2023

• Pearson W. Miller, Daniel Fortunato, Matteo Novaga, Stanislav Y. Shvartsman, Cyrill B. Muratov
  Generation and Motion of Interfaces in a Mass-Conserving Reaction-Diffusion System
  SIAM Journal on Applied Dynamical Systems (2023).
• Matthew R. Johnson, Sha Li, Christian F. Guerrero-Juarez, Pearson Miller, Benjamin J. Brack, Sarah A. Mereby, Jorge A. Moreno, Charles Y. Feigin, Jenna Gaska, Jaime A. Rivera-Perez, Qing Nie, Alexander Ploss, Stanislav Y. Shvartsman, Ricardo Mallarino
  A multifunctional Wnt regulator underlies the evolution of rodent stripe patterns
  Nature Ecology & Evolution (2023).
• Ekaterina P. Andrianova, Robert A. Marmion, Stanislav Y. Shvartsman, Igor B. Zhulin
  Evolutionary history of MEK1 illuminates the nature of deleterious mutations
  PNAS (2023).
• Stanislav Y. Shvartsman, Sarah McFann, Martin Wühr, Boris Y. Rubinstein
  Phase plane dynamics of ERK phosphorylation
  Journal of Biological Chemistry (2023).
• Celia M. Smits, Sayantan Dutta, Vishank Jain-Sharma, Sebastian J. Streichan, Stanislav Y. Shvartsman
  Maintaining symmetry during body axis elongation
  Current Biology (2023).
• Rocky Diegmiller, Jasmin Imran Alsous, Duojia Li, Yukiko M. Yamashita, Stanislav Y. Shvartsman
  Fusome topology and inheritance during insect gametogenesis
  PLOS Computational Biology (2023).
• Matthew Smart, Stanislav Y. Shvartsman, Hayden Nunley
  A model of replicating coupled oscillators generates naturally occurring cell networks
  Development (2023).
• Robert A. Marmion, Alison G. Simpkins, Lena A. Barrett, David W. Denberg, Susan Zusman, Jodi Schottenfeld-Roames, Trudi Schüpbach, Stanislav Y. Shvartsman
  Stochastic phenotypes in RAS-dependent developmental diseases
  Current Biology (2023).

2022

• Rocky Diegmiller, Hayden Nunley, Stanislav Y. Shvartsman and Jasmin Imran Alsous
  Quantitative models for building and growing fated small cell networks.
  Interface Focus (2022).
• Sarah McFann, Jared E. Toettcher, Stanislav Y. Shvartsman
  Putting in the Erk: Growth factor signaling and mesoderm morphogenesis.
  Current Topics in Developmental Biology (2022).
• Shannon E. Keenan, Maria Avdeeva, Liu Yang, Daniel S. Alber, Eric F. Wieschaus, Stanislav Y. Shvartsman
  Dynamics of Drosophila endoderm specification.
  PNAS (2022).
• Claire J. Weaver, Aleena L. Patel, Stanislav Y. Shvartsman, Michael S. Levine, Nicholas Treen
  ERK signaling dissolves ERF repression condensates in living embryos.
  PNAS (2022).
• Tomer Stern, Stanislav Y. Shvartsman, Eric F. Wieschaus
  Deconstructing gastrulation at single-cell resolution.
  Current Biology (2022).
• Caroline A. Doherty, Farners Amargant, Stanislav Y. Shvartsman, Francesca E. Duncan, Elizabeth R. Gavis
  Bidirectional communication in oogenesis: a dynamic conversation in mice and Drosophila.
  Trends in Cell Biology (2022).

