Eric Stone

Stone, E. A., & Singh, N. D. (2016, February). Bias-Variance Tradeoffs in Recombination Rate Estimation. https://doi.org/10.1534/genetics.115.185561

Skelly, D. A., Magwene, P. M., & Stone, E. A. (2016). Sporadic, Global Linkage Disequilibrium Between Unlinked Segregating Sites. GENETICS, 202(2), 427-+. https://doi.org/10.1534/genetics.115.177816

Olarte, R. A., Worthington, C. J., Horn, B. W., Moore, G. G., Singh, R., Monacell, J. T., … Carbone, I. (2015). Enhanced diversity and aflatoxigenicity in interspecific hybrids ofAspergillus flavusandAspergillus parasiticus. Molecular Ecology, 24(8), 1889–1909. https://doi.org/10.1111/mec.13153

Vensko, S. P., II, & Stone, E. A. (2015). [Review of Recent progress and open questions in Drosophila dosage compensation]. FLY, 9(1), 29–35. https://doi.org/10.1080/19336934.2015.1074786

Strope, P. K., Skelly, D. A., Kozmin, S. G., Mahadevan, G., Stone, E. A., Magwene, P. M., … McCusker, J. H. (2015). The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen. GENOME RESEARCH, 25(5), 762–774. https://doi.org/10.1101/gr.185538.114

Vensko, S. P., II, & Stone, E. A. (2015). X-to-autosome expression and msl-2 transcript abundance correlate among Drosophila melanogaster somatic tissues. PEERJ, 3. https://doi.org/10.7717/peerj.771

Durham, M. F., Magwire, M. M., Stone, E. A., & Leips, J. (2014). Genome-wide analysis in Drosophila reveals age-specific effects of SNPs on fitness traits. NATURE COMMUNICATIONS, 5. https://doi.org/10.1038/ncomms5338

Huang, W., Massouras, A., Inoue, Y., Peiffer, J., Ramia, M., Tarone, A. M., … Highnam, G. (2014). Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines. Genome Research, 24(7), 1193–1208.

Vensko, S. P., II, & Stone, E. A. (2014). No Evidence for a Global Male-Specific Lethal Complex-Mediated Dosage Compensation Contribution to the Demasculinization of the Drosophila melanogaster X Chromosome. PLOS ONE, 9(8). https://doi.org/10.1371/journal.pone.0103659

Robinson, M. C., Stone, E. A., & Singh, N. D. (2014). Population Genomic Analysis Reveals No Evidence for GC-Biased Gene Conversion in Drosophila melanogaster. MOLECULAR BIOLOGY AND EVOLUTION, 31(2), 425–433. https://doi.org/10.1093/molbev/mst220

Stone, E. A. (2014, August). Predictor performance with stratified data and imbalanced classes. https://doi.org/10.1038/nmeth.3045

Griffing, A. R., Lynch, B. R., & Stone, E. A. (2014). Structural properties of the minimum cut of partially-supplied graphs. DISCRETE APPLIED MATHEMATICS, 177, 152–157. https://doi.org/10.1016/j.dam.2014.05.043

Griffing, A. R., Lynch, B. R., & Stone, E. A. (2013). An eigenvector interlacing property of graphs that arise from trees by Schur complementation of the Laplacian. LINEAR ALGEBRA AND ITS APPLICATIONS, 438(3), 1078–1094. https://doi.org/10.1016/j.laa.2012.10.005

Guo, L., Tsai, S. Q., Hardison, N. E., James, A. H., Motsinger-Reif, A. A., Thames, B., … Piedrahita, J. A. (2013). Differentially expressed microRNAs and affected biological pathways revealed by modulated modularity clustering (MMC) analysis of human preeclamptic and IUGR placentas. Placenta, 34(7), 599–605. https://doi.org/10.1016/j.placenta.2013.04.007

Singh, N. D., Stone, E. A., Aquadro, C. F., & Clark, A. G. (2013). Fine-scale heterogeneity in crossover rate in the garnet-scalloped region of the Drosophila melanogaster X chromosome. Genetics, 194(2), 375–112.

