1 Timothy Ravasi King Abdullah University of Science and Technology Division of Biological and Environmental Sciences & Engineering /Biosciences Division of Computer, Electrical and Mathematical Sciences & Engineering /Computer Sciences Email: [email protected]PROFESSIONAL EXPERIENCE 2016-present 2009-2016 Full Professor, Division of Biological and Environmental Sciences & Engineering, KAUST Associate Professor, Division of Biological and Environmental Sciences & Engineering, KAUST 2009-present Adjunct Associate Professor, Department of Medicine, School of Medicine, University of California San Diego, USA 2005-present Permanent Senior Visiting Scientist, Institute of Chemicals and Physical Research (RIKEN), Japan 2009-2014 Principal Investigator, Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering, KAUST 2006-2009 Co-Director, Systems Biology and Integrative Networks Core of the Scripps NeuroAIDS Preclinical Studies Center (SNAPS), The Scripps Research Institute, University of California San Diego, USA 2005-2009 Research Scientist, Department of Bioengineering, Jacobs School of Engineering, University of California, San Diego, USA 2001-2009 Post-Doctoral, Special Research Center for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Australia 2001-2002 Post-Doctoral, Genomic Sciences Center, The Institute of Chemicals and Physical Research (RIKEN), Japan HONORS AND SCHOLARLY AWARDS (Student or post-doc advisees are underlined) - 2012 ScienceDirect’s Top 10 Hottest Articles: (Ramaprasad A, Pain A, Ravasi T. Defining the protein interaction network of human malaria parasite Plasmodium falciparum. Genomics. 2012 Feb;99(2):69-75. doi: 10.1016/j.ygeno.2011.11.006) - 2010 Nature Biotechnology, Top 10 Trends in computational biology—2010
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Timothy Ravasi CV 2016 - Integrative Systems …...Timothy Ravasi. 1st January 2002-31 December 2004 (AUD 3,000,000). - Expression profiling the LPS response in macrophages. Japan
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HONORSANDSCHOLARLYAWARDS(Studentorpost-docadviseesareunderlined)- 2012 ScienceDirect’s Top 10Hottest Articles: (Ramaprasad A, Pain A, Ravasi T. Defining theproteininteractionnetworkofhumanmalariaparasitePlasmodiumfalciparum.Genomics.2012Feb;99(2):69-75.doi:10.1016/j.ygeno.2011.11.006)-2010NatureBiotechnology,Top10Trendsincomputationalbiology—2010
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- 2010 Facultyof 1000: (Ravasi T, et al.Anatlasof combinatorial transcriptional regulation inmouse andman. Cell. 2010Mar 5;140(5):744-52. doi: 10.1016/j.cell.2010.01.044. Erratum in:Cell.2010Apr16;141(2):369.PMID:20211142.)- 2008 ScienceDirect’s Top 5 Hottest Articles: (Tan K, Tegner J and Ravasi T. Integratedapproaches to uncovering transcription regulatory networks in mammalian cells. Genomics.2008Mar;91(3):219-31.doi:10.1016/j.ygeno.2007.11.005.PMID:18191937)-2007ScienceDirect’sTop10HottestArticles: (Tegner J,NilssonR,BajicVB,Bjurkegren JandRavasiT.Systemsbiologyofinnateimmunity.CellImmunol.2006Dec;244(2):105-9.Epub2007Apr11.PubMedPMID:17433274;PMC1947944)- 2008 Winner of the Dolph Adams prize, for the most-cited article in Journal of LeukocyteBiology: (Schroder K, Hertzog PJ, Ravasi T and Hume DA. Interferon-gamma: an overview ofsignals, mechanisms and functions. J Leukoc Biol. 2004 Feb;75(2):163-89. Epub 2003 Oct 2.PMID:14525967)-2006FASEBJ.,The20Most-Frequentlydownloadedarticles:(AungHT,SchroderK,HimesSR,BrionK,vanZuylenW,TrieuA,SuzukiH,HayashizakiY,HumeDA,SweetMJandRavasiT.LPSregulates proinflammatory gene expression in macrophages by altering histone deacetylaseexpression.FASEBJ.2006Jul;20(9):1315-27.PMID:16816106)- 2006 ScienceDirect’s Top 10 Hottest Articles: (Nilsson R, Bajic VB, Suzuki H, di Bernardo D,BjurkegrenJ,KatayamaS,ReidJF,SweetMJ,GariboldiM,CarninciP,HayashizakiY,HumeDA,Tegner JandRavasiT.Transcriptionalnetworkdynamics inmacrophageactivation.Genomics.2006Aug;88(2):133-42.PMID:16698233)-2005PermanentpositionofSeniorVisitingScientistintheInstituteofChemicalsandPhysicalResearch(RIKEN),Japan-2004ScienceDirect’sTop10HottestArticles: (RavasiT,HsuK,GoyetteJ,SchroderK,YangZ,Rahimi F, Miranda LP, Alewood PF, Hume DA and Geczy C. Probing the S100 protein familythroughgenomicandfunctionalanalysis.Genomics.2004Jul;84(1):10-22.PMID:15203200)- 2002Original Research award, Institute forMolecular Bioscience,University ofQueensland,Australia-2001Fellowship,JapanScienceandTechnologyAgency,fortheanalysisandannotationofthemousegenome
UNIVERSITYSERVICEANDOUTREACHUniversityCommittees- 2015, Member of the KAUST Environmental Epigenetic Program, Division of Biological andEnvironmentalSciences&EngineeringFacultySearchCommittee- 2014, Member of the Marine Science Program Division of Biological andEnvironmentalSciences&EngineeringandRedSeaResearchCenterFacultySearchCommittee-2010,2011,2012,2013and2014,ElectedMemberandChairoftheBioscienceCoreLabuserscommittee
PROFESSIONALSERVICE-EditorforGenomics(Elsevier)-EditorforPloSONE-EditorImmunogenomics-EditorOpenJournalofBiology-EditorWileyEuropepublishers-EditorISRNGeneticsREVIEWERFORJOURNALSNature; Genome Research, Genomics, Bioinformatics, Scientific Reports, Electronic Journal ofBiotechnology,CellsTissuesOrgans,InflammationResearch,GenomeBiology,TheOpenBiologyJournal, Current Medicinal Chemistry, Journal of Bioinformatics, InternationalImmunopharmacology, Computational Biology, BMC Systems Biology, PLoS ComputationalBiology,PLoSONE,MolecularSystemsBiology,AmericanJournalofPhysiology.RESEARCHFUNDS- Genomic evidence for adaptation of marine fishes to ocean acidification. KAUST’s CRG4.PrincipalInvestigator:TimothyRavasi;Co-PrincipleInvestigators:Prof.PhilMunday(JamesCookUniversity,Australia).July1st,2016-June31st,2019($1,349,555).