Sun Lab

Publications

The publications from our lab are listed below in reverse chronological order. Please reach out if you would like a copy of any publication.

      * Co-first authors

      + Co-corresponding authors

Highlighted

Spatial transcriptomic clocks reveal cell proximity effects in brain ageing
Spatial transcriptomic clocks reveal cell proximity effects in brain ageing
Eric D. Sun, Olivia Y. Zhou, Max Hauptschein, Nimrod Rappoport, Lucy Xu, Paloma Navarro Negredo, Ling Liu, Thomas A. Rando, James Zou+, Anne Brunet+
Nature  ·  18 Dec 2024  ·  doi:10.1038/s41586-024-08334-8
TISSUE: uncertainty-calibrated prediction of single-cell spatial transcriptomics improves downstream analyses
TISSUE: uncertainty-calibrated prediction of single-cell spatial transcriptomics improves downstream analyses
Eric D. Sun, Rong Ma, Paloma Navarro Negredo, Anne Brunet, James Zou
Nature Methods  ·  12 Feb 2024  ·  doi:10.1038/s41592-024-02184-y
Dynamic visualization of high-dimensional data
Dynamic visualization of high-dimensional data
Eric D. Sun, Rong Ma, James Zou
Nature Computational Science  ·  30 Dec 2022  ·  doi:10.1038/s43588-022-00380-4
Cell-type-specific aging clocks to quantify aging and rejuvenation in neurogenic regions of the brain
Cell-type-specific aging clocks to quantify aging and rejuvenation in neurogenic regions of the brain
Matthew T. Buckley*, Eric D. Sun*, Benson M. George, Ling Liu, Nicholas Schaum, …, Margaret A. Goodell, Irving L. Weissman, Tony Wyss-Coray, Thomas A. Rando, Anne Brunet
Nature Aging  ·  19 Dec 2022  ·  doi:10.1038/s43587-022-00335-4
Optimal control of aging in complex networks
Optimal control of aging in complex networks
Eric D. Sun*, Thomas C. T. Michaels*, L. Mahadevan
Proceedings of the National Academy of Sciences  ·  12 Aug 2020  ·  doi:10.1073/pnas.2006375117

All

2025

Brain aging and rejuvenation at single-cell resolution
Brain aging and rejuvenation at single-cell resolution
Eric D. Sun*, Rahul Nagvekar*, Angela N. Pogson*, Anne Brunet
Neuron  ·  01 Jan 2025  ·  doi:10.1016/j.neuron.2024.12.007

2024

Spatial transcriptomic clocks reveal cell proximity effects in brain ageing
Spatial transcriptomic clocks reveal cell proximity effects in brain ageing
Eric D. Sun, Olivia Y. Zhou, Max Hauptschein, Nimrod Rappoport, Lucy Xu, Paloma Navarro Negredo, Ling Liu, Thomas A. Rando, James Zou+, Anne Brunet+
Nature  ·  18 Dec 2024  ·  doi:10.1038/s41586-024-08334-8
CRISPR Cas9 screens reveal regulators of ageing in neural stem cells
CRISPR–Cas9 screens reveal regulators of ageing in neural stem cells
Tyson J. Ruetz, Angela N. Pogson, Chloe M. Kashiwagi, Stephanie D. Gagnon, Bhek Morton, …, David W. Morgens, C. Kimberly Tsui, Amy Li, Michael C. Bassik, Anne Brunet
Nature  ·  02 Oct 2024  ·  doi:10.1038/s41586-024-07972-2
SPRITE: improving spatial gene expression imputation with gene and cell networks
SPRITE: improving spatial gene expression imputation with gene and cell networks
Eric D. Sun+, Rong Ma, James Zou+
Bioinformatics  ·  28 Jun 2024  ·  doi:10.1093/bioinformatics/btae253
Restoration of neuronal progenitors by partial reprogramming in the aged neurogenic niche
Restoration of neuronal progenitors by partial reprogramming in the aged neurogenic niche
Lucy Xu, Julliana Ramirez-Matias, Max Hauptschein, Eric D. Sun, Judith C. Lunger, Matthew T. Buckley, Anne Brunet
Nature Aging  ·  29 Mar 2024  ·  doi:10.1038/s43587-024-00594-3
Principled and interpretable alignability testing and integration of single-cell data
Principled and interpretable alignability testing and integration of single-cell data
Rong Ma, Eric D. Sun, David Donoho, James Zou
Proceedings of the National Academy of Sciences  ·  28 Feb 2024  ·  doi:10.1073/pnas.2313719121
TISSUE: uncertainty-calibrated prediction of single-cell spatial transcriptomics improves downstream analyses
TISSUE: uncertainty-calibrated prediction of single-cell spatial transcriptomics improves downstream analyses
Eric D. Sun, Rong Ma, Paloma Navarro Negredo, Anne Brunet, James Zou
Nature Methods  ·  12 Feb 2024  ·  doi:10.1038/s41592-024-02184-y

