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 Animals  [Clear All Filters]
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A
M. L. Aardema, Zhen, Y., and Andolfatto, P., “The evolution of cardenolide-resistant forms of Na⁺,K⁺ -ATPase in Danainae butterflies.”, Mol Ecol, vol. 21, no. 2, pp. 340-9, 2012.
P. Barron Abitua, Wagner, E., Navarrete, I. A., and Levine, M., “Identification of a rudimentary neural crest in a non-vertebrate chordate.”, Nature, vol. 492, no. 7427, pp. 104-7, 2012.
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.
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.
T. L. Adelman, Bialek, W., and Olberg, R. M., “The information content of receptive fields.”, Neuron, vol. 40, no. 4, pp. 823-33, 2003.
Y. Ahmed, Hayashi, S., Levine, A., and Wieschaus, E., “Regulation of armadillo by a Drosophila APC inhibits neuronal apoptosis during retinal development.”, Cell, vol. 93, no. 7, pp. 1171-82, 1998.
Y. Ahmed, Nouri, A., and Wieschaus, E., “Drosophila Apc1 and Apc2 regulate Wingless transduction throughout development.”, Development, vol. 129, no. 7, pp. 1751-62, 2002.
P. Andolfatto, Davison, D., Erezyilmaz, D., Hu, T. T., Mast, J., Sunayama-Morita, T., and Stern, D. L., “Multiplexed shotgun genotyping for rapid and efficient genetic mapping.”, Genome Res, vol. 21, no. 4, pp. 610-7, 2011.
P. Andolfatto, “Adaptive evolution of non-coding DNA in Drosophila.”, Nature, vol. 437, no. 7062, pp. 1149-52, 2005.
P. Andolfatto, “Controlling type-I error of the McDonald-Kreitman test in genomewide scans for selection on noncoding DNA.”, Genetics, vol. 180, no. 3, pp. 1767-71, 2008.
P. Andolfatto, Wong, K. M., and Bachtrog, D., “Effective population size and the efficacy of selection on the X chromosomes of two closely related Drosophila species.”, Genome Biol Evol, vol. 3, pp. 114-28, 2011.
P. Andolfatto and Wall, J. D., “Linkage disequilibrium patterns across a recombination gradient in African Drosophila melanogaster.”, Genetics, vol. 165, no. 3, pp. 1289-305, 2003.
P. Andolfatto, “Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome.”, Genome Res, vol. 17, no. 12, pp. 1755-62, 2007.
P. Andolfatto, J Scriber, M., and Charlesworth, B., “No association between mitochondrial DNA haplotypes and a female-limited mimicry phenotype in Papilio glaucus.”, Evolution, vol. 57, no. 2, pp. 305-16, 2003.
P. Armand, Knapp, A. C., Hirsch, A. J., Wieschaus, E. F., and Cole, M. D., “A novel basic helix-loop-helix protein is expressed in muscle attachment sites of the Drosophila epidermis.”, Mol Cell Biol, vol. 14, no. 6, pp. 4145-54, 1994.
J. F. Ayroles and Gibson, G., “Analysis of variance of microarray data.”, Methods Enzymol, vol. 411, pp. 214-33, 2006.
J. F. Ayroles, Hughes, K. A., Rowe, K. C., Reedy, M. M., Rodriguez-Zas, S. L., Drnevich, J. M., Cáceres, C. E., and Paige, K. N., “A genomewide assessment of inbreeding depression: gene number, function, and mode of action.”, Conserv Biol, vol. 23, no. 4, pp. 920-30, 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.
J. F. Ayroles, Laflamme, B. A., Stone, E. A., Wolfner, M. F., and Mackay, T. F. C., “Functional genome annotation of Drosophila seminal fluid proteins using transcriptional genetic networks.”, Genet Res (Camb), vol. 93, no. 6, pp. 387-95, 2011.
B
D. Bachtrog, Thornton, K., Clark, A., and Andolfatto, P., “Extensive introgression of mitochondrial DNA relative to nuclear genes in the Drosophila yakuba species group.”, Evolution, vol. 60, no. 2, pp. 292-302, 2006.