2021

• Sarah McFann, Sayantan Dutta, Jared E. Toettcher, Stanislav Y. Shvartsman
  Temporal integration of inductive cues on the way to gastrulation.
  PNAS (2021).
• Joseph Crapse, Nishant Pappireddi, Meera Gupta, Stanislav Y Shvartsman, Eric Wieschaus, Martin Wühr
  Evaluating the Arrhenius equation for developmental processes.
  Molecular Systems Biology (2021).
• Aleena L. Patel, Lili Zhang, Shannon E. Keenan, Christine A. Rushlow, Cécile Fradin, Stanislav Y. Shvartsman
  Capicua is a fast-acting transcriptional brake.
  Current Biology (2021).
• Binglun Shao, Rocky Diegmiller, Stanislav Y. Shvartsman
  Collective oscillations of coupled cell cycles.
  Biophysical Journal (2021).
• Sayantan Dutta, Aleena L. Patel, Shannon E. Keenan, Stanislav Y. Shvartsman
  From complex datasets to predictive models of embryonic development.
  Nature Computational Science (2021).
• Shao-Kuei Huang, Peter H. Whitney, Sayantan Dutta, Stanislav Y. Shvartsman, Christine A. Rushlow
  Spatial organization of transcribing loci during early genome activation in Drosophila.
  Current Biology (2021).
• Jasmin Imran Alsous, Jan Rozman, Robert A. Marmion, Andrej Košmrlj, Stanislav Y. Shvartsman
  Clonal dominance in excitable cell networks.
  Nature Physics (2021).
• Rocky Diegmiller, Caroline A. Doherty, Tomer Stern, Jasmin Imran Alsous, Stanislav Y. Shvartsman
  Size scaling in collective cell growth.
  Development (2021).
• Sarah McFann, Sayantan Dutta, Jared E. Toettcher, Stanislav Y. Shvartsman
  Temporal integration of inductive cues on the way to gastrulation.
  PNAS (2021).
• Caroline A. Doherty, Rocky Diegmiller, Manisha Kapasiawala, Elizabeth R. Gavis, Stanislav Y. Shvartsman
  Coupled oscillators coordinate collective germline growth.
  Developmental Cell (2021).
• Rocky Diegmiller, Lun Zhang, Marcio Gameiro, Justine Barr, Jasmin Imran Alsous, Paul Schedl, Stanislav Y. Shvartsman, Konstantin Mischaikow
  Mapping parameter spaces of biological switches.
  PLoS Computational Biology (2021).
• Robert A. Marmion, Liu Yang, Yogesh Goyal, Granton A. Jindal, Joshua L. Wetzel, Mona Singh, Trudi Schüpbach, Stanislav Y. Shvartsman
  Molecular mechanisms underlying cellular effects of human MEK1 mutations.
  Molecular Biology of the Cell (2021).

2020

• Vincent F. Fiore, Matej Krajnc, Felipe Garcia Quiroz, John Levorse, H Amalia Pasolli, Stanislav Y. Shvartsman, Elaine Fuchs
  Mechanics of a multilayer epithelium instruct tumor architecture and function.
  Nature (2020).
• Tomer Stern, Stanislav Y. Shvartsman, Eric F. Wieschaus
  Template-based mapping of dynamic motifs in tissue morphogenesis.
  PLoS Computational Biology (2020).
• Heath E. Johnson, Nareg J.V. Djabrayan, Stanislav Y. Shvartsman, Jared E. Toettcher
  Optogenetic Rescue of a Patterning Mutant.
  Current Biology (2020).
• Yonghyun Song, Stanislav Y. Shvartsman
  Chemical embryology redux: metabolic control of developement.
  Trends in Genetics (2020).
• Sayantan Dutta, Nareg J.V. Djabrayan, Celia M. Smits, Clarence W. Rowley, Stanislav Y. Shvartsman
  Excess dNTPs trigger oscillatory surface flow in the early Drosophila embryo.
  Biophysical Journal (2020).
• Shannon E. Keenan, Shelby A. Blythe, Robert A. Marmion, Nareg J.-V. Djabrayan, Eric F. Wieschaus, Stanislav Y. Shvartsman.
  Rapid dynamics of signal-dependent transcriptional repression by Capicua.
  Developmental Cell (2020).
• Sayantanee Paul, Liu Yang, Henry Mattingly, Yogesh Goyal, Stanislav Y. Shvartsman, Alexey Veraksa.
  Activation-induced substrate engagement in ERK signaling.
  Molecular Biology of the Cell (2020).
• Celia M. Smits, Stanislav Y. Shvartsman
  The design and logic of terminal patterning in Drosophila.
  Current Topics in Developmental Biology (2020).
• Eyan Yeung, Sarah McFann, Lewis Marsh, Emilie Dufresne, Sarah Filippi, Heather A. Harrington, Stanislav Y. Shvartsman, and Martin Wühr.
  Inference of multisite phosphorylation rate constants and their modulation by pathogenic mutations.
  Current Biology (2020).