- Transcriptional program and the epigenome of transgenerational acclimation to climatechange in reef fishes. KAUST’s CRG3. Principal Investigator: Timothy Ravasi; Co-PrincipleInvestigators:Prof.PhilMunday(JamesCookUniversity,Australia).February1st,2015-January31st,2018($1,350,000).- Effects ofMagnet Nanostructures on Leukemic Cells. KACST (GDRG) Saudi Arabia. PrincipalInvestigator:Prof.JurgenP.Kosel;Co-PrincipleInvestigators:TimothyRavasiandProf.JasmeenMarzaban.January2014-December31st2015(SAR600,000).- Regulatory Systems in the Innate Immune Response. Australia National Health andMedicalResearch Council. Principal Investigator: Prof. Paul Hertzog Sweet (Monash University,Australia); Co-Principle Investigators: Timothy Ravasi. 01 January 2015 - 31 December 2018(AUD771,978).-TheSpongeMicrobiomeProject:symbioticecosystemsinachangingclimate.DOECommunitySequencing Programme. Join Genome Institute, Department of Energy (DOE), USA. PrincipalInvestigator: Prof. Ute Hentschel (The University of Wuerzburg, Germany); Co-PrincipleInvestigators:TimothyRavasi.January1st,2013-December31st,2014($1,000,000).-RoleofmacrophagesinUropathogenicE.coliinfections.AustraliaNationalHealthandMedicalResearch Council. Principal Investigator: Prof. Matthew Sweet (University of Queensland,
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Australia); Co-Principle Investigators: Timothy Ravasi. January 2011-December 2013 (AUD555,048).- Association of Genetic Variation with Phenotype at the Network and Function Level. AnObesity-inducedinsulinresistancecasestudyintheSaudiArabianpopulationKAUSTAEA-GCR.Principal Investigator: Timothy Ravasi; Co-Principle Investigators: Prof. David Dill (StanfordUniversity,USA).September1st2011-30August2014($3,341,673).-ThegenomesequenceofthedinoflagellateSymbiodiniumsp.,asymbiontfromRedSeacorals.KAUST AEA-GCR. Principal Investigator: Prof Christian Voolstra; Co-Principle Investigators:Timothy Ravasi and Prof. Gos Micklem (University of Cambridge, UK). 1st February 2010-30September2012($539,403).- The genetic basis of obesity/diabetes in the Saudi population. KAUST FIC-CRG. PrincipalInvestigator: Timothy Ravasi; Co-Principle Investigators: Prof. Kumar Sharma (University ofCalifornia,SanDiego,USA).10June2011-July1st2013($1,678,422.77)- NeuroAIDS Preclinical Studies Center (SNAPS). National Institute of Health (NIH). PrincipalInvestigator:Prof.HowardFox(TheScrippsResearchInstitute,USA);Co-PrincipleInvestigators:TimothyRavasi.24August2006-24August2009($1,750,000).- Urine exosome biomarkers in anti-fibrotic trial for diabetic nephropathy. Juvenile DiabetesResearchFoundation(JDRF).PrincipalInvestigator:Prof.KumarSharma(UniversityofCalifornia,SanDiego,USA);Co-PrincipleInvestigators:TimothyRavasi.10January2008-30December2011($180,000).- CRC for Chronic Inflammatory Diseases. Identification of new therapeutic targets forRheumatoid arthritis and COPD diseases. Australia National Health and Medical ResearchCouncil. Prof.DavidH.Hume (University ofQueensland,Australia);Co-Principle Investigators:TimothyRavasi.1stJanuary2002-31December2004(AUD3,000,000).-ExpressionprofilingtheLPSresponseinmacrophages.JapanScienceandTechnologyAgency.PrincipleInvestigators:TimothyRavasi.10February2001-31st-January2002($70,000).PUBLICATIONSTotal106Peer-ReviewedJournalArticles(*correspondingauthor;studentorpost-docadviseesareunderlined).12,132totalcitations.h-Index38Booksandbookchapters1. *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
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pathogen.Toll-Like Receptors: 2015 Practice andMethods (2nd Edition), Ed: ClaireMcCoy,Publisher:Springer,NewYork.
2. Ravasi T*. Integrative Systems Approaches to study Innate Immunity. Clinical Applied
Immunogenomics.Springer.233SpringStreet,NewYork,NY10013,U.S.A.2008.3. Tegner J, Björkegren J, Ravasi T* and Bajic V. Transcription Regulatory Networks Analysis
UsingCAGE.(JohnWiley&Sons,Chichester,UK),2008.4. Hume DA, Wells CA and Ravasi T*. Transcriptional regulatory networks in macrophages
Decoding theGenomicControl of ImmuneReactionsNovartis Foundation Symposium,No281,2007.
molecularinsightsfromtranscriptomeanalysis.ScientificReports,2016.Underreview5. Bustamante E, Najera J, Bortell N, Ravasi T, Morsey B, Fox HJ and. Marcondes MC
Methamphetamineabuseaffectsgeneexpressioninbrain-derivedmicrogliaofSIV-infectedmacaques to enhance inflammation and promote virus targets. BMC Immunol. 2016 Apr23;17(1):7.doi:10.1186/s12865-016-0145-0.
Transcriptomicandproteomicshiftrevealsmechanismsofadaptation in larvaeofRedSeabarnacleBalanusamphitrite.BMCGenomics.2015Dec15;16(1):1063.doi:10.1186/s12864-015-2262-1.
13. Margineanu MJ, Julfakyan K, Sommer C, Pere JE, Contreras MF, Khashab N, Kosel J and
19. ContrerasMF,SougratR,ZaherA,RavasiT*andKoselJ*.Non-chemotoxicCancerCellDeathInduction Using Magnetic Nanowires. International Journal of Nanomedicine. 2015. Int JNanomedicine.2015Mar17;10:2141-53.doi:10.2147/IJN.S77081.
based insights into the microbial functional gene repertoire of marine sponges (highmicrobial abundance, lowmicrobial abundance) and seawater. FEMSMicrobiol Ecol. 2014Dec;90(3):832-43. doi: 10.1111/1574-6941.12441. Epub 2014 Nov 10. PubMed PMID:25318900.
24. Wong YH, Ryu T, Seridi L,Ghosheh Y, Bougouffa S,Qian PY andRavasi T*. Transcriptome
27. Zhang Y, Sun J, ZhangH, Chandramouli KH, Xu Y,He LS, Ravasi T andQianPY. Proteomicprofiling during the pre-competent to competent transition of the biofouling polychaeteHydroideselegans.Biofouling.2014Sep;30(8):921-8.doi:10.1080/08927014.2014.951341.PubMedPMID:25237770.
Red Sea sponges: sources for chemical and phylogenetic diversity.Mar Drugs. 2014May12;12(5):2771-89. doi: 10.3390/md12052771. PubMed PMID: 24824024; PubMed CentralPMCID:PMC4052315.
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 specifictranscriptional regulation. Proc Natl Acad Sci U S A. 2014 Apr 8;111(14):5289-94. doi:10.1073/pnas.1312717110.Epub2014Mar27.PubMedPMID:24706905;PubMedCentralPMCID:PMC3986152.
