Publications

2026

1. In prep.

   A branching process model of cell lineage links positional signaling to the canalization of clonal fate

   Weixiang Fang, Yi Yang, Jessica D Lin, and Reza Kalhor

   2026

   Manuscript in preparation
2. Submitted

   Genomic recording of gene-expression history along lineage trees

   James E Forsmo, Weixiang Fang, Jessica D Lin, Melanie Vazquez-Arroyo, Luca Fang, Jinwoo Jun, WanYing Lin, and Reza Kalhor

   2026

   In submission

2025

1. Cell Rep.

   

   A cell-state axis underlying colonization in carcinomas with implications for metastasis risk prediction and interception

   Jesse S Handler, Zijie Li, Rachel K Dveirin, Weixiang Fang, Hani Goodarzi, Elana J Fertig, and Reza Kalhor

   Cell Reports, 2025

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2. Methods Mol. Biol.

   

   Reconstructing progenitor state hierarchy and dynamics using lineage barcoding data

   Weixiang Fang, Yi Yang, Hongkai Ji, and Reza Kalhor

   In Lineage Tracing: Methods and Protocols, 2025

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2024

1. bioRxiv

   

   Quantifying functional conservation of human and mouse regulatory elements via FUNCODE

   Weixiang Fang, Chaoran Chen, Boyang Zhang, Yi Wang, Ruzhang Zhao, Weiqiang Zhou, and Hongkai Ji

   bioRxiv (in revision at Genome Biology), 2024

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   Evolutionary conservation is crucial for understanding genome functions and lays the foundation for using animal models in studying human diseases. However, conventional conservation scores based on DNA sequence evolution do not capture the dynamic biochemical activities of DNA elements, termed functional conservation. Quantifying functional conservation has been limited by the availability of functional genomic data matched across species. To address this, we developed FUNCODE, a framework for characterizing functional conservation through in silico sample matching. Applying FUNCODE to 2,595 uniformly processed datasets from the Encyclopedia of DNA Elements (ENCODE), we generated genome-wide FUNCODE scores for human and mouse regulatory elements, identifying 3.3 million functionally conserved human-mouse element pairs. We demonstrate FUNCODE’s diverse applications, including annotating 78,501 novel regulatory elements, transferring 37,968 high-resolution human ENCODE Hi-C loops in immune lineages to mice, identifying conserved functional signals for disease modeling, and enhancing cross-species integration of single-cell omics data.

2. bioRxiv

   A consensus variant-to-function score to functionally prioritize variants for disease

   Tabassum Fabiha, Ivy Evergreen, Soumya Kundu, Anusri Pampari, Sergey Abramov, Alexandr Boytsov, Kari Strouse, Katherine Dura, Weixiang Fang, Gaspard Kerner, John Butts, Thahmina Ali, Andreas Gschwind, Kristy S Mualim, Jill E Moore, Zhiping Weng, Jacob Ulirsch, Hongkai Ji, Jeff Vierstra, Timothy E Reddy, Stephen B Montgomery, Jesse Engreitz, Anshul Kundaje, Ryan Tewhey, Alkes Price, and Kushal Dey

   bioRxiv, 2024

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2023

1. iScience

   

   High-throughput screening for myelination promoting compounds using human stem cell-derived oligodendrocyte progenitor cells

   Weifeng Li, Cynthia Berlinicke, Yinyin Huang, Stefanie Giera, Anna G McGrath, Weixiang Fang, Chaoran Chen, Felipe Takaesu, Xiaoli Chang, Yukan Duan, D Kumar, Calvin Chang, Hai-Quan Mao, G Sheng, James C Dodge, Hongkai Ji, S Madden, Donald J Zack, and Xitiz Chamling

   iScience, 2023

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2. IJMS

   

   Regional gene expression in the retina, optic nerve head, and optic nerve of mice with optic nerve crush and experimental glaucoma

   Casey J Keuthan, Julie A Schaub, Meihan Wei, Weixiang Fang, Sarah Quillen, Elizabeth Kimball, Thomas V Johnson, Hongkai Ji, Donald J Zack, and Harry A Quigley

   International Journal of Molecular Sciences, 2023

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2022

1. Cell

   

   Quantitative fate mapping: A general framework for analyzing progenitor state dynamics via retrospective lineage barcoding

   Weixiang Fang, Claire M Bell, Abel Sapirstein, Soichiro Asami, Kathleen Leeper, Donald J Zack, Hongkai Ji, and Reza Kalhor

   Cell, 2022

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2021

1. Nat. Commun.

   

   Single-cell transcriptomic reveals molecular diversity and developmental heterogeneity of human stem cell-derived oligodendrocyte lineage cells

   Xitiz Chamling, Alyssa Kallman, Weixiang Fang, Cynthia A Berlinicke, Joseph L Mertz, Prajwal Devkota, Itzy E Morales Pantoja, Matthew D Smith, Zhicheng Ji, Calvin Chang, A Kaushik, L Chen, Kathleen A Whartenby, Peter A Calabresi, Hai-Quan Mao, Hongkai Ji, Tza-Huei Wang, and Donald J Zack

   Nature Communications, 2021

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2019

1. NAR

   

   Global prediction of chromatin accessibility using small-cell-number and single-cell RNA-seq

   Weiqiang Zhou, Zhicheng Ji, Weixiang Fang, and Hongkai Ji

   Nucleic Acids Research, 2019

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