Book chapters

Ravasi T, Mavromatis C., Bokil N.J. and Sweet M.J.

Co-transcriptomic analysis by RNA sequencing to simultaneously measure regulated gene expression in host and bacterial pathogen. 

Toll-Like Receptors, Practice and Methods (2nd Edition)

Claire McCoy, Publisher: Springer, New York, U.S.A. 2015

Ravasi T.
Integrative Systems Approaches to study Innate Immunity.

Clinical Applied Immunogenomics.
Springer. 233  Spring Street, New York, NY 10013, U.S.A. 2008  

Tegner J, Björkegren J, Ravasi T and Bajic V.
Transcription Regulatory Networks Analysis Using CAGE.
(John Wiley & Sons, Chichester, UK), 2008  

Hume DA, Wells CA and Ravasi T
Transcriptional regulatory networks in macrophages
Decoding the Genomic Control of Immune Reactions
Novartis Foundation Symposium, No 281
Novartis Foundation, ISBN: 978-0-470-02755-4, May 2007  

Ravasi T and Hume DA.
Noncoding RNAs in mammals
Encyclopedia of Genetics, Genomics, Proteomics, and Bioinformatics,
L. B. Jorde, P. F. R. Little, M. J. Dunn, S. Subramaniam, Eds.
(John Wiley & Sons, Chichester, UK), April 2006  

Scientific publications 

Chandramouli KH, Reish D, Zhang H, Qian PY and Ravasi T. Proteomic changes associated with successive reproductive periods in male polychaetous Neanthes arenaceodentata. Scientific Reports 2015. In press


ReFuGe consortium. The role of genomic data and genetic tools in the management of coral reefs. Frontiers in Ecology and the Environment. 2015 In press


Bustamante E, Najera J, Bortell N, Ravasi T, Morsey B, Fox HJ and. Marcondes MC Methamphetamine abuse affects gene expression in brain-derived microglia of SIV-infected macaques to enhance inflammation and promote virus targets. BMC Genomics 2015. In press


Ryu T, Veilleux HD, Donelson JM, van Herwerden L, Seridi L, Ghosheh Y, Berumen ML, Leggat W, Munday PL and Ravasi T. Mechanisms of transgenerational acclimation to a warming ocean. Nature Climate Change 2015. doi:10.1038/nclimate2724.


Giles EM, Saenz-Agudelo P, Hussey NE, Berumen ML and Ravasi T. Exploring seascape genetics and kinship in the reef sponge Stylissa carteri in the Red Sea. Ecology and Evolution 5 (13), 2487-2502, 1 Jun 2015 DOI: 10.1002/ece3.1511.


Contreras MF, Sougrat R, Zaher A, Ravasi T and Kosel J. Non-chemotoxic Cancer Cell Death Induction Using Magnetic Nanowires. International Journal of Nanomedicine. 2015. Int J Nanomedicine. 2015 Mar 17;10:2141-53. doi: 10.2147/IJN.S77081.


Alanis-Lobato G, Cannistraci CV, Eriksson A, Manica A and Ravasi T. Highlighting nonlinear patterns in population genetics datasets. Sci Rep. 2015 Jan 30;5:8140. doi: 10.1038/srep08140. PMID: 25633916

Mavromatis CH, Bokil NJ, Totsika M, Kakkanat A, Schaale K, Cannistraci CV, Ryu T, Beatson SA, Ulett GC, Schembri MA, Sweet MJ, Ravasi T. The Co-Transcriptome of Uropathogenic Escherichia coli-Infected Mouse Macrophages Reveals New Insights into Host-Pathogen Interactions. Cell Microbiol. 2014 Nov 20.

Bayer K, Moitinho-Silva L, Brümmer F, Cannistraci CV, Ravasi T, Hentschel U. GeoChip-based insights into the microbial functional gene repertoire of marine sponges (high microbial abundance, low microbial abundance) and seawater. FEMS Microbiol Ecol. 2014 Dec;90(3):832-43. 

Wong YH, Ryu T, Seridi L, Ghosheh Y, Bougouffa S, Qian PY, Ravasi T. Transcriptome analysis elucidates key developmental components of bryozoan lophophore development. Sci Rep. 2014 Oct 10;4:6534. 

