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 Body Patterning  [Clear All Filters]
Journal Article
O. Grimm and Wieschaus, E., The Bicoid gradient is shaped independently of nuclei., Development, vol. 137, no. 17, pp. 2857-62, 2010.
J. J. Zartman, Yakoby, N., Bristow, C. A., Zhou, X., Schlichting, K., Dahmann, C., and Shvartsman, S. Y., Cad74A is regulated by BR and is required for robust dorsal appendage formation in Drosophila oogenesis., Dev Biol, vol. 322, no. 2, pp. 289-301, 2008.
S. E. Cole, Levorse, J. M., Tilghman, S. M., and Vogt, T. F., Clock regulatory elements control cyclic expression of Lunatic fringe during somitogenesis., Dev Cell, vol. 3, no. 1, pp. 75-84, 2002.
M. E. Kavousanakis, Kanodia, J. S., Kim, Y., Kevrekidis, I. G., and Shvartsman, S. Y., A compartmental model for the bicoid gradient., Dev Biol, vol. 345, no. 1, pp. 12-7, 2010.
F. Biemar, Nix, D. A., Piel, J., Peterson, B., Ronshaugen, M., Sementchenko, V., Bell, I., J Manak, R., and Levine, M. S., Comprehensive identification of Drosophila dorsal-ventral patterning genes using a whole-genome tiling array., Proc Natl Acad Sci U S A, vol. 103, no. 34, pp. 12763-8, 2006.
G. T. Reeves, Kalifa, R., Klein, D. E., Lemmon, M. A., and Shvartsman, S. Y., Computational analysis of EGFR inhibition by Argos., Dev Biol, vol. 284, no. 2, pp. 523-35, 2005.
J. Cande, Goltsev, Y., and Levine, M. S., Conservation of enhancer location in divergent insects., Proc Natl Acad Sci U S A, vol. 106, no. 34, pp. 14414-9, 2009.
M. Markstein and Levine, M., Decoding cis-regulatory DNAs in the Drosophila genome., Curr Opin Genet Dev, vol. 12, no. 5, pp. 601-6, 2002.
J. Bothma and Levine, M., Development: lights, camera, action--the Drosophila embryo goes live!, Curr Biol, vol. 23, no. 21, pp. R965-7, 2013.
T. Gregor, Bialek, W., van Steveninck, R. R. de Ruyte, Tank, D. W., and Wieschaus, E. F., Diffusion and scaling during early embryonic pattern formation., Proc Natl Acad Sci U S A, vol. 102, no. 51, pp. 18403-7, 2005.
M. Pribyl, Muratov, C. B., and Shvartsman, S. Y., Discrete models of autocrine cell communication in epithelial layers., Biophys J, vol. 84, no. 6, pp. 3624-35, 2003.
A. Stathopoulos and Levine, M., Dorsal gradient networks in the Drosophila embryo., Dev Biol, vol. 246, no. 1, pp. 57-67, 2002.
S. De Renzis, Yu, J., Zinzen, R., and Wieschaus, E., Dorsal-ventral pattern of Delta trafficking is established by a Snail-Tom-Neuralized pathway., Dev Cell, vol. 10, no. 2, pp. 257-64, 2006.
N. Yakoby, Lembong, J., Schüpbach, T., and Shvartsman, S. Y., Drosophila eggshell is patterned by sequential action of feedforward and feedback loops., Development, vol. 135, no. 2, pp. 343-51, 2008.
D. Papatsenko and Levine, M. S., Dual regulation by the Hunchback gradient in the Drosophila embryo., Proc Natl Acad Sci U S A, vol. 105, no. 8, pp. 2901-6, 2008.
F. Liu, Morrison, A. H., and Gregor, T., Dynamic interpretation of maternal inputs by the Drosophila segmentation gene network., Proc Natl Acad Sci U S A, vol. 110, no. 17, pp. 6724-9, 2013.
