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

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Adaptation, Physiological
P. Andolfatto, Adaptive evolution of non-coding DNA in Drosophila., Nature, vol. 437, no. 7062, pp. 1149-52, 2005.
Aging
C. T. Murphy, Aging: miRacles of longevity?, Curr Biol, vol. 20, no. 24, pp. R1076-8, 2010.
Algorithms
Z. Barutcuoglu, Airoldi, E. M., Dumeaux, V., Schapire, R. E., and Troyanskaya, O. G., Aneuploidy prediction and tumor classification with heterogeneous hidden conditional random fields., Bioinformatics, vol. 25, no. 10, pp. 1307-13, 2009.
C. Huttenhower and Troyanskaya, O. G., Assessing the functional structure of genomic data., Bioinformatics, vol. 24, no. 13, pp. i330-8, 2008.
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.
T. Sharpee, Rust, N. C., and Bialek, W., Analyzing neural responses to natural signals: maximally informative dimensions., Neural Comput, vol. 16, no. 2, pp. 223-50, 2004.
J. Zhou, Schor, I. E., Yao, V., Theesfeld, C. L., Marco-Ferreres, R., Tadych, A., Furlong, E. E. M., and Troyanskaya, O. G., Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development., PLoS Genet, vol. 15, no. 9, p. e1008382, 2019.
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.
Z. Khan, Amini, S., Bloom, J. S., Ruse, C., Caudy, A. A., Kruglyak, L., Singh, M., Perlman, D. H., and Tavazoie, S., Accurate proteome-wide protein quantification from high-resolution 15N mass spectra., Genome Biol, vol. 12, no. 12, p. R122, 2011.
J. P. Nguyen, Linder, A. N., Plummer, G. S., Shaevitz, J. W., and Leifer, A. M., Automatically tracking neurons in a moving and deforming brain., PLoS Comput Biol, vol. 13, no. 5, p. e1005517, 2017.
Analysis of Variance
J. F. Ayroles and Gibson, G., Analysis of variance of microarray data., Methods Enzymol, vol. 411, pp. 214-33, 2006.
Animals
M. D. Chikina and Troyanskaya, O. G., Accurate quantification of functional analogy among close homologs., PLoS Comput Biol, vol. 7, no. 2, p. e1001074, 2011.
H. A. Müller and Wieschaus, E., armadillo, bazooka, and stardust are critical for early stages in formation of the zonula adherens and maintenance of the polarized blastoderm epithelium in Drosophila., J Cell Biol, vol. 134, no. 1, pp. 149-63, 1996.
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.
B. D. Bennett, Yuan, J., Kimball, E. H., and Rabinowitz, J. D., Absolute quantitation of intracellular metabolite concentrations by an isotope ratio-based approach., Nat Protoc, vol. 3, no. 8, pp. 1299-311, 2008.
J. Zhou, Schor, I. E., Yao, V., Theesfeld, C. L., Marco-Ferreres, R., Tadych, A., Furlong, E. E. M., and Troyanskaya, O. G., Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development., PLoS Genet, vol. 15, no. 9, p. e1008382, 2019.
S. L. Grady, Purdy, J. G., Rabinowitz, J. D., and Shenk, T., Argininosuccinate synthetase 1 depletion produces a metabolic state conducive to herpes simplex virus 1 infection., Proc Natl Acad Sci U S A, vol. 110, no. 51, pp. E5006-15, 2013.
J. F. Ayroles and Gibson, G., Analysis of variance of microarray data., Methods Enzymol, vol. 411, pp. 214-33, 2006.
J. D. Rabinowitz and White, E., Autophagy and metabolism., Science, vol. 330, no. 6009, pp. 1344-8, 2010.
T. Sharpee, Rust, N. C., and Bialek, W., Analyzing neural responses to natural signals: maximally informative dimensions., Neural Comput, vol. 16, no. 2, pp. 223-50, 2004.
