Bioinformatics Research Center
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Bioinformatics Research Center
NC State University
Raleigh, NC 27695-7566
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NOTE: BRC under renovation in 2013-2014
Nomadic in Fall 2013
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Departmental Site:
Biological Sciences
Office Hours:
By appointment
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Eric A. Stone
Associate Professor, Department of Biological Sciences
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Dr. Eric A. Stone began his career at North Carolina State University in 2005. He received his B.S. (Mathematics) in 1996 from the University of Florida and his M.S. (Statistics) in 2001 from Stanford University. He received his Ph.D. (Statistics) in 2004 from Stanford University.
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Course Course Title/Link to Syllabus Semester
ST 590A Bioinformatics I Fall 2013
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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

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
Guo L, Tsai SQ, Hardison NE, James AH, Motsinger-Reif AA, Thames B, 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

Huang W, Richards S., Carbone MA, Zhu D, Anholt RR, Ayroles JF, et al:
Epistasis dominates the genetic architecture of Drosophila quantitative traits
PNAS 2012, 109: 15553-15559

Massouras A, Waszak SM, Albarca-Aguilera M, Hens K, Holcombe W, Ayroles JF, Dermitzakis ET, et al:
Genomic variation and its impact on gene expression in Drosophila melanogaster
PLoS Genetics 2012, 8: e1003055
Stone EA:
Joint genotyping on the fly: identifying variation among a sequenced panel of inbred lines

Genome Research 2012: 22, 966-974
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
Ober U, Ayroles JF, Stone EA, Richards S, Zhu D, Gibbs RA, Stricker C, Gianola D, Schlather M, Mackay TFC, Simianer H:
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 Drosophila transcriptome
PLoS Genetics, 2012: 8, e1002593
Mackay TFC†, Richards S†, Stone EA†, Barbadilla A†, Ayroles JF, et al.:
The Drosophila melanogaster genetic 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

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

Maragh S, Miller RA, Bessling SL, McGaughey DM, Wessels MW, de Graaf B, Stone EA, Bertoli-Avella AM, Gearhart JD, Fisher S, McCallion AS:
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 of Drosophila 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,..., Stone EA, Hurles ME, Awadalla P for the 1000 Genomes Project:
Variation in genome-wide mutation rates within and between human families
Nature Genetics 2011, 43: 712-714

Myers RA, Casals F, Gauthier J, Keebler JEM,...,Stone EA, Rouleau GA, Awadalla P:
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
Stone EA:
Why the phylogenetic regression appears robust to tree misspecification
Systematic Biology 2011, 60: 245-260

The 1000 Genomes Project Consortium:
A map of human genome variation from population-scale sequencing
Nature 2010, 467: 1061-1073

Awadalla P, Gauthier J, Myers RA, Casals F,..., Stone EA, Lafrenière RG, Rouleau GA:
Direct measure of the de novo mutation rate in Autism and Schizophrenia.
American Journal of Human Genetics 2010, 87: 316-324
Gauthier J, Champagne N, Lafrenière RG, Xiong L, Spiegelman D, et al:
De novo mutations in the gene encoding the synaptic scaffolding protein SHANK3 in patients ascertained for schizophrenia
PNAS 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 ONE 2010, 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 Research
2010, 20: 142-154

Zhou S, Stone EA, Mackay TFC, Anholt RRH:
Plasticity of the Chemoreceptor Repertoire in Drosophila melanogaster.
PLoS Genetics 2009, 5 :e1000681
Morozova TV, Ayroles JF, Jordan KW, Duncan LH, Carbone MA, Lyman RF, Stone EA, Govindaraju DR, Ellison CR, Mackay TFC, Anholt RRH:
Alcohol sensitivity in Drosophila: translational potential of systems genetics.
Genetics 2009, 183: 733-745
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
Hobolth A, Stone EA:
Efficient simulation from finite-state, continuous-time Markov chains with incomplete observations, with applications to molecular evolution
Annals of Applied Statistics 2009, 3: 1204-1231
Stone EA, Ayroles JF:
Modulated modularity clustering as a tool for functional genomic inference.
PLoS Genetics 2009, 5: e1000479
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
Mackay TFC, Stone EA, Ayroles JF:
The genetics of quantitative traits: Challenges and prospects.
Nature Reviews Genetics 2009, 10: 565-577
Ayroles JF†, Carbone MA†, Stone EA†, Jordan KW, Lyman RF, et al:
Systems genetics of complex traits in Drosophila melanogaster.
Nature Genetics 2009, 41: 299-307 († Equal contributors)
Harbison ST, Carbone MA, Ayroles MF, Stone EA, Lyman RF, Mackay TFC:
Co-regulated transcriptional networks contribute to natural genetic variation in Drosophila sleep.
Nature Genetics 2009, 41: 371-375
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
Stone EA, Nielsen DM:
Bioinformatics, in Molecular and Biochemical Toxicology 4th ed.
Edited by RC Smart and E Hodgson, Wiley (2008)
Stone EA, Sidow A:
Constructing a meaningful evolutionary average at the phylogenetic center of mass
BMC Bioinformatics 2007, 8: 222
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
Hsieh W-P, Passador-Gurgel G, Stone EA, Gibson G:
Mixture modeling of transcript abundance classes in natural populations.
Genome Biology 2007, 8: R98
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
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
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
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
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.
PNAS 2005, 102: 8949-8954 († Equal contributors)
The ENCODE Consortium:
The ENCODE (ENCylopedia of DNA Elements) Project.
Science 2004, 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.
PNAS 2002, 99: 2912-2917
Software: (click here for software page)
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Joint Genotyper for Inbred Lines (JGIL) Link to software page
Modulated Modularity Clustering (MMC) Link to website
Multivariate Analysis of Protein Polymorphism (MAPP) Link to download site
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North Carolina State University
Raleigh, North Carolina 27695

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