Seridi L, Ryu T, Ravasi T. Dynamic epigenetic control of highly conserved noncoding elements. PLoS One. 2014 Oct 7;9(10):e109326.

Zhang Y, Sun J, Zhang H, Chandramouli KH, Xu Y, He LS, Ravasi T, Qian PY. Proteomic profiling during the pre-competent to competent transition of the biofouling polychaete Hydroides elegans. Biofouling. 2014 Sep;30(8):921-8. 

Hasegawa Y, Tang D, Takahashi N, Hayashizaki Y, Forrest AR; FANTOM Consortium, Suzuki H. CCL2 enhances pluripotency of human induced pluripotent stem cells by activating hypoxia related genes. Sci Rep. 2014 Jun 24;4:5228. 

Moitinho-Silva L, Seridi L, Ryu T, Voolstra CR, Ravasi T, Hentschel U. Revealing microbial functional activities in the Red Sea sponge Stylissa carteri by metatranscriptomics. Environ Microbiol. 2014 Jun 11. 

Abdelmohsen UR, Yang C, Horn H, Hajjar D, Ravasi T, Hentschel U. Actinomycetes from Red Sea sponges: sources for chemical and phylogenetic diversity. Mar Drugs. 2014 May 12;12(5):2771-89. 

Morikawa H, Ohkura N, Vandenbon A, Itoh M, Nagao-Sato S, Kawaji H, Lassmann T, Carninci P, Hayashizaki Y, Forrest AR, Standley DM, Date H, Sakaguchi S; FANTOM Consortium. Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation. Proc Natl Acad Sci U S A. 2014 Apr 8;111(14):5289-94. 

Arner E, Forrest AR, Ehrlund A, Mejhert N, Itoh M, Kawaji H, Lassmann T, Laurencikiene J, Rydén M, Arner P; FANTOM Consortium. Ceruloplasmin is a novel adipokine which is overexpressed in adipose tissue of obese subjects and in obesity-associated cancer cells. PLoS One. 2014 Mar 27;9(3):e80274. 

FANTOM Consortium and the RIKEN PMI and CLST (DGT). A promoter-level mammalian expression atlas. Nature. 2014 Mar 27;507(7493):462-70. 
Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO, Jørgensen M, Andersen PR, Bertin N, Rackham O, Burroughs AM, Baillie JK, Ishizu Y, Shimizu Y, Furuhata E, Maeda S, Negishi Y, Mungall CJ, Meehan TF, Lassmann T, Itoh M, Kawaji H, Kondo N, Kawai J, Lennartsson A, Daub CO, Heutink P, Hume DA, Jensen TH, Suzuki H, Hayashizaki Y, Müller F; FANTOM Consortium, Forrest AR, Carninci P, Rehli M, Sandelin A. An atlas of active enhancers across human cell types and tissues. Nature. 2014 Mar 27;507(7493):455-61. 

Harjes J, Ryu T, Abdelmohsen UR, Moitinho-Silva L, Horn H, Ravasi T, Hentschel U. Draft Genome Sequence of the Antitrypanosomally Active Sponge-Associated Bacterium Actinokineospora sp. Strain EG49. Genome Announc. 2014 Mar 6;2(2). pii: e00160-14. 

Chen ZF, Zhang H, Wang H, Matsumura K, Wong YH, Ravasi T, Qian PY. Quantitative proteomics study of larval settlement in the Barnacle Balanus amphitrite. PLoS One. 2014 Feb 13;9(2):e88744. 

GIGA Community of Scientists, Bracken-Grissom H, Collins AG, Collins T, Crandall K, Distel D, Dunn C, Giribet G, Haddock S, Knowlton N, Martindale M, Medina M, Messing C, O'Brien SJ, Paulay G, Putnam N, Ravasi T, Rouse GW, Ryan JF, Schulze A, Wörheide G, Adamska M, Bailly X, Breinholt J, Browne WE, Diaz MC, Evans N, Flot JF, Fogarty N, Johnston M, Kamel B, Kawahara AY, Laberge T, Lavrov D, Michonneau F, Moroz LL, Oakley T, Osborne K, Pomponi SA, Rhodes A, Santos SR, Satoh N, Thacker RW, Van de Peer Y, Voolstra CR, Welch DM, Winston J, Zhou X. The Global Invertebrate Genomics Alliance (GIGA): developing community resources to study diverse invertebrate genomes. J Hered. 2014 Jan-Feb;105(1):1-18. 

