研究领域
【1】基因大数据科学、三代基因测序软件技术。合作发布如下大型基因测序软件技术:
DBG2OLC,SPARC,SparseAssembler,10x-assisted-3GSHybridAssembly.
【2】人类微生物群系（菌群）医学生态学理论和方法。
主编《生物信息学：计算技术与软件导论》（科学出版社，该书获国家科技出版基金奖励资助），并在ISMEJournal,EcologicalMonographs,MolecularEcology,ScienceTranslationalMedicine等发表论文近50篇。
【3】网络安全可靠性、可存活性理论、进化博弈论、计算智能、人工智能。
编著：《Reliability,SurvivabilityandResilience:AUnifiedTheoreticApproachwith
SurvivalAnalysis,DynamicHybridFaultModelsandExtendedEvolutionaryGameTheory》
(inPress)Springer.并在IEEETranslationsonReliability等期刊和IEEE/ACM主办国际会议发表论文30余篇。
软件技术：
DBG2OLC,SPARC,SparseAssembler,10x-assisted-3GSHybridAssembly,
[1]DBG2OLC[三代基因测序组装软件:AnultraefficientdeNovogenomeassemblerforthe3rdgenerationsequencingtechnologies(PacBio&OxfordNanopore)].Availableat:
https://sites.google.com/site/dbg2olc/
https://sourceforge.net/projects/dbg2olc/
[2]Sparc[三代基因测序纠错软件:Asparsity-basedconsensusalgorithmforlongerroneous3rdGSsequencingreads].Availableat:
https://sourceforge.net/projects/sparc-consensus/
https://github.com/yechengxi/Sparc
[3]SparseAssembler[二代基因测序组装软件:Sparsek-merGraphforMemoryEfficientdenovoGenomeAssembly).Thecorealgorithm(Sparsek-mer)wasusedinBGI’sSoapDenovo-II,theupdatedversionofBGI’sflagshipsoftwareSoapDenovo].Availableat:
https://sites.google.com/site/sparseassembler/
https://sourceforge.net/projects/sparseassembler/
[4]10x-assisted-3GSHybridAssembly:
MaZSetal.(2018)Hybridassemblyofultra-longNanoporereadsaugmentedwith10×-genomicscontigs:Demonstratedwithahumangenome.Genomics,vol.110,https://doi.org/10.1016/j.ygeno.2018.12.013
[5]HPTree:Reconstructingevolutionarytreesinparallelformassivesequences.BMCSystemBiology.
http://lab.malab.cn/soft/HPtree/contact.html
近期论文
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1.LiWendy&ZSMa(2019)FBAEcologicalGuild:TrioofFirmicutes-BacteroidetesAllianceagainstActinobacteriainHumanOralMicrobiome.(UnderReview)
2.LiWendy&ZSMa(2019)AtheoreticapproachtothemechanismofgutmicrobiometranslocationinSIV-infectedAsianmacaques.(UnderReview)
3.LiLianwei,WendyLi,QuanZou,ZSMa(2019)Networkanalysisofthehotspringmicrobiomesketchespossiblenichedifferentiationsamongecologicalguilds.(UnderReview)
4.LiLianwei&ZSMa(2019)Speciessortingandneutraltheoryanalysesrevealarchaealandbacterialcommunitiesareassembleddifferentlyinhotsprings.(UnderReview)
5.MaZS&WendyLi(2019)Howmanandwomanaredifferentintheirmicrobiome—Ecologicalandnetworkanalysesofthemicrogenderome.(UnderReview)
6.MaZS&LianweiLi(2019)Estimatingtheoptimumcoverageandqualityofampliconsequencing.(UnderRreview)
7.MaZS&LianweiLi(2019)Themicrobiometransmissionincomplementaryseminovaginalmicrobiomeisarandomwalkdrivenbyneutralprocess(UnderReview)
8.MaZS(2019)Assessingandinterpretingtheheterogeneityofhumangutmetagenome.(UnderReview)
9.MaZS(2019)Whythereisnotaconsistentdiversity-diseaserelationshipinhumanmicrobiome-associateddiseases(UnderReview)
10.MaZS,LWLiandYPZhang(2019)Individual-LevelSNPDiversityandSimilarityProfiles.https://arxiv.org/abs/1903.04512
11.MaZS(2019)Humanreproductivesystemmicrobiomesexhibitedsignificantlydifferentheterogeneityscalingwithgutmicrobiome,buttheintra-systemscalingisinvariant.https://www.biorxiv.org/content/10.1101/680355v1
12.MaZS&AMEllison(2019)Dominancenetworkanalysisprovidesanewframeworkforstudyingthediversity-stabilityrelationship.EcologicalMonographs.DOI:https://doi.org/10.1002/ecm.1358
13.MaZS,LiL,GotelliNJ(2019)Diversity-diseaserelationshipsandsharedspeciesanalysesforhumanmicrobiome-associateddiseases.TheISMEJournal.DOI:https://doi.org/10.1038/s41396-019-0395-y
14.LiLW&MaZS(2019)Comparativepowerlawanalysisforthespatialheterogeneityscalingofthehot-springandhumanmicrobiomes.MolecularEcology.DOI:http://dx.doi.org/10.1111/mec.15124
15.MaZS(2019)AnewDTAR(diversity–time–arearelationship)modeldemonstratedwiththeindoormicrobiome.JournalofBiogeography,https://doi.org/10.1111/jbi.13636
16.MaZS,LiLW,YeCX,PengMS,ZhangYP(2019)Hybridassemblyofultra-longNanoporereadsaugmentedwith10×-genomicscontigs:Demonstratedwithahumangenome.Genomics,vol.110,https://doi.org/10.1016/j.ygeno.2018.12.013
17.MaZS&AMEllison(2018)Aunifiedconceptofdominanceapplicableatbothcommunityandspeciesscale.Ecosphere,https://doi.org/10.1002/ecs2.2477.
