2013
- Thomas J Levario, Mei Zhan, Bomyi Lim, Stanislav Y. Shvartsman, and Hang Lu
Microfluidic trap array for massively parallel imaging of Drosophila embryos
Nature Protocols, 8, 721-736 (2013).
- Peter V. Gordon, Cyrill B. Muratov, and Stanislav Y. Shvartsman
Local accumulation times for source, diffusion, and degradation models in two and three dimensions
The Journal of Chemical Physics, 138, 104121 (2013).
- Miriam Osterfield, XinXin Du, Trudi Schupbach, Eric Wieschaus, and Stanislav Y. Shvartsman
Three-dimensional epithelial morphogenesis in the developing Drosophila egg
Developmental Cell, 24, 400-410 (2013).
2012
- Oliver Grimm, Victoria Sanchez Zini, Yoosik Kim, Jordi Casanova, Stanislav Y. Shvartsman, and Eric Wieschaus
Torso RTK controls Capicua degradation by changing its subcellular localization
Development, 139, 3962-3968 (2012).
- Christine A. Rushlow and Stanislav Y. Shvartsman
Temporal dynamics, spatial range, and transcriptional interpretation of the Dorsal morphogen gradient
Current Opinion in Genetics & Development 22 (2012).
- Stanislav Y. Shvartsman and Ruth E. Baker
Mathematical models of morphogen gradients and their effects on gene expression
WIREs Dev Biol. doi:10.1002/wdev.55 (2012)
- Gerardo Jimenez, Stanislav Y. Shvartsman and Ze'ev Paroush
The Capicua repressor - a general sensor of RTK signaling in development and disease
Journal of Cell Science 125, 1383-1391 (2012).
- David S. A. Simakov, Lily S. Cheung, Len M. Pismen and Stanislav Y. Shvartsman
EGFR-dependent network interactions that pattern Drosophila eggshell appendages
Development, 139, 2814-2820 (2012).
- Aharon Helman, Bomyi Lim, Maria Jose Andreu, Yoosik Kim, Tatyana Shestkin, Hang Lu, Gerardo Jimenez, Stanislav Y. Shvartsman and Ze'ev Paroush
RTK signaling modulates the Dorsal gradient
Development, 139, 3032-3039 (2012).
- Jitendra S. Kanodia, Hsiao-Lan Liang, Yoosik Kim, Bomyi Lim, Mei Zhan, Hang Lu, Christine A. Rushlow, and Stanislav Y. Shvartsman
Pattern formation by graded and uniform signals in the early Drosophila embryo
Biophysical Journal, Vol.102, 427-433 (2012).
- Alisa Fuchs, Lily S. Cheung, Enrica Charbonnier, Stanislav Y. Shvartsman, and George Pyrowolakis
Transcriptional interpretation of the EGF receptor signaling gradient
PNAS Vol.109, No.5,1572-1577 (2012).
2011
- Ping Liu, Ioannis G. Kevrekidis, and Stanislav Y. Shvartsman
Substrate-dependent control of ERK phosphorylation can lead to oscillations
Biophysical Journal, Vol.101, 2572-2581 (2011).
- Alexander Berezhkovskii and Stanislav Y. Shvartsman.
Physical interpretation of mean local accumulation time of morphogen gradient formation.
J. Chem. Phys. 135, 154115 (2011).
- Jitendra S. Kanodia, Yoosik Kim, Raju Tomer, Zia Khan, Kwanghun Chung, John D. Storey, Hang Lu, Philipp J. Keller and Stanislav Y. Shvartsman.
A computational statistics approach for estimating the spatial range of morphogen gradients.
Development 138, 4867-4874 (2011).
- Cyrill B. Muratov, Peter V. Gordon and Stanislav Y Shvartsman.
Self-similar dynamics of morphogen gradients.
PHYSICAL REVIEW E 84, 041916 (2011).
- Lily S Cheung, Trudi Schupbach and Stanislav Y Shvartsman.
Pattern formation by receptor tyrosine kinases: analysis of the Gurken gradient in Drosophila oogenesis.
Current Opinion in Genetics and Development 21:1-7 (2011).
- Jeremiah J Zartman, Lily S Cheung, Matthew G Niepielko, Christine Bonini, Benjamin Haley, Nir Yakoby and Stanislav Y Shvartsman.
Pattern formation by a moving morphogen source.
Physical Biology 8, (2011).