2019

• Aleena L. Patel, Eyan Yeung, Sarah E. McGuire, Andrew Y. Wu, Jared E. Toettcher, Rebecca D. Burdine, Stanislav Y. Shvartsman
  Optimizing photoswitchable MEK.
  PNAS (2019).
• Yonghyun Song, Junyoung O. Park, Lukas Tanner, Yatsuhisa Nagano, Joshua D. Rabinowitz, Stanislav Y. Shvartsman
  Energy budget of Drosophila embryogenesis.
  Current Biology (2019).
• Clinton A. Taylor IV, Kevin W. Cormier, Shannon E. Keenan, Svetlana Earnest, Steve Stippec, Chonlarat Wichaidit, Yu-Chi Juang, Junmei Wang, Stanislav Y. Shvartsman, Elizabeth J. Goldsmith and Melanie H. Cobb
  Functional divergence caused by mutations in an energetic hotspot in ERK2.
  PNAS (2019).
• Sayantan Dutta, Nareg J.V. Djabrayan, Salvatore Torquato, Stanislav Y. Shvartsman, Matej Krajnc
  Self-similar dynamics of nuclear packing in the early Drosophila embryo.
  Biophysical Journal (2019).
• Nareg J.V. Djabrayan, Celia M. Smits, Matej Krajnc, Tomer Stern, Shigehiro Yamada, William C. Lemon, Philipp J. Keller, Christine A. Rushlow and Stanislav Y. Shvartsman
  Metabolic Regulation of Developmental Cell Cycles and Zygotic Transcription.
  Current Biology (2019).

2018

• Aleena L. Patel and Stanislav Y. Shvartsman
  Outstanding questions in developmental ERK signaling.
  Development (2018).
• Jasmin Imran Alsous, Paul Villoutreix, Norbert Stoop, Stanislav Y. Shvartsman, Jörn Dunkel
  Entropic effects in cell lineage tree packings.
  Nature Physics (2018).
• Yogesh Goyal, Trudi Schüpbach, Stanislav Y. Shvartsman
  A quantitative model of developmental RTK signaling.
  Developmental Biology (2018).
• Rocky Diegmiller, Hadrien Montanelli, Cyrill B. Muratov, Stanislav Y. Shvartsman
  Spherical caps in cell polarization.
  Biophysical Journal (2018).

2017

• Granton A. Jindal, Yogesh Goyal, John M. Humphreys, Eyan Yeung, Kaijia Tian, Victoria L. Patterson, Haixia He, Rebecca D. Burdine, Stanislav Y. Shvartsman, and Elizabeth J. Goldsmith
  How activating mutations affect MEK1 regulation and function.
  J Biol Chem (2017).
• Shannon E. Keenan and Stanislav Y. Shvartsman
  Mechanisms and causality in molecular diseases.
  History and Philosophy of the Life Sciences (2017).
• Paul Villoutreix , Joakim Andén , Bomyi Lim, Hang Lu, Ioannis G. Kevrekidis, Amit Singer and Stanislav Y. Shvartsman
  Synthesizing developmental trajectories.
  PLoS Comput Biol (2017).
• Jasmin Imran Alsous, Paul Villoutreix, Alexander M. Berezhkovskii, and Stanislav Y. Shvartsman
  Collective growth in a small cell network.
  Current Biology (2017).
• Maira Arruda Cardoso, Marcio Fontenele, Bomyi Lim, Paulo Mascarello Bisch, Stanislav Y. Shvartsman, and Helena Marcolla Araujo
  A novel function for the IκB inhibitor Cactus in promoting Dorsal nuclear localization and activity in the Drosophila embryo.
  Development (2017).
• Yogesh Goyal, Thomas J. Levario, Henry H. Mattingly, Susan Holmes, Stanislav Y. Shvartsman, and Hang Lu
  Parallel imaging of Drosophila embryos for quantitative analysis of genetic perturbations of the Ras pathway.
  Disease Models & Mechanisms (2017).
• Henry H. Mattingly, Moshe Sheintuch, and Stanislav Y. Shvartsman
  The Design Space of the Embryonic Cell Cycle Oscillator.
  Biophysical Journal (2017).
• Yonghyun Song, Robert A. Marmion, Junyoung O. Park, Debopriyo Biswas, Joshua D. Rabinowitz, and Stanislav Y. Shvartsman
  Dynamic Control of dNTP Synthesis in Early Embryos.
  Developmental Cell (2017).
• George Pyrowolakis, Ville Veikkolainen, Nir Yakoby, and Stanislav Y. Shvartsman
  Gene regulation during Drosophila eggshell patterning.
  PNAS (2017).
• Miriam Osterfield, Celeste A. Berg, and Stanislav Y. Shvartsman
  Epithelial Patterning, Morphogenesis, and Evolution: Drosophila Eggshell as a Model.
  Developmental Cell (2017).
• William A. Rogers, Yogesh Goyal, Kei Yamaya, Stanislav Y. Shvartsman and Michael S. Levine
  Uncoupling neurogenic gene networks in the Drosophila embryo.
  Genes and Development (2017).
• Mahim Misra, Basile Audoly, Stanislav Y. Shvartsman
  Complex structures from patterned cell sheets.
  Philos Trans R Soc Lond B Biol Sci. (2017).
• Bomyi Lim, Carmeline J. Dsilva, Ioannis G. Kevrekidis, Stanislav Y. Shvartsman
  Reconstructing ERK Signaling in the Drosophila Embryo from Fixed Images.
  Methods Mol Biol. (2017).
• Natasha Arora, Jasmin Imran Alsous, Jacob W. Guggenheim, Michael Mak, Jorge Munera, James M. Wells, Roger D. Kamm, H. Harry Asada, Stanislav Y. Shvartsman, Linda G. Griffith
  A process engineering approach to increase organoid yield
  Development (2017).
• Yogesh Goyal, Granton A Jindal, José L Pelliccia, Kei Yamaya, Eyan Yeung, Alan S Futran, Rebecca D Burdine, Trudi Schüpbach & Stanislav Y Shvartsman
  Divergent effects of intrinsically active MEK variants on developmental Ras signaling
  Nature Genetics (2017).
• Heath E. Johnson, Yogesh Goyal, Nicole L. Pannucci, Trudi Schüpbach, Stanislav Y. Shvartsman, Jared E. Toettcher
  The Spatiotemporal Limits of Developmental Erk Signaling
  Developmental Cell (2017).
• Granton A. Jindal, Yogesh Goyal, Kei Yamaya, Alan S. Futran, Iason Kountouridis, Courtney A. Balgobin, Trudi Schüpbach, Rebecca D. Burdine, and Stanislav Y. Shvartsman
  In vivo severity ranking of Ras pathway mutations associated with developmental disorders
  PNAS (2017).

