Author

Zichen Jiang

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· 3 Cancer Biology· 1 Genomics· 1

Signature Assays, Organisms & Methods

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Organism:human· 5 Research Focus:variant calling· 4 Assay:whole-genome sequencing· 4 Approach:statistical model· 3 Approach:experimental assay· 2 Assay:whole-exome sequencing· 2 Approach:benchmark study· 1 Research Focus:benchmarking· 1

Frequent Co-Authors

Ludmil B. AlexandroviD· 4 shared Marcos Díaz‐GayiD· 2 shared Mariya KazachkovaiD· 2 shared Michael R. StrattoniD· 2 shared Paul BrennaniD· 2 shared Raviteja VangaraiD· 2 shared Sarah MoodyiD· 2 shared Ammal AbbasiiD· 1 shared

Activity by Year

2023-2026 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 28 mutual co-author links

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4 shared papersBioinformatics

Ludmil B. AlexandrovORCID

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5 papers

Recent·Most cited

Identification and Validation of a Previously Missed Mutational Signature in Colorectal Cancer

Mariya Kazachkova, Burçak Otlu, Marcos Díaz‐Gay, Ammal Abbasi, Sarah Moody, Zichen Jiang, Sandra P. Perdomo, David C. Wedge, Paul Brennan, Michael R. Stratton, Ludmil B. Alexandrov

The paper identifies and validates a previously missed mutational signature in microsatellite-stable colorectal cancer, showing it is distinct from known signatures and not caused by canonical DNA repair defects.

Nature Communications · Aug 12, 2026Peer-reviewedCancer Biology

The Impact of Variant Calling on Substitution Mutational Signature Inference

Zichen Jiang, Jessica N. Au, Mariya Kazachkova, Marcos Díaz-Gay, Raviteja Vangara, Ludmil B. Alexandrov

This study evaluates how variant calling strategies affect mutational signature inference, finding that consensus calling reduces artifacts while preserving true signals.

bioRxiv · Dec 12, 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

Loop Catalog: a comprehensive HiChIP database of human and mouse samples

Joaquin Reyna, Kyra Fetter, Romeo Ignacio, Cemil Can Ali Marandi, Astoria Ma, Nikhil Rao, Zichen Jiang, Daniela Salgado Figueroa, Sourya Bhattacharyya, Ferhat Ay

Loop Catalog compiles HiChIP data from 1000+ human and mouse samples to provide a resource for analyzing chromatin loops and their regulatory roles.

Genome biology · Jun 20, 2025Peer-reviewedBioinformatics

Assigning mutational signatures to individual samples and individual somatic mutations with SigProfilerAssignment

Marcos Díaz‐Gay, Raviteja Vangara, Mark D. Barnes, Xi Wang, S. M. Ashiqul Islam, Ian Vermes, Stephen Oscar Duke, Nithish Bharadhwaj Narasimman, Ting Yang, Zichen Jiang, Sarah Moody, Sergey Senkin, Paul Brennan, Michael R. Stratton, Ludmil B. Alexandrov

SigProfilerAssignment refits known substitution, doublet, indel and copy-number mutational signatures to single samples and probabilistically to individual mutations, outperforming four refitting tools on 2,700 synthetic genomes.

Bioinformatics · Dec 1, 2023Peer-reviewedBioinformatics✦ In-depth digest