Extracellular vesicles from dental pulp mesenchymal stem cells modulate macrophage phenotype during acute and chronic cardiac inflammation in athymic nude rats with myocardial infarction

Authors: Elena Amaro-Prellezo, Marta Gómez-Ferrer, Lusine Hakobyan, Imelda Ontoria-Oviedo, Esteban Peiró-Molina, Sonia Tarazona, Pedro Salguero, Amparo Ruiz-Saurí, Marta Selva-Roldán, Rosa Vives-Sanchez, Pilar Sepúlveda

Source: Inflammation and Regeneration, Vol 44, Iss 1, Pp 1-20 (2024)

Subject Terms: Extracellular vesicles, Mesenchymal stromal cells, Acute myocardial infarction, Inflammation, Macrophage, Pathology, RB1-214

File Description: electronic resource

Relation: https://doaj.org/toc/1880-8190

Access URL: https://doaj.org/article/2e9200040b54470badfe995a73dc2d3f

Advancing microbiome research with machine learning: key findings from the ML4Microbiome COST action

Authors: Domenica D’Elia, Jaak Truu, Leo Lahti, Magali Berland, Georgios Papoutsoglou, Michelangelo Ceci, Aldert Zomer, Marta B. Lopes, Eliana Ibrahimi, Aleksandra Gruca, Alina Nechyporenko, Marcus Frohme, Thomas Klammsteiner, Enrique Carrillo-de Santa Pau, Laura Judith Marcos-Zambrano, Karel Hron, Gianvito Pio, Andrea Simeon, Ramona Suharoschi, Isabel Moreno-Indias, Andriy Temko, Miroslava Nedyalkova, Elena-Simona Apostol, Ciprian-Octavian Truică, Rajesh Shigdel, Jasminka Hasić Telalović, Erik Bongcam-Rudloff, Piotr Przymus, Naida Babić Jordamović, Laurent Falquet, Sonia Tarazona, Alexia Sampri, Gaetano Isola, David Pérez-Serrano, Vladimir Trajkovik, Lubos Klucar, Tatjana Loncar-Turukalo, Aki S. Havulinna, Christian Jansen, Randi J. Bertelsen, Marcus Joakim Claesson

Source: Frontiers in Microbiology, Vol 14 (2023)

Subject Terms: microbiome, machine learning, artificial intelligence, standards, best practices, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fmicb.2023.1257002/full; https://doaj.org/toc/1664-302X

Access URL: https://doaj.org/article/5f8da7afb1744c6687be2586111ac38e

Machine learning approaches in microbiome research: challenges and best practices

Authors: Georgios Papoutsoglou, Sonia Tarazona, Marta B. Lopes, Thomas Klammsteiner, Eliana Ibrahimi, Julia Eckenberger, Pierfrancesco Novielli, Alberto Tonda, Andrea Simeon, Rajesh Shigdel, Stéphane Béreux, Giacomo Vitali, Sabina Tangaro, Leo Lahti, Andriy Temko, Marcus J. Claesson, Magali Berland

Source: Frontiers in Microbiology, Vol 14 (2023)

Subject Terms: microbiome data analysis, machine learning methods, preprocessing, feature selection, predictive modeling, model selection, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fmicb.2023.1261889/full; https://doaj.org/toc/1664-302X

Access URL: https://doaj.org/article/a35769259f1946d3b9af729120cec4fd

acorde unravels functionally interpretable networks of isoform co-usage from single cell data

Authors: Angeles Arzalluz-Luque, Pedro Salguero, Sonia Tarazona, Ana Conesa

Source: Nature Communications, Vol 13, Iss 1, Pp 1-18 (2022)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/9f2429f68ce346fc859786e13647afc3

Multi-omic analysis unveils biological pathways in peripheral immune system associated to minimal hepatic encephalopathy appearance in cirrhotic patients

Authors: Teresa Rubio, Vicente Felipo, Sonia Tarazona, Roberta Pastorelli, Desamparados Escudero-García, Joan Tosca, Amparo Urios, Ana Conesa, Carmina Montoliu

Source: Scientific Reports, Vol 11, Iss 1, Pp 1-14 (2021)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/dbe0975e446a4472953af02c8fc7c53a

