Stanislav Shvartsman

Summary

Affiliation: Princeton University
Country: USA

Publications

  1. doi request reprint Mathematical models of morphogen gradients and their effects on gene expression
    Stanislav Y Shvartsman
    Department of Chemical and Biological Engineering and Lewis Sigler Institute for Integrative Genomics, Princeton University, NJ, USA
    Wiley Interdiscip Rev Dev Biol 1:715-30. 2012
  2. doi request reprint Unit operations of tissue development: epithelial folding
    Jeremiah J Zartman
    Department of Chemical Engineering, Carl Icahn Laboratory, Princeton University, Princeton, NJ 08544, USA
    Annu Rev Chem Biomol Eng 1:231-46. 2010
  3. pmc MAPK signaling in equations and embryos
    Stanislav Y Shvartsman
    Lewis Sigler Institute for Integrative Genomics and Department of Chemical Engineering, Princeton University, Princeton, New Jersey, USA
    Fly (Austin) 3:62-7. 2009
  4. pmc Dynamics of maternal morphogen gradients in Drosophila
    Stanislav Y Shvartsman
    Department of Chemical Engineering and Lewis Sigler Institute for Integrative Genomics, Princeton University, New Jersey, United States
    Curr Opin Genet Dev 18:342-7. 2008
  5. ncbi request reprint Modeling and computational analysis of EGF receptor-mediated cell communication in Drosophila oogenesis
    Stanislav Y Shvartsman
    Department of Chemical Engineering and Lewis Sigler Institute for Integrative Genomics, Princeton University, NJ 08544, USA
    Development 129:2577-89. 2002
  6. pmc Shooting from the hip: spatial control of signal release by intracellular waves
    Stanislav Y Shvartsman
    Department of Chemical Engineering and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
    Proc Natl Acad Sci U S A 99:9087-9. 2002
  7. ncbi request reprint Computational analysis of EGFR inhibition by Argos
    Gregory T Reeves
    Department of Chemical Engineering, Princeton University, Princeton, NJ 08544, USA Lewis Sigler Institute for Integrative Genomics, Princeton University, Carl Icahn Laboratory, Washington Road, Princeton, NJ 08544, USA
    Dev Biol 284:523-35. 2005
  8. pmc Discrete models of autocrine cell communication in epithelial layers
    Michal Pribyl
    Department of Chemical Engineering and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
    Biophys J 84:3624-35. 2003
  9. pmc Feedback control of the EGFR signaling gradient: superposition of domain-splitting events in Drosophila oogenesis
    Jeremiah J Zartman
    Lewis Sigler Institute and Department of Chemical Engineering, Carl Icahn Laboratory, Washington Road, Princeton University, Princeton, NJ 08544, USA
    Development 136:2903-11. 2009
  10. pmc Cad74A is regulated by BR and is required for robust dorsal appendage formation in Drosophila oogenesis
    Jeremiah J Zartman
    Lewis Sigler Institute and Department of Chemical Engineering, Carl Icahn Laboratory, Princeton University, Princeton, NJ 08544, USA
    Dev Biol 322:289-301. 2008

Collaborators

  • Trudi Schupbach
  • Douglas Lauffenburger
  • Ruth E Baker
  • H Wiley
  • Jennifer Lippincott-Schwartz
  • Jeremiah J Zartman
  • Nir Yakoby
  • Alexander M Berezhkovskii
  • Jessica Lembong
  • Jitendra S Kanodia
  • Yoosik Kim
  • Gregory T Reeves
  • Mathieu Coppey
  • Michal Pribyl
  • Cyrill B Muratov
  • Lea A Goentoro
  • Michael I Monine
  • Daryl E Klein
  • Michail E Kavousanakis
  • Christine Sample
  • Lazaros Batsilas
  • Karin Schlichting
  • Ioannis G Kevrekidis
  • Christian Dahmann
  • Xenia Schafer
  • Christopher A Bristow
  • Alistair N Boettiger
  • Liang Qiao
  • Mark A Lemmon
  • Ze ev Paroush
  • Gerardo JimĂ©nez
  • Leiore Ajuria
  • Rona Grossman
  • Lily S Cheung
  • Robert DeLotto
  • Viktor K Lund
  • Richa Rikhy
  • Colin Watson
  • Danielle Gong
  • Marc S Halfon
  • Xiaofeng Zhou
  • Robert B Nachbar
  • Luigi Martinelli
  • Craig P Kowal
  • Joseph Goodhouse
  • Rachel Kalifa
  • Elizabeth J Joslin
  • Valerie M Nappi

