360
Views
4
CrossRef citations to date
0
Altmetric
Review

Parallel computing in genomic research: advances and applications

&
Pages 23-35 | Published online: 13 Nov 2015

References

  • PevsnerJBioinformatics and Functional GenomicsHoboken, NJJohn Wiley & Sons, Inc2009
  • DaiLGaoXGuoYXiaoJZhangZBioinformatics clouds for big data manipulationBiol Direct2012714323190475
  • MarxVBiology: the big challenges of big dataNature2013498745325526023765498
  • MillerWMakovaKDNekrutenkoAHardisonRCComparative genomicsAnnu Rev Genomics Hum Genet200451155615485342
  • KoboldtDCSteinbergKMLarsonDEWilsonRKMardisERThe next-generation sequencing revolution and its impact on genomicsCell20131551273824074859
  • WallDPKudtarkarPFusaroVAPivovarovRPatilPTonellatoPJCloud computing for comparative genomicsBMC Bioinformatics201011125920482786
  • ArmbrustMFoxAGriffithRA view of cloud computingCommun ACM20105345058
  • BuyyaRBrobergJGoscinskiAMCloud Computing: Principles and Paradigms1st edWileyNew Jersey, NJ2011
  • CarpenterBGetovVJuddGSkjellumAFoxGMPJ: MPI-like message passing for JavaConcurr Comput2000121110191038
  • AilamakiAIoannidisYELivnyMScientific workflow management by database managementProceedings of the Tenth International Conference on Scientific and Statistical Database ManagementCapri, Italy1998Washington, DCIEEE Computer Society1998190199
  • AbouelhodaMIssaSGhanemMTavaxy: integrating Taverna and Galaxy workflows with cloud computing supportBMC Bioinformatics2012137722559942
  • LeeKPatonNWSakellariouRDeelmanEFernandesAAAMehtaGAdaptive workflow processing and execution in PegasusProceedings of the 3rd International Conference on Grid and Pervasive ComputingKunming, China2008Washington, DCIEEE Computer Society199899106
  • WozniakJMArmstrongTGWildeMKatzDSLuskEFosterITSwift/T: large-scale application composition via distributed-memory dataflow processingProceedings of the 13th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid)Washington, DCIEEE Computer Society201395102
  • OliveiraDOgasawaraEBaiãoFMattosoMSciCumulus: a lightweight cloud middleware to explore many task computing paradigm in scientific workflowsProceedings of the 3rd International Conference on Cloud ComputingWashington, DCIEEE Computer Society2010378385
  • KitchenhamBBreretonPTurnerMThe impact of limited search procedures for systematic literature reviews: a participant-observer case studyProceedings of the 2009 3rd International Symposium on Empirical Software Engineering and MeasurementLake Buena Vista, FL, USA15–16 October 2009Washington, DCIEEE Computer Society2009336345
  • UrrútiaGBonfillXDeclaración PRISMA: una propuesta para mejorar la publicación de revisiones sistemáticas y metaanálisisMed Clín201013511507511
  • BernardesJSDávilaAMCostaVSZaveruchaGImproving model construction of profile HMMs for remote homology detection through structural alignmentBMC Bioinformatics20078143517999748
  • WuMScottAJPhylogenomic analysis of bacterial and archaeal sequences with AMPHORA2Bioinformatics20122871033103422332237
  • AhmedMAhmadIKhanSUA comparative analysis of parallel computing approaches for genome assemblyInterdiscip Sci201131576321369889
  • NiemenmaaMKallioASchumacherAKlemelaPKorpelainenEHeljankoKHadoop-BAM: directly manipulating next generation sequencing data in the cloudBioinformatics201228687687722302568
  • BlomJAlbaumSPDoppmeierDEDGAR: a software framework for the comparative analysis of prokaryotic genomesBMC Bioinformatics200910115419457249
  • LordELeclercqMBocADialloABMakarenkovVArmadillo 1.1: an original workflow platform for designing and conducting phylogenetic analysis and simulationsPLoS One201271e2990322253821
  • SeverinJBealKVilellaAJeHive: an artificial intelligence workflow system for genomic analysisBMC Bioinformatics201011124020459813
  • HuberWCareyVJGentlemanROrchestrating high-throughput genomic analysis with BioconductorNat Methods201512211512125633503
  • KleftogiannisDKalnisPBajicVBComparing memory-efficient genome assemblers on stand-alone and cloud infrastructuresPLoS One201389e7550524086547
  • NefedovAVSadygovRGA parallel method for enumerating amino acid compositions and masses of all theoretical peptidesBMC Bioinformatics201112143222059886
