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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Animals
M. Tipping, Kim, Y., Kyriakakis, P., Tong, M., Shvartsman, S. Y., and Veraksa, A., “β-arrestin Kurtz inhibits MAPK and Toll signalling in Drosophila development.”, EMBO J, vol. 29, no. 19, pp. 3222-35, 2010.
A. Marie Sokac and Wieschaus, E., “Zygotically controlled F-actin establishes cortical compartments to stabilize furrows during Drosophila cellularization.”, J Cell Sci, vol. 121, no. Pt 11, pp. 1815-24, 2008.
L. Simpson and Wieschaus, E., “Zygotic activity of the nullo locus is required to stabilize the actin-myosin network during cellularization in Drosophila.”, Development, vol. 110, no. 3, pp. 851-63, 1990.
J. A. Emerson, Vacher, J., Cirillo, L. A., Tilghman, S. M., and Tyner, A. L., “The zonal expression of alpha-fetoprotein transgenes in the livers of adult mice.”, Dev Dyn, vol. 195, no. 1, pp. 55-66, 1992.
G. S. Ducker and Rabinowitz, J. D., “ZMP: a master regulator of one-carbon metabolism.”, Mol Cell, vol. 57, no. 2, pp. 203-4, 2015.
D. Botstein and Fink, G. R., “Yeast: an experimental organism for 21st Century biology.”, Genetics, vol. 189, no. 3, pp. 695-704, 2011.
L. Christiaen, Wagner, E., Shi, W., and Levine, M., “X-gal staining of electroporated sea squirt (Ciona) embryos.”, Cold Spring Harb Protoc, vol. 2009, no. 12, p. pdb.prot5346, 2009.
K. Thornton, Bachtrog, D., and Andolfatto, P., “X chromosomes and autosomes evolve at similar rates in Drosophila: no evidence for faster-X protein evolution.”, Genome Res, vol. 16, no. 4, pp. 498-504, 2006.
P. M. Ferree, Frydman, H. M., Li, J. M., Cao, J., Wieschaus, E., and Sullivan, W., “Wolbachia utilizes host microtubules and Dynein for anterior localization in the Drosophila oocyte.”, PLoS Pathog, vol. 1, no. 2, p. e14, 2005.
H. A. Müller, Samanta, R., and Wieschaus, E., “Wingless signaling in the Drosophila embryo: zygotic requirements and the role of the frizzled genes.”, Development, vol. 126, no. 3, pp. 577-86, 1999.
M. Peifer, Sweeton, D., Casey, M., and Wieschaus, E., “wingless signal and Zeste-white 3 kinase trigger opposing changes in the intracellular distribution of Armadillo.”, Development, vol. 120, no. 2, pp. 369-80, 1994.
D. Botstein, “Willing to do the math: an interview with David Botstein. Interview by Jane Gitschier.”, PLoS Genet, vol. 2, no. 5, p. e79, 2006.
L. Christiaen, Wagner, E., Shi, W., and Levine, M., “Whole-mount in situ hybridization on sea squirt (Ciona intestinalis) embryos.”, Cold Spring Harb Protoc, vol. 2009, no. 12, p. pdb.prot5348, 2009.
A. Stathopoulos and Levine, M., “Whole-genome expression profiles identify gene batteries in Drosophila.”, Dev Cell, vol. 3, no. 4, pp. 464-5, 2002.
A. Stathopoulos and Levine, M., “Whole-genome analysis of Drosophila gastrulation.”, Curr Opin Genet Dev, vol. 14, no. 5, pp. 477-84, 2004.
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.
N. S. Tolwinski, Wehrli, M., Rives, A., Erdeniz, N., DiNardo, S., and Wieschaus, E., “Wg/Wnt signal can be transmitted through arrow/LRP5,6 and Axin independently of Zw3/Gsk3beta activity.”, Dev Cell, vol. 4, no. 3, pp. 407-18, 2003.
E. Schneidman, Berry, M. J., Segev, R., and Bialek, W., “Weak pairwise correlations imply strongly correlated network states in a neural population.”, Nature, vol. 440, no. 7087, pp. 1007-12, 2006.
