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 Storey, John D  [Clear All Filters]
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Adolescent
K. H. Desai, Tan, C. Seng, Leek, J. T., Maier, R. V., Tompkins, R. G., and Storey, J. D., “Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study.”, PLoS Med, vol. 8, no. 9, p. e1001093, 2011.
Adult
K. H. Desai, Tan, C. Seng, Leek, J. T., Maier, R. V., Tompkins, R. G., and Storey, J. D., “Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study.”, PLoS Med, vol. 8, no. 9, p. e1001093, 2011.
Algorithms
L. S. Chen and Storey, J. D., “Eigen-R2 for dissecting variation in high-dimensional studies.”, Bioinformatics, vol. 24, no. 19, pp. 2260-2, 2008.
Animals
J. S. Kanodia, Kim, Y., Tomer, R., Khan, Z., Chung, K., Storey, J. D., Lu, H., Keller, P. J., and Shvartsman, S. Y., “A computational statistics approach for estimating the spatial range of morphogen gradients.”, Development, vol. 138, no. 22, pp. 4867-74, 2011.
Antigen Presentation
K. H. Desai, Tan, C. Seng, Leek, J. T., Maier, R. V., Tompkins, R. G., and Storey, J. D., “Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study.”, PLoS Med, vol. 8, no. 9, p. e1001093, 2011.
Biostatistics
J. S. Kanodia, Kim, Y., Tomer, R., Khan, Z., Chung, K., Storey, J. D., Lu, H., Keller, P. J., and Shvartsman, S. Y., “A computational statistics approach for estimating the spatial range of morphogen gradients.”, Development, vol. 138, no. 22, pp. 4867-74, 2011.
Chromatin
T. T. Marstrand and Storey, J. D., “Identifying and mapping cell-type-specific chromatin programming of gene expression.”, Proc Natl Acad Sci U S A, vol. 111, no. 6, pp. E645-54, 2014.
Cleavage Stage, Ovum
J. S. Kanodia, Kim, Y., Tomer, R., Khan, Z., Chung, K., Storey, J. D., Lu, H., Keller, P. J., and Shvartsman, S. Y., “A computational statistics approach for estimating the spatial range of morphogen gradients.”, Development, vol. 138, no. 22, pp. 4867-74, 2011.
Computational Biology
J. S. Kanodia, Kim, Y., Tomer, R., Khan, Z., Chung, K., Storey, J. D., Lu, H., Keller, P. J., and Shvartsman, S. Y., “A computational statistics approach for estimating the spatial range of morphogen gradients.”, Development, vol. 138, no. 22, pp. 4867-74, 2011.
Computer Simulation
J. S. Kanodia, Kim, Y., Tomer, R., Khan, Z., Chung, K., Storey, J. D., Lu, H., Keller, P. J., and Shvartsman, S. Y., “A computational statistics approach for estimating the spatial range of morphogen gradients.”, Development, vol. 138, no. 22, pp. 4867-74, 2011.
Deoxyribonuclease I
T. T. Marstrand and Storey, J. D., “Identifying and mapping cell-type-specific chromatin programming of gene expression.”, Proc Natl Acad Sci U S A, vol. 111, no. 6, pp. E645-54, 2014.
Drosophila
J. S. Kanodia, Kim, Y., Tomer, R., Khan, Z., Chung, K., Storey, J. D., Lu, H., Keller, P. J., and Shvartsman, S. Y., “A computational statistics approach for estimating the spatial range of morphogen gradients.”, Development, vol. 138, no. 22, pp. 4867-74, 2011.
Drosophila Proteins
J. S. Kanodia, Kim, Y., Tomer, R., Khan, Z., Chung, K., Storey, J. D., Lu, H., Keller, P. J., and Shvartsman, S. Y., “A computational statistics approach for estimating the spatial range of morphogen gradients.”, Development, vol. 138, no. 22, pp. 4867-74, 2011.
