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TimothyRavasiKingAbdullahUniversityofScienceandTechnology

DivisionofBiologicalandEnvironmentalSciences&Engineering/BiosciencesDivisionofComputer,ElectricalandMathematicalSciences&Engineering/ComputerSciences

Email:timothy.ravasi@kaust.edu.sa

PROFESSIONALEXPERIENCE

2016-present2009-2016

FullProfessor,DivisionofBiologicalandEnvironmentalSciences&Engineering,KAUSTAssociateProfessor,DivisionofBiologicalandEnvironmentalSciences&Engineering,KAUST

2009-present AdjunctAssociateProfessor,DepartmentofMedicine,SchoolofMedicine,UniversityofCaliforniaSanDiego,USA

2005-present PermanentSeniorVisitingScientist,InstituteofChemicalsandPhysicalResearch(RIKEN),Japan

2009-2014

PrincipalInvestigator,ComputationalBioscienceResearchCenter(CBRC),Computer,ElectricalandMathematicalSciencesandEngineering,KAUST

2006-2009

Co-Director,SystemsBiologyandIntegrativeNetworksCoreoftheScrippsNeuroAIDSPreclinicalStudiesCenter(SNAPS),TheScrippsResearchInstitute,UniversityofCaliforniaSanDiego,USA

2005-2009

ResearchScientist,DepartmentofBioengineering,JacobsSchoolofEngineering,UniversityofCalifornia,SanDiego,USA

2001-2009

Post-Doctoral,SpecialResearchCenterforFunctionalandAppliedGenomics,InstituteforMolecularBioscience,UniversityofQueensland,Australia

2001-2002

Post-Doctoral,GenomicSciencesCenter,TheInstituteofChemicalsandPhysicalResearch(RIKEN),Japan

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

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PROFESSIONALAFFILIATIONS

-FoundingmemberoftheGlobalInvertebrateGenomicsAlliance(GIGA)

-FoundingmemberoftheSea-quenceproject,Refuge20/20consortium

-MemberofthesteeringcommitteeforthePanAsianPopulationGeneticInitiative(PAPGI)-MemberoftheprogramcommitteefortheDREAMconferencesfortheDialogueonReverseEngineering.

-MemberoftheInternationalProgramCommitteeComputationalBioscience(CompBio)

-MemberoftheRIKENFunctionalAnnotationofMammalianGenomesconsortium(FANTOM6).

PROFESSIONALREGISTRATION

-MemberoftheHumanGenomeOrganization(HUGO)

-MemberoftheInternationalSocietyofComputationalBiology(ISCB)

-MemberoftheInternationalSocietyforReefStudies(ISRS)

-MemberoftheAustralianCoralReefSociety(ACRS)

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

-2012,MemberofStrategyWorkingGroup7-2012MemberoftheKAUSTTemporaryBioethicalcommittee.-2010,2011and2012MemberoftheKAUSTFacultyITgovernancecommittee

-2011and2012,MemberoftheVisualizationCoreLabUserscommittee-2010and2011,ElectedMemberofKAUSTAcademicCouncil-2011,MemberoftheKAUSTFacultyTravelPolicycommittee.

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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.

Peer-reviewedmanuscripts1. SchunterS,WelchMJ,RyuT,ZhangH,BerumenML,NilssonGE,MundayPLandRavasiT*.

Molecularsignaturesoftransgenerationalbrainresponsetooceanacidificationinareeffish.NatureClimateChange.2016.UnderReview

2. Aranda M, Y. Li, Y.J. Liew, S. Baumgarten, O. Simakov, M. Wilson, J. Piel, H. Ashoor, S.

Bougouffa,V.B.Bajic,T.Ryu,T.Ravasi,T.Bayer,G.Micklem,H.Kim,J.Bhak,T.C.LaJeunesse,C.R. Voolstra. Comparative analysis of coral dinoflagellate symbionts genomes highlightsevolutionaryadaptationstoasymbioticlifestyle.ISME,2016.Underreview

3. Martin JT, Markert SM, Ryu T, Ravasi T, Stigloher S, Hentschel U, and Moitinho-Silva L.

Shedding light on the candidate phylum Poribacteria by high-resolution visualization andtranscriptionalprofiling.mBIO,2016.Underreview

4. CasasL,Saborido-ReyF,RyuT,MichellCT,RavasiTandIrigoienX..Sexchangeinclownfish:

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.

