Publications

You can also find my articles on my Google Scholar profile.

Patents

Machine learning pipeline for genome-wide association studies

Published in United States Patent Application US20240120024A1, 2024

A machine learning approach to predict causal genes from GWAS summary statistics, substantially improving identification precision and recall. Assignee: Illumina Inc.

Recommended citation: Field, Y., Ulirsch, J. C., Malangone, C., Madrid-Mencia, M., et al. (2024). Machine learning pipeline for genome-wide association studies. U.S. Patent Application No. 18/483,313 (Publication No. US20240120024A1).

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Journal Articles

STAG2 loss-of-function affects short-range genomic contacts and modulates the basal-luminal transcriptional program of bladder cancer cells

Published in Nucleic Acids Research, 2021 · Cited by 32

STAG2 loss-of-function links cohesin variant distribution to a basal transcriptional shift in bladder cancer, offering new insights into tumor suppressor mechanisms.

Recommended citation: Richart, L., Lapi, E., Pancaldi, V., Cuenca-Ardura, M., Carrillo-de-Santa Pau, E., Madrid-Mencía, M., … & Real, F. X. (2021). STAG2 loss-of-function affects short-range genomic contacts and modulates the basal-luminal transcriptional program of bladder cancer cells. Nucleic Acids Research, 49(19), 11005-11021.

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Using GARDEN-NET and ChAseR to explore human haematopoietic 3D chromatin interaction networks

Published in Nucleic Acids Research, 2020 · Cited by 24

First-author. An R package and web-based visualization tool for the representation, analysis, and integration of epigenomic data in the context of 3D chromatin interaction networks.

Recommended citation: Madrid-Mencía, M., Raineri, E., Cao, T. B. N., & Pancaldi, V. (2020). Using GARDEN-NET and ChAseR to explore human haematopoietic 3D chromatin interaction networks. Nucleic Acids Research, 48(8), 4066-4080.

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Cytidine deaminase resolves replicative stress and protects pancreatic cancer from DNA-targeting drugs

Published in Cancer Research, 2024 · Cited by 18

CDA overexpression in pancreatic adenocarcinoma resolves replicative stress at forks and correlates with resistance to DNA-damaging chemotherapy.

Recommended citation: Lumeau, A., Bery, N., Francès, A., Gayral, M., Labrousse, G., Ribeyre, C., … Madrid-Mencía, M., … & Cordelier, P. (2024). Cytidine deaminase resolves replicative stress and protects pancreatic cancer from DNA-targeting drugs. Cancer Research, 84(7), 1013-1028.

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Single-Cell Virtual Cytometer allows user-friendly and versatile analysis and visualization of multimodal single cell RNAseq datasets

Published in NAR Genomics and Bioinformatics, 2020 · Cited by 17

Open-source software for flow cytometry-like visualization and exploration of pre-processed multi-omics single cell datasets.

Recommended citation: Pont, F., Tosolini, M., Gao, Q., Perrier, M., Madrid-Mencía, M., Huang, T. S., … & Fournié, J. J. (2020). Single-Cell Virtual Cytometer allows user-friendly and versatile analysis and visualization of multimodal single cell RNAseq datasets. NAR Genomics and Bioinformatics, 2(2), lqaa025.

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Insights on TAM formation from a Boolean model of macrophage polarization based on in vitro studies

Published in Cancers, 2020 · Cited by 15

A Boolean model of macrophage polarization extended to tumor microenvironment conditions, predicting potential regulators such as STAT1 and EGF as immunotherapy targets.

Recommended citation: Marku, M., Verstraete, N., Raynal, F., Madrid-Mencía, M., Domagala, M., Fournié, J. J., … & Pancaldi, V. (2020). Insights on TAM formation from a Boolean model of macrophage polarization based on in vitro studies. Cancers, 12(12), 3664.

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Low replicative stress triggers cell-type specific inheritable advanced replication timing

Published in International Journal of Molecular Sciences, 2021 · Cited by 10

Low replicative stress induces inheritable advances in replication timing at specific chromosomal domains, with potential impacts on cellular identity and gene expression.

Recommended citation: Courtot, L., Bournique, E., Maric, C., Guitton-Sert, L., Madrid-Mencía, M., Pancaldi, V., … & Bergoglio, V. (2021). Low replicative stress triggers cell-type specific inheritable advanced replication timing. International Journal of Molecular Sciences, 22(9), 4959.

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DoriTool: a bioinformatics integrative tool for post-association functional annotation

Published in Public Health Genomics, 2017 · Cited by 7

An integrative bioinformatics pipeline for post-association functional annotation, combining data from multiple functional tools to maximize reproducibility and reduce researcher workload.

Recommended citation: Martín-Antoniano, I., Alonso, L., Madrid, M., Lopez de Maturana, E., & Malats, N. (2017). DoriTool: a bioinformatics integrative tool for post-association functional annotation. Public Health Genomics, 20(2), 126-135.

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