Embryo, Nonmammalian
J. S. Kanodia, Kim, Y., Tomer, R., Khan, Z., Chung, K., Storey, J. D., Lu, H., Keller, P. J., and Shvartsman, S. Y., “A computational statistics approach for estimating the spatial range of morphogen gradients.”, Development, vol. 138, no. 22, pp. 4867-74, 2011.
Female
K. H. Desai, Tan, C. Seng, Leek, J. T., Maier, R. V., Tompkins, R. G., and Storey, J. D., “Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study.”, PLoS Med, vol. 8, no. 9, p. e1001093, 2011.
Gene Deletion
D. G. Robinson, Chen, W., Storey, J. D., and Gresham, D., “Design and analysis of Bar-seq experiments.”, G3 (Bethesda), vol. 4, no. 1, pp. 11-8, 2014.
Gene Expression Profiling
T. T. Marstrand and Storey, J. D., “Identifying and mapping cell-type-specific chromatin programming of gene expression.”, Proc Natl Acad Sci U S A, vol. 111, no. 6, pp. E645-54, 2014.
L. S. Chen and Storey, J. D., “Eigen-R2 for dissecting variation in high-dimensional studies.”, Bioinformatics, vol. 24, no. 19, pp. 2260-2, 2008.
Gene Expression Regulation
K. H. Desai, Tan, C. Seng, Leek, J. T., Maier, R. V., Tompkins, R. G., and Storey, J. D., “Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study.”, PLoS Med, vol. 8, no. 9, p. e1001093, 2011.
Gene Expression Regulation, Developmental
J. S. Kanodia, Kim, Y., Tomer, R., Khan, Z., Chung, K., Storey, J. D., Lu, H., Keller, P. J., and Shvartsman, S. Y., “A computational statistics approach for estimating the spatial range of morphogen gradients.”, Development, vol. 138, no. 22, pp. 4867-74, 2011.
Gene Library
D. G. Robinson, Chen, W., Storey, J. D., and Gresham, D., “Design and analysis of Bar-seq experiments.”, G3 (Bethesda), vol. 4, no. 1, pp. 11-8, 2014.
Genes, Developmental
J. S. Kanodia, Kim, Y., Tomer, R., Khan, Z., Chung, K., Storey, J. D., Lu, H., Keller, P. J., and Shvartsman, S. Y., “A computational statistics approach for estimating the spatial range of morphogen gradients.”, Development, vol. 138, no. 22, pp. 4867-74, 2011.
Genes, Fungal
D. Gresham, Boer, V. M., Caudy, A., Ziv, N., Brandt, N. J., Storey, J. D., and Botstein, D., “System-level analysis of genes and functions affecting survival during nutrient starvation in Saccharomyces cerevisiae.”, Genetics, vol. 187, no. 1, pp. 299-317, 2011.
Genes, MHC Class II
K. H. Desai, Tan, C. Seng, Leek, J. T., Maier, R. V., Tompkins, R. G., and Storey, J. D., “Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study.”, PLoS Med, vol. 8, no. 9, p. e1001093, 2011.
Genetic Variation
L. S. Chen and Storey, J. D., “Eigen-R2 for dissecting variation in high-dimensional studies.”, Bioinformatics, vol. 24, no. 19, pp. 2260-2, 2008.
High-Throughput Nucleotide Sequencing
D. G. Robinson, Chen, W., Storey, J. D., and Gresham, D., “Design and analysis of Bar-seq experiments.”, G3 (Bethesda), vol. 4, no. 1, pp. 11-8, 2014.
Humans
T. T. Marstrand and Storey, J. D., “Identifying and mapping cell-type-specific chromatin programming of gene expression.”, Proc Natl Acad Sci U S A, vol. 111, no. 6, pp. E645-54, 2014.
K. H. Desai, Tan, C. Seng, Leek, J. T., Maier, R. V., Tompkins, R. G., and Storey, J. D., “Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study.”, PLoS Med, vol. 8, no. 9, p. e1001093, 2011.
Imaging, Three-Dimensional
J. S. Kanodia, Kim, Y., Tomer, R., Khan, Z., Chung, K., Storey, J. D., Lu, H., Keller, P. J., and Shvartsman, S. Y., “A computational statistics approach for estimating the spatial range of morphogen gradients.”, Development, vol. 138, no. 22, pp. 4867-74, 2011.