6. GhoshehY,SeridiL,RyuT,TakahashiH,OrlandoV,CarninciPandRavasiT*.Discoveryand

characterization of piRNAs in adult mouse brain. Sci Rep. 2016 Apr 26;6:25039. doi:10.1038/srep25039.

7. DineshramR,ChandramouliKH,ZhangH,QianPY,KoWKGingerRavasiTandVengatesen

Thiyagarajan. Quantitative analysis of oyster larval proteome provides new insights intomoleculareffectsofmultipleclimate-relatedstressors.GlobChangBiol.2016Mar17.doi:10.1111/gcb.13249.

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8. FelixLP,PerezJE,ContrerasMF,RavasiT*andKoselJ*.Cytotoxiceffectsofnickelnanowiresinhumanfibroblasts.ToxicologyReports.3,2016,373–380.doi:10.1016/j.toxrep.2016.03.004

9. Ryu T, Seridi L, Silva L, OatesM, LiewYJ, MarvromatisH, Wang X, Haywood A, F. Lafi F,KupresaninM, Sougrat R, , AlzahraniMA, Ghoseh Y, Giles EC, Schunter C, Baumgarten S,BerumenML,GaoX,ArandaM,ForetS,Gough J,VoolstraCR,HentschelUandRavasiT*.Hologenomeanalysis of twomarine spongeswith differentmicrobiomes. BMCGenomics,2016Feb29;17(1):158.doi:10.1186/s12864-016-2501-0.

10. LiewYJ,RyuT,ArandaMandRavasiT*.miRNArepertoiresofdemospongesStylissacarteri

andXestospongiatestudinaria.PLoSOne.2016Feb12;11(2):e0149080.doi:10.1371/journal.pone.0149080.PMID:26871907

11. Perez JE, ContrerasMF, Vilanova E, Felix LP, Luongo G, Dunlop I, Ravasi T* and Kosel J*.

Cytotoxicityanddissolutionrateofnickelnanowires.Nanotoxicology.2015Dec22:1-38.12. ChandramouliKH,Al-AqeelS,RyuT,ZhangH,Seridi L,GhoshehY,QianPYandRavasiT*.

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

RavasiT*.Quantificationofnanowireuptakebylivingcells.JNanobiotechnology.2016Jan15;14(1):4.doi:10.1186/s12951-015-0153-x

14. ChandramouliKH,ReishD,ZhangH,QianPYandRavasiT*.Proteomicchangesassociated

withsuccessivereproductiveperiodsinmalepolychaetousNeanthesarenaceodentata.SciRep.2015Sep4;5:13561.doi:10.1038/srep13561.

15. ReFuGeconsortium.Theroleofgenomicdataandgenetictoolsinthemanagementofcoral

reefs.Front.Mar.Sci.,15September2015.http://dx.doi.org/10.3389/fmars.2015.00068.16. ZhangH,QianPY,RavasiT*.Selectivephosphorylationduringearlymacrophage

differentiation.Proteomics.2015Aug26.doi:10.1002/pmic.201400511.17. VeilleuxHD,RyuT,DonelsonJM,vanHerwerdenL,SeridiL,GhoshehY,BerumenML,Leggat

W,RavasiT*andMundayPL*.Mechanismsoftransgenerationalacclimationtoawarmingocean.NatureClimateChange2015.doi:10.1038/nclimate2724.

