Publications

Synthesis of Long RNA with a Site-Specific Modification by EnZymatic Splint Ligation.
Gamper H, McCormick CA, Tavakoli S, Wanunu M, Rouhanifard SH, Hou YM. bioRxiv. 2022 Sep 18.
https://doi.org/10.1101/2022.09.17.508400.

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. Nature Methods. 2022 Oct 24.

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.

eTOC v2

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. 

 


clampExponential 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

 


editingVisualizing 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.

 


bonesNeutrophils and Ly6Chi monocytes collaborate in generating an optimal cytokine response that protects against pulmonary Legionella pneumophila infection.

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


chompCHoMP: 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.


glycan.pngChemical probing of glycans in cells and organisms

SH Rouhanifard, LU Nordstrøm, T Zheng, P Wu. Chemical Society Reviews 42 (10), 4284-4296


MNPDetection 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