki, T, Suzuki, T, Piccirilli, JA, Wanunu, M, Seifert, E, Wallace, DC, Hou, YM. (2024) Post-transcriptional methylation of mitochondrial-tRNA differentially contributes to mitochondrial pathology. Nature Commun 15(1):9008, doi: 10.1038/s41467-024-53318-x; PMID: 39424798; PMCID:PMC11489592 Makhamreh, A, Tavakoli, S, Fallahi, A, Kang, X, Gamper, H, Nabizadehmashhadtoroghi, M, Jain, M, Hou, YM, Rouhanifard, SH, Wanunu, M. (2024) Nanopore signal deviations from pseudouridine modifications in RNA are sequence-specific; quantification requires dedicated synthetic controls. Sci Rep. 14(1): 22457. DOI: 10.1038/s41598-024-72994-9; PMID: 39341872; PMCID:PMC11438862. Nakano, Y, Gamper, H, McGuigan, H, Maharjan, S, Sun, Z, Yigit, E, Grunberg, S, Krishnan, K, Li, NS, Piccirilli, JA, Kleiner, R, Nichols, N, Hou, YM. (2025) Genome-wide profiling of tRNA modifications by Induro-tRNAseq reveals coordinated changes. Nat Commun, PMID: 39865096; PMCID: PMC 11770116; DOI: 10.1038/s41467-025-56348-1. Fanari, O, Tavakoli, S, Qiu, Y, Makhamreh, A, Nilan, K, Akeson, S, Meseonznik, M, McCormick, CA, Block, D, Gamper, H, Jain, M, Hou, YM, Wanunu, M, Rouhanifard, SH. (2025) Probing enzyme-dependent pseudouridylation using direct RNA sequencing to assess neuronal epitranscriptome plasticity. Cell Systems, 2025 Mar 18:101238, doi: 10.1016/j.cels.2025.101238; PMID: 40118059

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