Publications

Research & presentations.

Peer-reviewed articles, scientific reviews, collaborative studies and conference abstracts spanning cancer epigenomics, computational methods, multiomics and precision oncology.

Underlined author names identify current or former Epigenome Lab members. Conference abstracts are identified separately from full research papers.

2026

Chromatin accessibility landscapes define stromal cell identities across tissues

Amin Nooranikhojasteh, Ghazaleh Tavallaee, Nicholas Khuu, Shu Yi Shen, Shaida Ouladan, Ayush Raman, Elias Orouji

Communications Biology · Single-cell epigenomics

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2025

Benchmarking peak calling methods for CUT&RUN

Amin Nooranikhojasteh, Ghazaleh Tavallaee, Elias Orouji

Bioinformatics · Computational methods

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2025

Chimeric Antigen Receptor-T Cells in Colorectal Cancer: Pioneering New Avenues in Solid Tumor Immunotherapy

Shaida Ouladan, Elias Orouji

Journal of Clinical Oncology · Oncology perspective

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2024

Mapping the 3D genome architecture

Ghazaleh Tavallaee, Elias Orouji

Computational and Structural Biotechnology Journal (online December 2024) · 3D genome

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2024

Beyond traditional subtyping: a multilayered genomic perspective on colorectal cancer

Shaida Ouladan, Elias Orouji

Gut · Precision oncology

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2023

MYC reshapes CTCF-mediated chromatin architecture in prostate cancer

Zhao Wei, Song Wang, Yaning Xu, Wenzheng Wang, Fraser Soares, Musaddeque Ahmed, Ping Su, Tingting Wang, Elias Orouji, Xin Xu, Yong Zeng, Sujun Chen, Xiaoyu Liu, Tianwei Jia, Zhaojian Liu, Lutao Du, Yunshan Wang, Shaoyong Chen, Chuanxin Wang, Housheng Hansen He, Haiyang Guo

Nature Communications · Cancer genome architecture

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2022

Chromatin state dynamics confers specific therapeutic strategies in enhancer subtypes of colorectal cancer

Elias Orouji, Ayush T Raman, et al.

Gut · Cancer epigenomics

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2022

Computational methods to explore chromatin state dynamics

Elias Orouji, Ayush T Raman

Briefings in Bioinformatics · Computational epigenomics

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2021

Methylation-eQTL analysis in cancer research

Yusha Liu, Keith A Baggerly, Elias Orouji, Ganiraju Manyam, Huiqin Chen, Michael Lam, Jennifer S Davis, Michael S Lee, Bradley M Broom, David G Menter, Kunal Rai, Scott Kopetz, Jeffrey S Morris

Bioinformatics · Statistical genomics

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2021

Reprogramming of bivalent chromatin states in NRAS mutant melanoma suggests PRC2 inhibition as a therapeutic strategy

Christopher J Terranova, Ming Tang, Mayinuer Maitituoheti, Ayush T Raman, Archit K Ghosh, Jonathan Schulz, Samir B Amin, Elias Orouji, Katarzyna Tomczak, Sharmistha Sarkar, Junna Oba, Caitlin Creasy, Chang-Jiun Wu, Samia Khan, Rossana Lazcano, Khalida Wani, Anand Singh, Praveen Barrodia, Dongyu Zhao, Kaifu Chen, Lauren E Haydu, Wei-Lien Wang, Alexander J Lazar, Scott E Woodman, Chantale Bernatchez, Kunal Rai

Cell Reports · Cancer epigenomics

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2026

Chromatin Landscape of Cancer Cell Lines Identifies Enhancer Subtypes

Mahinur Mattohti, Emre Arslan, Ayush T. Raman, Christopher Terranova, Zhiyi Liu, Elias Orouji, Sanjana Srinivasan, Veena Kochat, Ming Tang, Samirkumar B. Amin, Jonathan Schulz, Neha S. Samant, Anand K. Singh, Emmanuel Martinez-Ledesma, Sharmistha Sarkar, Marcus Coyle, Christopher Bristow, Faye M. Johnson, Curtis R. Pickering, Keila E. Torres, Jeffery N. Myers, Kunal Rai

bioRxiv (preprint, not peer reviewed) · Preprint · Pan-cancer epigenomics

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2025

A novel framework for deciphering 3D genome structure in colorectal cancer

Amin Nooranikhojasteh, Jakob Zerbs, Ghazaleh Tavallaee, Elias Orouji

AACR Annual Meeting · Cancer Research, Abstract 215 · Meeting abstract · Not a full paper

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2025

Deciphering colorectal cancer progression through integrative epigenomic analysis for precision therapeutics

Ghazaleh Tavallaee, Amin Nooranikhojasteh, Elias Orouji

ASCO Annual Meeting · Journal of Clinical Oncology, e15561 · Meeting abstract · Not a full paper

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Explore additional collaborative publications and our extended research record through Elias Orouji on Google Scholar or PubMed . Citation details are provided by linked publishers.