@article{ozsoy_yilmaz_patlar_emecen_durmaz_magwire_zhou_huang_anholt_mackay_2021, title={Epistasis for head morphology in Drosophila melanogaster}, volume={11}, ISSN={["2160-1836"]}, DOI={10.1093/g3journal/jkab285}, abstractNote={Abstract}, number={10}, journal={G3-GENES GENOMES GENETICS}, author={Ozsoy, Ergi D. and Yilmaz, Murat and Patlar, Bahar and Emecen, Guzin and Durmaz, Esra and Magwire, Michael M. and Zhou, Shanshan and Huang, Wen and Anholt, Robert R. H. and Mackay, Trudy F. C.}, year={2021}, month={Oct} }
 @article{everett_huang_zhou_carbone_lyman_arya_geisz_ma_morgante_st armour_et al._2020, title={Gene expression networks in the Drosophila Genetic Reference Panel}, volume={30}, ISSN={["1549-5469"]}, DOI={10.1101/gr.257592.119}, abstractNote={A major challenge in modern biology is to understand how naturally occurring variation in DNA sequences affects complex organismal traits through networks of intermediate molecular phenotypes. This question is best addressed in a genetic mapping population in which all molecular polymorphisms are known and for which molecular endophenotypes and complex traits are assessed on the same genotypes. Here, we performed deep RNA sequencing of 200 Drosophila Genetic Reference Panel inbred lines with complete genome sequences and for which phenotypes of many quantitative traits have been evaluated. We mapped expression quantitative trait loci for annotated genes, novel transcribed regions, transposable elements, and microbial species. We identified host variants that affect expression of transposable elements, independent of their copy number, as well as microbiome composition. We constructed sex-specific expression quantitative trait locus regulatory networks. These networks are enriched for novel transcribed regions and target genes in heterochromatin and euchromatic regions of reduced recombination, as well as genes regulating transposable element expression. This study provides new insights regarding the role of natural genetic variation in regulating gene expression and generates testable hypotheses for future functional analyses.}, number={3}, journal={GENOME RESEARCH}, author={Everett, Logan J. and Huang, Wen and Zhou, Shanshan and Carbone, Mary Anna and Lyman, Richard F. and Arya, Gunjan H. and Geisz, Matthew S. and Ma, Junwu and Morgante, Fabio and St Armour, Genevieve and et al.}, year={2020}, month={Mar}, pages={485–496} }
 @article{zhou_morgante_geisz_ma_anholt_mackay_2020, title={Systems genetics of the Drosophila metabolome}, volume={30}, ISSN={["1549-5469"]}, DOI={10.1101/gr.243030.118}, abstractNote={How effects of DNA sequence variants are transmitted through intermediate endophenotypes to modulate organismal traits remains a central question in quantitative genetics. This problem can be addressed through a systems approach in a population in which genetic polymorphisms, gene expression traits, metabolites, and complex phenotypes can be evaluated on the same genotypes. Here, we focused on the metabolome, which represents the most proximal link between genetic variation and organismal phenotype, and quantified metabolite levels in 40 lines of the Drosophila melanogaster Genetic Reference Panel. We identified sex-specific modules of genetically correlated metabolites and constructed networks that integrate DNA sequence variation and variation in gene expression with variation in metabolites and organismal traits, including starvation stress resistance and male aggression. Finally, we asked to what extent SNPs and metabolites can predict trait phenotypes and generated trait- and sex-specific prediction models that provide novel insights about the metabolomic underpinnings of complex phenotypes.}, number={3}, journal={GENOME RESEARCH}, author={Zhou, Shanshan and Morgante, Fabio and Geisz, Matthew S. and Ma, Junwu and Anholt, Robert R. H. and Mackay, Trudy F. C.}, year={2020}, month={Mar}, pages={392–405} }
