Mahmoud Ahmed, a postdoc researcher in genomics

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Contribute to the research topic I am coordinating for Frontiers (here)
Check out our two recent preprints on bioRxiv and medRxiv

Bio

I graduated from Cairo University with a medical degree. After graduation, I spent a year traveling and volunteering with youth organizations to bring a bit of fun and nature to underserved school kids. In 2016, I joined a lab in Jinju, South Korea, to do research. I studied autophagy and its role in development and disease using high-throughput sequencing data. I developed several open-source R packages and Shiny apps to work with gene expression and regulation data. Now I am building an open-source platform to discover and repurpose drugs for cancer. I also try my hand at the exciting field of cancer evolution. I spend most days between the Linux terminal, the R console, and the LaTex editor.

Work Experience

Senior Researcher. Gyeongsang National University, South Korea (2021 - Present)

Education

PhD. Gyeongsang National University - 2021
- Thesis: Transcriptional Regulation of Autophagy During Adipocyte Differentiation
MS. Gyeongsang National University - 2018
- Thesis: Systematic characterization of autophagy-related genes during the adipocyte differentiation using public-access data
MBBCh. Cairo University - 2014
Lots of online courses

Awards & Fellowships

Fellowship. Center for Human Resource Development in the Bio-health Industry (2021 - 2022)
Young Scientist Program Award. FAOBMB (2021)
Young Scientist Program Award. KSBMB (2020 & 2021)
Young Pioneer Research Award. Gyeongsang National University (2018 & 2019)

Interests

Cancer evolution
Drug discovery and repurposing
Regulation of gene expression
Adipocyte differentiation
Autophagy

Projects

Task specialization in evolving cancer cells

Studying task specialization and trade-offs in evolving cancer cells.

Perturbing biological networks in cancer cell lines

Studying causal biological networks and their perturbation using existing biological knowledge and data.

Transcriptional regulation of RKIP in cancer

Deciphering the regulatory circuits responsible for RKIP loss in different cancer cell models.

(Archived) Regulation of autophagy in development and disease

Studying the regulation of autophagy in development (adipocyte differentiation) and disease (cancer).

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Publications

Tissue-specific gene expression in obese hyperglycemic mice

Mahmoud Ahmed, Omar Elashkar, Jong Youl Lee, Eun Ae Jeong, Kyung Eun Kim, Gu Seob Roh, Deok Ryong Kim

All Life, vol. 15(1), Taylor & Francis, 2022, pp. 555-561

Disruption of cancer cell functions by task-specific drug perturbations

Mahmoud Ahmed, Deok Ryong Kim

Frontiers in Pharmacology, vol. 13, 2022

Meta-analysis of the Effect of Orlistat on The Body Mass Index in Obese Subjects

Gyeonghwa Jeong, Dongwoo Han, Mahmoud Ahmed, Deok Ryong Kim

medRxiv, Cold Spring Harbor Laboratory Press, 2022

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Posts

Jan 5, 2023

Public data for the public good

The human genome project galvanized the scientific community around an ambitious goal. It produced several crucial discoveries, and a new era of research began. For the first time, it became possible to estimate the number of human genes and compile a ...

The evolutionary war — how to beat cancer in its own game

Cancer evolves. That much is known and agreed upon. Researchers still, however, debate the detailed picture of how cancer came to be and why it still plages our species is subject to debate. Studying cancer through an evolutionary lens could provide an...

Gene expression adaptation in yeast, mice, and humans

Coding vs. non-coding variants Mutations produce novelty. The kind of novel variants on which selection acts. These variants fall within two broad categories depending on location in the genome: protein-coding and regulatory sequences. The former pro...

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