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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Protein Binding
S. H Wiley, Shvartsman, S. Y., and Lauffenburger, D. A., “Computational modeling of the EGF-receptor system: a paradigm for systems biology.”, Trends Cell Biol, vol. 13, no. 1, pp. 43-50, 2003.
D. E. Klein, Nappi, V. M., Reeves, G. T., Shvartsman, S. Y., and Lemmon, M. A., “Argos inhibits epidermal growth factor receptor signalling by ligand sequestration.”, Nature, vol. 430, no. 7003, pp. 1040-4, 2004.
C. B. Muratov and Shvartsman, S. Y., “Signal propagation and failure in discrete autocrine relays.”, Phys Rev Lett, vol. 93, no. 11, p. 118101, 2004.
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.
M. Pribyl, Muratov, C. B., and Shvartsman, S. Y., “Long-range signal transmission in autocrine relays.”, Biophys J, vol. 84, no. 2 Pt 1, pp. 883-96, 2003.
Protein Kinase Inhibitors
D. E. Klein, Nappi, V. M., Reeves, G. T., Shvartsman, S. Y., and Lemmon, M. A., “Argos inhibits epidermal growth factor receptor signalling by ligand sequestration.”, Nature, vol. 430, no. 7003, pp. 1040-4, 2004.
Protein Kinases
D. E. Klein, Nappi, V. M., Reeves, G. T., Shvartsman, S. Y., and Lemmon, M. A., “Argos inhibits epidermal growth factor receptor signalling by ligand sequestration.”, Nature, vol. 430, no. 7003, pp. 1040-4, 2004.
Protein Transport
C. B. Muratov and Shvartsman, S. Y., “Signal propagation and failure in discrete autocrine relays.”, Phys Rev Lett, vol. 93, no. 11, p. 118101, 2004.
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.
L. A. Goentoro, Reeves, G. T., Kowal, C. P., Martinelli, L., Schüpbach, T., and Shvartsman, S. Y., “Quantifying the Gurken morphogen gradient in Drosophila oogenesis.”, Dev Cell, vol. 11, no. 2, pp. 263-72, 2006.
Protein Tyrosine Phosphatases
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.
Protein-Tyrosine Kinases
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.
Proto-Oncogene Proteins
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.
Reactive Oxygen Species
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.
Receptor Protein-Tyrosine Kinases
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.
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. 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.
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. 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.
G. Jiménez, Shvartsman, S. Y., and Paroush, Z. 'ev, “The Capicua repressor--a general sensor of RTK signaling in development and disease.”, J Cell Sci, vol. 125, no. Pt 6, pp. 1383-91, 2012.
Receptor, Epidermal Growth Factor
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.
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.
S. H Wiley, Shvartsman, S. Y., and Lauffenburger, D. A., “Computational modeling of the EGF-receptor system: a paradigm for systems biology.”, Trends Cell Biol, vol. 13, no. 1, pp. 43-50, 2003.
D. E. Klein, Nappi, V. M., Reeves, G. T., Shvartsman, S. Y., and Lemmon, M. A., “Argos inhibits epidermal growth factor receptor signalling by ligand sequestration.”, Nature, vol. 430, no. 7003, pp. 1040-4, 2004.
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.
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, 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, 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.
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.
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. 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.
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.
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.
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.
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.
W. A. Rogers, Goyal, Y., Yamaya, K., Shvartsman, S. Y., and Levine, M. S., “Uncoupling neurogenic gene networks in the Drosophila embryo.”, Genes Dev, vol. 31, no. 7, pp. 634-638, 2017.
M. I. Monine, Berezhkovskii, A. M., Joslin, E. J., H Wiley, S., Lauffenburger, D. A., and Shvartsman, S. Y., “Ligand accumulation in autocrine cell cultures.”, Biophys J, vol. 88, no. 4, pp. 2384-90, 2005.
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.
Receptors, Cell Surface
C. B. Muratov and Shvartsman, S. Y., “Signal propagation and failure in discrete autocrine relays.”, Phys Rev Lett, vol. 93, no. 11, p. 118101, 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, Batsilas, L., and Shvartsman, S. Y., “Ligand trapping in epithelial layers and cell cultures.”, Biophys Chem, vol. 107, no. 3, pp. 221-7, 2004.
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.
M. Pribyl, Muratov, C. B., and Shvartsman, S. Y., “Long-range signal transmission in autocrine relays.”, Biophys J, vol. 84, no. 2 Pt 1, pp. 883-96, 2003.
Receptors, Invertebrate Peptide
D. E. Klein, Nappi, V. M., Reeves, G. T., Shvartsman, S. Y., and Lemmon, M. A., “Argos inhibits epidermal growth factor receptor signalling by ligand sequestration.”, Nature, vol. 430, no. 7003, pp. 1040-4, 2004.
