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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2011
V. Hilgers, Perry, M. W., Hendrix, D., Stark, A., Levine, M., and Haley, B., Neural-specific elongation of 3' UTRs during Drosophila development., Proc Natl Acad Sci U S A, vol. 108, no. 38, pp. 15864-9, 2011.
V. Hilgers, Perry, M. W., Hendrix, D., Stark, A., Levine, M., and Haley, B., Neural-specific elongation of 3' UTRs during Drosophila development., Proc Natl Acad Sci U S A, vol. 108, no. 38, pp. 15864-9, 2011.
V. Hilgers, Perry, M. W., Hendrix, D., Stark, A., Levine, M., and Haley, B., Neural-specific elongation of 3' UTRs during Drosophila development., Proc Natl Acad Sci U S A, vol. 108, no. 38, pp. 15864-9, 2011.
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. 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.
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.
M. Levine, Paused RNA polymerase II as a developmental checkpoint., Cell, vol. 145, no. 4, pp. 502-11, 2011.
A. M. Berezhkovskii and Shvartsman, S. Y., Physical interpretation of mean local accumulation time of morphogen gradient formation., J Chem Phys, vol. 135, no. 15, p. 154115, 2011.
C. S. Greene and Troyanskaya, O. G., PILGRM: an interactive data-driven discovery platform for expert biologists., Nucleic Acids Res, vol. 39, no. Web Server issue, pp. W368-74, 2011.
C. S. Greene and Troyanskaya, O. G., PILGRM: an interactive data-driven discovery platform for expert biologists., Nucleic Acids Res, vol. 39, no. Web Server issue, pp. W368-74, 2011.
C. S. Greene and Troyanskaya, O. G., PILGRM: an interactive data-driven discovery platform for expert biologists., Nucleic Acids Res, vol. 39, no. Web Server issue, pp. W368-74, 2011.
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, 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.
D. J. Wilson, Hernandez, R. D., Andolfatto, P., and Przeworski, M., A population genetics-phylogenetics approach to inferring natural selection in coding sequences., PLoS Genet, vol. 7, no. 12, p. e1002395, 2011.
D. J. Wilson, Hernandez, R. D., Andolfatto, P., and Przeworski, M., A population genetics-phylogenetics approach to inferring natural selection in coding sequences., PLoS Genet, vol. 7, no. 12, p. e1002395, 2011.
L. Vastag, Jorgensen, P., Peshkin, L., Wei, R., Rabinowitz, J. D., and Kirschner, M. W., Remodeling of the metabolome during early frog development., PLoS One, vol. 6, no. 2, p. e16881, 2011.
S. C. Little and Wieschaus, E. F., Shifting patterns: merging molecules, morphogens, motility, and methodology., Dev Cell, vol. 21, no. 1, pp. 2-4, 2011.
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.
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.
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.
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.
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.
D. Botstein and Fink, G. R., Yeast: an experimental organism for 21st Century biology., Genetics, vol. 189, no. 3, pp. 695-704, 2011.
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.
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.
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.
J. D. Rabinowitz and White, E., Autophagy and metabolism., Science, vol. 330, no. 6009, pp. 1344-8, 2010.
O. Grimm and Wieschaus, E., The Bicoid gradient is shaped independently of nuclei., Development, vol. 137, no. 17, pp. 2857-62, 2010.
X. Lu, Drocco, J., and Wieschaus, E. F., Cell cycle regulation via inter-nuclear communication during the early embryonic development of Drosophila melanogaster., Cell Cycle, vol. 9, no. 14, pp. 2908-10, 2010.
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.
S. Neumann, Hansen, C. H., Wingreen, N. S., and Sourjik, V., Differences in signalling by directly and indirectly binding ligands in bacterial chemotaxis., EMBO J, vol. 29, no. 20, pp. 3484-95, 2010.
Y. Guan, Ackert-Bicknell, C. L., Kell, B., Troyanskaya, O. G., and Hibbs, M. A., Functional genomics complements quantitative genetics in identifying disease-gene associations., PLoS Comput Biol, vol. 6, no. 11, p. e1000991, 2010.