Rydon M, Arner P; FANTOM Consortium. Ceruloplasmin is a novel adipokine which isoverexpressed in adipose tissue of obese subjects and in obesity-associated cancer cells.PLoSOne.2014Mar27;9(3):e80274.doi:10.1371/journal.pone.0080274.eCollection2014.PubMedPMID:24676332;PubMedCentralPMCID:PMC3968011.
Genome Sequence of the Antitrypanosomally Active Sponge-Associated BacteriumActinokineosporasp.StrainEG49.GenomeAnnounc.2014Mar6;2(2).pii:e00160-14.doi:10.1128/genomeA.00160-14. PubMed PMID: 24604655; PubMed Central PMCID:PMC3945511.
DunnC,GiribetG,HaddockS,KnowltonN,MartindaleM,MedinaM,MessingC,O'BrienSJ,PaulayG, PutnamN, Ravasi T, RouseGW,Ryan JF, SchulzeA,WörheideG, AdamskaM,BaillyX,BreinholtJ,BrowneWE,DiazMC,EvansN,FlotJF,FogartyN,JohnstonM,KamelB,KawaharaAY,LabergeT,LavrovD,MichonneauF,MorozLL,OakleyT,OsborneK,PomponiSA, Rhodes A, Santos SR, SatohN, Thacker RW, Van de Peer Y, Voolstra CR,Welch DM,Winston J, Zhou X. The Global Invertebrate Genomics Alliance (GIGA): developingcommunity resources to study diverse invertebrate genomes. J Hered. 2014 Jan-Feb;105(1):1-18. doi: 10.1093/jhered/est084. PubMed PMID: 24336862; PubMed CentralPMCID:PMC4072906.
38. Giles EC, Saenz-Agudelo P, Berumen ML and Ravasi T. Novel polymorphic microsatellite
markers developed for a common reef sponge, Stylissa carteri. Marine Biodiversity, Sep.2013,43(3),237-241.Doi:10.1007/s12526-013-0151-x.
39. Chandramouli KH, Ravasi T, Reish D and Qian PY. Proteomic changes betweenmale and
female worms of the polychaetous annelid Neanthes arenaceodentata before and afterspawning. PLoS One. 2013 Aug 30;8(8):e72990. doi: 10.1371/journal.pone.0072990..PubMedPMID:24023665;PubMedCentralPMCID:PMC3758283.
U*. Specificity and transcriptional activity of microbiota associated with low and highmicrobial abundance sponges from the Red Sea. Mol Ecol. 2014Mar;23(6):1348-63. doi:10.1111/mec.12365.Epub2013Aug20.PubMedPMID:23957633.
topology for the prediction of epistatic behavior. Genomics. 2013 Oct;102(4):202-8. doi:10.1016/j.ygeno.2013.07.010.Epub2013Jul25.PubMedPMID:23892246.
43. Chandramouli KH, Dash S, Zhang Y, Ravasi T* and Qian PY*. Proteomic andmetabolomic
profiles of marine Vibrio sp. 010 in response to an antifoulant challenge. Biofouling.2013;29(7):789-802.doi:10.1080/08927014.2013.805209.Epub2013Jul4.PubMedPMID:23822634.
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44. Cannistraci CV, Alanis-Lobato G and Ravasi T*. Minimum curvilinearity to enhancetopologicalpredictionofprotein interactionsbynetworkembedding.Bioinformatics.2013Jul 1;29(13):i199-209. doi: 10.1093/bioinformatics/btt208. PubMed PMID: 23812985;PubMedCentralPMCID:PMC3694668.
45. Ammirati E, Cristell N, Cianflone D, Vermi AC,Marenzi G, DeMetrioM, Uren NG, Hu D,
Ravasi T,Maseri A andCannistraci CV.Questing for circadian dependence in ST-segment-elevationacutemyocardial infarction:amulticentricandmultiethnic study.CircRes.2013May10;112(10):e110-4.doi:10.1161/CIRCRESAHA.112.300778.PubMedPMID:23661713.
46. Cannistraci CV, Alanis-LobatoG and Ravasi T*. From link-prediction in brain connectomes
andprotein interactomes to the local-community-paradigm in complexnetworks. SciRep.2013;3:1613. doi: 10.1038/srep01613. PubMedPMID: 23563395; PubMedCentral PMCID:PMC3619147.
contraction pathway in cryptorchidism and evidence for genomic connections withcardiomyopathy pathways in RASopathies. BMC Med Genomics. 2013 Feb 14;6:5. doi:10.1186/1755-8794-6-5.PubMedPMID:23410028;PubMedCentralPMCID:PMC3626861.
48. ChandramouliKH,SunJ,MokFS,LiuL,QiuJW,RavasiT*andQianPY*.Transcriptomeandquantitative proteome analysis reveals molecular processes associated with larvalmetamorphosis in the polychaete Pseudopolydora vexillosa. J Proteome Res. 2013 Mar1;12(3):1344-58.doi:10.1021/pr3010088.Epub2013Jan29.PubMedPMID:23294167.
Viability of Nickel Nanowires. Proceedings of the 2013 International Conference onBiological,MedicalandChemicalEngineering(BMCE2013).2013,HongKong,PRC.
51. Ryu T, Seridi L and Ravasi T*. The evolution of ultraconserved elements with different
phylogenetic origins. BMC Evol Biol. 2012 Dec 5;12:236. doi: 10.1186/1471-2148-12-236.PubMedPMID:23217155;PubMedCentralPMCID:PMC3556307.
MiendlarzewskaEA,SangalliLM,MonelloA,PernowJ,BjurnstedtBennermoM,MarenziG,Hu D, Uren NG, Cianflone D, Ravasi T, Manfredi AA and Maseri A. Identification andpredictivevalueofinterleukin-6+interleukin-10+andinterleukin-6-interleukin-10+cytokinepatternsinST-elevationacutemyocardialinfarction.CircRes.2012Oct26;111(10):1336-48.doi:10.1161/CIRCRESAHA.111.262477.Epub2012Aug29.PubMedPMID:22931953.
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53. Giles EC, Kamke J, Moitinho-Silva L, Taylor MW, Hentschel U, Ravasi T and Schmitt S.Bacterial community profiles in lowmicrobial abundance sponges. FEMS Microbiol Ecol.2013 Jan;83(1):232-41.doi:10.1111/j.1574-6941.2012.01467.x.Epub2012Sep4.PubMedPMID:22882238.
54. FanM,Wong KC, Ryu T, Ravasi T andGao X. SECOM: a novel hash seed and community
detection based-approach for genome-scale protein domain identification. PLoS One.2012;7(6):e39475. doi: 10.1371/journal.pone.0039475. Epub 2012 Jun 28. PubMed PMID:22761802;PubMedCentralPMCID:PMC3386278.
proteomics identify molecular targets that are crucial in larval settlement andmetamorphosis of Bugula neritina. J Proteome Res. 2011 Jan 7;10(1):349-60. doi:10.1021/pr100817v.Epub2010Dec16.PubMedPMID:21090758.
