2024
Syndrome-informed phenotyping identifies a polygenic background for achondroplasia-like facial variation in the general population
Vanneste M, Hoskens H, Goovaerts S, Matthews H, Devine J, Aponte J, Cole J, Shriver M, Marazita M, Weinberg S, Walsh S, Richmond S, Klein O, Spritz R, Peeters H, Hallgrímsson B, Claes P. Syndrome-informed phenotyping identifies a polygenic background for achondroplasia-like facial variation in the general population. Nature Communications 2024, 15: 10458. PMID: 39622794, PMCID: PMC11612227, DOI: 10.1038/s41467-024-54839-1.Peer-Reviewed Original ResearchConceptsMultivariate GWASMendelian phenotypesComplex traitsPolygenic backgroundMendelian disordersPolygenic basisGenetic variationGenetic variantsGenetic intersectionAchondroplasia phenotypePhenotypic spectrumPhenotypeGenesSkeletal developmentShape axesCraniofacial shapeGWASFacial variationsThree-dimensional facial scansGeneral populationTraitsControl scoresVariationControl samplesVariantsMapping genes for human face shape: Exploration of univariate phenotyping strategies.
Yuan M, Goovaerts S, Vanneste M, Matthews H, Hoskens H, Richmond S, Klein O, Spritz R, Hallgrimsson B, Walsh S, Shriver M, Shaffer J, Weinberg S, Peeters H, Claes P. Mapping genes for human face shape: Exploration of univariate phenotyping strategies. PLOS Computational Biology 2024, 20: e1012617. PMID: 39621772, DOI: 10.1371/journal.pcbi.1012617.Peer-Reviewed Original ResearchGenome-wide association studiesMultiple genome-wide association studiesPhenotyping strategiesSNP-based heritabilityInter-landmark distancesLD score regressionFacial gestaltMap genesGenetic lociAssociation studiesCraniofacial shapeUnivariate traitsMorphological traitsEuropean ancestryScore regressionLow heritabilityPhenotyping approachFacial resemblanceFacial shapePhenotypeGenetic factorsTraitsHuman face shapeHeritabilityGenetic influencesA novel approach to craniofacial analysis using automated 3D landmarking of the skull
Wilke F, Matthews H, Herrick N, Dopkins N, Claes P, Walsh S. A novel approach to craniofacial analysis using automated 3D landmarking of the skull. Scientific Reports 2024, 14: 12381. PMID: 38811771, PMCID: PMC11137148, DOI: 10.1038/s41598-024-63137-1.Peer-Reviewed Original ResearchConceptsHuman skullCone-beam computed tomographyCentroid sizeCranial anatomyBone variationLandmark setsVault regionCraniofacial analysisSkullMorphological researchBone masksEvolutionary underpinningsIntraclass coefficientQuantification of variationCT imageryBone surfaceLandmarksCraniofacial structuresBone phenotypeLevel of concordanceManually placed landmarksShape analysisAutomatic landmarkingSkull scanIndependent observersA common cis-regulatory variant impacts normal-range and disease-associated human facial shape through regulation of PKDCC during chondrogenesis
Mohammed J, Arora N, Matthews H, Hansen K, Bader M, Walsh S, Shaffer J, Weinberg S, Swigut T, Claes P, Selleri L, Wysocka J. A common cis-regulatory variant impacts normal-range and disease-associated human facial shape through regulation of PKDCC during chondrogenesis. ELife 2024, 13: e82564. PMID: 38483448, PMCID: PMC10939500, DOI: 10.7554/elife.82564.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesSingle nucleotide polymorphismsGenome-wide association study studiesDisease predispositionComplex morphological traitsEmbryonic cell typesSkull elementsCognate enhancersAssociation studiesAssociated with quantitative changesPhenotypic traitsPhenotypic variationMorphological traitsJaw shapeNucleotide polymorphismsGenetic variantsMorphological variationTyrosine kinaseCell typesNormal rangeRisk of non-syndromic orofacial cleftsFacial morphogenesisNon-syndromic orofacial cleftsHuman populationSkeletal development
2023
Data-driven trait heritability-based extraction of human facial phenotypes
