马占山，研究员，博导，计算生物与医学生态学学科负责人。美国爱达荷大学计算机科学(2008年)和昆虫学(1997年)双博士;计算机科学和计算生物学研究科学家。具有在美国硅谷等地近10年的涵盖电子、网络、软件、信息安全领域的计算机高级工程师经历,并曾担任人类微生物菌群研究计划(HumanMicrobiomeProject)主要研发科学家;受邀为英国

“Facultyof1000Biology&Medicine”撰写学术评论(2008-2016)。2011年分别入选云南省高端科技人才和海外高层次人才;2015年入选云岭产业领军人才。在计算机科学、工程数学、计算智能与人工智能、昆虫学、生态学、生物信息学、人类微生物群系、宏基因组等领域的重要期刊发表论文近百篇；合作研发出大型二、三代基因测序软件、超大规模进化树构建软件（DBG2OLC，SPARC，SparseAssembler,HPTree)，并申请10多项发明专利。在计算科学领域（非生物学领域）论文可见DBLP计算机科学数据库和MathSciNet数学网数据库：http://dblp.uni-trier.de/pers/hd/m/Ma:Zhanshan_=Sam=

http://genealogy.math.ndsu.nodak.edu/id.php?id=132255

承担科研项目

(1)国家自然科学基金(信息科学部)：生态“舞台”与进化计算“演出”(2012－2015年)

(2)国家自然科学基金(管理科学部)：网络系统可存活性理论的扩展及实证研究(2015－2018年)

(3)国家自科学基金(生命科学部)：基于宏遗传技术的生物多样性检测法(2012－2015年)

(4)云南省引进高端科技人才项目:面向计算生物信息学的GP-GPU计算技术（2012-2016）

(5)海外高层次人才引进计划(2012-2015年)

(6)云岭产业技术领军人才基金（2015-2019年）

(7)国际合作项目：基因大数据信息技术及其应用（2017-2019年）

(8)国家自科学基金(生命科学部):菌群多样性与疾病关系的生态机制及病因研究（2020-2023）

【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

Faculty1000ofBiologyandMedicine,UK(2008-2016)

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