18. Giles EM, Saenz-Agudelo P, HusseyNE, BerumenML* and Ravasi T*. Exploring seascape

geneticsandkinshipinthereefspongeStylissacarteriintheRedSea.EcologyandEvolution5(13),2487-2502,1Jun2015DOI:10.1002/ece3.1511.

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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.

20. Alanis-LobatoG,CannistraciCV,ErikssonA,ManicaAandRavasiT*.Highlightingnonlinear

patterns in population genetics datasets. Sci Rep. 2015 Jan 30;5:8140. doi:10.1038/srep08140.PMID:25633916

21. Thestatisticalgeometryoftranscriptomedivergenceincell-typeevolutionandcancer.Liang

C; FANTOMConsortium,ForrestAR,WagnerGP.Et al.NatCommun.2015 Jan14;6:6066.doi:10.1038/ncomms7066.PMID:25585899.

22. MavromatisCH,BokilNJ,TotsikaM,KakkanatA,SchaaleK,CannistraciCV,RyuT,Beatson

SA, Ulett GC, Schembri MA, Sweet MJ and Ravasi T*. The Co-Transcriptome ofUropathogenic Escherichia coli-Infected Mouse Macrophages Reveals New Insights intoHost-PathogenInteractions.CellMicrobiol.2014Nov20.doi:10.1111/cmi.12397.PubMedPMID:25410299.

23. BayerK,Moitinho-SilvaL,BrommerF,CannistraciCV,RavasiT*andHentschelU*.GeoChip-

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

analysiselucidates keydevelopmental componentsofbryozoan lophophoredevelopment.Sci Rep. 2014 Oct 10;4:6534. doi: 10.1038/srep06534.PubMed PMID: 25300304; PubMedCentralPMCID:PMC4192642.

25. Seridi L, Ryu T and Ravasi T*. Dynamic epigenetic control of highly conserved noncoding

elements. PLoS One. 2014 Oct 7;9(10):e109326. doi: 10.1371/journal.pone.0109326.PubMedPMID:25289637;PubMedCentralPMCID:PMC4188601.

26. ChandramouliKH,QianPY,andRavasiT.Proteomicsinsights:proteinsrelatedtolarval

attachmentandmetamorphosisofmarineinvertebrates.Front.Mar.Sci.,31October2014.http://dx.doi.org/10.3389/fmars.2014.00052.

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.

28. HasegawaY,TangD,TakahashiN,HayashizakiY,ForrestAR;FANTOMConsortium,SuzukiH.

CCL2enhancespluripotencyofhumaninducedpluripotentstemcellsbyactivatinghypoxia

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related genes. Sci Rep. 2014 Jun 24;4:5228. doi: 10.1038/srep05228. PubMed PMID:24957798;PubMedCentralPMCID:PMC4067614.

29. Moitinho-Silva L, Seridi L, Ryu T, Voolstra CR, Ravasi T* and Hentschel U*. Revealing

microbialfunctionalactivitiesintheRedSeaspongeStylissacarteribymetatranscriptomics.Environ Microbiol. 2014 Jun 11. doi: 10.1111/1462-2920.12533. [Epub ahead of print]PubMedPMID:24920529.

30. AbdelmohsenUR,YangC,HornH,HajjarD,RavasiT*andHentschelU*.Actinomycetesfrom

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.

31. MorikawaH,OhkuraN,VandenbonA,ItohM,Nagao-SatoS,KawajiH,LassmannT,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 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.

32. ArnerE,ForrestAR,EhrlundA,MejhertN, ItohM,KawajiH,LassmannT,Laurencikiene J,

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.

33. FANTOMConsortiumandtheRIKENPMIandCLST(DGT),ForrestAR,etal.Apromoter-level

mammalian expression atlas. Nature. 2014 Mar 27;507(7493):462-70. doi:10.1038/nature13182.PubMedPMID:24670764.