- Yoosik Kim, Maria Jose Andreu, Bomyi Lim, Kwanghun Chung, Mark Terayama, Gerardo Jimenez, Celeste A. Berg, Hang Lu and Stanislav Y Shvartsman.
Gene Regulation by MAPK Substrate Competition.
Developmental Cell 20, 880-887 (2011).
- Alexander Berezhkovskii, Christine Sample and Stanislav Y Shvartsman.
Formation of morphogen gradients: Local accumulation time.
Physical Review E 83, 051906 (2011).
- Peter V. Gordon, Christine Sample, Alexander Berezhkovskii, Cyrill B. Muratov and Stanislav Y Shvartsman.
Local kinetics of morphogen gradients.
PNAS Vol.1087, No.15, 6157-6162 (2011).
- Yoosik Kim, Ze'ev Paroush, Knud Nairz, Ernst Hafen, Gerardo Jimenez and Stanislav Y Shvartsman.
Substrate-dependent control of MAPK phosphorylation in vivo.
Molecular Systems Biology 7:467 (2011).
- Kwanghun Chung, Yoosik Kim, Jitendra S Kanodia, Emily Gong, Stanislav Y Shvartsman and Hang Lu.
A microfluidic array for large-scale ordering and orientation of embryos.
Nature Methods. Vol. 8, No. 2, pp. 171-177 (2011).
2010
- Alexander Berezhkovskii, Christine Sample and Stanislav Shvartsman.
How long does it take to establish a morphogen gradient.
Biophysical Journal. 99, pp. 59-61 (2010).
- Marla Tipping, Yoosik Kim, Phillip Kyriakakis, Mei Tong, Stanislav Shvartsman and Alexey Veraksa.
Beta-arrestin Kurtz inhibits MAPK and Toll signalling in Drosophila development.
The EMBO Journal. 29, pp. 3222-3235 (2010).
- C.B.Muratov and S.Y.Shvartsman.
Waves of Autocrine Signaling in Patterned Epithelia.
Math. Model. Nat. Phenom. Vol 5, No. 5, 2010, pp. 46-63. - Kavousanakis ME, Kanodia JS, Kim,Kevrekidis IG, Shvartsman SY.
A compartmental model for the bicoid gradient.
Developmental Biology 345:12-17 (2010). - Sample C and Shvartsman SY.
Multiscale modeling of diffusion in the early Drosophila embryo.
Proc Natl Acad Sci USA 107(22):10092-6 (2010). Supporting Information - Zartman JJ and Shvartsman SY.
Unit Operations of Tissue Development: Epithelial Folding.
Annual Review of Chemical and Biomolecular Engineering 1:231-46 (2010). - Kim Y, Coppey M, Grossman R, Ajuria L, Jimenez G, Paroush Z, Shvartsman SY.
MAPK Substrate Competition Integrates Patterning Signals in the Drosophila Embryo.
Current Biology 20(5):1-6 (2010).
2009
-
Kanodia JS, Rikhy R, Kim Y, Lund VK, DeLotto R, Lippincott-Schwartz Jand Shvartsman SY.
Dynamics of the Dorsal morphogen gradient.
Proc Natl Acad Sci USA 106(4):1087-92 (2009). Supporting Information,Table,Appendix - Zartman JJ, Kanodia JS, Cheung LS and Shvartsman SY.
Feedback control of the EGFR signaling gradient: superposition of domain-splitting events in Drosophilaoogenesis.
Development 136:2903 (2009). - Yan S-J, Zartman JJ, Zhang M, Scott A, Shvartsman SY and Li WX.
Bistability coordinates activation of the EGFR and DPP pathways in Drosophila vein differentiation.
Molecular Systems Biology 5:278 (2009). - Muratov CB, Posta F, and Shvartsman SY.
Autocrine signal transmission with extracellular ligand degradation.
Physical Biology 6:016006 (2009). - Lembong J, Yakoby N, Shvartsman SY.
Pattern formation by dynamically interacting network motifs.
Proc Natl Acad Sci USA 106(9):3213-3218 (2009). - Berezhkovskii AM, Coppey M, and Shvartsman SY.
Signaling gradients in cascades of two-state reaction-diffusion systems.
Proc Natl Acad Sci USA 106(4):1087-92 (2009). - Shvartsman SY, Coppey M, and Berezhkovskii AM.
MAPK signaling in equations and embryos.
Fly 3(1):62-67 (2009). - Zartman JJ, Kanodia JS, Yakoby N, Schafer X, Watson C, Schlichting K, Dahmann C, and Shvartsman SY.
