List of Faculty Publications

Below is a list of Faculty publications imported from PubMed or manually added. By default, publications are sorted by year with titles displayed in ascending alphabetical order.
Shortcuts: Wühr, Martin | Wingreen, Ned | Wieschaus, Eric | Troyanskaya, Olga | Tilghman, Shirley | Storey, John | Singh, Mona | Shvartsman, Stanislav | Shaevitz, Joshua | Rabinowitz, Joshua | Murphy, Coleen | Levine, Michael {Levine, Michael S.} | Gregor, Thomas | Botstein, David | Bialek, William | Ayroles, Julien | Andolfatto, Peter | Akey, Joshua

Filters: Author is Stone, Eric A  [Clear All Filters]
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Aggression
A. C. Edwards, Ayroles, J. F., Stone, E. A., Carbone, M. Anna, Lyman, R. F., and Mackay, T. F. C., “A transcriptional network associated with natural variation in Drosophila aggressive behavior.”, Genome Biol, vol. 10, no. 7, p. R76, 2009.
Alcohol Drinking
T. V. Morozova, Ayroles, J. F., Jordan, K. W., Duncan, L. H., Carbone, M. Anna, Lyman, R. F., Stone, E. A., Govindaraju, D. R., R Ellison, C., Mackay, T. F. C., and Anholt, R. R. H., “Alcohol sensitivity in Drosophila: translational potential of systems genetics.”, Genetics, vol. 183, no. 2, pp. 733-45, 1SI-12SI, 2009.
Alleles
T. F. C. Mackay, Richards, S., Stone, E. A., Barbadilla, A., Ayroles, J. F., Zhu, D., Casillas, S., Han, Y., Magwire, M. M., Cridland, J. M., Richardson, M. F., Anholt, R. R. H., Barrón, M., Bess, C., Blankenburg, K. Petra, Carbone, M. Anna, Castellano, D., Chaboub, L., Duncan, L., Harris, Z., Javaid, M., Jayaseelan, J. Christina, Jhangiani, S. N., Jordan, K. W., Lara, F., Lawrence, F., Lee, S. L., Librado, P., Linheiro, R. S., Lyman, R. F., Mackey, A. J., Munidasa, M., Muzny, D. Marie, Nazareth, L., Newsham, I., Perales, L., Pu, L. - L., Qu, C., Ràmia, M., Reid, J. G., Rollmann, S. M., Rozas, J., Saada, N., Turlapati, L., Worley, K. C., Wu, Y. - Q., Yamamoto, A., Zhu, Y., Bergman, C. M., Thornton, K. R., Mittelman, D., and Gibbs, R. A., “The Drosophila melanogaster Genetic Reference Panel.”, Nature, vol. 482, no. 7384, pp. 173-8, 2012.
Allelic Imbalance
A. Massouras, Waszak, S. M., Albarca-Aguilera, M., Hens, K., Holcombe, W., Ayroles, J. F., Dermitzakis, E. T., Stone, E. A., Jensen, J. D., Mackay, T. F. C., and Deplancke, B., “Genomic variation and its impact on gene expression in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 11, p. e1003055, 2012.
Amino Acid Sequence
J. F. Ayroles, Carbone, M. Anna, Stone, E. A., Jordan, K. W., Lyman, R. F., Magwire, M. M., Rollmann, S. M., Duncan, L. H., Lawrence, F., Anholt, R. R. H., and Mackay, T. F. C., “Systems genetics of complex traits in Drosophila melanogaster.”, Nat Genet, vol. 41, no. 3, pp. 299-307, 2009.
Animals
U. Ober, Ayroles, J. F., Stone, E. A., Richards, S., Zhu, D., Gibbs, R. A., Stricker, C., Gianola, D., Schlather, M., Mackay, T. F. C., and Simianer, H., “Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 5, p. e1002685, 2012.
J. F. Ayroles, Laflamme, B. A., Stone, E. A., Wolfner, M. F., and Mackay, T. F. C., “Functional genome annotation of Drosophila seminal fluid proteins using transcriptional genetic networks.”, Genet Res (Camb), vol. 93, no. 6, pp. 387-95, 2011.
S. D. Kocher, Ayroles, J. F., Stone, E. A., and Grozinger, C. M., “Individual variation in pheromone response correlates with reproductive traits and brain gene expression in worker honey bees.”, PLoS One, vol. 5, no. 2, p. e9116, 2010.
J. F. Ayroles, Carbone, M. Anna, Stone, E. A., Jordan, K. W., Lyman, R. F., Magwire, M. M., Rollmann, S. M., Duncan, L. H., Lawrence, F., Anholt, R. R. H., and Mackay, T. F. C., “Systems genetics of complex traits in Drosophila melanogaster.”, Nat Genet, vol. 41, no. 3, pp. 299-307, 2009.
S. T. Harbison, Carbone, M. Anna, Ayroles, J. F., Stone, E. A., Lyman, R. F., and Mackay, T. F. C., “Co-regulated transcriptional networks contribute to natural genetic variation in Drosophila sleep.”, Nat Genet, vol. 41, no. 3, pp. 371-5, 2009.
W. Huang, Richards, S., Carbone, M. Anna, Zhu, D., Anholt, R. R. H., Ayroles, J. F., Duncan, L., Jordan, K. W., Lawrence, F., Magwire, M. M., Warner, C. B., Blankenburg, K., Han, Y., Javaid, M., Jayaseelan, J., Jhangiani, S. N., Muzny, D., Ongeri, F., Perales, L., Wu, Y. - Q., Zhang, Y., Zou, X., Stone, E. A., Gibbs, R. A., and Mackay, T. F. C., “Epistasis dominates the genetic architecture of Drosophila quantitative traits.”, Proc Natl Acad Sci U S A, vol. 109, no. 39, pp. 15553-9, 2012.
A. C. Edwards, Ayroles, J. F., Stone, E. A., Carbone, M. Anna, Lyman, R. F., and Mackay, T. F. C., “A transcriptional network associated with natural variation in Drosophila aggressive behavior.”, Genome Biol, vol. 10, no. 7, p. R76, 2009.
A. Massouras, Waszak, S. M., Albarca-Aguilera, M., Hens, K., Holcombe, W., Ayroles, J. F., Dermitzakis, E. T., Stone, E. A., Jensen, J. D., Mackay, T. F. C., and Deplancke, B., “Genomic variation and its impact on gene expression in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 11, p. e1003055, 2012.
E. A. Stone and Ayroles, J. F., “Modulated modularity clustering as an exploratory tool for functional genomic inference.”, PLoS Genet, vol. 5, no. 5, p. e1000479, 2009.
T. V. Morozova, Ayroles, J. F., Jordan, K. W., Duncan, L. H., Carbone, M. Anna, Lyman, R. F., Stone, E. A., Govindaraju, D. R., R Ellison, C., Mackay, T. F. C., and Anholt, R. R. H., “Alcohol sensitivity in Drosophila: translational potential of systems genetics.”, Genetics, vol. 183, no. 2, pp. 733-45, 1SI-12SI, 2009.
T. F. C. Mackay, Richards, S., Stone, E. A., Barbadilla, A., Ayroles, J. F., Zhu, D., Casillas, S., Han, Y., Magwire, M. M., Cridland, J. M., Richardson, M. F., Anholt, R. R. H., Barrón, M., Bess, C., Blankenburg, K. Petra, Carbone, M. Anna, Castellano, D., Chaboub, L., Duncan, L., Harris, Z., Javaid, M., Jayaseelan, J. Christina, Jhangiani, S. N., Jordan, K. W., Lara, F., Lawrence, F., Lee, S. L., Librado, P., Linheiro, R. S., Lyman, R. F., Mackey, A. J., Munidasa, M., Muzny, D. Marie, Nazareth, L., Newsham, I., Perales, L., Pu, L. - L., Qu, C., Ràmia, M., Reid, J. G., Rollmann, S. M., Rozas, J., Saada, N., Turlapati, L., Worley, K. C., Wu, Y. - Q., Yamamoto, A., Zhu, Y., Bergman, C. M., Thornton, K. R., Mittelman, D., and Gibbs, R. A., “The Drosophila melanogaster Genetic Reference Panel.”, Nature, vol. 482, no. 7384, pp. 173-8, 2012.
T. F. C. Mackay, Stone, E. A., and Ayroles, J. F., “The genetics of quantitative traits: challenges and prospects.”, Nat Rev Genet, vol. 10, no. 8, pp. 565-77, 2009.
Animals, Genetically Modified
S. T. Harbison, Carbone, M. Anna, Ayroles, J. F., Stone, E. A., Lyman, R. F., and Mackay, T. F. C., “Co-regulated transcriptional networks contribute to natural genetic variation in Drosophila sleep.”, Nat Genet, vol. 41, no. 3, pp. 371-5, 2009.
Animals, Inbred Strains
S. T. Harbison, Carbone, M. Anna, Ayroles, J. F., Stone, E. A., Lyman, R. F., and Mackay, T. F. C., “Co-regulated transcriptional networks contribute to natural genetic variation in Drosophila sleep.”, Nat Genet, vol. 41, no. 3, pp. 371-5, 2009.
