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Published:
56- Lea, A. J., Clark, A. G., Dahl, A. W., Devinsky, O., Garcia, A. R., Golden, C. D., … & Ayroles, J. F. (2023). Evolutionary mismatch and the role of GxE interactions in human disease.. arXiv preprint 2301.05255
55- Wolf, S*, Melo, D*, Garske, KM, Pallares, LF, & Ayroles, JF. (2022). Characterizing the landscape of gene expression variance in humans.bioRxiv
54- Lea, A. J., Caldas, I. V., Garske, K. M., Echwa, J., Gurven, M., Handley, C., … & Ayroles, J. F. (2023). Adaptations to water stress and pastoralism in the Turkana of northwest Kenya. bioRxiv
53- Lea, A. J., Garcia, A., Arevalo, J., Ayroles, J. F., Buetow, K., Cole, S. W., … & Gurven, M. D. (2023). Natural selection of immune and metabolic genes associated with health in two lowland Bolivian populations. Proceedings of the National Academy of Sciences, 120 (1) e2207544120
52- Lea, A. J., Peng, J., & Ayroles, J. F. (2022). Diverse environmental perturbations reveal the evolution and context-dependency of genetic effects on gene expression levels. Genome Research, 32(10), 1826-1839
51- Pettie, KP, Mumbach, M, Lea, AJ, Ayroles, JF, Chang, HY, Kasowski, M, & Fraser, HB. (2022). Chromatin activity identifies differential gene regulation across human ancestries. bioRxiv
50- Bruijning, M., Henry, L. P., Forsberg, S. K., Metcalf, C. J. E., & Ayroles, J. F. (2022). Natural selection for imprecise vertical transmission in host–microbiota systems. Nature ecology & evolution 6(1):77-87.
49- Henry, L. P., & Ayroles, J. F. (2022). Latitudinal cline does not predict variation in the microbiome of wild Drosophila melanogaster. Molecular Ecology 31(22), 5861-5871.
48- Henry, L. P., Fernandez, M., Wolf, S., & Ayroles, J. (2022). Wolbachia interacts with the microbiome to shape fitness-associated traits during seasonal adaptation in Drosophila melanogaster. bioRxiv.
47- de Bivort, B., Buchanan, S., Skutt-Kakaria, K., Gajda, E., Ayroles, J., O’Leary, C., … & Smith, M. A. Y. (2022). Precise quantification of behavioral individuality from 80 million decisions across 183,000 flies. Frontiers in Behavioral Neuroscience, 16.
46- Golden, C. D., Ayroles, J., Eurich, J. G., Gephart, J. A., Seto, K. L., Sharp, M. K., … & Timeon, E. (2022). Study Protocol: Interactive Dynamics of Coral Reef Fisheries and the Nutrition Transition in Kiribati. Frontiers in Public Health, 10:890381.
45- Bruijning, M., Ayroles, J. F., Henry, L. P., Koskella, B., Meyer, K. M., & Metcalf, C. J. E. (2022). Relative abundance data can misrepresent heritability of the microbiome. bioRxiv.
44- Werkhoven, Z., Bravin, A., Skutt-Kakaria, K., Reimers, P., Pallares, L.F., Ayroles, J. and de Bivort, B.L., 2021. The structure of behavioral variation within a genotype. Elife, 10, p.e64988.
43- Choi, J.Y., Dai, X., Alam, O., Peng, J.Z., Rughani, P., Hickey, S., Harrington, E., Juul, S., Ayroles, J.F., Purugganan, M.D. and Stacy, E.A., 2021. Ancestral polymorphisms shape the adaptive radiation of Metrosideros across the Hawaiian Islands. Proceedings of the National Academy of Sciences, 118(37).
42- Henry, L.P., Bruijning, M., Forsberg, S.K. and Ayroles, J.F., 2021. The microbiome extends host evolutionary potential. Nature Communications, 12(1):1-13.
41- Akhund-Zade, J., Lall, S., Gajda, E., Yoon, D., Ayroles, J.F. and de Bivort, B.L., 2021. Genetic basis of offspring number-body weight tradeoff in Drosophila melanogaster. G3 Genes| Genomes| Genetics.
40- Lea, A.J., Siford, R., Phung, T., Taravella, A., Lutukoi, F., Lowasa, S., Muhoya, B., Waigwa, C., Davidson, S., Handley, C. and Kamau, J., 2021, March. Uncovering the evolutionary history of the Turkana, a desert pastoralist group. American Journal or Physical Anthropology (174):60-60.
39- Lea, A.J., Waigwa, C., Muhoya, B., Lotukoi, F., Peng, J., Henry, L., Abhyankar, V., Kamau, J., Martins, D., Gurven, M. and Ayroles, J.F., 2021. Social gradients in health vary between rural and urban Turkana. Evolution, Medicine, and Public Health 9(1), 406–419.