Coevolution within a transcriptional network by compensatory trans and cis mutations.Genome Res. 2010 Dec;20(12):1672-8. doi: 10.1101/gr.111765.110. Epub 2010 Oct 26.PubMedPMID:20978140;PubMedCentralPMCID:PMC2989993.
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62. Cannistraci CV, Ravasi T, Montevecchi FM, Ideker T and Alessio M. Nonlinear dimensionreduction and clustering by Minimum Curvilinearity unfold neuropathic pain and tissueembryological classes. Bioinformatics. 2010 Sep 15;26(18):i531-9. doi:10.1093/bioinformatics/btq376. PubMed PMID: 20823318; PubMed Central PMCID:PMC2935424.
and proteome profiling of a non-modelmarine invertebrate, Bugula neritina. Proteomics.2010Aug;10(16):2972-81.doi:10.1002/pmic.201000056.PubMedPMID:20540116.
synthesis and proteomic changes during metamorphosis of the marine bryozoan Bugulaneritina. Proteome Sci. 2010 May 24;8:25. doi: 10.1186/1477-5956-8-25. PubMed PMID:20497544;PubMedCentralPMCID:PMC2890537.
of monocyte membrane proteome perturbation during lipopolysaccharide-inducedtolerance using iTRAQ-based quantitative proteomic approach. Proteomics. 2010Aug;10(15):2780-9.doi:10.1002/pmic.201000066.PubMedPMID:20486119.
2010 Mar 5;140(5):744-52. doi: 10.1016/j.cell.2010.01.044. Erratum in: Cell. 2010 Apr16;141(2):369.PubMedPMID:20211142;PubMedCentralPMCID:PMC2836267.
68. Gersten M, Alirezaei M, Marcondes MC, Flynn C, Ravasi T, Ideker T and Fox HS. An
integrated systems analysis implicates EGR1 downregulation in simian immunodeficiencyvirusencephalitis-inducedneuraldysfunction.JNeurosci.2009Oct7;29(40):12467-76.doi:10.1523/JNEUROSCI.3180-09.2009. PubMed PMID:19812322; PubMed Central PMCID:PMC2802851.
71. Tan K, Feizi H, Luo C, Fan SH, Ravasi T and Ideker TG. A systems approach to delineatefunctions of paralogous transcription factors: role of the Yap family in the DNA damageresponse. Proc Natl Acad Sci U S A. 2008 Feb 26;105(8):2934-9. doi:10.1073/pnas.0708670105.Epub2008Feb19.PubMedPMID:18287073;PubMedCentralPMCID:PMC2268563.
CA, Hume DA, Reddel RR and Clark SJ. Concordant epigenetic silencing of transforminggrowth factor-beta signaling pathway genes occurs early in breast carcinogenesis. CancerRes.2007Dec15;67(24):11517-27.PubMedPMID:18089780.
StaceyKJ,DeckerT,HumeDA,DalpkeAHandSweetMJ.DifferentialeffectsofCpGDNAonIFN-beta induction and STAT1 activation in murine macrophages versus dendritic cells:alternativelyactivatedSTAT1negativelyregulatesTLRsignalinginmacrophages.JImmunol.2007Sep15;179(6):3495-503.PubMedPMID:17785783.
76. Bode KA, Schroder K, Hume DA, Ravasi T, Heeg K, Sweet MJ and Dalpke AH. Histone
deacetylase inhibitors decrease Toll-like receptor-mediated activation of proinflammatorygene expression by impairing transcription factor recruitment. Immunology. 2007Dec;122(4):596-606.Epub2007Jul16.PubMedPMID:17635610;PubMedCentralPMCID:PMC2266046.
77. Hume DA, Wells CA and Ravasi T*. Transcriptional regulatory networks in macrophages.
GariboldiM, Carninci P, Hayashizaki Y, Hume DA, Tegner J and Ravasi T*. Transcriptionalnetworkdynamicsinmacrophageactivation.Genomics.2006Aug;88(2):133-42.Epub2006May12.PubMedPMID:16698233.
BatalovS,BeiselKW,BultCJ,FletcherCF,ForrestAR,FurunoM,HillD, ItohM,Kanamori-KatayamaM,KatayamaS,KatohM,KawashimaT,QuackenbushJ,RavasiT,RingBZ,ShibataK,SugiuraK,TakenakaY,TeasdaleRD,WellsCA,ZhuY,KaiC,KawaiJ,HumeDA,CarninciPand Hayashizaki Y. Transcript annotation in FANTOM3: mouse gene catalog based onphysicalcDNAs.PLoSGenet.2006Apr;2(4):e62.PubMedPMID:16683036;PubMedCentralPMCID:PMC1449903.
for development and survival of macrophages. J Immunol. 2006 Feb 15;176(4):2219-28.PubMedPMID:16455978.
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88. *RavasiT,SuzukiH,PangKC,KatayamaS,FurunoM,OkunishiR,FukudaS,RuK,FrithMC,Gongora MM, Grimmond SM, Hume DA, Hayashizaki Y and Mattick JS. Experimentalvalidationoftheregulatedexpressionoflargenumbersofnon-codingRNAsfromthemousegenome.GenomeRes.2006 Jan;16(1):11-9.Epub2005Dec12.PubMedPMID:16344565;PubMedCentralPMCID:PMC1356124.
SuzukiM,KawaiJ,SuzukiH,CarninciP,HayashizakiY,WellsC,FrithM,RavasiT,PangKC,HallinanJ,Mattick J,HumeDA,LipovichL,BatalovS,EngstromPG,MizunoY,FaghihiMA,SandelinA,ChalkAM,Mottagui-TabarS,LiangZ,LenhardB,WahlestedtC;RIKENGenomeExploration Research Group; Genome Science Group (Genome Network Project CoreGroup); FANTOM Consortium. Antisense transcription in the mammalian transcriptome.Science.2005Sep2;309(5740):1564-6.PubMedPMID:16141073.
91. Carninci P, et al. FANTOM Consortium; RIKEN Genome Exploration Research Group and
Genome Science Group (Genome Network Project Core Group). The transcriptionallandscape of the mammalian genome. Science. 2005 Sep 2;309(5740):1559-63. Science.2006Mar24;311(5768):1713.PubMedPMID:16141072.
DA, Kobe B and Martin JL. An inflammatory role for the mammalian carboxypeptidaseinhibitor latexin: relationship to cystatins and the tumor suppressor TIG1. Structure. 2005Feb;13(2):309-17.PubMedPMID:15698574.
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96. RavasiT,HsuK,GoyetteJ,SchroderK,YangZ,RahimiF,MirandaLP,AlewoodPF,HumeDAand Geczy C. Probing the S100 protein family through genomic and functional analysis.Genomics.2004Jul;84(1):10-22.PubMedPMID:15203200.
102. Wells CA, Ravasi T, Sultana R, Yagi K, Carninci P, Bono H, Faulkner G, Okazaki Y,
QuackenbushJ,HumeDA,LyonsPA;RIKENGERGroup;GSLMembers.Continueddiscoveryof transcriptional units expressed in cells of the mouse mononuclear phagocyte lineage.GenomeRes. 2003 Jun;13(6B):1360-5. PubMedPMID:12819134;PubMedCentral PMCID:PMC403663.
