Sara Rouhanifard
@srouhanifard.bsky.social
Asst. Prof of bioengineering @Northeastern University | RNA modifications | RNA localization | click chemistry | single-molecule studies | www.rouhanifardlab.com
Reposted by Sara Rouhanifard
Multi-Scale Kinetics Modeling and Advanced Assay for mRNA-Lipid Nanoparticle Potency Assessment https://www.biorxiv.org/content/10.1101/2025.09.29.679406v1
October 1, 2025 at 11:05 PM
Multi-Scale Kinetics Modeling and Advanced Assay for mRNA-Lipid Nanoparticle Potency Assessment https://www.biorxiv.org/content/10.1101/2025.09.29.679406v1
Reposted by Sara Rouhanifard
Protocol for differential analysis of pseudouridine modifications using nanopore DRS and unmodified transcriptome control #protocol #starprotocols #cellpress
Protocol for differential analysis of pseudouridine modifications using nanopore DRS and unmodified transcriptome control
In this protocol, we detect pseudouridine using nanopore direct RNA sequencing (DRS 002/004) and analyze dynamic changes to mRNA modifications in response to perturbation. We cover RNA extraction, poly(A) selection, DRS, unmodified transcriptome (in vitro transcribed [IVT]) library preparation, and knockdowns of writer proteins as critical controls. We detail preprocessing, psi-site identification, and differential analysis, quantifying the direction and magnitude of changes across cellular type...
dlvr.it
July 25, 2025 at 3:09 PM
Protocol for differential analysis of pseudouridine modifications using nanopore DRS and unmodified transcriptome control #protocol #starprotocols #cellpress
Reposted by Sara Rouhanifard
RNA modifications in T cells are more stable than expected—primary and immortalized cells share most sites, suggesting common regulatory features can be studied across systems bit.ly/3GP97C8
August 5, 2025 at 7:46 PM
RNA modifications in T cells are more stable than expected—primary and immortalized cells share most sites, suggesting common regulatory features can be studied across systems bit.ly/3GP97C8
1/🧵
🚨 New paper published in RNA!
Scientists often say anecdotally that RNA modifications are disrupted in immortalized cells — but no one’s really tested it.
So we did: ψ-mapping in primary T cells vs. Jurkat cells using direct RNA-seq.
📄 tinyurl.com/TCellPsiRNA
#nanopore #RNA #pseudouridine
🚨 New paper published in RNA!
Scientists often say anecdotally that RNA modifications are disrupted in immortalized cells — but no one’s really tested it.
So we did: ψ-mapping in primary T cells vs. Jurkat cells using direct RNA-seq.
📄 tinyurl.com/TCellPsiRNA
#nanopore #RNA #pseudouridine
July 17, 2025 at 5:22 PM
1/🧵
🚨 New paper published in RNA!
Scientists often say anecdotally that RNA modifications are disrupted in immortalized cells — but no one’s really tested it.
So we did: ψ-mapping in primary T cells vs. Jurkat cells using direct RNA-seq.
📄 tinyurl.com/TCellPsiRNA
#nanopore #RNA #pseudouridine
🚨 New paper published in RNA!
Scientists often say anecdotally that RNA modifications are disrupted in immortalized cells — but no one’s really tested it.
So we did: ψ-mapping in primary T cells vs. Jurkat cells using direct RNA-seq.
📄 tinyurl.com/TCellPsiRNA
#nanopore #RNA #pseudouridine
Reposted by Sara Rouhanifard
In this incredible work, @srouhanifard.bsky.social developed a new catalyst, which makes CuAAC truly biocompatible
rdcu.be/enfHz
rdcu.be/enfHz
inCu-click: DNA-enhanced ligand enables live-cell, intracellular click chemistry reaction with copper catalyst
Nature Communications - Tracking biomolecules in living cells requires fast but gentle labeling. Here, authors introduce inCu-click, a DNA-conjugated ligand that localizes copper to enable...
rdcu.be
June 17, 2025 at 1:15 AM
In this incredible work, @srouhanifard.bsky.social developed a new catalyst, which makes CuAAC truly biocompatible
rdcu.be/enfHz
rdcu.be/enfHz
Just published: “inCu-click: DNA-enhanced ligand enables live-cell click chemistry with copper catalyst” in @natcomms.nature.com! 🚀
A DNA-conjugated chelator locks Cu⁺ ions for in situ CuAAC at nanomolar doses—zero toxicity.