D. Bachtrog and Andolfatto, P., “Selection, recombination and demographic history in Drosophila miranda.”, Genetics, vol. 174, no. 4, pp. 2045-59, 2006.
E. Bae, Calhoun, V. C., Levine, M., Lewis, E. B., and Drewell, R. A., “Characterization of the intergenic RNA profile at abdominal-A and Abdominal-B in the Drosophila bithorax complex.”, Proc Natl Acad Sci U S A, vol. 99, no. 26, pp. 16847-52, 2002.
W. Bailis, Shyer, J. A., Zhao, J., Canaveras, J. Carlos Gar, Khazal, F. J. Al, Qu, R., Steach, H. R., Bielecki, P., Khan, O., Jackson, R., Kluger, Y., Maher, L. J., Rabinowitz, J., Craft, J., and Flavell, R. A., “Distinct modes of mitochondrial metabolism uncouple T cell differentiation and function.”, Nature, vol. 571, no. 7765, pp. 403-407, 2019.
E. Banks, Nabieva, E., Chazelle, B., and Singh, M., “Organization of physical interactomes as uncovered by network schemas.”, PLoS Comput Biol, vol. 4, no. 10, p. e1000203, 2008.
E. Banks, Nabieva, E., Peterson, R., and Singh, M., “NetGrep: fast network schema searches in interactomes.”, Genome Biol, vol. 9, no. 9, p. R138, 2008.
T. M. Bartlett, Bratton, B. P., Duvshani, A., Miguel, A., Sheng, Y., Martin, N. R., Nguyen, J. P., Persat, A., Desmarais, S. M., VanNieuwenhze, M. S., Huang, K. Casey, Zhu, J., Shaevitz, J. W., and Gitai, Z., “A Periplasmic Polymer Curves Vibrio cholerae and Promotes Pathogenesis.”, Cell, vol. 168, no. 1-2, pp. 172-185.e15, 2017.
M. S. Bartolomei, Zemel, S., and Tilghman, S. M., “Parental imprinting of the mouse H19 gene.”, Nature, vol. 351, no. 6322, pp. 153-5, 1991.
M. S. Bartolomei, Webber, A. L., Brunkow, M. E., and Tilghman, S. M., “Epigenetic mechanisms underlying the imprinting of the mouse H19 gene.”, Genes Dev, vol. 7, no. 9, pp. 1663-73, 1993.
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.
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.
A. Bejsovec and Wieschaus, E., “Segment polarity gene interactions modulate epidermal patterning in Drosophila embryos.”, Development, vol. 119, no. 2, pp. 501-17, 1993.
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.
K. K. Benson, Hu, W., Weller, A. H., Bennett, A. H., Chen, E. R., Khetarpal, S. A., Yoshino, S., Bone, W. P., Wang, L., Rabinowitz, J. D., Voight, B. F., and Soccio, R. E., “Natural human genetic variation determines basal and inducible expression of , an obesity-associated gene.”, Proc Natl Acad Sci U S A, vol. 116, no. 46, pp. 23232-23242, 2019.
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. M. Berezhkovskii, Batsilas, L., and Shvartsman, S. Y., “Ligand trapping in epithelial layers and cell cultures.”, Biophys Chem, vol. 107, no. 3, pp. 221-7, 2004.
A. M. Berezhkovskii and Shvartsman, S. Y., “Kinetics of receptor occupancy during morphogen gradient formation.”, J Chem Phys, vol. 138, no. 24, p. 244105, 2013.
A. M. Berezhkovskii and Shvartsman, S. Y., “On the GFP-based analysis of dynamic concentration profiles.”, Biophys J, vol. 106, no. 3, pp. L13-5, 2014.
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.
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.
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.
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.
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. 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.
S. M. Block, Asbury, C. L., Shaevitz, J. W., and Lang, M. J., “Probing the kinesin reaction cycle with a 2D optical force clamp.”, Proc Natl Acad Sci U S A, vol. 100, no. 5, pp. 2351-6, 2003.