S. Y. Shvartsman, Coppey, M., and Berezhkovskii, A. M., Dynamics of maternal morphogen gradients in Drosophila., Curr Opin Genet Dev, vol. 18, no. 4, pp. 342-7, 2008.
J. S. Kanodia, Rikhy, R., Kim, Y., Lund, V. K., DeLotto, R., Lippincott-Schwartz, J., and Shvartsman, S. Y., Dynamics of the Dorsal morphogen gradient., Proc Natl Acad Sci U S A, vol. 106, no. 51, pp. 21707-12, 2009.
D. S. A. Simakov, Cheung, L. S., Pismen, L. M., and Shvartsman, S. Y., EGFR-dependent network interactions that pattern Drosophila eggshell appendages., Development, vol. 139, no. 15, pp. 2814-20, 2012.
N. Haupaix, Abitua, P. B., Sirour, C., Yasuo, H., Levine, M., and Hudson, C., Ephrin-mediated restriction of ERK1/2 activity delimits the number of pigment cells in the Ciona CNS., Dev Biol, vol. 394, no. 1, pp. 170-80, 2014.
B. Houchmandzadeh, Wieschaus, E., and Leibler, S., Establishment of developmental precision and proportions in the early Drosophila embryo., Nature, vol. 415, no. 6873, pp. 798-802, 2002.
B. P. Berman, Nibu, Y., Pfeiffer, B. D., Tomancak, P., Celniker, S. E., Levine, M., Rubin, G. M., and Eisen, M. B., Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome., Proc Natl Acad Sci U S A, vol. 99, no. 2, pp. 757-62, 2002.
J. J. Zartman, Kanodia, J. S., Yakoby, N., Schafer, X., Watson, C., Schlichting, K., Dahmann, C., and Shvartsman, S. Y., Expression patterns of cadherin genes in Drosophila oogenesis., Gene Expr Patterns, vol. 9, no. 1, pp. 31-6, 2009.
J. J. Zartman, Kanodia, J. S., Cheung, L. S., and Shvartsman, S. Y., Feedback control of the EGFR signaling gradient: superposition of domain-splitting events in Drosophila oogenesis., Development, vol. 136, no. 17, pp. 2903-11, 2009.
E. Wagner and Levine, M., FGF signaling establishes the anterior border of the Ciona neural tube., Development, vol. 139, no. 13, pp. 2351-9, 2012.
L. Abouchar, Petkova, M. D., Steinhardt, C. R., and Gregor, T., Fly wing vein patterns have spatial reproducibility of a single cell., J R Soc Interface, vol. 11, no. 97, p. 20140443, 2014.
R. E. Dawes-Hoang, Parmar, K. M., Christiansen, A. E., Phelps, C. B., Brand, A. H., and Wieschaus, E. F., folded gastrulation, cell shape change and the control of myosin localization., Development, vol. 132, no. 18, pp. 4165-78, 2005.
S. C. Little, Tkačik, G., Kneeland, T. B., Wieschaus, E. F., and Gregor, T., The formation of the Bicoid morphogen gradient requires protein movement from anteriorly localized mRNA., PLoS Biol, vol. 9, no. 3, p. e1000596, 2011.
M. Levine and Davidson, E. H., Gene regulatory networks for development., Proc Natl Acad Sci U S A, vol. 102, no. 14, pp. 4936-42, 2005.
J. Grosshans and Wieschaus, E., A genetic link between morphogenesis and cell division during formation of the ventral furrow in Drosophila., Cell, vol. 101, no. 5, pp. 523-31, 2000.
E. Farley and Levine, M., HOT DNAs: a novel class of developmental enhancers., Genes Dev, vol. 26, no. 9, pp. 873-6, 2012.
J. - W. Hong, Hendrix, D. A., Papatsenko, D., and Levine, M. S., How the Dorsal gradient works: insights from postgenome technologies., Proc Natl Acad Sci U S A, vol. 105, no. 51, pp. 20072-6, 2008.
