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Matteo Pellegrini
Phone: X50012
Office: 3000C Terasaki Life Science Bldg

Research Interests

Our lab is interested in the development of computational approaches to interpret genomic data. We seek to develop large-scale models of transcriptional and epigenetic regulation as well as signal transduction. Our approach is to build models that integrate varied data that sheds light on these phenomena. This data is produced using the latest generation of high throughput sequencers. Our research focuses on the development of both low and high-level analyses. For instance we are developing suites of tools for the analysis of high throughput sequencing data, including epigenomics and transcriptomics. Our goal is to make these tools, and the resulting databases, generally available to the scientific community.

Selected Publications

Massoud AH, Charbonnier LM, Lopez D, Pellegrini M, Phipatanakul W, Chatila TA., "An asthma-associated IL4R variant exacerbates airway inflammation by promoting conversion of regulatory T cells to T(H)17-like cells", Nat Med (2016). [link]

Escuin-Ordinas H, Li S, Xie MW, Sun L, Hugo W, Huang RR, Jiao J, de-Faria FM, Realegeno S, Krystofinski P, Azhdam A, Komenan SM, Atefi M, Comin-Anduix B, Pellegrini M, Cochran AJ, Modlin RL, Herschman HR, Lo RS, McBride WH, Segura T, Ribas A, "Cutaneous wound healing through paradoxical MAPK activation by BRAF inhibitors", Nat Commun 7: (2016). [link]

Hoban MD, Lumaquin D, Kuo CY, Romero Z, Long J, Ho M, Young CS, Mojadidi M, Fitz-Gibbon S, Cooper AR, Lill GR, Urbinati F, Campo-Fernandez B, Bjurstrom CF, Pellegrini M, Hollis RP, Kohn DB, "CRISPR/Cas9-Mediated Correction of the Sickle Mutation in Human CD34+ cells", Mol Ther (2016). [link]

Vega-Vaquero A, Bonora G, Morselli M, Vaquero-Sedas MI, Rubbi L, Pellegrini M, Vega-Palas MA, "Novel features of telomere biology revealed by the absence of telomeric DNA methylation", Genome Res 26 (8): 1047-1056 (2016). [link]

Brumm AJ, Nunez S, Doroudchi MM, Kawaguchi R, Duan J, Pellegrini M, Lam L, Carmichael ST, Deb A, Hinman JD, "Astrocytes Can Adopt Endothelial Cell Fates in a p53-Dependent Manner", Mol Neurobiol (2016). [link]

Lam L, Chin L, Halder RC, Sagong B, Famenini S, Sayre J, Montoya D, Rubbi L, Pellegrini M, Fiala M, "Epigenetic changes in T-cell and monocyte signatures and production of neurotoxic cytokines in ALS patients", FASEB J (2016). [link]

Schokrpur S, Hu J, Moughon DL, Liu P, Lin LC, Hermann K, Mangul S, Guan W, Pellegrini M, Xu H, Wu L., "CRISPR-Mediated VHL Knockout Generates an Improved Model for Metastatic Renal Cell Carcinoma", Sci Rep 6: (2016). [link]

Realegeno S, Kelly-Scumpia KM, Dang AT, Lu J, Teles R, Liu PT, Schenk M, Lee EY, Schmidt NW, Wong GC, Sarno EN, Rea TH, Ochoa MT, Pellegrini M, Modlin RL, "S100A12 Is Part of the Antimicrobial Network against Mycobacterium leprae in Human Macrophages", PLoS Pathog 12 (6): (2016). [link]

Zhang H, Prado K, Zhang KX, Peek EM, Lee J, Wang X, Huang J, Li G, Pellegrini M, Chin AI., "Biased Expression of the FOXP3?3 Isoform in Aggressive Bladder Cancer Mediates Differentiation and Cisplatin Chemotherapy Resistance", Clin Cancer Res (2016). [link]

Flinders C, Lam L, Rubbi L, Ferrari R, Fitz-Gibbon S, Chen PY, Thompson M, Christofk H, B Agus D, Ruderman D, Mallick P, Pellegrini M, "Epigenetic changes mediated by polycomb repressive complex 2 and E2a are associated with drug resistance in a mouse model of lymphoma", Genome Med 8 (1): (2016). [link]

Meng Q, Ying Z, Noble E, Zhao Y, Agrawal R, Mikhail A, Zhuang Y, Tyagi E, Zhang Q, Lee JH, Morselli M, Orozco L, Guo W, Kilts TM, Zhu J, Zhang B, Pellegrini M, Xiao X, Young MF, Gomez-Pinilla F, Yang X., "Systems Nutrigenomics Reveals Brain Gene Networks Linking Metabolic and Brain Disorders", EBioMedicine 7: 157-166 (2016). [link]

Janowitz Koch I, Clark MM, Thompson MJ, Deere-Machemer KA, Wang J, Duarte L, Gnanadesikan GE, McCoy EL, Rubbi L, Stahler DR, Pellegrini M, Ostrander EA, Wayne RK, Sinsheimer JS, vonHoldt BM, "The concerted impact of domestication and transposon insertions on methylation patterns between dogs and grey wolves", Mol Ecol 25 (8): 1838-1855 (2016). [link]

Gugger PF, Fitz-Gibbon S, PellEgrini M, Sork VL, "Species-wide patterns of DNA methylation variation in Quercus lobata and their association with climate gradients", Mol Ecol 25 (8): 1665-1680 (2016). [link]

Chen H, Orozco LD, Wang J, Rau CD, Rubbi L, Ren S, Wang Y, Pellegrini M, Lusis AJ, Vondriska TM, "DNA Methylation Indicates Susceptibility to Isoproterenol-Induced Cardiac Pathology and Is Associated With Chromatin States", Circ Res 118 (5): 786-797 (2016). [link]

Liu W, Jiang X, Pellegrini M, Wang X., "Discovering communities in complex networks by edge label propagation", Sci Rep 6: (2016). [link]