Harmonization of quality metrics and power calculation in multi-omic studies

Authors: Sonia Tarazona, Leandro Balzano-Nogueira, David Gómez-Cabrero, Andreas Schmidt, Axel Imhof, Thomas Hankemeier, Jesper Tegnér, Johan A. Westerhuis, Ana Conesa

Source: Nature Communications, Vol 11, Iss 1, Pp 1-13 (2020)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/0c51984a3d59449daf214ba0b39baeb7

tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing

Authors: Lorena de la Fuente, Ángeles Arzalluz-Luque, Manuel Tardáguila, Héctor del Risco, Cristina Martí, Sonia Tarazona, Pedro Salguero, Raymond Scott, Alberto Lerma, Ana Alastrue-Agudo, Pablo Bonilla, Jeremy R. B. Newman, Shunichi Kosugi, Lauren M. McIntyre, Victoria Moreno-Manzano, Ana Conesa

Source: Genome Biology, Vol 21, Iss 1, Pp 1-32 (2020)

Subject Terms: Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s13059-020-02028-w; https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/43d2bfbe25f9461c9529a9f3e3a7f87d

A Nextflow pipeline for T-cell receptor repertoire reconstruction and analysis from RNA sequencing data

Authors: Teresa Rubio, Maria Chernigovskaya, Susanna Marquez, Cristina Marti, Paula Izquierdo-Altarejos, Amparo Urios, Carmina Montoliu, Vicente Felipo, Ana Conesa, Victor Greiff, Sonia Tarazona

Source: ImmunoInformatics, Vol 6, Iss , Pp 100012- (2022)

Subject Terms: T-cell receptor, CD4 isolation, RNA sequencing, Immune repertoire analysis, Minimal Hepatic Encephalopathy, Computer applications to medicine. Medical informatics, R858-859.7

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2667119022000040; https://doaj.org/toc/2667-1190

Access URL: https://doaj.org/article/a9c87492a74c495fa73825fe5daae9e2

Gene-environment interaction analysis of redox-related metals and genetic variants with plasma metabolic patterns in a general population from Spain: The Hortega Study

Authors: Marta Galvez-Fernandez, Francisco Sanchez-Saez, Arce Domingo-Relloso, Zulema Rodriguez-Hernandez, Sonia Tarazona, Vannina Gonzalez-Marrachelli, Maria Grau-Perez, Jose M. Morales-Tatay, Nuria Amigo, Tamara Garcia-Barrera, Jose L. Gomez-Ariza, F. Javier Chaves, Ana Barbara Garcia-Garcia, Rebeca Melero, Maria Tellez-Plaza, Juan C. Martin-Escudero, Josep Redon, Daniel Monleon

Source: Redox Biology, Vol 52, Iss , Pp 102314- (2022)

Subject Terms: Metals, Metabolomics, Oxidative stress, Candidate genes, Gene-environment interaction, Medicine (General), R5-920, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2213231722000866; https://doaj.org/toc/2213-2317

Access URL: https://doaj.org/article/3b5f1db5a1cf4b80a5c8ac0605461c93

Association Between Sex Hormone Levels and Clinical Outcomes in Patients With COVID-19 Admitted to Hospital: An Observational, Retrospective, Cohort Study

Authors: Anna Beltrame, Pedro Salguero, Emanuela Rossi, Ana Conesa, Lucia Moro, Laura Rachele Bettini, Eleonora Rizzi, Mariella D’Angió, Michela Deiana, Chiara Piubelli, Paola Rebora, Silvia Duranti, Paolo Bonfanti, Ilaria Capua, Sonia Tarazona, Maria Grazia Valsecchi

Source: Frontiers in Immunology, Vol 13 (2022)

Subject Terms: sex hormones, COVID-19, outcome, ARDS, severity, testosterone, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2022.834851/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/94a766d8d295465f9d321c38c511de0b

Machine-learning-derived predictive score for early estimation of COVID-19 mortality risk in hospitalized patients.

