@article{yamamoto_huang_anholt_mackay_2024, title={Article The genetic basis of variation in Drosophila melanogaster mating behavior}, volume={27}, ISSN={["2589-0042"]}, DOI={10.1016/j.isci.2024.109837}, abstractNote={Mating behavior is an essential fitness trait. We used the inbred, sequenced lines of the}, number={5}, journal={ISCIENCE}, author={Yamamoto, Akihiko and Huang, Wen and Anholt, Robert R. H. and Mackay, Trudy F. C.}, year={2024}, month={May} }
 @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{baker_carbone_huang_anholt_mackay_2021, title={Genetic basis of variation in cocaine and methamphetamine consumption in outbred populations of Drosophila melanogaster}, volume={118}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.2104131118}, abstractNote={Significance}, number={23}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Baker, Brandon M. and Carbone, Mary Anna and Huang, Wen and Anholt, Robert R. H. and Mackay, Trudy F. C.}, year={2021}, month={Jun} }
 @article{huang_campbell_carbone_jones_unselt_anholt_mackay_2020, title={Context-dependent genetic architecture of Drosophila life span}, volume={18}, ISSN={["1545-7885"]}, DOI={10.1371/journal.pbio.3000645}, abstractNote={Understanding the genetic basis of variation in life span is a major challenge that is difficult to address in human populations. Evolutionary theory predicts that alleles affecting natural variation in life span will have properties that enable them to persist in populations at intermediate frequencies, such as late-life–specific deleterious effects, antagonistic pleiotropic effects on early and late-age fitness components, and/or sex- and environment-specific or antagonistic effects. Here, we quantified variation in life span in males and females reared in 3 thermal environments for the sequenced, inbred lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) and an advanced intercross outbred population derived from a subset of DGRP lines. Quantitative genetic analyses of life span and the micro-environmental variance of life span in the DGRP revealed significant genetic variance for both traits within each sex and environment, as well as significant genotype-by-sex interaction (GSI) and genotype-by-environment interaction (GEI). Genome-wide association (GWA) mapping in both populations implicates over 2,000 candidate genes with sex- and environment-specific or antagonistic pleiotropic allelic effects. Over 1,000 of these genes are associated with variation in life span in other D. melanogaster populations. We functionally assessed the effects of 15 candidate genes using RNA interference (RNAi): all affected life span and/or micro-environmental variance of life span in at least one sex and environment and exhibited sex-and environment-specific effects. Our results implicate novel candidate genes affecting life span and suggest that variation for life span may be maintained by variable allelic effects in heterogeneous environments.}, number={3}, journal={PLOS BIOLOGY}, author={Huang, Wen and Campbell, Terry and Carbone, Mary Anna and Jones, W. Elizabeth and Unselt, Desiree and Anholt, Robert R. H. and Mackay, Trudy F. C.}, year={2020}, month={Mar} }
 @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{parker_kohn_spirina_mcmillen_huang_mackay_2020, title={Genetic Basis of Increased Lifespan and Postponed Senescence in Drosophila melanogaster}, volume={10}, ISSN={["2160-1836"]}, DOI={10.1534/g3.120.401041}, abstractNote={Abstract}, number={3}, journal={G3-GENES GENOMES GENETICS}, author={Parker, Grace A. and Kohn, Nathan and Spirina, Ally and McMillen, Anna and Huang, Wen and Mackay, Trudy F. C.}, year={2020}, month={Mar}, pages={1087–1098} }
 @article{yanagawa_huang_yamamoto_wada-katsumata_schal_mackay_2020, title={Genetic Basis of Natural Variation in Spontaneous Grooming in Drosophila melanogaster}, volume={10}, ISSN={["2160-1836"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85090276700&partnerID=MN8TOARS}, DOI={10.1534/g3.120.401360}, abstractNote={Abstract}, number={9}, journal={G3-GENES GENOMES GENETICS}, author={Yanagawa, Aya and Huang, Wen and Yamamoto, Akihiko and Wada-Katsumata, Ayako and Schal, Coby and Mackay, Trudy F. C.}, year={2020}, month={Sep}, pages={3453–3460} }
