2023
Integrated analysis of competitive endogenous RNA networks in elder patients with non-small cell lung cancer
Chen Z, Yu F, Zhu B, Li Q, Yu Y, Zong F, Liu W, Zhang M, Wu S. Integrated analysis of competitive endogenous RNA networks in elder patients with non-small cell lung cancer. Medicine 2023, 102: e33192. PMID: 36897674, PMCID: PMC9997791, DOI: 10.1097/md.0000000000033192.Peer-Reviewed Original ResearchConceptsMRNA ceRNA networkEndogenous RNA (ceRNA) networkCeRNA networkMessenger RNAsRNA networkLncRNA-miRNACompetitive endogenous RNA (ceRNA) networkLong non-coding RNAsPotential ceRNA networksNon-coding RNAsFunctions of DEmRNAsCancer-related processesCancer Genome AtlasGenome analysisGene OntologyKyoto EncyclopediaDevelopment of NSCLCGene Expression Omnibus (GEO) cohortNovel insightsGenome AtlasSurvival packageExpression levelsIntegrated analysisDEmRNAsMiRNAs
2022
Whole Genome Analyses Accurately Identify Neisseria spp. and Limit Taxonomic Ambiguity
Khoder M, Osman M, Kassem I, Rafei R, Shahin A, Fournier P, Rolain J, Hamze M. Whole Genome Analyses Accurately Identify Neisseria spp. and Limit Taxonomic Ambiguity. International Journal Of Molecular Sciences 2022, 23: 13456. PMID: 36362240, PMCID: PMC9657967, DOI: 10.3390/ijms232113456.Peer-Reviewed Original ResearchConceptsDraft genomeComplete genome sequenceWhole-genome analysisNCBI GenBank databaseMatrix-assisted laser desorptionGenomic toolsPhylogenetic relationshipsTaxonomic ambiguityBacterial taxonomyGenome sequenceGenome analysisGenomic levelTaxonomic relationshipsTaxonomic toolGenBank databaseGenome sequencingGenomeLaser desorptionSpeciesNeisseria sppWGS analysisSppNeisseriaSequencingStrainsMutation spectrum of congenital heart disease in a consanguineous Turkish population
Dong W, Kaymakcalan H, Jin SC, Diab NS, Tanıdır C, Yalcin ASY, Ercan‐Sencicek A, Mane S, Gunel M, Lifton RP, Bilguvar K, Brueckner M. Mutation spectrum of congenital heart disease in a consanguineous Turkish population. Molecular Genetics & Genomic Medicine 2022, 10: e1944. PMID: 35481623, PMCID: PMC9184665, DOI: 10.1002/mgg3.1944.Peer-Reviewed Original ResearchConceptsWhole-exome sequencingLaterality defectsUnique genetic architectureCongenital heart diseaseConsanguineous familyGenetic architectureCausal genesCHD genesGenome analysisHomozygous variantGenetic landscapeGenetic lesionsGenomic alterationsHeart diseaseConsanguineous populationFunction variantsRecessive variantsCHD probandsGenesType of CHDMutation spectrumStructural congenital heart diseaseVariantsCHD subjectsAdditional patients
2021
Structural insights into the evolution of the RAG recombinase
Liu C, Zhang Y, Liu CC, Schatz DG. Structural insights into the evolution of the RAG recombinase. Nature Reviews Immunology 2021, 22: 353-370. PMID: 34675378, DOI: 10.1038/s41577-021-00628-6.Peer-Reviewed Original ResearchConceptsRAG recombinaseComparative genome analysisGenomes of eukaryotesProtein-DNA complexesSingle amino acid mutationAntigen receptor genesMolecular domesticationRag familyAmino acid mutationsJawed vertebratesVertebrate immunityTransposable elementsEvolutionary adaptationGenome analysisStructural biologyDNA bindingStructural insightsGene 1Acid mutationsCleavage activityRecombinaseReceptor geneStructural evidenceRecombinationAdaptive immunity
2020
Analysis of Cell and Nucleus Genome by Next-Generation Sequencing
