2024
AXIN1 mutations in nonsyndromic craniosynostosis.
Timberlake A, Hemal K, Gustafson J, Hao L, Valenzuela I, Slavotinek A, Cunningham M, Kahle K, Lifton R, Persing J. AXIN1 mutations in nonsyndromic craniosynostosis. Journal Of Neurosurgery Pediatrics 2024, 34: 246-251. PMID: 38905707, PMCID: PMC11200303, DOI: 10.3171/2024.5.peds24115.Peer-Reviewed Original ResearchSequence dataAXIN1 mutationsCase-parent triosGenome-wide significanceCS casesNonsyndromic CSGenome sequencing projectsWnt signalingExome sequencing dataRNA sequencing dataPhenotypes associated with mutationsSequencing projectsGenetic testingInhibitor of Wnt signalingLive birthsNonsyndromic casesGenetic etiologyGenetic causeCS patientsAXIN1Nonsyndromic craniosynostosisMutationsHealthy controlsBirth defectsExome
2021
Neptune: an environment for the delivery of genomic medicine
Eric V, Yi V, Murdock D, Kalla S, Wu T, Sabo A, Li S, Meng Q, Tian X, Murugan M, Cohen M, Kovar C, Wei W, Chung W, Weng C, Wiesner G, Jarvik G, Muzny D, Gibbs R, Abrams D, Adunyah S, Albertson-Junkans L, Almoguera B, Ames D, Appelbaum P, Aronson S, Aufox S, Babb L, Balasubramanian A, Bangash H, Basford M, Bastarache L, Baxter S, Behr M, Benoit B, Bhoj E, Bielinski S, Bland S, Blout C, Borthwick K, Bottinger E, Bowser M, Brand H, Brilliant M, Brodeur W, Caraballo P, Carrell D, Carroll A, Castillo L, Castro V, Chandanavelli G, Chiang T, Chisholm R, Christensen K, Chung W, Chute C, City B, Cobb B, Connolly J, Crane P, Crew K, Crosslin D, Dayal J, De Andrade M, De la Cruz J, Denny J, Denson S, DeSmet T, Dikilitas O, Dinsmore M, Dodge S, Dunlea P, Edwards T, Eng C, Fasel D, Fedotov A, Feng Q, Fleharty M, Foster A, Freimuth R, Friedrich C, Fullerton S, Funke B, Gabriel S, Gainer V, Gharavi A, Gibbs R, Glazer A, Glessner J, Goehringer J, Gordon A, Graham C, Green R, Gundelach J, Hain H, Hakonarson H, Harden M, Harley J, Harr M, Hartzler A, Hayes M, Hebbring S, Henrikson N, Hershey A, Hoell C, Holm I, Howell K, Hripcsak G, Hu J, Hynes E, Jarvik G, Jayaseelan J, Jiang Y, Joo Y, Jose S, Josyula N, Justice A, Kalra D, Karlson E, Keating B, Kelly M, Kenny E, Key D, Kiryluk K, Kitchner T, Klanderman B, Klee E, Kochan D, Korchina V, Kottyan L, Kudalkar E, Rahm A, Kullo I, Lammers P, Larson E, Lebo M, Leduc M, Lee M, Lennon N, Leppig K, Leslie N, Li R, Liang W, Lin C, Linder J, Lindor N, Lingren T, Linneman J, Liu C, Liu W, Liu X, Lynch J, Lyon H, Macbeth A, Mahadeshwar H, Mahanta L, Malin B, Manolio T, Marasa M, Marsolo K, McGowan M, McNally E, Meldrim J, Mentch F, Rasouly H, Mosley J, Mukherjee S, Mullen T, Muniz J, Murdock D, Murphy S, Murugan M, Muzny D, Myers M, Namjou B, Ni Y, Onofrio R, Obeng A, Person T, Peterson J, Petukhova L, Pisieczko C, Pratap S, Prows C, Puckelwartz M, Raj R, Ralston J, Ramaprasan A, Ramirez A, Rasmussen L, Rasmussen-Torvik L, Raychaudhuri S, Rehm H, Ritchie M, Rives C, Riza B, Roden D, Rosenthal E, Santani A, Dan S, Scherer S, Scott S, Scrol A, Sengupta S, Shang N, Sharma H, Sharp R, Singh R, Sleiman P, Slowik K, Smith J, Smith M, Smoot D, Smoller J, Sohn S, Stanaway I, Starren J, Stroud M, Su J, Taylor C, Tolwinski K, Van Driest S, Vargas S, Varugheese M, Veenstra D, Venner E, Verbitsky M, Vicente G, Wagner M, Walker K, Walunas T, Wang L, Wang Q, Wei W, Weiss S, Wells Q, Weng C, White P, Wiesner G, Wiley K, Williams J, Williams M, Wilson M, Witkowski L, Woods L, Woolf B, Wynn J, Yang Y, Zhang G, Zhang L, Zouk H. Neptune: an environment for the delivery of genomic medicine. Genetics In Medicine 2021, 23: 1838-1846. PMID: 34257418, PMCID: PMC8487966, DOI: 10.1038/s41436-021-01230-w.Peer-Reviewed Original Research
2016
Carcinogenesis: UV Radiation
