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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H
B. Haarer, Viggiano, S., Hibbs, M. A., Troyanskaya, O. G., and Amberg, D. C., Modeling complex genetic interactions in a simple eukaryotic genome: actin displays a rich spectrum of complex haploinsufficiencies., Genes Dev, vol. 21, no. 2, pp. 148-59, 2007.
P. R. Haddrill, Thornton, K. R., Charlesworth, B., and Andolfatto, P., Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations., Genome Res, vol. 15, no. 6, pp. 790-9, 2005.
B. He, Caudy, A., Parsons, L., Rosebrock, A., Pane, A., Raj, S., and Wieschaus, E., Mapping the pericentric heterochromatin by comparative genomic hybridization analysis and chromosome deletions in Drosophila melanogaster., Genome Res, vol. 22, no. 12, pp. 2507-19, 2012.
D. Hendrix, Levine, M., and Shi, W., miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data., Genome Biol, vol. 11, no. 4, p. R39, 2010.
C. Hei Ho, Magtanong, L., Barker, S. L., Gresham, D., Nishimura, S., Natarajan, P., L Y Koh, J., Porter, J., Gray, C. A., Andersen, R. J., Giaever, G., Nislow, C., Andrews, B., Botstein, D., Graham, T. R., Yoshida, M., and Boone, C., A molecular barcoded yeast ORF library enables mode-of-action analysis of bioactive compounds., Nat Biotechnol, vol. 27, no. 4, pp. 369-77, 2009.
K. Casey Huang, Ehrhardt, D. W., and Shaevitz, J. W., The molecular origins of chiral growth in walled cells., Curr Opin Microbiol, vol. 15, no. 6, pp. 707-14, 2012.
K. Casey Huang and Wingreen, N. S., Min-protein oscillations in round bacteria., Phys Biol, vol. 1, no. 3-4, pp. 229-35, 2004.
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M. Lagha, Bothma, J. P., and Levine, M., Mechanisms of transcriptional precision in animal development., Trends Genet, vol. 28, no. 8, pp. 409-16, 2012.
T. J. Levario, Zhan, M., Lim, B., Shvartsman, S. Y., and Lu, H., Microfluidic trap array for massively parallel imaging of Drosophila embryos., Nat Protoc, vol. 8, no. 4, pp. 721-36, 2013.
S. Li, Stone, H. A., and Murphy, C. T., A microfluidic device and automatic counting system for the study of C. elegans reproductive aging., Lab Chip, 2014.
S. Li, Stone, H. A., and Murphy, C. T., A microfluidic device and automatic counting system for the study of C. elegans reproductive aging., Lab Chip, vol. 15, no. 2, pp. 524-31, 2015.
A. M. Li, Ducker, G. S., Li, Y., Seoane, J. A., Xiao, Y., Melemenides, S., Zhou, Y., Liu, L., Vanharanta, S., Graves, E. E., Rankin, E. B., Curtis, C., Massague, J., Rabinowitz, J. D., Thompson, C. B., and Ye, J., Metabolic profiling reveals a dependency of human metastatic breast cancer on mitochondrial serine and one-carbon unit metabolism., Mol. Cancer Res., vol. 18, no. 4, pp. 599-611, 2020.
L. Liu, Shah, S., Fan, J., Park, J. O., Wellen, K. E., and Rabinowitz, J. D., Malic enzyme tracers reveal hypoxia-induced switch in adipocyte NADPH pathway usage., Nat Chem Biol, vol. 12, no. 5, pp. 345-52, 2016.
W. Lu, Clasquin, M. F., Melamud, E., Amador-Noguez, D., Caudy, A. A., and Rabinowitz, J. D., Metabolomic analysis via reversed-phase ion-pairing liquid chromatography coupled to a stand alone orbitrap mass spectrometer., Anal Chem, vol. 82, no. 8, pp. 3212-21, 2010.
W. Lu, Su, X., Klein, M. S., Lewis, I. A., Fiehn, O., and Rabinowitz, J. D., Metabolite Measurement: Pitfalls to Avoid and Practices to Follow., Annu Rev Biochem, vol. 86, pp. 277-304, 2017.