Oh J, Abyzov A. Analysis of Cell and Nucleus Genome by Next-Generation Sequencing. 2020, 35-65. DOI: 10.1007/978-3-030-62532-0_3.Peer-Reviewed Original ResearchSingle-cell genomesBulk of cellsNext-generation sequencing technologiesMosaic variantsNuclear genomeNucleus genomeGenomic mosaicismAnalysis of cellsGenome analysisNext-generation sequencingCell genomeSequencing technologiesGenomeGenomic variantsSingle cellsCellsVariantsMosaicismDiscoverySequencingValuable insightsEnvironmental exposures
2019
Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2
Zhou B, Ho S, Greer S, Spies N, Bell J, Zhang X, Zhu X, Arthur J, Byeon S, Pattni R, Saha I, Huang Y, Song G, Perrin D, Wong W, Ji H, Abyzov A, Urban A. Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2. Nucleic Acids Research 2019, 47: 3846-3861. PMID: 30864654, PMCID: PMC6486628, DOI: 10.1093/nar/gkz169.Peer-Reviewed Original ResearchConceptsGenome sequenceStructural variantsGenomic structural featuresSomatic genomic rearrangementsFunctional genomics dataAllele-specific expressionEntire chromosome armsIntegrated genome analysisCRISPR/Cas9Cell linesMain cell linesGenome structureEpigenomic characteristicsChromosome armsGenome analysisDNA methylationGenome characteristicsRetrotransposon insertionChromosomal segmentsGenomic rearrangementsGenomic dataRegulatory complexityCell line HepG2Copy numberLoss of heterozygosityGenomic Analysis in the Age of Human Genome Sequencing
Lappalainen T, Scott AJ, Brandt M, Hall IM. Genomic Analysis in the Age of Human Genome Sequencing. Cell 2019, 177: 70-84. PMID: 30901550, PMCID: PMC6532068, DOI: 10.1016/j.cell.2019.02.032.Peer-Reviewed Original ResearchMeSH KeywordsBiological Specimen BanksChromosome MappingGenetic Predisposition to DiseaseGenetic TestingGenetic VariationGenome-Wide Association StudyGenome, HumanGenomicsHigh-Throughput Nucleotide SequencingHuman Genome ProjectHumansPolymorphism, Single NucleotideSequence Analysis, DNAWhole Genome SequencingConceptsFunctional genomics approachAllele frequency spectrumHuman genome sequencingGene mapping studiesGenome sequencing technologiesRare human diseasesWhole-genome sequencingGenomic approachesGenetic variant discoveryGenome variationHuman genomeGenome analysisGenomic analysisSequencing technologiesGenome sequencingVariant discoveryHuman diseasesHuman geneticsGenomeFunctional interpretationMapping studiesFunctional effectsSequencingGermline variantsGenetics
2018
Genome Analyses of >200,000 Individuals Identify 58 Loci for Chronic Inflammation and Highlight Pathways that Link Inflammation and Complex Disorders
Ligthart S, Vaez A, Võsa U, Stathopoulou M, de Vries P, Prins B, Van der Most P, Tanaka T, Naderi E, Rose L, Wu Y, Karlsson R, Barbalic M, Lin H, Pool R, Zhu G, Macé A, Sidore C, Trompet S, Mangino M, Sabater-Lleal M, Kemp J, Abbasi A, Kacprowski T, Verweij N, Smith A, Huang T, Marzi C, Feitosa M, Lohman K, Kleber M, Milaneschi Y, Mueller C, Huq M, Vlachopoulou E, Lyytikäinen L, Oldmeadow C, Deelen J, Perola M, Zhao J, Feenstra B, Amini M, Lahti J, Schraut K, Fornage M, Suktitipat B, Chen W, Li X, Nutile T, Malerba G, Luan J, Bak T, Schork N, Del Greco M. F, Thiering E, Mahajan A, Marioni R, Mihailov E, Eriksson J, Ozel A, Zhang W, Nethander M, Cheng Y, Aslibekyan S, Ang W, Gandin I, Yengo L, Portas L, Kooperberg C, Hofer E, Rajan K, Schurmann C, Hollander W, Ahluwalia