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Instructor
Biography
Dr. Lin was recruited to the Adams Center from Harvard in 2024. He received his PhD at the prestigious Peking University, one of China’s highest ranked educational institutions under the tutelage of Prof. Xing Wang Deng, a fellow of the U.S. National Academy of Sciences in 2019.
Dr. Lin’s research is focused on revealing the causal relationships between genome variants, epigenetic marks, gene expression, and quantitative traits. Dr. Lin has published on complex and quantitative trait genetics during his graduate studies as first author in Lin et al. PNAS, 2020 and as co-first author in Wang*, Lin* et al., Nature Genetics, 2020.
In these high-profile publications, Dr. Lin honed the quantitative trait locus and causal inference analyses, that he is now applying at the single-cell level to Parkinson’s disease in the Parkinson Cell Atlas in 5D project.
Last Updated on November 17, 2025.
Appointments
Education & Training
- Postdoc Research Fellow
- Harvard Medical School/Brigham and Women's Hospital (2023)
- PhD
- Peking University, College of Life Sciences (2019)
Research
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Overview
My research programs are dedicated to a central question: how to translate these complex human brain-cell-spatial gene activity map into druggable targets of human brain diseases for combating complex diseases like Parkinson's? To address this question, my group is developing novel statistical model, and also apply statistical genetics, functional genomics, and computational biology approaches to construct a brain-cell-spatial gene activity map, and then reveal novel therapeutic strategies of Parkinson’s disease by connecting brain-cell-spatial gene regulation insights with disease risk.
ORCID
0000-0003-2270-5194- View Lab Website
Scherzer's Lab
Research at a Glance
Publications Timeline
A big-picture view of Zechuan Lin's research output by year.
20Publications
632Citations
Publications
2025
Experimental and Computational Methods for Allelic Imbalance Analysis from Single-Nucleus RNA-seq Data.
Simmons SK, Adiconis X, Haywood N, Parker J, Lin Z, Liao Z, Tuncali I, Al'Khafaji AM, Shin A, Jagadeesh K, Gosik K, Gatzen M, Smith JT, El Kodsi DN, Kuras Y, Baecher-Allan C, Serrano GE, Beach TG, Garimella K, Rozenblatt-Rosen O, Regev A, Dong X, Scherzer CR, Levin JZ. Experimental and Computational Methods for Allelic Imbalance Analysis from Single-Nucleus RNA-seq Data. BioRxiv 2025 PMID: 39185246, DOI: 10.1101/2024.08.13.607784.Peer-Reviewed Original Research
2022
qHD5 encodes an AP2 factor that suppresses rice heading by down-regulating Ehd2 expression
Sun B, Xue P, Wen X, Gong K, Wang B, Xu P, Lin Z, Peng Z, Fu J, Yu P, Sun L, Zhang Y, Cao L, Cao L, Cheng S, Wu W, Zhan X. qHD5 encodes an AP2 factor that suppresses rice heading by down-regulating Ehd2 expression. Plant Science 2022, 324: 111446. PMID: 36041562, DOI: 10.1016/j.plantsci.2022.111446.Peer-Reviewed Original ResearchCitationsMeSH Keywords and ConceptsConceptsHomozygous mutant linesTransactivation activity assayLong-day conditionsSemi-dominant geneExpansion of cultivationHeading dateRice reproductionAP2 transcription factorsRice headingQHD5QRT-PCR analysisRice domesticationShort daysMutant linesRiceAP2 factorsGeographic expansionGene editing experimentsTransient expressionQRT-PCRFlowersAP2Activity assayIndicaProgenyThe telomere‐to‐telomere gap‐free genome of four rice parents reveals SV and PAV patterns in hybrid rice breeding
Zhang Y, Fu J, Wang K, Han X, Yan T, Su Y, Li Y, Lin Z, Qin P, Fu C, Deng X, Zhou D, Yang Y, He H. The telomere‐to‐telomere gap‐free genome of four rice parents reveals SV and PAV patterns in hybrid rice breeding. Plant Biotechnology Journal 2022, 20: 1642-1644. PMID: 35748695, PMCID: PMC9398309, DOI: 10.1111/pbi.13880.Peer-Reviewed Original ResearchCitationsMeSH Keywords and ConceptsTranscriptome profiling of two super hybrid rice provides insights into the genetic basis of heterosis
Fu J, Zhang Y, Yan T, Li Y, Jiang N, Zhou Y, Zhou Q, Qin P, Fu C, Lin H, Zhong J, Han X, Lin Z, Wang F, He H, Wang K, Yang Y. Transcriptome profiling of two super hybrid rice provides insights into the genetic basis of heterosis. BMC Plant Biology 2022, 22: 314. PMID: 35773646, PMCID: PMC9245205, DOI: 10.1186/s12870-022-03697-4.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsAllele-specifically expressed genesSuper hybrid riceHybrid riceGenetic bases of heterosisSuper hybrid rice varietiesMolecular basis of heterosisHybrid rice varietiesExploitation of heterosisHybrid rice breedingUtilization of heterosisFormation of heterosisIonotropic glutamate receptor signaling pathwayExpressed genesGenetic basisTranscriptome profilingResponse to water deprivationRice breedingRice varietiesYoung paniclesMolecular basisGlutamate receptor signaling pathwayRice productionHeterosisAmino acid sensorsRiceGenomic insights on the contribution of introgressions from Xian/Indica to the genetic improvement of Geng/Japonica rice cultivars