Detail Information

Publications34

  1. doi request reprint Mathematical models of morphogen gradients and their effects on gene expression
    Stanislav Y Shvartsman
    Department of Chemical and Biological Engineering and Lewis Sigler Institute for Integrative Genomics, Princeton University, NJ, USA
    Wiley Interdiscip Rev Dev Biol 1:715-30. 2012
    ..Transcriptional control by morphogens is discussed within the framework of thermodynamic site occupancy models of gene regulatory regions...
  2. doi request reprint Unit operations of tissue development: epithelial folding
    Jeremiah J Zartman
    Department of Chemical Engineering, Carl Icahn Laboratory, Princeton University, Princeton, NJ 08544, USA
    Annu Rev Chem Biomol Eng 1:231-46. 2010
    ..In turn, quantitative models of embryogenesis can inspire novel methods for creating synthetic organs and treating degenerative tissue diseases...
  3. pmc MAPK signaling in equations and embryos
    Stanislav Y Shvartsman
    Lewis Sigler Institute for Integrative Genomics and Department of Chemical Engineering, Princeton University, Princeton, New Jersey, USA
    Fly (Austin) 3:62-7. 2009
    ..Here we discuss a biophysical model that can describe the observed dynamics and guide future experiments for exploring the relative importance of multiple layers of MAPK cascade regulation...
  4. pmc Dynamics of maternal morphogen gradients in Drosophila
    Stanislav Y Shvartsman
    Department of Chemical Engineering and Lewis Sigler Institute for Integrative Genomics, Princeton University, New Jersey, United States
    Curr Opin Genet Dev 18:342-7. 2008
    ..The results of these quantitative studies provide critical tests of classical models and reveal new modes of morphogen regulation and readout in one of the most extensively studied patterning systems...
  5. ncbi request reprint Modeling and computational analysis of EGF receptor-mediated cell communication in Drosophila oogenesis
    Stanislav Y Shvartsman
    Department of Chemical Engineering and Lewis Sigler Institute for Integrative Genomics, Princeton University, NJ 08544, USA
    Development 129:2577-89. 2002
    ..We propose that versatility in signaling mediated by autocrine loops can be systematically explored using experiment-based mechanistic models and their analysis...
  6. pmc Shooting from the hip: spatial control of signal release by intracellular waves
    Stanislav Y Shvartsman
    Department of Chemical Engineering and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
    Proc Natl Acad Sci U S A 99:9087-9. 2002
  7. ncbi request reprint Computational analysis of EGFR inhibition by Argos
    Gregory T Reeves
    Department of Chemical Engineering, Princeton University, Princeton, NJ 08544, USA Lewis Sigler Institute for Integrative Genomics, Princeton University, Carl Icahn Laboratory, Washington Road, Princeton, NJ 08544, USA
    Dev Biol 284:523-35. 2005
    ..Thus, the spatial range of Argos does not have to be tightly regulated or may act at different ranges in distinct developmental contexts...
  8. pmc Discrete models of autocrine cell communication in epithelial layers
    Michal Pribyl
    Department of Chemical Engineering and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
    Biophys J 84:3624-35. 2003
    ..We use our model to interpret recent experimental studies of the EGFR/Rhomboid/Spitz module in Drosophila development...
  9. pmc Feedback control of the EGFR signaling gradient: superposition of domain-splitting events in Drosophila oogenesis
    Jeremiah J Zartman
    Lewis Sigler Institute and Department of Chemical Engineering, Carl Icahn Laboratory, Washington Road, Princeton University, Princeton, NJ 08544, USA
    Development 136:2903-11. 2009
    ..Thus, the processes that define the two-domain patterns of Broad and EGFR activation are distinct; their actions are separated in time and have different effects on eggshell morphology...
  10. pmc Cad74A is regulated by BR and is required for robust dorsal appendage formation in Drosophila oogenesis
    Jeremiah J Zartman
    Lewis Sigler Institute and Department of Chemical Engineering, Carl Icahn Laboratory, Princeton University, Princeton, NJ 08544, USA
    Dev Biol 322:289-301. 2008
    ..Based on these results, we propose that Cad74A is part of the adhesive machinery that enables robust dorsal appendage formation, and as such provides a link between the patterning of the follicle cells and eggshell morphogenesis...
  11. pmc Nuclear trapping shapes the terminal gradient in the Drosophila embryo
    Mathieu Coppey
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA
    Curr Biol 18:915-9. 2008
    ..Inside the syncytial embryo, nuclei play the role of traps that localize diffusible dpERK. We argue that the length scale of the terminal-patterning gradient is determined mainly by the intracellular module...
  12. doi request reprint Expression patterns of cadherin genes in Drosophila oogenesis
    Jeremiah J Zartman
    Lewis Sigler Institute, Department of Chemical Engineering, Princeton University, Princeton, NJ 08544, USA