Brash D, Heffernan T, Nghiem P, Cho R. Carcinogenesis: UV Radiation. 2016, 887-902. DOI: 10.1007/978-3-662-47398-6_56.ChaptersLarge-scale sequencing projectsUV-damaged cellsSequencing projectsDNA repairTumor suppressorSomatic point mutationsSurveillance mechanismClonal growthLow-frequency mutationsDNA damageBase changesCell behaviorPoint mutationsMutationsSomatic mutationsFree radical clearanceHuman skin cancerFrequency mutationsSpecific somatic mutationsUltraviolet radiationPTCH mutationsGenetic factorsNOTCH1 mutationsCellsVast number
2015
Carcinogenesis: UV Radiation
Brash D, Heffernan T, Nghiem P, Cho R. Carcinogenesis: UV Radiation. 2015, 1-17. DOI: 10.1007/978-3-642-27814-3_56-2.ChaptersLarge-scale sequencing projectsUV-damaged cellsSequencing projectsDNA repairTumor suppressorSomatic point mutationsSurveillance mechanismClonal growthLow-frequency mutationsDNA damageBase changesCell behaviorPoint mutationsMutationsSomatic mutationsFree radical clearanceHuman skin cancerFrequency mutationsSpecific somatic mutationsUltraviolet radiationPTCH mutationsGenetic factorsNOTCH1 mutationsCellsVast number
2013
Adjusting for Background Mutation Frequency Biases Improves the Identification of Cancer Driver Genes
Evans P, Avey S, Kong Y, Krauthammer M. Adjusting for Background Mutation Frequency Biases Improves the Identification of Cancer Driver Genes. IEEE Transactions On NanoBioscience 2013, 12: 150-157. PMID: 23694700, PMCID: PMC3989533, DOI: 10.1109/tnb.2013.2263391.Peer-Reviewed Original ResearchConceptsMore non-synonymous mutationsMutation frequencyTumor sequencing projectsGene-specific mannerCancer driver genesNon-synonymous mutationsSynonymous mutation ratioMutation biasSequencing projectsBackground mutation frequencyGene expressionDriver genesGenesTumor developmentMutation burdenMutation ratioHigher non-synonymous mutation burdenMutationsMutation countsExpressionBackground frequencyFrequency biasesIdentification
2012
VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment
Habegger L, Balasubramanian S, Chen DZ, Khurana E, Sboner A, Harmanci A, Rozowsky J, Clarke D, Snyder M, Gerstein M. VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment. Bioinformatics 2012, 28: 2267-2269. PMID: 22743228, PMCID: PMC3426844, DOI: 10.1093/bioinformatics/bts368.Peer-Reviewed Original ResearchConceptsCloud-computing environmentVariant annotation toolsAmazon Machine ImageCommand line interfaceLarge data filesMachine imagesWeb servicesVirtual machinesDemand accessWeb applicationSource codeAnnotation toolData filesComputational frameworkPersonal genomesDifferent variantsGenomic coordinatesSimple intersectionDetailed documentationPHPMachineSequencing projectsAnnotationEnvironmentFiles
2011
Population Genetic Analysis of Plasmodium falciparum Parasites Using a Customized Illumina GoldenGate Genotyping Assay
Campino S, Auburn S, Kivinen K, Zongo I, Ouedraogo J, Mangano V, Djimde A, Doumbo O, Kiara S, Nzila A, Borrmann S, Marsh K, Michon P, Mueller I, Siba P, Jiang H, Su X, Amaratunga C, Socheat D, Fairhurst R, Imwong M, Anderson T, Nosten F, White N, Gwilliam R, Deloukas P, MacInnis B, Newbold C, Rockett K, Clark T, Kwiatkowski D. Population Genetic Analysis of Plasmodium falciparum Parasites Using a Customized Illumina GoldenGate Genotyping Assay. PLOS ONE 2011, 6: e20251. PMID: 21673999, PMCID: PMC3108946, DOI: 10.1371/journal.pone.0020251.Peer-Reviewed Original ResearchConceptsPopulation genetic studiesIllumina GoldenGateGenetic studiesSingle nucleotide polymorphism (SNP) discoveryLarge-scale population genetic studiesLaboratory clonesPopulation genetic diversityPopulation genetic analysesGenome sequencing projectsPlasmodium falciparum genomeTotal genomic DNAParasite population dynamicsMinor frequency allelesFalciparum genomePolymorphism discoveryGenetic diversitySequencing projectsWhole genomeP. falciparumGenetic analysisImportant phenotypesGenomic DNAHigh SNPPopulation dynamicsMultiple-clone infectionsHigher-level metazoan relationships: recent progress and remaining questions