A. Vincent, Blankenship, J. T., and Wieschaus, E., Integration of the head and trunk segmentation systems controls cephalic furrow formation in Drosophila., Development, vol. 124, no. 19, pp. 3747-54, 1997.
B. Lim, Samper, N., Lu, H., Rushlow, C., Jiménez, G., and Shvartsman, S. Y., Kinetics of gene derepression by ERK signaling., Proc Natl Acad Sci U S A, vol. 110, no. 25, pp. 10330-5, 2013.
A. Stathopoulos and Levine, M., Linear signaling in the Toll-Dorsal pathway of Drosophila: activated Pelle kinase specifies all threshold outputs of gene expression while the bHLH protein Twist specifies a subset., Development, vol. 129, no. 14, pp. 3411-9, 2002.
P. V. Gordon, Sample, C., Berezhkovskii, A. M., Muratov, C. B., and Shvartsman, S. Y., Local kinetics of morphogen gradients., Proc Natl Acad Sci U S A, vol. 108, no. 15, pp. 6157-62, 2011.
A. Stathopoulos and Levine, M., Localized repressors delineate the neurogenic ectoderm in the early Drosophila embryo., Dev Biol, vol. 280, no. 2, pp. 482-93, 2005.
Y. Kim, Coppey, M., Grossman, R., Ajuria, L., Jiménez, G., Paroush, Z. 'ev, and Shvartsman, S. Y., MAPK substrate competition integrates patterning signals in the Drosophila embryo., Curr Biol, vol. 20, no. 5, pp. 446-51, 2010.
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.
M. Coppey, Berezhkovskii, A. M., Kim, Y., Boettiger, A. N., and Shvartsman, S. Y., Modeling the bicoid gradient: diffusion and reversible nuclear trapping of a stable protein., Dev Biol, vol. 312, no. 2, pp. 623-30, 2007.
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.
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.
A. Stolfi, Wagner, E., J Taliaferro, M., Chou, S., and Levine, M., Neural tube patterning by Ephrin, FGF and Notch signaling relays., Development, vol. 138, no. 24, pp. 5429-39, 2011.
M. Coppey, Boettiger, A. N., Berezhkovskii, A. M., and Shvartsman, S. Y., Nuclear trapping shapes the terminal gradient in the Drosophila embryo., Curr Biol, vol. 18, no. 12, pp. 915-9, 2008.
J. J. Zartman, Cheung, L. S., Niepielko, M. G., Bonini, C., Haley, B., Yakoby, N., and Shvartsman, S. Y., Pattern formation by a moving morphogen source., Phys Biol, vol. 8, no. 4, p. 045003, 2011.
J. Lembong, Yakoby, N., and Shvartsman, S. Y., Pattern formation by dynamically interacting network motifs., Proc Natl Acad Sci U S A, vol. 106, no. 9, pp. 3213-8, 2009.
J. A. Zallen and Wieschaus, E., Patterned gene expression directs bipolar planar polarity in Drosophila., Dev Cell, vol. 6, no. 3, pp. 343-55, 2004.
B. Houchmandzadeh, Wieschaus, E., and Leibler, S., Precise domain specification in the developing Drosophila embryo., Phys Rev E Stat Nonlin Soft Matter Phys, vol. 72, no. 6 Pt 1, p. 061920, 2005.
P. Barron Abitua, T Gainous, B., Kaczmarczyk, A. N., Winchell, C. J., Hudson, C., Kamata, K., Nakagawa, M., Tsuda, M., Kusakabe, T. G., and Levine, M., The pre-vertebrate origins of neurogenic placodes., Nature, vol. 524, no. 7566, pp. 462-5, 2015.
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.
A. Stathopoulos, Tam, B., Ronshaugen, M., Frasch, M., and Levine, M., pyramus and thisbe: FGF genes that pattern the mesoderm of Drosophila embryos., Genes Dev, vol. 18, no. 6, pp. 687-99, 2004.
