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 Reproducibility of Results  [Clear All Filters]
Journal Article
C. L. Myers, Dunham, M. J., Kung, S. Y., and Troyanskaya, O. G., Accurate detection of aneuploidies in array CGH and gene expression microarray data., Bioinformatics, vol. 20, no. 18, pp. 3533-43, 2004.
C. S. Greene and Troyanskaya, O. G., Accurate evaluation and analysis of functional genomics data and methods., Ann N Y Acad Sci, vol. 1260, pp. 95-100, 2012.
J. O. Dubuis, Samanta, R., and Gregor, T., Accurate measurements of dynamics and reproducibility in small genetic networks., Mol Syst Biol, vol. 9, p. 639, 2013.
T. V. Morozova, Ayroles, J. F., Jordan, K. W., Duncan, L. H., Carbone, M. Anna, Lyman, R. F., Stone, E. A., Govindaraju, D. R., R Ellison, C., Mackay, T. F. C., and Anholt, R. R. H., Alcohol sensitivity in Drosophila: translational potential of systems genetics., Genetics, vol. 183, no. 2, pp. 733-45, 1SI-12SI, 2009.
C. Huttenhower and Troyanskaya, O. G., Bayesian data integration: a functional perspective., Comput Syst Bioinformatics Conf, pp. 341-51, 2006.
C. L. Myers, Robson, D., Wible, A., Hibbs, M. A., Chiriac, C., Theesfeld, C. L., Dolinski, K., and Troyanskaya, O. G., Discovery of biological networks from diverse functional genomic data., Genome Biol, vol. 6, no. 13, p. R114, 2005.
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. L. Myers, Barrett, D. R., Hibbs, M. A., Huttenhower, C., and Troyanskaya, O. G., Finding function: evaluation methods for functional genomic data., BMC Genomics, vol. 7, p. 187, 2006.
J. F. Ayroles, Laflamme, B. A., Stone, E. A., Wolfner, M. F., and Mackay, T. F. C., Functional genome annotation of Drosophila seminal fluid proteins using transcriptional genetic networks., Genet Res (Camb), vol. 93, no. 6, pp. 387-95, 2011.
Y. Guan, Ackert-Bicknell, C. L., Kell, B., Troyanskaya, O. G., and Hibbs, M. A., Functional genomics complements quantitative genetics in identifying disease-gene associations., PLoS Comput Biol, vol. 6, no. 11, p. e1000991, 2010.
M. D. Chikina, Huttenhower, C., Murphy, C. T., and Troyanskaya, O. G., Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans., PLoS Comput Biol, vol. 5, no. 6, p. e1000417, 2009.
J. Zhou and Troyanskaya, O. G., Global quantitative modeling of chromatin factor interactions., PLoS Comput Biol, vol. 10, no. 3, p. e1003525, 2014.
W. Lu, Kimball, E., and Rabinowitz, J. D., A high-performance liquid chromatography-tandem mass spectrometry method for quantitation of nitrogen-containing intracellular metabolites., J Am Soc Mass Spectrom, vol. 17, no. 1, pp. 37-50, 2006.
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.
A. Pop, Huttenhower, C., Iyer-Pascuzzi, A., Benfey, P. N., and Troyanskaya, O. G., Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana., BMC Syst Biol, vol. 4, p. 180, 2010.
V. N. Kristensen, Vaske, C. J., Ursini-Siegel, J., Van Loo, P., Nordgard, S. H., Sachidanandam, R., Sørlie, T., Wärnberg, F., Haakensen, V. D., Helland, Å., Naume, B., Perou, C. M., Haussler, D., Troyanskaya, O. G., and Børresen-Dale, A. - L., Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling., Proc Natl Acad Sci U S A, vol. 109, no. 8, pp. 2802-7, 2012.
D. Gorenshteyn, Zaslavsky, E., Fribourg, M., Park, C. Y., Wong, A. K., Tadych, A., Hartmann, B. M., Albrecht, R. A., García-Sastre, A., Kleinstein, S. H., Troyanskaya, O. G., and Sealfon, S. C., Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases., Immunity, vol. 43, no. 3, pp. 605-14, 2015.
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.
A. V. Persikov, Osada, R., and Singh, M., Predicting DNA recognition by Cys2His2 zinc finger proteins., Bioinformatics, vol. 25, no. 1, pp. 22-9, 2009.
J. H. Fong, Keating, A. E., and Singh, M., Predicting specificity in bZIP coiled-coil protein interactions., Genome Biol, vol. 5, no. 2, p. R11, 2004.
T. Gregor, Tank, D. W., Wieschaus, E. F., and Bialek, W., Probing the limits to positional information., Cell, vol. 130, no. 1, pp. 153-64, 2007.
S. U. Bajad, Lu, W., Kimball, E. H., Yuan, J., Peterson, C., and Rabinowitz, J. D., Separation and quantitation of water soluble cellular metabolites by hydrophilic interaction chromatography-tandem mass spectrometry., J Chromatogr A, vol. 1125, no. 1, pp. 76-88, 2006.
C. Y. Park, Hess, D. C., Huttenhower, C., and Troyanskaya, O. G., Simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway components., PLoS Comput Biol, vol. 6, no. 11, p. e1001009, 2010.
R. Mukhopadhyay, Emberly, E., Tang, C., and Wingreen, N. S., Statistical mechanics of RNA folding: importance of alphabet size., Phys Rev E Stat Nonlin Soft Matter Phys, vol. 68, no. 4 Pt 1, p. 041904, 2003.
N. Novoradovskaya, Whitfield, M. L., Basehore, L. S., Novoradovsky, A., Pesich, R., Usary, J., Karaca, M., Wong, W. K., Aprelikova, O., Fero, M., Perou, C. M., Botstein, D., and Braman, J., Universal Reference RNA as a standard for microarray experiments., BMC Genomics, vol. 5, no. 1, p. 20, 2004.
R. G. Endres, Oleksiuk, O., Hansen, C. H., Meir, Y., Sourjik, V., and Wingreen, N. S., Variable sizes of Escherichia coli chemoreceptor signaling teams., Mol Syst Biol, vol. 4, p. 211, 2008.