2016

• Liu Yang, Sayantanee Paul, Kenneth G. Trieu, Lucas G. Dent, Francesca Froldi, Marta Forés, Kaitlyn Webster, Kellee R. Siegfried, Shu Kondo, Kieran Harvey, Louise Cheng, Gerardo Jiménez, Stanislav Y. Shvartsman, and Alexey Veraksa
  Minibrain and Wings apart control organ growth and tissue patterning through down-regulation of Capicua
  PNAS (2016).
• Alexander M. Berezhkovskii and Stanislav Y. Shvartsman
  Diffusive Flux in a Model of Stochastically Gated Oxygen Transport in Insect Respiration
  J. Chem. Phys. 144, 204101 (2016).
• Boris Y. Rubinstein, Henry H. Mattingly, Alexander M. Berezhkovskii, and Stanislav Y. Shvartsman
  Long-Term Dynamics of Multi-Site Phosphorylation
  Mol. Biol. Cell E16-03-0137 (2016).
• Mahim Misra, Basile Audoly, Ioannis G. Kevrekidis & Stanislav Y. Shvartsman
  Shape Transformations of Epithelial Shells
  Biophysical Journal, Vol. 110 (7) 1670–1678 (2016).
• Thomas J. Levario, Bomyi Lim, Stanislav Y. Shvartsman & Hang Lu
  Microfluidics for High-Throughput Quantitative Studies of Early Development
  Annual Review of Biomedical Engineering, Vol. 18 (2016).
• Thomas J. Levario, Charles Zhao, Tel Rouse1, Stanislav Y. Shvartsman & Hang Lu
  An integrated platform for large-scale data collection and precise perturbation of live Drosophila embryos
  Scientific Reports 6: 21366 (2016).