T, Zhao J, Draisma H, Ford I, Timpson N, Teumer A, Huang H, Wahl S, Liu Y, Huang J, Uh H, Geller F, Joshi P, Yanek L, Trabetti E, Lehne B, Vozzi D, Verbanck M, Biino G, Saba Y, Meulenbelt I, O’Connell J, Laakso M, Giulianini F, Magnusson P, Ballantyne C, Hottenga J, Montgomery G, Rivadineira F, Rueedi R, Steri M, Herzig K, Stott D, Menni C, Frånberg M, St. Pourcain B, Felix S, Pers T, Bakker S, Kraft P, Peters A, Vaidya D, Delgado G, Smit J, Großmann V, Sinisalo J, Seppälä I, Williams S, Holliday E, Moed M, Langenberg C, Räikkönen K, Ding J, Campbell H, Sale M, Chen Y, James A, Ruggiero D, Soranzo N, Hartman C, Smith E, Berenson G, Fuchsberger C, Hernandez D, Tiesler C, Giedraitis V, Liewald D, Fischer K, Mellström D, Larsson A, Wang Y, Scott W, Lorentzon M, Beilby J, Ryan K, Pennell C, Vuckovic D, Balkau B, Concas M, Schmidt R, de Leon C, Bottinger E, Kloppenburg M, Paternoster L, Boehnke M, Musk A, Willemsen G, Evans D, Madden P, Kähönen M, Kutalik Z, Zoledziewska M, Karhunen V, Kritchevsky S, Sattar N, Lachance G, Clarke R, Harris T, Raitakari O, Attia J, van Heemst D, Kajantie E, Sorice R, Gambaro G, Scott R, Hicks A, Ferrucci L, Standl M, Lindgren C, Starr J, Karlsson M, Lind L, Li J, Chambers J, Mori T, de Geus E, Heath A, Martin N, Auvinen J, Buckley B, de Craen A, Waldenberger M, Strauch K, Meitinger T, Scott R, McEvoy M, Beekman M, Bombieri C, Ridker P, Mohlke K, Pedersen N, Morrison A, Boomsma D, Whitfield J, Strachan D, Hofman A, Vollenweider P, Cucca F, Jarvelin M, Jukema J, Spector T, Hamsten A, Zeller T, Uitterlinden A, Nauck M, Gudnason V, Qi L, Grallert H, Borecki I, Rotter J, März W, Wild P, Lokki M, Boyle M, Salomaa V, Melbye M, Eriksson J, Wilson J, Penninx B, Becker D, Worrall B, Gibson G, Krauss R, Ciullo M, Zaza G, Wareham N, Oldehinkel A, Palmer L, Murray S, Pramstaller P, Bandinelli S, Heinrich J, Ingelsson E, Deary I, Mägi R, Vandenput L, van der Harst P, Desch K, Kooner J, Ohlsson C, Hayward C, Lehtimäki T, Shuldiner A, Arnett D, Beilin L, Robino A, Froguel P, Pirastu M, Jess T, Koenig W, Loos R, Evans D, Schmidt H, Smith G, Slagboom E, Eiriksdottir G, Morris A, Psaty B, Tracy R, Nolte I, Boerwinkle E, Visvikis-Siest S, Reiner A, Gross M, Bis J, Franke L, Franco O, Benjamin E, Chasman D, Dupuis J, Snieder H, Dehghan A, Alizadeh B, Alizadeh B, Boezen H, Franke L, van der Harst P, Navis G, Rots M, Snieder H, Swertz M, Wolffenbuttel B, Wijmenga C, Benjamin E, Chasman D, Dehghan A, Ahluwalia T, Meigs J, Tracy R, Alizadeh B, Ligthart S, Bis J, Eiriksdottir G, Pankratz N, Gross M, Rainer A, Snieder H, Wilson J, Psaty B, Dupuis J, Prins B, Vaso U, Stathopoulou M, Franke L, Lehtimaki T, Koenig W, Jamshidi Y, Siest S, Abbasi A, Uitterlinden A, Abdollahi M, Schnabel R, Schick U, Nolte I, Kraja A, Hsu Y, Tylee D, Zwicker A, Uher R, Davey-Smith G, Morrison A, Hicks A, van Duijn C, Ward-Caviness C, Boerwinkle E, Rotter J, Rice K, Lange L, Perola M, de Geus E, Morris A, Makela K, Stacey D, Eriksson J, Frayling T, Slagboom P. Genome Analyses of >200,000 Individuals Identify 58 Loci for Chronic Inflammation and Highlight Pathways that Link Inflammation and Complex Disorders. American Journal Of Human Genetics 2018, 103: 691-706. PMID: 30388399, PMCID: PMC6218410, DOI: 10.1016/j.ajhg.2018.09.009.Peer-Reviewed Original ResearchConceptsC-reactive proteinAmount of CRPGenome-wide association studiesMendelian randomization analysisClinical outcomesChronic inflammationChronic low-grade inflammationLow-grade inflammationRandomization analysisBody mass indexBiology of inflammationCausal protective effectDistinct genetic lociRisk-increasing effectSilico functional analysisMass indexProtective effectClinical consequencesMultiple complex diseasesImmune pathwaysInflammationBipolar disorderSensitive biomarkerGenome analysisHighlight pathwaysChapter 16 Genetic Variations of Long Noncoding RNAs in Cancer