Cui D, Zhou H, Ma X, Lin Z, Sun L, Han B, Li M, Sun J, Liu J, Jin G, Wang X, Cao G, Deng X, He H, Han L. Genomic insights on the contribution of introgressions from Xian/Indica to the genetic improvement of Geng/Japonica rice cultivars. Plant Communications 2022, 3: 100325. PMID: 35576158, PMCID: PMC9251437, DOI: 10.1016/j.xplc.2022.100325.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsRice cultivarsGenetic improvementTrait improvementDisease resistanceImprovement of plant typeContribution of introgressionGenetic effects of genesGenetic effectsGenomic contributionYield componentsPanicle numberTillering plantsGrain numberPlant ideotypePanicle sizeBreeding pedigreesGenomic landscape analysisPi-d2Plant architectureCultivarsTranscription factor genesPlant typesGenomic breedingGene haplotypesRice
2020
Genome-wide selection and genetic improvement during modern maize breeding
Wang B, Lin Z, Li X, Zhao Y, Zhao B, Wu G, Ma X, Wang H, Xie Y, Li Q, Song G, Kong D, Zheng Z, Wei H, Shen R, Wu H, Chen C, Meng Z, Wang T, Li Y, Li X, Chen Y, Lai J, Hufford M, Ross-Ibarra J, He H, Wang H. Genome-wide selection and genetic improvement during modern maize breeding. Nature Genetics 2020, 52: 565-571. PMID: 32341525, DOI: 10.1038/s41588-020-0616-3.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsModern maize breedingMaize breedingMaize breeding programsElite inbred linesGenome-wide selectionBreeding signaturesMaize yieldBreeding programsGenetic improvementInbred linesAgronomic phenotypesBreedingGenome-wide associationPhenotypic changesTargets of selectionMaizeGenomic regionsGenomic basisTwentieth century1GermplasmPlantsYieldChronological samplesToleranceLociThe Asymmetric Expression of SAUR Genes Mediated by ARF7/19 Promotes the Gravitropism and Phototropism of Plant Hypocotyls
Wang X, Yu R, Wang J, Lin Z, Han X, Deng Z, Fan L, He H, Deng X, Chen H. The Asymmetric Expression of SAUR Genes Mediated by ARF7/19 Promotes the Gravitropism and Phototropism of Plant Hypocotyls. Cell Reports 2020, 31: 107529. PMID: 32320660, DOI: 10.1016/j.celrep.2020.107529.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsSubfamily genesSAUR genesAsymmetric expressionPhototropic responseEctopic expressionAsymmetric distribution of auxinTropic responsesAsymmetric auxin distributionDownstream of auxinLateral redistribution of auxinRedistribution of auxinDistribution of auxinPlant hypocotylGrowth of hypocotylsAuxin distributionSAUR19Arabidopsis hypocotylsGenesSoybean hypocotylsLateral redistributionAuxinARF7ArabidopsisHypocotylBending growthDivergent selection and genetic introgression shape the genome landscape of heterosis in hybrid rice
Lin Z, Qin P, Zhang X, Fu C, Deng H, Fu X, Huang Z, Jiang S, Li C, Tang X, Wang X, He G, Yang Y, He H, Deng X. Divergent selection and genetic introgression shape the genome landscape of heterosis in hybrid rice. Proceedings Of The National Academy Of Sciences Of The United States Of America 2020, 117: 4623-4631. PMID: 32071222, PMCID: PMC7060695, DOI: 10.1073/pnas.1919086117.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsHeterotic lociHybrid riceRice subpopulationsHybrid rice varietiesGenomic landscapeRice hybrid breedingPyramiding breedingHybrid breedingRice varietiesRice landracesWild riceFemale parentHybrid parentsRice productionHeterosisField trialsGenome resequencingSNP chipGenomic introgressionRiceDivergent selectionExogenous genomesGenetic basisBreedingGenetic mechanisms
2019
The hybrid protein interactome contributes to rice heterosis as epistatic effects
Li H, Jiang S, Li C, Liu L, Lin Z, He H, Deng X, Zhang Z, Wang X. The hybrid protein interactome contributes to rice heterosis as epistatic effects. The Plant Journal 2019, 102: 116-128. PMID: 31736145, DOI: 10.1111/tpj.14616.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsEpistatic effectsParental genomesMetabolic biosynthesis pathwaysMetabolic gene clustersGenomic selection analysesGenomic divergenceInteractome datasetsPPI predictionGene clusterGenomic variationProtein interactomeGenomic regionsBiosynthesis pathwayEpistasis interactionsInteraction partnersCultivar NipponbareInteractomeTrait predictionSelection analysisHybrid progenyGenetic effectsMetabolic enzymesGenetic hypothesisRice heterosisGenome
2017
Genome-wide study of an elite rice pedigree reveals a complex history of genetic architecture for breeding improvement
Chen S, Lin Z, Zhou D, Wang C, Li H, Yu R, Deng H, Tang X, Zhou S, Wang Deng X, He H. Genome-wide study of an elite rice pedigree reveals a complex history of genetic architecture for breeding improvement. Scientific Reports 2017, 7: 45685. PMID: 28374863, PMCID: PMC5379486, DOI: 10.1038/srep45685.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsQuantitative trait lociMinor-effect quantitative trait lociBreeding improvementEffect quantitative trait lociLow levels of phenotypic variationConventional indica riceGenotypes of quantitative trait lociGenetic architectureLevels of phenotypic variationExcellent cultivarsIndica riceBreeding workCrop breedingTrait improvementBreeding generationsMolecular breedingTrait lociBreedingHuanghuazhanPhenotypic variationSelective sweepsCultivarsPhenotypic dataTraitsGenomic regions
Academic Achievements & Community Involvement
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Honors
honor Resource-Limited Award
10/14/2025National AwardThe American Society for Human GeneticsDetailsUnited States
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101 College Street
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Fl 10, Ste 1029
New Haven, CT 06510