 @article{huang_carbone_lyman_anholt_mackay_2020, title={Genotype by environment interaction for gene expression in Drosophila melanogaster}, volume={11}, ISSN={["2041-1723"]}, DOI={10.1038/s41467-020-19131-y}, abstractNote={Abstract}, number={1}, journal={NATURE COMMUNICATIONS}, author={Huang, Wen and Carbone, Mary Anna and Lyman, Richard F. and Anholt, Robert R. H. and Mackay, Trudy F. C.}, year={2020}, month={Oct} }
 @article{morgante_huang_sorensen_maltecca_mackay_2020, title={Leveraging Multiple Layers of Data To Predict Drosophila Complex Traits}, volume={10}, ISSN={["2160-1836"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85097210372&partnerID=MN8TOARS}, DOI={10.1534/g3.120.401847}, abstractNote={Abstract}, number={12}, journal={G3-GENES GENOMES GENETICS}, author={Morgante, Fabio and Huang, Wen and Sorensen, Peter and Maltecca, Christian and Mackay, Trudy F. C.}, year={2020}, month={Dec}, pages={4599–4613} }
 @article{matute_comeault_earley_serrato-capuchina_peede_monroy-eklund_huang_jones_mackay_coyne_2020, title={Rapid and Predictable Evolution of Admixed Populations Between Two Drosophila Species Pairs}, volume={214}, ISSN={["1943-2631"]}, DOI={10.1534/genetics.119.302685}, abstractNote={Abstract}, number={1}, journal={GENETICS}, author={Matute, Daniel R. and Comeault, Aaron A. and Earley, Eric and Serrato-Capuchina, Antonio and Peede, David and Monroy-Eklund, Anais and Huang, Wen and Jones, Corbin D. and Mackay, Trudy F. C. and Coyne, Jerry A.}, year={2020}, month={Jan}, pages={211–230} }
 @article{harbison_kumar_huang_mccoy_smith_mackay_2019, title={Genome-Wide Association Study of Circadian Behavior in Drosophila melanogaster}, volume={49}, ISSN={["1573-3297"]}, DOI={10.1007/s10519-018-9932-0}, abstractNote={Circadian rhythms influence physiological processes from sleep-wake cycles to body temperature and are controlled by highly conserved cycling molecules. Although the mechanistic basis of the circadian clock has been known for decades, the extent to which circadian rhythms vary in nature and the underlying genetic basis for that variation is not well understood. We measured circadian period (Ʈ) and rhythmicity index in the Drosophila Genetic Reference Panel (DGRP) and observed extensive genetic variation in both. Seven DGRP lines had sexually dimorphic arrhythmicity and one line had an exceptionally long Ʈ. Genome-wide analyses identified 584 polymorphisms in 268 genes. We observed differences among transcripts for nine genes predicted to interact among themselves and canonical clock genes in the long period line and a control. Mutations/RNAi knockdown targeting these genes also affected circadian behavior. Our observations reveal that complex genetic interactions influence high levels of variation in circadian phenotypes.}, number={1}, journal={BEHAVIOR GENETICS}, author={Harbison, Susan T. and Kumar, Shailesh and Huang, Wen and McCoy, Lenovia J. and Smith, Kirklin R. and Mackay, Trudy F. C.}, year={2019}, month={Jan}, pages={60–82} }
 @article{morgante_huang_maltecca_mackay_2018, title={Effect of genetic architecture on the prediction accuracy of quantitative traits in samples of unrelated individuals}, volume={120}, ISSN={["1365-2540"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85041836520&partnerID=MN8TOARS}, DOI={10.1038/s41437-017-0043-0}, abstractNote={Predicting complex phenotypes from genomic data is a fundamental aim of animal and plant breeding, where we wish to predict genetic merits of selection candidates; and of human genetics, where we wish to predict disease risk. While genomic prediction models work well with populations of related individuals and high linkage disequilibrium (LD) (e.g., livestock), comparable models perform poorly for populations of unrelated individuals and low LD (e.g., humans). We hypothesized that low prediction accuracies in the latter situation may occur when the genetics architecture of the trait departs from the infinitesimal and additive architecture assumed by most prediction models. We used simulated data for 10,000 lines based on sequence data from a population of unrelated, inbred Drosophila melanogaster lines to evaluate this hypothesis. We show that, even in very simplified scenarios meant as a stress test of the commonly used Genomic Best Linear Unbiased Predictor (G-BLUP) method, using all common variants yields low prediction accuracy regardless of the trait genetic architecture. However, prediction accuracy increases when predictions are informed by the genetic architecture inferred from mapping the top variants affecting main effects and interactions in the training data, provided there is sufficient power for mapping. When the true genetic architecture is largely or partially due to epistatic interactions, the additive model may not perform well, while models that account explicitly for interactions generally increase prediction accuracy. Our results indicate that accounting for genetic architecture can improve prediction accuracy for quantitative traits.