Fri Feb 14, 2025 5:47 pm
2025-Viswanath et al-preprint
"HiPoNet: A Topology-Preserving Multi-View Neural Network For High Dimensional Point Cloud and Single-Cell Data"
Siddharth Viswanath, Hiren Madhu, Dhananjay Bhaskar, Jake Kovalic, Dave Johnson, Rex Ying, Christopher Tape, Ian Adelstein, Michael Perlmutter, Smita Krishnaswamy
arXiv, posted 11 Feb 2025
https://doi.org/10.48550/arXiv.2502.07746
- will update when/if this is peer-reviewed and published
- claims to reuse:
Melanoma: MIBI-TOF: "We use data originally collected by Ptacek et al. (2021) and published in Vesely & Johnson (2025)"
- however, Ptacek reference is a conference abstract (no experimental details, and not further published, as far as I know), and Vesely and Johnson Mendeley dataset are CSV not TIFF or other raw data
PDO: CyTOF: 2023-Ramos Zapatero et al-Cell
- this paper does contain CyTOF data that was released. However, this Viswanath paper's Appendix says "Patient-derived organoids (PDOs) are cell cultures grown from patient tumor samples. Each culture, representing a PDO sample, is characterized by 44 gene expression markers and contains approximately 1137 cells. Collectively, we consider 1,678 such cultures, forming 44 dimensional point clouds, resulting in a total of 2 million cells."
- since the Ramos Zapatero paper *also* performs scRNAseq, it is therefore unclear whether this PDO dataset reuses CyTOF or scRNAseq.
Siddharth Viswanath, Hiren Madhu, Dhananjay Bhaskar, Jake Kovalic, Dave Johnson, Rex Ying, Christopher Tape, Ian Adelstein, Michael Perlmutter, Smita Krishnaswamy
arXiv, posted 11 Feb 2025
https://doi.org/10.48550/arXiv.2502.07746
- will update when/if this is peer-reviewed and published
- claims to reuse:
Melanoma: MIBI-TOF: "We use data originally collected by Ptacek et al. (2021) and published in Vesely & Johnson (2025)"
- however, Ptacek reference is a conference abstract (no experimental details, and not further published, as far as I know), and Vesely and Johnson Mendeley dataset are CSV not TIFF or other raw data
PDO: CyTOF: 2023-Ramos Zapatero et al-Cell
- this paper does contain CyTOF data that was released. However, this Viswanath paper's Appendix says "Patient-derived organoids (PDOs) are cell cultures grown from patient tumor samples. Each culture, representing a PDO sample, is characterized by 44 gene expression markers and contains approximately 1137 cells. Collectively, we consider 1,678 such cultures, forming 44 dimensional point clouds, resulting in a total of 2 million cells."
- since the Ramos Zapatero paper *also* performs scRNAseq, it is therefore unclear whether this PDO dataset reuses CyTOF or scRNAseq.