CONFERENCEPRESENTATIONS-InvitedKeynotespeaker:RavasiT.Mechanismsoftransgenerationalacclimationtoawarmingocean. Integration of ‘omic’ datasets in non-model organisms. 7th Annual Next-GenerationSequencingCongress.12-13November2015,London,UK.- Invited speaker: Ravasi T. 2nd Next Generation Sequencing & Bioinformatics Conference,October5-7,2015,Berlin,Germany.- Invited Keynote speaker: Ravasi T.Rethinking theGWAS.Anew integrativemethod for theanalysisofdiseaseassociationdatasets.KarolinskaInstitute’sFirstEuropeanSummerSchoolinSystemsMedicine2015.22-26June2015,StockholmArchipelago.- Invited speaker: Ravasi T. Challenges in the studies of co-transcriptomes. From Sponges toMan.InstituteforMolecularInfectionBiology,UniversityofWürzburg.March23,2015.-Steeringcommitteemember:RavasiT.SyntheticandSystemsBiologySummerSchool:BiologymeetsEngineeringandComputerScience-2ndEdition.Taormina-Sicily,Italy,July5-9,2015-InvitedLecturer:RavasiT.AnoverviewofMarineGenomics.KAUSTRedSeaSummerProgram.Thuwal–KSA,July24-August14,2015.- Invitedspeaker:RavasiT.HumanGenomeMeeting2015“TransformingHumanGenomicsforASustainableTomorrow”.KualaLumpurMarch14-17,2015- Invited speaker: Ravasi T. The genomes and transcriptomes of Red Sea Sponges. GIGAconsortiumforMarineInvertebrateGenomics.March1st-3rd.2013.DaniaBeach,FL,USA.-Invitedspeaker:RavasiT.ModelingGWASbyGeneticInteractionNetworks.PAPGIWorkshopinComputationalBiology.March19th-22nd.2013.Manila,Philippines.-Invitedspeaker:RavasiT.TopologicalpredictionofEpistaticBehaviorfromGeneticInteractionNetworks.10thAPCHGconferences.December5thto-8thKualaLumpur,Malaysia.2013.-Invitedspeaker:RavasiT.Dean’sseminarseries,CenterforMolecularMedicineandGeneticsandDepartmentofNeurology,SchoolofMedicine,WayneStateUniversity.Detroit,MIMarch222012.
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- Section Chair: Ravasi T. Marine Genomics, a lesson from the Sponges. InternationalConferencesofReefStudies(ICRS).July2012,Cairns,Australia.-Invitedspeaker:RavasiT.AssessingcombinatorialtranscriptionalregulationinMetazoaWellcomeTrustAdvanceCourse,Hinxton,Cambridge,March9-12,2011.- Section Chair: Ravasi T. The Saudi Arabian Population Structure. Human GenomeMeeting,Dubai,March14-17,2011- SectionChair:RavasiT.TheSaudiGenome Initiative.WorkingSummit,“GlobalandRegionalInitiatives:PanAsianPersonalGenomicsInitiative”HGMDubai,March14-17,2011.Dubai,UAE.- Invited speaker: Ravasi T. Assessing Combinatorial Transcriptional Regulation. 3rd AnnualIAMCSSpringSymposium,May30-31,2011.TexasA&MUniversity,USA.- Invited speaker: RavasiT.Genome-widemappingofcombinatorial regulation inmouseandman.23rdAnnualInternationalConferenceonIntelligentSystemsforMolecularBiologyandthe 14th European Conference on Computational Biology (ISMB/ECCB). 16-20 July 2011.Vienna,Austria.-Keynote lectures:RavasiT.AnAtlasofcombinatorialregulationinmouseandman.The84thAnnualMeetingoftheJapaneseBiochemicalSociety,September22,2011Kyoto,Japan.- Invited speaker: Ravasi T. Combinatorial regulation in mammals. The Human GenomeMeeting.May18-21,2010.Montpellier,France.- Invited speaker: Ravasi T. Transcriptional Regulation in Reef Building Corals. Euro ISRSsymposium 2010: Reefs in a changing environment. 13-17 December 2010.Wageningen, TheNetherlands.-Invitedspeaker:RavasiT.ThecomplexityoftranscriptionalregulationinReefBuildingCorals.2ndAsiaPacificCoralReefSymposium(APCRS).20-20June2010,PhuketThailand.-Invitedspeaker:RavasiT.InferringTranscriptionRegulatoryNetworksinmammal.CambridgeComputationalBiologyInstitute5thAnnualsSymposium.20-22May2009,CambridgeUK.
- Invited speaker: Ravasi T. Genome-wide survey of the transcription factors combinatorialregulationinmammals.TheScrippsResearchInstitute.April,2008,LaJolla,CA,USA.
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- Invited speaker: Ravasi T. Epigenetic regulation duringmacrophages activation. The SouthAfricaBioinformaticsInstitute,UniversityofWesternCape,March03,2008,CapeTown,SouthAfrica.- Invited speaker: Ravasi T. Systems Biology in Immunity. Center for Genome Regulation.February5,2007,BarcelonaSpain.- Invited speaker: Ravasi T. Inferring mammalian Transcriptional Regulatory Networks usingprotein-protein interactions. The Gordon Research Conference-Protein, June 17-22, 2007,HoldernessSchool,NHUSA.- Invited speaker: Ravasi T. Systems Biology and diseases. Sidney Kimmel Cancer Center.January30,2007,SanDiego,CAUSA.- Invited speaker: Ravasi T. A Systems Approach to infer transcriptional networks inmacrophages. InternationalCongressof Innunogenomicand Immunomics.October8-12,2006Budapest,Hungary.-Invitedspeaker:RavasiT.Howtoinferdynamicsofgeneregulatorynetworksfromexpressiondata.MiniNetworkWorkshop,FANTOMconference,January8-12,2006,Yokohama,Japan.- Invited speaker:RavasiT.RegulatoryNetworksevolutionandAdaptation.Agilentworkshop,invitedlecture,thePlantandAnimalGenomeXIVConference.January14-18,2006,SanDiego,CA,USA.- Invited speaker:RavasiT. Mechanismof LPS-inducibleofgeneexpression.The Institute forInfocommResearchinSingapore,October2004,Singapore.- Invited speaker: Ravasi T. SystemBiology is takingplace. TheMolecularOncology InstituteIFOM.October2004,Milan,Italy.- Invited speaker: Ravasi T. Transcriptional networks in macrophage. The First InternationalconferenceinBasicandClinicalImmunogenomic.October2004,Budapest,Hungary.- Invited speaker: Ravasi T. Epigenetic ofmacrophages activation. TheGarvan Institute. June2003,Sydney,Australia.- Oral presentation: Chandramouli C, Reish D, Zhang H, Qian PY and Ravasi T. ProteomicChanges Associated with Successive Reproductive Periods in Male Polychaetous Neanthesarenaceodentata. EuropeanProteomicAssociation (EuPACongress), 23-28 June2015,Milano,Italy.-Posterpresentation:PerezJE,ContrerasMF,VilanovaE,FelixLP,LuongoG,PorterAE,DunlopIE,RavasiTandKosel J.NickelNanowires IntracellularDissolutionAnd InductionOfApoptosisOn HCT 116 Cells. ASME 2015 4th Global Conference on Nanoengineering for Medicine andBiology,19-22April2015,Minneapolis,MN,USA.
