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: Keyword is Gene Expression  [Clear All Filters]
2019
J. Zhou, Park, C. Y., Theesfeld, C. L., Wong, A. K., Yuan, Y., Scheckel, C., Fak, J. J., Funk, J., Yao, K., Tajima, Y., Packer, A., Darnell, R. B., and Troyanskaya, O. G., “Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk.”, Nat Genet, vol. 51, no. 6, pp. 973-980, 2019.
2018
J. Zhou, Theesfeld, C. L., Yao, K., Chen, K. M., Wong, A. K., and Troyanskaya, O. G., “Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk.”, Nat Genet, vol. 50, no. 8, pp. 1171-1179, 2018.
S. E. McKee, Zhang, S., Chen, L., Rabinowitz, J. D., and Reyes, T. M., “Perinatal high fat diet and early life methyl donor supplementation alter one carbon metabolism and DNA methylation in the brain.”, J Neurochem, vol. 145, no. 5, pp. 362-373, 2018.
2015
S. D. Kocher, Tsuruda, J. M., Gibson, J. D., Emore, C. M., Arechavaleta-Velasco, M. E., Queller, D. C., Strassmann, J. E., Grozinger, C. M., Gribskov, M. R., San Miguel, P., Westerman, R., and Hunt, G. J., “A Search for Parent-of-Origin Effects on Honey Bee Gene Expression.”, G3 (Bethesda), vol. 5, no. 8, pp. 1657-62, 2015.
2012
A. Massouras, Waszak, S. M., Albarca-Aguilera, M., Hens, K., Holcombe, W., Ayroles, J. F., Dermitzakis, E. T., Stone, E. A., Jensen, J. D., Mackay, T. F. C., and Deplancke, B., “Genomic variation and its impact on gene expression in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 11, p. e1003055, 2012.
2010
P. Jumbo-Lucioni, Ayroles, J. F., Chambers, M. Moses, Jordan, K. W., Leips, J., Mackay, T. Fc, and De Luca, M., “Systems genetics analysis of body weight and energy metabolism traits in Drosophila melanogaster.”, BMC Genomics, vol. 11, p. 297, 2010.
2009
J. F. Ayroles, Hughes, K. A., Rowe, K. C., Reedy, M. M., Rodriguez-Zas, S. L., Drnevich, J. M., Cáceres, C. E., and Paige, K. N., “A genomewide assessment of inbreeding depression: gene number, function, and mode of action.”, Conserv Biol, vol. 23, no. 4, pp. 920-30, 2009.
L. Christiaen, Wagner, E., Shi, W., and Levine, M., “Whole-mount in situ hybridization on sea squirt (Ciona intestinalis) embryos.”, Cold Spring Harb Protoc, vol. 2009, no. 12, p. pdb.prot5348, 2009.
2008
P. Mehta, Mukhopadhyay, R., and Wingreen, N. S., “Exponential sensitivity of noise-driven switching in genetic networks.”, Phys Biol, vol. 5, no. 2, p. 026005, 2008.
2007
M. A. Hibbs, Hess, D. C., Myers, C. L., Huttenhower, C., Li, K., and Troyanskaya, O. G., “Exploring the functional landscape of gene expression: directed search of large microarray compendia.”, Bioinformatics, vol. 23, no. 20, pp. 2692-9, 2007.
C. Huttenhower, Flamholz, A. I., Landis, J. N., Sahi, S., Myers, C. L., Olszewski, K. L., Hibbs, M. A., Siemers, N. O., Troyanskaya, O. G., and Coller, H. A., “Nearest Neighbor Networks: clustering expression data based on gene neighborhoods.”, BMC Bioinformatics, vol. 8, p. 250, 2007.
2005
M. J. Brauer, Saldanha, A. J., Dolinski, K., and Botstein, D., “Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures.”, Mol Biol Cell, vol. 16, no. 5, pp. 2503-17, 2005.
C. L. Myers, Chen, X., and Troyanskaya, O. G., “Visualization-based discovery and analysis of genomic aberrations in microarray data.”, BMC Bioinformatics, vol. 6, p. 146, 2005.
2004
I. S. Lossos, Czerwinski, D. K., Alizadeh, A. A., Wechser, M. A., Tibshirani, R., Botstein, D., and Levy, R., “Prediction of survival in diffuse large-B-cell lymphoma based on the expression of six genes.”, N Engl J Med, vol. 350, no. 18, pp. 1828-37, 2004.
2003
S. C. Linn, West, R. B., Pollack, J. R., Zhu, S., Hernandez-Boussard, T., Nielsen, T. O., Rubin, B. P., Patel, iv, R., Goldblum, J. R., Siegmund, D., Botstein, D., Brown, P. O., C Gilks, B., and van de Rijn, M., “Gene expression patterns and gene copy number changes in dermatofibrosarcoma protuberans.”, Am J Pathol, vol. 163, no. 6, pp. 2383-95, 2003.
J. Cowden and Levine, M., “Ventral dominance governs sequential patterns of gene expression across the dorsal-ventral axis of the neuroectoderm in the Drosophila embryo.”, Dev Biol, vol. 262, no. 2, pp. 335-49, 2003.