Y. Guan, Ackert-Bicknell, C. L., Kell, B., Troyanskaya, O. G., and Hibbs, M. A., Functional genomics complements quantitative genetics in identifying disease-gene associations., PLoS Comput Biol, vol. 6, no. 11, p. e1000991, 2010.
The Gene Ontology in 2010: extensions and refinements., Nucleic Acids Res, vol. 38, no. Database issue, pp. D331-5, 2010.
The Gene Ontology in 2010: extensions and refinements., Nucleic Acids Res, vol. 38, no. Database issue, pp. D331-5, 2010.
The Gene Ontology in 2010: extensions and refinements., Nucleic Acids Res, vol. 38, no. Database issue, pp. D331-5, 2010.
J. A. Capra, Paeschke, K., Singh, M., and Zakian, V. A., G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae., PLoS Comput Biol, vol. 6, no. 7, p. e1000861, 2010.
J. A. Capra, Paeschke, K., Singh, M., and Zakian, V. A., G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae., PLoS Comput Biol, vol. 6, no. 7, p. e1000861, 2010.
A. M. Berezhkovskii, Sample, C., and Shvartsman, S. Y., How long does it take to establish a morphogen gradient?, Biophys J, vol. 99, no. 8, pp. L59-61, 2010.
A. M. Berezhkovskii, Sample, C., and Shvartsman, S. Y., How long does it take to establish a morphogen gradient?, Biophys J, vol. 99, no. 8, pp. L59-61, 2010.
A. C. Martin, Gelbart, M., Fernandez-Gonzalez, R., Kaschube, M., and Wieschaus, E. F., Integration of contractile forces during tissue invagination., J Cell Biol, vol. 188, no. 5, pp. 735-49, 2010.
A. C. Martin, Gelbart, M., Fernandez-Gonzalez, R., Kaschube, M., and Wieschaus, E. F., Integration of contractile forces during tissue invagination., J Cell Biol, vol. 188, no. 5, pp. 735-49, 2010.
C. S. Greene and Troyanskaya, O. G., Integrative systems biology for data-driven knowledge discovery., Semin Nephrol, vol. 30, no. 5, pp. 443-54, 2010.
D. Botstein, It's the data!, Mol Biol Cell, vol. 21, no. 1, pp. 4-6, 2010.
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.
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.
O. Grimm, Coppey, M., and Wieschaus, E., Modelling the Bicoid gradient., Development, vol. 137, no. 14, pp. 2253-64, 2010.
O. Grimm, Coppey, M., and Wieschaus, E., Modelling the Bicoid gradient., Development, vol. 137, no. 14, pp. 2253-64, 2010.
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, Levine, M., and Boettiger, A., Morphogen gradients: limits to signaling or limits to measurement?, Curr Biol, vol. 20, no. 5, pp. R232-4, 2010.
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.
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.
T. Gregor, Fujimoto, K., Masaki, N., and Sawai, S., The onset of collective behavior in social amoebae., Science, vol. 328, no. 5981, pp. 1021-5, 2010.
D. Gresham, Curry, B., Ward, A., D Gordon, B., Brizuela, L., Kruglyak, L., and Botstein, D., Optimized detection of sequence variation in heterozygous genomes using DNA microarrays with isothermal-melting probes., Proc Natl Acad Sci U S A, vol. 107, no. 4, pp. 1482-7, 2010.
H. Goodarzi, Bennett, B. D., Amini, S., Reaves, M. L., Hottes, A. K., Rabinowitz, J. D., and Tavazoie, S., Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli., Mol Syst Biol, vol. 6, p. 378, 2010.
S. R. Engel, Balakrishnan, R., Binkley, G., Christie, K. R., Costanzo, M. C., Dwight, S. S., Fisk, D. G., Hirschman, J. E., Hitz, B. C., Hong, E. L., Krieger, C. J., Livstone, M. S., Miyasato, S. R., Nash, R., Oughtred, R., Park, J., Skrzypek, M. S., Weng, S., Wong, E. D., Dolinski, K., Botstein, D., and J Cherry, M., Saccharomyces Genome Database provides mutant phenotype data., Nucleic Acids Res, vol. 38, no. Database issue, pp. D433-6, 2010.
