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Selected publications

• Vensko SP, Stone EA. “X-to-autosome expression and msl-2 transcript abundance correlate among Drosophila melanogaster somatic tissues”. Peer J 3, e771.
• Olarte RA, Worthington CJ, Horn BW, Moore GG, Singh R, et al. “Enhanced diversity and aflatoxigenicity in interspecific hybrids of Aspergillus flavus and Aspergillus parasiticus”. Molecular Ecology 2015: 24, 1889-1909.
• Strope PK, Skelly DA, Kozmin SG, Mahadevan G, Stone EA, Magwene PM, Dietrich FS, McCusker JH. “The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen”. Genome Research,2015 25: 762-774.
• 2014
• Stone EA. “Predictor performance with stratified data and imbalanced classes”. Nature Methods2014: 11, 782-783.
• Vensko SP, Stone EA. “No evidence for a global male-specific lethal complex-mediated dosage compensation contribution to the demasculinization of the Drosophila melanogaster Xchromosome”. PLoS ONE 2014: e103659.
• Griffing AR, Lynch BR, Stone EA. “Structural properties of the minimum cut of partially-supplied graphs”. Discrete Applied Mathematics 2014: 177, 152-157.
• Durham MF, Magwire MM, Stone EA, Leips JL. “Genome-wide analysis in Drosophila reveals age-specific effects of SNPs on fitness traits”. Nature Communications 5, Article 4338.
• Huang W, Massouras A, Inoue Y, Peiffer J, Rámia M, et al. “Natural variation in genome architecture among 205 Drosophila melanogaster genetic reference panel lines”. Genome Research2014: 24, 1193-1208.
• 2013
• Moore GG, Elliott JL, Singh R, Horn BW, Dorner JW, et al. “Sexuality generates diversity in the aflatoxin gene cluster: evidence on a global scale.” PLoS Pathogens 2013: 9, e1003574.
• Guo L, Tsai SQ, Hardison NE, James AH, Motsinger-Reif AA, et al. “Differentially expressed microRNAs and affected biological pathways revealed by modulated modularity clustering (MMC) analysis of human preeclamptic and IUGR placentas”. Placenta 2013: 34, 599-605.
• Singh ND, Stone EA, Aquadro CF, Clark AG. “Fine-scale heterogeneity in crossover rate in the garnet-scalloped region of the Drosophila melanogaster X chromosome”. Genetics 2013: 194, 375-387.
• Griffing AR, Lynch BR, Stone EA. “An eigenvector interlacing property of graphs that arise from trees by Schur complementation of the Laplacian”. Linear Algebra and its Applications 2013: 438, 1078-1094.
• 2012
• Massouras A, Waszak SM, Albarca-Aguilera M, Hens K, Holcombe W, et al. “Genomic variation and its impact on gene expression in Drosophila melanogaster.” PLoS Genetics 2012: 8, e1003055.
• Huang W, Richards S, Carbone MA, Zhu D, Anholt RRH, et al. “Epistasis dominates the genetic architecture of Drosophila quantitative traits”. Proceedings of the National Academy of Sciences2012: 109, 15553-15559.
• Stone EA. “Joint genotyping on the fly: identifying variation among a sequenced panel of inbred lines”. Genome Research, 2012: 22, 966-974.
• Ober U, Ayroles JF, Stone EA, Richards S, Zhu D, et al. “Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster.” PLoS Genetics, 2012: 8, e1002685.
• Zhou S, Campbell TG, Stone EA, Mackay TFC, Anholt RRH. “Phenotypic plasticity of the Drosophilatranscriptome”. PLoS Genetics, 2012: 8, e1002593.
• Mackay TFC†, Richards S†, Stone EA†, Barbadilla A†, Ayroles JF, et al. “The Drosophila melanogastergenetic reference panel. “ Nature, 2012: 482, 173-178. (†equal contributors)
• Cartwright RA, Hussin J, Keebler JEM, Stone EA, Awadalla P. “A family-based probabilistic method for capturing de novo mutations from high-throughput short-read sequencing data.” Statistical Applications in Genetics and Molecular Biology, 2012: 11, 6.
