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

Fu K, Bonora G, Pellegrini M, "Interactions between core histone marks and DNA methyltransferases predict DNA methylation patterns observed in human cells and tissues", Epigenetics (2019). [link]

Weiss DI, Ma F, Merleev AA, Maverakis E, Gilliet M, Balin SJ, Bryson BD, Ochoa MT, Pellegrini M, Bloom BR, Modlin RL., "IL-1beta Induces the Rapid Secretion of the Antimicrobial Protein IL-26 from Th17 Cells", J Immunol 203 (4): 911-921 (2019).

Snir S, Farrell C, Pellegrini M, "Human epigenetic ageing is logarithmic with time across the entire lifespan", Epigenetics 14 (9): 912-926 (2019).

Shigeta A, Huang V, Zuo J, Besada R, Nakashima Y, Lu Y, Ding Y, Pellegrini M, Kulkarni RP, Hsiai T, Deb A, Zhou B, Nakano H, Nakano A., "Endocardially Derived Macrophages Are Essential for Valvular Remodeling", Dev Cell 48 (5): 617-630 (2019).

R Andrade P, Mehta M, Lu J, M B Teles R, Montoya D, O Scumpia P, Nunes Sarno E, Ochoa MT, Ma F, Pellegrini M, Modlin RL., "The cell fate regulator NUPR1 is induced by Mycobacterium leprae via type I interferon in human leprosy", PLoS Negl Trop Dis 13 (7): (2019). [link]

Montoya DJ, Andrade P, Silva BJA, Teles RMB, Ma F, Bryson B, Sadanand S, Noel T, Lu J, Sarno E, Arnvig KB, Young D, Lahiri R, Williams DL, Fortune S, Bloom BR, Pellegrini M, Modlin RL., "Dual RNA-Seq of Human Leprosy Lesions Identifies Bacterial Determinants Linked to Host Immune Response", Cell Rep 26 (13): 3574-3585 (2019).

Montoya D, Mehta M, Ferguson BG, Teles RMB, Krutzik SR, Cruz D, Pellegrini M, Modlin RL, "Plasticity of antimicrobial and phagocytic programs in human macrophages", Immunology 156 (2): 164-173 (2019).

Ma F, Pellegrini M, "ACTINN: Automated Identification of Cell Types in Single Cell RNA Sequencing", Bioinformatics (2019). [link]

Ma F, Fuqua BK, Hasin Y, Yukhtman C, Vulpe CD, Lusis AJ, Pellegrini M, "A comparison between whole transcript and 3' RNA sequencing methods using Kapa and Lexogen library preparation methods", BMC Genomics 20: (2019). [link]

Leung CS, Douglass SM, Morselli M, Obusan MB, Pavlyukov MS, Pellegrini M, Johnson TL, "H3K36 Methylation and the Chromodomain Protein Eaf3 Are Required for Proper Cotranscriptional Spliceosome Assembly", Cell Rep 27 (13): 3760-3769 (2019).

Frausto RF, Chung DD, Boere PM, Swamy VS, Duong HNV, Kao L, Azimov R, Zhang W, Carrigan L, Wong D, Morselli M, Zakharevich M, Hanser EM, Kassels AC, Kurtz I, Pellegrini M, Aldave AJ., "ZEB1 insufficiency causes corneal endothelial cell state transition and altered cellular processing", PLoS One 14 (6): (2019). [link]

Fan X, Han W, Teng L, Jiang P, Zhang X, Xu D, Li C, Pellegrini M, Wu C, Wang Y, Kaczurowski MJS, Lin X, Tirichine L, Mock T, Ye N., "Single-base methylome profiling of the giant kelp Saccharina japonica reveals significant differences in DNA methylation to microalgae and plants", New Phytol (2019). [link]

Charbonnier LM, Cui Y, Stephen-Victor E, Harb H, Lopez D, Bleesing JJ, Garcia-Lloret MI, Chen K, Ozen A, Carmeliet P, Li MO, Pellegrini M, Chatila TA, "Functional reprogramming of regulatory T cells in the absence of Foxp3", Nat Immunol 20 (9): 1208-1219 (2019).

Cantarella S, Carnevali D, Morselli M, Conti A, Pellegrini M, Montanini B, Dieci G:, "Alu RNA Modulates the Expression of Cell Cycle Genes in Human Fibroblasts", Int J Mol Sci 20: (2019).

Bulterys PL, Toesca IJ, Norris MH, Maloy JP, Fitz-Gibbon ST, France B, Toffig B, Morselli M, Somprasong N, Pellegrini M, Schweizer HP, Tuanyok A, Damoiseaux R, French CT, Miller JF., "An in situ high-throughput screen identifies inhibitors of intracellular Burkholderia pseudomallei with therapeutic efficacy", Proc Natl Acad Sci U S A 116 (37): 18597-18606 (2019).