Featured Publications
Deconvolution of in vivo protein-RNA contacts using fractionated eCLIP-seq
Biancon G, Busarello E, Joshi P, Lesch B, Halene S, Tebaldi T. Deconvolution of in vivo protein-RNA contacts using fractionated eCLIP-seq. STAR Protocols 2022, 3: 101823. PMID: 36595959, PMCID: PMC9676202, DOI: 10.1016/j.xpro.2022.101823.Peer-Reviewed Original ResearchConceptsProtein-RNA interactionsIndividual RNA-binding proteinsTranscriptome-wide analysisThousands of RNAsProtein-RNA contactsRNA-binding proteinSingle nucleotide levelComputational analysis pipelineRNA processingMulticomponent complexesRNA immunoprecipitationRead countsComplete detailsAnalysis pipelineAdditional levelProteinImmunoprecipitationRNAInteractionComplexesIs it the time to integrate novel sequencing technologies into clinical practice?
VanOudenhove J, Halene S, Mendez L. Is it the time to integrate novel sequencing technologies into clinical practice? Current Opinion In Hematology 2022, 30: 70-77. PMID: 36602939, DOI: 10.1097/moh.0000000000000754.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsMeSH KeywordsGenetic Association StudiesHigh-Throughput Nucleotide SequencingHumansMutationSequence Analysis, DNAConceptsNovel sequencing technologiesSequencing technologiesUnprecedented biological insightsNext-generation sequencing techniquesDNA sequencing technologiesHigh-throughput NGSRare cell populationsBiological insightsMultiomics approachSequencing techniquesGenotype-phenotype correlationClonal diversityCellular resolutionMechanistic insightsCell populationsPhenotype correlationMyeloid diseasesClonesClonal hierarchyClonal haematopoiesisResidual clonesInsightsSeqDiversityImproved capture
2022
Spatial profiling of chromatin accessibility in mouse and human tissues
Deng Y, Bartosovic M, Ma S, Zhang D, Kukanja P, Xiao Y, Su G, Liu Y, Qin X, Rosoklija GB, Dwork AJ, Mann JJ, Xu ML, Halene S, Craft JE, Leong KW, Boldrini M, Castelo-Branco G, Fan R. Spatial profiling of chromatin accessibility in mouse and human tissues. Nature 2022, 609: 375-383. PMID: 35978191, PMCID: PMC9452302, DOI: 10.1038/s41586-022-05094-1.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBrainCell DifferentiationCell LineageChromatinChromatin Assembly and DisassemblyChromatin Immunoprecipitation SequencingEpigenomicsGene Expression ProfilingGenomeHigh-Throughput Nucleotide SequencingHumansMicePalatine TonsilConceptsChromatin accessibilityATAC-seqSpecific epigenetic landscapesChromatin accessibility profilingCell fate decisionsEpigenetic informationEpigenetic landscapeGenome scaleFate decisionsAccessible genomeCell identityEpigenetic underpinningsNext-generation sequencingGene regulatorsCell statesMouse embryosSpatial biologySpatial transcriptomicsCell typesCellular levelImmune cell typesDistinct organizationHuman tissuesProfilingSpatial profiling
2019
The minimal that kills: Why defining and targeting measurable residual disease is the “Sine Qua Non” for further progress in management of acute myeloid leukemia
Bewersdorf JP, Shallis RM, Boddu PC, Wood B, Radich J, Halene S, Zeidan AM. The minimal that kills: Why defining and targeting measurable residual disease is the “Sine Qua Non” for further progress in management of acute myeloid leukemia. Blood Reviews 2019, 43: 100650. PMID: 31883804, DOI: 10.1016/j.blre.2019.100650.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsMeSH KeywordsAnimalsDisease ManagementHigh-Throughput Nucleotide SequencingHumansImmune Checkpoint InhibitorsLeukemia, Myeloid, AcuteNeoplasm, ResidualConceptsAcute myeloid leukemiaMyeloid leukemiaHard clinical outcomesClinical trial evidenceMeasurable residual diseaseResidual leukemic cellsRisk of relapseApprovable endpointsMRD statusDeep remissionMorphologic remissionMRD assessmentOverall survivalMRD levelsClinical outcomesDisease relapseInitial treatmentResidual diseaseTrial evidenceClinical trialsTreatment decisionsSurrogate endpointsBone marrowPreemptive interventionLeukemic cells