P. Mehta and Gregor, T., Approaching the molecular origins of collective dynamics in oscillating cell populations., Curr Opin Genet Dev, vol. 20, no. 6, pp. 574-80, 2010.
C. T. Murphy, Aging: miRacles of longevity?, Curr Biol, vol. 20, no. 24, pp. R1076-8, 2010.
N. S. Tolwinski and Wieschaus, E., Armadillo nuclear import is regulated by cytoplasmic anchor Axin and nuclear anchor dTCF/Pan., Development, vol. 128, no. 11, pp. 2107-17, 2001.
L. Poillet-Perez, Xie, X., Zhan, L., Yang, Y., Sharp, D. W., Hu, Z. Sherrie, Su, X., Maganti, A., Jiang, C., Lu, W., Zheng, H., Bosenberg, M. W., Mehnert, J. M., Guo, J. Yanxiang, Lattime, E., Rabinowitz, J. D., and White, E., Autophagy maintains tumour growth through circulating arginine., Nature, vol. 563, no. 7732, pp. 569-573, 2018.
B. He, Doubrovinski, K., Polyakov, O., and Wieschaus, E., Apical constriction drives tissue-scale hydrodynamic flow to mediate cell elongation., Nature, vol. 508, no. 7496, pp. 392-6, 2014.
P. Andolfatto, Adaptive evolution of non-coding DNA in Drosophila., Nature, vol. 437, no. 7062, pp. 1149-52, 2005.
K. Thornton and Andolfatto, P., Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster., Genetics, vol. 172, no. 3, pp. 1607-19, 2006.
D. E. Klein, Nappi, V. M., Reeves, G. T., Shvartsman, S. Y., and Lemmon, M. A., Argos inhibits epidermal growth factor receptor signalling by ligand sequestration., Nature, vol. 430, no. 7003, pp. 1040-4, 2004.
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.
E. Wieschaus and Riggleman, R., Autonomous requirements for the segment polarity gene armadillo during Drosophila embryogenesis., Cell, vol. 49, no. 2, pp. 177-84, 1987.
J. P. Nguyen, Linder, A. N., Plummer, G. S., Shaevitz, J. W., and Leifer, A. M., Automatically tracking neurons in a moving and deforming brain., PLoS Comput Biol, vol. 13, no. 5, p. e1005517, 2017.
A. L. Webber and Tilghman, S. M., The absence of enhancer competition between Igf2 and H19 following transfer into differentiated cells., Mol Cell Biol, vol. 18, no. 4, pp. 1903-10, 1998.
A. Di Gregorio and Levine, M., Analyzing gene regulation in ascidian embryos: new tools for new perspectives., Differentiation, vol. 70, no. 4-5, pp. 132-9, 2002.
M. J. O'Neill, Ingram, R. S., Vrana, P. B., and Tilghman, S. M., Allelic expression of IGF2 in marsupials and birds., Dev Genes Evol, vol. 210, no. 1, pp. 18-20, 2000.
J. D. Jensen, Thornton, K. R., and Andolfatto, P., An approximate bayesian estimator suggests strong, recurrent selective sweeps in Drosophila., PLoS Genet, vol. 4, no. 9, p. e1000198, 2008.
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.
S. R. Browning, Browning, B. L., Zhou, Y., Tucci, S., and Akey, J. M., Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture., Cell, vol. 173, no. 1, pp. 53-61.e9, 2018.
N. N. Pavlova, Hui, S., Ghergurovich, J. M., Fan, J., Intlekofer, A. M., White, R. M., Rabinowitz, J. D., Thompson, C. B., and Zhang, J., As Extracellular Glutamine Levels Decline, Asparagine Becomes an Essential Amino Acid., Cell Metab, vol. 27, no. 2, pp. 428-438.e5, 2018.
Biological Transport
R. G. Endres and Wingreen, N. S., Accuracy of direct gradient sensing by single cells., Proc Natl Acad Sci U S A, vol. 105, no. 41, pp. 15749-54, 2008.
