Gregory R. Granthttps://orcid.org/0000-0002-0139-7658https://www.wikidata.org/entity/Q41045552https://id.loc.gov/authorities/names/n00006983https://d-nb.info/gnd/17347389XThomas G. BrooksNicholas F. LahensAntonijo MrcelaDimitra SarantopoulouSoumyashant NayakAmruta NaikShaon SenguptaPeter S. ChoiGregory R. GrantBEERS2: RNA-Seq simulation through high fidelity in silico modeling.202425Briefings Bioinform.3https://doi.org/10.1093/bib/bbae164db/journals/bib/bib25.html#BrooksLMSNNSCG24Dimitra SarantopoulouThomas G. BrooksSoumyashant NayakAntonijo MrcelaNicholas F. LahensGregory R. GrantComparative evaluation of full-length isoform quantification from RNA-Seq.266202122BMC Bioinform.1https://doi.org/10.1186/s12859-021-04198-1db/journals/bmcbi/bmcbi22.html#SarantopoulouBN21Scott S. NortonJorge Vaquero-GarciaNicholas F. LahensGregory R. GrantYoseph BarashOutlier detection for improved differential splicing quantification from RNA-Seq experiments with replicates.1488-1497201834Bioinform.9https://doi.org/10.1093/bioinformatics/btx790https://www.wikidata.org/entity/Q47252957db/journals/bioinformatics/bioinformatics34.html#NortonVLGB18Qiwen HuEun Ji KimJian FengGregory R. GrantElizabeth A. HellerHistone posttranslational modifications predict specific alternative exon subtypes in mammalian brain.201713PLoS Comput. Biol.6https://doi.org/10.1371/journal.pcbi.1005602https://www.wikidata.org/entity/Q36400544db/journals/ploscb/ploscb13.html#HuKFGH17Katharina E. HayerAngel D. PizarroNicholas F. LahensJohn B. HogeneschGregory R. GrantBenchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data.3938-3945201531Bioinform.24https://doi.org/10.1093/bioinformatics/btv488https://www.wikidata.org/entity/Q30991504db/journals/bioinformatics/bioinformatics31.html#HayerPLHG15Cristina AurrecoecheaAna BarretoJohn BrestelliBrian P. BrunkShon CadeRyan DohertySteve FischerBindu GajriaXin Gao 0002Alan R. GingleGregory R. GrantOmar S. HarbMark HeigesSufen HuJohn IodiceJessica C. KissingerEileen T. KraemerWei Li 0031Deborah F. PinneyBrian PittsDavid S. RoosGanesh SrinivasamoorthyChristian J. Stoeckert Jr.Haiming WangSusanne WarrenfeltzEuPathDB: The Eukaryotic Pathogen database.684-691201341Nucleic Acids Res.Database-Issuehttps://doi.org/10.1093/nar/gks1113https://www.wikidata.org/entity/Q34313331db/journals/nar/nar41.html#AurrecoecheaBBBCDFGGGGHHHIKKLPPRSSWW13Gregory R. GrantMichael H. FarkasAngel D. PizarroNicholas F. LahensJonathan SchugBrian P. BrunkChristian J. Stoeckert Jr.John B. HogeneschEric A. PierceComparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM).2518-2528201127Bioinform.18https://doi.org/10.1093/bioinformatics/btr427https://www.wikidata.org/entity/Q33966703db/journals/bioinformatics/bioinformatics27.html#GrantFPLSBSHP11Cristina AurrecoecheaAna BarretoJohn BrestelliBrian P. BrunkElisabet V. CalerSteve FischerBindu GajriaXin Gao 0002Alan R. GingleGregory R. GrantOmar S. HarbMark HeigesJohn IodiceJessica C. KissingerEileen T. KraemerWei Li 0031Vishal NayakCary PenningtonDeborah F. PinneyBrian PittsDavid S. RoosGanesh SrinivasamoorthyChristian J. Stoeckert Jr.Charles TreatmanHaiming WangAmoebaDB and MicrosporidiaDB: functional genomic resources for Amoebozoa and Microsporidia species.612-619201139Nucleic Acids Res.Database-Issuehttps://doi.org/10.1093/nar/gkq1006https://www.wikidata.org/entity/Q24616782db/journals/nar/nar39.html#AurrecoecheaBBBCFGGGGHHIKKLNPPPRSSTW11Cristina AurrecoecheaJohn BrestelliBrian P. BrunkSteve FischerBindu GajriaXin Gao 0002Alan R. GingleGregory R. GrantOmar S. HarbMark HeigesFrank InnamoratoJohn IodiceJessica