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A list of all the posts and pages found on the site. For you robots out there, there is an XML version available for digesting as well.
Pages
Posts
portfolio
Computer Vision adapted to Optical Coherence Tomographies (Bachelor’s Thesis)
Published:
Developed an automated image processing algorithm using Python and OpenCV to measure uvea thickness and monitor uveitis evolution in OCT scans. 
Structure-PPi v2.0
Published:
Module for annotating cancer-related single-nucleotide variants at protein-protein interfaces. 
AQuAS: Health System Observatory Visualization Platform
Published:
Developed an interactive geospatial platform for the Catalan Agency for Health Quality and Evaluation (AQuAS) to visualize and analyze regional health system indicators. 
GARDEN-NET & ChAseR: 3D Chromatin Interaction Networks
Published:
Developed an R package and a web-based visualization tool for the analysis and integration of epigenomic data within 3D chromatin networks. 
Invention: ML Pipeline for Genome-Wide Association Studies (Patent)
Published:
Co-authored a patent (US20240120024A1) for a machine learning approach that significantly improves causal gene identification in GWAS. 
publications
DoriTool: a bioinformatics integrative tool for post-association functional annotation
Published in Public Health Genomics, 2017 (Cited by 7)
In this paper, we present DoriTool, a comprehensive, easy, and friendly pipeline integrating biological data from different functional tools. The tool was designed with the aim to maximize reproducibility and reduce the working time of the researchers.
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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Using GARDEN-NET and ChAseR to explore human haematopoietic 3D chromatin interaction networks
Published in Nucleic Acids Research, 2020 (Cited by 24)
We introduce an R package and a web-based visualization tool for the representation, analysis and integration of epigenomic data in the context of 3D chromatin interaction networks. GARDEN-NET allows for the projection of user-submitted genomic features on pre-loaded 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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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)
We introduce Single-Cell Virtual Cytometer, an open-source software for flow cytometry-like visualization and exploration of pre-processed multi-omics single cell datasets. Using an original CITE-seq dataset of PBMC from an healthy donor, we illustrate its use for the integrated analysis of transcriptomes and epitopes.
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 16)
Here we start from an existing model of macrophage polarization and extend it to the specific conditions encountered inside a tumour by adding signals, receptors, transcription factors and cytokines that are known to be the key components in establishing the cancer cell-macrophage interaction.
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)
We report that RT advances are cell-type-specific and involve large heterochromatin domains. Importantly, we found that some major late to early RT advances can be inherited by the unstressed next-cellular generation, which is a unique process that correlates with enhanced chromatin accessibility.
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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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)
Cohesin exists in two variants containing STAG1 or STAG2. STAG2 is one of the most mutated genes in cancer and a major bladder tumor suppressor. Here, we analyze the genomic distribution of STAG1 and STAG2 and perform STAG2 loss-of-function experiments using RT112 bladder cancer cells; we then analyze the genomic effects by integrating gene expression and chromatin interaction data.
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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Cytidine deaminase resolves replicative stress and protects pancreatic cancer from DNA-targeting drugs
Published in Cancer Research, 2024 (Cited by 14)
In this study, we observed that CDA was overexpressed in pancreatic adenocarcinoma from patients at baseline and was essential for experimental tumor growth. Mechanistic investigations revealed that CDA localized to replication forks where it increased replication speed, improved replication fork restart efficiency, reduced endogenous replication stress, minimized DNA breaks, and regulated genetic stability.
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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Machine learning pipeline for genome-wide association studies
Published in United States Patent Application US20240120024A1, 2024
This patent discloses machine learning techniques to predict causal genes from genome-wide association study (GWAS) summary statistics, improving identification precision and recall.
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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talks
teaching
Text Mining for Bioinformatics
Graduate Course, Instituto de Salud Carlos III (ISCIII), 2017
Designed and delivered an intensive 15-hour module on Text Mining and Natural Language Processing (NLP) within the Master in Bioinformatics and Computational Biology program.