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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2019
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.
2018
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.
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.
2017
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.
2016
J. Yanxiang Guo, Teng, X., Laddha, S. V., Ma, S., Van Nostrand, S. C., Yang, Y., Khor, S., Chan, C. S., Rabinowitz, J. D., and White, E., “Autophagy provides metabolic substrates to maintain energy charge and nucleotide pools in Ras-driven lung cancer cells.”, Genes Dev, vol. 30, no. 15, pp. 1704-17, 2016.
2015
Y. - F. Xu, Lu, W., and Rabinowitz, J. D., “Avoiding misannotation of in-source fragmentation products as cellular metabolites in liquid chromatography-mass spectrometry-based metabolomics.”, Anal Chem, vol. 87, no. 4, pp. 2273-81, 2015.
2014
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.
J. Zhang, Fan, J., Venneti, S., Cross, J. R., Takagi, T., Bhinder, B., Djaballah, H., Kanai, M., Cheng, E. H., Judkins, A. R., Pawel, B., Baggs, J., Cherry, S., Rabinowitz, J. D., and Thompson, C. B., “Asparagine plays a critical role in regulating cellular adaptation to glutamine depletion.”, Mol Cell, vol. 56, no. 2, pp. 205-18, 2014.
G. Karsli-Uzunbas, Guo, J. Yanxiang, Price, S., Teng, X., Laddha, S. V., Khor, S., Kalaany, N. Y., Jacks, T., Chan, C. S., Rabinowitz, J. D., and White, E., “Autophagy is required for glucose homeostasis and lung tumor maintenance.”, Cancer Discov, vol. 4, no. 8, pp. 914-27, 2014.
2013
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. 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.
K. Dolinski and Botstein, D., “Automating the construction of gene ontologies.”, Nat Biotechnol, vol. 31, no. 1, pp. 34-5, 2013.
2012
M. Louis Reaves, Sinha, S., Rabinowitz, J. D., Kruglyak, L., and Redfield, R. J., “Absence of detectable arsenate in DNA from arsenate-grown GFAJ-1 cells.”, Science, vol. 337, no. 6093, pp. 470-3, 2012.
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.
2011
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.
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.
D. Swanson and Wingreen, N. S., “Active biopolymers confer fast reorganization kinetics.”, Phys Rev Lett, vol. 107, no. 21, p. 218103, 2011.
S. - W. Teng, Schaffer, J. N., Tu, K. C., Mehta, P., Lu, W., Ong, N. P., Bassler, B. L., and Wingreen, N. S., “Active regulation of receptor ratios controls integration of quorum-sensing signals in Vibrio harveyi.”, Mol Syst Biol, vol. 7, p. 491, 2011.
2010
S. Goyal, Yuan, J., Chen, T., Rabinowitz, J. D., and Wingreen, N. S., “Achieving optimal growth through product feedback inhibition in metabolism.”, PLoS Comput Biol, vol. 6, no. 6, p. e1000802, 2010.
S. Wang, Arellano-Santoyo, H., Combs, P. A., and Shaevitz, J. W., “Actin-like cytoskeleton filaments contribute to cell mechanics in bacteria.”, Proc Natl Acad Sci U S A, vol. 107, no. 20, pp. 9182-5, 2010.
D. Gresham, Usaite, R., Germann, S. Manuela, Lisby, M., Botstein, D., and Regenberg, B., “Adaptation to diverse nitrogen-limited environments by deletion or extrachromosomal element formation of the GAP1 locus.”, Proc Natl Acad Sci U S A, vol. 107, no. 43, pp. 18551-6, 2010.
C. T. Murphy, “Aging: miRacles of longevity?”, Curr Biol, vol. 20, no. 24, pp. R1076-8, 2010.
Y. Kyung Kwon, Higgins, M. B., and Rabinowitz, J. D., “Antifolate-induced depletion of intracellular glycine and purines inhibits thymineless death in E. coli.”, ACS Chem Biol, vol. 5, no. 8, pp. 787-95, 2010.
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.
J. D. Rabinowitz and White, E., “Autophagy and metabolism.”, Science, vol. 330, no. 6009, pp. 1344-8, 2010.
2009
B. D. Bennett, Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., and Rabinowitz, J. D., “Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli.”, Nat Chem Biol, vol. 5, no. 8, pp. 593-9, 2009.
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.
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.
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.
2008
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.
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.
T. Mignot and Shaevitz, J. W., “Active and passive mechanisms of intracellular transport and localization in bacteria.”, Curr Opin Microbiol, vol. 11, no. 6, pp. 580-5, 2008.
W. Lu, Bennett, B. D., and Rabinowitz, J. D., “Analytical strategies for LC-MS-based targeted metabolomics.”, J Chromatogr B Analyt Technol Biomed Life Sci, vol. 871, no. 2, pp. 236-42, 2008.
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.
C. Huttenhower and Troyanskaya, O. G., “Assessing the functional structure of genomic data.”, Bioinformatics, vol. 24, no. 13, pp. i330-8, 2008.
2007
J. D. Rabinowitz and Kimball, E., “Acidic acetonitrile for cellular metabolome extraction from Escherichia coli.”, Anal Chem, vol. 79, no. 16, pp. 6167-73, 2007.
A. Chi, Huttenhower, C., Geer, L. Y., Coon, J. J., Syka, J. E. P., Bai, D. L., Shabanowitz, J., Burke, D. J., Troyanskaya, O. G., and Hunt, D. F., “Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.”, Proc Natl Acad Sci U S A, vol. 104, no. 7, pp. 2193-8, 2007.
2006
J. Akiko Heck, Gresham, D., Botstein, D., and Alani, E., “Accumulation of recessive lethal mutations in Saccharomyces cerevisiae mlh1 mismatch repair mutants is not associated with gross chromosomal rearrangements.”, Genetics, vol. 174, no. 1, pp. 519-23, 2006.
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.
J. F. Ayroles and Gibson, G., “Analysis of variance of microarray data.”, Methods Enzymol, vol. 411, pp. 214-33, 2006.
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.
2005
P. Andolfatto, “Adaptive evolution of non-coding DNA in Drosophila.”, Nature, vol. 437, no. 7062, pp. 1149-52, 2005.
2004
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.
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.
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.
2002
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. Lang, Asbury, C. L., Shaevitz, J. W., and Block, S. M., “An automated two-dimensional optical force clamp for single molecule studies.”, Biophys J, vol. 83, no. 1, pp. 491-501, 2002.
2001
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.
2000
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.
1998
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.
1996
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.
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.
1987
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.