J. F. Ayroles, Carbone, M. Anna, Stone, E. A., Jordan, K. W., Lyman, R. F., Magwire, M. M., Rollmann, S. M., Duncan, L. H., Lawrence, F., Anholt, R. R. H., and Mackay, T. F. C., “Systems genetics of complex traits in Drosophila melanogaster.”, Nat Genet, vol. 41, no. 3, pp. 299-307, 2009.
Base Sequence
J. F. Ayroles, Carbone, M. Anna, Stone, E. A., Jordan, K. W., Lyman, R. F., Magwire, M. M., Rollmann, S. M., Duncan, L. H., Lawrence, F., Anholt, R. R. H., and Mackay, T. F. C., “Systems genetics of complex traits in Drosophila melanogaster.”, Nat Genet, vol. 41, no. 3, pp. 299-307, 2009.
Bayes Theorem
U. Ober, Ayroles, J. F., Stone, E. A., Richards, S., Zhu, D., Gibbs, R. A., Stricker, C., Gianola, D., Schlather, M., Mackay, T. F. C., and Simianer, H., “Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 5, p. e1002685, 2012.
Bees
S. D. Kocher, Ayroles, J. F., Stone, E. A., and Grozinger, C. M., “Individual variation in pheromone response correlates with reproductive traits and brain gene expression in worker honey bees.”, PLoS One, vol. 5, no. 2, p. e9116, 2010.
Behavior, Animal
A. C. Edwards, Ayroles, J. F., Stone, E. A., Carbone, M. Anna, Lyman, R. F., and Mackay, T. F. C., “A transcriptional network associated with natural variation in Drosophila aggressive behavior.”, Genome Biol, vol. 10, no. 7, p. R76, 2009.
Brain
S. D. Kocher, Ayroles, J. F., Stone, E. A., and Grozinger, C. M., “Individual variation in pheromone response correlates with reproductive traits and brain gene expression in worker honey bees.”, PLoS One, vol. 5, no. 2, p. e9116, 2010.
Centromere
T. F. C. Mackay, Richards, S., Stone, E. A., Barbadilla, A., Ayroles, J. F., Zhu, D., Casillas, S., Han, Y., Magwire, M. M., Cridland, J. M., Richardson, M. F., Anholt, R. R. H., Barrón, M., Bess, C., Blankenburg, K. Petra, Carbone, M. Anna, Castellano, D., Chaboub, L., Duncan, L., Harris, Z., Javaid, M., Jayaseelan, J. Christina, Jhangiani, S. N., Jordan, K. W., Lara, F., Lawrence, F., Lee, S. L., Librado, P., Linheiro, R. S., Lyman, R. F., Mackey, A. J., Munidasa, M., Muzny, D. Marie, Nazareth, L., Newsham, I., Perales, L., Pu, L. - L., Qu, C., Ràmia, M., Reid, J. G., Rollmann, S. M., Rozas, J., Saada, N., Turlapati, L., Worley, K. C., Wu, Y. - Q., Yamamoto, A., Zhu, Y., Bergman, C. M., Thornton, K. R., Mittelman, D., and Gibbs, R. A., “The Drosophila melanogaster Genetic Reference Panel.”, Nature, vol. 482, no. 7384, pp. 173-8, 2012.
Chromosome Mapping
T. F. C. Mackay, Stone, E. A., and Ayroles, J. F., “The genetics of quantitative traits: challenges and prospects.”, Nat Rev Genet, vol. 10, no. 8, pp. 565-77, 2009.
U. Ober, Ayroles, J. F., Stone, E. A., Richards, S., Zhu, D., Gibbs, R. A., Stricker, C., Gianola, D., Schlather, M., Mackay, T. F. C., and Simianer, H., “Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 5, p. e1002685, 2012.
J. F. Ayroles, Carbone, M. Anna, Stone, E. A., Jordan, K. W., Lyman, R. F., Magwire, M. M., Rollmann, S. M., Duncan, L. H., Lawrence, F., Anholt, R. R. H., and Mackay, T. F. C., “Systems genetics of complex traits in Drosophila melanogaster.”, Nat Genet, vol. 41, no. 3, pp. 299-307, 2009.
A. Massouras, Waszak, S. M., Albarca-Aguilera, M., Hens, K., Holcombe, W., Ayroles, J. F., Dermitzakis, E. T., Stone, E. A., Jensen, J. D., Mackay, T. F. C., and Deplancke, B., “Genomic variation and its impact on gene expression in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 11, p. e1003055, 2012.
Chromosomes, Insect
T. F. C. Mackay, Richards, S., Stone, E. A., Barbadilla, A., Ayroles, J. F., Zhu, D., Casillas, S., Han, Y., Magwire, M. M., Cridland, J. M., Richardson, M. F., Anholt, R. R. H., Barrón, M., Bess, C., Blankenburg, K. Petra, Carbone, M. Anna, Castellano, D., Chaboub, L., Duncan, L., Harris, Z., Javaid, M., Jayaseelan, J. Christina, Jhangiani, S. N., Jordan, K. W., Lara, F., Lawrence, F., Lee, S. L., Librado, P., Linheiro, R. S., Lyman, R. F., Mackey, A. J., Munidasa, M., Muzny, D. Marie, Nazareth, L., Newsham, I., Perales, L., Pu, L. - L., Qu, C., Ràmia, M., Reid, J. G., Rollmann, S. M., Rozas, J., Saada, N., Turlapati, L., Worley, K. C., Wu, Y. - Q., Yamamoto, A., Zhu, Y., Bergman, C. M., Thornton, K. R., Mittelman, D., and Gibbs, R. A., “The Drosophila melanogaster Genetic Reference Panel.”, Nature, vol. 482, no. 7384, pp. 173-8, 2012.
Cluster Analysis
S. D. Kocher, Ayroles, J. F., Stone, E. A., and Grozinger, C. M., “Individual variation in pheromone response correlates with reproductive traits and brain gene expression in worker honey bees.”, PLoS One, vol. 5, no. 2, p. e9116, 2010.
E. A. Stone and Ayroles, J. F., “Modulated modularity clustering as an exploratory tool for functional genomic inference.”, PLoS Genet, vol. 5, no. 5, p. e1000479, 2009.
T. V. Morozova, Ayroles, J. F., Jordan, K. W., Duncan, L. H., Carbone, M. Anna, Lyman, R. F., Stone, E. A., Govindaraju, D. R., R Ellison, C., Mackay, T. F. C., and Anholt, R. R. H., “Alcohol sensitivity in Drosophila: translational potential of systems genetics.”, Genetics, vol. 183, no. 2, pp. 733-45, 1SI-12SI, 2009.
Computational Biology
A. C. Edwards, Ayroles, J. F., Stone, E. A., Carbone, M. Anna, Lyman, R. F., and Mackay, T. F. C., “A transcriptional network associated with natural variation in Drosophila aggressive behavior.”, Genome Biol, vol. 10, no. 7, p. R76, 2009.
Computer Simulation
E. A. Stone and Ayroles, J. F., “Modulated modularity clustering as an exploratory tool for functional genomic inference.”, PLoS Genet, vol. 5, no. 5, p. e1000479, 2009.
Data Interpretation, Statistical
E. A. Stone and Ayroles, J. F., “Modulated modularity clustering as an exploratory tool for functional genomic inference.”, PLoS Genet, vol. 5, no. 5, p. e1000479, 2009.
Databases, Genetic
E. A. Stone and Ayroles, J. F., “Modulated modularity clustering as an exploratory tool for functional genomic inference.”, PLoS Genet, vol. 5, no. 5, p. e1000479, 2009.
DNA Transposable Elements
A. C. Edwards, Ayroles, J. F., Stone, E. A., Carbone, M. Anna, Lyman, R. F., and Mackay, T. F. C., “A transcriptional network associated with natural variation in Drosophila aggressive behavior.”, Genome Biol, vol. 10, no. 7, p. R76, 2009.
Drosophila
S. T. Harbison, Carbone, M. Anna, Ayroles, J. F., Stone, E. A., Lyman, R. F., and Mackay, T. F. C., “Co-regulated transcriptional networks contribute to natural genetic variation in Drosophila sleep.”, Nat Genet, vol. 41, no. 3, pp. 371-5, 2009.
Drosophila melanogaster
T. V. Morozova, Ayroles, J. F., Jordan, K. W., Duncan, L. H., Carbone, M. Anna, Lyman, R. F., Stone, E. A., Govindaraju, D. R., R Ellison, C., Mackay, T. F. C., and Anholt, R. R. H., “Alcohol sensitivity in Drosophila: translational potential of systems genetics.”, Genetics, vol. 183, no. 2, pp. 733-45, 1SI-12SI, 2009.
U. Ober, Ayroles, J. F., Stone, E. A., Richards, S., Zhu, D., Gibbs, R. A., Stricker, C., Gianola, D., Schlather, M., Mackay, T. F. C., and Simianer, H., “Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 5, p. e1002685, 2012.