Z. Khan, Wang, Y. - C., Wieschaus, E. F., and Kaschube, M., Quantitative 4D analyses of epithelial folding during Drosophila gastrulation., Development, vol. 141, no. 14, pp. 2895-900, 2014.
D. Papatsenko and Levine, M., Quantitative analysis of binding motifs mediating diverse spatial readouts of the Dorsal gradient in the Drosophila embryo., Proc Natl Acad Sci U S A, vol. 102, no. 14, pp. 4966-71, 2005.
H. G. Garcia, Tikhonov, M., Lin, A., and Gregor, T., Quantitative imaging of transcription in living Drosophila embryos links polymerase activity to patterning., Curr Biol, vol. 23, no. 21, pp. 2140-5, 2013.
G. T. Reeves, Muratov, C. B., Schüpbach, T., and Shvartsman, S. Y., Quantitative models of developmental pattern formation., Dev Cell, vol. 11, no. 3, pp. 289-300, 2006.
V. S. Chopra, Hong, J. - W., and Levine, M., Regulation of Hox gene activity by transcriptional elongation in Drosophila., Curr Biol, vol. 19, no. 8, pp. 688-93, 2009.
A. Helman, Lim, B., Andreu, M. José, Kim, Y., Shestkin, T., Lu, H., Jiménez, G., Shvartsman, S. Y., and Paroush, Z. 'ev, RTK signaling modulates the Dorsal gradient., Development, vol. 139, no. 16, pp. 3032-9, 2012.
J. - W. Hong, Hendrix, D. A., and Levine, M. S., Shadow enhancers as a source of evolutionary novelty., Science, vol. 321, no. 5894, p. 1314, 2008.
T. Gregor, McGregor, A. P., and Wieschaus, E. F., Shape and function of the Bicoid morphogen gradient in dipteran species with different sized embryos., Dev Biol, vol. 316, no. 2, pp. 350-8, 2008.
J. P. Bothma, Magliocco, J., and Levine, M., The snail repressor inhibits release, not elongation, of paused Pol II in the Drosophila embryo., Curr Biol, vol. 21, no. 18, pp. 1571-7, 2011.
T. Gregor, Wieschaus, E. F., McGregor, A. P., Bialek, W., and Tank, D. W., Stability and nuclear dynamics of the bicoid morphogen gradient., Cell, vol. 130, no. 1, pp. 141-52, 2007.
C. A. Rushlow and Shvartsman, S. Y., Temporal dynamics, spatial range, and transcriptional interpretation of the Dorsal morphogen gradient., Curr Opin Genet Dev, vol. 22, no. 6, pp. 542-6, 2012.
O. Grimm, Zini, V. Sanchez, Kim, Y., Casanova, J., Shvartsman, S. Y., and Wieschaus, E., Torso RTK controls Capicua degradation by changing its subcellular localization., Development, vol. 139, no. 21, pp. 3962-8, 2012.
M. Pribyl, Muratov, C. B., and Shvartsman, S. Y., Transitions in the model of epithelial patterning., Dev Dyn, vol. 226, no. 1, pp. 155-9, 2003.
J. T. Blankenship and Wieschaus, E., Two new roles for the Drosophila AP patterning system in early morphogenesis., Development, vol. 128, no. 24, pp. 5129-38, 2001.
J. Cowden and Levine, M., Ventral dominance governs sequential patterns of gene expression across the dorsal-ventral axis of the neuroectoderm in the Drosophila embryo., Dev Biol, vol. 262, no. 2, pp. 335-49, 2003.
A. Stathopoulos, Van Drenth, M., Erives, A., Markstein, M., and Levine, M., Whole-genome analysis of dorsal-ventral patterning in the Drosophila embryo., Cell, vol. 111, no. 5, pp. 687-701, 2002.