M. A. Gelbart, He, B., Martin, A. C., Thiberge, S. Y., Wieschaus, E. F., and Kaschube, M., “Volume conservation principle involved in cell lengthening and nucleus movement during tissue morphogenesis.”, Proc Natl Acad Sci U S A, vol. 109, no. 47, pp. 19298-303, 2012.
M. Peifer, McCrea, P. D., Green, K. J., Wieschaus, E., and Gumbiner, B. M., “The vertebrate adhesive junction proteins beta-catenin and plakoglobin and the Drosophila segment polarity gene armadillo form a multigene family with similar properties.”, J Cell Biol, vol. 118, no. 3, pp. 681-91, 1992.
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.
B. Haley, Foys, B., and Levine, M., “Vectors and parameters that enhance the efficacy of RNAi-mediated gene disruption in transgenic Drosophila.”, Proc Natl Acad Sci U S A, vol. 107, no. 25, pp. 11435-40, 2010.
J. Parsch, Novozhilov, S., Saminadin-Peter, S. S., Wong, K. M., and Andolfatto, P., “On the utility of short intron sequences as a reference for the detection of positive and negative selection in Drosophila.”, Mol Biol Evol, vol. 27, no. 6, pp. 1226-34, 2010.
U. Ober, Ayroles, J. F., Stone, E. A., Richards, S., Zhu, D., Gibbs, R. A., Stricker, C., Gianola, D., Schlather, M., Mackay, T. F. C., and Simianer, H., “Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 5, p. e1002685, 2012.
A. Ochoa, Llinás, M., and Singh, M., “Using context to improve protein domain identification.”, BMC Bioinformatics, vol. 12, p. 90, 2011.
W. J. Gehring, Wieschaus, E., and Holliger, M., “The use of 'normal' and 'transformed' gynandromorphs in mapping the primordial germ cells and the gonadal mesoderm in Drosophila.”, J Embryol Exp Morphol, vol. 35, no. 3, pp. 607-16, 1976.
W. Shi, Levine, M., and Davidson, B., “Unraveling genomic regulatory networks in the simple chordate, Ciona intestinalis.”, Genome Res, vol. 15, no. 12, pp. 1668-74, 2005.
S. De Renzis, Elemento, O., Tavazoie, S., and Wieschaus, E. F., “Unmasking activation of the zygotic genome using chromosomal deletions in the Drosophila embryo.”, PLoS Biol, vol. 5, no. 5, p. e117, 2007.
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.
J. J. Zartman and Shvartsman, S. Y., “Unit operations of tissue development: epithelial folding.”, Annu Rev Chem Biomol Eng, vol. 1, pp. 231-46, 2010.
B. Davidson, Shi, W., and Levine, M., “Uncoupling heart cell specification and migration in the simple chordate Ciona intestinalis.”, Development, vol. 132, no. 21, pp. 4811-8, 2005.
J. D. Rabinowitz, Lloyd, P. M., Munzar, P., Myers, D. J., Cross, S., Damani, R., Quintana, R., Spyker, D. A., Soni, P., and Cassella, J. V., “Ultra-fast absorption of amorphous pure drug aerosols via deep lung inhalation.”, J Pharm Sci, vol. 95, no. 11, pp. 2438-51, 2006.
H. Yoo-Warren, Pachnis, V., Ingram, R. S., and Tilghman, S. M., “Two regulatory domains flank the mouse H19 gene.”, Mol Cell Biol, vol. 8, no. 11, pp. 4707-15, 1988.
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.
T. J. Vasicek, Zeng, L., Guan, X. J., Zhang, T., Costantini, F., and Tilghman, S. M., “Two dominant mutations in the mouse fused gene are the result of transposon insertions.”, Genetics, vol. 147, no. 2, pp. 777-86, 1997.
V. Sourjik and Wingreen, N. S., “Turning to the cold.”, Nat Cell Biol, vol. 9, no. 9, pp. 1029-31, 2007.
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.
L. Christiaen, Davidson, B., Kawashima, T., Powell, W., Nolla, H., Vranizan, K., and Levine, M., “The transcription/migration interface in heart precursors of Ciona intestinalis.”, Science, vol. 320, no. 5881, pp. 1349-52, 2008.