J. F. Ayroles, Laflamme, B. A., Stone, E. A., Wolfner, M. F., and Mackay, T. F. C., “Functional genome annotation of Drosophila seminal fluid proteins using transcriptional genetic networks.”, Genet Res (Camb), vol. 93, no. 6, pp. 387-95, 2011.
J. F. Ayroles, Carbone, M. Anna, Stone, E. A., Jordan, K. W., Lyman, R. F., Magwire, M. M., Rollmann, S. M., Duncan, L. H., Lawrence, F., Anholt, R. R. H., and Mackay, T. F. C., “Systems genetics of complex traits in Drosophila melanogaster.”, Nat Genet, vol. 41, no. 3, pp. 299-307, 2009.
W. Huang, Richards, S., Carbone, M. Anna, Zhu, D., Anholt, R. R. H., Ayroles, J. F., Duncan, L., Jordan, K. W., Lawrence, F., Magwire, M. M., Warner, C. B., Blankenburg, K., Han, Y., Javaid, M., Jayaseelan, J., Jhangiani, S. N., Muzny, D., Ongeri, F., Perales, L., Wu, Y. - Q., Zhang, Y., Zou, X., Stone, E. A., Gibbs, R. A., and Mackay, T. F. C., “Epistasis dominates the genetic architecture of Drosophila quantitative traits.”, Proc Natl Acad Sci U S A, vol. 109, no. 39, pp. 15553-9, 2012.
A. Massouras, Waszak, S. M., Albarca-Aguilera, M., Hens, K., Holcombe, W., Ayroles, J. F., Dermitzakis, E. T., Stone, E. A., Jensen, J. D., Mackay, T. F. C., and Deplancke, B., “Genomic variation and its impact on gene expression in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 11, p. e1003055, 2012.
T. F. C. Mackay, Richards, S., Stone, E. A., Barbadilla, A., Ayroles, J. F., Zhu, D., Casillas, S., Han, Y., Magwire, M. M., Cridland, J. M., Richardson, M. F., Anholt, R. R. H., Barrón, M., Bess, C., Blankenburg, K. Petra, Carbone, M. Anna, Castellano, D., Chaboub, L., Duncan, L., Harris, Z., Javaid, M., Jayaseelan, J. Christina, Jhangiani, S. N., Jordan, K. W., Lara, F., Lawrence, F., Lee, S. L., Librado, P., Linheiro, R. S., Lyman, R. F., Mackey, A. J., Munidasa, M., Muzny, D. Marie, Nazareth, L., Newsham, I., Perales, L., Pu, L. - L., Qu, C., Ràmia, M., Reid, J. G., Rollmann, S. M., Rozas, J., Saada, N., Turlapati, L., Worley, K. C., Wu, Y. - Q., Yamamoto, A., Zhu, Y., Bergman, C. M., Thornton, K. R., Mittelman, D., and Gibbs, R. A., “The Drosophila melanogaster Genetic Reference Panel.”, Nature, vol. 482, no. 7384, pp. 173-8, 2012.
A. C. Edwards, Ayroles, J. F., Stone, E. A., Carbone, M. Anna, Lyman, R. F., and Mackay, T. F. C., “A transcriptional network associated with natural variation in Drosophila aggressive behavior.”, Genome Biol, vol. 10, no. 7, p. R76, 2009.
E. A. Stone and Ayroles, J. F., “Modulated modularity clustering as an exploratory tool for functional genomic inference.”, PLoS Genet, vol. 5, no. 5, p. e1000479, 2009.
Drosophila Proteins
J. F. Ayroles, Laflamme, B. A., Stone, E. A., Wolfner, M. F., and Mackay, T. F. C., “Functional genome annotation of Drosophila seminal fluid proteins using transcriptional genetic networks.”, Genet Res (Camb), vol. 93, no. 6, pp. 387-95, 2011.
S. T. Harbison, Carbone, M. Anna, Ayroles, J. F., Stone, E. A., Lyman, R. F., and Mackay, T. F. C., “Co-regulated transcriptional networks contribute to natural genetic variation in Drosophila sleep.”, Nat Genet, vol. 41, no. 3, pp. 371-5, 2009.
A. C. Edwards, Ayroles, J. F., Stone, E. A., Carbone, M. Anna, Lyman, R. F., and Mackay, T. F. C., “A transcriptional network associated with natural variation in Drosophila aggressive behavior.”, Genome Biol, vol. 10, no. 7, p. R76, 2009.
T. V. Morozova, Ayroles, J. F., Jordan, K. W., Duncan, L. H., Carbone, M. Anna, Lyman, R. F., Stone, E. A., Govindaraju, D. R., R Ellison, C., Mackay, T. F. C., and Anholt, R. R. H., “Alcohol sensitivity in Drosophila: translational potential of systems genetics.”, Genetics, vol. 183, no. 2, pp. 733-45, 1SI-12SI, 2009.
Epistasis, Genetic
W. Huang, Richards, S., Carbone, M. Anna, Zhu, D., Anholt, R. R. H., Ayroles, J. F., Duncan, L., Jordan, K. W., Lawrence, F., Magwire, M. M., Warner, C. B., Blankenburg, K., Han, Y., Javaid, M., Jayaseelan, J., Jhangiani, S. N., Muzny, D., Ongeri, F., Perales, L., Wu, Y. - Q., Zhang, Y., Zou, X., Stone, E. A., Gibbs, R. A., and Mackay, T. F. C., “Epistasis dominates the genetic architecture of Drosophila quantitative traits.”, Proc Natl Acad Sci U S A, vol. 109, no. 39, pp. 15553-9, 2012.
Ethanol
T. V. Morozova, Ayroles, J. F., Jordan, K. W., Duncan, L. H., Carbone, M. Anna, Lyman, R. F., Stone, E. A., Govindaraju, D. R., R Ellison, C., Mackay, T. F. C., and Anholt, R. R. H., “Alcohol sensitivity in Drosophila: translational potential of systems genetics.”, Genetics, vol. 183, no. 2, pp. 733-45, 1SI-12SI, 2009.
Female
S. D. Kocher, Ayroles, J. F., Stone, E. A., and Grozinger, C. M., “Individual variation in pheromone response correlates with reproductive traits and brain gene expression in worker honey bees.”, PLoS One, vol. 5, no. 2, p. e9116, 2010.
J. F. Ayroles, Carbone, M. Anna, Stone, E. A., Jordan, K. W., Lyman, R. F., Magwire, M. M., Rollmann, S. M., Duncan, L. H., Lawrence, F., Anholt, R. R. H., and Mackay, T. F. C., “Systems genetics of complex traits in Drosophila melanogaster.”, Nat Genet, vol. 41, no. 3, pp. 299-307, 2009.
S. T. Harbison, Carbone, M. Anna, Ayroles, J. F., Stone, E. A., Lyman, R. F., and Mackay, T. F. C., “Co-regulated transcriptional networks contribute to natural genetic variation in Drosophila sleep.”, Nat Genet, vol. 41, no. 3, pp. 371-5, 2009.
T. V. Morozova, Ayroles, J. F., Jordan, K. W., Duncan, L. H., Carbone, M. Anna, Lyman, R. F., Stone, E. A., Govindaraju, D. R., R Ellison, C., Mackay, T. F. C., and Anholt, R. R. H., “Alcohol sensitivity in Drosophila: translational potential of systems genetics.”, Genetics, vol. 183, no. 2, pp. 733-45, 1SI-12SI, 2009.
Gene Expression
A. Massouras, Waszak, S. M., Albarca-Aguilera, M., Hens, K., Holcombe, W., Ayroles, J. F., Dermitzakis, E. T., Stone, E. A., Jensen, J. D., Mackay, T. F. C., and Deplancke, B., “Genomic variation and its impact on gene expression in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 11, p. e1003055, 2012.
Gene Expression Profiling
J. F. Ayroles, Laflamme, B. A., Stone, E. A., Wolfner, M. F., and Mackay, T. F. C., “Functional genome annotation of Drosophila seminal fluid proteins using transcriptional genetic networks.”, Genet Res (Camb), vol. 93, no. 6, pp. 387-95, 2011.
S. D. Kocher, Ayroles, J. F., Stone, E. A., and Grozinger, C. M., “Individual variation in pheromone response correlates with reproductive traits and brain gene expression in worker honey bees.”, PLoS One, vol. 5, no. 2, p. e9116, 2010.
A. C. Edwards, Ayroles, J. F., Stone, E. A., Carbone, M. Anna, Lyman, R. F., and Mackay, T. F. C., “A transcriptional network associated with natural variation in Drosophila aggressive behavior.”, Genome Biol, vol. 10, no. 7, p. R76, 2009.
E. A. Stone and Ayroles, J. F., “Modulated modularity clustering as an exploratory tool for functional genomic inference.”, PLoS Genet, vol. 5, no. 5, p. e1000479, 2009.
Gene Expression Regulation
S. T. Harbison, Carbone, M. Anna, Ayroles, J. F., Stone, E. A., Lyman, R. F., and Mackay, T. F. C., “Co-regulated transcriptional networks contribute to natural genetic variation in Drosophila sleep.”, Nat Genet, vol. 41, no. 3, pp. 371-5, 2009.
