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machine learning • transcriptomics • epigenomics • alveolar macrophages
Inflammation is central to many diseases. It is a signalling process transmitted by dozens of signalling molecules in many combinations. Our lab focuses on understanding the types of inflammation in the lung that lead to disease. We use machine learning models on next-generation sequencing datasets to predict patterns associated with cytokine activation and use these to deconvolute the inflammatory response as seen by the resident macrophage population.
Fonseca GJ, Tao J, et. al. Diverse motif ensembles specify non-redundant DNA binding activities of AP-1 family members in macrophages. Nat Commun. 2019 Jan 24;10(1):414. PMID: 30679424.
Lopez-Ramirez MA, Fonseca G, et. a. Thrombospondin1 (TSP1) replacement prevents cerebral cavernous malformations. J Exp Med. 2017 Nov 6;214(11):3331-3346. PMID: 28970240.
Sajti E, Link VM, Ouyang Z, Spann NJ, Westin E, Romanoski CE, Fonseca GJ, Prince LS, Glass CK. Transcriptomic and epigenetic mechanisms underlying myeloid diversity in the lung. Nat Immunol. 2020 Feb;21(2):221-231. PMID: 31959980.