2025
Structural insights into RNA targeting with de novo small molecule
Xu L, Chung K, Liu T, Pyle A. Structural insights into RNA targeting with de novo small molecule. Structural Dynamics 2025, 12: a41-a41. DOI: 10.1063/4.0000350.Peer-Reviewed Original ResearchRNA-small molecule interactionsChemical space explorationRNA-ligand recognitionMedicinal chemistry campaignHigh-throughput screening assayChemistry campaignSelf-splicing intronsInhibitor discoveryNon-coding genesMolecule interactionsCryo-EM structureSmall moleculesAtomic detailRNA bindersStructural insightsMolecular interactionsC. albicansTarget RNASplicing inhibitorsGene productsRNA moleculesRNA targetsDruggable genomeDrug developmentMolecules
2022
Building integrative functional maps of gene regulation
Xu J, Pratt HE, Moore JE, Gerstein MB, Weng Z. Building integrative functional maps of gene regulation. Human Molecular Genetics 2022, 31: r114-r122. PMID: 36083269, PMCID: PMC9585680, DOI: 10.1093/hmg/ddac195.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsGene regulationRegulatory mapSame genetic informationNon-coding genesSuch regulatory elementsEvolutionary analysisHuman genomeRegulatory elementsGenetic informationGene expressionType diversityRegulatory roleGenomeBase pairsIndividual cellsFunctional assaysSpecific functionsRegulationCellsFunctional mapsGenesDNADiversityCopiesSequence
2020
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes
Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, Shuai S, Lanzós A, Herrmann C, Maruvka YE, Shen C, Amin SB, Bandopadhayay P, Bertl J, Boroevich KA, Busanovich J, Carlevaro-Fita J, Chakravarty D, Chan CWY, Craft D, Dhingra P, Diamanti K, Fonseca NA, Gonzalez-Perez A, Guo Q, Hamilton MP, Haradhvala NJ, Hong C, Isaev K, Johnson TA, Juul M, Kahles A, Kahraman A, Kim Y, Komorowski J, Kumar K, Kumar S, Lee D, Lehmann KV, Li Y, Liu EM, Lochovsky L, Park K, Pich O, Roberts ND, Saksena G, Schumacher SE, Sidiropoulos N, Sieverling L, Sinnott-Armstrong N, Stewart C, Tamborero D, Tubio JMC, Umer HM, Uusküla-Reimand L, Wadelius C, Wadi L, Yao X, Zhang CZ, Zhang J, Haber JE, Hobolth A, Imielinski M, Kellis M, Lawrence MS, von Mering C, Nakagawa H, Raphael BJ, Rubin MA, Sander C, Stein LD, Stuart JM, Tsunoda T, Wheeler DA, Johnson R, Reimand J, Gerstein M, Khurana E, Campbell PJ, López-Bigas N, Weischenfeldt J, Beroukhim R, Martincorena I, Pedersen J, Getz G. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature 2020, 578: 102-111. PMID: 32025015, PMCID: PMC7054214, DOI: 10.1038/s41586-020-1965-x.Peer-Reviewed Original ResearchConceptsInternational Cancer Genome ConsortiumStructural variantsPoint mutationsDriver discoveryProtein-coding genesNon-coding genesNon-coding regionsPan-cancer analysisDriver point mutationsSomatic driversCancer Genome AtlasRegulatory sequencesCancer genomesUntranslated regionGenome ConsortiumFocal deletionsGenesGenome AtlasGenomeNovel candidatesMutationsRecurrent breakpointsRegion of TP53DiscoveryVariants
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