V. S. Chopra, Kong, N., and Levine, M., “Transcriptional repression via antilooping in the Drosophila embryo.”, Proc Natl Acad Sci U S A, vol. 109, no. 24, pp. 9460-4, 2012.
A. C. Edwards, Ayroles, J. F., Stone, E. A., Carbone, M. Anna, Lyman, R. F., and Mackay, T. F. C., “A transcriptional network associated with natural variation in Drosophila aggressive behavior.”, Genome Biol, vol. 10, no. 7, p. R76, 2009.
A. Fuchs, Cheung, L. S., Charbonnier, E., Shvartsman, S. Y., and Pyrowolakis, G., “Transcriptional interpretation of the EGF receptor signaling gradient.”, Proc Natl Acad Sci U S A, vol. 109, no. 5, pp. 1572-7, 2012.
M. Levine and Tjian, R., “Transcription regulation and animal diversity.”, Nature, vol. 424, no. 6945, pp. 147-51, 2003.
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. H. Feuerman, Godbout, R., Ingram, R. S., and Tilghman, S. M., “Tissue-specific transcription of the mouse alpha-fetoprotein gene promoter is dependent on HNF-1.”, Mol Cell Biol, vol. 9, no. 10, pp. 4204-12, 1989.
Y. Guan, Gorenshteyn, D., Burmeister, M., Wong, A. K., Schimenti, J. C., Handel, M. Ann, Bult, C. J., Hibbs, M. A., and Troyanskaya, O. G., “Tissue-specific functional networks for prioritizing phenotype and disease genes.”, PLoS Comput Biol, vol. 8, no. 9, p. e1002694, 2012.
C. T. Murphy, Lee, S. - J., and Kenyon, C., “Tissue entrainment by feedback regulation of insulin gene expression in the endoderm of Caenorhabditis elegans.”, Proc Natl Acad Sci U S A, vol. 104, no. 48, pp. 19046-50, 2007.
L. C. Osborne, Hohl, S. S., Bialek, W., and Lisberger, S. G., “Time course of precision in smooth-pursuit eye movements of monkeys.”, J Neurosci, vol. 27, no. 11, pp. 2987-98, 2007.
L. C. Osborne, Bialek, W., and Lisberger, S. G., “Time course of information about motion direction in visual area MT of macaque monkeys.”, J Neurosci, vol. 24, no. 13, pp. 3210-22, 2004.
M. Osterfield, Du, X. X., Schüpbach, T., Wieschaus, E., and Shvartsman, S. Y., “Three-dimensional epithelial morphogenesis in the developing Drosophila egg.”, Dev Cell, vol. 24, no. 4, pp. 400-10, 2013.
S. Luo, Kleemann, G. A., Ashraf, J. M., Shaw, W. M., and Murphy, C. T., “TGF-β and insulin signaling regulate reproductive aging via oocyte and germline quality maintenance.”, Cell, vol. 143, no. 2, pp. 299-312, 2010.
S. Luo, Shaw, W. M., Ashraf, J., and Murphy, C. T., “TGF-beta Sma/Mab signaling mutations uncouple reproductive aging from somatic aging.”, PLoS Genet, vol. 5, no. 12, p. e1000789, 2009.
J. D. Wall, Andolfatto, P., and Przeworski, M., “Testing models of selection and demography in Drosophila simulans.”, Genetics, vol. 162, no. 1, pp. 203-16, 2002.
A. C. Martin and Wieschaus, E. F., “Tensions divide.”, Nat Cell Biol, vol. 12, no. 1, pp. 5-7, 2010.
M. K. Shin, Levorse, J. M., Ingram, R. S., and Tilghman, S. M., “The temporal requirement for endothelin receptor-B signalling during neural crest development.”, Nature, vol. 402, no. 6761, pp. 496-501, 1999.
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.
A. Di Gregorio, Harland, R. M., Levine, M., and Casey, E. Silva, “Tail morphogenesis in the ascidian, Ciona intestinalis, requires cooperation between notochord and muscle.”, Dev Biol, vol. 244, no. 2, pp. 385-95, 2002.
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A., “T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”, PLoS Biol, vol. 1, no. 2, p. E53, 2003.
