Publications

Paired aptamer capture and FISH detection of individual virions enables cell-free determination of infectious titer.
Liu Y, Potts JL, Bloch D, Nian K, McCormick CA, Fanari O, Rouhanifard SH. bioRxiv. 2022 Nov 14.
https://doi.org/10.1101/2022.11.13.516306

DNA-enhanced CuAAC ligand enables live-cell detection of intracellular biomolecules.
Nian K, Liu Y, Brigandi L, Rouhanifard SH. bioRxiv. 2022 Nov 10.
https://doi.org/10.1101/2022.11.10.515969

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.