38- Pallares, L.F., Lea, A.J., Han, C., Filippova, E.V., Andolfatto, P. and Ayroles, J.F., 2023. Diet unmasks genetic variants that regulate lifespan in outbred Drosophila. Nat Genet 55, 123–129.
37- Rau, C.D., Gonzales, N.M., Bloom, J.S., Park, D., Ayroles, J., Palmer, A.A., Lusis, A.J. and Zaitlen, N., 2020. Modeling epistasis in mice and yeast using the proportion of two or more distinct genetic backgrounds: Evidence for “polygenic epistasis. PLoS genetics, 16(10):e1009165.
36- Lea, A.J., Martins, D., Kamau, J., Gurven, M. and Ayroles, J.F., 2020. Urbanization and market integration have strong, nonlinear effects on cardiometabolic health in the Turkana. Science advances, 6(43):eabb1430.
35- Akhund-Zade, J., Yoon, D., Bangerter, A., Polizos, N., Campbell, M., Soloshenko, A., Zhang, T., Wice, E., Albright, A., Narayanan, A. and Schmidt, P., 2020. Wild flies hedge their thermal preference bets in response to seasonal fluctuations. Biorxiv (2020.09.16.300731).
34- Henry, L., Fernandez, M. and Ayroles, J.F., 2020. GxGxE interactions and adaptive potential of the microbiome in Drosophila melanogaster. bioRxiv (2020.09.21.306779).
33- Henry, L.P. and Ayroles, J.F., 2021. Meta-analysis suggests the microbiome responds to Evolve and Resequence experiments in Drosophila melanogaster. BMC microbiology, 21(1):1-14.
32- Bruijning, M., Metcalf, C.J.E., Jongejans, E. and Ayroles, J.F., 2020. The evolution of variance control. Trends in ecology & evolution, 35(1):22-33.
31- Pallares, L.F., Picard, S. and Ayroles, J.F., 2020. TM3’seq: a tagmentation-mediated 3’sequencing approach for improving scalability of RNAseq experiments. G3: Genes, Genomes, Genetics, 10(1):143-150.
30- A J Lea, M Subramaniam, A Ko, T Lehtimäki, E Raitoharju, MikaKähönen, I Seppälä, N Mononen, O Raitakari, M Ala-Korpela, P Pajukanta, N Zaitlen, Ayroles JF. (2019). Genetic and environmental perturbations lead to regulatory decoherence. eLife 2019;8:e40538
29- S Musharoff, DS Park, A Dahl, JM Galanter, X Liu, S Huntsman, C Eng, Burchard EG, Ayroles JF *, Zaitlen N* (2018) Existence and implications of population variance structure. bioRxiv, 439661 (*equal contribution)
28- Schrider DR, Ayroles JF, Matute DR, AD Kern AD. (2018). Supervised machine learning reveals introgressed loci in the genomes of Drosophila simulans and D. sechellia. PLoS genetics 14 (4), e1007341.
27- Dumitrascu B, Darnell G, Ayroles JF, Engelhardt BE. (2018). Statistical tests for detecting variance effects in quantitative trait studies. Bioinformatics 1, 11.
24 – Zwarts L, Broeck LV, Cappuyns E, Ayroles JF, Magwire MM, Vulsteke V, Clements J, Mackay TF, Callaerts P. (2015) The genetic basis of natural variation in mushroom body size in Drosophila melanogaster. Nature communications.11:6.
23 – Ayroles JF, Buchanan SM, O’Leary C, Skutt-Kakaria K, Grenier JK, Clark AG, Hartl DL, de Bivort BL. (2015). Behavioral idiosyncrasy reveals genetic control of phenotypic variability. Proceedings of the National Academy of Sciences 112(21):6706-11.
21 – Matute DR*, Ayroles JF*. (2014) Hybridization occurs between Drosophila simulans and D. sechellia in the Seychelles archipelago. Journal of evolutionary biology. 27(6):1057-68.
20- Corbett-Detig RB, Zhou J, Clark AG, Hartl DL, Ayroles JF . (2013). Genetic Incompatibilities Within Species are Widespread. Nature, 504, 135–137.
19- Huang W, Richards S, Carbone MA, Zhu D, Anholt RRH, Ayroles JF, et al. (2012) Epistasis Dominates The Genetic Architecture Of Drosophila Quantitative Traits. PNAS, 109:15553-15559.
18- Massouras A, Waszak SM, Albarca M, Hens K, Holcombe K, Ayroles JF, Dermitzakis ET, Eric A Stone EA, Jensen J D, Mackay T.F.C, Deplancke B. (2012) Genomic Variation And Its Impact On Gene Expression In Drosophila Melanogaster. Plos Genetics. 8 (11): e1003055.