Read the full paper here ➡️ rdcu.be/enfHz #clickchemistry
A DNA-conjugated chelator locks Cu⁺ ions for in situ CuAAC at nanomolar doses—zero toxicity.
Read the full paper here ➡️ rdcu.be/enfHz #clickchemistry
inCu-click: DNA-enhanced ligand enables live-cell, intracellular click chemistry reaction with copper catalyst
Nature Communications - Tracking biomolecules in living cells requires fast but gentle labeling. Here, authors introduce inCu-click, a DNA-conjugated ligand that localizes copper to enable...
rdcu.be
May 29, 2025 at 1:08 PM
Just published: “inCu-click: DNA-enhanced ligand enables live-cell click chemistry with copper catalyst” in @natcomms.nature.com! 🚀
A DNA-conjugated chelator locks Cu⁺ ions for in situ CuAAC at nanomolar doses—zero toxicity.
Read the full paper here ➡️ rdcu.be/enfHz #clickchemistry
A DNA-conjugated chelator locks Cu⁺ ions for in situ CuAAC at nanomolar doses—zero toxicity.
Read the full paper here ➡️ rdcu.be/enfHz #clickchemistry
1/6 🧬New paper at @cp-cellsystems.bsky.social led by @sashafanari.bsky.social! Does pseudouridine (Ψ) dynamically respond to cell state? We used nanopore DRS + Mod-p ID to map Ψ in neuron-like cells under “normal” and “perturbed” conditions (healthy differentiation and unhealthy Pb2+ poisoning).
March 21, 2025 at 3:42 PM
1/6 🧬New paper at @cp-cellsystems.bsky.social led by @sashafanari.bsky.social! Does pseudouridine (Ψ) dynamically respond to cell state? We used nanopore DRS + Mod-p ID to map Ψ in neuron-like cells under “normal” and “perturbed” conditions (healthy differentiation and unhealthy Pb2+ poisoning).
Reposted by Sara Rouhanifard
Sitting in a journal club-style class right now and after the main presenters present, there are "roles" from others in the group, like the "archeologist" who looks into the citation trail, the "private investigator" who tries to dig into the history, and the "industry practitioner", etc. Cool idea!
March 18, 2025 at 3:15 PM
Sitting in a journal club-style class right now and after the main presenters present, there are "roles" from others in the group, like the "archeologist" who looks into the citation trail, the "private investigator" who tries to dig into the history, and the "industry practitioner", etc. Cool idea!
Reposted by Sara Rouhanifard
🧪🧬👩🔬🖥️
Do immortalized cells have a different RNA modification profile compared to primary cells? 🤔
@sashafanari.bsky.social @wanunupore.bsky.social @srouhanifard.bsky.social assess the most abundant RNA modification, pseudouridine, in primary and immortalized human T cells
👇
doi.org/10.1101/2025...
Do immortalized cells have a different RNA modification profile compared to primary cells? 🤔
@sashafanari.bsky.social @wanunupore.bsky.social @srouhanifard.bsky.social assess the most abundant RNA modification, pseudouridine, in primary and immortalized human T cells
👇
doi.org/10.1101/2025...
Direct RNA sequencing of primary human T cells reveals the impact of immortalization on mRNA pseudouridine modifications.
Immortalized cell lines are commonly used as proxies for primary cells in human biology research. For example, Jurkat leukemic T cells fundamentally contributed to uncovering T cell signaling, activat...
doi.org
March 10, 2025 at 8:49 PM
🧪🧬👩🔬🖥️
Do immortalized cells have a different RNA modification profile compared to primary cells? 🤔
@sashafanari.bsky.social @wanunupore.bsky.social @srouhanifard.bsky.social assess the most abundant RNA modification, pseudouridine, in primary and immortalized human T cells
👇
doi.org/10.1101/2025...
Do immortalized cells have a different RNA modification profile compared to primary cells? 🤔
@sashafanari.bsky.social @wanunupore.bsky.social @srouhanifard.bsky.social assess the most abundant RNA modification, pseudouridine, in primary and immortalized human T cells
👇
doi.org/10.1101/2025...
