Author

Mohamed Ameen

Illumina (United States)

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Genomics· 2 Genetics· 1

Signature Assays, Organisms & Methods

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Research Focus:gene regulatory network inference· 3 Organism:human· 3 Approach:deep learning· 2 Assay:ATAC-seq· 1 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Research Focus:database / resource· 1 Research Focus:differential expression· 1

Frequent Co-Authors

Akshay BalsubramaniiD· 2 shared Anshul Bharat KundajeiD· 2 shared Ioannis KarakikesiD· 2 shared Ke WangiD· 2 shared Laksshman SundaramiD· 2 shared Surag NairiD· 2 shared A Blocker· 1 shared Abhimanyu BanerjeeiD· 1 shared

Activity by Year

2022-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 24 mutual co-author links

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2 shared papersGenetics

Akshay BalsubramaniORCID

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3 papers

Recent·Most cited

X-Atlas/Orion: Genome-wide Perturb-seq Datasets via a Scalable Fix-Cryopreserve Platform for Training Dose-Dependent Biological Foundation Models

Ann C Huang, Tsung-Han S. Hsieh, Jiang Zhu, Jackson Michuda, Ashton Teng, Soohong Kim, Elizabeth M Rumsey, Sharon K Lam, Ikenna Anigbogu, Philip Wright, Mohamed Ameen, Kwontae You, Christopher J Graves, Hyunsung John Kim, Adam J. Litterman, , Ci Chu

The paper introduces a scalable Perturb-seq platform called FiCS Perturb-seq and releases X-Atlas/Orion, a large Perturb-seq atlas, to improve foundation model development through dose-dependent genetic effects.

bioRxiv · Jun 11, 2025 · PreprintGenomics

Deep learning the cis-regulatory code of chromatin dynamics during cellular reprogramming

Surag Nair, Mohamed Ameen, Laksshman Sundaram, Anusri Pampari, Jacob Matthew Schreiber, Akshay Balsubramani, Yu Xin Wang, David Burns, Helen M. Blau, Ioannis Karakikes, Ke Wang, Anshul Bharat Kundaje

The paper uses deep learning to analyze chromatin accessibility and gene expression during reprogramming, revealing how TF concentrations and motif syntax influence cis-regulatory networks.

bioRxiv · Oct 4, 2023 · PreprintGenetics

Integrative single-cell analysis of cardiogenesis identifies developmental trajectories and non-coding mutations in congenital heart disease

Mohamed Ameen, Laksshman Sundaram, Mengcheng Shen, Abhimanyu Banerjee, Soumya Kundu, Surag Nair, Anna Shcherbina, Mingxia Gu, Kitchener D. Wilson, Avyay Varadarajan, Nirmal Vadgama, Akshay Balsubramani, Joseph C. Wu, J Engreitz, Kyle Kai‐How Farh, , Anshul Bharat Kundaje

This study uses single-cell chromatin accessibility analysis to identify developmental trajectories and non-coding mutations associated with congenital heart disease.

Cell · Dec 1, 2022Peer-reviewedGenomics