T. V. Morozova, Ayroles, J. F., Jordan, K. W., Duncan, L. H., Carbone, M. Anna, Lyman, R. F., Stone, E. A., Govindaraju, D. R., R Ellison, C., Mackay, T. F. C., and Anholt, R. R. H., “Alcohol sensitivity in Drosophila: translational potential of systems genetics.”, Genetics, vol. 183, no. 2, pp. 733-45, 1SI-12SI, 2009.
Gene Frequency
A. C. Edwards, Ayroles, J. F., Stone, E. A., Carbone, M. Anna, Lyman, R. F., and Mackay, T. F. C., “A transcriptional network associated with natural variation in Drosophila aggressive behavior.”, Genome Biol, vol. 10, no. 7, p. R76, 2009.
Gene Regulatory Networks
S. D. Kocher, Ayroles, J. F., Stone, E. A., and Grozinger, C. M., “Individual variation in pheromone response correlates with reproductive traits and brain gene expression in worker honey bees.”, PLoS One, vol. 5, no. 2, p. e9116, 2010.
J. F. Ayroles, Laflamme, B. A., Stone, E. A., Wolfner, M. F., and Mackay, T. F. C., “Functional genome annotation of Drosophila seminal fluid proteins using transcriptional genetic networks.”, Genet Res (Camb), vol. 93, no. 6, pp. 387-95, 2011.
J. F. Ayroles, Carbone, M. Anna, Stone, E. A., Jordan, K. W., Lyman, R. F., Magwire, M. M., Rollmann, S. M., Duncan, L. H., Lawrence, F., Anholt, R. R. H., and Mackay, T. F. C., “Systems genetics of complex traits in Drosophila melanogaster.”, Nat Genet, vol. 41, no. 3, pp. 299-307, 2009.
S. T. Harbison, Carbone, M. Anna, Ayroles, J. F., Stone, E. A., Lyman, R. F., and Mackay, T. F. C., “Co-regulated transcriptional networks contribute to natural genetic variation in Drosophila sleep.”, Nat Genet, vol. 41, no. 3, pp. 371-5, 2009.
A. C. Edwards, Ayroles, J. F., Stone, E. A., Carbone, M. Anna, Lyman, R. F., and Mackay, T. F. C., “A transcriptional network associated with natural variation in Drosophila aggressive behavior.”, Genome Biol, vol. 10, no. 7, p. R76, 2009.
T. V. Morozova, Ayroles, J. F., Jordan, K. W., Duncan, L. H., Carbone, M. Anna, Lyman, R. F., Stone, E. A., Govindaraju, D. R., R Ellison, C., Mackay, T. F. C., and Anholt, R. R. H., “Alcohol sensitivity in Drosophila: translational potential of systems genetics.”, Genetics, vol. 183, no. 2, pp. 733-45, 1SI-12SI, 2009.
Genes, Insect
T. V. Morozova, Ayroles, J. F., Jordan, K. W., Duncan, L. H., Carbone, M. Anna, Lyman, R. F., Stone, E. A., Govindaraju, D. R., R Ellison, C., Mackay, T. F. C., and Anholt, R. R. H., “Alcohol sensitivity in Drosophila: translational potential of systems genetics.”, Genetics, vol. 183, no. 2, pp. 733-45, 1SI-12SI, 2009.
S. T. Harbison, Carbone, M. Anna, Ayroles, J. F., Stone, E. A., Lyman, R. F., and Mackay, T. F. C., “Co-regulated transcriptional networks contribute to natural genetic variation in Drosophila sleep.”, Nat Genet, vol. 41, no. 3, pp. 371-5, 2009.
W. Huang, Richards, S., Carbone, M. Anna, Zhu, D., Anholt, R. R. H., Ayroles, J. F., Duncan, L., Jordan, K. W., Lawrence, F., Magwire, M. M., Warner, C. B., Blankenburg, K., Han, Y., Javaid, M., Jayaseelan, J., Jhangiani, S. N., Muzny, D., Ongeri, F., Perales, L., Wu, Y. - Q., Zhang, Y., Zou, X., Stone, E. A., Gibbs, R. A., and Mackay, T. F. C., “Epistasis dominates the genetic architecture of Drosophila quantitative traits.”, Proc Natl Acad Sci U S A, vol. 109, no. 39, pp. 15553-9, 2012.
A. C. Edwards, Ayroles, J. F., Stone, E. A., Carbone, M. Anna, Lyman, R. F., and Mackay, T. F. C., “A transcriptional network associated with natural variation in Drosophila aggressive behavior.”, Genome Biol, vol. 10, no. 7, p. R76, 2009.
Genetic Linkage
T. F. C. Mackay, Stone, E. A., and Ayroles, J. F., “The genetics of quantitative traits: challenges and prospects.”, Nat Rev Genet, vol. 10, no. 8, pp. 565-77, 2009.
Genetic Techniques
E. A. Stone and Ayroles, J. F., “Modulated modularity clustering as an exploratory tool for functional genomic inference.”, PLoS Genet, vol. 5, no. 5, p. e1000479, 2009.
Genetic Variation
J. F. Ayroles, Carbone, M. Anna, Stone, E. A., Jordan, K. W., Lyman, R. F., Magwire, M. M., Rollmann, S. M., Duncan, L. H., Lawrence, F., Anholt, R. R. H., and Mackay, T. F. C., “Systems genetics of complex traits in Drosophila melanogaster.”, Nat Genet, vol. 41, no. 3, pp. 299-307, 2009.
S. T. Harbison, Carbone, M. Anna, Ayroles, J. F., Stone, E. A., Lyman, R. F., and Mackay, T. F. C., “Co-regulated transcriptional networks contribute to natural genetic variation in Drosophila sleep.”, Nat Genet, vol. 41, no. 3, pp. 371-5, 2009.
A. Massouras, Waszak, S. M., Albarca-Aguilera, M., Hens, K., Holcombe, W., Ayroles, J. F., Dermitzakis, E. T., Stone, E. A., Jensen, J. D., Mackay, T. F. C., and Deplancke, B., “Genomic variation and its impact on gene expression in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 11, p. e1003055, 2012.
A. C. Edwards, Ayroles, J. F., Stone, E. A., Carbone, M. Anna, Lyman, R. F., and Mackay, T. F. C., “A transcriptional network associated with natural variation in Drosophila aggressive behavior.”, Genome Biol, vol. 10, no. 7, p. R76, 2009.
T. V. Morozova, Ayroles, J. F., Jordan, K. W., Duncan, L. H., Carbone, M. Anna, Lyman, R. F., Stone, E. A., Govindaraju, D. R., R Ellison, C., Mackay, T. F. C., and Anholt, R. R. H., “Alcohol sensitivity in Drosophila: translational potential of systems genetics.”, Genetics, vol. 183, no. 2, pp. 733-45, 1SI-12SI, 2009.
Genetics, Population
U. Ober, Ayroles, J. F., Stone, E. A., Richards, S., Zhu, D., Gibbs, R. A., Stricker, C., Gianola, D., Schlather, M., Mackay, T. F. C., and Simianer, H., “Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 5, p. e1002685, 2012.
J. F. Ayroles, Carbone, M. Anna, Stone, E. A., Jordan, K. W., Lyman, R. F., Magwire, M. M., Rollmann, S. M., Duncan, L. H., Lawrence, F., Anholt, R. R. H., and Mackay, T. F. C., “Systems genetics of complex traits in Drosophila melanogaster.”, Nat Genet, vol. 41, no. 3, pp. 299-307, 2009.
Genome
A. Massouras, Waszak, S. M., Albarca-Aguilera, M., Hens, K., Holcombe, W., Ayroles, J. F., Dermitzakis, E. T., Stone, E. A., Jensen, J. D., Mackay, T. F. C., and Deplancke, B., “Genomic variation and its impact on gene expression in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 11, p. e1003055, 2012.
Genome, Insect
T. V. Morozova, Ayroles, J. F., Jordan, K. W., Duncan, L. H., Carbone, M. Anna, Lyman, R. F., Stone, E. A., Govindaraju, D. R., R Ellison, C., Mackay, T. F. C., and Anholt, R. R. H., “Alcohol sensitivity in Drosophila: translational potential of systems genetics.”, Genetics, vol. 183, no. 2, pp. 733-45, 1SI-12SI, 2009.
U. Ober, Ayroles, J. F., Stone, E. A., Richards, S., Zhu, D., Gibbs, R. A., Stricker, C., Gianola, D., Schlather, M., Mackay, T. F. C., and Simianer, H., “Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 5, p. e1002685, 2012.
J. F. Ayroles, Laflamme, B. A., Stone, E. A., Wolfner, M. F., and Mackay, T. F. C., “Functional genome annotation of Drosophila seminal fluid proteins using transcriptional genetic networks.”, Genet Res (Camb), vol. 93, no. 6, pp. 387-95, 2011.
