Author

Shams Al-Azzam

University of California San Diego

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 Bioinformatics· 1 Cancer Biology· 1

Signature Assays, Organisms & Methods

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Assay:whole-genome sequencing· 4 Organism:human· 3 Approach:statistical model· 3 Research Focus:variant calling· 3 Organism:mouse· 2 Assay:bulk RNA-seq· 1 Research Focus:cell-cell communication· 1 Research Focus:chromatin & epigenetic regulation· 1

Frequent Co-Authors

Ludmil B. AlexandroviD· 4 shared Isabella StueweiD· 3 shared Maria ZhivaguiiD· 3 shared Shuvro Prokash NandiiD· 3 shared Audrey Kristin· 2 shared Luka CulibrkiD· 2 shared Mia PetljakiD· 2 shared Yuhe ChengiD· 2 shared

Activity by Year

2025-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 40 mutual co-author links

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4 shared papersGenomics

Ludmil B. AlexandrovORCID

Mutual co-authors in cluster

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4 papers

Recent·Most cited

A Compendium of 49 Experimental SBS Signatures for Decoding Human Cancer Mutational Processes

Maria Zhivagui, Jessica N. Au, Sanskruti Sharma, Peter T. Nguyen, Shams Al-Azzam, Jiang Zhang, Mark D. Barnes, Ludmil B. Alexandrov

The paper curates 49 experimental single-base substitution signatures from cancer genomes to link mutational processes to DNA damage mechanisms.

bioRxiv · Sep 4, 2026 · PreprintGenomics

Multi-omics profiling reveals microenvironmental remodeling as a key driver of house dust mite-induced lung cancer progression

Shams Al-Azzam, Isabella Stuewe, Sunandini Sharma, Miki Yamada-Hara, Arisachi Tanaka, Kegan Stringer, Merna Behnam, Norah Al-Azzam, Shuvro Prokash Nandi, Maria Zhivagui, Janelle Duong, Ting Yang, Scott Herdman, Maripat Corr, Nicholas J. G. Webster, , Samuel Bertin

This study uses multi-omics profiling to show that house dust mite exposure accelerates lung tumor growth through immune-mediated mechanisms by altering the tumor microenvironment.

Neoplasia · Jan 28, 2026Peer-reviewedCancer Biology

A Universal Duplex Sequencing Approach for Accurate Detection of Somatic Mutations

Shuvro Prokash Nandi, Yuhe Cheng, Shams Al-Azzam, Safa Saeed, Audrey Kristin, Nadia Sunico, Isabella Stuewe, Zichen Jiang, Luka Culibrk, Maria Zhivagui, Xiaoxu Yang, Rachel M. Wise, Foster C. Jacobs, Bérénice Chavanel, Michael Korenjak, , Ludmil B. Alexandrov

This paper introduces UDSeq, a duplex sequencing protocol for accurate somatic mutation detection with low DNA input and high coverage, achieving a low error rate and enabling cross-species profiling.

bioRxiv · Sep 14, 2025 · PreprintGenomics

Improved Mutation Detection in Duplex Sequencing Data with Sample-Specific Error Profiles

Yuhe Cheng, Shuvro Prokash Nandi, Luka Culibrk, Audrey Kristin, Isabella Stuewe, Shams Al-Azzam, Mia Petljak, Ludmil B. Alexandrov

DupCaller improves mutation detection in duplex sequencing by using sample-specific error profiles and a strand-aware model, increasing sensitivity across various samples and conditions.

bioRxiv · Jul 13, 2025 · PreprintBioinformatics