Yuan M, Goovaerts S, Hoskens H, Richmond S, Walsh S, Shriver M, Shaffer J, Marazita M, Weinberg S, Peeters H, Claes P. Data-driven trait heritability-based extraction of human facial phenotypes. 2023, 00: 312-319. DOI: 10.1109/bibm58861.2023.10385885.Peer-Reviewed Original ResearchTrait heritabilityGenome-wide association scanAssociation scansSNP heritabilityGenetic lociAssociation studiesGenetic variationModel shape variationsPhenotypic traitsMorphological traitsEffect traitsRelevant phenotypesDimension reduction techniquesPhenotypic measurementsData-driven optimizationPhenotypic descriptorsFeature spaceHuman expertsGenetic search algorithmPhenotypeAutomatic extractionTraitsHuman faceDegree of variationSearch algorithmnetMUG: a novel network-guided multi-view clustering workflow for dissecting genetic and facial heterogeneity
Li Z, Melograna F, Hoskens H, Duroux D, Marazita M, Walsh S, Weinberg S, Shriver M, Müller-Myhsok B, Claes P, Van Steen K. netMUG: a novel network-guided multi-view clustering workflow for dissecting genetic and facial heterogeneity. Frontiers In Genetics 2023, 14: 1286800. PMID: 38125750, PMCID: PMC10731261, DOI: 10.3389/fgene.2023.1286800.Peer-Reviewed Original ResearchMulti-view clustering frameworkHeterogeneous data sourcesSingle-view dataMulti-view dataMultiple Canonical Correlation AnalysisMulti-view clusteringMulti-view featuresClustering frameworkTrue labelsData structureFacial imagesExtraneous dataRand indexBenchmark methodsNetwork representationSynthetic dataSparse multiple canonical correlation analysisData sourcesHierarchical clusteringClusteringCanonical correlation analysisSuperior performanceNetworkGenomic dataReal data analysisJoint multi-ancestry and admixed GWAS reveals the complex genetics behind human cranial vault shape
Goovaerts S, Hoskens H, Eller R, Herrick N, Musolf A, Justice C, Yuan M, Naqvi S, Lee M, Vandermeulen D, Szabo-Rogers H, Romitti P, Boyadjiev S, Marazita M, Shaffer J, Shriver M, Wysocka J, Walsh S, Weinberg S, Claes P. Joint multi-ancestry and admixed GWAS reveals the complex genetics behind human cranial vault shape. Nature Communications 2023, 14: 7436. PMID: 37973980, PMCID: PMC10654897, DOI: 10.1038/s41467-023-43237-8.Peer-Reviewed Original ResearchILIAD: a suite of automated Snakemake workflows for processing genomic data for downstream applications
Herrick N, Walsh S. ILIAD: a suite of automated Snakemake workflows for processing genomic data for downstream applications. BMC Bioinformatics 2023, 24: 424. PMID: 37940870, PMCID: PMC10633908, DOI: 10.1186/s12859-023-05548-x.Peer-Reviewed Original ResearchConceptsRaw genomic dataSoftware toolsHigh-performance computing clusterOwn big dataRaw data typesVariant call format filesOpen-source suiteBioinformatics software toolsDownstream applicationsDocker containersGenomic dataLocal machineComputing clusterBig dataConfiguration filesJob executionWindows platformData workflowIntermediate filesSingle commandFormat fileReproducible workflowsVCF filesData typesStorage limitations
2008
Management of pediatric penetrating oropharyngeal trauma.
Zonfrillo MR, Roy AD, Walsh SA. Management of pediatric penetrating oropharyngeal trauma. Pediatric Emergency Care 2008, 24: 172-5. PMID: 18347498, DOI: 10.1097/PEC.0b013e3181669072.Peer-Reviewed Original Research
2007
Hematoma of the Labia Majora in an Adolescent Girl
Bechtel K, Santucci K, Walsh S. Hematoma of the Labia Majora in an Adolescent Girl. Pediatric Emergency Care 2007, 23: 407-408. PMID: 17572528, DOI: 10.1097/01.pec.0000278399.47999.0b.Peer-Reviewed Original Research
2002
Case report: persistent dysuria and a suprapubic mass in a 3-year-old boy.
Walsh SA, Weiss RM. Case report: persistent dysuria and a suprapubic mass in a 3-year-old boy. Current Opinion In Pediatrics 2002, 14: 647-8. PMID: 12352261, DOI: 10.1097/00008480-200210000-00013.Peer-Reviewed Original Research