Moore, G. G., Elliott, J. L., Singh, R., Horn, B. W., Dorner, J. W., Stone, E. A., … Carbone, I. (2013). Sexuality Generates Diversity in the Aflatoxin Gene Cluster: Evidence on a Global Scale. PLoS Pathogens, 9(8), e1003574. https://doi.org/10.1371/journal.ppat.1003574

Felix, T. M., Hughes, K. A., Stone, E. A., Drnevich, J. M., & Leips, J. (2012). Age-specific variation in immune response in drosophila melanogaster has a genetic basis. Genetics, 191(3), 989–584.

Olarte, R. A., Horn, B. W., Dorner, J. W., Monacell, J. T., Singh, R., Stone, E. A., & Carbone, I. (2012). Effect of sexual recombination on population diversity in aflatoxin production by Aspergillus flavus and evidence for cryptic heterokaryosis. MOLECULAR ECOLOGY, 21(6), 1453–1476. https://doi.org/10.1111/j.1365-294x.2011.05398.x

Stone, E. A. (2012). Joint genotyping on the fly: Identifying variation among a sequenced panel of inbred lines. GENOME RESEARCH, 22(5), 966–974. https://doi.org/10.1101/gr.129122.111

Myers, R. A., Casals, F., Gauthier, J., Hamdan, F. F., Keebler, J., Boyko, A. R., … Stone, E. A. (2011). A population genetic approach to mapping neurological disorder genes using deep resequencing. PLoS Genetics, 7(2).

Maragh, S., Miller, R. A., Bessling, S. L., McGaughey, D. M., Wessels, M. W., Graaf, B., … McCallion, A. S. (2011). Identification of RNA binding motif proteins essential for cardiovascular development. BMC DEVELOPMENTAL BIOLOGY, 11. https://doi.org/10.1186/1471-213x-11-62

Dworkin, I., Anderson, J. A., Idaghdour, Y., Parker, E. K., Stone, E. A., & Gibson, G. (2011). The Effects of Weak Genetic Perturbations on the Transcriptome of the Wing Imaginal Disc and Its Association With Wing Shape in Drosophila melanogaster. GENETICS, 187(4), 1171–U314. https://doi.org/10.1534/genetics.110.125922

McFerrin, L. G., & Stone, E. A. (2011). The non-random clustering of non-synonymous substitutions and its relationship to evolutionary rate. BMC GENOMICS, 12. https://doi.org/10.1186/1471-2164-12-415

Conrad, D. F., Keebler, J. E. M., DePristo, M. A., Lindsay, S. J., Zhang, Y. J., Casals, F., … Hurles, M. E. (2011). Variation in genome-wide mutation rates within and between human families. Nature Genetics, 43(7), 712–137.

Stone, E. A. (2011). Why the Phylogenetic Regression Appears Robust to Tree Misspecification. SYSTEMATIC BIOLOGY, 60(3), 245–260. https://doi.org/10.1093/sysbio/syq098

Gauthier, J., Champagne, N., Lafreniere, R. G., Xiong, L., Spiegelman, D., Brustein, E., … Fathalli, F. (2010). De novo mutations in the gene encoding the synaptic scaffolding protein SHANK3 in patients ascertained for schizophrenia. Proceedings of the National Academy of Sciences of the United States of America, 107(17), 7863–7868.

Awadalla, P., Gauthier, J., Myers, R. A., Casals, F., Hamdan, F. F., Griffing, A. R., … DeLisi, J. L. E. (2010). Direct measure of the de novo mutation rate in autism and schizophrenia cohorts. American Journal of Human Genetics, 87(3), 316–324.