18.MaZS(2018)Extendingspecies-arearelationships(SAR)todiversity-arearelationships(DAR),EcologyandEvolution,DOI:10.1002/ece3.4425
19.MaZS(2018)Diversitytime-periodanddiversity-time-arearelationshipsexemplifiedbythehumanmicrobiome.ScientificReports,8(1):7214.
20.MaZS(2018)SketchingthehumanmicrobiomebiogeographywithDAR(diversity-arearelationship)profiles.MicrobialEcology,vol.76,https://doi.org/10.1007/s00248-018-1245-6
21.MaZS,LiLW,LiW(2018)Assessingandinterpretingthewithin-Bodybiogeographyofhumanmicrobiomediversity.FrontiersinMicrobiology,9:1619.
22.MaZS,LiLW(2018)MeasuringmetagenomediversityandsimilaritywithHillnumbers.MolecularEcologyResources,https://doi.org/10.1111/1755-0998.12923
23.LiW,YuanY,XiaY,SunY,MiaoY,MaZS(2018)Across-scaleneutraltheoryapproachtotheinfluenceofobesityoncommunityassemblyofhumangutmicrobiome.FrontiersinMicrobiology,2018
24.SunY,LiLW,XiaY,LiW,WangK,WangL,MiaoY,MaZS(2018)ThegutmicrobiotaheterogeneityandassemblychangesassociatedwiththeIBD.ScientificReports.DOI:10.1038/s41598-018-37143-z
25.LiLW&MaZS(2018)GlobalmicrobiomediversityscalinginhotspringswithDAR(diversity-arearelationship)profiles.FrontiersinMicrobiology.DOI:https://doi.org/10.3389/fmicb.2019.00118
26.MaZS,LiLW(2018)Semenmicrobiomebiogeography:ananalysisbasedonaChinesepopulationstudy.FrontiersinMicrobiology.DOI:10.3389/fmicb.2018.03333.
27.MaZS,YeDD(2017)Trios—promisinginsilicobiomarkersfordifferentiatingtheeffectofdiseaseonthehumanmicrobiomenetwork.ScientificReports,7(1):13259.
28.MaZS(2017)TheP/N(Positive-to-NegativeLinks)ratioincomplexnetworks—apromisinginsilicobiomarkerfordetectingchangesoccurringinthehumanmicrobiome.MicrobialEcology,vol.75(4):DOI:10.1007/s00248-017-1079-7.
29.MaZS,LiL(2017)Quantifyingthehumanvaginalcommunitystatetypes(CSTs)withthespeciesspecificityindex.PeerJ,2017,5(6).DOI:10.7717/peerj.3366.
30.ChenHJ,PengS,DaiL,ZouQ,YiB,YangX,MaZS(2017)Oralmicrobialcommunityassemblyundertheinfluenceofperiodontitis.PLOSONE,12(8):e0182259.doi:10.1371/journal.pone.0182259.
31.DaiL,KouH,XiaY,WenX,MaZS(2017)Doescolorectalcancersignificantlyinfluencetheassemblyofgutmicrobialcommunities?.PeerJ,5(8):e3383.DOI:10.7717/peerj.3383.
32.WeiL,XingPW,SuR,ShiG,MaZS,ZouQ(2017)CPPred-RF:ASequence-basedpredictorforidentifyingcell-penetratingpeptidesandtheiruptakeefficiency.JournalofProteomeResearch,2017:acs.jproteome.7b00019.
33.ZouQ,WanS,ZengX,MaZS(2017)Reconstructingevolutionarytreesinparallelformassivesequences.BMCSystemsBiology,11(S6):100.DOI:10.1186/s12918-017-0476-3.