Chandramouli KH, Ravasi T, Reish D, Qian PY. Proteomic changes between male and female worms of the polychaetous annelid Neanthes arenaceodentata before and after spawning. PLoS One. 2013 Aug 30;8(8):e72990. 

Moitinho-Silva L, Bayer K, Cannistraci CV, Giles EC, Ryu T, Seridi L, Ravasi T, Hentschel U. Specificity and transcriptional activity of microbiota associated with low and high microbial abundance sponges from the Red Sea. Mol Ecol. 2014 Mar;23(6):1348-63. 

Alanis-Lobato G, Cannistraci CV, Ravasi T. Exploitation of genetic interaction network topology for the prediction of epistatic behavior. Genomics. 2013 Oct;102(4):202-8. 

Chandramouli KH, Dash S, Zhang Y, Ravasi T, Qian PY. Proteomic and metabolomic profiles of marine Vibrio sp. 010 in response to an antifoulant challenge. Biofouling. 2013;29(7):789-802. 
Cannistraci CV, Alanis-Lobato G, Ravasi T. Minimum curvilinearity to enhance topological prediction of protein interactions by network embedding. Bioinformatics. 2013 Jul 1;29(13):i199-209. 

Ammirati E, Cristell N, Cianflone D, Vermi AC, Marenzi G, De Metrio M, Uren NG, Hu D, Ravasi T, Maseri A, Cannistraci CV. Questing for circadian dependence in ST-segment-elevation acute myocardial infarction: a multicentric and multiethnic study. Circ Res. 2013 May 10;112(10):e110-4. 

Cannistraci CV, Alanis-Lobato G, Ravasi T. From link-prediction in brain connectomes and protein interactomes to the local-community-paradigm in complex networks. Sci Rep. 2013;3:1613. 

Cannistraci CV, Ogorevc J, Zorc M, Ravasi T, Dovc P, Kunej T. Pivotal role of the muscle-contraction pathway in cryptorchidism and evidence for genomic connections with cardiomyopathy pathways in RASopathies. BMC Med Genomics. 2013 Feb 14;6:5. 

Chandramouli KH, Sun J, Mok FS, Liu L, Qiu JW, Ravasi T, Qian PY. Transcriptome and quantitative proteome analysis reveals molecular processes associated with larval metamorphosis in the polychaete Pseudopolydora vexillosa. J Proteome Res. 2013 Mar 1;12(3):1344-58. 

Ryu T, Seridi L, Ravasi T. The evolution of ultraconserved elements with different phylogenetic origins. BMC Evol Biol. 2012 Dec 5;12:236. 

Ammirati E, Cannistraci CV, Cristell NA, Vecchio V, Palini AG, Tornvall P, Paganoni AM, Miendlarzewska EA, Sangalli LM, Monello A, Pernow J, Björnstedt Bennermo M, Marenzi G, Hu D, Uren NG, Cianflone D, Ravasi T, Manfredi AA, Maseri A. Identification and predictive value of interleukin-6+ interleukin-10+ and interleukin-6- interleukin-10+ cytokine patterns in ST-elevation acute myocardial infarction. Circ Res. 2012 Oct 26;111(10):1336-48. 

Giles EC, Kamke J, Moitinho-Silva L, Taylor MW, Hentschel U, Ravasi T, Schmitt S. Bacterial community profiles in low microbial abundance sponges. FEMS Microbiol Ecol. 2013 Jan;83(1):232-41. 

Fan M, Wong KC, Ryu T, Ravasi T, Gao X. SECOM: A Novel Hash Seed and Community Detection Based-Approach for Genome-Scale Protein Domain Identification. PLoS One. 2012;7(6):e39475. Epub 2012 Jun 28.


