2024
A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders
Lee A, Ayers L, Kosicki M, Chan W, Fozo L, Pratt B, Collins T, Zhao B, Rose M, Sanchis-Juan A, Fu J, Wong I, Zhao X, Tenney A, Lee C, Laricchia K, Barry B, Bradford V, Jurgens J, England E, Lek M, MacArthur D, Lee E, Talkowski M, Brand H, Pennacchio L, Engle E. A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders. Nature Communications 2024, 15: 8268. PMID: 39333082, PMCID: PMC11436875, DOI: 10.1038/s41467-024-52463-7.Peer-Reviewed Original ResearchConceptsNon-coding variantsCranial motor neuronsMendelian disordersIn vivo transgenic assayPredictor of enhancer activityCis-regulatory elementsMulti-omic frameworkWhole-genome sequencingEnhanced activityVariant discoveryGenome sequenceChromatin accessibilityPutative enhancersHistone modificationsRegulatory elementsGene expression assaysGene predictionTransgenic assaysEpigenomic profilingMendelian casesExpression assaysMutational enhancementCongenital cranial dysinnervation disordersCell typesFunctional impactCGMega: explainable graph neural network framework with attention mechanisms for cancer gene module dissection
Li H, Han Z, Sun Y, Wang F, Hu P, Gao Y, Bai X, Peng S, Ren C, Xu X, Liu Z, Chen H, Yang Y, Bo X. CGMega: explainable graph neural network framework with attention mechanisms for cancer gene module dissection. Nature Communications 2024, 15: 5997. PMID: 39013885, PMCID: PMC11252405, DOI: 10.1038/s41467-024-50426-6.Peer-Reviewed Original Research
2023
Enhancing Cancer Gene Prediction through Aligned Fusion of Multiple PPI Networks Using Graph Transformer Models
Han Z, Yu G, Yang Y. Enhancing Cancer Gene Prediction through Aligned Fusion of Multiple PPI Networks Using Graph Transformer Models. 2023, 00: 542-547. DOI: 10.1109/bibm58861.2023.10385593.Peer-Reviewed Original ResearchProtein-protein interaction networkProtein-protein interactionsCancer gene predictionCancer genesGene predictionCancer cell line datasetsGene interaction relationshipsCell line datasetsCancer driver genesMulti-omics dataPan-cancer datasetProtein-proteinPPI networkGene associationsGene representationMulti-OmicsDriver genesGenesGraph neural networksCancer researchGraph transformer networkState-of-the-art performanceCancerState-of-the-artGraph transformation model
2022
The complete sequence of a human genome
Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze AV, Mikheenko A, Vollger MR, Altemose N, Uralsky L, Gershman A, Aganezov S, Hoyt SJ, Diekhans M, Logsdon GA, Alonge M, Antonarakis SE, Borchers M, Bouffard GG, Brooks SY, Caldas GV, Chen NC, Cheng H, Chin CS, Chow W, de Lima LG, Dishuck PC, Durbin R, Dvorkina T, Fiddes IT, Formenti G, Fulton RS, Fungtammasan A, Garrison E, Grady PGS, Graves-Lindsay TA, Hall IM, Hansen NF, Hartley GA, Haukness M, Howe K, Hunkapiller MW, Jain C, Jain M, Jarvis ED, Kerpedjiev P, Kirsche M, Kolmogorov M, Korlach J, Kremitzki M, Li H, Maduro VV, Marschall T, McCartney AM, McDaniel J, Miller DE, Mullikin JC, Myers EW, Olson ND, Paten B, Peluso P, Pevzner PA, Porubsky D, Potapova T, Rogaev EI, Rosenfeld JA, Salzberg SL, Schneider VA, Sedlazeck FJ, Shafin K, Shew CJ, Shumate A, Sims Y, Smit AFA, Soto DC, Sović I, Storer JM, Streets A, Sullivan BA, Thibaud-Nissen F, Torrance J, Wagner J, Walenz BP, Wenger A, Wood JMD, Xiao C, Yan SM, Young AC, Zarate S, Surti U, McCoy RC, Dennis MY, Alexandrov IA, Gerton JL, O’Neill R, Timp W, Zook JM, Schatz MC, Eichler EE, Miga KH, Phillippy AM. The complete sequence of a human genome. Science 2022, 376: 44-53. PMID: 35357919, PMCID: PMC9186530, DOI: 10.1126/science.abj6987.Peer-Reviewed Original ResearchConceptsHuman genomeRecent segmental duplicationsHuman reference genomeProtein codingSegmental duplicationsGapless assemblyHeterochromatic regionsReference genomeGene predictionSatellite arraysComplete sequenceGenomeAcrocentric chromosomesPair sequenceBase pairsShort armFunctional studiesChromosomesSequenceComplex regionTelomeresDuplicationRegionAssemblyConsortium
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