• Felix TM, Hughes KA, Stone EA, Drnevich JM, Leips J. “Age-specific variation in immune response in Drosophila melanogaster has a genetic basis”. Genetics, 2012: 191: 989-1002.
• Olarte RA, Horn BW, Dorner JW, Monacell JT, Singh R, Stone EA, Carbone I. “Effect of sexual recombination on population diversity in aflatoxin production by Aspergillus flavus and evidence for cryptic heterokaryosis”. Molecular Ecology, 2012: 21, 1453-1476.
• 2011
• Maragh S, Miller RA, Bessling SL, McGaughey DM, Wessels MW, et al. “Identification of RNA binding motif proteins essential for cardiovascular development”. BMC Developmental Biology, 2011: 11, 62.
• Ayroles JF, Laflamme BA, Stone EA, Wolfner MF, Mackay TFC. “Functional genome annotation ofDrosophila seminal fluid proteins using transcriptional genetic networks”. Genetics Research, 2011: 93, 387-395.
• McFerrin LG, Stone EA. “The non-random clustering of non-synonymous substitutions and its relationship to evolutionary rate”. BMC Genomics 2011: 12, 415.
• Conrad DF, Keebler JEM, DePristo MA, Lindsay SJ, Zhang Y, et al. “Variation in genome-wide mutation rates within and between human families”. Nature Genetics 2011: 43, 712-714.
• Stone EA. “Why the phylogenetic regression appears robust to tree misspecification”. Systematic Biology 2011: 60, 245-260.
• Myers RA, Casals F, Gauthier J, Hamdan FF, Keebler JEM, et al. “A population genetic approach to mapping neurological disorder genes using deep resequencing“. PLoS Genetics 2011: 7, e1001318.
• Dworkin I, Anderson JAB, Idaghdour Y, Parker EK, Stone EA, Gibson G. “The effects of weak genetic perturbations on the transcriptome of the wing imaginal disc, and its association with wing shape in Drosophila melanogaster”. Genetics 2011: 187, 1171-1184.
• 2010
• Awadalla P, Gauthier J, Myers RA, Casals F, Hamdan FF, et al. “Direct measure of the de novomutation rate in autism and schizophrenia cohorts”. American Journal of Human Genetics 2010: 87, 316-324.
• The 1000 Genomes Project Consortium. “A map of human genome variation from population-level sequencing”. Nature 2010: 467, 1071-1073.
• Gauthier J, Champagne N, Lafreniere RG, Xiong L, Spiegelman D, et al. “De novo mutations in the gene encoding the synaptic scaffolding protein SHANK3 in patients ascertained for schizophrenia”. Proceedings of the National Academy of Sciences 2010: 107, 7863-7868.
• Kocher SD, Ayroles JF, Stone EA, Grozinger CM. “Individual variation in pheromone response correlates with reproductive traits and brain gene expression in worker honey bees”. PLoS ONE2010: 5:e9116.
• Binkley J, Karra K, Kirby A, Hosobuchi M, Stone EA, Sidow A. “ProPhylER: a curated online resource for protein function and structure based on evolutionary constraint analyses”. Genome Research2010, 20:142-152.
• 2009
• Zhou S, Stone EA, Mackay TFC, Anholt RRH. “Plasticity of the chemoreceptor repertoire inDrosophila melanogaster”. PLoS Genetics 2009, 5:e1000681.
• Ayroles JF†, Carbone MA†, Stone EA†, Jordan KW, Lyman RF, Magwire MM, Rollman SM, Duncan LH, Lawrence F, Anholt RRH, Mackay TFC. “Systems genetics of complex traits in Drosophila melanogaster”. Nature Genetics 2009, 41: 299-307. (†equal contributors)
• Morozova TV, Ayroles JF, Jordan KW, Duncan LH, Carbone MA, Lyman RF, Stone EA, Mackay TFC, Anholt RRH. “Alcohol sensitivity in Drosophila: translational potential of systems genetics”. Genetics2009, 183:733-745.
• Hobolth A, Stone EA. “Efficient simulation from finite-state, continuous-time Markov chains with incomplete observations”. Annals of Applied Statistics 2009, 3: 1204-1231.
