Research

Publications

Renée L. Flaherty, Flavia Hughes, George Sflomos, Carlos Ronchi, et al. “LOX inhibition disrupts a collagen–integrin–MYC axis to suppress progression of invasive lobular carcinoma.” Cancer Research 86(10), 2487–2507 (2026). doi:10.1158/0008-5472.CAN-25-3490
Carlos Ronchi, Giovanna Ambrosini, Flavia Hughes, Renée L. Flaherty, Hazel M. Quinn, Daria Matvienko, Andrea Agnoletto, Cathrin Brisken. “biogrowleR: enhancing longitudinal data analysis.” Journal of Mammary Gland Biology and Neoplasia 30, 9 (2025). doi:10.1007/s10911-025-09583-7
Dorian V. Ziegler, Kanishka Parashar, Lucia Leal-Esteban, …, Carlos Ronchi, …, Lluis Fajas. “CDK4 inactivation inhibits apoptosis via mitochondria-ER contact remodeling in triple-negative breast cancer.” Nature Communications 16, 541 (2025). doi:10.1038/s41467-024-55605-z
Carlos Ronchi, Syed Haider, Cathrin Brisken. “EMBER creates a unified space for independent breast cancer transcriptomic datasets enabling precision oncology.” npj Breast Cancer 10, 56 (2024). doi:10.1038/s41523-024-00665-z
Carlos Ronchi, Cathrin Brisken. “Targeting the progesterone receptor in breast cancer: mind the short form!” Clinical Cancer Research 29(5), 833–834 (2023). doi:10.1158/1078-0432.CCR-22-3374

EMBER: a universal framework that embeds independent breast cancer transcriptomes into a single unified space, enabling molecular subtype and pathway scoring on a single-sample basis. Code: github.com/chronchi/ember.
biogrowleR: Extracting insights from growth measurement data; a R package. Link to the website with further tutorials and instructions: upbri.gitlab.io/biogrowleR/. For bugs and issues, create a new issue on gitlab: gitlab.com/upbri/biogrowleR

Persistent homology applied to the protein stability (pdf) - 22/01/2020
Homologia persistente, machine learning e o estudo de proteínas (pdf) - 22/10/2018
Homologia persistente e o algoritmo de redução (ipynb), (algo) - 08/10/2018

Estrogen signature and gene coexpression network for breast cancer stratification and survival analysis
- Basel Computational Biology Conference - BC2, Switzerland, Sep 2021
A topological approach to protein stability (Poster)
- XII Regional Topology Meeting, Oct 2019
Persistent Homology and the Protein Folding Problem
- Geometric Data Analysis, May 2019
- Data Driven Dynamics: Algebraic Topology, Combinatorics and Analysis, Apr 2019
Optimal cycles and applications in machine learning (Poster)
- TRIPODS Summer Bootcamp: Topology and Machine Learning, Aug 2018
- XXI Brazilian Topology Meeting, Aug 2018
- Workshop de Teses e Dissertações, Aug 2018 (Best poster presentation award)