Author

Safa Saeed

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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Bioinformatics· 1 Genomics· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 2 Organism:human· 2 Assay:bulk RNA-seq· 1 Research Focus:differential expression· 1 Research Focus:gene regulatory network inference· 1 Organism:mouse· 1 Approach:statistical model· 1 Research Focus:variant calling· 1

Frequent Co-Authors

Ludmil B. AlexandroviD· 2 shared Shuvro Prokash NandiiD· 2 shared Arturo Bujarrabal-DuesoiD· 1 shared Audrey Kristin· 1 shared Bérénice ChavaneliD· 1 shared Björn SchumacheriD· 1 shared David H. MeyeriD· 1 shared Foster C. Jacobs· 1 shared

Activity by Year

2025-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 29 mutual co-author links

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2 shared papersBioinformatics

Ludmil B. AlexandrovORCID

Mutual co-authors in cluster

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2 papers

Recent·Most cited

The DREAM complex links somatic mutation, lifespan, and disease

Zane Koch, Shuvro Prokash Nandi, Kate Licon, Arturo Bujarrabal-Dueso, David H. Meyer, Safa Saeed, Pirunthan Perampalam, Frederick A. Dick, Björn Schumacher, Ludmil B. Alexandrov, Trey E. Ideker

This study shows that DREAM complex activity influences somatic mutation burden, lifespan, and age-related disease, with reduced activity linked to longer lifespan and lower disease risk.

bioRxiv · Sep 15, 2025 · PreprintBioinformatics

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