 @article{zhou_campbell_stone_mackay_anholt_2012, title={Phenotypic Plasticity of the Drosophila Transcriptome}, volume={8}, ISSN={["1553-7404"]}, DOI={10.1371/journal.pgen.1002593}, abstractNote={Phenotypic plasticity is the ability of a single genotype to produce different phenotypes in response to changing environments. We assessed variation in genome-wide gene expression and four fitness-related phenotypes of an outbred Drosophila melanogaster population under 20 different physiological, social, nutritional, chemical, and physical environments; and we compared the phenotypically plastic transcripts to genetically variable transcripts in a single environment. The environmentally sensitive transcriptome consists of two transcript categories, which comprise ∼15% of expressed transcripts. Class I transcripts are genetically variable and associated with detoxification, metabolism, proteolysis, heat shock proteins, and transcriptional regulation. Class II transcripts have low genetic variance and show sexually dimorphic expression enriched for reproductive functions. Clustering analysis of Class I transcripts reveals a fragmented modular organization and distinct environmentally responsive transcriptional signatures for the four fitness-related traits. Our analysis suggests that a restricted environmentally responsive segment of the transcriptome preserves the balance between phenotypic plasticity and environmental canalization.}, number={3}, journal={PLOS GENETICS}, author={Zhou, Shanshan and Campbell, Terry G. and Stone, Eric A. and Mackay, Trudy F. C. and Anholt, Robert R. H.}, year={2012}, month={Mar} }
 @article{zhou_luoma_armour_thakkar_mackay_anholt, title={A drosophila model for toxicogenomics: Genetic variation in susceptibility to heavy metal exposure}, volume={13}, number={7}, journal={PLoS Genetics}, author={Zhou, S. S. and Luoma, S. E. and Armour, G. E. S. and Thakkar, E. and Mackay, T. F. C. and Anholt, R. R. H.} }
 @article{garlapow_everett_zhou_gearhart_fay_huang_morozova_arya_turlapati_st armour_et al., title={Genetic and genomic response to selection for food consumption in Drosophila melanogaster}, volume={47}, number={2}, journal={Behavior Genetics}, author={Garlapow, M. E. and Everett, L. J. and Zhou, S. S. and Gearhart, A. W. and Fay, K. A. and Huang, W. and Morozova, T. V. and Arya, G. H. and Turlapati, L. and St Armour, G. and et al.}, pages={227–243} }
 @article{zhou_stone_mackay_anholt, title={Plasticity of the chemoreceptor repertoire in Drosophila melanogaster}, volume={5}, number={10}, journal={PLoS Genetics}, author={Zhou, S. S. and Stone, E. A. and Mackay, T. F. C. and Anholt, R. R. H.} }
 @article{zhou_morozova_hussain_luoma_mccoy_yamamoto_mackay_anholt, title={The genetic basis for variation in sensitivity to lead toxicity in Drosophila melanogaster}, volume={124}, number={7}, journal={Environmental Health Perspectives}, author={Zhou, S. S. and Morozova, T. V. and Hussain, Y. N. and Luoma, S. E. and McCoy, L. and Yamamoto, A. and Mackay, T. F. C. and Anholt, R. R. H.}, pages={1062–1070} }
 @article{carnes_campbell_huang_butler_carbone_duncan_harbajan_king_peterson_weitzel_et al., title={The genomic basis of postponed senescence in Drosophila melanogaster}, volume={10}, number={9}, journal={PLoS One}, author={Carnes, M. U. and Campbell, T. and Huang, W. and Butler, D. G. and Carbone, M. A. and Duncan, L. H. and Harbajan, S. V. and King, E. M. and Peterson, K. R. and Weitzel, A. and et al.} }
 @article{zhou_mackay_anholt, title={Tuning the chemosensory window A fly's perspective}, volume={4}, number={3}, journal={Fly}, author={Zhou, S. S. and Mackay, T. F. C. and Anholt, R. R. H.}, pages={230–235} }