In Situ Hybridization, Fluorescence
J. S. Kanodia, Kim, Y., Tomer, R., Khan, Z., Chung, K., Storey, J. D., Lu, H., Keller, P. J., and Shvartsman, S. Y., “A computational statistics approach for estimating the spatial range of morphogen gradients.”, Development, vol. 138, no. 22, pp. 4867-74, 2011.
Inflammation
K. H. Desai, Tan, C. Seng, Leek, J. T., Maier, R. V., Tompkins, R. G., and Storey, J. D., “Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study.”, PLoS Med, vol. 8, no. 9, p. e1001093, 2011.
Leucine
D. Gresham, Boer, V. M., Caudy, A., Ziv, N., Brandt, N. J., Storey, J. D., and Botstein, D., “System-level analysis of genes and functions affecting survival during nutrient starvation in Saccharomyces cerevisiae.”, Genetics, vol. 187, no. 1, pp. 299-317, 2011.
Leukocytes
K. H. Desai, Tan, C. Seng, Leek, J. T., Maier, R. V., Tompkins, R. G., and Storey, J. D., “Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study.”, PLoS Med, vol. 8, no. 9, p. e1001093, 2011.
Longitudinal Studies
K. H. Desai, Tan, C. Seng, Leek, J. T., Maier, R. V., Tompkins, R. G., and Storey, J. D., “Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study.”, PLoS Med, vol. 8, no. 9, p. e1001093, 2011.
Male
K. H. Desai, Tan, C. Seng, Leek, J. T., Maier, R. V., Tompkins, R. G., and Storey, J. D., “Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study.”, PLoS Med, vol. 8, no. 9, p. e1001093, 2011.
MAP Kinase Signaling System
K. H. Desai, Tan, C. Seng, Leek, J. T., Maier, R. V., Tompkins, R. G., and Storey, J. D., “Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study.”, PLoS Med, vol. 8, no. 9, p. e1001093, 2011.
Middle Aged
K. H. Desai, Tan, C. Seng, Leek, J. T., Maier, R. V., Tompkins, R. G., and Storey, J. D., “Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study.”, PLoS Med, vol. 8, no. 9, p. e1001093, 2011.
Models, Statistical
L. S. Chen and Storey, J. D., “Eigen-R2 for dissecting variation in high-dimensional studies.”, Bioinformatics, vol. 24, no. 19, pp. 2260-2, 2008.
Morphogenesis
J. S. Kanodia, Kim, Y., Tomer, R., Khan, Z., Chung, K., Storey, J. D., Lu, H., Keller, P. J., and Shvartsman, S. Y., “A computational statistics approach for estimating the spatial range of morphogen gradients.”, Development, vol. 138, no. 22, pp. 4867-74, 2011.
Multiple Organ Failure
K. H. Desai, Tan, C. Seng, Leek, J. T., Maier, R. V., Tompkins, R. G., and Storey, J. D., “Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study.”, PLoS Med, vol. 8, no. 9, p. e1001093, 2011.
Mutation
D. Gresham, Boer, V. M., Caudy, A., Ziv, N., Brandt, N. J., Storey, J. D., and Botstein, D., “System-level analysis of genes and functions affecting survival during nutrient starvation in Saccharomyces cerevisiae.”, Genetics, vol. 187, no. 1, pp. 299-317, 2011.
Oligonucleotide Array Sequence Analysis
K. H. Desai, Tan, C. Seng, Leek, J. T., Maier, R. V., Tompkins, R. G., and Storey, J. D., “Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study.”, PLoS Med, vol. 8, no. 9, p. e1001093, 2011.
Osmolar Concentration
J. S. Kanodia, Kim, Y., Tomer, R., Khan, Z., Chung, K., Storey, J. D., Lu, H., Keller, P. J., and Shvartsman, S. Y., “A computational statistics approach for estimating the spatial range of morphogen gradients.”, Development, vol. 138, no. 22, pp. 4867-74, 2011.
