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 Proteins  [Clear All Filters]
2010
J. D. Rabinowitz and White, E., Autophagy and metabolism., Science, vol. 330, no. 6009, pp. 1344-8, 2010.
P. Jiang and Singh, M., SPICi: a fast clustering algorithm for large biological networks., Bioinformatics, vol. 26, no. 8, pp. 1105-11, 2010.
2009
D. C. Hess, Myers, C. L., Huttenhower, C., Hibbs, M. A., Hayes, A. P., Paw, J., Clore, J. J., Mendoza, R. M., San Luis, B., Nislow, C., Giaever, G., Costanzo, M., Troyanskaya, O. G., and Caudy, A. A., Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis., PLoS Genet, vol. 5, no. 3, p. e1000407, 2009.
J. Song and Singh, M., How and when should interactome-derived clusters be used to predict functional modules and protein function?, Bioinformatics, vol. 25, no. 23, pp. 3143-50, 2009.
C. Huttenhower, Hibbs, M. A., Myers, C. L., Caudy, A. A., Hess, D. C., and Troyanskaya, O. G., The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction., Bioinformatics, vol. 25, no. 18, pp. 2404-10, 2009.
M. Anna Carbone, Ayroles, J. F., Yamamoto, A., Morozova, T. V., West, S. A., Magwire, M. M., Mackay, T. F. C., and Anholt, R. R. H., Overexpression of myocilin in the Drosophila eye activates the unfolded protein response: implications for glaucoma., PLoS One, vol. 4, no. 1, p. e4216, 2009.
J. A. Capra, Laskowski, R. A., Thornton, J. M., Singh, M., and Funkhouser, T. A., Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure., PLoS Comput Biol, vol. 5, no. 12, p. e1000585, 2009.
Z. Khan, Bloom, J. S., Garcia, B. A., Singh, M., and Kruglyak, L., Protein quantification across hundreds of experimental conditions., Proc Natl Acad Sci U S A, vol. 106, no. 37, pp. 15544-8, 2009.
2008
J. A. Capra and Singh, M., Characterization and prediction of residues determining protein functional specificity., Bioinformatics, vol. 24, no. 13, pp. 1473-80, 2008.
L. Peña-Castillo, Tasan, M., Myers, C. L., Lee, H., Joshi, T., Zhang, C., Guan, Y., Leone, M., Pagnani, A., Kim, W. Kyu, Krumpelman, C., Tian, W., Obozinski, G., Qi, Y., Mostafavi, S., Lin, G. Ning, Berriz, G. F., Gibbons, F. D., Lanckriet, G., Qiu, J., Grant, C., Barutcuoglu, Z., Hill, D. P., Warde-Farley, D., Grouios, C., Ray, D., Blake, J. A., Deng, M., Jordan, M. I., Noble, W. S., Morris, Q., Klein-Seetharaman, J., Bar-Joseph, iv, Z., Chen, T., Sun, F., Troyanskaya, O. G., Marcotte, E. M., Xu, D., Hughes, T. R., and Roth, F. P., A critical assessment of Mus musculus gene function prediction using integrated genomic evidence., Genome Biol, vol. 9 Suppl 1, p. S2, 2008.
C. L. Vizcarra, Zhang, N., Marshall, S. A., Wingreen, N. S., Zeng, C., and Mayo, S. L., An improved pairwise decomposable finite-difference Poisson-Boltzmann method for computational protein design., J Comput Chem, vol. 29, no. 7, pp. 1153-62, 2008.
Y. Guan, Myers, C. L., Hess, D. C., Barutcuoglu, Z., Caudy, A. A., and Troyanskaya, O. G., Predicting gene function in a hierarchical context with an ensemble of classifiers., Genome Biol, vol. 9 Suppl 1, p. S3, 2008.
P. Mehta, Goyal, S., and Wingreen, N. S., A quantitative comparison of sRNA-based and protein-based gene regulation., Mol Syst Biol, vol. 4, p. 221, 2008.
2002
E. G. Emberly, Wingreen, N. S., and Tang, C., Designability of alpha-helical proteins., Proc Natl Acad Sci U S A, vol. 99, no. 17, pp. 11163-8, 2002.
H. Li, Tang, C., and Wingreen, N. S., Designability of protein structures: a lattice-model study using the Miyazawa-Jernigan matrix., Proteins, vol. 49, no. 3, pp. 403-12, 2002.
J. Miller, Zeng, C., Wingreen, N. S., and Tang, C., Emergence of highly designable protein-backbone conformations in an off-lattice model., Proteins, vol. 47, no. 4, pp. 506-12, 2002.
D. J. Brooks, Fresco, J. R., Lesk, A. M., and Singh, M., Evolution of amino acid frequencies in proteins over deep time: inferred order of introduction of amino acids into the genetic code., Mol Biol Evol, vol. 19, no. 10, pp. 1645-55, 2002.
M. L. Whitfield, Sherlock, G., Saldanha, A. J., Murray, J. I., Ball, C. A., Alexander, K. E., Matese, J. C., Perou, C. M., Hurt, M. M., Brown, P. O., and Botstein, D., Identification of genes periodically expressed in the human cell cycle and their expression in tumors., Mol Biol Cell, vol. 13, no. 6, pp. 1977-2000, 2002.
E. G. Emberly, Miller, J., Zeng, C., Wingreen, N. S., and Tang, C., Identifying proteins of high designability via surface-exposure patterns., Proteins, vol. 47, no. 3, pp. 295-304, 2002.
J. A. Zallen, Cohen, Y., Hudson, A. M., Cooley, L., Wieschaus, E., and Schejter, E. D., SCAR is a primary regulator of Arp2/3-dependent morphological events in Drosophila., J Cell Biol, vol. 156, no. 4, pp. 689-701, 2002.