Expression patterns of cadherin genes in Drosophila oogenesis.
Gene Expression Patterns 9(1):31-36 (2009).
2008
- Yakoby N, Bristow CA, Gong D, Schafer X, Lembong J, Zartman JJ, Halfon MS, Schupbach T, and Shvartsman SY.
A combinatorial code for pattern formation in Drosophila oogenesis.
Developmental Cell 15:1-13 (2008). - Zartman JJ, Yakoby N, Bristow CA, Zhou X, Schlichting K, Dahmann C, and Shvartsman SY.
Cad74A is regulated by BR and is required for robust dorsal appendage formation in Drosophila oogenesis.
Developmental Biology 322:289-301 (2008). - Lembong J., Yakoby N., and Shvartsman SY.
Spatial Regulation of BMP Signaling by Patterned Receptor Expression
Tissue Engineering 14(9):1469-1477 (2008). - Shvartsman SY, Coppey M, and Berezhkovskii AM.
Dynamics of maternal morphogen gradients in Drosophila.
Current Opinion in Genetics and Development 18:1-6 (2008). - Posta F, Shvartsman SY, and Muratov CB.
Compensated optimal grids for elliptic boundary-value problems.
J. Comp. Phys. 227:8622-8635 (2008). - Coppey M, Boettiger AN, Berezhkovskii AM, Shvartsman SY.
Nuclear trapping shapes the terminal gradient in the Drosophila embryo.
Curr Biol 18(12):915-9. (2008). Supplemental Data - Berezhkovskii A.M., Coppey M., Sealfon S.C., and Shvartsman S.Y.
Cell-to-cell communication: Time and length scales of ligand internalization in cultures of suspended cells.
J. Chem. Phys. 128:225102 (2008). - Muratov CB and Shvartsman SY.
Boundary homogenization for periodic arrays of absorbers.
Multiscale Model. Simul. 7(1):44-61 (2008). - Yakoby N., Lembong J., Schupbach T., and Shvartsman SY.
Drosophila eggshell is patterned by sequential action of feedforward and feedback loops.
Development 135:343-351 (2008).
2007
- Zartman JJ and Shvartsman SY.
Enhancer Organization: Transistor with a Twist or Something in a Different Vein?
Current Biology Vol 17 No 24:R1048 (2007). - Coppey M, Berezhkovskii AM., Kim Y., Boettiger AN., Shvartsman SY.
Modeling the bicoid gradient: diffusion and nuclear trapping of a stable protein.
Developmental Biology 312(2):623-30 (2007). - Coppey M, Berezhkovskii AM, Sealfon SC, Shvartsman SY.
Time and length scales of autocrine signals in three dimensions.
Biophys J. 2007 Sep 15;93(6):1917-22. - Qiao L, Nachbar R, Kevrekidis I, Shvartsman S.
Bistability and oscillations in the Huang-Ferrell model of MAPK signaling.
PLoS Computational Biology, 2007
2006
- Reeves GT, Muratov CB, Schupbach T, Shvartsman SY.
Quantitative Models of Developmental Pattern Formation.
Dev Cell. 11(3):289-300. 2006 - Lea A. Goentoro, Gregory T. Reeves, Craig P. Kowal, Luigi Martinelli, Trudi Schupbach, and Stanislav Y. Shvartsman.
Quantifying the Gurken Morphogen Gradient in Drosophila Oogenesis,
Develpmental Cell 11:263-272. 2006 - Djordje L. Nikolic, Alistair N. Boettiger, Dafna Bar-Sagi, Jeffrey D. Carbeck and Stanislav Y. Shvartsman.
Role of boundary conditions in an experimental model of epithelial wound healing,
Am J Physiol Cell Physiol. 291(1):C68-75. 2006 - Berezhkovskii AM, Monine MI, Muratov CB, Shvartsman SY.
Homogenization of boundary conditions for surfaces with regular arrays of traps,
J Chem Phys. 124(3):036103. 2006 - Goentoro LA, Yakoby N, Goodhouse J, Schupbach T, Shvartsman SY.
Quantitative analysis of the GAL4/UAS system in Drosophila oogenesis.
Genesis. 44(2):66-74. 2006
2005
- N. Yakoby, C.A. Bristow, I. Gouzman, M.P. Rossi, Y. Gogotsi, T. Schupbach and S.Y. Shvartsman.
