Sara H. Rouhanifard

NanoCortex provides a unified agentic framework for nanopore sequencing analysis, improving usability over general-purpose models by integrating data processing and biological interpretation.

The paper develops a multi-scale kinetic model and advanced assays to assess mRNA-LNP potency by integrating mechanistic understanding with multi-omics data.

This study shows that PUS7's cytoplasmic localization enhances stress tolerance by increasing pseudouridylation of mRNAs involved in metal and ROS homeostasis.

The paper introduces a quality control method for synthetic RNA using Oxford Nanopore sequencing to assess integrity, sequence accuracy, and modification sites, improving synthesis fidelity and yield.

NuclampFISH enables cell sorting based on nuclear RNA expression for chromatin analysis by using reversible crosslinkers and amplified FISH signals.

The paper compares pseudouridine modification sites in primary and immortalized human T cells using direct RNA sequencing, finding most sites are conserved with some cell-type specific differences.

This paper develops machine learning models to quantitatively measure pseudouridine occupancy in human mRNAs using synthetic controls, revealing site-specific requirements for accurate classification.

The paper generates and characterizes modification-free RNA transcripts from human cell lines for use as controls in nanopore direct RNA sequencing analysis.

The paper maps pseudouridylation sites in human cell lines using nanopore sequencing and shows how psi modifications affect translation through distinct mechanisms.

This study uses direct RNA sequencing to examine pseudouridylation dynamics in neurons under healthy and unhealthy conditions, finding changes in psi writer expression and site occupancy.

The paper develops a semi-quantitative method to detect pseudouridine modifications in human mRNAs using long-read nanopore sequencing and validates it with synthetic RNA controls.

This paper develops a cell-free method to directly measure infectious viral titer by capturing intact virions with an aptamer and detecting their genomes using FISH.

The paper develops a DNA-enhanced CuAAC ligand for intracellular biomolecule labeling in live cells, demonstrating reduced copper toxicity and effective labeling.

This paper introduces clampFISH, a method for detecting RNA with high-gain signal amplification, enabling single-cell and single-molecule resolution using fluorescent probes.

The paper develops an RNA FISH method to visualize adenosine-to-inosine editing in single cells and finds no correlation with nuclear localization or paraspeckle association.