S. R. Engel, Balakrishnan, R., Binkley, G., Christie, K. R., Costanzo, M. C., Dwight, S. S., Fisk, D. G., Hirschman, J. E., Hitz, B. C., Hong, E. L., Krieger, C. J., Livstone, M. S., Miyasato, S. R., Nash, R., Oughtred, R., Park, J., Skrzypek, M. S., Weng, S., Wong, E. D., Dolinski, K., Botstein, D., and J Cherry, M., Saccharomyces Genome Database provides mutant phenotype data., Nucleic Acids Res, vol. 38, no. Database issue, pp. D433-6, 2010.
S. R. Engel, Balakrishnan, R., Binkley, G., Christie, K. R., Costanzo, M. C., Dwight, S. S., Fisk, D. G., Hirschman, J. E., Hitz, B. C., Hong, E. L., Krieger, C. J., Livstone, M. S., Miyasato, S. R., Nash, R., Oughtred, R., Park, J., Skrzypek, M. S., Weng, S., Wong, E. D., Dolinski, K., Botstein, D., and J Cherry, M., Saccharomyces Genome Database provides mutant phenotype data., Nucleic Acids Res, vol. 38, no. Database issue, pp. D433-6, 2010.
S. R. Engel, Balakrishnan, R., Binkley, G., Christie, K. R., Costanzo, M. C., Dwight, S. S., Fisk, D. G., Hirschman, J. E., Hitz, B. C., Hong, E. L., Krieger, C. J., Livstone, M. S., Miyasato, S. R., Nash, R., Oughtred, R., Park, J., Skrzypek, M. S., Weng, S., Wong, E. D., Dolinski, K., Botstein, D., and J Cherry, M., Saccharomyces Genome Database provides mutant phenotype data., Nucleic Acids Res, vol. 38, no. Database issue, pp. D433-6, 2010.
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.
C. Y. Park, Hess, D. C., Huttenhower, C., and Troyanskaya, O. G., Simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway components., PLoS Comput Biol, vol. 6, no. 11, p. e1001009, 2010.
P. Jiang and Singh, M., SPICi: a fast clustering algorithm for large biological networks., Bioinformatics, vol. 26, no. 8, pp. 1105-11, 2010.
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.
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.
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.
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.
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.
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.
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.
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.
S. - J. Yan, Zartman, J. J., Zhang, M., Scott, A., Shvartsman, S. Y., and Li, W. X., Bistability coordinates activation of the EGFR and DPP pathways in Drosophila vein differentiation., Mol Syst Biol, vol. 5, p. 278, 2009.
S. - J. Yan, Zartman, J. J., Zhang, M., Scott, A., Shvartsman, S. Y., and Li, W. X., Bistability coordinates activation of the EGFR and DPP pathways in Drosophila vein differentiation., Mol Syst Biol, vol. 5, p. 278, 2009.
C. Huttenhower, Myers, C. L., Hibbs, M. A., and Troyanskaya, O. G., Computational analysis of the yeast proteome: understanding and exploiting functional specificity in genomic data., Methods Mol Biol, vol. 548, pp. 273-93, 2009.
C. Huttenhower, Myers, C. L., Hibbs, M. A., and Troyanskaya, O. G., Computational analysis of the yeast proteome: understanding and exploiting functional specificity in genomic data., Methods Mol Biol, vol. 548, pp. 273-93, 2009.
C. Huttenhower, Myers, C. L., Hibbs, M. A., and Troyanskaya, O. G., Computational analysis of the yeast proteome: understanding and exploiting functional specificity in genomic data., Methods Mol Biol, vol. 548, pp. 273-93, 2009.
R. P. Oliveira, Abate, J. Porter, Dilks, K., Landis, J., Ashraf, J., Murphy, C. T., and T Blackwell, K., Condition-adapted stress and longevity gene regulation by Caenorhabditis elegans SKN-1/Nrf., Aging Cell, vol. 8, no. 5, pp. 524-41, 2009.