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. P. Bothma, Levine, M., and Boettiger, A., “Morphogen gradients: limits to signaling or limits to measurement?”, Curr Biol, vol. 20, no. 5, pp. R232-4, 2010.
J. P. Bothma, Garcia, H. G., Ng, S., Perry, M. W., Gregor, T., and Levine, M., “Enhancer additivity and non-additivity are determined by enhancer strength in the Drosophila embryo.”, Elife, vol. 4, 2015.
J. P. Bothma, Garcia, H. G., Esposito, E., Schlissel, G., Gregor, T., and Levine, M., “Dynamic regulation of eve stripe 2 expression reveals transcriptional bursts in living Drosophila embryos.”, Proc Natl Acad Sci U S A, vol. 111, no. 29, pp. 10598-603, 2014.
J. Bothma and Levine, M., “Development: lights, camera, action--the Drosophila embryo goes live!”, Curr Biol, vol. 23, no. 21, pp. R965-7, 2013.
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.
D. Botstein, “Genome-sequencing anniversary. Fruits of genome sequences for biology.”, Science, vol. 331, no. 6020, p. 1025, 2011.
D. Botstein and Fink, G. R., “Yeast: an experimental organism for 21st Century biology.”, Genetics, vol. 189, no. 3, pp. 695-704, 2011.
D. Botstein, “Lasker∼Koshland to genetics pioneer.”, Cell, vol. 158, no. 6, pp. 1230-2, 2014.
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.
A. B. Bowman, Levorse, J. M., Ingram, R. S., and Tilghman, S. M., “Functional characterization of a testis-specific DNA binding activity at the H19/Igf2 imprinting control region.”, Mol Cell Biol, vol. 23, no. 22, pp. 8345-51, 2003.
C. I. Brannan, Dees, E. C., Ingram, R. S., and Tilghman, S. M., “The product of the H19 gene may function as an RNA.”, Mol Cell Biol, vol. 10, no. 1, pp. 28-36, 1990.
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.
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.
M. E. Brunkow and Tilghman, S. M., “Ectopic expression of the H19 gene in mice causes prenatal lethality.”, Genes Dev, vol. 5, no. 6, pp. 1092-101, 1991.
D. T. Burke, Rossi, J. M., Leung, J., Koos, D. S., and Tilghman, S. M., “A mouse genomic library of yeast artificial chromosome clones.”, Mamm Genome, vol. 1, no. 1, p. 65, 1991.
C
V. C. Calhoun, Stathopoulos, A., and Levine, M., “Promoter-proximal tethering elements regulate enhancer-promoter specificity in the Drosophila Antennapedia complex.”, Proc Natl Acad Sci U S A, vol. 99, no. 14, pp. 9243-7, 2002.
V. C. Calhoun and Levine, M., “Coordinate regulation of an extended chromosome domain.”, Cell, vol. 113, no. 3, pp. 278-80, 2003.
V. C. Calhoun and Levine, M., “Long-range enhancer-promoter interactions in the Scr-Antp interval of the Drosophila Antennapedia complex.”, Proc Natl Acad Sci U S A, vol. 100, no. 17, pp. 9878-83, 2003.
B. Callahan, Neher, R. A., Bachtrog, D., Andolfatto, P., and Shraiman, B. I., “Correlated evolution of nearby residues in Drosophilid proteins.”, PLoS Genet, vol. 7, no. 2, p. e1001315, 2011.
S. A. Camper and Tilghman, S. M., “Postnatal repression of the alpha-fetoprotein gene is enhancer independent.”, Genes Dev, vol. 3, no. 4, pp. 537-46, 1989.
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.
J. Doran Cande, Chopra, V. S., and Levine, M., “Evolving enhancer-promoter interactions within the tinman complex of the flour beetle, Tribolium castaneum.”, Development, vol. 136, no. 18, pp. 3153-60, 2009.