34.MaZS(2017)MeasuringmicrobiomediversityandsimilaritywithHillNumbers.Chapter8,in“Metagenomics”https://doi.org/10.1016/B978-0-08-102268-9.00008-2,Elsevier
35.YeCX&ZSMa(2016)Sparc:asparsity-basedconsensusalgorithmforlongerroneoussequencingreads.PeerJ.4:e2016;DOI10.7717/peerj.2016https://peerj.com/articles/2016/
36.YeCX,CHill,JRuan,ZSMa(2016)DBG2OLC:EfficientAssemblyofLargeGenomesUsingLongErroneousReadsoftheThirdGenerationSequencingTechnologies.http://www.nature.com/articles/srep31900
37.LiLW&MaZS(2016)TestingtheNeutralTheoryofBiodiversitywithHumanMicrobiomeDatasets.ScientificReports.6,ArticleNo.31448
38.MaZS,LWLi,WendyLi,JieLi,HJChen(2016)Integratednetwork-diversityanalysessuggestsuppressiveeffectofHodgkin’slymphomaandslightlyrelievingeffectofchemotherapyonhumanmilkmicrobiome.ScientificReports,vol.6,ArticleNumber28048,doi:10.1038/srep28048
39.WangY,WangR,LiY,MaZS*(2016)SexRatioElasticityInfluencestheSelectionofSexRatioStrategy.ScientificReports,2016,6(1):39807
40.MaZSetal(2016)ABriefReviewontheEcologicalNetworkAnalysiswithApplicationsintheEmergingMedicalEcology.pp7-41,In“HydrocarbonandLipidMicrobiologyProtocols,SpringerProtocolsHandbooks”.Editors:McGenityT.etal.Springer.
41.MaZSetal.(2015)Networkanalysissuggestsapotentially‘evil’allianceofopportunisticpathogensinhibitedbyacooperativenetworkinhumanmilkbacterialcommunities.ScientificReports5,Articlenumber:8275
42.MaZS(2015)Powerlawanalysisofthehumanmicrobiome.MolecularEcology,vol.24,DOI:10.1111/mec.13394.
43.MaZS(2015)Towardscomputationalmodelsofanimalcognition,anintroductionforcomputerscientists.CognitiveSystemsResearch33:42-69
44.MaZS(2015)Towardscomputationalmodelsofanimalcommunication,anintroductionforcomputerscientists.CognitiveSystemsResearch33:70-99
45.YeCX,HillC,RuanJ,MaZS*(2014).DBG2OLC:efficientassemblyoflargegenomesusingthecompressedoverlapgraph.Paper:http://adsabs.harvard.edu/cgi-bin/bib_query?arXiv:1410.2801Software:http://sites.google.com/site/dbg2olc/
46.LiH,YeDD,WangX,SettlesML,WangJ,ZhouL,DongP,MaZS*(2014)SoilbacterialcommunitiesofdifferentnaturalforesttypesinChina.PlantandSoil383.
47.GuanQ&MaZS*(2014).Ecologicalanalysisofthehumanmilkmicrobiome.ChineseScienceBulletin59(22):2205-2212.http://www.eurekalert.org/pub_releases/2014-09/scp-ahb090214.php
48.Ma,ZS,LiexunYang,RonaldP.Neilson,AndrewHess,RichardMillar(2014)ASurvivability-CenteredResearchAgendaforCloudComputingSupportedEmergencyResponseandManagementSystems.17pp.The35thIEEE-AIAAAerospaceConference(Aerospace2014),BigSky,Montana,USA,March7-15th,2014.doi:10.1109/AERO.2014.6836515
49.ZhangZG,GengJW,TangXD,FanH,XuJC,WenXJ,ZSMa*,P.Shi*(2014)Spatialheterogeneityandco-occurrencepatternsofhumanmucosalassociatedintestinalmicrobiota.TheISMEJournal,doi:10.1038/ismej.2013.185
50.Ma,ZS(2013)StochasticPopulations,PowerLaw,andFitnessAggregationinGeneticAlgorithms.FundamentaInformaticae,vol.122,pp173-206.
51.Ma,ZS(2013)Firstpassagetimeandfirstpassagepercolationmodelsforanalyzingnetworkresilienceandeffectivestrategiesinstrategicinformationwarfareresearch.I.J.InformationandComputerSecurity.5(4):334-358.
52.Ma,ZS(2012)ChaoticpopulationsinGeneticAlgorithms.AppliedSoftComputing,12(8):2409-2424.
53.Ma,ZS(2012)Aunifieddefinitionforreliability,survivabilityandresilienceinspiredbythehandicapprincipleandecologicalstability.I.J.ofCriticalInfrastructures,8(2):242-272.