C. KissingerEileen T. KraemerWei Li 0031John A. Miller 0001Vishal NayakCary PenningtonDeborah F. PinneyDavid S. RoosChris RossGanesh SrinivasamoorthyChristian J. Stoeckert Jr.Ryan ThibodeauCharles TreatmanHaiming WangEuPathDB: a portal to eukaryotic pathogen databases.415-419201038Nucleic Acids Res.Database-Issuehttps://doi.org/10.1093/nar/gkp941https://www.wikidata.org/entity/Q33600902db/journals/nar/nar38.html#AurrecoecheaBBFGGGGHHIIKKLMNPPRRSSTTW10Martin AslettCristina AurrecoecheaMatthew BerrimanJohn BrestelliBrian P. BrunkMark CarringtonDaniel P. DepledgeSteve FischerBindu GajriaXin Gao 0002Malcolm J. GardnerAlan R. GingleGregory R. GrantOmar S. HarbMark HeigesChristiane Hertz-FowlerRobin HoustonFrank InnamoratoJohn IodiceJessica C. KissingerEileen T. KraemerWei Li 0031Flora J. LoganJohn A. Miller 0001Siddhartha MitraPeter J. MylerVishal NayakCary PenningtonIsabelle PhanDeborah F. PinneyGowthaman RamasamyMatthew B. RogersDavid S. RoosChris RossDhileep SivamDeborah F. SmithGanesh SrinivasamoorthyChristian J. Stoeckert Jr.Sandhya SubramanianRyan ThibodeauAdrian TiveyCharles TreatmanGiles VelardeHaiming WangTriTrypDB: a functional genomic resource for the Trypanosomatidae.457-462201038Nucleic Acids Res.Database-Issuehttps://doi.org/10.1093/nar/gkp851https://www.wikidata.org/entity/Q33601045db/journals/nar/nar38.html#AslettAB10Ruth HellerElisabetta ManduchiGregory R. GrantWarren J. EwensA flexible two-stage procedure for identifying gene sets that are differentially expressed.1019-1025200925Bioinform.8https://doi.org/10.1093/bioinformatics/btp076https://www.wikidata.org/entity/Q83338108db/journals/bioinformatics/bioinformatics25.html#HellerMGE09Cristina AurrecoecheaJohn BrestelliBrian P. BrunkJane M. CarltonJennifer DommerSteve FischerBindu GajriaXin Gao 0002Alan R. GingleGregory R. GrantOmar S. HarbMark HeigesFrank InnamoratoJohn IodiceJessica C. KissingerEileen T. KraemerWei Li 0031John A. Miller 0001Hilary G. MorrisonVishal NayakCary PenningtonDeborah F. PinneyDavid S. RoosChris RossChristian J. Stoeckert Jr.Steven SullivanCharles TreatmanHaiming WangGiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis.526-530200937Nucleic Acids Res.Database-Issuehttps://doi.org/10.1093/nar/gkn631https://www.wikidata.org/entity/Q24656241db/journals/nar/nar37.html#AurrecoecheaBBCDFGGGGHHIIKKLMMNPPRRSSTW09Cristina AurrecoecheaJohn BrestelliBrian P. BrunkJennifer DommerSteve FischerBindu GajriaXin Gao 0002Alan R. GingleGregory R. GrantOmar S. HarbMark HeigesFrank InnamoratoJohn IodiceJessica C. KissingerEileen T. KraemerWei Li 0031John A. Miller 0001Vishal NayakCary PenningtonDeborah F. PinneyDavid S. RoosChris RossChristian J. Stoeckert Jr.Charles TreatmanHaiming WangPlasmoDB: a functional genomic database for malaria parasites.539-543200937Nucleic Acids Res.Database-Issuehttps://doi.org/10.1093/nar/gkn814https://www.wikidata.org/entity/Q29618004db/journals/nar/nar37.html#AurrecoecheaBBDFGGGGHHIIKKLMNPPRRSTW09Gregory R. GrantJunmin LiuChristian J. Stoeckert Jr.A practical false discovery rate approach to identifying patterns of differential expression in microarray data.2684-2690200521Bioinform.11https://doi.org/10.1093/bioinformatics/bti407https://www.wikidata.org/entity/Q30986006db/journals/bioinformatics/bioinformatics21.html#GrantLS05Elisabetta ManduchiGregory R. GrantH. HeJunmin LiuMatthew D. MailmanAngel D. PizarroPatricia L. WhetzelChristian J. Stoeckert Jr.RAD and the RAD Study-Annotator: an approach to collection, organization and exchange of all relevant information for high-throughput gene expression