J. Cande, Andolfatto, P., Prud'homme, B., Stern, D. L., and Gompel, N., “Evolution of multiple additive loci caused divergence between Drosophila yakuba and D. santomea in wing rowing during male courtship.”, PLoS One, vol. 7, no. 8, p. e43888, 2012.
C. Cao, Lemaire, L. A., Wang, W., Yoon, P. H., Choi, Y. A., Parsons, L. R., Matese, J. C., Wang, W., Levine, M., and Chen, K., “Comprehensive single-cell transcriptome lineages of a proto-vertebrate.”, Nature, vol. 571, no. 7765, pp. 349-354, 2019.
M. Anna Carbone, Ayroles, J. F., Yamamoto, A., Morozova, T. V., West, S. A., Magwire, M. M., Mackay, T. F. C., and Anholt, R. R. H., “Overexpression of myocilin in the Drosophila eye activates the unfolded protein response: implications for glaucoma.”, PLoS One, vol. 4, no. 1, p. e4216, 2009.
T. Caspary, Cleary, M. A., Baker, C. C., Guan, X. J., and Tilghman, S. M., “Multiple mechanisms regulate imprinting of the mouse distal chromosome 7 gene cluster.”, Mol Cell Biol, vol. 18, no. 6, pp. 3466-74, 1998.
T. Caspary, Cleary, M. A., Perlman, E. J., Zhang, P., Elledge, S. J., and Tilghman, S. M., “Oppositely imprinted genes p57(Kip2) and igf2 interact in a mouse model for Beckwith-Wiedemann syndrome.”, Genes Dev, vol. 13, no. 23, pp. 3115-24, 1999.
L. S. Cheung, Schüpbach, T., and Shvartsman, S. Y., “Pattern formation by receptor tyrosine kinases: analysis of the Gurken gradient in Drosophila oogenesis.”, Curr Opin Genet Dev, vol. 21, no. 6, pp. 719-25, 2011.
L. S. Cheung, Simakov, D. S. A., Fuchs, A., Pyrowolakis, G., and Shvartsman, S. Y., “Dynamic model for the coordination of two enhancers of broad by EGFR signaling.”, Proc Natl Acad Sci U S A, vol. 110, no. 44, pp. 17939-44, 2013.
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.
M. D. Chikina, Huttenhower, C., Murphy, C. T., and Troyanskaya, O. G., “Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans.”, PLoS Comput Biol, vol. 5, no. 6, p. e1000417, 2009.
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.
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.
V. S. Chopra, Hendrix, D. A., Core, L. J., Tsui, C., Lis, J. T., and Levine, M., “The polycomb group mutant esc leads to augmented levels of paused Pol II in the Drosophila embryo.”, Mol Cell, vol. 42, no. 6, pp. 837-44, 2011.
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.
L. Christiaen, Wagner, E., Shi, W., and Levine, M., “Electroporation of transgenic DNAs in the sea squirt Ciona.”, Cold Spring Harb Protoc, vol. 2009, no. 12, p. pdb.prot5345, 2009.
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.
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.
L. Christiaen, Stolfi, A., and Levine, M., “BMP signaling coordinates gene expression and cell migration during precardiac mesoderm development.”, Dev Biol, vol. 340, no. 2, pp. 179-87, 2010.
L. Christiaen, Wagner, E., Shi, W., and Levine, M., “Microinjection of morpholino oligos and RNAs in sea squirt (Ciona) embryos.”, Cold Spring Harb Protoc, vol. 2009, no. 12, p. pdb.prot5347, 2009.
L. Christiaen, Wagner, E., Shi, W., and Levine, M., “Isolation of sea squirt (Ciona) gametes, fertilization, dechorionation, and development.”, Cold Spring Harb Protoc, vol. 2009, no. 12, p. pdb.prot5344, 2009.
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.
L. Christiaen, Wagner, E., Shi, W., and Levine, M., “Isolation of individual cells and tissues from electroporated sea squirt (Ciona) embryos by fluorescence-activated cell sorting (FACS).”, Cold Spring Harb Protoc, vol. 2009, no. 12, p. pdb.prot5349, 2009.