54.Ma,ZS(2012)ANoteonExtendingTaylor’sPowerLawforCharacterizingHumanMicrobialCommunities:InspirationfromComparativeStudiesontheDistributionPatternsofInsectsandGalaxies,andasaCaseStudyforMedicalEcologyandPersonalizedMedicine.http://adsabs.harvard.edu/abs/2012arXiv1205.3504M
55.Ye,CX,ZSMa,CH.Cannon,MPopandDW.Yu.2012.Exploitingsparsenessindenovogenomeassembly.BMCBioinformatics,13(Suppl6):S1.
56.Gajer,P,RM.Brotman,GBai,JSakamoto,UMESchütte,XZhong,SSKKoenig,LFu,ZSMa,XZhou,ZAbdo,LJForneyandJRavel.(2012)TemporalDynamicsoftheHumanVaginalMicrobiota.ScienceTranslationalMedicine.4:(132):132ra52.
57.MaZSetal(2012)ABird'sEyeViewofMicrobialCommunityDynamics.In“MicrobialEcologicalTheory:CurrentPerspectives.”Editors:LAOgilvieandPRHirsch.CaisterAcademicPress.
58.Ma,ZS&AWKrings(2011)DynamichybridfaultmodelingandextendedevolutionaryGametheoryforreliability,survivabilityandfaulttoleranceanalyses.IEEETransactionsonReliability.vol.60(1):180-196.
59.Ma,ZS(2011)Ecological‘theater’forevolutionarycomputing‘play’:someinsightsfrompopulationecologyandevolutionaryecology.I.JournalofBio-InspiredComputing4(1):31-55.
60.Ma,ZS(2011)Didwemisssomeevidenceofchaosinlaboratoryinsectpopulations?PopulationEcology,53:405–412.
61.Ma,ZS(2011)Frailtymodelingforriskanalysisinnetworksecurityandsurvivability.I.J.ComputerandInformationSecurity,4:276-294.
62.Ma,ZSetal(2011).Insectnavigationandcommunicationinflightandmigration:apotentialmodelforjoiningandcollisionavoidanceinMAVs(Micro-AerialVehicle)andmobilerobotsfleetcontrol.Proc.ofthe32ndIEEE-AIAAAerospaceConference.14pp,BigSky,Montana,USA.
63.Ye,CX.,C.Cannon,ZSMa*,DW.Yu,andM.Pop*(2011)SparseAssembler2:Sparsek-merGraphforMemoryEfficientGenomeAssembly.http://adsabs.harvard.edu/cgi-bin/bib_query?arXiv:1108.3556
64.Ma,ZS,etal(2011)Hasthecyberwarfarethreatbeenoverstated?Acheaptalkgame-theoreticperspectiveontheGoogle-hackingclaim.The7thCyberspaceSciencesandInformationIntelligenceResearchWorkshop,7thCSIIRW11.October14-16,2011.OakRidgeNationalLab,OakRidge,USA.
65.Ma,ZSetal(2011)Caringabouttreesintheforest:incorporatingfrailtyinriskanalysisforpersonalizedmedicine.PersonalizedMedicine,8(6):681-688
66.Ma,ZS(2010)IsStrategicInformationWarfareReallyAsymmetric?—aNewPerspectivefromtheHandicapPrinciple.JournalofInformationWarfare,9(3):51-61.
67.Ma,ZS(2010)SurvivalAnalysisApproachtoLifeTableAnalysisandHypothesisTestingforRussianWheatAphidPopulations.BulletinofEntomologicalResearch.vol.100(3):315-324
68.Ma,ZSetal(2010)LogicsinAnimalCognition:AreTheyImportanttoBrainComputerInterfaces(BCI)andFutureSpaceMissions?Proc.31stIEEE-AIAAAerospaceConference2010,8pp.BigSky,Montana,USA.
69.MaZS(2010)Anintegratedapproachtonetworkintrusiondetectionwithblockclusteringanalysis,generalisedlogisticregressionandlineardiscriminantanalysis.I.J.InformationandComputerSecurity.DOI:http://dx.doi.org/10.1504/IJICS.2010.03186
70.MaZS(2010)ANewExtendedEvolutionaryGameTheoryApproachtoStrategicInformationWarfareResearch.J.ofInformationWarfare,vol.8(2).
71.MaZS(2010)TowardsaPopulationDynamicsTheoryforEvolutionaryComputing:LearningfromBiologicalPopulationDynamicsinNature.SpringerLectureNotesinArtificialIntelligence,vol.5855,pp195-205
72.MaZS(2010)TowardsanExtendedEvolutionaryGameTheorywithSurvivalAnalysisandAgreementAlgorithmsforModelingUncertainty,Vulnerability,andDeception.SpringerLectureNotesinArtificialIntelligence,vol.5855,pp608-618
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