R. P. Oliveira, Abate, J. Porter, Dilks, K., Landis, J., Ashraf, J., Murphy, C. T., and T Blackwell, K., Condition-adapted stress and longevity gene regulation by Caenorhabditis elegans SKN-1/Nrf., Aging Cell, vol. 8, no. 5, pp. 524-41, 2009.
R. P. Oliveira, Abate, J. Porter, Dilks, K., Landis, J., Ashraf, J., Murphy, C. T., and T Blackwell, K., Condition-adapted stress and longevity gene regulation by Caenorhabditis elegans SKN-1/Nrf., Aging Cell, vol. 8, no. 5, pp. 524-41, 2009.
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. 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.
S. T. Harbison, Carbone, M. Anna, Ayroles, J. F., Stone, E. A., Lyman, R. F., and Mackay, T. F. C., Co-regulated transcriptional networks contribute to natural genetic variation in Drosophila sleep., Nat Genet, vol. 41, no. 3, pp. 371-5, 2009.
S. T. Harbison, Carbone, M. Anna, Ayroles, J. F., Stone, E. A., Lyman, R. F., and Mackay, T. F. C., Co-regulated transcriptional networks contribute to natural genetic variation in Drosophila sleep., Nat Genet, vol. 41, no. 3, pp. 371-5, 2009.
X. Lu, Li, J. M., Elemento, O., Tavazoie, S., and Wieschaus, E. F., Coupling of zygotic transcription to mitotic control at the Drosophila mid-blastula transition., Development, vol. 136, no. 12, pp. 2101-10, 2009.
X. Lu, Li, J. M., Elemento, O., Tavazoie, S., and Wieschaus, E. F., Coupling of zygotic transcription to mitotic control at the Drosophila mid-blastula transition., Development, vol. 136, no. 12, pp. 2101-10, 2009.
Y. Goltsev, Rezende, G. L., Vranizan, K., Lanzaro, G., Valle, D., and Levine, M., Developmental and evolutionary basis for drought tolerance of the Anopheles gambiae embryo., Dev Biol, vol. 330, no. 2, pp. 462-70, 2009.
G. Tkačik and Bialek, W., Diffusion, dimensionality, and noise in transcriptional regulation., Phys Rev E Stat Nonlin Soft Matter Phys, vol. 79, no. 5 Pt 1, p. 051901, 2009.
C. L. Myers, Chiriac, C., and Troyanskaya, O. G., Discovering biological networks from diverse functional genomic data., Methods Mol Biol, vol. 563, pp. 157-75, 2009.
C. L. Myers, Chiriac, C., and Troyanskaya, O. G., Discovering biological networks from diverse functional genomic data., Methods Mol Biol, vol. 563, pp. 157-75, 2009.
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.
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.
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, 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.
M. Rebeiz, Ramos-Womack, M., Jeong, S., Andolfatto, P., Werner, T., True, J., Stern, D. L., and Carroll, S. B., Evolution of the tan locus contributed to pigment loss in Drosophila santomea: a response to Matute et al., Cell, vol. 139, no. 6, pp. 1189-96, 2009.
M. Rebeiz, Ramos-Womack, M., Jeong, S., Andolfatto, P., Werner, T., True, J., Stern, D. L., and Carroll, S. B., Evolution of the tan locus contributed to pigment loss in Drosophila santomea: a response to Matute et al., Cell, vol. 139, no. 6, pp. 1189-96, 2009.
M. Rebeiz, Ramos-Womack, M., Jeong, S., Andolfatto, P., Werner, T., True, J., Stern, D. L., and Carroll, S. B., Evolution of the tan locus contributed to pigment loss in Drosophila santomea: a response to Matute et al., Cell, vol. 139, no. 6, pp. 1189-96, 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. 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.
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.
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.
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.
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.
S. - J. Lee, Murphy, C. T., and Kenyon, C., Glucose shortens the life span of C. elegans by downregulating DAF-16/FOXO activity and aquaporin gene expression., Cell Metab, vol. 10, no. 5, pp. 379-91, 2009.