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-Oralpresentation:ErikssonA,ManicaAandRavasiT.Usingmodernandancientgenomestoreconstruct ancient expansions: detecting and controlling for coverage bias and deamination.HumanGenomeMeeting2015,inKualaLumpur,Malaysia.-Oral presentation:MargineanuM. B., Julfakyan K., Sommer C., Perez J. E., ContrerasM. F.,KhashabN., Kosel J. P., andRavasi T.Quantificationof nanowire uptakeby living cells. ASME2015 4thGlobal Conference onNanoengineering forMedicine and Biology. 19-22April 2015,Minneapolis,USA.-Oral presentation:MargineanuM. B., Julfakyan K., Sommer C., Perez J. E., ContrerasM. F.,Khashab N., Kosel J. P., and Ravasi T. Quantification of nanowire uptake by living cells.BioNanoMed2015 - 6th InternationalCongressNanotechnology inMedicine&Biology, 08-10April2015,Graz,Austria.-Oralpresentation:ChandramouliC,RyuT,ZhangH,GhoshehY,Al-AqeelS,QianPYandRavasiT. Molecular evidences of thermal and osmo-adaptation in Red Sea larvae of BalanusAmphitrite."MarineEnvironmentoftheRedSea.10-13November2014,Jeddah,SaudiArabia.-Posterpresentation:ErikssonA,ManicaAandRavasiT.Theeffectofpopulationstructureonsharedgeneticvariationamongrecentlydivergedspecies.CellSymposia:EvolutionofModernHumans-FromBonestoGenomes,2014,inSitges,Spain.-Oralpresentation: ErikssonA,ManicaAandRavasiT.Theeffectofpopulationstructureonsharedgeneticvariationamongrecentlydivergedspecies.Humanevolutioninthegenomicera:Origins,populationsandphenotypes,2014,inLeicester,UK.OrganizedbyEuropeanMolecularBiologyOrganisation(EMBO).- Poster presentation: Al-Aqeel S, Ryu T, Zhang H, Chandramouli KH, Qian PY, Ravasi T.ASystem-wide Approach to IdentifyMechanisms of Barnacle Attachment, TowardIdentificationof New AntifoulingCompounds.The 16th International Biodegradation and BiodeteriorationSymposium,2-5,September,2014.Lodz,Poland-Oralpresentation:Al-AqeelS,RyuT,ZhangH,ChandramouliKH,QianPY,RavasiT.ASystem-wideApproach to IdentifyMechanismsofBarnacleAttachment,Toward IdentificationofNewAntifouling Compounds.International conference on themarineenvironment of the Red Sea,10-13,NOVEMBER,2014,KingAbdulazizuniversity,Jeddah,SaudiArabia.- Oral presentation: Alanis-Lobato, G., Cannistraci, C.V. & Ravasi, T. Exploring the GeneticsUnderlying Autoimmune Diseases with Network Analysis and Link Prediction. Middle EastConferenceonBiomedicalEngineering2014,February2014,Doha,Qatar.-Oralpresentation:ChandramouliC,RyuT,ZhangH,GhoshehY,Al-AqeelS,QianPYandRavasiT.Marineproteomics:FindingmechanismsofadaptationinlarvaeofRedSeabarnacleBalanus
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amphitrite 13th Human Proteome Organization world Congress. 5-8October 2014, Madrid,Spain.-Posterpresentation:RyuTandRavasiT.HologenomeanalysisoftwoRedSeaspongesshedlight on the coevolution of animal host and symbionts. 15th International Symposium onMicrobialEcology,24-29August2014,Seoul,Korea.-Oralpresentation:RyuTandRavasiT.IntegrativehologenomeanalysisoftheRedSeasponges,Stylissa carteri and Xestospongia testudinaria. 3rd Asia-Pacific Coral Reef Symposium, 23-27June2014,Kenting,Taiwan.- Oral presentation: Chandramouli C, Qian PY and Ravasi T. Transcriptomic and proteomicinsights into larval metamorphosis of the polychaete Pseudopolydora vexillosa. 11thInternationalPolychaeteConference,4-9August2013,Sydney,Australia.-Oralpresentation:ErikssonA,ManicaAandRavasiT.ReconstructingthecolonisationofAsiausinggenomesandspatiallyexplicitmodels.PAPGIgenomicsworkshop,2013 inSeoul,Korea.Oralpresentation.-Oralpresentation:PerezJE,ContrerasMF,VilanovaE,RavasiTandKosel J.CytotoxicityandEffects on Cell Viability of Nickel Nanowires. 2013 International Conference on Biological,MedicalandChemicalEngineering,1-2December2013,HongKong.-Posterpresentation:PerezJE,ContrerasMF,RavasiT,andKoselT.CytotoxicityandEffectsonCellViabilityofNickelNanowires.KAUSTPresidentInternationalAdvisoryCouncilPosterSession,Apr19th,2013,Thuwal,KSA.-Posterpresentation:PerezJE,ContrerasMF,RavasiTandKoselJ.CytotoxicityandEffectsonCellViabilityofNickelNanowires.12thJointMMM/IntermagConference,14-18January2013,Chicago,IL,USA.-Oralpresentation:Cannistraci,C.V.,Alanis-Lobato,G.andRavasi,T.HeartAttacks:Leveraginga Cardiovascular Systems Biology Strategy to Predict Future Outcomes. TBC/ISCB-Asia 2013,Seoul,Korea.SelectedTalkinHighlightstrack.-Oralpresentation:Cannistraci,C.V.,Alanis-Lobato,G.andRavasi,T.HeartAttacks:LeveragingaCardiovascularSystemsBiologyStrategytoPredictFutureOutcomes.ISMB/ECCB2013,Berlin,Germany.SelectedTalkinHighlightstrack-Oralpresentation:Cannistraci,C.V.,Alanis-Lobato,G.andRavasi,T.Minimumcurvilinearitytoenhancetopologicalpredictionofproteininteractionsbynetworkembedding.ISMB/ECCB2013,Berlin,Germany,SelectedtalkinProceedingstrack(andarticlepublicationinBioinformatics)
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- Oral presentation: Cannistraci, C.V., Alanis-Lobato, G. and Ravasi, T. From link-prediction inbrain connectomes and protein interactomes to the local-community-paradigm in complexnetworks.The7th InternationalWorkshoponMachineLearning inSystemsBiology (MLSB13),ISMB/ECCB2013SpecialInterestGroup,Berlin,Germany.-Oralpresentation:RyuT,HentschelU,andRavasiT.IntegrativetranscriptomeanalysisoftwoRedSeasponges,StylissacarteriandXestospongiatestudinaria.9thWorldSpongeConference,4-8November2013,Perth,Australia.- Oral presentation: Cannistraci, C.V., Alanis-Lobato, G. and Ravasi, T. Network science andmachine learning for systems biology. KAUST-McGill Research Workshop, King AbdullahUniversityofScienceandTechnology(KAUST),May15,2013,SaudiArabia.