Publications

Link to all publications via Google Scholar.
Publications in reversed chronological order. Generated by jekyll-scholar.
† co-corresponding authors; * equal contribution.

Preprints

  1. On the consistent and scalable detection of spatial patterns
    Jiayu Su†, Jun Hou Fung, Haoyu Wang, Dian Yang, David A. Knowles†, Raul Rabadan†
    2026
    Detecting spatial patterns is fundamental to scientific discovery, yet current methods lack statistical consensus and face computational barriers when applied to large-scale spatial omics datasets. We unify major approaches through a single quadratic form and derive general consistency conditions. We reveal that several widely used methods, including Moran’s I, are inconsistent, and propose scalable corrections. The resulting test enables robust pattern detection across millions of spatial locations and single-cell lineage-tracing datasets.
    Link to paper Code Website
  2. Perplexity as a metric for isoform diversity in the human transcriptome
    Megan D Schertzer, Stella H Park, Jiayu Su, Gloria M Sheynkman, David A Knowles
    bioRxiv, 2025
    Link to paper

Peer-reviewed papers

  1. Mapping isoforms and regulatory mechanisms from spatial transcriptomics data with splisosm
    Jiayu Su†, Yiming Qu, Megan Schertzer, Haochen Yang, Jiahao Jiang, Tenzin Lhakhang, Theodore M Nelson, Stella Park, Qiliang Lai, Xi Fu, Seung-won Choi, David A Knowles†, Raul Rabadan†
    Nature Biotechnology, 2026
    Link to paper Code Website
  2. A foundation model of transcription across human cell types
    Xi Fu, Shentong Mo, Alejandro Buendia, Anouchka P Laurent, Anqi Shao, Maria del Mar Alvarez-Torres, Tianji Yu, Jimin Tan, Jiayu Su, Romella Sagatelian, Alberto Ferrando, Yanyan Lan, David M Owens, Teresa Palomero, Eric P Xing, Raul Rabadan
    Nature, 2025
  3. A niche driven mechanism determines response and a mutation-independent therapeutic approach for myeloid malignancies
    Ioanna Mosialou, Abdullah M Ali, Rossella Labella, Brygida Bisikirska, Alvaro Cuesta-Dominguez, Paraskevi Vgenopoulou, Ismarc Reyes, Sanjana M Rao, Anqi Wang, Na Luo, Marta Galan-Diez, Junfei Zhao, Brian J Chernak, Jan Philipp Bewersdorf, Kazuya Fukasawa, Jiayu Su, Jason Higa, Rachel A Adams, Adam L Corper, Sergey Pampou, Catherine M Woods, Xiaomin Fan, Roshan P Shah, Julie Feldstein, Na Liu, Cui Liang, Mael Heiblig, Steven Kornblau, Guillermo Garcia-Manero, Ellin Berman, Joseph G Jurcic, Raul Rabadan, Azra Raza, Stavroula Kousteni
    Cancer Cell, 2025
  4. Disentangling interpretable factors with supervised independent subspace principal component analysis
    Jiayu Su†, David A. Knowles†, Raul Rabadan†
    In Advances in Neural Information Processing Systems (NeurIPS), 2024
    Link to paper Code Website
  5. Smoother: a unified and modular framework for incorporating structural dependency in spatial omics data
    Jiayu Su†, Jean-Baptiste Reynier, Xi Fu, Guojie Zhong, Jiahao Jiang, Rydberg Supo Escalante, Yiping Wang, Luis Aparicio, Benjamin Izar, David A Knowles, Raul Rabadan†
    Genome Biology, 2023
    Link to paper Code Website
  6. A transcriptome-based single-cell biological age model and resource for tissue-specific aging measures
    Shulin Mao*, Jiayu Su*, Longteng Wang, Xiaochen Bo, Cheng Li†, Hebing Chen†
    Genome Research, 2023
    Link to paper Code Website
  7. Single-cell multi-omics defines the cell-type-specific impact of splicing aberrations in human hematopoietic clonal outgrowths
    Mariela Cortés-López, Paulina Chamely, Allegra G. Hawkins, Robert F. Stanley, Ariel D. Swett, Saravanan Ganesan, Tarek H. Mouhieddine, Xiaoguang Dai, Lloyd Kluegel, Celine Chen, Kiran Batta, Nili Furer, Rahul S. Vedula, John Beaulaurier, Alexander W. Drong, Scott Hickey, Neville Dusaj, Gavriel Mullokandov, Adam M. Stasiw, Jiayu Su, Ronan Chaligné, Sissel Juul, Eoghan Harrington, David A. Knowles, Catherine J. Potenski, Daniel H. Wiseman, Amos Tanay, Liran Shlush, Robert C. Lindsley, Irene M. Ghobrial, Justin Taylor, Omar Abdel-Wahab, Federico Gaiti, Dan A. Landau
    Cell Stem Cell, 2023
  8. Immunotherapy for breast cancer using epcam aptamer tumor-targeted gene knockdown
    Ying Zhang, Xuemei Xie, Pourya Naderi Yeganeh, Dian-Jang Lee, David Valle-Garcia, Karla F. Meza-Sosa, Caroline Junqueira, Jiayu Su, Hongbo R. Luo, Winston Hide, Judy Lieberman
    Proceedings of the National Academy of Sciences, 2021
  9. Single-cell transcriptome profiling reveals neutrophil heterogeneity in homeostasis and infection
    Xuemei Xie*, Qiang Shi*, Peng Wu, Xiaoyu Zhang, Hiroto Kambara, Jiayu Su, Hongbo Yu, Shin-Young Park, Rongxia Guo, Qian Ren, Sudong Zhang, Yuanfu Xu, Leslie E. Silberstein, Tao Cheng, Fengxia Ma†, Cheng Li†, Hongbo R. Luo†
    Nature Immunology, 2020
    Link to paper Code