S. - J. Lee, Murphy, C. T., and Kenyon, C., Glucose shortens the life span of C. elegans by downregulating DAF-16/FOXO activity and aquaporin gene expression., Cell Metab, vol. 10, no. 5, pp. 379-91, 2009.
C. Huttenhower, Mehmood, S. O., and Troyanskaya, O. G., Graphle: Interactive exploration of large, dense graphs., BMC Bioinformatics, vol. 10, p. 417, 2009.
J. Song and Singh, M., How and when should interactome-derived clusters be used to predict functional modules and protein function?, Bioinformatics, vol. 25, no. 23, pp. 3143-50, 2009.
C. Huttenhower, Hibbs, M. A., Myers, C. L., Caudy, A. A., Hess, D. C., and Troyanskaya, O. G., The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction., Bioinformatics, vol. 25, no. 18, pp. 2404-10, 2009.
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.
J. S. Bloom, Khan, Z., Kruglyak, L., Singh, M., and Caudy, A. A., Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays., BMC Genomics, vol. 10, p. 221, 2009.
J. S. Bloom, Khan, Z., Kruglyak, L., Singh, M., and Caudy, A. A., Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays., BMC Genomics, vol. 10, p. 221, 2009.
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.
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.
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.
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.
D. Papatsenko, Goltsev, Y., and Levine, M., Organization of developmental enhancers in the Drosophila embryo., Nucleic Acids Res, vol. 37, no. 17, pp. 5665-77, 2009.
D. Papatsenko, Goltsev, Y., and Levine, M., Organization of developmental enhancers in the Drosophila embryo., Nucleic Acids Res, vol. 37, no. 17, pp. 5665-77, 2009.
D. Papatsenko, Goltsev, Y., and Levine, M., Organization of developmental enhancers in the Drosophila embryo., Nucleic Acids Res, vol. 37, no. 17, pp. 5665-77, 2009.
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.
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.
G. Sella, Petrov, D. A., Przeworski, M., and Andolfatto, P., Pervasive natural selection in the Drosophila genome?, PLoS Genet, vol. 5, no. 6, p. e1000495, 2009.
A. V. Persikov, Osada, R., and Singh, M., Predicting DNA recognition by Cys2His2 zinc finger proteins., Bioinformatics, vol. 25, no. 1, pp. 22-9, 2009.
A. V. Persikov, Osada, R., and Singh, M., Predicting DNA recognition by Cys2His2 zinc finger proteins., Bioinformatics, vol. 25, no. 1, pp. 22-9, 2009.
A. V. Persikov, Osada, R., and Singh, M., Predicting DNA recognition by Cys2His2 zinc finger proteins., Bioinformatics, vol. 25, no. 1, pp. 22-9, 2009.
Z. Khan, Bloom, J. S., Garcia, B. A., Singh, M., and Kruglyak, L., Protein quantification across hundreds of experimental conditions., Proc Natl Acad Sci U S A, vol. 106, no. 37, pp. 15544-8, 2009.
A. C. Martin, Kaschube, M., and Wieschaus, E. F., Pulsed contractions of an actin-myosin network drive apical constriction., Nature, vol. 457, no. 7228, pp. 495-9, 2009.
A. C. Martin, Kaschube, M., and Wieschaus, E. F., Pulsed contractions of an actin-myosin network drive apical constriction., Nature, vol. 457, no. 7228, pp. 495-9, 2009.
L. Salwinski, Licata, L., Winter, A., Thorneycroft, D., Khadake, J., Ceol, A., Aryamontri, A. Chatr, Oughtred, R., Livstone, M., Boucher, L., Botstein, D., Dolinski, K., Berardini, T., Huala, E., Tyers, M., Eisenberg, D., Cesareni, G., and Hermjakob, H., Recurated protein interaction datasets., Nat Methods, vol. 6, no. 12, pp. 860-1, 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, 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.
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.
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, 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.
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.
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. 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.
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.
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. 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. 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.
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.
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.
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.
C. Huttenhower and Troyanskaya, O. G., Assessing the functional structure of genomic data., Bioinformatics, vol. 24, no. 13, pp. i330-8, 2008.