Systems-level questions in Drosophila oogenesis,
IEE Proc.-Sys. Biol. 15:276-284. 2005 - Gregory T. Reeves, Rachel Kalifa, Daryl E. Klein, Mark A. Lemmon and Stanislav Y. Shvartsman.
Computational analysis of EGFR inhibition by Argos.
Developmental Biology, 284: 523-535, 2005 - Stanislav Y. Shvartsman ,
Quantitative Analysis of Developing Tissues
AIChE Journal. Volume 51, Issue 5 , Pages 1312 - 1318 - M.Monine, A. M. Berezhkovskii , E.J. Joslin , H.Wiley , D.A. Lauffenburger and S.Y.Shvartsman.
Ligand Accumulation in Autocrine Cell Cultures.
Biophysical Journal Vol. 88, pp. 2384-2390, 2005.
2004
- Shvartsman SY, A.M. Berezhkovskii, Y.M. Makhnovskii, M. Monine, and V.Y. Zitserman,
Boundary homogenization for trapping by patchy surfaces,
J Chem Phys, Vol 121(22), 2004. - Shvartsman SY, Wiley HS, Lauffenburger DA,
Epidermal growth factor receptor signaling in tissues.
IEEE CONTROL SYSTEMS MAGAZINE 24 (4): 53-61 AUG 2004. - Muratov CB, Shvartsman SY,
Signal propagation and failure in discrete autocrine relays.
Phys Rev Lett. 2004 Sep 10;93(11):118101. Epub 2004 Sep 10. - Klein DE, Nappi VM, Reeves GT, Shvartsman SY, Lemmon MA.
Argos inhibits epidermal growth factor receptor signalling by ligand sequestration.
Nature. 2004 Aug 26;430(7003):1040-4. - Berezhkovskii AM, Batsilas L, Shvartsman SY,
Ligand Trapping in epithelial layers and cell cultures,
Biophysical Chemistry, 2004,107(3), 221-227
2003
- Berezhkovskii AM, Zitserman VYu, Shvartsman SY,
Effective diffusivity in periodic porous materials,
J. Chem. Phys., 2003, 119(14), 6991-6993 - Berezhkovskii AM, Zitserman VYu, Shvartsman SY,
Diffusivity in periodic arrays of spherical cavities,
J. Chem. Phys., 2003, 118(15), 7146-7147 - Muratov CB, Shvartsman SY.
An asymptotic study of the inductive pattern formation mechanism in Drosophila egg development,
Physica D, Nonlinear Phenomena 186(1-2) (2003) 93-108 - Batsilas L, Berezhkovskii AM, Shvartsman SY,
Stochastic model for autocrine and paracrine signals in cell culture assays,
Biophys J., 2003, 85: 3659-3665 - Pribyl M, Muratov CB, Shvartsman SY.
Discrete models of autocrine cell communication in epithelial layers.
Biophys J., 2003, 84: 3624-3635 - Pribyl M, Muratov CB, Shvartsman SY.
Long-range signal transmission in autocrine relays.
Biophys J., 2003, 84: 883-896 - Wiley HS, Shvartsman SY, Lauffenburger DA.
Computational modeling of the EGF receptor system: a paradigm for systems biology.
Trends Cell Biol, 2003 13(1), 43-50. - Pribyl M, Muratov CB, Shvartsman SY.
Transitions in the model of epithelial patterning.
Dev Dyn., 2003, 226(1):155-9.
2002
- Shvartsman SY, Hagan MP, Yacoub A, Dent P, Wiley HS, Lauffenburger DA.
Autocrine loops with positive feedback enable context-dependent cell signaling.
Am J Physiol Cell Physiol., 2002, 282:C545-C559. - Shvartsman SY,
Shooting from the hip,
PNAS, 2002, 99(14), 9087-9089. - Shvartsman SY, Muratov CB, Lauffenburger DA.
Modeling and computational analysis of EGF receptor-mediated cell communication in Drosophila oogenesis.
Development 2002,129(11):2577-2589.
2001
Microfluidic trap array for massively parallel imaging of Drosophila embryos
Local accumulation times for source, diffusion, and degradation models in two and three dimensions
Three-dimensional epithelial morphogenesis in the developing Drosophila egg
Torso RTK controls Capicua degradation by changing its subcellular localization
Temporal dynamics, spatial range, and transcriptional interpretation of the Dorsal morphogen gradient
Mathematical models of morphogen gradients and their effects on gene expression
The Capicua repressor - a general sensor of RTK signaling in development and disease
EGFR-dependent network interactions that pattern Drosophila eggshell appendages
RTK signaling modulates the Dorsal gradient
Pattern formation by graded and uniform signals in the early Drosophila embryo
Transcriptional interpretation of the EGF receptor signaling gradient
Substrate-dependent control of ERK phosphorylation can lead to oscillations
Physical interpretation of mean local accumulation time of morphogen gradient formation.
