2024
Effective genome editing with an enhanced ISDra2 TnpB system and deep learning-predicted ωRNAs
Marquart K, Mathis N, Mollaysa A, Müller S, Kissling L, Rothgangl T, Schmidheini L, Kulcsár P, Allam A, Kaufmann M, Matsushita M, Haenggi T, Cathomen T, Kopf M, Krauthammer M, Schwank G. Effective genome editing with an enhanced ISDra2 TnpB system and deep learning-predicted ωRNAs. Nature Methods 2024, 1-10. PMID: 39313558, DOI: 10.1038/s41592-024-02418-z.Peer-Reviewed Original ResearchPublisher Correction: Machine learning prediction of prime editing efficiency across diverse chromatin contexts
Mathis N, Allam A, Tálas A, Kissling L, Benvenuto E, Schmidheini L, Schep R, Damodharan T, Balázs Z, Janjuha S, Ioannidi E, Böck D, van Steensel B, Krauthammer M, Schwank G. Publisher Correction: Machine learning prediction of prime editing efficiency across diverse chromatin contexts. Nature Biotechnology 2024, 1-1. PMID: 39134755, DOI: 10.1038/s41587-024-02383-0.Peer-Reviewed Original ResearchExplainable deep learning for disease activity prediction in chronic inflammatory joint diseases
Trottet C, Allam A, Horvath A, Finckh A, Hügle T, Adler S, Kyburz D, Micheroli R, Krauthammer M, Ospelt C. Explainable deep learning for disease activity prediction in chronic inflammatory joint diseases. PLOS Digital Health 2024, 3: e0000422. PMID: 38935600, PMCID: PMC11210792, DOI: 10.1371/journal.pdig.0000422.Peer-Reviewed Original ResearchNeural networkMulti-task learning modelShort-term memory networkMedical expert knowledgeFeature representationAttention layerLatent representationLatent embeddingsDeep learningK-nearestMemory networkTree-basedLearning modelsExpert knowledgeBaseline strategyActivity predictionScoring networkRegression algorithmAttribution methodsNetworkChronic inflammatory joint diseaseStatic baselinesRepresentationModular modelPatient representationCOL10A1 expression distinguishes a subset of cancer-associated fibroblasts present in the stroma of high-risk basal cell carcinoma
Esposito M, Yerly L, Shukla P, Hermes V, Sella F, Balazs Z, Lattmann E, Tastanova A, Turko P, Lang R, Kolm I, Staeger R, Kuonen F, Krauthammer M, Hafner J, Levesque M, Restivo G. COL10A1 expression distinguishes a subset of cancer-associated fibroblasts present in the stroma of high-risk basal cell carcinoma. British Journal Of Dermatology 2024, 191: 775-790. PMID: 38916477, DOI: 10.1093/bjd/ljae258.Peer-Reviewed Original ResearchBasal cell carcinoma subtypesBasal cell carcinomaCancer-associated fibroblastsHigh-risk basal cell carcinomasInvasive BCCCancer-associated fibroblast populationsLaser capture microdissectionCell carcinomaHigh-risk BCC subtypesSubtypes of basal cell carcinomaHigh risk of recurrenceBasal cell carcinoma developmentBasal cell carcinoma progressionHigh-risk subtypesBasal cell carcinoma samplesGene expression signaturesTailored treatment optionsBasosquamous subtypesHealthy skin samplesRNA sequencingStromal featuresTumor microenvironmentMorphological subtypesTreatment optionsPrognostic biomarkerMachine learning prediction of prime editing efficiency across diverse chromatin contexts
Mathis N, Allam A, Tálas A, Kissling L, Benvenuto E, Schmidheini L, Schep R, Damodharan T, Balázs Z, Janjuha S, Ioannidi E, Böck D, van Steensel B, Krauthammer M, Schwank G. Machine learning prediction of prime editing efficiency across diverse chromatin contexts. Nature Biotechnology 2024, 1-8. PMID: 38907037, DOI: 10.1038/s41587-024-02268-2.Peer-Reviewed Original ResearchInnate acting memory Th1 cells modulate heterologous diseases
Rakebrandt N, Yassini N, Kolz A, Schorer M, Lambert K, Goljat E, Brull A, Rauld C, Balazs Z, Krauthammer M, Carballido J, Peters A, Joller N. Innate acting memory Th1 cells modulate heterologous diseases. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2312837121. PMID: 38838013, PMCID: PMC11181110, DOI: 10.1073/pnas.2312837121.Peer-Reviewed Original ResearchConceptsIFN-gAutoimmune model of multiple sclerosisIFN-g productionInnate-like responsesMemory Th1 cellsModel of multiple sclerosisResponse to IL-12T helper 1Heterologous challengeTh1 cellsAutoimmune modelsIL-33IL-12Immune memoryDisease onsetIL-18Viral infectionUnrelated diseaseMultiple sclerosisDiseaseEnhanced responseInfectionHeterologous diseasesCellsRechallengeLongitudinal cell-free DNA characterization by low-coverage whole-genome sequencing in patients undergoing high-dose radiotherapy