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F. Markowetz, Mulder, K. W., Airoldi, E. M., Lemischka, I. R., and Troyanskaya, O. G., Mapping dynamic histone acetylation patterns to gene expression in nanog-depleted murine embryonic stem cells., PLoS Comput Biol, vol. 6, no. 12, p. e1001034, 2010.
E. Melamud, Vastag, L., and Rabinowitz, J. D., Metabolomic analysis and visualization engine for LC-MS data., Anal Chem, vol. 82, no. 23, pp. 9818-26, 2010.
J. H. Millonig, Emerson, J. A., Levorse, J. M., and Tilghman, S. M., Molecular analysis of the distal enhancer of the mouse alpha-fetoprotein gene., Mol Cell Biol, vol. 15, no. 7, pp. 3848-56, 1995.
P. S. Minhas, Liu, L., Moon, P. K., Joshi, A. U., Dove, C., Mhatre, S., Contrepois, K., Wang, Q., Lee, B. A., Coronado, M., Bernstein, D., Snyder, M. P., Migaud, M., Majeti, R., Mochly-Rosen, D., Rabinowitz, J. D., and Andreasson, K. I., Macrophage de novo NAD synthesis specifies immune function in aging and inflammation., Nat Immunol, vol. 20, no. 1, pp. 50-63, 2019.
J. G. Moloughney, Kim, P. K., Vega-Cotto, N. M., Wu, C. - C., Zhang, S., Adlam, M., Lynch, T., Chou, P. - C., Rabinowitz, J. D., Werlen, G., and Jacinto, E., mTORC2 Responds to Glutamine Catabolite Levels to Modulate the Hexosamine Biosynthesis Enzyme GFAT1., Mol Cell, vol. 63, no. 5, pp. 811-26, 2016.
T. Mora, Walczak, A. M., Bialek, W., and Callan, C. G., Maximum entropy models for antibody diversity., Proc Natl Acad Sci U S A, vol. 107, no. 12, pp. 5405-10, 2010.
T. Mora, Yu, H., and Wingreen, N. S., Modeling torque versus speed, shot noise, and rotational diffusion of the bacterial flagellar motor., Phys Rev Lett, vol. 103, no. 24, p. 248102, 2009.
R. J. Morscher, Ducker, G. S., Li, S. Hsin- Jung, Mayer, J. A., Gitai, Z., Sperl, W., and Rabinowitz, J. D., Mitochondrial translation requires folate-dependent tRNA methylation., Nature, vol. 554, no. 7690, pp. 128-132, 2018.
P
J. O. Park, Rubin, S. A., Xu, Y. - F., Amador-Noguez, D., Fan, J., Shlomi, T., and Rabinowitz, J. D., Metabolite concentrations, fluxes and free energies imply efficient enzyme usage., Nat Chem Biol, 2016.
M. Peifer and Wieschaus, E., Mutations in the Drosophila gene extradenticle affect the way specific homeo domain proteins regulate segmental identity., Genes Dev, vol. 4, no. 7, pp. 1209-23, 1990.
M. W. Perry, Boettiger, A. N., and Levine, M., Multiple enhancers ensure precision of gap gene-expression patterns in the Drosophila embryo., Proc Natl Acad Sci U S A, vol. 108, no. 33, pp. 13570-5, 2011.
M. D. Petkova, Little, S. C., Liu, F., and Gregor, T., Maternal origins of developmental reproducibility., Curr Biol, vol. 24, no. 11, pp. 1283-8, 2014.
J. R. Pollack, Sørlie, T., Perou, C. M., Rees, C. A., Jeffrey, S. S., Lonning, P. E., Tibshirani, R., Botstein, D., Børresen-Dale, A. - L., and Brown, P. O., Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors., Proc Natl Acad Sci U S A, vol. 99, no. 20, pp. 12963-8, 2002.
M. A. Postner, Miller, K. G., and Wieschaus, E. F., Maternal effect mutations of the sponge locus affect actin cytoskeletal rearrangements in Drosophila melanogaster embryos., J Cell Biol, vol. 119, no. 5, pp. 1205-18, 1992.