J. Munger, Bennett, B. D., Parikh, A., Feng, X. - J., McArdle, J., Rabitz, H. A., Shenk, T., and Rabinowitz, J. D., “Systems-level metabolic flux profiling identifies fatty acid synthesis as a target for antiviral therapy.”, Nat Biotechnol, vol. 26, no. 10, pp. 1179-86, 2008.
R. Lu, Markowetz, F., Unwin, R. D., Leek, J. T., Airoldi, E. M., MacArthur, B. D., Lachmann, A., Rozov, R., Ma'ayan, A., Boyer, L. A., Troyanskaya, O. G., Whetton, A. D., and Lemischka, I. R., “Systems-level dynamic analyses of fate change in murine embryonic stem cells.”, Nature, vol. 462, no. 7271, pp. 358-62, 2009.
J. F. Ayroles, Carbone, M. Anna, Stone, E. A., Jordan, K. W., Lyman, R. F., Magwire, M. M., Rollmann, S. M., Duncan, L. H., Lawrence, F., Anholt, R. R. H., and Mackay, T. F. C., “Systems genetics of complex traits in Drosophila melanogaster.”, Nat Genet, vol. 41, no. 3, pp. 299-307, 2009.
P. Jumbo-Lucioni, Ayroles, J. F., Chambers, M. Moses, Jordan, K. W., Leips, J., Mackay, T. Fc, and De Luca, M., “Systems genetics analysis of body weight and energy metabolism traits in Drosophila melanogaster.”, BMC Genomics, vol. 11, p. 297, 2010.
S. R McIsaac, Oakes, B. L., Wang, X., Dummit, K. A., Botstein, D., and Noyes, M. B., “Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast.”, Nucleic Acids Res, vol. 41, no. 4, p. e57, 2013.
J. A. Drocco, Wieschaus, E. F., and Tank, D. W., “The synthesis-diffusion-degradation model explains Bicoid gradient formation in unfertilized eggs.”, Phys Biol, vol. 9, no. 5, p. 055004, 2012.
E. Schneidman, Bialek, W., and Berry, M. J., “Synergy, redundancy, and independence in population codes.”, J Neurosci, vol. 23, no. 37, pp. 11539-53, 2003.
E. Schneidman, Puchalla, J. L., Segev, R., Harris, R. A., Bialek, W., and Berry, M. J., “Synergy from silence in a combinatorial neural code.”, J Neurosci, vol. 31, no. 44, pp. 15732-41, 2011.
A. N. Boettiger and Levine, M., “Synchronous and stochastic patterns of gene activation in the Drosophila embryo.”, Science, vol. 325, no. 5939, pp. 471-3, 2009.
J. W. Shaevitz, “Super-resolution for a 3D world.”, Nat Methods, vol. 5, no. 6, pp. 471-2, 2008.
Y. Kim, Paroush, Z. 'ev, Nairz, K., Hafen, E., Jiménez, G., and Shvartsman, S. Y., “Substrate-dependent control of MAPK phosphorylation in vivo.”, Mol Syst Biol, vol. 7, p. 467, 2011.
V. Pachnis, Brannan, C. I., and Tilghman, S. M., “The structure and expression of a novel gene activated in early mouse embryogenesis.”, EMBO J, vol. 7, no. 3, pp. 673-81, 1988.
K. Pfeifer, Leighton, P. A., and Tilghman, S. M., “The structural H19 gene is required for transgene imprinting.”, Proc Natl Acad Sci U S A, vol. 93, no. 24, pp. 13876-83, 1996.
L. Batsilas, Berezhkovskii, A. M., and Shvartsman, S. Y., “Stochastic model of autocrine and paracrine signals in cell culture assays.”, Biophys J, vol. 85, no. 6, pp. 3659-65, 2003.
N. Brenner, Agam, O., Bialek, W., and van Steveninck, Rde Ruyter, “Statistical properties of spike trains: universal and stimulus-dependent aspects.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 66, no. 3 Pt 1, p. 031907, 2002.