P. A. DiMaggio, McAllister, S. R., Floudas, C. A., Feng, X. - J., Rabinowitz, J. D., and Rabitz, H. A., Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies., BMC Bioinformatics, vol. 9, p. 458, 2008.
P. A. DiMaggio, McAllister, S. R., Floudas, C. A., Feng, X. - J., Rabinowitz, J. D., and Rabitz, H. A., Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies., BMC Bioinformatics, vol. 9, p. 458, 2008.
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.
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.
N. Yakoby, Bristow, C. A., Gong, D., Schafer, X., Lembong, J., Zartman, J. J., Halfon, M. S., Schüpbach, T., and Shvartsman, S. Y., A combinatorial code for pattern formation in Drosophila oogenesis., Dev Cell, vol. 15, no. 5, pp. 725-37, 2008.
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, 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.
S. R. McAllister, Feng, X. - J., DiMaggio, P. A., Floudas, C. A., Rabinowitz, J. D., and Rabitz, H., Descriptor-free molecular discovery in large libraries by adaptive substituent reordering., Bioorg Med Chem Lett, vol. 18, no. 22, pp. 5967-70, 2008.
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.
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.
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.
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.
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.
S. Jeong, Rebeiz, M., Andolfatto, P., Werner, T., True, J., and Carroll, S. B., The evolution of gene regulation underlies a morphological difference between two Drosophila sister species., Cell, vol. 132, no. 5, pp. 783-93, 2008.
S. Jeong, Rebeiz, M., Andolfatto, P., Werner, T., True, J., and Carroll, S. B., The evolution of gene regulation underlies a morphological difference between two Drosophila sister species., Cell, vol. 132, no. 5, pp. 783-93, 2008.
S. Jeong, Rebeiz, M., Andolfatto, P., Werner, T., True, J., and Carroll, S. B., The evolution of gene regulation underlies a morphological difference between two Drosophila sister species., Cell, vol. 132, no. 5, pp. 783-93, 2008.
E. L. Hong, Balakrishnan, R., Dong, Q., Christie, K. R., Park, J., Binkley, G., Costanzo, M. C., Dwight, S. S., Engel, S. R., Fisk, D. G., Hirschman, J. E., Hitz, B. C., Krieger, C. J., Livstone, M. S., Miyasato, S. R., Nash, R. S., Oughtred, R., Skrzypek, M. S., Weng, S., Wong, E. D., Zhu, K. K., Dolinski, K., Botstein, D., and J Cherry, M., Gene Ontology annotations at SGD: new data sources and annotation methods., Nucleic Acids Res, vol. 36, no. Database issue, pp. D577-81, 2008.
Y. Guan, Myers, C. L., Lu, R., Lemischka, I. R., Bult, C. J., and Troyanskaya, O. G., A genomewide functional network for the laboratory mouse., PLoS Comput Biol, vol. 4, no. 9, p. e1000165, 2008.
Y. Guan, Myers, C. L., Lu, R., Lemischka, I. R., Bult, C. J., and Troyanskaya, O. G., A genomewide functional network for the laboratory mouse., PLoS Comput Biol, vol. 4, no. 9, p. e1000165, 2008.
Y. Guan, Myers, C. L., Lu, R., Lemischka, I. R., Bult, C. J., and Troyanskaya, O. G., A genomewide functional network for the laboratory mouse., PLoS Comput Biol, vol. 4, no. 9, p. e1000165, 2008.
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.
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.
G. Tkačik, Callan, C. G., and Bialek, W., Information capacity of genetic regulatory elements., Phys Rev E Stat Nonlin Soft Matter Phys, vol. 78, no. 1 Pt 1, p. 011910, 2008.
G. Tkačik, Callan, C. G., and Bialek, W., Information flow and optimization in transcriptional regulation., Proc Natl Acad Sci U S A, vol. 105, no. 34, pp. 12265-70, 2008.
G. Tkačik, Callan, C. G., and Bialek, W., Information flow and optimization in transcriptional regulation., Proc Natl Acad Sci U S A, vol. 105, no. 34, pp. 12265-70, 2008.