Sun J, Zhang H, Wang H, Heras H, Dreon MS, Ituarte S, Ravasi T, Qian PY, Qiu JW. First proteome of the egg perivitelline fluid of a freshwater gastropod with aerial oviposition. J Proteome Res. 2012 Aug 3;11(8):4240-8. Epub 2012 Jul 13.

Wong YH, Wang H, Ravasi T, Qian PY. Involvement of Wnt signaling pathways in the metamorphosis of the bryozoan Bugula neritina. PLoS One. 2012;7(3):e33323. Epub 2012 Mar 20.


Ramaprasad A, Pain A, Ravasi T. Defining the protein interaction network of human malaria parasite Plasmodium falciparum. Genomics. 2012 Feb;99(2):69-75. Epub 2011 Dec 8. (2012 ScienceDirect TOP 10 DOWNLOADED ARTICLES)


Bokila NJ, Totsikab M, Careyc AJ, Stacey KJ, Hancocke V, Saundersf BM, Ravasi T, Ulettc G, Schembri MA, and Sweet MJ. Intramacrophage survival of uropathogenic Escherichia coli: differences between diverse clinical isolates and between mouse and human macrophages. Immunobiology. Immunobiology. 2011 Nov;216(11):1164-71.


Ryu T, Mavromatis C, Bayer T, Voolstra CR and Ravasi T. Unexpected complexity of the Reef-Building Coral Acropora millepora transcription factor network. BMC Syst Biol. 2011 Apr 28;5:58.


Zhang H, Wong YH, Wang H, Chen Z, Arellano SM, Ravasi T, Qian PY. Quantitative proteomics identify molecular targets that are crucial in larval settlement and metamorphosis of Bugula neritina. J Proteome Res. 2011 Jan 7;10(1):349-60. Epub 2010 Dec 16.


Kuo D, Licon K, Bandyopadhyay S, Chuang R, Luo C, Catalana J, Ravasi T, Tan K, Ideker T. Coevolution within a transcriptional network by compensatory trans and cis mutations. Genome Res. 2010 Dec;20(12):1672-8. Epub 2010 Oct 26.


Cannistraci CV, Ravasi T, Montevecchi FM, Ideker T, Alessio M. Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathic pain and tissue embryological classes. Bioinformatics. 2010 Sep 15;26(18):i531-9.


Kuo D, Tan K, Zinman G, Ravasi T, Bar-Joseph Z, Ideker T. Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering. Genome Biol. 2010;11(7):R77.


Ramachandra Rao S, Talwar P, Ravasi T and Sharma K. Novel systems biology insights using antifribrotic approaches for diabetic kidney disease. Expert Rev. Endocrino. Metab. 5(1), 127-135 (2010).


Wang H, Zhang H, Wong YH, Voolstra C, Ravasi T, B Bajic V, Qian PY. Rapid transcriptome and proteome profiling of a non-model marine invertebrate, Bugula neritina. Proteomics. 2010 Aug;10(16):2972-81.


Wong YH, Arellano SM, Zhang H, Ravasi T, Qian PY. Dependency on de novo protein synthesis and proteomic changes during metamorphosis of the marine bryozoan Bugula neritina. Proteome Sci. 2010 May 24;8:25.


Zhang H, Zhao C, Li X, Zhu Y, Gan CS, Wang Y, Ravasi T, Qian PY, Wong SC, Sze SK. Study of monocyte membrane proteome perturbation during lipopolysaccharide-induced tolerance using iTRAQ-based quantitative proteomic approach. Proteomics. 2010 Aug;10(15):2780-9.


Timothy Ravasi, Carlo Vittorio Cannistraci, Shintaro Katayama, Vladimir B. Bajic, Kai Tan, et al. An atlas of combinatorial transcriptional regulation in mouse and man. Cell, 140-5, 744-752, 5 March 2010. (Faculty of 1000).

Merril Gersten, Mehrdad Alirezaei, Maria Cecilia Garibaldi Marcondes, Claudia Flynn, Timothy Ravasi, Trey Ideker, and Howard S. Fox. An integrated systems analysis implicates EGR1 downregulation in SIVE- induced neural dysfunction. J Neurosci. 2009 Oct 7;29(40):12467-76.


