2018
Genomic Comparison Among Global Isolates of L. interrogans Serovars Copenhageni and Icterohaemorrhagiae Identified Natural Genetic Variation Caused by an Indel
Santos LA, Adhikarla H, Yan X, Wang Z, Fouts DE, Vinetz JM, Alcantara LCJ, Hartskeerl RA, Goris MGA, Picardeau M, Reis MG, Townsend JP, Zhao H, Ko AI, Wunder EA. Genomic Comparison Among Global Isolates of L. interrogans Serovars Copenhageni and Icterohaemorrhagiae Identified Natural Genetic Variation Caused by an Indel. Frontiers In Cellular And Infection Microbiology 2018, 8: 193. PMID: 29971217, PMCID: PMC6018220, DOI: 10.3389/fcimb.2018.00193.Peer-Reviewed Original ResearchConceptsSerovar CopenhageniPublic health relevanceSevere casesSerogroup IcterohaemorrhagiaeSerovar IcterohaemorrhagiaeWorldwide zoonosisHealth relevanceIcterohaemorrhagiaeCopenhageniVirulent strainHigh discriminatory powerSerovarsGlobal isolatesFrameshift mutationDiscriminatory powerFirst studyPathogenic speciesIsolates
2014
An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
Brownstein CA, Beggs AH, Homer N, Merriman B, Yu TW, Flannery KC, DeChene ET, Towne MC, Savage SK, Price EN, Holm IA, Luquette LJ, Lyon E, Majzoub J, Neupert P, McCallie Jr D, Szolovits P, Willard HF, Mendelsohn NJ, Temme R, Finkel RS, Yum SW, Medne L, Sunyaev SR, Adzhubey I, Cassa CA, de Bakker P, Duzkale H, Dworzyński P, Fairbrother W, Francioli L, Funke BH, Giovanni MA, Handsaker RE, Lage K, Lebo MS, Lek M, Leshchiner I, MacArthur DG, McLaughlin HM, Murray MF, Pers TH, Polak PP, Raychaudhuri S, Rehm HL, Soemedi R, Stitziel NO, Vestecka S, Supper J, Gugenmus C, Klocke B, Hahn A, Schubach M, Menzel M, Biskup S, Freisinger P, Deng M, Braun M, Perner S, Smith R, Andorf JL, Huang J, Ryckman K, Sheffield VC, Stone EM, Bair T, Black-Ziegelbein EA, Braun TA, Darbro B, DeLuca AP, Kolbe DL, Scheetz TE, Shearer AE, Sompallae R, Wang K, Bassuk AG, Edens E, Mathews K, Moore SA, Shchelochkov OA, Trapane P, Bossler A, Campbell CA, Heusel JW, Kwitek A, Maga T, Panzer K, Wassink T, Van Daele D, Azaiez H, Booth K, Meyer N, Segal MM, Williams MS, Tromp G, White P, Corsmeier D, Fitzgerald-Butt S, Herman G, Lamb-Thrush D, McBride KL, Newsom D, Pierson CR, Rakowsky AT, Maver A, Lovrečić L, Palandačić A, Peterlin B, Torkamani A, Wedell A, Huss M, Alexeyenko A, Lindvall JM, Magnusson M, Nilsson D, Stranneheim H, Taylan F, Gilissen C, Hoischen A, van Bon B, Yntema H, Nelen M, Zhang W, Sager J, Zhang L, Blair K, Kural D, Cariaso M, Lennon GG, Javed A, Agrawal S, Ng PC, Sandhu KS, Krishna S, Veeramachaneni V, Isakov O, Halperin E, Friedman E, Shomron N, Glusman G, Roach JC, Caballero J, Cox HC, Mauldin D, Ament SA, Rowen L, Richards DR, Lucas F, Gonzalez-Garay ML, Caskey CT, Bai Y, Huang Y, Fang F, Zhang Y, Wang Z, Barrera J, Garcia-Lobo JM, González-Lamuño D, Llorca J, Rodriguez MC, Varela I, Reese MG, De La Vega FM, Kiruluta E, Cargill M, Hart RK, Sorenson JM, Lyon GJ, Stevenson DA, Bray BE, Moore BM, Eilbeck K, Yandell M, Zhao H, Hou L, Chen X, Yan X, Chen M, Li C, Yang C, Gunel M, Li P, Kong Y, Alexander AC, Albertyn ZI, Boycott KM, Bulman DE, Gordon P, Innes AM, Knoppers BM, Majewski J, Marshall CR, Parboosingh JS, Sawyer SL, Samuels ME, Schwartzentruber J, Kohane IS, Margulies DM. An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge. Genome Biology 2014, 15: r53. PMID: 24667040, PMCID: PMC4073084, DOI: 10.1186/gb-2014-15-3-r53.Peer-Reviewed Original Research
2011
On optimal pooling designs to identify rare variants through massive resequencing
Lee JS, Choi M, Yan X, Lifton RP, Zhao H. On optimal pooling designs to identify rare variants through massive resequencing. Genetic Epidemiology 2011, 35: 139-147. PMID: 21254222, PMCID: PMC3176340, DOI: 10.1002/gepi.20561.Peer-Reviewed Original Research
2007
Inferring activity changes of transcription factors by binding association with sorted expression profiles
Cheng C, Yan X, Sun F, Li LM. Inferring activity changes of transcription factors by binding association with sorted expression profiles. BMC Bioinformatics 2007, 8: 452. PMID: 18021409, PMCID: PMC2194743, DOI: 10.1186/1471-2105-8-452.Peer-Reviewed Original ResearchConceptsTranscription factorsExpression profilesMicroarray dataTarget gene selectionPost-transcriptional modificationsChIP-chip dataMicroarray expression profilesExpression differentiationLow expression levelsProfile of expressionTarget genesRegulatory mechanismsGene expressionBiological processesMicroarray studiesAffinity dataGene selectionSame machineryExpression levelsGenesActivity changesSignificance cutoffDifferentiationMeaningful hypothesesAffinity scores
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