@book {798,
	title = {Cell-Level Pathway Scoring Comparison with~a~Biologically Constrained Variational Autoencoder},
	series = {Lecture Notes in Computer Science. Computational Methods in Systems Biology},
	volume = {14137},
	year = {2023},
	pages = {62 - 77},
	publisher = {Springer Nature Switzerland},
	organization = {Springer Nature Switzerland},
	address = {Cham},
	isbn = {978-3-031-42696-4},
	issn = {0302-9743},
	doi = {10.1007/978-3-031-42697-110.1007/978-3-031-42697-1_5},
	url = {https://link.springer.com/chapter/10.1007/978-3-031-42697-1_5},
	author = {Gundogdu, Pelin and Pay{\'a}-Milans, Miriam and Alamo-Alvarez, Inmaculada and Nepomuceno-Chamorro, Isabel A. and Dopazo, Joaquin and Loucera, Carlos}
}
@article {771,
	title = {Crosstalk between Metabolite Production and Signaling Activity in Breast Cancer.},
	journal = {Int J Mol Sci},
	volume = {24},
	year = {2023},
	month = {2023 Apr 18},
	abstract = {<p>The reprogramming of metabolism is a recognized cancer hallmark. It is well known that different signaling pathways regulate and orchestrate this reprogramming that contributes to cancer initiation and development. However, recent evidence is accumulating, suggesting that several metabolites could play a relevant role in regulating signaling pathways. To assess the potential role of metabolites in the regulation of signaling pathways, both metabolic and signaling pathway activities of Breast invasive Carcinoma (BRCA) have been modeled using mechanistic models. Gaussian Processes, powerful machine learning methods, were used in combination with SHapley Additive exPlanations (SHAP), a recent methodology that conveys causality, to obtain potential causal relationships between the production of metabolites and the regulation of signaling pathways. A total of 317 metabolites were found to have a strong impact on signaling circuits. The results presented here point to the existence of a complex crosstalk between signaling and metabolic pathways more complex than previously was thought.</p>},
	issn = {1422-0067},
	doi = {10.3390/ijms24087450},
	author = {Cubuk, Cankut and Loucera, Carlos and Pe{\~n}a-Chilet, Maria and Dopazo, Joaquin}
}
@article {701,
	title = {CSVS, a crowdsourcing database of the Spanish population genetic variability.},
	journal = {Nucleic Acids Res},
	volume = {49},
	year = {2021},
	month = {2021 01 08},
	pages = {D1130-D1137},
	abstract = {<p>The knowledge of the genetic variability of the local population is of utmost importance in personalized medicine and has been revealed as a critical factor for the discovery of new disease variants. Here, we present the Collaborative Spanish Variability Server (CSVS), which currently contains more than 2000 genomes and exomes of unrelated Spanish individuals. This database has been generated in a collaborative crowdsourcing effort collecting sequencing data produced by local genomic projects and for other purposes. Sequences have been grouped by ICD10 upper categories. A web interface allows querying the database removing one or more ICD10 categories. In this way, aggregated counts of allele frequencies of the pseudo-control Spanish population can be obtained for diseases belonging to the category removed. Interestingly, in addition to pseudo-control studies, some population studies can be made, as, for example, prevalence of pharmacogenomic variants, etc. In addition, this genomic data has been used to define the first Spanish Genome Reference Panel (SGRP1.0) for imputation. This is the first local repository of variability entirely produced by a crowdsourcing effort and constitutes an example for future initiatives to characterize local variability worldwide. CSVS is also part of the GA4GH Beacon network. CSVS can be accessed at: http://csvs.babelomics.org/.</p>},
	keywords = {Alleles, Chromosome Mapping, Crowdsourcing, Databases, Genetic, Exome, Gene Frequency, Genetic Variation, Genetics, Population, Genome, Human, Genomics, Humans, Internet, Precision Medicine, Software, Spain},
	issn = {1362-4962},
	doi = {10.1093/nar/gkaa794},
	author = {Pe{\~n}a-Chilet, Maria and Rold{\'a}n, Gema and Perez-Florido, Javier and Ortuno, Francisco M and Carmona, Rosario and Aquino, Virginia and L{\'o}pez-L{\'o}pez, Daniel and Loucera, Carlos and Fernandez-Rueda, Jose L and Gallego, Asunci{\'o}n and Garcia-Garcia, Francisco and Gonz{\'a}lez-Neira, Anna and Pita, Guillermo and N{\'u}{\~n}ez-Torres, Roc{\'\i}o and Santoyo-L{\'o}pez, Javier and Ayuso, Carmen and Minguez, Pablo and Avila-Fernandez, Almudena and Corton, Marta and Moreno-Pelayo, Miguel {\'A}ngel and Morin, Mat{\'\i}as and Gallego-Martinez, Alvaro and Lopez-Escamez, Jose A and Borrego, Salud and Anti{\v n}olo, Guillermo and Amigo, Jorge and Salgado-Garrido, Josefa and Pasalodos-Sanchez, Sara and Morte, Beatriz and Carracedo, {\'A}ngel and Alonso, {\'A}ngel and Dopazo, Joaquin}
}