Satish RamachandraRao, Timothy Ravasi, Yanqing Zhu, Tracy A. McGowan, Irene Toh, Stephen R. Dunn, Michael A. Shaw and Kumar Sharma. Renoprotective Role of Pirfenidone in Diabetic Kidney Disease. J Am Soc Nephrol published July 2, 2009.


§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.


Tan K, Feizi H, Luo C, Fan SH, Ravasi T and Ideker T. A systems approach to delineate functions of paralogous transcription factors: Role of the Yap family in the DNA damage response. PNAS, 2008 Feb. 19, 10.1073. (Faculty of 1000).


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).


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)


Hinshelwood RA, Huschtscha LI, Melki J, Stirzaker C, Ravasi T, Wells CA, Hume DA, Reddel RR and Clark SJ. Concordant epigenetic silencing of TGFb signaling pathway genes occurs early in breast carcinogenesis. Cancer Res. 2007 Dec 15;67(24):11517-27.


Ravasi T, Wells C and Hume DA. Systems Biology of Transcription Control in Macrophages. Bioessays. 2007 Nov 15;29(12):1215-1226. (Invited review)


Schroder K, Spille M, Pilz A, Lattin J, Bode KA, Burrows AD, Ravasi T, Weighardt H, Stacey KJ, Decker T, Hume DA, Dalpke AH and Sweet MJ. Differential effects of CpG DNA on IFNb induction and STAT1 activation in murine macrophages versus dendritic cells: identification of a novel functions for STAT1 in toll-like receptor signaling. J Immunol. 2007 Sep 15;179(6):3495-503.


Bode KA, Schroder K, Hume DA, Ravasi T, Heeg K, Sweet MJ, and Dalpke AH. Histone deacetylase inhibitors decrease Toll-like receptor mediated cytokine production. Immunology. 2007 Jul 16.


Ripoll VM, Irvine KM, Ravasi T, Sweet MJ, Hume DA. Gpnmb Is Induced in Macrophages by IFN-{gamma} and Lipopolysaccharide and Acts as a Feedback Regulator of Proinflammatory Responses. J Immunol. 2007 May 15;178(10):6557-66.


Hume DA, Wells C and Ravasi T. Transcriptional Regulatory Networks in Macrophages. Novartis Found Symp. 2007;281:2-18. (Invited review)


Sasmono RT, Ehrnsperger A, Cronau SL, Ravasi T, Kandane R, Hickey MJ, Cook, Himes SR, Hamilton JA and Hume DA. Mouse neutrophilic granulocytes express mRNA encoding the macrophage colony stimulating factor receptor (CSF-1R) as well as many other macrophage-specific transcripts, and can transdifferentiate into macrophages in vitro in response to CSF-1. Journal of Leukocytes Biology, J Leukoc Biol. 2007 Apr 16.


Schroder K, Lichtinger M, Irvine KM, Brion K, Trieu A, Ross I,  Ravasi T, Stacey KJ, Rehli M, Hume DA and Sweet MJ. PU.1 and ICSBP are required for tlr9 promoter regulation in mouse macrophages. J Leukoc Biol. 2007 Jun;81(6):1577-90.


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)


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


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.


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)


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.


Himes SR, Ravasi T, Sester DP, Cronau S, Sasmono T, and Hume DA. c-Jun N-terminal kinases are important for development and survival of macrophages. Journal of Immunology. 2006 Feb 15;176(4):2219-28.


Sester DP, Trieu A, McDonald R, Ravasi T, Sasmono T, Ripoll V, Stacey KJ, Hume DA and Sweet ML. LPS regulates sensitivity of primary murine macrophage to bacterial/CpG DNA in a CSF-1-dependent manner: a novel mechanism for LPS-inducible gene expression. Immunobiology. 2005;210(2-4):97-107.


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)


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.


Rehli, M., Sulzbacher, S., Pape, S., Ravasi T., Wells, C.A., Heinz, S., Sollner, L., El   Chartouni, C., Krause, S.W., Steingrimsson, E., Hume, D.A., Andreesen, R., (2005). Transcription factor Tfec contributes to the interleukin 4-inducible expression of a small group of genes in mouse macrophages including the granulocyte colony- stimulating factor receptor. J Immunol. 2005 Jun 1;174(11):7111-22.


