A proposed workflow to robustly analyze bacterial transcripts in RNAseq data from extracellular vesicles

Authors: Alex M. Ascensión, Miriam Gorostidi-Aicua, Ane Otaegui-Chivite, Ainhoa Alberro, Rocio del Carmen Bravo-Miana, Tamara Castillo-Trivino, Laura Moles, David Otaegui

Source: Frontiers in Microbiology, Vol 16 (2025)

Subject Terms: extracellular vesicles, bacteria, RNA-seq, multiple sclerosis, taxa profiling, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fmicb.2025.1486661/full; https://doaj.org/toc/1664-302X

Access URL: https://doaj.org/article/fa011e3f1dc44d5cbd262424add36496

Inflammation-mediated fibroblast activation and immune dysregulation in collagen VII-deficient skin

Authors: Morgan Anderson-Crannage, Alex M. Ascensión, Olga Ibanez-Solé, Hongwen Zhu, Edo Schaefer, Darcy Ottomanelli, Bruno Hochberg, Jian Pan, Wen Luo, Meijuan Tian, Yaya Chu, Mitchell S. Cairo, Ander Izeta, Yanling Liao

Source: Frontiers in Immunology, Vol 14 (2023)

Subject Terms: epidermolysis bullosa, inflammation, immune suppression, dermal microenvironment, fibroblast activation, interleukin-1, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2023.1211505/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/34e1d4686234451eb208aeefa7d3b96f

The need to reassess single-cell RNA sequencing datasets: the importance of biological sample processing [version 2; peer review: 2 approved]

Authors: Alex M. Ascensión, Marcos J. Araúzo-Bravo, Ander Izeta

Source: F1000Research, Vol 10 (2022)

Subject Terms: single-cell RNA-seq, skin, fibroblasts, reproducibility, computational analysis, Python, eng, Medicine, Science

File Description: electronic resource

Relation: https://f1000research.com/articles/10-767/v2; https://doaj.org/toc/2046-1402

Access URL: https://doaj.org/article/690da4bb04f0423098155cce0ef3ef67

FOntCell: Fusion of Ontologies of Cells

Authors: Javier Cabau-Laporta, Alex M. Ascensión, Mikel Arrospide-Elgarresta, Daniela Gerovska, Marcos J. Araúzo-Bravo

Source: Frontiers in Cell and Developmental Biology, Vol 9 (2021)

Subject Terms: ontology alignment, ontology merging, automatic ontology merging, cell ontology, Human Cell Atlas (HCA), Ontology Alignment Evaluation Initiative (OAEI), Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fcell.2021.562908/full; https://doaj.org/toc/2296-634X

Access URL: https://doaj.org/article/7ba878be2c9748e696c76b3f44ebdad2

Challenges and Opportunities for the Translation of Single-Cell RNA Sequencing Technologies to Dermatology

Authors: Alex M. Ascensión, Marcos J. Araúzo-Bravo, Ander Izeta

Source: Life, Vol 12, Iss 1, p 67 (2022)

Subject Terms: single-cell, skin, cell population heterogeneity, dermatological disease, Science

File Description: electronic resource

Relation: https://www.mdpi.com/2075-1729/12/1/67; https://doaj.org/toc/2075-1729

Access URL: https://doaj.org/article/e4ca7f2958ce4cd39db428f0ac8bc81a

NaviSE: superenhancer navigator integrating epigenomics signal algebra

Authors: Alex M. Ascensión, Mikel Arrospide-Elgarresta, Ander Izeta, Marcos J. Araúzo-Bravo

Source: BMC Bioinformatics, Vol 18, Iss 1, Pp 1-18 (2017)

Subject Terms: Superenhancers, Next-generation sequencing, Parallel computing, Epigenomics, Computational biology, Graphics user interface, 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/s12859-017-1698-5; https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/d59ca3be9fa54b21a2b182796752f05e

Signal Integration and Transcriptional Regulation of the Inflammatory Response Mediated by the GM-/M-CSF Signaling Axis in Human Monocytes

Authors: Ramon M. Rodriguez, Beatriz Suarez-Alvarez, Jose L. Lavín, Alex M. Ascensión, Monika Gonzalez, Juan J. Lozano, Aroa B. Raneros, Paula D. Bulnes, Jose R. Vidal-Castiñeira, Covadonga Huidobro, Cristina Martin-Martin, Ana B. Sanz, Marta Ruiz-Ortega, Amaya Puig-Kröger, Angel L. Corbí, Marcos J. Araúzo-Bravo, Ana M. Aransay, Carlos Lopez-Larrea

Source: Cell Reports, Vol 29, Iss 4, Pp 860-872.e5 (2019)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2211124719312239; https://doaj.org/toc/2211-1247

Access URL: https://doaj.org/article/69b31ac581ed459390e887cfe1dc0c24

Lack of evidence for increased transcriptional noise in aged tissues

Authors: Olga Ibañez-Solé, Alex M Ascensión, Marcos J Araúzo-Bravo, Ander Izeta

Source: eLife, Vol 11 (2022)

Subject Terms: aging, transcription, variability, single-cell RNA sequencing, lung, cell identity, Medicine, Science, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://elifesciences.org/articles/80380; https://doaj.org/toc/2050-084X

Access URL: https://doaj.org/article/571f3e8ff36b403c9e488f25c331141d