2025
Precision medicine in the pediatric and neonatal intensive care units through genomics
Duy P, Dylik B, Deniz E. Precision medicine in the pediatric and neonatal intensive care units through genomics. Current Opinion In Pediatrics 2025, 37: 211-215. PMID: 40298123, PMCID: PMC12055474, DOI: 10.1097/mop.0000000000001471.Peer-Reviewed Original ResearchConceptsNeonatal intensive care unitGenome-wide sequencing technologiesSingle nucleotide resolutionWhole-genome sequencingIntensive care unitGene therapyPrecision medicineNucleotide resolutionSequencing technologiesGenetic perturbationsGenomic medicineGenomic technologiesCare unitFDA-approved gene therapyGenetic associationGenetic diagnosisHuman disordersCritically Ill ChildrenOmics technologiesMolecular diagnosisGenetic conditionsDisease biologyClinically actionable findingsPathological workupDiagnostic adjunct
2024
A user guide to RT-based mapping of RNA modifications
Fang D, Babich J, Dangelmaier E, Wall V, Nachtergaele S. A user guide to RT-based mapping of RNA modifications. Methods In Enzymology 2024, 705: 51-79. PMID: 39389673, DOI: 10.1016/bs.mie.2024.07.006.Peer-Reviewed Original Research
2022
Integrative genome-wide analysis reveals EIF3A as a key downstream regulator of translational repressor protein Musashi 2 (MSI2)
Karmakar S, Ramirez O, Paul KV, Gupta AK, Kumari V, Botti V, de los Mozos IR, Neuenkirchen N, Ross RJ, Karanicolas J, Neugebauer KM, Pillai MM. Integrative genome-wide analysis reveals EIF3A as a key downstream regulator of translational repressor protein Musashi 2 (MSI2). NAR Cancer 2022, 4: zcac015. PMID: 35528200, PMCID: PMC9070473, DOI: 10.1093/narcan/zcac015.Peer-Reviewed Original ResearchRNA binding proteinMusashi-2Functional targetIntegrative genome-wide analysisGenome-wide analysisIndividual-nucleotide resolutionAsymmetric cell divisionCell fate decisionsThousands of mRNAsKey downstream regulatorProtein Musashi-2Polysome profilingFate decisionsEukaryotic translation initiation factor 3aNucleotide resolutionCell divisionDirect RNATranslational inductionCancer stem cellsDownstream regulatorsUntranslated regionIndirect targetsBinding proteinDirect targetMere bindingSecondary structural ensembles of the SARS-CoV-2 RNA genome in infected cells
Lan TCT, Allan MF, Malsick LE, Woo JZ, Zhu C, Zhang F, Khandwala S, Nyeo SSY, Sun Y, Guo JU, Bathe M, Näär A, Griffiths A, Rouskin S. Secondary structural ensembles of the SARS-CoV-2 RNA genome in infected cells. Nature Communications 2022, 13: 1128. PMID: 35236847, PMCID: PMC8891300, DOI: 10.1038/s41467-022-28603-2.Peer-Reviewed Original ResearchConceptsRNA genomeSARS-CoV-2 RNA genomeStructural ensemblesAlternative RNA conformationsSingle-nucleotide resolutionInfected cellsRNA biologyGenomic structureSARS-CoV-2 genomeCellular contextNucleotide resolutionFunctional characterizationGenomeRNA conformationEntire SARS-CoV-2 genomeProfiling studiesFull lengthRNAStimulation elementCellsBiologyBetacoronavirusesLittle experimental dataConformationPromotes
2011
Mapping copy number variation by population-scale genome sequencing
Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stütz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO. Mapping copy number variation by population-scale genome sequencing. Nature 2011, 470: 59-65. PMID: 21293372, PMCID: PMC3077050, DOI: 10.1038/nature09708.Peer-Reviewed Original ResearchConceptsMost structural variantsStructural variantsSequencing-based association studiesUnbalanced structural variantsGenomic structural variantsFunctional impactDNA sequencing dataSV hotspotsSV discoveryHuman genomeNucleotide resolutionGene disruptionAdditional structural variantsHigh-frequency deletionSequencing dataGenome sequencingAssociation studiesTandem duplicationNumber variationsGene deletionPartial gene deletionsDeletionCommon mechanismForm of variationSize spectra
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