2023

Chromatin accessibility dynamics of neurogenic niche cells reveal defects in neural stem cell adhesion and migration during aging
Chromatin accessibility dynamics of neurogenic niche cells reveal defects in neural stem cell adhesion and migration during aging
Robin W. Yeo*, Olivia Y. Zhou*, Brian L. Zhong, Eric D. Sun, Paloma Navarro Negredo, …, Tyson J. Ruetz, Mikaela Wilson, Anshul Kundaje, Alexander R. Dunn, Anne Brunet
Nature Aging  ·  13 Jul 2023  ·  doi:10.1038/s43587-023-00449-3
A spectral method for assessing and combining multiple data visualizations
A spectral method for assessing and combining multiple data visualizations
Rong Ma, Eric D. Sun, James Zou
Nature Communications  ·  11 Feb 2023  ·  doi:10.1038/s41467-023-36492-2

2022

Dynamic visualization of high-dimensional data
Dynamic visualization of high-dimensional data
Eric D. Sun, Rong Ma, James Zou
Nature Computational Science  ·  30 Dec 2022  ·  doi:10.1038/s43588-022-00380-4
Cell-type-specific aging clocks to quantify aging and rejuvenation in neurogenic regions of the brain
Cell-type-specific aging clocks to quantify aging and rejuvenation in neurogenic regions of the brain
Matthew T. Buckley*, Eric D. Sun*, Benson M. George, Ling Liu, Nicholas Schaum, …, Margaret A. Goodell, Irving L. Weissman, Tony Wyss-Coray, Thomas A. Rando, Anne Brunet
Nature Aging  ·  19 Dec 2022  ·  doi:10.1038/s43587-022-00335-4

2021

Predicting physiological aging rates from a range of quantitative traits using machine learning
Predicting physiological aging rates from a range of quantitative traits using machine learning
Eric D. Sun, Yong Qian, Richard Oppong, Thomas J. Butler, Jesse Zhao, …, Myriam Gorospe, Luigi Ferrucci, David Schlessinger, Ilya Goldberg, Jun Ding
Aging  ·  29 Oct 2021  ·  doi:10.18632/aging.203660
ImageNet-trained deep neural networks exhibit illusion-like response to the Scintillating grid
ImageNet-trained deep neural networks exhibit illusion-like response to the Scintillating grid
Eric D. Sun+, Ron Dekel+
Journal of Vision  ·  22 Oct 2021  ·  doi:10.1167/jov.21.11.15
The cusp of an apple
The cusp of an apple
Aditi Chakrabarti*, Thomas C. T. Michaels*, Sifan Yin, Eric D. Sun, L. Mahadevan
Nature Physics  ·  01 Oct 2021  ·  doi:10.1038/s41567-021-01335-8

2020

Optimal control of aging in complex networks
Optimal control of aging in complex networks
Eric D. Sun*, Thomas C. T. Michaels*, L. Mahadevan
Proceedings of the National Academy of Sciences  ·  12 Aug 2020  ·  doi:10.1073/pnas.2006375117
Sex Chromosome Degeneration by Regulatory Evolution
Sex Chromosome Degeneration by Regulatory Evolution
Thomas Lenormand, Frederic Fyon, Eric D. Sun, Denis Roze
Current Biology  ·  01 Aug 2020  ·  doi:10.1016/j.cub.2020.05.052