S. T. Harbison, Carbone, M. Anna, Ayroles, J. F., Stone, E. A., Lyman, R. F., and Mackay, T. F. C., “Co-regulated transcriptional networks contribute to natural genetic variation in Drosophila sleep.”, Nat Genet, vol. 41, no. 3, pp. 371-5, 2009.
A. C. Edwards, Ayroles, J. F., Stone, E. A., Carbone, M. Anna, Lyman, R. F., and Mackay, T. F. C., “A transcriptional network associated with natural variation in Drosophila aggressive behavior.”, Genome Biol, vol. 10, no. 7, p. R76, 2009.
Genome-Wide Association Study
T. F. C. Mackay, Richards, S., Stone, E. A., Barbadilla, A., Ayroles, J. F., Zhu, D., Casillas, S., Han, Y., Magwire, M. M., Cridland, J. M., Richardson, M. F., Anholt, R. R. H., Barrón, M., Bess, C., Blankenburg, K. Petra, Carbone, M. Anna, Castellano, D., Chaboub, L., Duncan, L., Harris, Z., Javaid, M., Jayaseelan, J. Christina, Jhangiani, S. N., Jordan, K. W., Lara, F., Lawrence, F., Lee, S. L., Librado, P., Linheiro, R. S., Lyman, R. F., Mackey, A. J., Munidasa, M., Muzny, D. Marie, Nazareth, L., Newsham, I., Perales, L., Pu, L. - L., Qu, C., Ràmia, M., Reid, J. G., Rollmann, S. M., Rozas, J., Saada, N., Turlapati, L., Worley, K. C., Wu, Y. - Q., Yamamoto, A., Zhu, Y., Bergman, C. M., Thornton, K. R., Mittelman, D., and Gibbs, R. A., “The Drosophila melanogaster Genetic Reference Panel.”, Nature, vol. 482, no. 7384, pp. 173-8, 2012.
T. V. Morozova, Ayroles, J. F., Jordan, K. W., Duncan, L. H., Carbone, M. Anna, Lyman, R. F., Stone, E. A., Govindaraju, D. R., R Ellison, C., Mackay, T. F. C., and Anholt, R. R. H., “Alcohol sensitivity in Drosophila: translational potential of systems genetics.”, Genetics, vol. 183, no. 2, pp. 733-45, 1SI-12SI, 2009.
S. T. Harbison, Carbone, M. Anna, Ayroles, J. F., Stone, E. A., Lyman, R. F., and Mackay, T. F. C., “Co-regulated transcriptional networks contribute to natural genetic variation in Drosophila sleep.”, Nat Genet, vol. 41, no. 3, pp. 371-5, 2009.
Genomics
T. F. C. Mackay, Richards, S., Stone, E. A., Barbadilla, A., Ayroles, J. F., Zhu, D., Casillas, S., Han, Y., Magwire, M. M., Cridland, J. M., Richardson, M. F., Anholt, R. R. H., Barrón, M., Bess, C., Blankenburg, K. Petra, Carbone, M. Anna, Castellano, D., Chaboub, L., Duncan, L., Harris, Z., Javaid, M., Jayaseelan, J. Christina, Jhangiani, S. N., Jordan, K. W., Lara, F., Lawrence, F., Lee, S. L., Librado, P., Linheiro, R. S., Lyman, R. F., Mackey, A. J., Munidasa, M., Muzny, D. Marie, Nazareth, L., Newsham, I., Perales, L., Pu, L. - L., Qu, C., Ràmia, M., Reid, J. G., Rollmann, S. M., Rozas, J., Saada, N., Turlapati, L., Worley, K. C., Wu, Y. - Q., Yamamoto, A., Zhu, Y., Bergman, C. M., Thornton, K. R., Mittelman, D., and Gibbs, R. A., “The Drosophila melanogaster Genetic Reference Panel.”, Nature, vol. 482, no. 7384, pp. 173-8, 2012.
E. A. Stone and Ayroles, J. F., “Modulated modularity clustering as an exploratory tool for functional genomic inference.”, PLoS Genet, vol. 5, no. 5, p. e1000479, 2009.
Genotype
T. V. Morozova, Ayroles, J. F., Jordan, K. W., Duncan, L. H., Carbone, M. Anna, Lyman, R. F., Stone, E. A., Govindaraju, D. R., R Ellison, C., Mackay, T. F. C., and Anholt, R. R. H., “Alcohol sensitivity in Drosophila: translational potential of systems genetics.”, Genetics, vol. 183, no. 2, pp. 733-45, 1SI-12SI, 2009.
U. Ober, Ayroles, J. F., Stone, E. A., Richards, S., Zhu, D., Gibbs, R. A., Stricker, C., Gianola, D., Schlather, M., Mackay, T. F. C., and Simianer, H., “Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 5, p. e1002685, 2012.
T. F. C. Mackay, Richards, S., Stone, E. A., Barbadilla, A., Ayroles, J. F., Zhu, D., Casillas, S., Han, Y., Magwire, M. M., Cridland, J. M., Richardson, M. F., Anholt, R. R. H., Barrón, M., Bess, C., Blankenburg, K. Petra, Carbone, M. Anna, Castellano, D., Chaboub, L., Duncan, L., Harris, Z., Javaid, M., Jayaseelan, J. Christina, Jhangiani, S. N., Jordan, K. W., Lara, F., Lawrence, F., Lee, S. L., Librado, P., Linheiro, R. S., Lyman, R. F., Mackey, A. J., Munidasa, M., Muzny, D. Marie, Nazareth, L., Newsham, I., Perales, L., Pu, L. - L., Qu, C., Ràmia, M., Reid, J. G., Rollmann, S. M., Rozas, J., Saada, N., Turlapati, L., Worley, K. C., Wu, Y. - Q., Yamamoto, A., Zhu, Y., Bergman, C. M., Thornton, K. R., Mittelman, D., and Gibbs, R. A., “The Drosophila melanogaster Genetic Reference Panel.”, Nature, vol. 482, no. 7384, pp. 173-8, 2012.
Humans
E. A. Stone and Ayroles, J. F., “Modulated modularity clustering as an exploratory tool for functional genomic inference.”, PLoS Genet, vol. 5, no. 5, p. e1000479, 2009.
T. V. Morozova, Ayroles, J. F., Jordan, K. W., Duncan, L. H., Carbone, M. Anna, Lyman, R. F., Stone, E. A., Govindaraju, D. R., R Ellison, C., Mackay, T. F. C., and Anholt, R. R. H., “Alcohol sensitivity in Drosophila: translational potential of systems genetics.”, Genetics, vol. 183, no. 2, pp. 733-45, 1SI-12SI, 2009.
T. F. C. Mackay, Stone, E. A., and Ayroles, J. F., “The genetics of quantitative traits: challenges and prospects.”, Nat Rev Genet, vol. 10, no. 8, pp. 565-77, 2009.
Inbreeding
T. V. Morozova, Ayroles, J. F., Jordan, K. W., Duncan, L. H., Carbone, M. Anna, Lyman, R. F., Stone, E. A., Govindaraju, D. R., R Ellison, C., Mackay, T. F. C., and Anholt, R. R. H., “Alcohol sensitivity in Drosophila: translational potential of systems genetics.”, Genetics, vol. 183, no. 2, pp. 733-45, 1SI-12SI, 2009.
INDEL Mutation
A. Massouras, Waszak, S. M., Albarca-Aguilera, M., Hens, K., Holcombe, W., Ayroles, J. F., Dermitzakis, E. T., Stone, E. A., Jensen, J. D., Mackay, T. F. C., and Deplancke, B., “Genomic variation and its impact on gene expression in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 11, p. e1003055, 2012.
Insect Proteins
S. D. Kocher, Ayroles, J. F., Stone, E. A., and Grozinger, C. M., “Individual variation in pheromone response correlates with reproductive traits and brain gene expression in worker honey bees.”, PLoS One, vol. 5, no. 2, p. e9116, 2010.
Linkage Disequilibrium
U. Ober, Ayroles, J. F., Stone, E. A., Richards, S., Zhu, D., Gibbs, R. A., Stricker, C., Gianola, D., Schlather, M., Mackay, T. F. C., and Simianer, H., “Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 5, p. e1002685, 2012.
Lymphocytes
E. A. Stone and Ayroles, J. F., “Modulated modularity clustering as an exploratory tool for functional genomic inference.”, PLoS Genet, vol. 5, no. 5, p. e1000479, 2009.
Malate Dehydrogenase
T. V. Morozova, Ayroles, J. F., Jordan, K. W., Duncan, L. H., Carbone, M. Anna, Lyman, R. F., Stone, E. A., Govindaraju, D. R., R Ellison, C., Mackay, T. F. C., and Anholt, R. R. H., “Alcohol sensitivity in Drosophila: translational potential of systems genetics.”, Genetics, vol. 183, no. 2, pp. 733-45, 1SI-12SI, 2009.
Male
J. F. Ayroles, Laflamme, B. A., Stone, E. A., Wolfner, M. F., and Mackay, T. F. C., “Functional genome annotation of Drosophila seminal fluid proteins using transcriptional genetic networks.”, Genet Res (Camb), vol. 93, no. 6, pp. 387-95, 2011.