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.
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.
K. R. Christie, Weng, S., Balakrishnan, R., Costanzo, M. C., Dolinski, K., Dwight, S. S., Engel, S. R., Feierbach, B., Fisk, D. G., Hirschman, J. E., Hong, E. L., Issel-Tarver, L., Nash, R., Sethuraman, A., Starr, B., Theesfeld, C. L., Andrada, R., Binkley, G., Dong, Q., Lane, C., Schroeder, M., Botstein, D., and J Cherry, M., “Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms.”, Nucleic Acids Res, vol. 32, no. Database issue, pp. D311-4, 2004.
K. Chung, Kim, Y., Kanodia, J. S., Gong, E., Shvartsman, S. Y., and Lu, H., “A microfluidic array for large-scale ordering and orientation of embryos.”, Nat Methods, vol. 8, no. 2, pp. 171-6, 2011.
M. A. Cleary, van Raamsdonk, C. D., Levorse, J., Zheng, B., Bradley, A., and Tilghman, S. M., “Disruption of an imprinted gene cluster by a targeted chromosomal translocation in mice.”, Nat Genet, vol. 29, no. 1, pp. 78-82, 2001.
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.
R. M. Cooper, Wingreen, N. S., and Cox, E. C., “An excitable cortex and memory model successfully predicts new pseudopod dynamics.”, PLoS One, vol. 7, no. 3, p. e33528, 2012.
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. 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.
R. B. Corbett-Detig, Zhou, J., Clark, A. G., Hartl, D. L., and Ayroles, J. F., “Genetic incompatibilities are widespread within species.”, Nature, vol. 504, no. 7478, pp. 135-7, 2013.
M. Costa, Wilson, E. T., and Wieschaus, E., “A putative cell signal encoded by the folded gastrulation gene coordinates cell shape changes during Drosophila gastrulation.”, Cell, vol. 76, no. 6, pp. 1075-89, 1994.
D. E. Coulter, Swaykus, E. A., Beran-Koehn, M. A., Goldberg, D., Wieschaus, E., and Schedl, P., “Molecular analysis of odd-skipped, a zinc finger encoding segmentation gene with a novel pair-rule expression pattern.”, EMBO J, vol. 9, no. 11, pp. 3795-804, 1990.
D. E. Coulter and Wieschaus, E., “Gene activities and segmental patterning in Drosophila: analysis of odd-skipped and pair-rule double mutants.”, Genes Dev, vol. 2, no. 12B, pp. 1812-23, 1988.
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.
J. Cowden and Levine, M., “The Snail repressor positions Notch signaling in the Drosophila embryo.”, Development, vol. 129, no. 7, pp. 1785-93, 2002.
R. Cui, Schumer, M., Kruesi, K., Walter, R., Andolfatto, P., and Rosenthal, G. G., “Phylogenomics reveals extensive reticulate evolution in Xiphophorus fishes.”, Evolution, vol. 67, no. 8, pp. 2166-79, 2013.
D
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.
B. Davidson and Levine, M., “Evolutionary origins of the vertebrate heart: Specification of the cardiac lineage in Ciona intestinalis.”, Proc Natl Acad Sci U S A, vol. 100, no. 20, pp. 11469-73, 2003.
S. M. Davidson, Jonas, O., Keibler, M. A., Hou, H. Wei, Luengo, A., Mayers, J. R., Wyckoff, J., Del Rosario, A. M., Whitman, M., Chin, C. R., Condon, K. J., Lammers, A., Kellersberger, K. A., Stall, B. K., Stephanopoulos, G., Bar-Sagi, D., Han, J., Rabinowitz, J. D., Cima, M. J., Langer, R., and Heiden, M. G. Vander, “Direct evidence for cancer-cell-autonomous extracellular protein catabolism in pancreatic tumors.”, Nat Med, vol. 23, no. 2, pp. 235-241, 2017.
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