Featured Publications
GEM-NET: Lessons in Multi-Institution Teamwork Using Collaboration Software
Gaffney SG, Ad O, Smaga S, Schepartz A, Townsend JP. GEM-NET: Lessons in Multi-Institution Teamwork Using Collaboration Software. ACS Central Science 2019, 5: 1159-1169. PMID: 31404233, PMCID: PMC6661976, DOI: 10.1021/acscentsci.9b00111.Peer-Reviewed Original ResearchSoftware infrastructureMulti-institution teamOpen source codeCollaboration softwareCode editingData sharingSource codeTask managementCustom applicationsCollaborative documentInfrastructureCommunicationMultiple fieldsInternal communicationUsersUniversity campusSchedulingSecuritySharingSoftwareTeamCodeImplementationDocumentsGoal
2011
Getting the Most Out of Your Fungal Microarray Data: Two Cost- and Time-Effective Methods
Mathioni SM, Beló A, Townsend JP, Donofrio NM. Getting the Most Out of Your Fungal Microarray Data: Two Cost- and Time-Effective Methods. Methods In Molecular Biology 2011, 722: 61-77. PMID: 21590413, DOI: 10.1007/978-1-61779-040-9_5.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsExpensive softwareData generationMultiple platformsGenomic data generationEfficient waySuch dataPossible informationGenome sequencing technologiesKind of analysisData analysisFungal dataUsersDifferent environmentsMicroarray dataBioinformaticistsCostExperimental costSoftwareProtocolBottleneckPlatformTaskTechnologyDataAcademia
2009
The filamentous fungal gene expression database (FFGED)
Zhang Z, Townsend JP. The filamentous fungal gene expression database (FFGED). Fungal Genetics And Biology 2009, 47: 199-204. PMID: 20025988, PMCID: PMC2822089, DOI: 10.1016/j.fgb.2009.12.001.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsChromosome MappingComputational BiologyComputer GraphicsDatabase Management SystemsDatabases, GeneticGene ExpressionGene Expression ProfilingGene Expression Regulation, FungalGenes, FungalGenome, FungalInternetModels, GeneticModels, StatisticalOligonucleotide Array Sequence AnalysisSaccharomyces cerevisiaeSequence AlignmentSoftwareSystems IntegrationUser-Computer InterfaceConceptsEfficient web interfaceExpression databaseUser-friendly managementCollection of toolsGene expression databaseDifferent usersData sharingWeb interfaceCollaborative platformExperimental metadataFree databaseRaw dataData submissionUsersMultiple experimentsGene expression dataSharingDatabaseEssential informationAjaxMetadataExpression dataDifferent experimentsRetrievalRelated experiments
2008
Bringing Web 2.0 to bioinformatics
Zhang Z, Cheung KH, Townsend JP. Bringing Web 2.0 to bioinformatics. Briefings In Bioinformatics 2008, 10: 1-10. PMID: 18842678, PMCID: PMC2638627, DOI: 10.1093/bib/bbn041.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsData exchangeWeb 2.0Data integrationHeterogeneous data sourcesHarness collective intelligenceSharing of dataWeb 2.0 technologiesIntegration of dataMajor bioinformatics challengeWeb servicesData warehousingData creationData sharingCollaborative platformCollective intelligenceAutomatic analysisCommunication modelInformation technologyBioinformatics researchUsersData sourcesSharingMultiple sourcesBioinformatics challengesPlatform