  • HunterAAMacgregorABSzaboTOWellingtonCABellgardMIYabi: an online research environment for grid, high performance and cloud computingSource Code Biol Med201271122333270
  • GurtowskiJSchatzMCLangmeadBGenotyping in the cloud with crossbowBaxevanisADPetskoGASteinLDStormoGDCurrent Protocols in BioinformaticsHoboken, NJJohn Wiley & Sons, Inc2012
  • ZhaoSPrengerKSmithLRainbow: a tool for large-scale whole-genome sequencing data analysis using cloud computingBMC Genomics20131442523802613
  • PrinsPBelhachemiDMöllerSSmantGScalable computing for evolutionary genomicsMethods Mol Biol201285652954522399474
  • DongSLiuPCaoYDuZGrid computing methodology for protein structure prediction and analysisChenGPanYGuoMLuJParallel and Distributed Processing and Applications – ISPA 2005 WorkshopsBerlinSpringer2005257266
  • HeathAPGreenwayMPowellRBionimbus: a cloud for managing, analyzing and sharing large genomics datasetsJ Am Med Inform Assoc201421696997524464852
  • SinghAChenCLiuWMitchellWSchmidtBA hybrid computational grid architecture for comparative genomicsIEEE Trans Inf Technol Biomed200812221822518348951
  • MoustafaABhattacharyaDAllenAEiTree: a high-throughput phy-logenomic pipeline5th Cairo International Biomedical Engineering Conference (CIBEC)Cairo, Egypt16 December 2010Washington, DCIEEE Computer Society2010103107
  • El-KaliobyMAbouelhodaMKrügerJPersonalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC packageBMC Bioinformatics201213Suppl 17S2223281941
  • ReidJGCarrollAVeeraraghavanNLaunching genomics into the cloud: deployment of Mercury, a next generation sequence analysis pipelineBMC Bioinformatics20141513024475911
  • MinevichGParkDSBlankenbergDPooleRJHobertOCloudMap: a cloud-based pipeline for analysis of mutant genome sequencesGenetics201219241249126923051646
  • KrampisKBoothTChapmanBCloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics communityBMC Bioinformatics20121314222429538
  • OcañaKACSde OliveiraDDiasJOgasawaraEMattosoMDesigning a parallel cloud based comparative genomics workflow to improve phylogenetic analysesFuture Gener Comput Syst201329822052219
  • OcañaKACSde OliveiraDOgasawaraEDávilaAMRLimaAABMattosoMSciPhy: a cloud-based workflow for phylogenetic analysis of drug targets in protozoan genomesde SouzaONTellesGPPalakalMAdvances in Bioinformatics and Computational BiologyBerlinSpringer20116670
  • OliveiraDOcañaKACSOgasawaraEPerformance evaluation of parallel strategies in public clouds: a study with phylogenomic workflowsFuture Gener Comput Syst201329718161825
  • OcañaKACSde OliveiraDHortaFDiasJOgasawaraEMattosoMExploring molecular evolution reconstruction using a parallel cloud based scientific workflowde SoutoMCKannMGAdvances in Bioinformatics and Computational BiologyBerlinSpringer2012179191
  • OcañaKBenzaSOliveiraDDiasJMattosoMExploring large scale receptor-ligand pairs in molecular docking workflows in HPC cloudsIEEE 28th International Parallel and Distributed Processing Symposium Workshops 13th IEEE International Workshop on High Performance Computational Biology (HiComb 2014)Phoenix, AZ, USA19–23 May 2014Washington, DCIEEE Computer Society2014536545
  • OcañaKACSOliveiraDSilvaVBenzaSMattosoMLQExploiting the parallel execution of homology workflow alternatives in HPC compute cloudsToumaniFPerniciBGrigoriDService-Oriented Computing – ICSOC 2014 WorkshopsBerlinSpringer2014336350
  • DeelmanEGannonDShieldsMTaylorIWorkflows and e-Science: an overview of workflow system features and capabilitiesFuture Gener Comput Syst2009255528540
  • BayucanAHendersonRLJonesJPPortable Batch System Administration GuideMountain View, CAVeridian Systems2000
  • GentzschWSun Grid Engine: towards creating a compute power gridProceedings of First IEEE/ACM International Symposium on Cluster Computing and the GridBrisbane, QLD15–18 May 2001Washington, DCIEEE Computer Society20013536
  • Apache Software FoundationHadoopForest Hill, MDApache Software Foundation2009
  • DeanJGhemawatSMapReduce: simplified data processing on large clustersProceedings of the 6th Conference on Symposium on Opearting Systems Design and Implementation6Berkeley, CAUSENIX Association20041010
  • DingMZhengLLuYLiLGuoSGuoMMore convenient more overhead: the performance evaluation of Hadoop streamingProceedings of the 2011 ACM Symposium on Research in Applied ComputationNew York, NYACM2011307313