W. Bialek, Cavagna, A., Giardina, I., Mora, T., Silvestri, E., Viale, M., and Walczak, A. M., “Statistical mechanics for natural flocks of birds.”, Proc Natl Acad Sci U S A, vol. 109, no. 13, pp. 4786-91, 2012.
J. Gollub, Ball, C. A., Binkley, G., Demeter, J., Finkelstein, D. B., Hebert, J. M., Hernandez-Boussard, T., Jin, H., Kaloper, M., Matese, J. C., Schroeder, M., Brown, P. O., Botstein, D., and Sherlock, G., “The Stanford Microarray Database: data access and quality assessment tools.”, Nucleic Acids Res, vol. 31, no. 1, pp. 94-6, 2003.
V. S. Chopra, Cande, J., Hong, J. - W., and Levine, M., “Stalled Hox promoters as chromosomal boundaries.”, Genes Dev, vol. 23, no. 13, pp. 1505-9, 2009.
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.
J. H. Thomas and Wieschaus, E., “src64 and tec29 are required for microfilament contraction during Drosophila cellularization.”, Development, vol. 131, no. 4, pp. 863-71, 2004.
L. Christiaen, Stolfi, A., Davidson, B., and Levine, M., “Spatio-temporal intersection of Lhx3 and Tbx6 defines the cardiac field through synergistic activation of Mesp.”, Dev Biol, vol. 328, no. 2, pp. 552-60, 2009.
F. Biemar, Zinzen, R., Ronshaugen, M., Sementchenko, V., J Manak, R., and Levine, M. S., “Spatial regulation of microRNA gene expression in the Drosophila embryo.”, Proc Natl Acad Sci U S A, vol. 102, no. 44, pp. 15907-11, 2005.
J. Lembong, Yakoby, N., and Shvartsman, S. Y., “Spatial regulation of BMP signaling by patterned receptor expression.”, Tissue Eng Part A, vol. 14, no. 9, pp. 1469-77, 2008.
B. Riggleman, Schedl, P., and Wieschaus, E., “Spatial expression of the Drosophila segment polarity gene armadillo is posttranscriptionally regulated by wingless.”, Cell, vol. 63, no. 3, pp. 549-60, 1990.
M. Diehn, Sherlock, G., Binkley, G., Jin, H., Matese, J. C., Hernandez-Boussard, T., Rees, C. A., J Cherry, M., Botstein, D., Brown, P. O., and Alizadeh, A. A., “SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data.”, Nucleic Acids Res, vol. 31, no. 1, pp. 219-23, 2003.
H. M. Frydman, Li, J. M., Robson, D. N., and Wieschaus, E., “Somatic stem cell niche tropism in Wolbachia.”, Nature, vol. 441, no. 7092, pp. 509-12, 2006.
W. Bialek, Cavagna, A., Giardina, I., Mora, T., Pohl, O., Silvestri, E., Viale, M., and Walczak, A. M., “Social interactions dominate speed control in poising natural flocks near criticality.”, Proc Natl Acad Sci U S A, vol. 111, no. 20, pp. 7212-7, 2014.
J. Cowden and Levine, M., “The Snail repressor positions Notch signaling in the Drosophila embryo.”, Development, vol. 129, no. 7, pp. 1785-93, 2002.
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.
M. J. Rosenbluth, Crow, A., Shaevitz, J. W., and Fletcher, D. A., “Slow stress propagation in adherent cells.”, Biophys J, vol. 95, no. 12, pp. 6052-9, 2008.
T. Lecuit, Samanta, R., and Wieschaus, E., “slam encodes a developmental regulator of polarized membrane growth during cleavage of the Drosophila embryo.”, Dev Cell, vol. 2, no. 4, pp. 425-36, 2002.
S. M. Tilghman, “The sins of the fathers and mothers: genomic imprinting in mammalian development.”, Cell, vol. 96, no. 2, pp. 185-93, 1999.
B. Haley, Hendrix, D., Trang, V., and Levine, M., “A simplified miRNA-based gene silencing method for Drosophila melanogaster.”, Dev Biol, vol. 321, no. 2, pp. 482-90, 2008.
Y. Pritykin and Singh, M., “Simple topological features reflect dynamics and modularity in protein interaction networks.”, PLoS Comput Biol, vol. 9, no. 10, p. e1003243, 2013.