S. D. Kocher, Ayroles, J. F., Stone, E. A., and Grozinger, C. M., “Individual variation in pheromone response correlates with reproductive traits and brain gene expression in worker honey bees.”, PLoS One, vol. 5, no. 2, p. e9116, 2010.
J. F. Ayroles, Carbone, M. Anna, Stone, E. A., Jordan, K. W., Lyman, R. F., Magwire, M. M., Rollmann, S. M., Duncan, L. H., Lawrence, F., Anholt, R. R. H., and Mackay, T. F. C., “Systems genetics of complex traits in Drosophila melanogaster.”, Nat Genet, vol. 41, no. 3, pp. 299-307, 2009.
S. T. Harbison, Carbone, M. Anna, Ayroles, J. F., Stone, E. A., Lyman, R. F., and Mackay, T. F. C., “Co-regulated transcriptional networks contribute to natural genetic variation in Drosophila sleep.”, Nat Genet, vol. 41, no. 3, pp. 371-5, 2009.
A. C. Edwards, Ayroles, J. F., Stone, E. A., Carbone, M. Anna, Lyman, R. F., and Mackay, T. F. C., “A transcriptional network associated with natural variation in Drosophila aggressive behavior.”, Genome Biol, vol. 10, no. 7, p. R76, 2009.
T. V. Morozova, Ayroles, J. F., Jordan, K. W., Duncan, L. H., Carbone, M. Anna, Lyman, R. F., Stone, E. A., Govindaraju, D. R., R Ellison, C., Mackay, T. F. C., and Anholt, R. R. H., “Alcohol sensitivity in Drosophila: translational potential of systems genetics.”, Genetics, vol. 183, no. 2, pp. 733-45, 1SI-12SI, 2009.
Models, Biological
S. T. Harbison, Carbone, M. Anna, Ayroles, J. F., Stone, E. A., Lyman, R. F., and Mackay, T. F. C., “Co-regulated transcriptional networks contribute to natural genetic variation in Drosophila sleep.”, Nat Genet, vol. 41, no. 3, pp. 371-5, 2009.
Models, Genetic
U. Ober, Ayroles, J. F., Stone, E. A., Richards, S., Zhu, D., Gibbs, R. A., Stricker, C., Gianola, D., Schlather, M., Mackay, T. F. C., and Simianer, H., “Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 5, p. e1002685, 2012.
J. F. Ayroles, Laflamme, B. A., Stone, E. A., Wolfner, M. F., and Mackay, T. F. C., “Functional genome annotation of Drosophila seminal fluid proteins using transcriptional genetic networks.”, Genet Res (Camb), vol. 93, no. 6, pp. 387-95, 2011.
E. A. Stone and Ayroles, J. F., “Modulated modularity clustering as an exploratory tool for functional genomic inference.”, PLoS Genet, vol. 5, no. 5, p. e1000479, 2009.
Models, Theoretical
U. Ober, Ayroles, J. F., Stone, E. A., Richards, S., Zhu, D., Gibbs, R. A., Stricker, C., Gianola, D., Schlather, M., Mackay, T. F. C., and Simianer, H., “Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 5, p. e1002685, 2012.
Molecular Sequence Annotation
J. F. Ayroles, Laflamme, B. A., Stone, E. A., Wolfner, M. F., and Mackay, T. F. C., “Functional genome annotation of Drosophila seminal fluid proteins using transcriptional genetic networks.”, Genet Res (Camb), vol. 93, no. 6, pp. 387-95, 2011.
Molecular Sequence Data
J. F. Ayroles, Carbone, M. Anna, Stone, E. A., Jordan, K. W., Lyman, R. F., Magwire, M. M., Rollmann, S. M., Duncan, L. H., Lawrence, F., Anholt, R. R. H., and Mackay, T. F. C., “Systems genetics of complex traits in Drosophila melanogaster.”, Nat Genet, vol. 41, no. 3, pp. 299-307, 2009.
S. T. Harbison, Carbone, M. Anna, Ayroles, J. F., Stone, E. A., Lyman, R. F., and Mackay, T. F. C., “Co-regulated transcriptional networks contribute to natural genetic variation in Drosophila sleep.”, Nat Genet, vol. 41, no. 3, pp. 371-5, 2009.
Multigene Family
E. A. Stone and Ayroles, J. F., “Modulated modularity clustering as an exploratory tool for functional genomic inference.”, PLoS Genet, vol. 5, no. 5, p. e1000479, 2009.
Mutagenesis, Insertional
A. C. Edwards, Ayroles, J. F., Stone, E. A., Carbone, M. Anna, Lyman, R. F., and Mackay, T. F. C., “A transcriptional network associated with natural variation in Drosophila aggressive behavior.”, Genome Biol, vol. 10, no. 7, p. R76, 2009.
Mutation
A. C. Edwards, Ayroles, J. F., Stone, E. A., Carbone, M. Anna, Lyman, R. F., and Mackay, T. F. C., “A transcriptional network associated with natural variation in Drosophila aggressive behavior.”, Genome Biol, vol. 10, no. 7, p. R76, 2009.
Oligonucleotide Array Sequence Analysis
S. D. Kocher, Ayroles, J. F., Stone, E. A., and Grozinger, C. M., “Individual variation in pheromone response correlates with reproductive traits and brain gene expression in worker honey bees.”, PLoS One, vol. 5, no. 2, p. e9116, 2010.
J. F. Ayroles, Laflamme, B. A., Stone, E. A., Wolfner, M. F., and Mackay, T. F. C., “Functional genome annotation of Drosophila seminal fluid proteins using transcriptional genetic networks.”, Genet Res (Camb), vol. 93, no. 6, pp. 387-95, 2011.
Ovary
S. D. Kocher, Ayroles, J. F., Stone, E. A., and Grozinger, C. M., “Individual variation in pheromone response correlates with reproductive traits and brain gene expression in worker honey bees.”, PLoS One, vol. 5, no. 2, p. e9116, 2010.
Phenotype
T. V. Morozova, Ayroles, J. F., Jordan, K. W., Duncan, L. H., Carbone, M. Anna, Lyman, R. F., Stone, E. A., Govindaraju, D. R., R Ellison, C., Mackay, T. F. C., and Anholt, R. R. H., “Alcohol sensitivity in Drosophila: translational potential of systems genetics.”, Genetics, vol. 183, no. 2, pp. 733-45, 1SI-12SI, 2009.
U. Ober, Ayroles, J. F., Stone, E. A., Richards, S., Zhu, D., Gibbs, R. A., Stricker, C., Gianola, D., Schlather, M., Mackay, T. F. C., and Simianer, H., “Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 5, p. e1002685, 2012.
J. F. Ayroles, Carbone, M. Anna, Stone, E. A., Jordan, K. W., Lyman, R. F., Magwire, M. M., Rollmann, S. M., Duncan, L. H., Lawrence, F., Anholt, R. R. H., and Mackay, T. F. C., “Systems genetics of complex traits in Drosophila melanogaster.”, Nat Genet, vol. 41, no. 3, pp. 299-307, 2009.
A. Massouras, Waszak, S. M., Albarca-Aguilera, M., Hens, K., Holcombe, W., Ayroles, J. F., Dermitzakis, E. T., Stone, E. A., Jensen, J. D., Mackay, T. F. C., and Deplancke, B., “Genomic variation and its impact on gene expression in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 11, p. e1003055, 2012.
T. F. C. Mackay, Richards, S., Stone, E. A., Barbadilla, A., Ayroles, J. F., Zhu, D., Casillas, S., Han, Y., Magwire, M. M., Cridland, J. M., Richardson, M. F., Anholt, R. R. H., Barrón, M., Bess, C., Blankenburg, K. Petra, Carbone, M. Anna, Castellano, D., Chaboub, L., Duncan, L., Harris, Z., Javaid, M., Jayaseelan, J. Christina, Jhangiani, S. N., Jordan, K. W., Lara, F., Lawrence, F., Lee, S. L., Librado, P., Linheiro, R. S., Lyman, R. F., Mackey, A. J., Munidasa, M., Muzny, D. Marie, Nazareth, L., Newsham, I., Perales, L., Pu, L. - L., Qu, C., Ràmia, M., Reid, J. G., Rollmann, S. M., Rozas, J., Saada, N., Turlapati, L., Worley, K. C., Wu, Y. - Q., Yamamoto, A., Zhu, Y., Bergman, C. M., Thornton, K. R., Mittelman, D., and Gibbs, R. A., “The Drosophila melanogaster Genetic Reference Panel.”, Nature, vol. 482, no. 7384, pp. 173-8, 2012.
A. C. Edwards, Ayroles, J. F., Stone, E. A., Carbone, M. Anna, Lyman, R. F., and Mackay, T. F. C., “A transcriptional network associated with natural variation in Drosophila aggressive behavior.”, Genome Biol, vol. 10, no. 7, p. R76, 2009.
