Matteo Pellegrini
email: matteop@mcdb.ucla.edu
phone: X50012
office: 4219 LIFE SCIENCE BUILDING
lab: 4215
homepage: http://pellegrini.mcdb.ucla.edu
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, tiling and expression arrays along with mass spectrometry. 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 base calling and mapping. We are also developing multivariate regression methodologies that combine binding and expression data to infer transcriptional regulatory mechanisms. Our goal is to make these tools, and the resulting databases, generally available to the scientific community.
Selected Publications
Orozco, L.D., Cokus, S.J., Ghazalpour, A., Ingram-Drake, L., Wang, S., Van Nas, A., Che, N.,Araujo, J.A., Pellegrini, M., Lusis, A.J.. 2009. Copy number variation influences gene expression and metabolic traits in mice Hum Mol Genet : - .
Mark Chin, Mike Mason; Wei Xie; Stefano Violinia, Mike Singer; Cory Peterson; Gayane Ambartsumyan, Otaren Aimiuwu; Laura Richter; Jin Zhang; Ivan Khvorostov, Vanessa Ott, Michael Grunstein, Nissim Benvenisty, Carlo M Croce, Amander Clark, Tim Baxter; April Pyle, Mike Teitell, Matteo Pellegrini, Kathrin Plath and William E Lowry. 2009. Induced pluripotent stem cells and embryonic stem cells are distinguished by gene expression signatures Cell Stem Cell 5: 111-123 .
Zhang, X., Bernatavichute, Y.V., Cokus, S., Pellegrini, M. and Jacobsen, S.E.. 2009. Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana Genome Biology 10: - [link].
Jacob, Y., Feng, S., Leblanc, C.A., Bernatavichute, Y.V., Stroud, H., Cokus, S., Johnson, L.M., Pellegrini, M., Jacobsen, S.E., and Michaels, S.D.. 2009. ATXR5 and ATXR6 are H3K27 monomethyltransferases required for chromatin structure and gene silencing Nature Structural Molecular Biology 16: 763-768 .
Gekas, C., Rhodes, K.E., Gereige, L.M., Helgadottir, H., Ferrari, R., Kurdistani, S.K., Montecino-Rodriguez, E., Bassel-Duby, R., Olson, E., Krivtsov, A.V., Armstrong, S., Orkin, S.H., Pellegrini, M., Mikkola, H.K.. 2009. Mef2C is a lineage-restricted target of Scl/Tal1 and regulates megakaryopoiesis and B cell homeostasis Blood 113: 3461-3471 .
Widman, N., Jacobsen, S.E. and Pellegrini, M.. 2009. Determining the conservation of DNA methylation in Arabidopsis Epigenetics 4: 119-124 .
Conway, A.E., Lindgren, A., Galic, Z., Pyle, A.D., Wu, H., Zack, J.A., Pellegrini, M., Teitell, M.A., Clark, A.. 2009. A Pluripotency and Self-Renewal Program Controls the Expansion of Genetically Unstable Cancer Stem Cells in Pluripotent Stem Cell-Derived Tumors A Pluripotency and Self-Renewal Program Controls the Expansion of Genetically Unstable Cancer Stem Cells in Pluripotent Stem Cell-Derived Tumors 27: 18-28 .
Das, D., Pellegrini, M., and Gray, J.W.. 2009. A primer on regression methods for decoding cis-regulatory logic PLoS Computational Biology 5: - [link].
Cokus, S.J., Feng, S., Zhang, X., Chen, Z., Merriman, B., Haudenschild, C.D., Pradhan, S., Nelson, S.F., Pellegrini, M., Jacobsen, S.E.. 2008. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning Nature 452: 215-219 .
Ferrari, R., Pellegrini, M., Horwitz, G., Xie, W., Berk, A.J.. 2008. Epigenetic reprogramming by adenovirus e1a Science 321: 1086-1088 .