Improved reconstruction of single-cell developmental potential with CytoTRACE 2

Minji Kang; Gunsagar S Gulati; Erin L Brown; Zhen Qi; Susanna Avagyan; Jose Juan Almagro Armenteros; Rachel Gleyzer; Wubing Zhang; Chloé B Steen; Jeremy Philip D'Silva; Janella Schwab; Michael F Clarke; Aadel A Chaudhuri; Aaron M Newman

doi:10.1038/s41592-025-02857-2

Improved reconstruction of single-cell developmental potential with CytoTRACE 2

Nat Methods. 2025 Nov;22(11):2258-2263. doi: 10.1038/s41592-025-02857-2. Epub 2025 Oct 27.

Authors

Minji Kang^#^{1

2

3}, Gunsagar S Gulati^#⁴, Erin L Brown^#^{1

2}, Zhen Qi^#¹, Susanna Avagyan², Jose Juan Almagro Armenteros^{1

5}, Rachel Gleyzer^{1

2}, Wubing Zhang^{1

2}, Chloé B Steen^{6

7

8}, Jeremy Philip D'Silva^{1

2}, Janella Schwab^{1

2

9}, Michael F Clarke^{1

10}, Aadel A Chaudhuri^{11

12}, Aaron M Newman^{13

14

15

16}

Affiliations

¹ Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
² Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
³ Department of Computer Science, Stanford University, Stanford, CA, USA.
⁴ Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
⁵ Department of Genetics, Stanford University, Stanford, CA, USA.
⁶ Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway.
⁷ Institute for Cancer Research, Oslo University Hospital and University of Oslo, Oslo, Norway.
⁸ Precision Immunotherapy Alliance, University of Oslo, Oslo, Norway.
⁹ Department of Bioengineering, Stanford University, Stanford, CA, USA.
¹⁰ Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
¹¹ Department of Radiation Oncology, Mayo Clinic, Rochester, MN, USA.
¹² Mayo Clinic Comprehensive Cancer Center, Rochester, MN, USA.
¹³ Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA. amnewman@stanford.edu.
¹⁴ Department of Biomedical Data Science, Stanford University, Stanford, CA, USA. amnewman@stanford.edu.
¹⁵ Stanford Cancer Institute, Stanford University, Stanford, CA, USA. amnewman@stanford.edu.
¹⁶ Chan Zuckerberg Biohub - San Francisco, San Francisco, CA, USA. amnewman@stanford.edu.

^# Contributed equally.

Abstract

While single-cell RNA sequencing has advanced our understanding of cell fate, identifying molecular hallmarks of potency-a cell's ability to differentiate into other cell types-remains a challenge. Here we introduce CytoTRACE 2, an interpretable deep learning framework for predicting absolute developmental potential from single-cell RNA sequencing data. Across diverse platforms and tissues, CytoTRACE 2 outperformed previous methods in predicting developmental hierarchies, enabling detailed mapping of single-cell differentiation landscapes and expanding insights into cell potency.

MeSH terms

Animals
Cell Differentiation* / genetics
Deep Learning*
Humans
Mice
RNA-Seq / methods
Sequence Analysis, RNA* / methods
Single-Cell Analysis* / methods

Abstract

MeSH terms

Grants and funding