studies.200420Bioinform.4https://doi.org/10.1093/bioinformatics/btg428https://www.wikidata.org/entity/Q38462894db/journals/bioinformatics/bioinformatics20.html#ManduchiGHLMPWS04452-459Amit BahlBrian P. BrunkJonathan CrabtreeMartin J. FraunholzBindu GajriaGregory R. GrantHagai GinsburgDinesh GuptaJessica C. KissingerPhilip LaboLi LiMatthew D. MailmanArthur J. MilgramDavid S. PearsonDavid S. RoosJonathan SchugChristian J. Stoeckert Jr.Patricia L. WhetzelPlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data.212-215200331Nucleic Acids Res.1db/journals/nar/nar31.html#BahlBCFGGGGKLLMMPRSSW03https://doi.org/10.1093/nar/gkg081https://www.wikidata.org/entity/Q30760703Amit BahlBrian P. BrunkRoss L. CoppelJonathan CrabtreeSharon J. DiskinMartin J. FraunholzGregory R. GrantDinesh GuptaRobert L. HuestisJessica C. KissingerPhilip LaboLi LiShannon K. McWeeneyArthur J. MilgramDavid S. RoosJonathan SchugChristian J. Stoeckert Jr.PlasmoDB: the Plasmodium genome resource. An integrated database providing tools for accessing, analyzing and mapping expression and sequence data (both finished and unfinished).87-90200230Nucleic Acids Res.1db/journals/nar/nar30.html#BahlBCCDFGGHKLLMMRSS03https://doi.org/10.1093/nar/30.1.87https://www.wikidata.org/entity/Q30667264Elisabetta ManduchiGregory R. GrantSteven E. McKenzieG. Christian OvertonSaul SurreyChristian J. Stoeckert Jr.Generation of patterns from gene expression data by assigning confidence to differentially expressed genes.685-698200016Bioinform.8db/journals/bioinformatics/bioinformatics16.html#ManduchiGMOSSS00https://doi.org/10.1093/bioinformatics/16.8.685https://www.wikidata.org/entity/Q30620367Gregory R. GrantBioinformatics - The Machine Learning Approach.139-141200024Comput. Chem.1https://doi.org/10.1016/S0097-8485(00)80015-7db/journals/candc/candc24.html#Grant00Gregory R. GrantR. S. SpielmanElisabetta ManduchiVivian G. CheungWarren J. EwensSignificance testing for genomic mismatch scanning.182-1871999conf/recomb/1999RECOMBhttps://doi.org/10.1145/299432.299482db/conf/recomb/recomb1999.html#GrantSMCE99Martin AslettCristina AurrecoecheaAmit BahlYoseph BarashAna BarretoMatthew BerrimanJohn BrestelliThomas G. BrooksBrian P. BrunkShon CadeElisabet V. CalerJane M. CarltonMark CarringtonVivian G. CheungPeter S. ChoiRoss L. CoppelJonathan CrabtreeDaniel P. DepledgeSharon J. DiskinRyan DohertyJennifer DommerWarren J. EwensMichael H. FarkasJian FengSteve FischerMartin J. FraunholzBindu GajriaXin Gao 0002Malcolm J. GardnerAlan R. GingleHagai GinsburgDinesh GuptaOmar S. HarbKatharina HayerKatharina E. HayerH. HeMark HeigesElizabeth A. HellerRuth HellerChristiane Hertz-FowlerJohn B. HogeneschRobin HoustonQiwen HuSufen HuRobert L. HuestisFrank InnamoratoJohn IodiceEun Ji KimJessica C. KissingerEileen T. KraemerPhilip LaboNicholas F. LahensLi LiWei Li 0031Junmin LiuFlora J. Logan-KlumplerFlora J. LoganMatthew D. MailmanElisabetta ManduchiSteven E. McKenzieShannon K. McWeeneyArthur J. MilgramJohn A. Miller 0001Siddhartha MitraHilary G. MorrisonAntonijo MrcelaPeter J. MylerAmruta NaikSoumyashant NayakVishal NayakScott S. NortonG. Christian OvertonDavid S. PearsonCary PenningtonIsabelle PhanEric A. PierceDeborah F. PinneyBrian PittsAngel D. PizarroGowthaman RamasamyMatthew B. RogersDavid S. RoosChris RossDimitra SarantopoulouJonathan SchugShaon SenguptaDhileep SivamDeborah F. SmithR. S. SpielmanGanesh SrinivasamoorthyChristian J. Stoeckert Jr.Sandhya SubramanianSteven SullivanSaul SurreyRyan ThibodeauAdrian TiveyCharles TreatmanJorge Vaquero-GarciaGiles VelardeHaiming WangSusanne WarrenfeltzPatricia L. Whetzel