Edgecombe G, Giribet G, Dunn C, Hejnol A, Kristensen R, Neves R, Rouse G, Worsaae K, Sørensen M. Higher-level metazoan relationships: recent progress and remaining questions. Organisms Diversity & Evolution 2011, 11: 151-172. DOI: 10.1007/s13127-011-0044-4.Peer-Reviewed Original ResearchThousands of genesTarget gene approachSister-group relationBilaterian phylogenyBilaterian animalsPhylogenomic approachProtostome cladeMain cladesTaxonomic sampleSequencing projectsAcoelomorph flatwormsPhylogenetic analysisSister groupMultiple lociCladeProtostomesStable corePlacozoaBilateriansBilateriaDeuterostomesMetazoansSpiraliansPlatyzoaDeuterostomia
1998
Characterization of dacC, Which Encodes a New Low-Molecular-Weight Penicillin-Binding Protein in Bacillus subtilis
Pedersen L, Murray T, Popham D, Setlow P. Characterization of dacC, Which Encodes a New Low-Molecular-Weight Penicillin-Binding Protein in Bacillus subtilis. Journal Of Bacteriology 1998, 180: 4967-4973. PMID: 9733705, PMCID: PMC107527, DOI: 10.1128/jb.180.18.4967-4973.1998.Peer-Reviewed Original ResearchConceptsWeight penicillin-binding proteinsPenicillin-binding proteinsBacillus subtilis genome sequencing projectB. subtilis chromosomeGenome sequencing projectsWild-type cellsWild-type sporesInsertional mutantsPenicillin binding proteinsSequencing projectsSequence homologyUnknown functionBacillus subtilisEscherichia coliGenesPBP genesProteinSame heat resistanceOutgrowth kineticsExpressionSigmaHMutantsChromosomesHomologyPromoter
1996
Deciphering isozyme function: exploring cell biology with chemistry in the post-genomic era
Crews C. Deciphering isozyme function: exploring cell biology with chemistry in the post-genomic era. Cell Chemical Biology 1996, 3: 961-965. PMID: 9000005, DOI: 10.1016/s1074-5521(96)90162-3.Peer-Reviewed Original ResearchIdentification and characterization of pbpC, the gene encoding Bacillus subtilis penicillin-binding protein 3
Murray T, Popham D, Setlow P. Identification and characterization of pbpC, the gene encoding Bacillus subtilis penicillin-binding protein 3. Journal Of Bacteriology 1996, 178: 6001-6005. PMID: 8830698, PMCID: PMC178458, DOI: 10.1128/jb.178.20.6001-6005.1996.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceBacillus subtilisBacterial ProteinsBase SequenceCarrier ProteinsCell DivisionGene ExpressionGenes, BacterialHexosyltransferasesMolecular Sequence DataMultienzyme ComplexesMuramoylpentapeptide CarboxypeptidaseMutagenesisPenicillin-Binding ProteinsPeptidyl TransferasesRecombinant Fusion ProteinsRestriction MappingSpecies SpecificitySpores, BacterialTranscription, GeneticConceptsSignificant sequence similarityVegetative cell wallTranscriptional fusionsRedundant functionsDouble mutantLog-phase growthSequence similaritySequencing projectsPenicillin-binding protein 3Peptidoglycan structureSpore cortexCell wallB. subtilisBacillus subtilisGenesMajor promoterSpore germinationWeight PBPsSporulationCell morphologyFurther upstreamProtein 3GerminationSpore heat resistanceSubtilisTrends and Challenges in Experimental Macromolecular Crystallography
Chayen N, Boggon T, Cassetta A, Deacon A, Gleichmann T, Habash J, Harrop S, Helliwell J, Nieh Y, Peterson M, Raftery J, Snell E, Hädener A, Niemann A, Siddons D, Stojanoff V, Thompson A, Ursby T, Wulff M. Trends and Challenges in Experimental Macromolecular Crystallography. Quarterly Reviews Of Biophysics 1996, 29: 227-278. PMID: 8968112, DOI: 10.1017/s0033583500005837.Peer-Reviewed Original ResearchConceptsHuman genome sequencing projectGenome sequencing projectsModern drug discoveryStructural molecular biologyPrimary sequencingYeast genomeBiological chemistryStructural chemistrySequencing projectsBiological macromoleculesStructural DatabaseRational designMolecular biologyCognate ligandsDrug discoveryMolecular interactionsEnzyme reactivityMacromolecular crystallographyNovel inhibitorsChemistryNucleic acidsVirus structureFunctional detailsStructural detailsPharmaceutical industry
This site is protected by hCaptcha and its Privacy Policy and Terms of Service apply