Eric A Stone

Bias-Variance Tradeoffs in Recombination Rate Estimation

Stone, E. A., & Singh, N. D. (2016, February).

Sporadic, Global Linkage Disequilibrium Between Unlinked Segregating Sites

GENETICS, 202(2), 427-+.

Enhanced diversity and aflatoxigenicity in interspecific hybrids ofAspergillus flavusandAspergillus parasiticus

Molecular Ecology, 24(8), 1889–1909.

Recent progress and open questions in Drosophila dosage compensation

[Review of ]. FLY, 9(1), 29–35.

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.

X-to-autosome expression and msl-2 transcript abundance correlate among Drosophila melanogaster somatic tissues

PEERJ, 3.

Genome-wide analysis in Drosophila reveals age-specific effects of SNPs on fitness traits

NATURE COMMUNICATIONS, 5.

Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines

Genome Research, 24(7), 1193–1208.

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).

Population Genomic Analysis Reveals No Evidence for GC-Biased Gene Conversion in Drosophila melanogaster

MOLECULAR BIOLOGY AND EVOLUTION, 31(2), 425–433.

Predictor performance with stratified data and imbalanced classes

Stone, E. A. (2014, August).

Structural properties of the minimum cut of partially-supplied graphs

DISCRETE APPLIED MATHEMATICS, 177, 152–157.

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.

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.

Fine-scale heterogeneity in crossover rate in the garnet-scalloped region of the Drosophila melanogaster X chromosome

Genetics, 194(2), 375–112.

Sexuality Generates Diversity in the Aflatoxin Gene Cluster: Evidence on a Global Scale

PLoS Pathogens, 9(8), e1003574.

Age-specific variation in immune response in drosophila melanogaster has a genetic basis

Genetics, 191(3), 989–584.

Effect of sexual recombination on population diversity in aflatoxin production by Aspergillus flavus and evidence for cryptic heterokaryosis

MOLECULAR ECOLOGY, 21(6), 1453–1476.

Joint genotyping on the fly: Identifying variation among a sequenced panel of inbred lines

GENOME RESEARCH, 22(5), 966–974.

A population genetic approach to mapping neurological disorder genes using deep resequencing

PLoS Genetics, 7(2).

Identification of RNA binding motif proteins essential for cardiovascular development

BMC DEVELOPMENTAL BIOLOGY, 11.

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.

The non-random clustering of non-synonymous substitutions and its relationship to evolutionary rate

BMC GENOMICS, 12.

Variation in genome-wide mutation rates within and between human families

Nature Genetics, 43(7), 712–137.

Why the Phylogenetic Regression Appears Robust to Tree Misspecification

SYSTEMATIC BIOLOGY, 60(3), 245–260.

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.

Direct measure of the de novo mutation rate in autism and schizophrenia cohorts

American Journal of Human Genetics, 87(3), 316–324.

ProPhylER: A curated online resource for protein function and structure based on evolutionary constraint analyses

GENOME RESEARCH, 20(1), 142–154.

Estimates of natural selection due to protein tertiary structure inform the ancestry of biallelic loci

Gene, 441(1-2), 45–52.

Modulated Modularity Clustering as an Exploratory Tool for Functional Genomic Inference

PLOS GENETICS, 5(5).

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.

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.

Constructing a meaningful evolutionary average at the phylogenetic center of mass

BMC BIOINFORMATICS, 8.

Mixture modeling of transcript abundance classes in natural populations

GENOME BIOLOGY, 8(6).

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.

Epistasis dominates the genetic architecture of Drosophila quantitative traits

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

Functional genome annotation of Drosophila seminal fluid proteins using transcriptional genetic networks

Ayroles, J. F., Laflamme, B. A., Stone, E. A., Wolfner, M. F., & Mackay, T. F. C. Genetical Research, 93(6), 387–395.

Genetic basis of transcriptome diversity in Drosophila melanogaster

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

Genomic variation and its impact on gene expression in Drosophila melanogaster

Massouras, A., Waszak, S. M., Albarca-Aguilera, M., Hens, K., Holcombe, W., Ayroles, J. F., … Deplancke, B. PLoS Genetics, 8(11).

Plasticity of the chemoreceptor repertoire in Drosophila melanogaster

Zhou, S. S., Stone, E. A., Mackay, T. F. C., & Anholt, R. R. H. PLoS Genetics, 5(10).

The Drosophila melanogaster genetic reference panel

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

Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster

Ober, U., Ayroles, J. F., Stone, E. A., Richards, S., Zhu, D. H., Gibbs, R. A., … Simianer, H. PLoS Genetics, 8(5).