Author

Ahmed Abbas

The Jackson Laboratory for Genomic Medicine

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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Bioinformatics· 2 Cancer Biology· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 2 Assay:bulk RNA-seq· 1 Research Focus:cancer & tumor microenvironment· 1 Assay:ChIP-seq· 1 Research Focus:chromatin & epigenetic regulation· 1 Research Focus:dimensionality reduction· 1 Approach:experimental assay· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

Akio Kobayashi· 1 shared Andrew B. GladdeniD· 1 shared Bin ZhouiD· 1 shared Byoungkoo LeeiD· 1 shared Chao XingiD· 1 shared Chia‐Lin WeiiD· 1 shared Diego H. CastrillóniD· 1 shared Elena LucasiD· 1 shared

Activity by Year

2019-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 14 mutual co-author links

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1 shared paperCancer Biology

Akio Kobayashi

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Author profile →

3 papers

Recent·Most cited

PAX2 is Transcriptionally Silenced by a Distinct Mechanism of Epigenetic Reprogramming to Initiate Endometrial Carcinogenesis

Subhransu S. Sahoo, Susmita Gurjar Ramanand, Ileana Cuevas, Yunpeng Gao, Sora Lee, Ahmed Abbas, Xunzhi Zhang, Vinod Kumar, Prasad R. K. Koduru, Sambit Roy, Russell R. Broaddus, Victoria Lin Bae-Jump, Andrew B. Gladden, Jayanthi Sivasothy Lea, Elena Lucas, , Diego H. Castrillón

This study identifies a specific epigenetic mechanism that silences PAX2 to initiate most endometrial cancers.

Journal of Clinical Investigation · Aug 15, 2025Peer-reviewedCancer Biology

ChIA-PIPE: A fully automated pipeline for ChIA-PET data analysis and visualization

Byoungkoo Lee, Jiahui Wang, Liuyang Cai, Minji Kim, Sandeep Namburi, Harianto Tjong, Yuliang Feng, Ping Wang, Zhonghui Tang, Ahmed Abbas, Chia‐Lin Wei, Yijun Ruan, Sheng Li

ChIA-PIPE is a fully automated pipeline for analyzing and visualizing ChIA-PET data, including quality assessment and visualization tools.

Science Advances · Jul 10, 2020Peer-reviewedBioinformatics

Integrating Hi-C and FISH data for modeling 3D organizations of chromosomes

Ahmed Abbas, Xuan He, Jing Niu, Bin Zhou, Guangxiang Zhu, Tszshan Ma, Jiangpeikun Song, Juntao Tony Gao, Michael Q. Zhang, Jianyang Zeng

This paper introduces GEM-FISH, a method that integrates Hi-C and FISH data to improve 3D chromosome modeling, showing better accuracy in TADs, compartments, and super-enhancer distributions than Hi-C alone.

Nature Communications · May 3, 2019Peer-reviewedBioinformatics