Balázs Z, Balermpas P, Ivanković I, Willmann J, Gitchev T, Bryant A, Guckenberger M, Krauthammer M, Andratschke N. Longitudinal cell-free DNA characterization by low-coverage whole-genome sequencing in patients undergoing high-dose radiotherapy. Radiotherapy And Oncology 2024, 197: 110364. PMID: 38834154, DOI: 10.1016/j.radonc.2024.110364.Peer-Reviewed Original ResearchCopy number alterationsCell-free DNACancer patientsTumor fractionHead and neck cancer patientsPlasma cell-free DNAAssociated with tumor aggressivenessSCCHN patient samplesSystemic tumor spreadTumor-agnostic approachHigh-dose radiotherapyPlasma cfDNA samplesWhole-genome sequencingHead and neckCell-free DNA sequencing dataDetect viral DNAViral DNAOligometastatic patientsSCCHN patientsRadiotherapy guidelinesTumor spreadTumor aggressivenessImaging findingsCfDNA samplesTreatment strategiesSimple Contrastive Representation Learning for Time Series Forecasting
Zheng X, Chen X, Schürch M, Mollaysa A, Allam A, Krauthammer M. Simple Contrastive Representation Learning for Time Series Forecasting. 2024, 00: 6005-6009. DOI: 10.1109/icassp48485.2024.10446875.Peer-Reviewed Original ResearchFormer smoking, but not active smoking, is associated with delirium in postoperative ICU patients: a matched case-control study
Komninou M, Egli S, Rossi A, Ernst J, Krauthammer M, Schuepbach R, Delgado M, Bartussek J. Former smoking, but not active smoking, is associated with delirium in postoperative ICU patients: a matched case-control study. Frontiers In Psychiatry 2024, 15: 1347071. PMID: 38559401, PMCID: PMC10979642, DOI: 10.3389/fpsyt.2024.1347071.Peer-Reviewed Original ResearchIntensive care unitCase-control studyFormer smokingNon-delirious patientsAssociated with increased odds of deliriumActive smokersActive smokingNon-smokersSimplified Acute Physiology Score IIAcute Physiology Score IIRisk of postoperative deliriumSurgical intensive care unitIntensive care unit patientsIndependent risk factorGroup of patientsCritically ill patientsAssociated with deliriumAssociated with increased oddsOdds of deliriumIncidence of deliriumLogistic regression analysisOccurrence of deliriumPropensity score analysisMidazolam usageMorphine useFragmentstein—facilitating data reuse for cell-free DNA fragment analysis
Balázs Z, Gitchev T, Ivanković I, Krauthammer M. Fragmentstein—facilitating data reuse for cell-free DNA fragment analysis. Bioinformatics 2024, 40: btae017. PMID: 38224549, PMCID: PMC10805340, DOI: 10.1093/bioinformatics/btae017.Peer-Reviewed Original ResearchConceptsCopy number variantsNucleotide-level informationCell-free DNA sequencing dataDNA fragmentation analysisCell-free DNASensitive genomic dataFragment length analysisNucleosome occupancyBAM filesCommand-line toolSequence dataGenomic dataAnalysis of cell-free DNASequence informationGNU GPLv3Bioinformatics softwareFragment analysisFunctional analysisAlignment mapData sharingLength analysisFragmentsSimplified formatLimited data sharingGenome
2023
Exploring the Latest Highlights in Medical Natural Language Processing across Multiple Languages: A Survey
Shaitarova A, Zaghir J, Lavelli A, Krauthammer M, Rinaldi F. Exploring the Latest Highlights in Medical Natural Language Processing across Multiple Languages: A Survey. Yearbook Of Medical Informatics 2023, 32: 230-243. PMID: 38147865, PMCID: PMC10751112, DOI: 10.1055/s-0043-1768726.Peer-Reviewed Original ResearchConceptsLanguage modelNLP tasksNatural language processing researchTransformer-based language modelsLanguage processing researchMedical natural language processingNatural language processingCommon NLP tasksEuropean languagesLow-resource onesNLP downstream tasksMultiple languagesMedical NLPNLP researchMedical textsBiomedical NLPLanguage processingLanguageInformation lacunaClinical NLPInformation extractionMedical domainEntity recognitionNegation detectionDownstream tasksBoosting Radiology Report Generation by Infusing Comparison Prior
Kim S, Nooralahzadeh F, Rohanian M, Fujimoto K, Nishio M, Sakamoto R, Rinaldi F, Krauthammer M. Boosting Radiology Report Generation by Infusing Comparison Prior. 2023, 50-61. DOI: 10.18653/v1/2023.bionlp-1.4.Peer-Reviewed Original ResearchDisfluent Cues for Enhanced Speech Understanding in Large Language Models
