Timothy Ravasi Laboratory

Dr. Ravasi’s research applies integrative systems approaches with the aim to infer the structures and dynamics of transcription regulatory networks in eukaryotic cells with particular emphasis on networks governing immunological systems or diseases models. Genome-wide measurements of several cellular states, such as genes and proteins expression, protein-protein and protein-DNA interactions are integrated, graphically displayed, and ultimately modeled computationally to develop system-wide models of gene regulation. He is also interested in cataloging the microbial biodiversity within the Red Sea ecosystem through the use of DNA "barcoding" generated by ultra-high-throughput genomes sequencing, aiming to the discovery of new microbial bioactive molecules with potential industrial and medical use.

Selected Publications

1. Harukazu Suzuki, Alistair R. R. Forrest, Erik van Nimwegen, Carsten O. Daub, Timo Lassmann, Timothy Ravasi et al. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet. 2009 Apr 19.
2. Tan K, Tegner J and Ravasi T. Integrated data-driven approaches to uncover transcription regulatory networks in mammalian cells. Genomics, 2008 Mar 91;3: 219-231 (Invited review and Journal Cover and 2008 ScienceDirect TOP 5 HOTTEST ARTICLES).
3. Tegnér J, Nilsson R, Bajic VB, Björkegren J, and Ravasi T. Systems biology of innate immunity. Cell Immunol. 2006 Dec;244(2):105-9. (Invited review and 2007 ScienceDirect TOP 10 HOTTEST ARTICLES)
4. Ravasi T, Wells C and Hume DA. Systems Biology of Transcription Control in Macrophages. Bioessays. 2007 Nov 15;29(12):1215-1226. (Invited review)
5. Hume DA, Wells C and Ravasi T. Transcriptional Regulatory Networks in Macrophages. Novartis Found Symp. 2007;281:2-18. (Invited review)
6. Nilsson R, Bajic VB, Katayama K, Suzuki H, Reid JF, Sweet MJ, Gariboldi M, Carninici P, Hayashizaki Y, Hume DA, Tegner J, and Ravasi T. Transcriptional Network Dynamics governing Macrophage Activation, Genomics., 2006. 88, 2, 133-142. August 1. (2006 ScienceDirect TOP 10 DOWNLOADED ARTICLES)
7. Aung HT, Schroder K, Himes SR, Brion K, van Zuylen W, Trieu A, Suzuki H, Hayashizaki Y, Hume DA, Sweet MJ, and Ravasi T. LPS regulates proinflammatory gene expression in macrophages by altering histone deacetylase expression. FASEB J., 2006. 20, 9. June 30. (2006 FASEB J., The 20 Most-Frequently downloaded articles)
8. Maeda RT, Kasukawa T, Oyama R, Gough J, Frith M, Engström PG, Lenhard B, Aturaliya RN, Batalov S, Beisel KW, Bult CJ, Fletcher CF, Forrest ARR, Furuno. Hill D, Itoh M, Katayama KM, Katayama S, Katoh M, Kawashima T, Quackenbush J, Ravasi T, et al. Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs. PLoS Genetic. 2006, 2, 4. Apr 28.
9. Carninci P, Sandelin TA, Lenhard B, Katayama1 S, Shimokawa K, Ponjavic P, Semple CA, Taylor MS, Engstrom P, Frith M, Forrest ARR, Alkema WB, Tan SL, Plessy C, Kodzius K, Ravasi T et al. Genome-wide analysis of mammalian promoter architecture and evolution, Nat Genet. 2006 Jun;38(6):626-35. (Faculty of 1000)
10. Ravasi T, Harakazu Suzuki, Ken C. Pang, Shintaro Katayama, Masaaki Furuno, Rie Okunishi, Shiro Fukuda, Kelin Ru, Martin Frith, M. Milena Gongora, Sean M. Grimmond, David A. Hume, Yoshihide Hayashazaki and John S. Mattick. Experimental validation of the regulated expression of a large numbers of noncoding RNAs from the mouse genome. Genome Research, 2006 Jan;16(1):11-9.
11. Katayama S, Tomaru Y, Kasukawa T, Waki T, Nakanishi M, Nakamura M, Nishida H, Yap CC, Suzuki M, Kawai J, Suzuki H, Carninci P, Hayashizaki Y, Wells C, Frith M, Ravasi T, Pang K, Mattick J, Hume DA, et al. Antisense transcription in the mammalian transcriptome. Science, 309:1564-1566, 2005. (Faculty of 1000)
12. Carninci P, Kasukawa T, Katayama T, Gough J, Frith M, Maeda M, Oyama M, Ravasi T, et al. The Transcriptional Landscape of the Mammalian Genome. Science, 309:1559-1563, 2005.