2002
B. K. Jones, Levorse, J., and Tilghman, S. M., “A human H19 transgene exhibits impaired paternal-specific imprint acquisition and maintenance in mice.”, Hum Mol Genet, vol. 11, no. 4, pp. 411-8, 2002.
O. G. Troyanskaya, Garber, M. E., Brown, P. O., Botstein, D., and Altman, R. B., “Nonparametric methods for identifying differentially expressed genes in microarray data.”, Bioinformatics, vol. 18, no. 11, pp. 1454-61, 2002.
J. C. Boldrick, Alizadeh, A. A., Diehn, M., Dudoit, S., Liu, C. Long, Belcher, C. E., Botstein, D., Staudt, L. M., Brown, P. O., and Relman, D. A., “Stereotyped and specific gene expression programs in human innate immune responses to bacteria.”, Proc Natl Acad Sci U S A, vol. 99, no. 2, pp. 972-7, 2002.
2001
M. E. Garber, Troyanskaya, O. G., Schluens, K., Petersen, S., Thaesler, Z., Pacyna-Gengelbach, M., van de Rijn, M., Rosen, G. D., Perou, C. M., Whyte, R. I., Altman, R. B., Brown, P. O., Botstein, D., and Petersen, I., “Diversity of gene expression in adenocarcinoma of the lung.”, Proc Natl Acad Sci U S A, vol. 98, no. 24, pp. 13784-9, 2001.
P. B. Vrana, Matteson, P. G., Schmidt, J. V., Ingram, R. S., Joyce, A., Prince, K. L., Dewey, M. J., and Tilghman, S. M., “Genomic imprinting of a placental lactogen gene in Peromyscus.”, Dev Genes Evol, vol. 211, no. 11, pp. 523-32, 2001.
L. J. Kurihara, Kikuchi, T., Wada, K., and Tilghman, S. M., “Loss of Uch-L1 and Uch-L3 leads to neurodegeneration, posterior paralysis and dysphagia.”, Hum Mol Genet, vol. 10, no. 18, pp. 1963-70, 2001.
O. Troyanskaya, Cantor, M., Sherlock, G., Brown, P., Hastie, T., Tibshirani, R., Botstein, D., and Altman, R. B., “Missing value estimation methods for DNA microarrays.”, Bioinformatics, vol. 17, no. 6, pp. 520-5, 2001.
2000
J. Grosshans and Wieschaus, E., “A genetic link between morphogenesis and cell division during formation of the ventral furrow in Drosophila.”, Cell, vol. 101, no. 5, pp. 523-31, 2000.
1995
C. Rauskolb, Smith, K. M., Peifer, M., and Wieschaus, E., “extradenticle determines segmental identities throughout Drosophila development.”, Development, vol. 121, no. 11, pp. 3663-73, 1995.
A. Bejsovec and Wieschaus, E., “Signaling activities of the Drosophila wingless gene are separately mutable and appear to be transduced at the cell surface.”, Genetics, vol. 139, no. 1, pp. 309-20, 1995.
1994
K. Pfeifer and Tilghman, S. M., “Allele-specific gene expression in mammals: the curious case of the imprinted RNAs.”, Genes Dev, vol. 8, no. 16, pp. 1867-74, 1994.
K. D. Irvine and Wieschaus, E., “fringe, a Boundary-specific signaling molecule, mediates interactions between dorsal and ventral cells during Drosophila wing development.”, Cell, vol. 79, no. 4, pp. 595-606, 1994.
P. Armand, Knapp, A. C., Hirsch, A. J., Wieschaus, E. F., and Cole, M. D., “A novel basic helix-loop-helix protein is expressed in muscle attachment sites of the Drosophila epidermis.”, Mol Cell Biol, vol. 14, no. 6, pp. 4145-54, 1994.
M. A. Postner and Wieschaus, E. F., “The nullo protein is a component of the actin-myosin network that mediates cellularization in Drosophila melanogaster embryos.”, J Cell Sci, vol. 107 ( Pt 7), pp. 1863-73, 1994.
M. Peifer, Sweeton, D., Casey, M., and Wieschaus, E., “wingless signal and Zeste-white 3 kinase trigger opposing changes in the intracellular distribution of Armadillo.”, Development, vol. 120, no. 2, pp. 369-80, 1994.
1992
S. Zemel, Bartolomei, M. S., and Tilghman, S. M., “Physical linkage of two mammalian imprinted genes, H19 and insulin-like growth factor 2.”, Nat Genet, vol. 2, no. 1, pp. 61-5, 1992.
E. D. Schejter, Rose, L. S., Postner, M. A., and Wieschaus, E., “Role of the zygotic genome in the restructuring of the actin cytoskeleton at the cycle-14 transition during Drosophila embryogenesis.”, Cold Spring Harb Symp Quant Biol, vol. 57, pp. 653-9, 1992.
1991
M. E. Brunkow and Tilghman, S. M., “Ectopic expression of the H19 gene in mice causes prenatal lethality.”, Genes Dev, vol. 5, no. 6, pp. 1092-101, 1991.
1990
A. L. Tyner, Godbout, R., Compton, R. S., and Tilghman, S. M., “The ontogeny of alpha-fetoprotein gene expression in the mouse gastrointestinal tract.”, J Cell Biol, vol. 110, no. 4, pp. 915-27, 1990.