Pheromones
S. D. Kocher, Ayroles, J. F., Stone, E. A., and Grozinger, C. M., “Individual variation in pheromone response correlates with reproductive traits and brain gene expression in worker honey bees.”, PLoS One, vol. 5, no. 2, p. e9116, 2010.
Polymorphism, Genetic
S. T. Harbison, Carbone, M. Anna, Ayroles, J. F., Stone, E. A., Lyman, R. F., and Mackay, T. F. C., “Co-regulated transcriptional networks contribute to natural genetic variation in Drosophila sleep.”, Nat Genet, vol. 41, no. 3, pp. 371-5, 2009.
Polymorphism, Single Nucleotide
T. V. Morozova, Ayroles, J. F., Jordan, K. W., Duncan, L. H., Carbone, M. Anna, Lyman, R. F., Stone, E. A., Govindaraju, D. R., R Ellison, C., Mackay, T. F. C., and Anholt, R. R. H., “Alcohol sensitivity in Drosophila: translational potential of systems genetics.”, Genetics, vol. 183, no. 2, pp. 733-45, 1SI-12SI, 2009.
U. Ober, Ayroles, J. F., Stone, E. A., Richards, S., Zhu, D., Gibbs, R. A., Stricker, C., Gianola, D., Schlather, M., Mackay, T. F. C., and Simianer, H., “Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 5, p. e1002685, 2012.
W. Huang, Richards, S., Carbone, M. Anna, Zhu, D., Anholt, R. R. H., Ayroles, J. F., Duncan, L., Jordan, K. W., Lawrence, F., Magwire, M. M., Warner, C. B., Blankenburg, K., Han, Y., Javaid, M., Jayaseelan, J., Jhangiani, S. N., Muzny, D., Ongeri, F., Perales, L., Wu, Y. - Q., Zhang, Y., Zou, X., Stone, E. A., Gibbs, R. A., and Mackay, T. F. C., “Epistasis dominates the genetic architecture of Drosophila quantitative traits.”, Proc Natl Acad Sci U S A, vol. 109, no. 39, pp. 15553-9, 2012.
A. Massouras, Waszak, S. M., Albarca-Aguilera, M., Hens, K., Holcombe, W., Ayroles, J. F., Dermitzakis, E. T., Stone, E. A., Jensen, J. D., Mackay, T. F. C., and Deplancke, B., “Genomic variation and its impact on gene expression in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 11, p. e1003055, 2012.
T. F. C. Mackay, Richards, S., Stone, E. A., Barbadilla, A., Ayroles, J. F., Zhu, D., Casillas, S., Han, Y., Magwire, M. M., Cridland, J. M., Richardson, M. F., Anholt, R. R. H., Barrón, M., Bess, C., Blankenburg, K. Petra, Carbone, M. Anna, Castellano, D., Chaboub, L., Duncan, L., Harris, Z., Javaid, M., Jayaseelan, J. Christina, Jhangiani, S. N., Jordan, K. W., Lara, F., Lawrence, F., Lee, S. L., Librado, P., Linheiro, R. S., Lyman, R. F., Mackey, A. J., Munidasa, M., Muzny, D. Marie, Nazareth, L., Newsham, I., Perales, L., Pu, L. - L., Qu, C., Ràmia, M., Reid, J. G., Rollmann, S. M., Rozas, J., Saada, N., Turlapati, L., Worley, K. C., Wu, Y. - Q., Yamamoto, A., Zhu, Y., Bergman, C. M., Thornton, K. R., Mittelman, D., and Gibbs, R. A., “The Drosophila melanogaster Genetic Reference Panel.”, Nature, vol. 482, no. 7384, pp. 173-8, 2012.
Quantitative Trait Loci
T. F. C. Mackay, Richards, S., Stone, E. A., Barbadilla, A., Ayroles, J. F., Zhu, D., Casillas, S., Han, Y., Magwire, M. M., Cridland, J. M., Richardson, M. F., Anholt, R. R. H., Barrón, M., Bess, C., Blankenburg, K. Petra, Carbone, M. Anna, Castellano, D., Chaboub, L., Duncan, L., Harris, Z., Javaid, M., Jayaseelan, J. Christina, Jhangiani, S. N., Jordan, K. W., Lara, F., Lawrence, F., Lee, S. L., Librado, P., Linheiro, R. S., Lyman, R. F., Mackey, A. J., Munidasa, M., Muzny, D. Marie, Nazareth, L., Newsham, I., Perales, L., Pu, L. - L., Qu, C., Ràmia, M., Reid, J. G., Rollmann, S. M., Rozas, J., Saada, N., Turlapati, L., Worley, K. C., Wu, Y. - Q., Yamamoto, A., Zhu, Y., Bergman, C. M., Thornton, K. R., Mittelman, D., and Gibbs, R. A., “The Drosophila melanogaster Genetic Reference Panel.”, Nature, vol. 482, no. 7384, pp. 173-8, 2012.
U. Ober, Ayroles, J. F., Stone, E. A., Richards, S., Zhu, D., Gibbs, R. A., Stricker, C., Gianola, D., Schlather, M., Mackay, T. F. C., and Simianer, H., “Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 5, p. e1002685, 2012.
A. Massouras, Waszak, S. M., Albarca-Aguilera, M., Hens, K., Holcombe, W., Ayroles, J. F., Dermitzakis, E. T., Stone, E. A., Jensen, J. D., Mackay, T. F. C., and Deplancke, B., “Genomic variation and its impact on gene expression in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 11, p. e1003055, 2012.
Quantitative Trait, Heritable
T. F. C. Mackay, Stone, E. A., and Ayroles, J. F., “The genetics of quantitative traits: challenges and prospects.”, Nat Rev Genet, vol. 10, no. 8, pp. 565-77, 2009.
A. C. Edwards, Ayroles, J. F., Stone, E. A., Carbone, M. Anna, Lyman, R. F., and Mackay, T. F. C., “A transcriptional network associated with natural variation in Drosophila aggressive behavior.”, Genome Biol, vol. 10, no. 7, p. R76, 2009.
J. F. Ayroles, Carbone, M. Anna, Stone, E. A., Jordan, K. W., Lyman, R. F., Magwire, M. M., Rollmann, S. M., Duncan, L. H., Lawrence, F., Anholt, R. R. H., and Mackay, T. F. C., “Systems genetics of complex traits in Drosophila melanogaster.”, Nat Genet, vol. 41, no. 3, pp. 299-307, 2009.
W. Huang, Richards, S., Carbone, M. Anna, Zhu, D., Anholt, R. R. H., Ayroles, J. F., Duncan, L., Jordan, K. W., Lawrence, F., Magwire, M. M., Warner, C. B., Blankenburg, K., Han, Y., Javaid, M., Jayaseelan, J., Jhangiani, S. N., Muzny, D., Ongeri, F., Perales, L., Wu, Y. - Q., Zhang, Y., Zou, X., Stone, E. A., Gibbs, R. A., and Mackay, T. F. C., “Epistasis dominates the genetic architecture of Drosophila quantitative traits.”, Proc Natl Acad Sci U S A, vol. 109, no. 39, pp. 15553-9, 2012.
Reproducibility of Results
T. V. Morozova, Ayroles, J. F., Jordan, K. W., Duncan, L. H., Carbone, M. Anna, Lyman, R. F., Stone, E. A., Govindaraju, D. R., R Ellison, C., Mackay, T. F. C., and Anholt, R. R. H., “Alcohol sensitivity in Drosophila: translational potential of systems genetics.”, Genetics, vol. 183, no. 2, pp. 733-45, 1SI-12SI, 2009.
J. F. Ayroles, Laflamme, B. A., Stone, E. A., Wolfner, M. F., and Mackay, T. F. C., “Functional genome annotation of Drosophila seminal fluid proteins using transcriptional genetic networks.”, Genet Res (Camb), vol. 93, no. 6, pp. 387-95, 2011.
Reproduction
S. D. Kocher, Ayroles, J. F., Stone, E. A., and Grozinger, C. M., “Individual variation in pheromone response correlates with reproductive traits and brain gene expression in worker honey bees.”, PLoS One, vol. 5, no. 2, p. e9116, 2010.
Reverse Transcriptase Polymerase Chain Reaction
T. V. Morozova, Ayroles, J. F., Jordan, K. W., Duncan, L. H., Carbone, M. Anna, Lyman, R. F., Stone, E. A., Govindaraju, D. R., R Ellison, C., Mackay, T. F. C., and Anholt, R. R. H., “Alcohol sensitivity in Drosophila: translational potential of systems genetics.”, Genetics, vol. 183, no. 2, pp. 733-45, 1SI-12SI, 2009.
J. F. Ayroles, Laflamme, B. A., Stone, E. A., Wolfner, M. F., and Mackay, T. F. C., “Functional genome annotation of Drosophila seminal fluid proteins using transcriptional genetic networks.”, Genet Res (Camb), vol. 93, no. 6, pp. 387-95, 2011.