Rohanian M, Nooralahzadeh F, Rohanian O, Clifton D, Krauthammer M. Disfluent Cues for Enhanced Speech Understanding in Large Language Models. 2023, 3676-3684. DOI: 10.18653/v1/2023.findings-emnlp.238.Peer-Reviewed Original Research
2016
RASopathy Gene Mutations in Melanoma
Halaban R, Krauthammer M. RASopathy Gene Mutations in Melanoma. Journal Of Investigative Dermatology 2016, 136: 1755-1759. PMID: 27236105, PMCID: PMC4992636, DOI: 10.1016/j.jid.2016.05.095.Peer-Reviewed Original ResearchConceptsRASopathy mutationsRAS/mitogen-activated protein kinaseRAS/mitogen-activated protein kinase (MAPK) pathwayMitogen-activated protein kinase pathwayMitogen-activated protein kinaseProtein kinase pathwayAmino acid substitutionsNext-generation sequencingProtein kinasePathway genesKinase pathwaySequencing dataDriver genesAcid substitutionsGenomic abnormalitiesMutationsLegius syndromeGenesAbundant mutationsGermline mutationsGene mutationsPathwaySignificant overlapKinaseMelanomagenesis
2015
Exome sequencing identifies recurrent mutations in NF1 and RASopathy genes in sun-exposed melanomas
Krauthammer M, Kong Y, Bacchiocchi A, Evans P, Pornputtapong N, Wu C, McCusker JP, Ma S, Cheng E, Straub R, Serin M, Bosenberg M, Ariyan S, Narayan D, Sznol M, Kluger HM, Mane S, Schlessinger J, Lifton RP, Halaban R. Exome sequencing identifies recurrent mutations in NF1 and RASopathy genes in sun-exposed melanomas. Nature Genetics 2015, 47: 996-1002. PMID: 26214590, PMCID: PMC4916843, DOI: 10.1038/ng.3361.Peer-Reviewed Original ResearchMeSH KeywordsAntineoplastic AgentsBenzimidazolesDNA Mutational AnalysisDrug Resistance, NeoplasmExomeGenetic Association StudiesGenetic Predisposition to DiseaseHumansInhibitory Concentration 50Kaplan-Meier EstimateLoss of HeterozygosityMaleMelanomaMutation, MissenseNeurofibromin 1Ras ProteinsSequence Analysis, RNASkin NeoplasmsSunlightTumor Cells, Cultured
2012
Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma
Krauthammer M, Kong Y, Ha BH, Evans P, Bacchiocchi A, McCusker J, Cheng E, Davis MJ, Goh G, Choi M, Ariyan S, Narayan D, Dutton-Regester K, Capatana A, Holman EC, Bosenberg M, Sznol M, Kluger HM, Brash DE, Stern DF, Materin MA, Lo RS, Mane S, Ma S, Kidd KK, Hayward NK, Lifton RP, Schlessinger J, Boggon TJ, Halaban R. Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma. Nature Genetics 2012, 44: 1006-1014. PMID: 22842228, PMCID: PMC3432702, DOI: 10.1038/ng.2359.Peer-Reviewed Original ResearchMeSH KeywordsAgedAged, 80 and overCase-Control StudiesDNA Mutational AnalysisExomeFemaleGene FrequencyGenetic Predisposition to DiseaseHumansMaleMelanomaMiddle AgedModels, MolecularMutationProto-Oncogene Proteins B-rafProto-Oncogene Proteins p21(ras)Rac1 GTP-Binding ProteinSequence Analysis, DNASkin NeoplasmsUveal NeoplasmsConceptsSun-exposed melanomasA semantic web framework to integrate cancer omics data with biological knowledge
Holford ME, McCusker JP, Cheung KH, Krauthammer M. A semantic web framework to integrate cancer omics data with biological knowledge. BMC Bioinformatics 2012, 13: s10. PMID: 22373303, PMCID: PMC3471346, DOI: 10.1186/1471-2105-13-s1-s10.Peer-Reviewed Original ResearchConceptsBiological knowledgeOmics dataSemantic modelFundamental biological knowledgeGene ontology dataCancer omics dataEpigenomic dataRegulatory networksSemantic Web technologiesTranscription factorsSemantic Web frameworkUnified data sourceGene promoterDemethylating agentApoptosis pathwayAnti-cancer therapySemantic WebSPARQL endpointsWeb technologiesRDF triplesWeb frameworkOntology dataData warehouseUniform interfaceReasoning tools
2008
Yale Image Finder (YIF): a new search engine for retrieving biomedical images
Xu S, McCusker J, Krauthammer M. Yale Image Finder (YIF): a new search engine for retrieving biomedical images. Bioinformatics 2008, 24: 1968-1970. PMID: 18614584, PMCID: PMC2732221, DOI: 10.1093/bioinformatics/btn340.Peer-Reviewed Original ResearchConceptsImage of interestSearch enginesBiomedical imagesNew search engineSimilar image contentsAccessible search enginesImage querySearch scenariosImage captionsRelevant imagesImage contentRelated imagesHigh-resolution imagesSearch keywordsPaper abstractsUsersResolution imagesImagesEngineFinderSource papersRelated papersQueriesJournal papersThumbnails