34. AnderssonR,GebhardC,Miguel-Escalada I,Hoof I,Bornholdt J,BoydM,Chen Y,ZhaoX,

SchmidlC,SuzukiT,NtiniE,ArnerE,ValenE,LiK,SchwarzfischerL,GlatzD,RaithelJ,LiljeB,RapinN,BaggerFO,JurgensenM,AndersenPR,BertinN,RackhamO,BurroughsAM,BaillieJK,IshizuY,ShimizuY,FuruhataE,MaedaS,NegishiY,MungallCJ,MeehanTF,LassmannT,ItohM,KawajiH,KondoN,KawaiJ,LennartssonA,DaubCO,HeutinkP,HumeDA,JensenTH,SuzukiH,HayashizakiY,MullerF;FANTOMConsortium,ForrestAR,CarninciP,RehliM,SandelinA.Anatlasofactiveenhancersacrosshumancelltypesandtissues.Nature.2014Mar27;507(7493):455-61.doi:10.1038/nature12787.PubMedPMID:24670763.

35. HarjesJ,RyuT,AbdelmohsenUR,Moitinho-SilvaL,HornH,RavasiTandHentschelU.Draft

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.

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36. Chen ZF, Zhang H, Wang H, Matsumura K, Wong YH, Ravasi T*, Qian PY*. Quantitativeproteomicsstudyof larvalsettlement intheBarnacleBalanus amphitrite.PLoSOne.2014Feb13;9(2):e88744. doi: 10.1371/journal.pone.0088744. eCollection2014. PubMedPMID:24551147;PubMedCentralPMCID:PMC3923807.

37. GIGACommunityofScientists,Bracken-GrissomH,CollinsAG,CollinsT,CrandallK,DistelD,

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.

40. Moitinho-SilvaL,BayerK,CannistraciCV,GilesEC,RyuT,SeridiL,RavasiT*andHentschel

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.

41. M.F.Contreras,T.Ravasi*,andJ.Kosel*.TargetedcancercelldeathInducedbyInducedby

Biofunctionalized Magnetic Nanowires. Proceedings of the Middle East Conference onBiomedicalEngineering.Feb.17,2014.Doha,Qatar.

42. 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. 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.

47. CannistraciCV,OgorevcJ,ZorcM,RavasiT,DovcPandKunejT.Pivotalroleofthemuscle-

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.

49. MalasTandRavasiT*.ComputationalToolsforGenome-WidemiRNAPredictionandStudy.

TOBIOJ.2012Nov;5:23-30.doi:10.2174/1874196701205010023.50. PerezJE,ContrerasMF,VilanovaE,RavasiT*andKosel J*.CytotoxicityandEffectsonCell

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.

52. Ammirati E, Cannistraci CV, Cristell NA, Vecchio V, Palini AG, Tornvall P, Paganoni AM,

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.

55. SunJ,ZhangH,WangH,HerasH,DreonMS,ItuarteS,RavasiT,QianPYandQiuJW.First

proteomeoftheeggperivitellinefluidofafreshwatergastropodwith aerialoviposition.JProteome Res. 2012 Aug 3;11(8):4240-8. doi: 10.1021/pr3003613. Epub 2012 Jul 13.PubMedPMID:22738194.

56. Wong YH,WangH, Ravasi T andQian PY. Involvement ofWnt signaling pathways in the

metamorphosis of the bryozoan Bugula neritina. PLoS One. 2012;7(3):e33323. doi:10.1371/journal.pone.0033323. Epub 2012 Mar 20. PubMed PMID: 22448242; PubMedCentralPMCID:PMC3308966.

57. Ramaprasad A, Pain A and 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.Epub2011Dec8.Review.PubMedPMID:22178265.

58. Bokil NJ, Totsika M, Carey AJ, Stacey KJ, Hancock V, Saunders BM, Ravasi T, Ulett GC,

SchembriMA and SweetMJ. Intramacrophage survival of uropathogenic Escherichia coli:differencesbetweendiverseclinicalisolatesandbetweenmouseandhumanmacrophages.Immunobiology. 2011 Nov;216(11):1164-71. doi: 10.1016/j.imbio.2011.05.011. Epub 2011May24.PubMedPMID:21802164.

