Messenger-RNA modification standards and machine learning models facilitate absolute site-specific pseudouridine quantification
Makhamreh A, Tavakoli S, Gamper H, Nabizadehmashhadtoroghi M, Fallahi A, , Hou YM, Rouhanifard SH*, Wanunu M*. bioRxiv. 2022 May 6. https://doi.org/10.1101/2022.05.06.490948.
clampFISH 2.0 enables rapid, scalable amplified RNA detection in situ
Dardani I, Emert BL, Goyal Y, Jiang C, Kaur A, Lee J, Rouhanifard SH, Alicea GM, Fane EM, Xiao M, Herlyn M, Weeraratna AT, Raj A. bioRxiv. 2022 Mar 17. https://doi.org/10.1101/2022.03.16.484659.
Detection of pseudouridine modifications and type I/II hypermodifications in human mRNAs using direct, long-read sequencing
Tavakoli S, Nabizadehmashhadtoroghi M, Makhamreh A, Gamper H, Rezapour NK, Hou YM, Wanunu M, Rouhanifard SH. bioRxiv. 2021 Nov 4. doi:10.1101/2021.11.03.467190.
Click chemistry-based amplification and detection of endogenous RNA and DNA molecules in situ using clampFISH probes
Tavakoli S, Liu Y, Potts JL, Rouhanifard SH. Methods in Enzymology. 2020 Jan 1. doi: 101.1016/bs.mie.2020.049
ClampFISH detects individual nucleic acid molecules using click chemistry–based amplification
Rouhanifard SH, Mellis IA, Dunagin M, Bayatpour S, Jiang CL, Dardani I, Symmons O, Emert B, Torre E, Cote A, Sullivan A, Stamatoyannopoulos JA, Raj A. Nat Biotechnol. 2019 Jan 1. doi: 10.1038/nbt.4286.
Engineered Glycocalyx Regulates Stem Cell Proliferation in Murine Crypt Organoids
Rouhanifard SH, Lopez Aguilar A, Meng L, Moremen KW, Wu P. Cell Chem Biol. 2018 Apr 19;25(4):439-446.e5. doi: 10.1016/j.chembiol.2018.01.010.
Exponential fluorescent amplification of RNA using clampFISH probes
Sara H Rouhanifard,Ian A Mellis, Margaret Dunagin, Sareh Bayatpour, Orsolya Symmons, Allison Cote, Arjun Raj. BioRxiv. 2017
Visualizing adenosine-to-inosine RNA editing in single mammalian cells.
Mellis IA, Gupte R, Raj A, Rouhanifard SH. Nat Methods. 2017 Aug;14(8):801-804. doi: 10.1038/nmeth.4332.
Cierra N Casson, Jessica L Doerner, Alan M Copenhaver, Jasmine Ramirez, Alicia M Holmgren, Mark A Boyer, Ingharan J Siddarthan, Sara H Rouhanifard, Arjun Raj, Sunny Shin. PLoS pathogens 13 (4), e1006309
CHoMP: a chemoenzymatic histology method using clickable probes.
Rouhanifard SH, López-Aguilar A, Wu P. Chembiochem. 2014 Dec 15;15(18):2667-73. doi: 10.1002/cbic.201402433.
Chemical probing of glycans in cells and organisms
SH Rouhanifard, LU Nordstrøm, T Zheng, P Wu. Chemical Society Reviews 42 (10), 4284-4296
Detection and isolation of dendritic cells using Lewis X-functionalized magnetic nanoparticles
SH Rouhanifard, R Xie, G Zhang, X Sun, X Chen, P Wu. Biomacromolecules 13 (10), 3039-3045
Rouhanifard Lab 