Author

Amr K. Makhamreh

Northeastern UniversityORCID 0000-0002-4615-5820Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Research Focus:differential expression· 4 Organism:human· 4 Assay:bulk RNA-seq· 2 Assay:long-read sequencing· 2 Approach:statistical model· 2 Research Focus:database / resource· 1 Approach:experimental assay· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

Meni WanunuiD· 4 shared Sara H. RouhanifardiD· 4 shared Howard GamperiD· 3 shared Sepideh TavakoliiD· 3 shared Ya‐Ming HouiD· 3 shared Caroline A. McCormickiD· 2 shared Dylan BlochiD· 2 shared Michele MeseonznikiD· 2 shared

Activity by Year

2023-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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4 shared papersGenomics

Meni WanunuORCID

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4 papers

Recent·Most cited

Direct RNA sequencing of primary human T cells reveals the impact of immortalization on mRNA pseudouridine modifications.

Oleksandra Fanari, Dylan Bloch, Yuchen Qiu, Michele Meseonznik, Amr K. Makhamreh, Meni Wanunu, Sara H. Rouhanifard

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.

bioRxiv · Mar 2, 2025 · PreprintGenomics

Messenger-RNA Modification Standards and Machine Learning Models Facilitate Absolute Site-Specific Pseudouridine Quantification

Amr K. Makhamreh, Sepideh Tavakoli, Ali Fallahi, Xinqi Kang, Howard Gamper, Mohammad Nabizadehmashhadtoroghi, Miten Jain, Ya‐Ming Hou, Sara H. Rouhanifard, Meni Wanunu

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

Scientific Reports · Sep 28, 2024Peer-reviewedGenomics

Probing enzyme-dependent pseudouridylation using direct RNA sequencing to assess neuronal epitranscriptome plasticity

Oleksandra Fanari, Sepideh Tavakoli, Yuchen Qiu, Amr K. Makhamreh, Keqing Nian, Stuart Akeson, Michele Meseonznik, Caroline A. McCormick, Dylan Bloch, Howard Gamper, Miten Jain, Ya‐Ming Hou, Meni Wanunu, Sara H. Rouhanifard

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.

bioRxiv · Mar 26, 2024 · PreprintGenomics

Semi-quantitative detection of pseudouridine modifications and type I/II hypermodifications in human mRNAs using direct and long-read sequencing

Sepideh Tavakoli, Mohammad Nabizadeh, Amr K. Makhamreh, Howard Gamper, Caroline A. McCormick, Neda Kari Rezapour, Ya‐Ming Hou, Meni Wanunu, Sara H. Rouhanifard

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.

Nature Communications · Jan 19, 2023Peer-reviewedGenomics