Biopolymers
D. Swanson and Wingreen, N. S., Active biopolymers confer fast reorganization kinetics., Phys Rev Lett, vol. 107, no. 21, p. 218103, 2011.
Cation Transport Proteins
D. C. Hess, Lu, W., Rabinowitz, J. D., and Botstein, D., Ammonium toxicity and potassium limitation in yeast., PLoS Biol, vol. 4, no. 11, p. e351, 2006.
Cells
R. G. Endres and Wingreen, N. S., Accuracy of direct gradient sensing by single cells., Proc Natl Acad Sci U S A, vol. 105, no. 41, pp. 15749-54, 2008.
R. G. Endres and Wingreen, N. S., Accuracy of direct gradient sensing by cell-surface receptors., Prog Biophys Mol Biol, vol. 100, no. 1-3, pp. 33-9, 2009.
Chemotaxis
R. G. Endres and Wingreen, N. S., Accuracy of direct gradient sensing by cell-surface receptors., Prog Biophys Mol Biol, vol. 100, no. 1-3, pp. 33-9, 2009.
Cyclic AMP
R. G. Endres and Wingreen, N. S., Accuracy of direct gradient sensing by single cells., Proc Natl Acad Sci U S A, vol. 105, no. 41, pp. 15749-54, 2008.
Database Management Systems
C. Huttenhower and Troyanskaya, O. G., Assessing the functional structure of genomic data., Bioinformatics, vol. 24, no. 13, pp. i330-8, 2008.
Diffusion
R. G. Endres and Wingreen, N. S., Accuracy of direct gradient sensing by single cells., Proc Natl Acad Sci U S A, vol. 105, no. 41, pp. 15749-54, 2008.
R. G. Endres and Wingreen, N. S., Accuracy of direct gradient sensing by cell-surface receptors., Prog Biophys Mol Biol, vol. 100, no. 1-3, pp. 33-9, 2009.
Disease
J. D. Rabinowitz and White, E., Autophagy and metabolism., Science, vol. 330, no. 6009, pp. 1344-8, 2010.
DNA, Intergenic
P. Andolfatto, Adaptive evolution of non-coding DNA in Drosophila., Nature, vol. 437, no. 7062, pp. 1149-52, 2005.
Drosophila melanogaster
J. D. Jensen, Thornton, K. R., and Andolfatto, P., An approximate bayesian estimator suggests strong, recurrent selective sweeps in Drosophila., PLoS Genet, vol. 4, no. 9, p. e1000198, 2008.
H. A. Müller and Wieschaus, E., armadillo, bazooka, and stardust are critical for early stages in formation of the zonula adherens and maintenance of the polarized blastoderm epithelium in Drosophila., J Cell Biol, vol. 134, no. 1, pp. 149-63, 1996.
B. He, Doubrovinski, K., Polyakov, O., and Wieschaus, E., Apical constriction drives tissue-scale hydrodynamic flow to mediate cell elongation., Nature, vol. 508, no. 7496, pp. 392-6, 2014.
N. S. Tolwinski and Wieschaus, E., Armadillo nuclear import is regulated by cytoplasmic anchor Axin and nuclear anchor dTCF/Pan., Development, vol. 128, no. 11, pp. 2107-17, 2001.
K. Thornton and Andolfatto, P., Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster., Genetics, vol. 172, no. 3, pp. 1607-19, 2006.
P. Andolfatto, Adaptive evolution of non-coding DNA in Drosophila., Nature, vol. 437, no. 7062, pp. 1149-52, 2005.
E. Wieschaus and Riggleman, R., Autonomous requirements for the segment polarity gene armadillo during Drosophila embryogenesis., Cell, vol. 49, no. 2, pp. 177-84, 1987.
D. E. Klein, Nappi, V. M., Reeves, G. T., Shvartsman, S. Y., and Lemmon, M. A., Argos inhibits epidermal growth factor receptor signalling by ligand sequestration., Nature, vol. 430, no. 7003, pp. 1040-4, 2004.
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.

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