}, number={6}, journal={HEREDITY}, author={Morgante, Fabio and Huang, Wen and Maltecca, Christian and Mackay, Trudy F. C.}, year={2018}, month={Jun}, pages={500–514} }
 @article{zhou_sun_huang_smol_tang_sun_2015, title={The Pacific decadal oscillation and changes in anchovy populations in the Northwest Pacific}, volume={114}, journal={Journal of Asian Earth Sciences}, author={Zhou, X. and Sun, Y. and Huang, W. and Smol, J. P. and Tang, Q. S. and Sun, L. G.}, year={2015}, pages={504–511} }
 @article{qin_sun_blais_wang_huang_huang_xie_2014, title={From sea to land: assessment of the bio-transport of phosphorus by penguins in Antarctica}, volume={32}, number={1}, journal={Chinese Journal of Oceanology and Limnology = Zhongguo Hai Yang Hu Zhao Xue Bao}, author={Qin, X. Y. and Sun, L. G. and Blais, J. M. and Wang, Y. H. and Huang, T. and Huang, W. and Xie, Z. Q.}, year={2014}, pages={148–154} }
 @article{huang_massouras_inoue_peiffer_ramia_tarone_turlapati_zichner_zhu_lyman_et al._2014, title={Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines}, volume={24}, number={7}, journal={Genome Research}, author={Huang, W. and Massouras, A. and Inoue, Y. and Peiffer, J. and Ramia, M. and Tarone, A. M. and Turlapati, L. and Zichner, T. and Zhu, D. H. and Lyman, R. F. and et al.}, year={2014}, pages={1193–1208} }
 @article{zhou_sun_huang_liu_jia_cheng_2014, title={Relationship between magnetic susceptibility and grain size of sediments in the China Seas and its implications}, volume={72}, journal={Continental Shelf Research}, author={Zhou, X. and Sun, L. G. and Huang, W. and Liu, Y. and Jia, N. and Cheng, W. H.}, year={2014}, pages={131–137} }
 @article{driver_huang_kropp_penagaricano_khatib_2013, title={Knockdown of CDKN1C (p57(kip2)) and PHLDA2 results in developmental changes in bovine pre-implantation embryos}, volume={8}, number={7}, journal={PLoS One}, author={Driver, A. M. and Huang, W. and Kropp, J. and Penagaricano, F. and Khatib, H.}, year={2013} }
 @article{wu_li_huang_li_li_2012, title={Alternative splicing regulated by butyrate in bovine epithelial cells}, volume={7}, number={6}, journal={PLoS One}, author={Wu, S. T. and Li, C. J. and Huang, W. and Li, W. Z. and Li, R. W.}, year={2012} }
 @article{zhou_sun_huang_cheng_jia_2012, title={Precipitation in the Yellow River drainage basin and East Asian monsoon strength on a decadal time scale}, volume={78}, number={3}, journal={Quaternary Research}, author={Zhou, X. and Sun, L. G. and Huang, W. and Cheng, W. H. and Jia, N.}, year={2012}, pages={486–491} }
 @article{ober_huang_magwire_schlather_simianer_mackay, title={Accounting for genetic architecture improves sequence based genomic prediction for a Drosophila fitness trait}, volume={10}, number={5}, journal={PLoS One}, author={Ober, U. and Huang, W. and Magwire, M. and Schlather, M. and Simianer, H. and Mackay, T. F. C.} }
 @article{swarup_huang_mackay_anholt, title={Analysis of natural variation reveals neurogenetic networks for Drosophila olfactory behavior}, volume={110}, number={3}, journal={Proceedings of the National Academy of Sciences of the United States of America}, author={Swarup, S. and Huang, W. and Mackay, T. F. C. and Anholt, R. R. H.}, pages={1017–1022} }
 @article{huang_richards_carbone_zhu_anholt_ayroles_duncan_jordan_lawrence_magwire_et al., title={Epistasis dominates the genetic architecture of Drosophila quantitative traits}, volume={109}, number={39}, journal={Proceedings of the National Academy of Sciences of the United States of America}, author={Huang, W. and Richards, S. and Carbone, M. A. and Zhu, D. H. and Anholt, R. R. H. and Ayroles, J. F. and Duncan, L. and Jordan, K. W. and Lawrence, F. and Magwire, M. M. and et al.}, pages={15553–15559} }