2015

• Md. Abul Hassan Samee, Bomyi Lim, Nuria Samper, Hang Lu, Christine A. Rushlow, Gerardo Jimenez, Stanislav Y. Shvartsman, and Saurabh SinhaA Systematic Ensemble Approach to Thermodynamic Modeling of Gene Expression from Sequence DataCell Systems 1: 396-407 (2015).
• Henry H. Mattingly, Jessica J. Chen, Swathi Arur and Stanislav Y. Shvartsman
  A Transport Model for Estimating the Time Course of ERK Activation in the C. elegans Germline
  Biophysical Journal 109(11): 2436-45 (2015).
• Simon Jenni, Yogesh Goyal, Marcin von Grotthuss, Stanislav Y. Shvartsman and Daryl E. Klein
  Structural Basis of Neurohormone Perception by the Receptor Tyrosine Kinase Torso
  Molecular Cell, in press (2015).
• Alexander M. Berezhkovskii and Stanislav Y. Shvartsman
  Dynamics of gradient formation by intracellular shuttling
  J. Chem. Phys. 143, 074116 (2015).
• Granton A. Jindal, Yogesh Goyal, Rebecca D. Burdine, Katherine A. Rauen, and Stanislav Y. Shvartsman
  RASopathies: unraveling mechanisms with animal models
  Dis. Model. Mech.8:769-782 (2015).
• Nebojsa Murisic, Vincent Hakim, Ioannis G. Kevrekidis, Stanislav Y. Shvartsman, and Basile Audoly
  From Discrete to Continuum Models of Three-Dimensional Deformations in Epithelial Sheets
  Biophysical Journal, 109, 154–163 (2015).
• Alan S. Futran, Saw Kyin, Stanislav Y. Shvartsman, and A. James Link
  Mapping the Binding Interface of ERK and Transcriptional Repressor Capicua Using Photocrosslinking
  PNAS (2015).
• Bomyi Lim, Carmeline J. Dsilva, Thomas J. Levario, Hang Lu, Trudi Schüpbach, Ioannis G. Kevrekidis, and Stanislav Y. Shvartsman
  Dynamics of Inductive ERK Signaling in the Drosophila Embryo
  Current Biology, 25, 1784 – 1790 (2015).
• Miriam Osterfield, Trudi Schüpbach, Eric Wieschaus, and Stanislav Y. Shvartsman
  Diversity of epithelial morphogenesis during eggshell formation in drosophilids
  Development, 142, 1971-1977 (2015).
• Carmeline J. Dsilva, Bomyi Lim, Hang Lu, Amit Singer, Ioannis G. Kevrekidis, and Stanislav Y. Shvartsman
  Temporal ordering and registration of images in studies of developmental dynamics 
  Development, 142, 1-8 (2015).
• Enrica Charbonnier, Alisa Fuchs, Lily S. Cheung, Mrinal Chayengia, Ville Veikkolainen, Stanislav Y. Shvartsman, and George Pyrowolakis
  BMP-dependent gene repression cascade in Drosophila eggshell patterning
  Developmental Biology, 402, 263 (2015).

• Code for the “Temporal ordering and registration of images in studies of developmental dynamics”

2014

• Xinxin Du, Miriam Osterfield and Stanislav Y. Shvartsman
  Computational analysis of three-dimensional epithelial morphogenesis using vertex models
  Physical Biology, 11. 066007 (2014).
• Lily S. Cheung and Stanislav Y. Shvartsman
  A Multiplex Fluorescent In Situ Hybridization Protocol for Clonal Analysis of Drosophila Oogenesis
  Methods Mol Biol. 1189, 2015, p115-22 (2014).
• Sun Melody Foo, Yujia Sun, Bomyi Lim, Ruta Ziukaite, Kevin O’Brien, Chung-Yi Nien, Nikolai Kirov, Stanislav Y. Shvartsman, and Christine A. Rushlow
  Zelda Potentiates Morphogen Activity by Increasing Chromatin Accessibility
  Current Biology, 24, 1341-1346 (2014).
• Alexander G. Fletcher, Miriam Osterfield, Ruth E. Baker, and Stanislav Y. Shvartsman
  Vertex Models of Epithelial Morphogenesis
  Biophysical Journal. Vol 106 2291-2304 (2014).
• Alexander M. Berezhkovskii, and Stanislav Y. Shvartsman
  On the GFP-Based Analysis of Dynamic Concentration Profiles
  Biophysical Journal. Vol 106 L13-L15 (2014).

2013

• Alan S. Futran, A. James Link, Rony Seger, and Stanislav Y. Shvartsman
  ERK as a model for systems biology of enzyme kinetics in cells
  Current Biology 23(21):972-979 (2013).
• Lily S. Cheung, David S. Simakov, Alisa Fuchs, George Pyrowolakis, and Stanislav Y. Shvartsman
  Dynamic model for the coordination of two enancers of broad by EGFR signaling
  PNAS Vol.110, No.44, 17939-17944 (2013).
• Alexander M. Berezhkovskii, and Stanislav Y. Shvartsman
  Kinetics of receptor occupancy during morphogen gradient formation
  The Journal of Chemical Physics, 138, 244105 (2013).
• Bomyi Lim, Nuria Samper, Hang Lu, Christine Rushlow, Gerardo Jimenez, and Stanislav Y. Shvartsman
  Kinetics of gene derepression by ERK signaling
  PNAS Vol.110, No.25, 10330-10335 (2013).
• Yoosik Kim, Antonia Iagovitina, Keisuke Ishihara, Kate M. Fitzgerald, Bart Deplancke, Dmitri Papatsenko, and Stanislav Y. Shvartsman
  Context-dependent transcriptional interpretation of mitogen activated protein kinase signaling in the Drosophila embryo
  Chaos, 23, 025105 (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

• Shvartsman SY, Wiley HS, Deen WM, Lauffenburger DA.
  Spatial range of autocrine signaling: modeling and computational analysis.
  Biophys J., 2001, 81(4):1854-67.