59. RyuT,MavromatisCH,BayerT,VoolstraCRandRavasi T*.Unexpected complexityof the

reef-buildingcoralAcroporamilleporatranscriptionfactornetwork.BMCSystBiol.2011Apr28;5:58.doi:10.1186/1752-0509-5-58.PubMedPMID:21526989;PubMedCentralPMCID:PMC3096595.

60. Zhang H,Wong YH,Wang H, Chen Z, Arellano SM, Ravasi T* and Qian PY*. Quantitative

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.

61. KuoD,LiconK,BandyopadhyayS,ChuangR,LuoC,CatalanaJ,RavasiT,TanKandIdekerT.

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.

63. KuoD,TanK,ZinmanG,RavasiT,Bar-JosephZandIdekerT.Evolutionarydivergenceinthe

fungal response to fluconazole revealed by soft clustering. Genome Biol. 2010;11(7):R77.doi: 10.1186/gb-2010-11-7-r77. Epub 2010 Jul 23. PubMed PMID: 20653936; PubMedCentralPMCID:PMC2926788.

64. WangH,ZhangH,WongYH,VoolstraC,RavasiT,BBajicVandQianPY.Rapidtranscriptome

and proteome profiling of a non-modelmarine invertebrate, Bugula neritina. Proteomics.2010Aug;10(16):2972-81.doi:10.1002/pmic.201000056.PubMedPMID:20540116.

65. WongYH,ArellanoSM,ZhangH,RavasiT*andQianPY*.Dependencyondenovoprotein

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.

66. ZhangH,ZhaoC,LiX,ZhuY,GanCS,WangY,RavasiT,QianPY,WongSCandSzeSK.Study

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.

67. RavasiT,etal.Anatlasofcombinatorialtranscriptionalregulationinmouseandman.Cell.

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.

69. RamachandraRaoSP,ZhuY,RavasiT,McGowanTA,TohI,DunnSR,OkadaS,ShawMAand

SharmaK.Pirfenidoneisrenoprotectiveindiabetickidneydisease.JAmSocNephrol.2009Aug;20(8):1765-75. doi: 10.1681/ASN.2008090931. Epub 2009 Jul 2. PubMed PMID:19578007;PubMedCentralPMCID:PMC2723978.

70. FANTOMConsortium,SuzukiHatal.Thetranscriptionalnetworkthatcontrolsgrowtharrest

anddifferentiationinahumanmyeloidleukemiacell line.NatGenet.2009May;41(5):553-62.doi:10.1038/ng.375.Epub2009Apr19.PubMedPMID:19377474.

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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.

72. TanK,TegnerJandRavasiT*.Integratedapproachestouncoveringtranscriptionregulatory

networks in mammalian cells. Genomics. 2008 Mar;91(3):219-31. doi:10.1016/j.ygeno.2007.11.005.Epub2008Jan8.Review.PubMedPMID:18191937.

73. HinshelwoodRA,HuschtschaLI,MelkiJ,StirzakerC,AbdipranotoA,VisselB,RavasiT,Wells

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.

74. *RavasiT,WellsCAandHumeDA.Systemsbiologyoftranscriptioncontrolinmacrophages.

Bioessays.2007Dec;29(12):1215-26.Review.PubMedPMID:18008376.75. SchroderK,SpilleM,PilzA,LattinJ,BodeKA,IrvineKM,BurrowsAD,RavasiT,WeighardtH,

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.

NovartisFoundSymp.2007;281:2-18;discussion18-24,50-3,208-9.Review.PubMedPMID:17534062.