17- Mackay TFC*, Richards S*, Barbadilla A *, Stone EA*, Ayroles JF*, Zhu D, Sònia Casillas. et. al. (2012) The Drosophila Genetics Reference Panel: A Community Resource for Analysis of Population Genomics and Quantitative Traits. Nature, 482(7384):173-8. Faculty of 1000, Biology
16 – Ober U, Ayroles JF, Stone EA, Richards S, Zhu D,Gibbs RA, Stricker C, Gianola D, Schlather M, Mackay TFC, Simianer H. (2011) Using Whole Genome Sequence Data to Predict Quantitative Trait Phenotypes in Drosophila melanogaster. PLoS Genetics, 8(5): e1002685. Faculty of 1000, Biology
15 – Rowe K, Singhal S, MacManes M, Ayroles JF, Morelli TL, Rubidge E, Bi K, Moritz C (2012). Museum Genomics: Low Cost And High Accuracy Genetic Data From Historical Specimens. Molecular Ecology Ressources, 11(6): 1082–1092.
14 – Ayroles JF, Laflamme B, Wolfner MA, Mackay TFC. (2011) Sifting Through The Data: Identifying Top Candidates For Novelseminal Protein Genes From Drosophila Whole Genome Expression Data. Genetics Research, 93(6): 387-395.
13 – Jumbo-Lucioni P*, Ayroles JF*, Chambers MM, Jordan KW, Leips J, Mackay TF, De Luca M. (2010) Systems Genetics Analysis Of Body Weight And Energy Metabolism Traits In Drosophila Melanogaster. BMC Genomics, 11(11): 297. (* Contributed equally)
12 – Edwards, A, Ayroles JF, Stone EA, Mackay TFC. (2009) A Transcriptional Network Associated With Natural Variation In Drosophila Aggressive Behavior. Genome Biology, 10(7): R76.
11 – Mackay TFC, Stone EA, Ayroles JF. (2009) Quantitative Genetics: Prospects And Challenges. Nature Review Genetics, 10(8): 565-577.
10 – Morozova TV*, Ayroles JF*, Jordan KW, Duncan LH, Carbone MA, Lyman RF, Stone EA, Govindaraju DR, Ellison RC, Mackay TF, Anholt RR. (2009) Alcohol Sensitivity In Drosophila: Translational Potential Of Systems Genetics. Genetics, 183(2): 733-745 (* Contributed equally)
9 – Harbison ST, Carbone MA, Ayroles JF, Stone EA, Lyman RF, Mackay TFC (2009) Co-Regulated Transcriptional Networks Contribute to Natural Genetic Variation in Drosophila Sleep. Nature Genetics, 41(3): 371-375.
8 – Ayroles JF, Carbone MA, Stone EA, Jordan KW, Lyman RF, Magwire MM, Rollman SM, Duncan LH, Lawrence F, Anholt RH, Mackay TFC. (2009) Systems genetics of complex traits in Drosophila melanogaster. Nature Genetics, 41(3): 299-307. Faculty of 1000, Biology
7 – Kocher SD, Ayroles JF, Stone EA, Grozinger CM. (2009) Genomics Of Pheromone Response: Cooperation And Conflict In Honey Bees. Plos ONE, 5(2): e9116.
6 – Stone EA, Ayroles JF. (2009) Modulated Modularity Clustering As An Exploratory Tool For Functional Genomic Inference. PLoS Genetics, 5(5): e1000479.
5 – Ayroles JF, Hughes KA, Reedy MM, Rodriguez-Zas SL, Drnevich JM, Rowe KC, Cáceres CE, Paige KN. (2009) Genome-Wide Assessment Of Inbreeding Depression In Drosophila Melanogaster. Conservation Biology, 23(4): 920-930.
4 – Carbone MA, Ayroles JF, Yamamoto A, Morozova TV, West SA, Magwire MM, Mackay TF, Anholt RR. (2009) Overexpression Of Myocilin In The Drosophila Eye Activates The Unfolded Protein Response: Implications For Glaucoma. PLoS ONE, 4(1): e4216.
3 – Ayroles JF, Gibson G. (2006) Analysis Of Variance Of Microarray Data. Methods Enzymol, 411: -33.
2 – Hughes KA, Ayroles JF, Reedy MM, Drnevich JM, Rowe KC, Ruedi EA, Cáceres CE, Paige KN. (2006) Segregating Variation In The Transcriptome: Cis Regulation And Additivity Of Effects. Genetics 173(3): 1347-1355.
1 – Dejean A, Solano PJ, Ayroles JF, Corbara B, Orivel J. (2005) Insect Behaviour: Arboreal Ants Build Traps to Capture Prey. Nature, (434):973.
Book Chapter:
1- Metcalf CJE*, Ayroles JF*. (2019). Chapter: “Why does intra-genotypic variance persist?” In book titled “Unsolved Problems in Ecology’. Princeton University Press. (*equal contribution)