G. Tkačik, Callan, C. G., and Bialek, W., Information flow and optimization in transcriptional regulation., Proc Natl Acad Sci U S A, vol. 105, no. 34, pp. 12265-70, 2008.
A. Marie Sokac and Wieschaus, E., Local actin-dependent endocytosis is zygotically controlled to initiate Drosophila cellularization., Dev Cell, vol. 14, no. 5, pp. 775-86, 2008.
A. Marie Sokac and Wieschaus, E., Local actin-dependent endocytosis is zygotically controlled to initiate Drosophila cellularization., Dev Cell, vol. 14, no. 5, pp. 775-86, 2008.
I. Nemenman, Lewen, G. D., Bialek, W., and van Steveninck, R. R. de Ruyte, Neural coding of natural stimuli: information at sub-millisecond resolution., PLoS Comput Biol, vol. 4, no. 3, p. e1000025, 2008.
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.
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.
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.
P. R. Haddrill, Bachtrog, D., and Andolfatto, P., Positive and negative selection on noncoding DNA in Drosophila simulans., Mol Biol Evol, vol. 25, no. 9, pp. 1825-34, 2008.
P. R. Haddrill, Bachtrog, D., and Andolfatto, P., Positive and negative selection on noncoding DNA in Drosophila simulans., Mol Biol Evol, vol. 25, no. 9, pp. 1825-34, 2008.
P. R. Haddrill, Bachtrog, D., and Andolfatto, P., Positive and negative selection on noncoding DNA in Drosophila simulans., Mol Biol Evol, vol. 25, no. 9, pp. 1825-34, 2008.
P. R. Haddrill, Bachtrog, D., and Andolfatto, P., Positive and negative selection on noncoding DNA in Drosophila simulans., Mol Biol Evol, vol. 25, no. 9, pp. 1825-34, 2008.
D. A. Hendrix, Hong, J. - W., Zeitlinger, J., Rokhsar, D. S., and Levine, M. S., Promoter elements associated with RNA Pol II stalling in the Drosophila embryo., Proc Natl Acad Sci U S A, vol. 105, no. 22, pp. 7762-7, 2008.
D. A. Hendrix, Hong, J. - W., Zeitlinger, J., Rokhsar, D. S., and Levine, M. S., Promoter elements associated with RNA Pol II stalling in the Drosophila embryo., Proc Natl Acad Sci U S A, vol. 105, no. 22, pp. 7762-7, 2008.
D. A. Hendrix, Hong, J. - W., Zeitlinger, J., Rokhsar, D. S., and Levine, M. S., Promoter elements associated with RNA Pol II stalling in the Drosophila embryo., Proc Natl Acad Sci U S A, vol. 105, no. 22, pp. 7762-7, 2008.
D. A. Hendrix, Hong, J. - W., Zeitlinger, J., Rokhsar, D. S., and Levine, M. S., Promoter elements associated with RNA Pol II stalling in the Drosophila embryo., Proc Natl Acad Sci U S A, vol. 105, no. 22, pp. 7762-7, 2008.
G. Tkačik, Gregor, T., and Bialek, W., The role of input noise in transcriptional regulation., PLoS One, vol. 3, no. 7, p. e2774, 2008.
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. - 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. - 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.
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.
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.
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.
C. Huttenhower, Schroeder, M., Chikina, M. D., and Troyanskaya, O. G., The Sleipnir library for computational functional genomics., Bioinformatics, vol. 24, no. 13, pp. 1559-61, 2008.
C. Huttenhower, Schroeder, M., Chikina, M. D., and Troyanskaya, O. G., The Sleipnir library for computational functional genomics., Bioinformatics, vol. 24, no. 13, pp. 1559-61, 2008.
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.
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.
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.
A. J. Pompeani, Irgon, J. J., Berger, M. F., Bulyk, M. L., Wingreen, N. S., and Bassler, B. L., The Vibrio harveyi master quorum-sensing regulator, LuxR, a TetR-type protein is both an activator and a repressor: DNA recognition and binding specificity at target promoters., Mol Microbiol, vol. 70, no. 1, pp. 76-88, 2008.

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