    Gene Expr Patterns 9:31-6. 2009
    ..Of particular note is the complex patterning of the region of the follicular epithelium that gives rise to the dorsal appendages, which are tubular structures that serve as respiratory organs for the developing embryo...
  13. pmc MAPK substrate competition integrates patterning signals in the Drosophila embryo
    Yoosik Kim
    Department of Chemical Engineering and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
    Curr Biol 20:446-51. 2010
    ..Substrate competition can be a general signal integration strategy in networks where enzymes, such as MAPK, interact with their multiple regulators and targets...
  14. pmc A compartmental model for the bicoid gradient
    Michail E Kavousanakis
    Department of Chemical Engineering, Princeton University, Princeton, NJ, USA
    Dev Biol 345:12-7. 2010
    ..We formulate a compartmental model, constrain its parameters by experimental data, and demonstrate that it provides an adequate description of the Bcd gradient dynamics...
  15. ncbi request reprint Quantitative models of developmental pattern formation
    Gregory T Reeves
    Department of Chemical Engineering and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
    Dev Cell 11:289-300. 2006
    ..Using a number of problems in fruit fly development, we discuss how models can be used to test the feasibility of proposed patterning mechanisms and characterize their systems-level properties...
  16. doi request reprint Spatial regulation of BMP signaling by patterned receptor expression
    Jessica Lembong
    Department of Chemical Engineering and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
    Tissue Eng Part A 14:1469-77. 2008
    ..Quantitative understanding of the mechanisms of spatiotemporal control of signaling pathways in development is essential for successful harnessing of these pathways in tissue engineering...
  17. ncbi request reprint Transitions in the model of epithelial patterning
    Michal Pribyl
    Department of Chemical Engineering and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
    Dev Dyn 226:155-9. 2003
    ..The existence of complex patterns in the model can be used to account for complex eggshell morphologies in related fly species...
  18. pmc Pattern formation by dynamically interacting network motifs
    Jessica Lembong
    Department of Chemical Engineering and Lewis Sigler Institute for Integrative Genomics, Washington Road, Princeton University, Princeton, NJ 08544, USA
    Proc Natl Acad Sci U S A 106:3213-8. 2009
    ....
  19. ncbi request reprint Quantifying the Gurken morphogen gradient in Drosophila oogenesis
    Lea A Goentoro
    Department of Chemical Engineering and Lewis Sigler Institute for Integrative Genomics, Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
    Dev Cell 11:263-72. 2006
    ..This provides a direct characterization of the shape of the Gurken gradient and demonstrates how parameter estimation techniques can be used to quantify morphogen gradients in development...
  20. ncbi request reprint Drosophila eggshell is patterned by sequential action of feedforward and feedback loops
    Nir Yakoby
    Department of Chemical Engineering and Lewis Sigler Institute for Integrative Genomics, Princeton University, NJ 08544, USA
    Development 135:343-51. 2008
    ..This mechanism demonstrates how complex patterns of gene expression can emerge from simple inputs, through the interaction of regulatory network motifs...
  21. pmc Dynamics of the Dorsal morphogen gradient
    Jitendra S Kanodia
    Department of Chemical Engineering and Lewis Sigler Institute for Integrative Genomics, Princeton University, Washington Road, Princeton, NJ 08544, USA
    Proc Natl Acad Sci U S A 106:21707-12. 2009
    ..We attribute these striking differences in the dynamics of maternal morphogen gradients to the differences in the initial conditions and chemistries of the anterior, DV, and terminal systems...
  22. pmc Stochastic model of autocrine and paracrine signals in cell culture assays
    Lazaros Batsilas
    Department of Chemical Engineering and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
    Biophys J 85:3659-65. 2003
    ..We test these analytical results by stochastic simulations with efficient Brownian dynamics code and apply our model to analyze the spatial operation of autocrine epidermal growth factor receptor systems...
  23. pmc Multiscale modeling of diffusion in the early Drosophila embryo
    Christine Sample
    Department of Chemical Engineering and Lewis Sigler Institute for Integrative Genomics, Princeton University, Washington Road, Princeton, NJ 08544, USA
    Proc Natl Acad Sci U S A 107:10092-6. 2010
    ..A similar approach can be used to analyze the dynamics of all three maternal morphogen gradients in Drosophila...
  24. pmc A combinatorial code for pattern formation in Drosophila oogenesis
    Nir Yakoby
    Lewis Sigler Institute for Integrative Genomics and Department of Chemical Engineering, Princeton University, Princeton, NJ 08544, USA