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. - 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.
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.
W. A. Rogers, Goyal, Y., Yamaya, K., Shvartsman, S. Y., and Levine, M. S., “Uncoupling neurogenic gene networks in the Drosophila embryo.”, Genes Dev, vol. 31, no. 7, pp. 634-638, 2017.
Receptors, Notch
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.
Repressor Proteins
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.
Y. Kim, Iagovitina, A., Ishihara, K., Fitzgerald, K. M., Deplancke, B., Papatsenko, D., and Shvartsman, S. Y., “Context-dependent transcriptional interpretation of mitogen activated protein kinase signaling in the Drosophila embryo.”, Chaos, vol. 23, no. 2, p. 025105, 2013.
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.
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.
G. Jiménez, Shvartsman, S. Y., and Paroush, Z. 'ev, “The Capicua repressor--a general sensor of RTK signaling in development and disease.”, J Cell Sci, vol. 125, no. Pt 6, pp. 1383-91, 2012.
Y. Kim, Andreu, M. José, Lim, B., Chung, K., Terayama, M., Jiménez, G., Berg, C. A., Lu, H., and Shvartsman, S. Y., “Gene regulation by MAPK substrate competition.”, Dev Cell, vol. 20, no. 6, pp. 880-7, 2011.
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.
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.
Reverse Transcriptase Polymerase Chain Reaction
L. A. Goentoro, Yakoby, N., Goodhouse, J., Schüpbach, T., and Shvartsman, S. Y., “Quantitative analysis of the GAL4/UAS system in Drosophila oogenesis.”, Genesis, vol. 44, no. 2, pp. 66-74, 2006.
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.
RNA Probes
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.
RNA, Messenger
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.
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.
Saccharomyces cerevisiae Proteins
L. A. Goentoro, Yakoby, N., Goodhouse, J., Schüpbach, T., and Shvartsman, S. Y., “Quantitative analysis of the GAL4/UAS system in Drosophila oogenesis.”, Genesis, vol. 44, no. 2, pp. 66-74, 2006.
Signal Transduction
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.
D. E. Klein, Nappi, V. M., Reeves, G. T., Shvartsman, S. Y., and Lemmon, M. A., “Argos inhibits epidermal growth factor receptor signalling by ligand sequestration.”, Nature, vol. 430, no. 7003, pp. 1040-4, 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.
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.
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.
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.
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.
S. Y. Shvartsman and Baker, R. E., “Mathematical models of morphogen gradients and their effects on gene expression.”, Wiley Interdiscip Rev Dev Biol, vol. 1, no. 5, pp. 715-30, 2012.
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.
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.
C. B. Muratov and Shvartsman, S. Y., “Signal propagation and failure in discrete autocrine relays.”, Phys Rev Lett, vol. 93, no. 11, p. 118101, 2004.
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.
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.
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.
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.
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.
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.
Y. Kim, Andreu, M. José, Lim, B., Chung, K., Terayama, M., Jiménez, G., Berg, C. A., Lu, H., and Shvartsman, S. Y., “Gene regulation by MAPK substrate competition.”, Dev Cell, vol. 20, no. 6, pp. 880-7, 2011.
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.
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.
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.
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.
G. Jiménez, Shvartsman, S. Y., and Paroush, Z. 'ev, “The Capicua repressor--a general sensor of RTK signaling in development and disease.”, J Cell Sci, vol. 125, no. Pt 6, pp. 1383-91, 2012.
W. A. Rogers, Goyal, Y., Yamaya, K., Shvartsman, S. Y., and Levine, M. S., “Uncoupling neurogenic gene networks in the Drosophila embryo.”, Genes Dev, vol. 31, no. 7, pp. 634-638, 2017.
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.
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.
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.
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.
L. A. Goentoro, Reeves, G. T., Kowal, C. P., Martinelli, L., Schüpbach, T., and Shvartsman, S. Y., “Quantifying the Gurken morphogen gradient in Drosophila oogenesis.”, Dev Cell, vol. 11, no. 2, pp. 263-72, 2006.
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.
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.
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.
S. H Wiley, Shvartsman, S. Y., and Lauffenburger, D. A., “Computational modeling of the EGF-receptor system: a paradigm for systems biology.”, Trends Cell Biol, vol. 13, no. 1, pp. 43-50, 2003.
Smad Proteins
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.
Species Specificity
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.
Stochastic Processes
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.
Stress, Mechanical
D. L. Nikolić, Boettiger, A. N., Bar-Sagi, D., Carbeck, J. D., and Shvartsman, S. Y., “Role of boundary conditions in an experimental model of epithelial wound healing.”, Am J Physiol Cell Physiol, vol. 291, no. 1, pp. C68-75, 2006.