-Oralpresentation:Cannistraci,C.V.,Alanis-Lobato,G.andRavasi,T.Minimumcurvilinearitytoenhance topological prediction of protein interactions by network embedding. NetSci 2013,satellitesymposium"ComplexNetworksmeetMachineLearning",June3-7,2013,Copenhagen,Denmark.-Posterpresentation:PerezJE,ContrerasMF,RavasiTandKoselJ.CytotoxicityandEffectsonCellViabilityofNickelNanowires.KAUSTWEPGraduatePosterCompetition,21 January2013,Thuwal,KSA.- Oral presentation: Cannistraci, C.V., Alanis-Lobato, G. and Ravasi, T. Towards personalizedgenomic medicine. Bioinformatics Workshop for Health and Population Genomics Research,UniversityofPhilippines,May29-30,Manila,Philippines.- Oral presentation:Cannistraci, C.V.,Alanis-Lobato,G. andRavasi, T.MinimumCurvilienarityfornetworkembeddinginbiologicalnetworks.WorkshopinNetworkTheoryandParadigmsinComplex Systems, King Abdullah University of Science and Technology (KAUST), June 15-16,Thuwal,SaudiArabia.-Posterpresentation:Alanis-Lobato,G.,Cannistraci,C.V.&Ravasi,T.LearningnewbiologyfromGWASbymeansofnetworkanalysisand linkprediction.HumanGenomeMeeting2013,April2013,Singapore.-Oralpresentation:RyuT,LafiF,Moitinho-SilvaL,SeridiL,GilesEC,VoolstraCR,HentschelU,and Ravasi T. Comparative transcriptomics of the marine sponges, Stylissa carteri andXestospongiatestudinaria fromthecentralRedSea.12th InternationalCoralReefSymposium,9-13July2012,Cairns,Australia.
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- Oral presentation: Ryu T, Seridi L,Giles EC,Moitinho-Silva L,HentschelU, Voolstra CR, andRavasiT.Integrativeapproachesshedlightoncoralsandspongesasemergingmodelorganisms.12thInternationalCoralReefSymposium,9-13July2012,Cairns,Australia.-Oralpresentation:ChandramouliC,SYMokF,SunJ,QiuJW,QianPYandRavasiT.The10thInternationalLarvalBiologySymposium.July30-August3,2012,Berkely,California,USA.-Oralpresentation:Moitinho-SilvaL,RyuT,LafiF,GilesEC,VoolstraCR,RavasiT,andHentschelU. Comparative metatranscriptomics of Red Sea sponge symbionts. 12th International CoralReefSymposium,9-13July2012,Cairns,Australia.-PosterPresentation:GhoshehY,Ryu,R,SeridiL,ClintonM,CarninciP,FaulknerGandRavasiT.Genome-wide discovery of piRNA clusters dynamically regulated during brain and testisdevelopment. European Conference on Computational Biology, 9-12 September 2012, Basel,Switzerland.-Oralpresentation:HaywoodA,RyuT,andRavasiT.DivergentmiRNAinhighandlowmicrobialporifera of the Red Sea. MicroRNAs Europe 2012 Meeting, 1-2 November 2012, Cambridge,UnitedKingdom.-Posterpresentation:SeridiL,RyuT,andRavasiT.InvestigatingAssociationBetweenGenomeConservation, Gene Organization and Epigenetic Regulation in Drosophila.EuropeanConferenceonComputationalBiology(ECCB),9-12September2012,Basel,Switzerland.-Posterpresentation:Alanis-Lobato,G.,Cannistraci,C.V.&Ravasi,T.Anovelgraphdissimilarityindex for prediction of genetic interactions. European Conference in Computational Biology(ECCB)2012,September2012,Basel,Switzerland.- Poster presentation: Alanis-Lobato, G., Cannistraci, C.V. & Ravasi, T. Prediction of geneticinteractionsusingnetworktopology.IntelligentSystemsforMolecularBiology(ISMB)2012,July2012,LongBeach,CA,USA.-Posterpresentation:Cannistraci,C.V.,Alanis-Lobato,G.&Ravasi,T.Minimumcurvilinearitytoaddresshigh-throughputprotein-protein interactionexperiments. ISMB/ECCB2011, July2011,Vienna,Austria.-Oral presentation:Cannistraci,C.V.,Alanis-Lobato,G.&Ravasi,T.Minimumcurvilinearity toaddress high-throughput protein-protein interaction experiments. King Fahd University ofPetroleumandMineralsGraduateSeminar,Dhahran,May2011,SaudiArabia.-Oral presentation:Cannistraci,C.V.,Alanis-Lobato,G.&Ravasi,T.Minimumcurvilinearity toaddresshigh-throughputprotein-proteininteractionexperiments.1stKAUSTGraduateResearchSymposium,May2011,Thuwal,SaudiArabia.
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- Oral presentation:Cannistraci CV, Ravasi T, Montevecchi FM, Ideker T and Alessio M.Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathicpainandtissueembryologicalclasses.SelectedtalkinProceedingstrack(andarticlepublicationinBioinformatics).September26th-29th,ECCB2010,Ghent,Belgium.- Oral presentation: Ryu T, Mavromatis H, Bayer T, Voolstra CR, and Ravasi T. Unexpectedcomplexity of the reef-building coral Acropora millepora transcritptional network. EuroInternaltionalSocietyforReefstudies,13-18,December,2010,Wageningen,Netherlands-Posterpresentation:RavasiTandHumeDA.ProbingtheS100proteinfamilythroughgenomicand functionalanalysis. InternationalSociety for InterferonandCytokineResearch.November2003,Cairns,Australia.- Poster presentation: Ravasi T and Hume DA. Characterization of the zinc finger containingprotein in the mouse genome. International conference of Inflammation. August 2003,Vancouver,Canada.-Posterpresentation:Epigeneticmechanismsofgeneexpressioninmacrophage.InternationalconferenceofInflammation.August2003,Vancouver,Canada.-Oral presentation:RavasiTandHumeDA.Structureandevolutionof thezinc fingerproteinfamilies.ComBioconference.September2002,Sydney,Australia.- Oral presentation:Ravasi T and Hume DA Mechanisms of LPS-inducible gene expression.AnnualMeetingofAustralianSocietyofImmunology.September2002,Brisbane,Australia.- Poster presentation: Ravasi T. and Hume DA. Stochastic gene expression. Generation ofdiversity in the Innate Immunesystem”.TheCytokineOdyssey ICS-SLB.November8-11,2001,MauiHI,USA.RESEARCHSUPERVISEDPhD:Advisor1. GregorioAlenis-Lobato, Computer Sciences; Exploitationof complexnetwork topology for
linkpredictioninbiologicalinteractomes(Startdate:Spring2011;Graduated:Fall2014).2. Harris Mavromatis, Biosciences; Mapping ofthe Co-Transcriptomes of UPEC-Infected
3. Sarah Al-Aqeel, Chemical Biological Engineering; ASystem-wide approachto IdentifymechanismsofBarnacleattachment(Startdate:Spring2011;Graduated:Fall2015).