    Dev Cell 15:725-37. 2008
    ..The proposed combinatorial framework allows systematic analysis of the diversity and dynamics of two-dimensional transcriptional patterns and guides future studies of gene regulation...
  25. ncbi request reprint Quantitative analysis of the GAL4/UAS system in Drosophila oogenesis
    Lea A Goentoro
    Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544, USA
    Genesis 44:66-74. 2006
    ..The imaging-based strategy described here can be used to quantify other GAL4 drivers in Drosophila and other organisms...
  26. pmc Bistability and oscillations in the Huang-Ferrell model of MAPK signaling
    Liang Qiao
    Department of Chemical Engineering, Princeton University, Princeton, New Jersey, USA
    PLoS Comput Biol 3:1819-26. 2007
    ..We argue that this type of analysis should accompany nonlinear multiparameter studies of stationary as well as transient features in network dynamics...
  27. pmc Ligand accumulation in autocrine cell cultures
    Michael I Monine
    Department of Chemical Engineering and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
    Biophys J 88:2384-90. 2005
    ..We demonstrate how the theory works by analyzing the autocrine epidermal growth factor receptor system and discuss the extension of our methods to other experiments with cultured autocrine cells...
  28. pmc Modeling the bicoid gradient: diffusion and reversible nuclear trapping of a stable protein
    Mathieu Coppey
    Department of Chemical Engineering and Lewis Sigler Institute for Integrative Genomics, Princeton University, USA
    Dev Biol 312:623-30. 2007
    ..Consistent with experimental observations, the Bicoid gradient in our model is established before nuclei migrate to the periphery of the embryo and remains stable during subsequent nuclear divisions...
  29. ncbi request reprint Enhancer organization: transistor with a twist or something in a different vein?
    Jeremiah J Zartman
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
    Curr Biol 17:R1048-50. 2007
    ..Computational modeling of these enhancers suggests interesting parallels with electronic transistors and optical image processors...
  30. pmc Long-range signal transmission in autocrine relays
    Michal Pribyl
    Department of Chemical Engineering and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
    Biophys J 84:883-96. 2003
    ..We compare our results to recent observations of autocrine and paracrine systems and discuss the steps toward experimental tests of our predictions...
  31. ncbi request reprint Argos inhibits epidermal growth factor receptor signalling by ligand sequestration
    Daryl E Klein
    Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, 809C Stellar Chance Laboratories, 422 Curie Boulevard, Philadelphia, Pennsylvania 19104 6059, USA
    Nature 430:1040-4. 2004
    ..Our results provide an insight into the mechanism of Argos function, and suggest new strategies for EGFR inhibitor design...
  32. ncbi request reprint Ligand trapping in epithelial layers and cell cultures
    Alexander M Berezhkovskii
    Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA
    Biophys Chem 107:221-7. 2004
    ..We conclude that a thin layer approximation is applicable for ligand trapping in epithelial layers while a typical cell culture experiment is appropriately described within an infinite layer approximation...
  33. ncbi request reprint Computational modeling of the EGF-receptor system: a paradigm for systems biology
    H Steven Wiley
    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    Trends Cell Biol 13:43-50. 2003
    ..The success of EGFR modeling can be a guide to combining models and experiments productively to understand complex biological processes as integrated systems...
  34. ncbi request reprint Homogenization of boundary conditions for surfaces with regular arrays of traps
    Alexander M Berezhkovskii
    Mathematical and Statistical Computing Laboratory, Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Chem Phys 124:036103. 2006

Research Grants7

  1. Genome wide analysis and modeling of signal integration in the Drosophila ovary
    Stanislav Shvartsman; Fiscal Year: 2007
    ..Given the highly conserved nature of these signaling pathways, our results will provide quantitative insights into the mechanisms of signaling crosstalk in developing and adult tissues. ..
  2. MSM: CR Multiscale analysis of epithelial patterning: m*
    Stanislav Shvartsman; Fiscal Year: 2007
    ..The project will bring together researchers in biology, engineering and mathematics in an interdisciplinary research program aimed at bringing about new understanding of EGFR system. ..
  3. Genome wide analysis and modeling of signal integration in the Drosophila ovary
    Stanislav Shvartsman; Fiscal Year: 2009
    ..Given the highly conserved nature of these signaling pathways, our results will provide quantitative insights into the mechanisms of signaling crosstalk in developing and adult tissues. ..