Substrate Specificity
P. Liu, Kevrekidis, I. G., and Shvartsman, S. Y., “Substrate-dependent control of ERK phosphorylation can lead to oscillations.”, Biophys J, vol. 101, no. 11, pp. 2572-81, 2011.
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.
Surface Properties
A. M. Berezhkovskii, Monine, M. I., Muratov, C. B., and Shvartsman, S. Y., “Homogenization of boundary conditions for surfaces with regular arrays of traps.”, J Chem Phys, vol. 124, no. 3, p. 036103, 2006.
Systems Biology
A. S. Futran, A Link, J., Seger, R., and Shvartsman, S. Y., “ERK as a model for systems biology of enzyme kinetics in cells.”, Curr Biol, vol. 23, no. 21, pp. R972-9, 2013.
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.
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.
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.
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.
Temperature
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.
Time Factors
M. I. Monine, Berezhkovskii, A. M., Joslin, E. J., H Wiley, S., Lauffenburger, D. A., and Shvartsman, S. Y., “Ligand accumulation in autocrine cell cultures.”, Biophys J, vol. 88, no. 4, pp. 2384-90, 2005.
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.
A. M. Berezhkovskii, Sample, C., and Shvartsman, S. Y., “Formation of morphogen gradients: local accumulation time.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 83, no. 5 Pt 1, p. 051906, 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.
P. Liu, Kevrekidis, I. G., and Shvartsman, S. Y., “Substrate-dependent control of ERK phosphorylation can lead to oscillations.”, Biophys J, vol. 101, no. 11, pp. 2572-81, 2011.
J. S. Kanodia, Liang, H. - L., Kim, Y., Lim, B., Zhan, M., Lu, H., Rushlow, C. A., and Shvartsman, S. Y., “Pattern formation by graded and uniform signals in the early Drosophila embryo.”, Biophys J, vol. 102, no. 3, pp. 427-33, 2012.
Tissue Distribution
J. S. Kanodia, Kim, Y., Tomer, R., Khan, Z., Chung, K., Storey, J. D., Lu, H., Keller, P. J., and Shvartsman, S. Y., “A computational statistics approach for estimating the spatial range of morphogen gradients.”, Development, vol. 138, no. 22, pp. 4867-74, 2011.
Toll-Like Receptors
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.
Trans-Activators
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.
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.
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.
Y. Kim, Andreu, M. José, Lim, B., Chung, K., Terayama, M., Jiménez, G., Berg, C. A., Lu, H., and Shvartsman, S. Y., “Gene regulation by MAPK substrate competition.”, Dev Cell, vol. 20, no. 6, pp. 880-7, 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.
Transcription Factors
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.
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. 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. 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, 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.
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. J. Zartman and Shvartsman, S. Y., “Enhancer organization: transistor with a twist or something in a different vein?”, Curr Biol, vol. 17, no. 24, pp. R1048-50, 2007.
L. A. Goentoro, Yakoby, N., Goodhouse, J., Schüpbach, T., and Shvartsman, S. Y., “Quantitative analysis of the GAL4/UAS system in Drosophila oogenesis.”, Genesis, vol. 44, no. 2, pp. 66-74, 2006.
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.
J. S. Kanodia, Liang, H. - L., Kim, Y., Lim, B., Zhan, M., Lu, H., Rushlow, C. A., and Shvartsman, S. Y., “Pattern formation by graded and uniform signals in the early Drosophila embryo.”, Biophys J, vol. 102, no. 3, pp. 427-33, 2012.
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.
Transcription, Genetic
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.
Y. Kim, Iagovitina, A., Ishihara, K., Fitzgerald, K. M., Deplancke, B., Papatsenko, D., and Shvartsman, S. Y., “Context-dependent transcriptional interpretation of mitogen activated protein kinase signaling in the Drosophila embryo.”, Chaos, vol. 23, no. 2, p. 025105, 2013.
Transforming Growth Factor alpha
L. A. Goentoro, Reeves, G. T., Kowal, C. P., Martinelli, L., Schüpbach, T., and Shvartsman, S. Y., “Quantifying the Gurken morphogen gradient in Drosophila oogenesis.”, Dev Cell, vol. 11, no. 2, pp. 263-72, 2006.
Transforming Growth Factor beta
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.
Transistors, Electronic
J. J. Zartman and Shvartsman, S. Y., “Enhancer organization: transistor with a twist or something in a different vein?”, Curr Biol, vol. 17, no. 24, pp. R1048-50, 2007.
Wing
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.
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.
Wound Healing
D. L. Nikolić, Boettiger, A. N., Bar-Sagi, D., Carbeck, J. D., and Shvartsman, S. Y., “Role of boundary conditions in an experimental model of epithelial wound healing.”, Am J Physiol Cell Physiol, vol. 291, no. 1, pp. C68-75, 2006.
Zinc Fingers
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, 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.

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