78. RipollVM,IrvineKM,RavasiT,SweetMJandHumeDA.Gpnmbisinducedinmacrophages

byIFN-gammaandlipopolysaccharideandactsasafeedbackregulatorofproinflammatoryresponses.JImmunol.2007May15;178(10):6557-66.PubMedPMID:17475886.

79. Hume DA, Wells C and Ravasi T. Transcriptional Regulatory Networks in Macrophages.

NovartisFoundSymp.2007;281:2-18.80. SasmonoRT,EhrnspergerA,CronauSL,RavasiT,KandaneR,HickeyMJ,CookAD,HimesSR,

Hamilton JA andHumeDA.Mouse neutrophilic granulocytes expressmRNA encoding the

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macrophagecolony-stimulatingfactorreceptor(CSF-1R)aswellasmanyothermacrophage-specifictranscriptsandcantransdifferentiateintomacrophagesinvitroinresponsetoCSF-1.JLeukocBiol.2007Jul;82(1):111-23.Epub2007Apr16.PubMedPMID:17438263.

81. TegnerJ,NilssonR,BajicVB,BjurkegrenJandRavasiT*.Systemsbiologyofinnateimmunity.

Cell Immunol. 2006 Dec;244(2):105-9. Epub 2007 Apr 11. PubMed PMID: 17433274;PubMedCentralPMCID:PMC1947944.

82. SchroderK,LichtingerM, IrvineKM,BrionK,TrieuA,Ross IL,RavasiT,StaceyKJ,RehliM,

HumeDAandSweetMJ.PU.1andICSBPcontrolconstitutiveandIFN-gamma-regulatedTlr9geneexpressioninmousemacrophages.JLeukocBiol.2007Jun;81(6):1577-90.Epub2007Mar14.PubMedPMID:17360957.

83. AungHT, Schroder K, Himes SR, Brion K, van ZuylenW, Trieu A, Suzuki H, Hayashizaki Y,

Hume DA, Sweet MJ and Ravasi T*. LPS regulates proinflammatory gene expression inmacrophages by altering histonedeacetylase expression. FASEB J. 2006 Jul;20(9):1315-27.PubMedPMID:16816106.

84. NilssonR,BajicVB,SuzukiH,diBernardoD,BjurkegrenJ,KatayamaS,Reid JF,SweetMJ,

GariboldiM, Carninci P, Hayashizaki Y, Hume DA, Tegner J and Ravasi T*. Transcriptionalnetworkdynamicsinmacrophageactivation.Genomics.2006Aug;88(2):133-42.Epub2006May12.PubMedPMID:16698233.

85. MaedaN,KasukawaT,OyamaR,GoughJ,FrithM,EngstromPG,LenhardB,AturaliyaRN,

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.

86. CarninciP,SandelinA,LenhardB,KatayamaS,ShimokawaK,PonjavicJ,SempleCA,Taylor

MS,EngstromPG,FrithMC,ForrestAR,AlkemaWB,TanSL,PlessyC,KodziusR,RavasiT,KasukawaT, Fukuda S, Kanamori-KatayamaM,KitazumeY, KawajiH, Kai C,NakamuraM,KonnoH,NakanoK,Mottagui-TabarS,ArnerP,ChesiA,GustincichS,PersichettiF,SuzukiH,Grimmond SM,Wells CA, Orlando V,Wahlestedt C, Liu ET, HarbersM, Kawai J, Bajic VB,HumeDA andHayashizaki Y.Genome-wide analysis ofmammalian promoter architectureandevolution.NatGenet.2006Jun;38(6):626-35.Epub2006Apr28.Erratumin:NatGenet.2007Sep;39(9):1174.PubMedPMID:16645617.

87. HimesSR,SesterDP,RavasiT,CronauSL,SasmonoTandHumeDA.TheJNKareimportant

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.

89. SesterDP,TrieuA,BrionK,SchroderK,RavasiT,RobinsonJA,McDonaldRC,RipollV,Wells

CA,SuzukiH,HayashizakiY,StaceyKJ,HumeDAandSweetMJ.LPSregulatesasetofgenesinprimarymurinemacrophagesbyantagonisingCSF-1action.Immunobiology.2005;210(2-4):97-107.PubMedPMID:16164016.