Phosphates
D. Gresham, Boer, V. M., Caudy, A., Ziv, N., Brandt, N. J., Storey, J. D., and Botstein, D., “System-level analysis of genes and functions affecting survival during nutrient starvation in Saccharomyces cerevisiae.”, Genetics, vol. 187, no. 1, pp. 299-317, 2011.
Polymorphism, Single Nucleotide
T. T. Marstrand and Storey, J. D., “Identifying and mapping cell-type-specific chromatin programming of gene expression.”, Proc Natl Acad Sci U S A, vol. 111, no. 6, pp. E645-54, 2014.
Prospective Studies
K. H. Desai, Tan, C. Seng, Leek, J. T., Maier, R. V., Tompkins, R. G., and Storey, J. D., “Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study.”, PLoS Med, vol. 8, no. 9, p. e1001093, 2011.
Regulatory Elements, Transcriptional
T. T. Marstrand and Storey, J. D., “Identifying and mapping cell-type-specific chromatin programming of gene expression.”, Proc Natl Acad Sci U S A, vol. 111, no. 6, pp. E645-54, 2014.
Research Design
D. G. Robinson, Chen, W., Storey, J. D., and Gresham, D., “Design and analysis of Bar-seq experiments.”, G3 (Bethesda), vol. 4, no. 1, pp. 11-8, 2014.
RNA, Fungal
D. G. Robinson, Chen, W., Storey, J. D., and Gresham, D., “Design and analysis of Bar-seq experiments.”, G3 (Bethesda), vol. 4, no. 1, pp. 11-8, 2014.
Saccharomyces cerevisiae
D. Gresham, Boer, V. M., Caudy, A., Ziv, N., Brandt, N. J., Storey, J. D., and Botstein, D., “System-level analysis of genes and functions affecting survival during nutrient starvation in Saccharomyces cerevisiae.”, Genetics, vol. 187, no. 1, pp. 299-317, 2011.
D. G. Robinson, Chen, W., Storey, J. D., and Gresham, D., “Design and analysis of Bar-seq experiments.”, G3 (Bethesda), vol. 4, no. 1, pp. 11-8, 2014.
Sequence Analysis, DNA
D. Gresham, Boer, V. M., Caudy, A., Ziv, N., Brandt, N. J., Storey, J. D., and Botstein, D., “System-level analysis of genes and functions affecting survival during nutrient starvation in Saccharomyces cerevisiae.”, Genetics, vol. 187, no. 1, pp. 299-317, 2011.
Sequence Analysis, RNA
D. G. Robinson, Chen, W., Storey, J. D., and Gresham, D., “Design and analysis of Bar-seq experiments.”, G3 (Bethesda), vol. 4, no. 1, pp. 11-8, 2014.
Software
L. S. Chen and Storey, J. D., “Eigen-R2 for dissecting variation in high-dimensional studies.”, Bioinformatics, vol. 24, no. 19, pp. 2260-2, 2008.
Systems Biology
D. Gresham, Boer, V. M., Caudy, A., Ziv, N., Brandt, N. J., Storey, J. D., and Botstein, D., “System-level analysis of genes and functions affecting survival during nutrient starvation in Saccharomyces cerevisiae.”, Genetics, vol. 187, no. 1, pp. 299-317, 2011.
Tissue Distribution
J. S. Kanodia, Kim, Y., Tomer, R., Khan, Z., Chung, K., Storey, J. D., Lu, H., Keller, P. J., and Shvartsman, S. Y., “A computational statistics approach for estimating the spatial range of morphogen gradients.”, Development, vol. 138, no. 22, pp. 4867-74, 2011.
Wounds and Injuries
K. H. Desai, Tan, C. Seng, Leek, J. T., Maier, R. V., Tompkins, R. G., and Storey, J. D., “Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study.”, PLoS Med, vol. 8, no. 9, p. e1001093, 2011.
Young Adult
K. H. Desai, Tan, C. Seng, Leek, J. T., Maier, R. V., Tompkins, R. G., and Storey, J. D., “Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study.”, PLoS Med, vol. 8, no. 9, p. e1001093, 2011.