Dimitrova N. Chapter 16 Genetic Variations of Long Noncoding RNAs in Cancer. 2018, 289-308. DOI: 10.1016/b978-0-12-811022-5.00016-4.Peer-Reviewed Original ResearchComprehensive genome analysisFunction of lncRNAsLong noncoding RNALncRNA lociCancer susceptibility variantsGenome analysisGenetic variationRegulatory regionsNoncoding RNAsGenomic dataSomatic variationExpression patternsFocal amplificationCancer predispositionPhysiological roleLncRNAsFunctional consequencesHuman cancersNucleotide polymorphismsExpression levelsRNAMechanism of actionNovel classIntriguing associationStrong linkage
2017
Typing and comparative genome analysis of Brucella melitensis isolated from Lebanon
Zaki N, Salloum T, Osman M, Rafei R, Hamze M, Tokajian S. Typing and comparative genome analysis of Brucella melitensis isolated from Lebanon. FEMS Microbiology Letters 2017, 364: fnx199. PMID: 28961704, DOI: 10.1093/femsle/fnx199.Peer-Reviewed Original ResearchConceptsGenome analysisLateral gene transferComparative genome analysisDraft genome sequencingWhole-genome single nucleotide polymorphism (SNP) analysisB. melitensisZoonotic disease brucellosisDepth genomic characterizationMultiple virulence determinantsSingle nucleotide polymorphism analysisNucleotide polymorphism analysisSequence divergenceGenome comparisonGenomic islandsSingle nucleotide polymorphismsGenetic variationGenomic characterizationDisease brucellosisGene transferMobile elements
2016
Comparative genomics and the diversity of life
Dunn C, Munro C. Comparative genomics and the diversity of life. Zoologica Scripta 2016, 45: 5-13. DOI: 10.1111/zsc.12211.Peer-Reviewed Original ResearchGenomic analysisComparative genome analysisComparative genomic analysisNumber of speciesDiversity of lifeGenome functionGene duplicationComparative genomicsOrganism's phenotypeLaboratory model systemPhylogenetic analysisGene homologyGenome sequenceGenome analysisMore speciesBiodiversity researchGenomicsNomenclatural systemSpeciesModel systemCentral roleSystematicsOrthologsPhylogeneticsPowerful windowWhat Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira
Fouts DE, Matthias MA, Adhikarla H, Adler B, Amorim-Santos L, Berg DE, Bulach D, Buschiazzo A, Chang YF, Galloway RL, Haake DA, Haft DH, Hartskeerl R, Ko AI, Levett PN, Matsunaga J, Mechaly AE, Monk JM, Nascimento AL, Nelson KE, Palsson B, Peacock SJ, Picardeau M, Ricaldi JN, Thaipandungpanit J, Wunder EA, Yang XF, Zhang JJ, Vinetz JM. What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira. PLOS Neglected Tropical Diseases 2016, 10: e0004403. PMID: 26890609, PMCID: PMC4758666, DOI: 10.1371/journal.pntd.0004403.Peer-Reviewed Original ResearchConceptsGenes/gene familiesProtein secretion systemComparative genomic analysisSignal peptide motifsCRISPR/Cas systemComputational biology analysisMammalian host adaptationBacterial pathogensWhole-genome analysisSialic acid biosynthesisLeptospira speciesEvolutionary relatednessSaprophytic Leptospira speciesGene familyMetabolic reconstructionGenomic comparisonSecretion motifBacterial virulence factorsHost adaptationSecretion systemGenome analysisAcid biosynthesisGenomic analysisNew insightsMammalian hostsNeisseria cinerea isolates can adhere to human epithelial cells by type IV pilus-independent mechanisms