90. KatayamaS,TomaruY,KasukawaT,WakiK,NakanishiM,NakamuraM,NishidaH,YapCC,

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.

92. CowiesonNP,ListwanP,KurzM,AagaardA,RavasiT,WellsC,HuberT,HumeDAandKobeB,MartinJL.Pilotstudiesontheparallelproductionofsolublemouseproteinsinabacterialexpressionsystem.JStructFunctGenomics.2005;6(1):13-20.PubMedPMID:15965734.

93. RehliM,SulzbacherS,PapeS,RavasiT,WellsCA,HeinzS,ScollnerL,ElChartouniC,Krause

SW, Steingrimsson E,HumeDA andAndreesenR. Transcription factor Tfec contributes totheIL-4-inducibleexpressionofasmallgroupofgenesinmousemacrophagesincludingthegranulocyte colony-stimulating factor receptor. J Immunol. 2005 Jun 1;174(11):7111-22.PubMedPMID:15908341.

94. WellsCA,RavasiTandHumeDA.Inflammationsuppressorgenes:pleaseswitchoutallthe

lights. J Leukoc Biol. 2005 Jul;78(1):9-13. Epub 2005 Mar 17. Review. PubMed PMID:15774547.

95. AagaardA,ListwanP,CowiesonN,HuberT,RavasiT,WellsCA,FlanaganJU,KellieS,Hume

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.

97. SchroderK,HertzogPJ,RavasiTandHumeDA. Interferon-gamma:anoverviewofsignals,

mechanismsandfunctions.JLeukocBiol.2004Feb;75(2):163-89.Epub2003Oct2.Review.PubMedPMID:14525967.

98. WellsCA,RavasiT,FaulknerGJ,CarninciP,OkazakiY,HayashizakiY,SweetM,Wainwright

BJandHumeDA.Geneticcontroloftheinnateimmuneresponse.BMCImmunol.2003Jun26;4:5.Epub2003Jun26.PubMedPMID:12826024;PubMedCentralPMCID:PMC194878.

99. ForrestAR,RavasiT,TaylorD,HuberT,HumeDAandGrimmondS;RIKENGERGroup;GSL

Members.Phosphoregulators:proteinkinasesandproteinphosphatasesofmouse.GenomeRes. 2003 Jun;13(6B):1443-54. PubMed PMID: 12819143; PubMed Central PMCID:PMC403684.

100. RavasiT,HuberT,ZavolanM,ForrestA,GaasterlandT,GrimmondSandHumeDA;RIKEN

GERGroup;GSLMembers.Systematiccharacterizationofthezinc-finger-containingproteinsin the mouse transcriptome. Genome Res. 2003 Jun;13(6B):1430-42. PubMed PMID:12819142;PubMedCentralPMCID:PMC403681.

101. Tajul-Arifin K, Teasdale R, Ravasi T, Hume DA and Mattick JS; RIKEN GER Group; GSL

Members.Identificationandanalysisofchromodomain-containingproteinsencodedinthemouse transcriptome. Genome Res. 2003 Jun;13(6B):1416-29. PubMed PMID: 12819141;PubMedCentralPMCID:PMC403676.

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.

103. OkazakiY,etal.FANTOMConsortium;RIKENGenomeExplorationResearchGroupPhaseI

& IITeam.Analysisof themouse transcriptomebasedon functionalannotationof60,770full-lengthcDNAs.Nature.2002Dec5;420(6915):563-73.PubMedPMID:12466851.

104. Hume DA, Ross IL, Himes SR, Sasmono RT, Wells CA and Ravasi T*. The mononuclear

phagocyte system revisited. J Leukoc Biol. 2002 Oct;72(4):621-7. Review. PubMed PMID:12377929.