A. M. Berezhkovskii, Coppey, M., and Shvartsman, S. Y., “Signaling gradients in cascades of two-state reaction-diffusion systems.”, Proc Natl Acad Sci U S A, vol. 106, no. 4, pp. 1087-92, 2009.
A. Bejsovec and Wieschaus, E., “Signaling activities of the Drosophila wingless gene are separately mutable and appear to be transduced at the cell surface.”, Genetics, vol. 139, no. 1, pp. 309-20, 1995.
S. Di Talia and Wieschaus, E. F., “Short-term integration of Cdc25 dynamics controls mitotic entry during Drosophila gastrulation.”, Dev Cell, vol. 22, no. 4, pp. 763-74, 2012.
S. B. Zusman, Sweeton, D., and Wieschaus, E. F., “short gastrulation, a mutation causing delays in stage-specific cell shape changes during gastrulation in Drosophila melanogaster.”, Dev Biol, vol. 129, no. 2, pp. 417-27, 1988.
S. Y. Shvartsman, “Shooting from the hip: spatial control of signal release by intracellular waves.”, Proc Natl Acad Sci U S A, vol. 99, no. 14, pp. 9087-9, 2002.
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.
M. W. Perry, Boettiger, A. N., Bothma, J. P., and Levine, M., “Shadow enhancers foster robustness of Drosophila gastrulation.”, Curr Biol, vol. 20, no. 17, pp. 1562-7, 2010.
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.
J. L. Marsh and Wieschaus, E., “Is sex determination in germ line and soma controlled by separate genetic mechanisms?”, Nature, vol. 272, no. 5650, pp. 249-51, 1978.
L. C. Osborne, Lisberger, S. G., and Bialek, W., “A sensory source for motor variation.”, Nature, vol. 437, no. 7057, pp. 412-6, 2005.
D. Bachtrog and Andolfatto, P., “Selection, recombination and demographic history in Drosophila miranda.”, Genetics, vol. 174, no. 4, pp. 2045-59, 2006.
K. A. Hughes, Ayroles, J. F., Reedy, M. M., Drnevich, J. M., Rowe, K. C., Ruedi, E. A., Cáceres, C. E., and Paige, K. N., “Segregating variation in the transcriptome: cis regulation and additivity of effects.”, Genetics, vol. 173, no. 3, pp. 1347-55, 2006.
A. Bejsovec and Wieschaus, E., “Segment polarity gene interactions modulate epidermal patterning in Drosophila embryos.”, Development, vol. 119, no. 2, pp. 501-17, 1993.
M. Peifer, Rauskolb, C., Williams, M., Riggleman, B., and Wieschaus, E., “The segment polarity gene armadillo interacts with the wingless signaling pathway in both embryonic and adult pattern formation.”, Development, vol. 111, no. 4, pp. 1029-43, 1991.
M. Peifer and Wieschaus, E., “The segment polarity gene armadillo encodes a functionally modular protein that is the Drosophila homolog of human plakoglobin.”, Cell, vol. 63, no. 6, pp. 1167-76, 1990.
T. T. Hu, Eisen, M. B., Thornton, K. R., and Andolfatto, P., “A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence.”, Genome Res, vol. 23, no. 1, pp. 89-98, 2013.
G. J. Stephens, Osborne, L. C., and Bialek, W., “Searching for simplicity in the analysis of neurons and behavior.”, Proc Natl Acad Sci U S A, vol. 108 Suppl 3, pp. 15565-71, 2011.
G. Tkačik, Marre, O., Amodei, D., Schneidman, E., Bialek, W., and Berry, M. J., “Searching for collective behavior in a large network of sensory neurons.”, PLoS Comput Biol, vol. 10, no. 1, p. e1003408, 2014.
C. T. Murphy, “The search for DAF-16/FOXO transcriptional targets: approaches and discoveries.”, Exp Gerontol, vol. 41, no. 10, pp. 910-21, 2006.
L. Christiaen, Wagner, E., Shi, W., and Levine, M., “The sea squirt Ciona intestinalis.”, Cold Spring Harb Protoc, vol. 2009, no. 12, p. pdb.emo138, 2009.
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