 @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{dembeck_huang_magwire_lawrence_lyman_mackay, title={Genetic architecture of abdominal pigmentation in Drosophila melanogaster}, volume={11}, number={5}, journal={PLoS Genetics}, author={Dembeck, L. M. and Huang, W. and Magwire, M. M. and Lawrence, F. and Lyman, R. F. and Mackay, T. F. C.} }
 @article{dembeck_boroczky_huang_schal_anholt_mackay, title={Genetic architecture of natural variation in cuticular hydrocarbon composition in Drosophila melanogaster}, volume={4}, journal={Elife}, author={Dembeck, L. M. and Boroczky, K. and Huang, W. and Schal, C. and Anholt, R. R. H. and Mackay, T. F. C.} }
 @article{carbone_yamamoto_huang_lyman_meadors_yamamoto_anholt_mackay, title={Genetic architecture of natural variation in visual senescence in Drosophila}, volume={113}, number={43}, journal={Proceedings of the National Academy of Sciences of the United States of America}, author={Carbone, M. A. and Yamamoto, A. and Huang, W. and Lyman, R. A. and Meadors, T. B. and Yamamoto, R. and Anholt, R. R. H. and Mackay, T. F. C.}, pages={E6620–6629} }
 @article{dembeck_huang_carbone_mackay, title={Genetic basis of natural variation in body pigmentation in Drosophila melanogaster}, volume={9}, number={2}, journal={Fly}, author={Dembeck, L. M. and Huang, W. and Carbone, M. A. and Mackay, T. F. C.}, pages={75–81} }
 @article{huang_carbone_magwire_peiffer_lyman_stone_anholt_mackay, title={Genetic basis of transcriptome diversity in Drosophila melanogaster}, volume={112}, number={44}, journal={Proceedings of the National Academy of Sciences of the United States of America}, author={Huang, W. and Carbone, M. A. and Magwire, M. M. and Peiffer, J. A. and Lyman, R. F. and Stone, E. A. and Anholt, R. R. H. and Mackay, T. F. C.}, pages={E6010–6019} }
 @article{montgomery_vorojeikina_huang_mackay_anholt_rand, title={Genome-wide association analysis of tolerance to methylmercury toxicity in Drosophila implicates myogenic and neuromuscular developmental pathways}, volume={9}, number={10}, journal={PLoS One}, author={Montgomery, S. L. and Vorojeikina, D. and Huang, W. and Mackay, T. F. C. and Anholt, R. R. H. and Rand, M. D.} }
 @article{ellis_huang_quinn_ahuja_alfrejd_gomez_hjelmen_moore_mackay_johnston_et al., title={Intrapopulation genome size variation in D. melanogaster reflects life history variation and plasticity}, volume={10}, number={7}, journal={PLoS Genetics}, author={Ellis, L. L. and Huang, W. and Quinn, A. M. and Ahuja, A. and Alfrejd, B. and Gomez, F. E. and Hjelmen, C. E. and Moore, K. L. and Mackay, T. F. C. and Johnston, J. S. and et al.} }
 @article{morozova_huang_pray_whitham_anholt_mackay, title={Polymorphisms in early neurodevelopmental genes affect natural variation in alcohol sensitivity in adult drosophila}, volume={16}, journal={BMC Genomics}, author={Morozova, T. V. and Huang, W. and Pray, V. A. and Whitham, T. and Anholt, R. R. H. and Mackay, T. F. C.} }
 @article{garlapow_huang_yarboro_peterson_mackay, title={Quantitative genetics of food intake in Drosophila melanogaster}, volume={10}, number={9}, journal={PLoS One}, author={Garlapow, M. E. and Huang, W. and Yarboro, M. T. and Peterson, K. R. and Mackay, T. F. C.} }
 @article{huang_lyman_lyman_carbone_harbison_magwire_mackay, title={Spontaneous mutations and the origin and maintenance of quantitative genetic variation}, volume={5}, journal={Elife}, author={Huang, W. and Lyman, R. F. and Lyman, R. A. and Carbone, M. A. and Harbison, S. T. and Magwire, M. M. and Mackay, T. F. C.} }
 @inproceedings{zielinska_welk_mayhorn_murphy-hill, title={The Persuasive phish: examining the social psychological principles hidden in phishing emails}, booktitle={Symposium and Bootcamp on the Science of Security}, author={Zielinska, O. and Welk, A. and Mayhorn, C. B. and Murphy-Hill, E.}, pages={126–126} }
 @article{hunter_huang_mackay_singh, title={The genetic architecture of natural variation in recombination rate in Drosophila melanogaster}, volume={12}, number={4}, journal={PLoS Genetics}, author={Hunter, C. M. and Huang, W. and Mackay, T. F. C. and Singh, N. D.} }
 @article{arya_magwire_huang_serrano-negron_mackay_anholt, title={The genetic basis for variation in olfactory behavior in Drosophila melanogaster}, volume={40}, number={4}, journal={Chemical Senses}, author={Arya, G. H. and Magwire, M. M. and Huang, W. and Serrano-Negron, Y. L. and Mackay, T. F. C. and Anholt, R. R. H.}, pages={233–243} }
 @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.} }