Reposted by Sara Rouhanifard
Direct RNA sequencing of primary human T cells reveals the impact of immortalization on mRNA pseudouridine modifications. https://www.biorxiv.org/content/10.1101/2025.03.02.641090v1
March 10, 2025 at 5:34 PM
Direct RNA sequencing of primary human T cells reveals the impact of immortalization on mRNA pseudouridine modifications. https://www.biorxiv.org/content/10.1101/2025.03.02.641090v1
Office hours are starting
February 21, 2025 at 2:39 PM
Office hours are starting
Reposted by Sara Rouhanifard
Online Now: Identification of molecular determinants of gene-specific bursting patterns by high-throughput imaging screens
Identification of molecular determinants of gene-specific bursting patterns by high-throughput imaging screens
Sood et al. used high-throughput screening to identify regulators of gene bursting and find both gene- and cell-type-specific effectors. Acetylation alters burst size in a gene-specific manner but is independent of promoter acetylation. Rather,…
dlvr.it
February 19, 2025 at 11:57 PM
Online Now: Identification of molecular determinants of gene-specific bursting patterns by high-throughput imaging screens
Reposted by Sara Rouhanifard
Single-molecule live-cell RNA imaging with CRISPR–Csm - @doudna-lab.bsky.social @qb3-berkeley.bsky.social @innovativegenomics.bsky.social go.nature.com/3EJPKsM
Single-molecule live-cell RNA imaging with CRISPR–Csm - Nature Biotechnology
Single-molecule live-cell fluorescence in situ hybridization uses an RNA-targeting CRISPR–Csm complex to image and track endogenous RNAs.
go.nature.com
February 18, 2025 at 3:29 PM
Single-molecule live-cell RNA imaging with CRISPR–Csm - @doudna-lab.bsky.social @qb3-berkeley.bsky.social @innovativegenomics.bsky.social go.nature.com/3EJPKsM
Reposted by Sara Rouhanifard
Cool paper using LLM to discover a protein sequence code for subcellular localization 👏
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Protein codes promote selective subcellular compartmentalization
Cells have evolved mechanisms to distribute ~10 billion protein molecules to subcellular compartments where diverse proteins involved in shared functions must assemble. Here, we demonstrate that prote...
www.science.org
February 9, 2025 at 12:46 AM
Cool paper using LLM to discover a protein sequence code for subcellular localization 👏
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Sara Rouhanifard
Gene editing technology began by people studying salt marshes. Ozempic began by folks studying the venom of Gila Monsters. Support for basic science has empowered us to understand our world. Tethering it to applications health has transformed and saved countless lives.
February 8, 2025 at 1:45 PM
Gene editing technology began by people studying salt marshes. Ozempic began by folks studying the venom of Gila Monsters. Support for basic science has empowered us to understand our world. Tethering it to applications health has transformed and saved countless lives.
Reposted by Sara Rouhanifard
Check it out! Another novel RNA modification - ADP-ribosylation - that was previously only known on proteins. A cousin to #glycoRNA 👏
www.nature.com/articles/s41...
www.nature.com/articles/s41...
February 6, 2025 at 7:38 PM
Check it out! Another novel RNA modification - ADP-ribosylation - that was previously only known on proteins. A cousin to #glycoRNA 👏
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Sara Rouhanifard
"Imagine a DAPI-like stain, but for the extracellular matrix." That's basically how this work was pitched to me by Kayvon and Antonio a year or so ago. Now the final product really delivers. Read about their versatile label for ECM in living tissues here: www.nature.com/articles/s41...
February 6, 2025 at 4:02 PM
"Imagine a DAPI-like stain, but for the extracellular matrix." That's basically how this work was pitched to me by Kayvon and Antonio a year or so ago. Now the final product really delivers. Read about their versatile label for ECM in living tissues here: www.nature.com/articles/s41...
Reposted by Sara Rouhanifard
Liu, ... Rouhanifard have optimized nuclear FISH to the point where it's now possible to sort cells based on transcript production. They sort cells into bins and measure chromatin state at the locus whose tx was sorted on.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
NuclampFISH enables cell sorting based on nuclear RNA expression for chromatin analysis
Transcriptional bursts refer to periods when RNA polymerase interacts with a DNA locus, leading to active gene transcription. This bursting activity can vary across individual cells, and analyzing the...
www.biorxiv.org
January 8, 2025 at 7:52 PM
Liu, ... Rouhanifard have optimized nuclear FISH to the point where it's now possible to sort cells based on transcript production. They sort cells into bins and measure chromatin state at the locus whose tx was sorted on.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...