2023
iHerd: an integrative hierarchical graph representation learning framework to quantify network changes and prioritize risk genes in disease
Duan Z, Dai Y, Hwang A, Lee C, Xie K, Xiao C, Xu M, Girgenti M, Zhang J. iHerd: an integrative hierarchical graph representation learning framework to quantify network changes and prioritize risk genes in disease. PLOS Computational Biology 2023, 19: e1011444. PMID: 37695793, PMCID: PMC10513318, DOI: 10.1371/journal.pcbi.1011444.Peer-Reviewed Original ResearchConceptsDriver genesRisk genesCritical cellular functionsDeeper molecular insightsDivergent genesPhenotypic variationCellular functionsTranscriptome perturbationsGene embeddingsGCN analysisGene prioritizationPathway levelDifferent genesGene classificationMolecular insightsGenesNetwork modulesComplex networksDifferent diseasesHierarchical levelsCells
2022
Molecular and cellular evolution of the primate dorsolateral prefrontal cortex
Ma S, Skarica M, Li Q, Xu C, Risgaard RD, Tebbenkamp ATN, Mato-Blanco X, Kovner R, Krsnik Ž, de Martin X, Luria V, Martí-Pérez X, Liang D, Karger A, Schmidt DK, Gomez-Sanchez Z, Qi C, Gobeske KT, Pochareddy S, Debnath A, Hottman CJ, Spurrier J, Teo L, Boghdadi AG, Homman-Ludiye J, Ely JJ, Daadi EW, Mi D, Daadi M, Marín O, Hof PR, Rasin MR, Bourne J, Sherwood CC, Santpere G, Girgenti MJ, Strittmatter SM, Sousa AMM, Sestan N. Molecular and cellular evolution of the primate dorsolateral prefrontal cortex. Science 2022, 377: eabo7257. PMID: 36007006, PMCID: PMC9614553, DOI: 10.1126/science.abo7257.Peer-Reviewed Original ResearchConceptsMolecular differencesSingle-nucleus transcriptomesSubset of speciesNeuropsychiatric risk genesCellular evolutionCellular repertoireEvolutionary specializationDorsolateral prefrontal cortexRate-limiting enzymeDivergent featuresRisk genesAnthropoid primatesPrefrontal cortexPrimate dorsolateral prefrontal cortexCertain interneuronsNeuropeptide somatostatinDopamine productionGranular neuronsTyrosine hydroxylaseCell subtypesExpressionTranscriptomeAdult humansGenesPrimates