Binkley, J., Karra, K., Kirby, A., Hosobuchi, M., Stone, E. A., & Sidow, A. (2010). ProPhylER: A curated online resource for protein function and structure based on evolutionary constraint analyses. GENOME RESEARCH, 20(1), 142–154. https://doi.org/10.1101/gr.097121.109

Choi, S. C., Stone, E. A., Kishino, H., & Thorne, J. L. (2009). Estimates of natural selection due to protein tertiary structure inform the ancestry of biallelic loci. Gene, 441(1-2), 45–52. https://doi.org/10.1016/j.gene.2008.07.020

Stone, E. A., & Ayroles, J. F. (2009). Modulated Modularity Clustering as an Exploratory Tool for Functional Genomic Inference. PLOS GENETICS, 5(5). https://doi.org/10.1371/journal.pgen.1000479

Stone, E. A., & Griffing, A. R. (2009). On the Fiedler vectors of graphs that arise from trees by Schur complementation of the Laplacian. LINEAR ALGEBRA AND ITS APPLICATIONS, 431(10), 1869–1880. https://doi.org/10.1016/j.laa.2009.06.024

Hobolth, A., & Stone, E. A. (2009). SIMULATION FROM ENDPOINT-CONDITIONED, CONTINUOUS-TIME MARKOV CHAINS ON A FINITE STATE SPACE, WITH APPLICATIONS TO MOLECULAR EVOLUTION. ANNALS OF APPLIED STATISTICS, 3(3), 1204–1231. https://doi.org/10.1214/09-AOAS247

Stone, E. A., & Sidow, A. (2007). Constructing a meaningful evolutionary average at the phylogenetic center of mass. BMC BIOINFORMATICS, 8. https://doi.org/10.1186/1471-2105-8-222

Hsieh, W.-P., Passador-Gurgel, G., Stone, E. A., & Gibson, G. (2007). Mixture modeling of transcript abundance classes in natural populations. GENOME BIOLOGY, 8(6). https://doi.org/10.1186/gb-2007-8-6-r98

Cranston, A. N., Carniti, C., Oakhill, K., Radzio-Andzelm, E., Stone, E. A., McCallion, A. S., … Ponder, B. A. J. (2006). RET is constitutively activated by novel tandem mutations that alter the active site resulting in multiple endocrine neoplasia type 2B. CANCER RESEARCH, 66(20), 10179–10187. https://doi.org/10.1158/0008-5472.CAN-06-0884

Huang, W., Richards, S., Carbone, M. A., Zhu, D. H., Anholt, R. R. H., Ayroles, J. F., … Muzny, D. Epistasis dominates the genetic architecture of Drosophila quantitative traits. Proceedings of the National Academy of Sciences of the United States of America, 109(39), 15553–15559.

Ayroles, J. F., Laflamme, B. A., Stone, E. A., Wolfner, M. F., & Mackay, T. F. C. Functional genome annotation of Drosophila seminal fluid proteins using transcriptional genetic networks. Genetical Research, 93(6), 387–395.

Huang, W., Carbone, M. A., Magwire, M. M., Peiffer, J. A., Lyman, R. F., Stone, E. A., … Mackay, T. F. C. Genetic basis of transcriptome diversity in Drosophila melanogaster. Proceedings of the National Academy of Sciences of the United States of America, 112(44), E6010–6019.

Massouras, A., Waszak, S. M., Albarca-Aguilera, M., Hens, K., Holcombe, W., Ayroles, J. F., … Deplancke, B. Genomic variation and its impact on gene expression in Drosophila melanogaster. PLoS Genetics, 8(11).

Zhou, S. S., Stone, E. A., Mackay, T. F. C., & Anholt, R. R. H. Plasticity of the chemoreceptor repertoire in Drosophila melanogaster. PLoS Genetics, 5(10).

Mackay, T. F. C., Richards, S., Stone, E. A., Barbadilla, A., Ayroles, J. F., Zhu, D. H., … Carbone, M. A. The Drosophila melanogaster genetic reference panel. Nature, 482(7384), 173–178.

Ober, U., Ayroles, J. F., Stone, E. A., Richards, S., Zhu, D. H., Gibbs, R. A., … Simianer, H. Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster. PLoS Genetics, 8(5).