Authors: Alba González-Cebrián, Joan Borràs-Ferrís, Juan Pablo Ordovás-Baines, Marta Hermenegildo-Caudevilla, Mónica Climente-Marti, Sonia Tarazona, Raffaele Vitale, Daniel Palací-López, Jesús Francisco Sierra-Sánchez, Javier Saez de la Fuente, Alberto Ferrer

Source: PLoS ONE, Vol 17, Iss 9, p e0274171 (2022)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/0fb4528dffd24b298146c77e4c183360

Mutant PRPF8 Causes Widespread Splicing Changes in Spliceosome Components in Retinitis Pigmentosa Patient iPSC-Derived RPE Cells

Authors: Ángeles Arzalluz-Luque, Jose Luis Cabrera, Heli Skottman, Alberto Benguria, Arantxa Bolinches-Amorós, Nicolás Cuenca, Vincenzo Lupo, Ana Dopazo, Sonia Tarazona, Bárbara Delás, Miguel Carballo, Beatriz Pascual, Imma Hernan, Slaven Erceg, Dunja Lukovic

Source: Frontiers in Neuroscience, Vol 15 (2021)

Subject Terms: iPSC, RPE, RNA-Seq, retinitis pigmentosa, pre-mRNA splicing, alternative splicing, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fnins.2021.636969/full; https://doaj.org/toc/1662-453X

Access URL: https://doaj.org/article/347373adf3fd4a898beb0087c33bbc18

STATegra: Multi-Omics Data Integration – A Conceptual Scheme With a Bioinformatics Pipeline

Authors: Nuria Planell, Vincenzo Lagani, Patricia Sebastian-Leon, Frans van der Kloet, Ewoud Ewing, Nestoras Karathanasis, Arantxa Urdangarin, Imanol Arozarena, Maja Jagodic, Ioannis Tsamardinos, Sonia Tarazona, Ana Conesa, Jesper Tegner, David Gomez-Cabrero

Source: Frontiers in Genetics, Vol 12 (2021)

Subject Terms: multi-omic analyses, data-integration, next-generation sequencing, component analysis, non-parametric combination, GeneSetCluster, Genetics, QH426-470

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fgene.2021.620453/full; https://doaj.org/toc/1664-8021

Access URL: https://doaj.org/article/99f7643058d144149055b509b7075821

Feedforward regulation of Myc coordinates lineage-specific with housekeeping gene expression during B cell progenitor cell differentiation.

Authors: Isabel Ferreirós-Vidal, Thomas Carroll, Tianyi Zhang, Vincenzo Lagani, Ricardo N Ramirez, Elizabeth Ing-Simmons, Alicia G Gómez-Valadés, Lee Cooper, Ziwei Liang, Georgios Papoutsoglou, Gopuraja Dharmalingam, Ya Guo, Sonia Tarazona, Sunjay J Fernandes, Peri Noori, Gilad Silberberg, Amanda G Fisher, Ioannis Tsamardinos, Ali Mortazavi, Boris Lenhard, Ana Conesa, Jesper Tegner, Matthias Merkenschlager, David Gomez-Cabrero

Source: PLoS Biology, Vol 17, Iss 4, p e2006506 (2019)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1544-9173; https://doaj.org/toc/1545-7885

Access URL: https://doaj.org/article/9bf45eded0be40789c3b6f117e693ee1

RGmatch: matching genomic regions to proximal genes in omics data integration

Authors: Pedro Furió-Tarí, Ana Conesa, Sonia Tarazona

Source: BMC Bioinformatics, Vol 17, Iss S15, Pp 1-10 (2016)

Subject Terms: Associations, Gene, Genomic region, Peak, Omics integration, NGS, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12859-016-1293-1; https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/ab87acdb62e6458b8a6115ef760c4baa

Elucidating the Role of Chromatin State and Transcription Factors on the Regulation of the Yeast Metabolic Cycle: A Multi-Omic Integrative Approach

Authors: Víctor Sánchez-Gaya, Salvador Casaní-Galdón, Manuel Ugidos, Zheng Kuang, Jane Mellor, Ana Conesa, Sonia Tarazona

Source: Frontiers in Genetics, Vol 9 (2018)

Subject Terms: YMC, histone modifications, gene expression, omics integration, regression, Genetics, QH426-470

File Description: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fgene.2018.00578/full; https://doaj.org/toc/1664-8021

Access URL: https://doaj.org/article/ff3c54c32cbe4203bbd6c622af09b88f