Cowieson NP, Listwan P, Kurz M, Aagaard A, Ravasi T, Wells C, Huber T, Hume DA, Kobe B, Martin JL. Pilot studies on the parallel production of soluble mouse proteins in a bacterial expression system. J Struct Funct Genomics. 2005;6(1):13-20.


Wells CA, Ravasi T, Hume DA. Inflammation suppressor genes: please switch out all the lights. J Leukoc Biol. 2005 Mar 17.


Aagaard A, Listwan P, Cowieson N, Huber T, Ravasi T, Wells CA, Flanagan JU, Kellie S, Hume DA, Kobe B, Martin JL. An inflammatory role for the mammalian carboxypeptidase inhibitor latexin: relationship to cystatins and the tumor suppressor TIG1. Structure (Camb). 2005 Feb;13(2):309-17.


Ravasi T, Hsu K, Goyette J, Schroder K, Yang Z, Miranda LP, Alewood PF, Hume DA and Geczy C. Probing the S100 protein family through genomic and functional analysis. Genomics. 2004 Jul;84(1):10-22. (2004 ScienceDirect TOP 10 downloaded ARTICLES)


Schroder K, Hertzog PJ, Ravasi T, Hume DA. Interferon-{gamma}: an overview of signals, mechanisms, and functions. J. Leukoc. Biol. 2003 Oct 2. (Winner of the 2008 Dolph Adams prize. For the review published in Journal of Leukocyte Biology that receives the most independent citations during this time period).


Wells C, Ravasi T, Faulkner J, Carninci P, Okazaki Y, Hayashizaki Y, Sweet MJ, Wainwright BJ, Hume DA. Genetic control of the innate immune response. BMC Immunol. 2003 Jun 26;4(1):5.


Tajul-Arifin K, Teasdale T, Ravasi T, Hume DA, Mattick JS. Identification and Analysis of Chromodomain-containing Proteins Encoded in the Mouse Transcriptome. Genome Res. 2003 Jun;13(6B):1416-29.


Wells C, Ravasi T, Sultana R, Yagi K, Carninci P, Bono H, Faulkner G, Okazaki Y, Quackenbush J, Hume DA, Lyons PA. Continued discovery of transcriptional units expressed in cells of the mouse mononuclear phagocyte lineage. Genome Res. 2003 Jun;13(6B):1360-5.


Forrest A, Ravasi T, Hume DA, Grimmond S, Taylor D, Gabrielli B, Huber T. Phosphoregulators: protein kinases and protein phosphatases of mouse. Genome Research, 2003 Genome Res. 2003 Jun;13(6B):1443-54.


Ravasi T, Huber T, Zavolan M, Forrest A, Gaasterland T, Grimmond T, Hume DA Systematic characterization of the zinc finger containing proteins in the mouse transcriptome. Genome Res. 2003 Jun;13(6B):1430-42.


Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H, Yamanaka I, Kiyosawa H, Yagi K, Tomaru Y, Hasegawa Y, Nogami A, et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature, 2002 Dec 5; 420(6915): 512-4.


Hume DA, Ross IL, Himes SR, Sasmono RT, Wells CA, Ravasi T. The mononuclear phagocyte system revisited. J. Leukoc. Biol. 2002 Oct;72(4):621-7.


Wardrop SL, Wells CA, Ravasi T, Hume DA, Richardson DR. Induction of Nramp2 in activated mouse macrophages is dissociated from regulation of the Nramp1, classical inflammatory genes, and genes involved in iron metabolism. J. Leukoc. Biol. 2002 Jan;71(1):99-106.


Ravasi T, Wells CA, Forest A, Underhill DM, Wainwright BJ, Aderem A, Grimmond S Hume DA Generation of diversity in the innate immune system. Macrophage heterogeneity arises from gene-autonomous transcriptional probability of individual inducible genes. J. Immunology, 2002 Jan 1, 168(1):99-106.​​​