Author

Xuan Cindy Li

National Institutes of HealthORCID 0000-0002-4774-8230Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Assay:DNA methylation· 3 Organism:human· 3 Approach:statistical model· 3 Research Focus:benchmarking· 2 Research Focus:clustering· 2 Research Focus:differential expression· 2 Approach:optimal transport· 2 Assay:bulk RNA-seq· 1

Frequent Co-Authors

Alejandro A. SchäfferiD· 4 shared S. Cenk ŞahinalpiD· 4 shared Stephen M. MountiD· 3 shared Yuelin LiuiD· 3 shared Eytan RuppiniD· 2 shared Farid Rashidi MehrabadiiD· 2 shared Kenneth AldapeiD· 2 shared Salem MalikićiD· 2 shared

Activity by Year

2020-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 38 mutual co-author links

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4 shared papersBioinformatics

Alejandro A. SchäfferORCID

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4 papers

Recent·Most cited

Qombucha: Reconstructing unobserved progenitor methylation profiles reveals distinct developmental programs in glioblastoma

Xuan Cindy Li, H. Lalchungnunga, Ananth Hari, Yuelin Liu, Omkar Singh, Zhichao Wu, Zied Abdullaev, Stephen M. Mount, Kenneth Aldape, Eytan Ruppin, Alejandro A. Schäffer, S. Cenk Şahinalp

Qombucha infers unobserved progenitor methylation profiles in GBM, revealing subtype-specific developmental programs and improved subtype classification.

bioRxiv · Aug 12, 2026 · PreprintBioinformatics

Fair molecular feature selection unveils universally tumor lineage-informative methylation sites in colorectal cancer

Xuan Cindy Li, Yuelin Liu, Alejandro A. Schäffer, Stephen M. Mount, S. Cenk Şahinalp

This paper introduces FALAFL, a fair feature selection algorithm for single-cell methylation data, identifying universally tumor lineage-informative CpG sites in colorectal cancer.

Bioinformatics · Jul 1, 2025Peer-reviewedBioinformatics

Single-cell methylation sequencing data reveal succinct metastatic migration histories and tumor progression models

Yuelin Liu, Xuan Cindy Li, Farid Rashidi Mehrabadi, Alejandro A. Schäffer, Drew W. Pratt, David Robert Crawford, Salem Malikić, Erin K. Molloy, Vishaka Gopalan, Stephen M. Mount, Eytan Ruppin, Kenneth Aldape, S. Cenk Şahinalp

This paper introduces Sgootr, a method to infer tumor lineage trees from single-cell methylation data, revealing metastatic progression models and identifying lineage-informative CpG sites.

Genome Research · Jun 14, 2023Peer-reviewedBioinformatics

PhISCS-BnB: A Fast Branch and Bound Algorithm for the Perfect Tumor Phylogeny Reconstruction Problem

Erfan Sadeqi Azer, Farid Rashidi Mehrabadi, Salem Malikić, Xuan Cindy Li, Osnat Bartok, Kevin Litchfield, Ronen Levy, Yardena Samuels, Alejandro A. Schäffer, Edward Michael Gertz, Chi‐Ping Day, Eva Pérez‐Guijarro, Kerrie L. Marie, Maxwell P. Lee, Glenn T Merlino, , S. Cenk Şahinalp

PhISCS-BnB computes the most likely perfect tumor phylogeny from single-cell sequencing data, offering optimality guarantees and significant speed improvements over existing methods.

Bioinformatics · Jul 1, 2020Peer-reviewedBioinformatics