4. Maria Fernanda Contreras, Biosciences; Magnetic nanowires as materials for cancer celldestruction(Startdate:Fall2011;Graduated:Fall2015).
6. Dina Hajjar, Chemical Biological Engineering; Cytological Profiling of Red Sea NaturalProducts using Automated High-Content Imaging Technique. (Start date: Fall 2012;Graduated:Spring2016).
7. Yanal Ghosheh, Computer Sciences; An integrative approach to analyze subtypes of non-codingRNA(Startdate:Spring2011;ExpectedGraduation:Spring2016).
dependent and independent approaches to assess fisheries, abundance, diversity,distributionandgeneticconnectivityofRedSeaelasmobranchpopulations(Startdate:Fall2011;Graduated:Fall2013).
2. May M. Al Qurashi, (PhD Advisor: Prof. Christoph Gehring) Biosciences; The Arabidopsisthaliana Cyclic-Nucleotide-Dependent Response. A Quantitative Proteomic andPhosphoproteomicAnalysisStartdate:Spring2010;Graduated:Winter2013).
3. Chatchanit Arif, (PhD Advisor: Prof. Christian Voolstra) Marine Sciences; ComparativeProfilingofcoralsymbiontcommunitiesfromtheCaribbean,Indo-Pacific,andArabianSeas(Startdate:Fall2011;Graduated:Fall2014).
4. Lauren Kyung-A Yum, (PhD Advisor: Prof. Christian Voolstra) Marine Sciences; RevealingHolobiontStructureandFunctionofThreeRedSeaDeep-SeaCorals (Startdate:Fall2011;Graduated:Fall2014).
6. Ilona Turek, (PhD Advisor: Prof. Christoph Gehring) Biosciences; Elucidation of the SignalTransduction Pathways Activated by the Plant Natriuretic Peptide AtPNP-A (Start date:Winter2011;Graduated:Winter2014).
7. Yue Guan, (PhD Advisor: Prof. Uli Stingl) Exploring Archaeal Communities And GenomesAcrossFiveDeep-SeaBrineLakesOfTheRedSeaWithAFocusOnMethanogens(Startdate:Fall2010;Graduated:Fall2015).
8. Anna Roik, (PhD Advisor: Prof. Christian Voolstra) Marine Sciences; Environmental andbiological controls of coral reef framework development (Start date: Fall 2012; ExpectedGraduation:Summer2016).
9. Till Rothig, (PhD Advisor: Prof. Christian Voolstra)Marine Sciences; Functional Ecology ofRedSeaCorals(Startdate:Summer2012;ExpectedGraduation:Winter2015).
11. Song He, (PhD Advisor: Prof. Michael Berumen) Marine Sciences; Coral reef fishhybridization(Startdate:Winter2014;ExpectedGraduation:Winter2016).
12. Vanessa S. N. Robitzch, (PhD Advisor: Prof. Michael Berumen) Marine Sciences; TheAssessment of Current Biogeographic Patterns of Coral Reef Fishes in the Red Sea byIncorporating their Evolutionary and Ecological Background (Start date: Spring 2014;ExpectedGraduation:Winter2016).
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13. OctavioRubénSalazarMoya,(PhDAdvisor:Prof.MarkTester)Biosciences;IdentificationofVacuolar Proteins Involved in Salinity Tolerance in Salicornia bigelovii: In search of theVacuolarNa+/H+Antiporter(Startdate:Winter2014;ExpectedGraduation:Spring2016).
14. Jennifer Booth, (PhD Advisor: Prof. Daniele Daffonchio) Ecology of the MangroveMicrobiome(Startdate:Summer2014;ExpectedGraduation:Summer2017).
MS:ThesisCommittee1. Mohammed El Sayed El Saeedy, (Advisor: Prof. Panos Kalnis) Computer Sciences; GRAMI:
Generalized Frequent SubgraphMining in LargeGraphs (Start date: Fall 2010;Graduated:Summer2011).
2. Noha Ahmed Al-Harthi, (Advisor: Prof. David Keyes) Computer Sciences; PerformanceBenchmarking of Fast Multipole Methods (Start date: Spring 2012; Graduated: Summer2013).
3. Abhinay Ramaprasad, (Advisor: Prof. Arnab Pain) Biosciences; Studying Different ClinicalSyndromes Of Paediatric Severe Malaria Using Plasma Proteomics (Start date: Fall 2011;Graduated:Summer2012).
4. Yara Al Zahid, (Advisor: Prof. Arnab Pain) Biosciences; Comparative Genomics andTranscriptomics Analysis ofMycobacterium Kansasii (Start date: Spring 2013; Graduated:Spring2014).
6. Ge Gao, (Advisor: Prof. Arnab Pain) Biosciences; Comparative Proteomic Profiling ofMycobacterium bovis and BCG Vaccine Strains (Start date: Spring 2012; Graduated: Fall2013).
7. Brian Parrot, (Advisor: Prof. Christoph Gehring) Biosciences; Post-translational Analysis ofArabidopsis thalianaProteins inResponse toCyclicGuanosineMonophosphateTreatmentStartdate:Winter2010;Graduated:Winter2011).
8. Maha T. Khalil, (Advisor: Prof. Michael Berumen) Marine Sciences; Designing MarineProtectedAreaNetworks in theCentralSaudiArabianRedSea (Startdate:Summer2011;Graduated:Fall2012).
9. Francisco Jose Acosta Espinosa, (Advisor: Prof. Uli Stingl) Marine Sciences; Diversity ofPicoeukaryotesatanOligotrophicSiteofftheNorthernRedSeaCoast(Startdate:Summer2011;Graduated:Fall2012).
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10. Tullia Isotta Terraneo, (Advisor: Prof. Michael Berumen) Investigating Species Boundarieswithin theHardCoralGenusGoniopora (Cnidaria, Scleractinia) fromtheRedSeaUsinganIntegrativeMorphomolecularApproach(Startdate:Summer2014;Graduated:Fall2015).
11. AllisonMonroe, (Advisor: Prof. Michael Berumen) Genetic differentiation across multiplespatialscalesof theRedSeaof thecoralsStylophorapistillataandPocillopora (Startdate:Summer2014;Graduated:Fall2015).
12. NoraKandler,(Advisor:Prof.MichaelBerumen)BiodiversityofMacrofaunaAssociatedwithSponges across Ecological Gradients in the Central Red Sea (Start date: Summer 2014;Graduated:Fall2015).