A computational statistics approach for estimating the spatial range of morphogen gradients.
Self-similar dynamics of morphogen gradients.
Pattern formation by receptor tyrosine kinases: analysis of the Gurken gradient in Drosophila oogenesis.
Pattern formation by a moving morphogen source.
Gene Regulation by MAPK Substrate Competition.
Formation of morphogen gradients: Local accumulation time.
Local kinetics of morphogen gradients.
Substrate-dependent control of MAPK phosphorylation in vivo.
A microfluidic array for large-scale ordering and orientation of embryos.
How long does it take to establish a morphogen gradient.
Beta-arrestin Kurtz inhibits MAPK and Toll signalling in Drosophila development.
Waves of Autocrine Signaling in Patterned Epithelia.
A compartmental model for the bicoid gradient.
Multiscale modeling of diffusion in the early Drosophila embryo.
Unit Operations of Tissue Development: Epithelial Folding.
MAPK Substrate Competition Integrates Patterning Signals in the Drosophila Embryo.
Dynamics of the Dorsal morphogen gradient.
Feedback control of the EGFR signaling gradient: superposition of domain-splitting events in Drosophilaoogenesis.
Bistability coordinates activation of the EGFR and DPP pathways in Drosophila vein differentiation.
Autocrine signal transmission with extracellular ligand degradation.
Pattern formation by dynamically interacting network motifs.
Signaling gradients in cascades of two-state reaction-diffusion systems.
MAPK signaling in equations and embryos.
Expression patterns of cadherin genes in Drosophila oogenesis.
A combinatorial code for pattern formation in Drosophila oogenesis.
Cad74A is regulated by BR and is required for robust dorsal appendage formation in Drosophila oogenesis.
Spatial Regulation of BMP Signaling by Patterned Receptor Expression
Dynamics of maternal morphogen gradients in Drosophila.
Compensated optimal grids for elliptic boundary-value problems.
Nuclear trapping shapes the terminal gradient in the Drosophila embryo.
Cell-to-cell communication: Time and length scales of ligand internalization in cultures of suspended cells.
Boundary homogenization for periodic arrays of absorbers.
Drosophila eggshell is patterned by sequential action of feedforward and feedback loops.
Enhancer Organization: Transistor with a Twist or Something in a Different Vein?
Modeling the bicoid gradient: diffusion and nuclear trapping of a stable protein.
Time and length scales of autocrine signals in three dimensions.
Bistability and oscillations in the Huang-Ferrell model of MAPK signaling.
Quantitative Models of Developmental Pattern Formation.
Quantifying the Gurken Morphogen Gradient in Drosophila Oogenesis,
Role of boundary conditions in an experimental model of epithelial wound healing,
Homogenization of boundary conditions for surfaces with regular arrays of traps,
Quantitative analysis of the GAL4/UAS system in Drosophila oogenesis.
Systems-level questions in Drosophila oogenesis,
Computational analysis of EGFR inhibition by Argos.
Quantitative Analysis of Developing Tissues
Ligand Accumulation in Autocrine Cell Cultures.
Boundary homogenization for trapping by patchy surfaces,
Epidermal growth factor receptor signaling in tissues.
Signal propagation and failure in discrete autocrine relays.
Argos inhibits epidermal growth factor receptor signalling by ligand sequestration.
Ligand Trapping in epithelial layers and cell cultures,
Effective diffusivity in periodic porous materials,
Diffusivity in periodic arrays of spherical cavities,
An asymptotic study of the inductive pattern formation mechanism in Drosophila egg development,
Stochastic model for autocrine and paracrine signals in cell culture assays,
Discrete models of autocrine cell communication in epithelial layers.
Long-range signal transmission in autocrine relays.
Computational modeling of the EGF receptor system: a paradigm for systems biology.
Transitions in the model of epithelial patterning.
Autocrine loops with positive feedback enable context-dependent cell signaling.
Shooting from the hip,
Modeling and computational analysis of EGF receptor-mediated cell communication in Drosophila oogenesis.