• Stone EA, Griffing AR. “On the Fiedler vectors of graphs that arise from trees by Schur complementation of the Laplacian”. Linear Algebra and its Applications 2009, 431: 1869-1880.
• Edwards AC, Ayroles JF, Stone EA, Carbone MA, Lyman RF, Mackay TFC. “A transcriptional network associated with natural variation in Drosophila aggressive behavior”. Genome Biology 2009, 10: R76.
• Mackay TFC, Stone EA, Ayroles JF. “The genetics of quantitative traits: challenges and prospects”. Nature Reviews Genetics 2009, 10: 565-577.
• Choi SC, Stone EA, Kishino H, Thorne JL. “Estimates of natural selection due to protein tertiary structure inform the ancestry of biallelic loci”. Gene 2009, 441: 45-52.
• Harbison ST, Carbone MA, Ayroles JF, Stone EA, Lyman RF, Mackay TFC. “Co-regulated transcriptional networks contribute to natural genetic variation in Drosophila sleep”. Nature Genetics 2009, 41: 371-375.
• Stone EA, Ayroles JF. “Modulated modularity clustering as an exploratory tool for functional genomic inference”. PLoS Genetics 2009, 5: e1000479.
• Prior to 2009
• Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, et al. “Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome”.Genome Research 2007, 17: 760-774.
• Stone EA, Sidow A. “Constructing a meaningful evolutionary average at the phylogenetic center of mass”. BMC Bioinformatics 2007, 8: 222.
• The ENCODE Project Consortium. “Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project”. Nature 2007, 447: 799-816.
• Hsieh W-P, Passador-Gurgel G, Stone EA, Gibson G. “Mixture modeling of transcript abundance classes in natural populations”. Genome Biology 2007, 8: R98.
• Cranston AN, Carniti C, Oakhill K, Radzio-Andzelm E, Stone EA, et al. “RET is constitutively activated by novel tandem mutations that alter the active site resulting in multiple endocrine neoplasia type 2B”. Cancer Research 2006, 66: 10179-87.
• Kashuk CS†, Stone EA†, Grice EA, Portnoy ME, Green ED, et al. “Phentotype-genotype correlation in Hirschsprung disease is illuminated by comparative analysis of the RET protein sequence”.Proceedings of the National Academy of Sciences 2005, 102: 8949-8954. (†equal contributors)
• Stone EA, Sidow A. “Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity”. Genome Research 2005, 15: 978-986.
• Cooper GM, Stone EA, Asimenos G, Green ED, Batzoglou S, Sidow A. “Distribution and intensity of constraint in mammalian genomic sequence”. Genome Research 2005, 15: 901-913.
• Stone EA, Cooper GM, Sidow A. “Trade-offs in detecting evolutionary constrained sequence by comparative genomics”. Annual Review of Genomics and Human Genetics 2005, 6: 143-164.
• The ENCODE Project Consortium. “The ENCODE (ENCylopedia of DNA Elements) Project”. Science2004, 306: 636-640.
• Rat Genome Sequencing Project Consortium. “Genome sequence of the Brown Norway rat yields insights into mammalian evolution”. Nature 2004, 428: 493-521.
• Cooper GM, Brudno M, Stone EA, Dubchak I, Batzoglou S, Sidow A. “Characterization of evolutionary rates and constraints in three mammalian genomes”. Genome Research 2004, 14: 539-548.
• Simon AL, Stone EA, Sidow A. “Inference of functional regions in proteins by quantification of evolutionary constraints”. Proceedings of the National Academy of Sciences 2002, 99: 2912-2917.
• BOOK CHAPTERS
• Anholt RRH., Mackay TFC, Stone EA. “Systems genetics of behavior in Drosophila melanogaster, in Handbook of Behavioral Genetics of Drosophila melanogaster, Edited by J Dubnau, Cambridge University Press, Cambridge, UK (2012)
• Stone EA, Nielsen DM. “Bioinformatics”, in Molecular and Biochemical Toxicology 4th ed. Edited by RC Smart and E Hodgson, Wiley (2008)