M. O. Press, McCoy, R. C., Hall, A. N., Akey, J. M., and Queitsch, C., Massive variation of short tandem repeats with functional consequences across strains of Arabidopsis thaliana., Genome Res, vol. 28, no. 8, pp. 1169-1178, 2018.
S
C. Sample and Shvartsman, S. Y., Multiscale modeling of diffusion in the early Drosophila embryo., Proc Natl Acad Sci U S A, vol. 107, no. 22, pp. 10092-6, 2010.
D. Sargin, Chottekalapanda, R. U., Perit, K. E., Yao, V., Chu, D., Sparks, D. W., Kalik, S., Power, S. K., Troyanskaya, O. G., Schmidt, E. F., Greengard, P., and Lambe, E. K., Mapping the physiological and molecular markers of stress and SSRI antidepressant treatment in S100a10 corticostriatal neurons., Mol Psychiatry, 2019.
E. Segal, Shapira, M., Regev, iv, A., Pe'er, D., Botstein, D., Koller, D., and Friedman, N., Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data., Nat Genet, vol. 34, no. 2, pp. 166-76, 2003.
C. Shi, Runnels, A. M., and Murphy, C. T., Mating and male pheromone kill Caenorhabditis males through distinct mechanisms., Elife, vol. 6, 2017.
C. Shi and Murphy, C. T., Mating induces shrinking and death in Caenorhabditis mothers., Science, vol. 343, no. 6170, pp. 536-40, 2014.
M. K. Shin, Russell, L. B., and Tilghman, S. M., Molecular characterization of four induced alleles at the Ednrb locus., Proc Natl Acad Sci U S A, vol. 94, no. 24, pp. 13105-10, 1997.
S. Y. Shvartsman, Coppey, M., and Berezhkovskii, A. M., MAPK signaling in equations and embryos., Fly (Austin), vol. 3, no. 1, pp. 62-7, 2009.
S. Y. Shvartsman and Baker, R. E., Mathematical models of morphogen gradients and their effects on gene expression., Wiley Interdiscip Rev Dev Biol, vol. 1, no. 5, pp. 715-30, 2012.
S. Y. Shvartsman, Muratov, C. B., and Lauffenburger, D. A., Modeling and computational analysis of EGF receptor-mediated cell communication in Drosophila oogenesis., Development, vol. 129, no. 11, pp. 2577-89, 2002.
S. J. Silverman, Petti, A. A., Slavov, N., Parsons, L., Briehof, R., Thiberge, S. Y., Zenklusen, D., Gandhi, S. J., Larson, D. R., Singer, R. H., and Botstein, D., Metabolic cycling in single yeast cells from unsynchronized steady-state populations limited on glucose or phosphate., Proc Natl Acad Sci U S A, vol. 107, no. 15, pp. 6946-51, 2010.
N. Slavov, Macinskas, J., Caudy, A., and Botstein, D., Metabolic cycling without cell division cycling in respiring yeast., Proc Natl Acad Sci U S A, vol. 108, no. 47, pp. 19090-5, 2011.
E. A. Stone and Ayroles, J. F., Modulated modularity clustering as an exploratory tool for functional genomic inference., PLoS Genet, vol. 5, no. 5, p. e1000479, 2009.
X. Su, Wellen, K. E., and Rabinowitz, J. D., Metabolic control of methylation and acetylation., Curr Opin Chem Biol, vol. 30, pp. 52-60, 2016.
X. Su, Lu, W., and Rabinowitz, J. D., Metabolite Spectral Accuracy on Orbitraps., Anal Chem, vol. 89, no. 11, pp. 5940-5948, 2017.
M. Sun, Wartel, M., Cascales, E., Shaevitz, J. W., and Mignot, T., Motor-driven intracellular transport powers bacterial gliding motility., Proc Natl Acad Sci U S A, vol. 108, no. 18, pp. 7559-64, 2011.
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Y. Zhen and Andolfatto, P., Methods to detect selection on noncoding DNA., Methods Mol Biol, vol. 856, pp. 141-59, 2012.
W. - X. Zong, Rabinowitz, J. D., and White, E., Mitochondria and Cancer., Mol Cell, vol. 61, no. 5, pp. 667-76, 2016.