105. Wardrop SL, Wells C, Ravasi T and Hume DA, Richardson DR. Induction of Nramp2 in

activated mouse macrophages is dissociated from regulation of the Nramp1, classical

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inflammatory genes, and genes involved in iron metabolism. J Leukoc Biol. 2002Jan;71(1):99-106.PubMedPMID:11781385.

106. RavasiT,WellsC,ForestA,UnderhillDM,WainwrightBJ,AderemA,GrimmondSandHume

DA.Generationofdiversityintheinnateimmunesystem:macrophageheterogeneityarisesfromgene-autonomoustranscriptionalprobabilityofindividualinduciblegenes.JImmunol.2002Jan1;168(1):44-50.PubMedPMID:11751944.

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.

- Invitedspeaker:RavasiT.Aconservednetworkofcombinatorialtranscriptionalregulationinmouseandman.SystemsBiology:Integrative,Comparative,andMulti-ScaleModeling.June11-142009,AmesIA.

-Invitedspeaker:RavasiT.EvolutionofTranscriptionalRegulatoryNetworksinEukaryotes.2ndEmergingTopicsinEpigeneticsResearch.March5,2009,LaJollaCA,USA.

- 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

MacrophagesRevealsNewInsights intotheMolecularBasisofHost-Pathogen InteractionsinHumanandMouse(Startdate:Fall2009;Graduated:Fall2014).

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).

5. LoqmaneSeridi,Noncodingelements: evolutionandspatio-temporaldynamics(Startdate:Spring2011;Graduated:Sping2016).

26

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).

8. JoseEfrainPerez,Biosciences; Interactionsbetweenverticallyalignedmagneticnanowiresandstemcells(Startdate:Fall2013;ExpectedGraduation:Spring2017).

PhD:DissertationCommittee1. JuliaL.Y.Spät,(PhDAdvisor:Prof.MichaelBerumen)MarineSciences; Integratingfisheries

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).

5. LucasMoitinho-Silva,(PhDAdvisor:Prof.UteHentschel,UniversityofWuerzburg,Germany)MarineSciences;ExplorationofmicrobialdiversityandfunctioninRedSeaspongesbydeepsequencing(Startdate:Winter2010;Graduated:Summer2013).

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).

10. PhilippEmanuelWalter,(PhDAdvisor:Prof.ValerioOrlando)Biosciences;RoleofSINE/ALUandLINEelementsinthecontextofterminaldifferentiationandstressresponseofskeletalmusclecells(Startdate:Spring2013;ExpectedGraduation:Fall2015).

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).

27

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:Advisor1. MichaelBogdanMargineanu,Biosciences;Quantificationofnanowireuptakebylivingcells

(Startdate:Fall2014;Graduated:Spring2015).2. Laura Felix, Biosciences; Cytotoxic effects of nickel nanowires in human fibroblasts (Start

date:Fall2013;Graduated:Spring2014).3. Jose E. Perez Rodriguez, Biosciences; Cytotoxicity and Effects on Cell Viability of Nickel

Nanowires(Startdate:Spring2012;Graduated:Spring2013).4. Chen Yang, Biosciences; Isolation and Phylogenetic Analysis and Antibiotic

Activity Screening of Red Sea Sponge-Associated Actinobacteria (Start date: Spring 2012;Graduated:Summer2013).

5. AlanItakura,Biosciences;DecouplingLinearandNonlinearAssociationsofGeneExpression(Startdate:Spring2012;Graduated:Summer2013).

6. LuisDeLaMora,Biosciences;ASystem-WideApproachtoDiabeticNephropathy(Startdate:Fall2010;Graduated:Fall2011).

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).

5. ErikoPadronRegalado,(Advisor:Prof.ArnabPain)Biosciences;MolecularEpidemiologyofViralGastroenteritisinHajjpilgrimage(Startdate:Spring2013;Graduated:Fall2014).

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).

28

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).