2013
Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics
Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüş ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GRS, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F, Consortium 1, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M. Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics. Science 2013, 342: 1235587. PMID: 24092746, PMCID: PMC3947637, DOI: 10.1126/science.1235587.Peer-Reviewed Original ResearchNegligible impact of rare autoimmune-locus coding-region variants on missing heritability
Hunt KA, Mistry V, Bockett NA, Ahmad T, Ban M, Barker JN, Barrett JC, Blackburn H, Brand O, Burren O, Capon F, Compston A, Gough SC, Jostins L, Kong Y, Lee JC, Lek M, MacArthur DG, Mansfield JC, Mathew CG, Mein CA, Mirza M, Nutland S, Onengut-Gumuscu S, Papouli E, Parkes M, Rich SS, Sawcer S, Satsangi J, Simmonds MJ, Trembath RC, Walker NM, Wozniak E, Todd JA, Simpson MA, Plagnol V, van Heel DA. Negligible impact of rare autoimmune-locus coding-region variants on missing heritability. Nature 2013, 498: 232-235. PMID: 23698362, PMCID: PMC3736321, DOI: 10.1038/nature12170.Peer-Reviewed Original Research
2011
Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project
Mu XJ, Lu ZJ, Kong Y, Lam HY, Gerstein MB. Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project. Nucleic Acids Research 2011, 39: 7058-7076. PMID: 21596777, PMCID: PMC3167619, DOI: 10.1093/nar/gkr342.Peer-Reviewed Original ResearchStreptococcus pneumoniae Clonal Complex 199: Genetic Diversity and Tissue-Specific Virulence
Thomas JC, Figueira M, Fennie KP, Laufer AS, Kong Y, Pichichero ME, Pelton SI, Pettigrew MM. Streptococcus pneumoniae Clonal Complex 199: Genetic Diversity and Tissue-Specific Virulence. PLOS ONE 2011, 6: e18649. PMID: 21533186, PMCID: PMC3077395, DOI: 10.1371/journal.pone.0018649.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsChinchillaDisease Models, AnimalGenes, BacterialGenetic VariationPneumococcal InfectionsStreptococcus pneumoniaeVirulenceConceptsChinchilla modelHeptavalent pneumococcal conjugate vaccinePneumococcal conjugate vaccineSerotype 19A isolatesMiddle ear isolatesS. pneumoniae isolatesLong-term effectivenessConjugate vaccinePneumococcal diseaseOtitis mediaVaccinated populationReplacement diseaseBlood isolatesInvasive diseaseCarriage isolatesPneumoniae isolatesCerebrospinal fluidEar isolatesFuture vaccinesImportant causeStreptococcus pneumoniaeMiddle earDiseaseVirulence potentialVaccine
2010
MU2A—reconciling the genome and transcriptome to determine the effects of base substitutions
Garla V, Kong Y, Szpakowski S, Krauthammer M. MU2A—reconciling the genome and transcriptome to determine the effects of base substitutions. Bioinformatics 2010, 27: 416-418. PMID: 21149339, PMCID: PMC3031033, DOI: 10.1093/bioinformatics/btq658.Peer-Reviewed Original ResearchMeSH KeywordsGenetic VariationGenomeHumansInternetMolecular Sequence AnnotationMutationNeoplasmsSoftwareTranscriptomeConceptsProtein productsSequence variantsNext-generation sequencing technologiesGenomic sequence variantsTranscript librariesGenomic coordinatesGenomic positionsReference genomeSequencing technologiesSequence variationGenomeGenomic variantsBase substitutionsVariant annotationTranscriptomeTranscriptsVariantsAnnotationMapping