Wörmann ME, Horien CL, Johnson E, Liu G, Aho E, Tang CM, Exley RM. Neisseria cinerea isolates can adhere to human epithelial cells by type IV pilus-independent mechanisms. Microbiology 2016, 162: 487-502. PMID: 26813911, PMCID: PMC4891991, DOI: 10.1099/mic.0.000248.Peer-Reviewed Original ResearchConceptsHuman epithelial cellsN. cinereaFunction of piliEpithelial cellsType IV piliPathogen Neisseria meningitidisHost-pathogen interactionsClose taxonomic relationshipFormation of microcoloniesPilus-pilus interactionsGenome analysisTaxonomic relationshipsMajor pilinTfp expressionPilin expressionSpecies sharesPilin genePathogenic NeisseriaNon-pathogenic Neisseria speciesCell surfaceNeisseria cinereaCinereaRole of TFPGenesNon-pathogenic Neisseria
2012
Phenotype diversity in type 1 Gaucher disease: discovering the genetic basis of Gaucher disease/hematologic malignancy phenotype by individual genome analysis
Lo SM, Choi M, Liu J, Jain D, Boot RG, Kallemeijn WW, Aerts JM, Pashankar F, Kupfer GM, Mane S, Lifton RP, Mistry PK. Phenotype diversity in type 1 Gaucher disease: discovering the genetic basis of Gaucher disease/hematologic malignancy phenotype by individual genome analysis. Blood 2012, 119: 4731-4740. PMID: 22493294, PMCID: PMC3367875, DOI: 10.1182/blood-2011-10-386862.Peer-Reviewed Original ResearchConceptsGenome analysisGenetic basisCancer phenotypeWhole exome captureNovel mutationsGenomic analysisPhenotype annotationsPhenotype diversityParallel sequencingHomozygosity mappingT-cell acute lymphoblastic lymphomaGenetic modifiersNovel insightsGene sequencingGaucher diseaseMalignancy phenotypeMutationsLysosomal accumulationPhenotypeHomozygous novel mutationPathogenic mutationsGenesMSH6 proteinsSequencingEnzyme studies
2003
Genome‐wide scan for prostate cancer susceptibility genes using families from the University of Michigan prostate cancer genetics project finds evidence for linkage on chromosome 17 near BRCA1
Lange E, Gillanders E, Davis C, Brown W, Campbell J, Jones M, Gildea D, Riedesel E, Albertus J, Freas‐Lutz D, Markey C, Giri V, Dimmer J, Montie J, Trent J, Cooney K. Genome‐wide scan for prostate cancer susceptibility genes using families from the University of Michigan prostate cancer genetics project finds evidence for linkage on chromosome 17 near BRCA1. The Prostate 2003, 57: 326-334. PMID: 14601029, DOI: 10.1002/pros.10307.Peer-Reviewed Original ResearchConceptsProstate cancer susceptibility genesCancer susceptibility genesSusceptibility genesCandidate genesGenome-wide scan dataGenome-wide analysisChromosome 17Michigan Prostate Cancer Genetics ProjectWhole-genome analysisCancer candidate genesProstate Cancer Genetics ProjectSubset of pedigreesStratified linkage analysesPrevious linkage studiesGenome analysisLinkage scanChromosome 1Genetic markersLinkage analysisAffected individualsGenesLinkage regionGenetics ProjectChromosome 17qProstate cancer families
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