RNA, Messenger
J. F. Ayroles, Carbone, M. Anna, Stone, E. A., Jordan, K. W., Lyman, R. F., Magwire, M. M., Rollmann, S. M., Duncan, L. H., Lawrence, F., Anholt, R. R. H., and Mackay, T. F. C., “Systems genetics of complex traits in Drosophila melanogaster.”, Nat Genet, vol. 41, no. 3, pp. 299-307, 2009.
Selection, Genetic
U. Ober, Ayroles, J. F., Stone, E. A., Richards, S., Zhu, D., Gibbs, R. A., Stricker, C., Gianola, D., Schlather, M., Mackay, T. F. C., and Simianer, H., “Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 5, p. e1002685, 2012.
T. F. C. Mackay, Richards, S., Stone, E. A., Barbadilla, A., Ayroles, J. F., Zhu, D., Casillas, S., Han, Y., Magwire, M. M., Cridland, J. M., Richardson, M. F., Anholt, R. R. H., Barrón, M., Bess, C., Blankenburg, K. Petra, Carbone, M. Anna, Castellano, D., Chaboub, L., Duncan, L., Harris, Z., Javaid, M., Jayaseelan, J. Christina, Jhangiani, S. N., Jordan, K. W., Lara, F., Lawrence, F., Lee, S. L., Librado, P., Linheiro, R. S., Lyman, R. F., Mackey, A. J., Munidasa, M., Muzny, D. Marie, Nazareth, L., Newsham, I., Perales, L., Pu, L. - L., Qu, C., Ràmia, M., Reid, J. G., Rollmann, S. M., Rozas, J., Saada, N., Turlapati, L., Worley, K. C., Wu, Y. - Q., Yamamoto, A., Zhu, Y., Bergman, C. M., Thornton, K. R., Mittelman, D., and Gibbs, R. A., “The Drosophila melanogaster Genetic Reference Panel.”, Nature, vol. 482, no. 7384, pp. 173-8, 2012.
Seminal Plasma Proteins
J. F. Ayroles, Laflamme, B. A., Stone, E. A., Wolfner, M. F., and Mackay, T. F. C., “Functional genome annotation of Drosophila seminal fluid proteins using transcriptional genetic networks.”, Genet Res (Camb), vol. 93, no. 6, pp. 387-95, 2011.
Sequence Analysis, DNA
U. Ober, Ayroles, J. F., Stone, E. A., Richards, S., Zhu, D., Gibbs, R. A., Stricker, C., Gianola, D., Schlather, M., Mackay, T. F. C., and Simianer, H., “Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 5, p. e1002685, 2012.
Sequence Homology, Amino Acid
J. F. Ayroles, Carbone, M. Anna, Stone, E. A., Jordan, K. W., Lyman, R. F., Magwire, M. M., Rollmann, S. M., Duncan, L. H., Lawrence, F., Anholt, R. R. H., and Mackay, T. F. C., “Systems genetics of complex traits in Drosophila melanogaster.”, Nat Genet, vol. 41, no. 3, pp. 299-307, 2009.
Sexual Behavior, Animal
S. D. Kocher, Ayroles, J. F., Stone, E. A., and Grozinger, C. M., “Individual variation in pheromone response correlates with reproductive traits and brain gene expression in worker honey bees.”, PLoS One, vol. 5, no. 2, p. e9116, 2010.
Sleep
S. T. Harbison, Carbone, M. Anna, Ayroles, J. F., Stone, E. A., Lyman, R. F., and Mackay, T. F. C., “Co-regulated transcriptional networks contribute to natural genetic variation in Drosophila sleep.”, Nat Genet, vol. 41, no. 3, pp. 371-5, 2009.
Social Behavior
S. D. Kocher, Ayroles, J. F., Stone, E. A., and Grozinger, C. M., “Individual variation in pheromone response correlates with reproductive traits and brain gene expression in worker honey bees.”, PLoS One, vol. 5, no. 2, p. e9116, 2010.
Species Specificity
A. C. Edwards, Ayroles, J. F., Stone, E. A., Carbone, M. Anna, Lyman, R. F., and Mackay, T. F. C., “A transcriptional network associated with natural variation in Drosophila aggressive behavior.”, Genome Biol, vol. 10, no. 7, p. R76, 2009.
Starvation
T. F. C. Mackay, Richards, S., Stone, E. A., Barbadilla, A., Ayroles, J. F., Zhu, D., Casillas, S., Han, Y., Magwire, M. M., Cridland, J. M., Richardson, M. F., Anholt, R. R. H., Barrón, M., Bess, C., Blankenburg, K. Petra, Carbone, M. Anna, Castellano, D., Chaboub, L., Duncan, L., Harris, Z., Javaid, M., Jayaseelan, J. Christina, Jhangiani, S. N., Jordan, K. W., Lara, F., Lawrence, F., Lee, S. L., Librado, P., Linheiro, R. S., Lyman, R. F., Mackey, A. J., Munidasa, M., Muzny, D. Marie, Nazareth, L., Newsham, I., Perales, L., Pu, L. - L., Qu, C., Ràmia, M., Reid, J. G., Rollmann, S. M., Rozas, J., Saada, N., Turlapati, L., Worley, K. C., Wu, Y. - Q., Yamamoto, A., Zhu, Y., Bergman, C. M., Thornton, K. R., Mittelman, D., and Gibbs, R. A., “The Drosophila melanogaster Genetic Reference Panel.”, Nature, vol. 482, no. 7384, pp. 173-8, 2012.
Systems Biology
E. A. Stone and Ayroles, J. F., “Modulated modularity clustering as an exploratory tool for functional genomic inference.”, PLoS Genet, vol. 5, no. 5, p. e1000479, 2009.
Telomere
T. F. C. Mackay, Richards, S., Stone, E. A., Barbadilla, A., Ayroles, J. F., Zhu, D., Casillas, S., Han, Y., Magwire, M. M., Cridland, J. M., Richardson, M. F., Anholt, R. R. H., Barrón, M., Bess, C., Blankenburg, K. Petra, Carbone, M. Anna, Castellano, D., Chaboub, L., Duncan, L., Harris, Z., Javaid, M., Jayaseelan, J. Christina, Jhangiani, S. N., Jordan, K. W., Lara, F., Lawrence, F., Lee, S. L., Librado, P., Linheiro, R. S., Lyman, R. F., Mackey, A. J., Munidasa, M., Muzny, D. Marie, Nazareth, L., Newsham, I., Perales, L., Pu, L. - L., Qu, C., Ràmia, M., Reid, J. G., Rollmann, S. M., Rozas, J., Saada, N., Turlapati, L., Worley, K. C., Wu, Y. - Q., Yamamoto, A., Zhu, Y., Bergman, C. M., Thornton, K. R., Mittelman, D., and Gibbs, R. A., “The Drosophila melanogaster Genetic Reference Panel.”, Nature, vol. 482, no. 7384, pp. 173-8, 2012.
Tissue Distribution
J. F. Ayroles, Carbone, M. Anna, Stone, E. A., Jordan, K. W., Lyman, R. F., Magwire, M. M., Rollmann, S. M., Duncan, L. H., Lawrence, F., Anholt, R. R. H., and Mackay, T. F. C., “Systems genetics of complex traits in Drosophila melanogaster.”, Nat Genet, vol. 41, no. 3, pp. 299-307, 2009.
Transcription, Genetic
A. C. Edwards, Ayroles, J. F., Stone, E. A., Carbone, M. Anna, Lyman, R. F., and Mackay, T. F. C., “A transcriptional network associated with natural variation in Drosophila aggressive behavior.”, Genome Biol, vol. 10, no. 7, p. R76, 2009.
Transcriptome
J. F. Ayroles, Laflamme, B. A., Stone, E. A., Wolfner, M. F., and Mackay, T. F. C., “Functional genome annotation of Drosophila seminal fluid proteins using transcriptional genetic networks.”, Genet Res (Camb), vol. 93, no. 6, pp. 387-95, 2011.
X Chromosome
T. F. C. Mackay, Richards, S., Stone, E. A., Barbadilla, A., Ayroles, J. F., Zhu, D., Casillas, S., Han, Y., Magwire, M. M., Cridland, J. M., Richardson, M. F., Anholt, R. R. H., Barrón, M., Bess, C., Blankenburg, K. Petra, Carbone, M. Anna, Castellano, D., Chaboub, L., Duncan, L., Harris, Z., Javaid, M., Jayaseelan, J. Christina, Jhangiani, S. N., Jordan, K. W., Lara, F., Lawrence, F., Lee, S. L., Librado, P., Linheiro, R. S., Lyman, R. F., Mackey, A. J., Munidasa, M., Muzny, D. Marie, Nazareth, L., Newsham, I., Perales, L., Pu, L. - L., Qu, C., Ràmia, M., Reid, J. G., Rollmann, S. M., Rozas, J., Saada, N., Turlapati, L., Worley, K. C., Wu, Y. - Q., Yamamoto, A., Zhu, Y., Bergman, C. M., Thornton, K. R., Mittelman, D., and Gibbs, R. A., “The Drosophila melanogaster Genetic Reference Panel.”, Nature, vol. 482, no. 7384, pp. 173-8, 2012.