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Items: 1 to 50 of 116

1.

Editorial overview: Tissue, cell and pathway engineering.

Schaffer D, Shvartsman SY.

Curr Opin Biotechnol. 2018 Aug;52:iv-v. doi: 10.1016/j.copbio.2018.07.004. No abstract available.

PMID:
30086879
2.

Outstanding questions in developmental ERK signaling.

Patel AL, Shvartsman SY.

Development. 2018 Jul 26;145(14). pii: dev143818. doi: 10.1242/dev.143818. Review.

PMID:
30049820
3.

A quantitative model of developmental RTK signaling.

Goyal Y, Schüpbach T, Shvartsman SY.

Dev Biol. 2018 Oct 1;442(1):80-86. doi: 10.1016/j.ydbio.2018.07.012. Epub 2018 Jul 17. Review.

PMID:
30026122
4.

Spherical Caps in Cell Polarization.

Diegmiller R, Montanelli H, Muratov CB, Shvartsman SY.

Biophys J. 2018 Jul 3;115(1):26-30. doi: 10.1016/j.bpj.2018.05.033. Epub 2018 Jun 20.

PMID:
29933887
5.

Mechanisms and causality in molecular diseases.

Keenan SE, Shvartsman SY.

Hist Philos Life Sci. 2017 Oct 16;39(4):35. doi: 10.1007/s40656-017-0162-1.

PMID:
29038918
6.

How activating mutations affect MEK1 regulation and function.

Jindal GA, Goyal Y, Humphreys JM, Yeung E, Tian K, Patterson VL, He H, Burdine RD, Goldsmith EJ, Shvartsman SY.

J Biol Chem. 2017 Nov 17;292(46):18814-18820. doi: 10.1074/jbc.C117.806067. Epub 2017 Oct 10.

7.

Synthesizing developmental trajectories.

Villoutreix P, Andén J, Lim B, Lu H, Kevrekidis IG, Singer A, Shvartsman SY.

PLoS Comput Biol. 2017 Sep 18;13(9):e1005742. doi: 10.1371/journal.pcbi.1005742. eCollection 2017 Sep.

8.

Collective Growth in a Small Cell Network.

Imran Alsous J, Villoutreix P, Berezhkovskii AM, Shvartsman SY.

Curr Biol. 2017 Sep 11;27(17):2670-2676.e4. doi: 10.1016/j.cub.2017.07.038. Epub 2017 Aug 31.

9.

The Design Space of the Embryonic Cell Cycle Oscillator.

Mattingly HH, Sheintuch M, Shvartsman SY.

Biophys J. 2017 Aug 8;113(3):743-752. doi: 10.1016/j.bpj.2017.06.045.

10.

Dynamic Control of dNTP Synthesis in Early Embryos.

Song Y, Marmion RA, Park JO, Biswas D, Rabinowitz JD, Shvartsman SY.

Dev Cell. 2017 Aug 7;42(3):301-308.e3. doi: 10.1016/j.devcel.2017.06.013. Epub 2017 Jul 20.

11.

A novel function for the IκB inhibitor Cactus in promoting Dorsal nuclear localization and activity in the Drosophila embryo.

Cardoso MA, Fontenele M, Lim B, Bisch PM, Shvartsman SY, Araujo HM.

Development. 2017 Aug 15;144(16):2907-2913. doi: 10.1242/dev.145557. Epub 2017 Jul 13.

12.

Gene regulation during Drosophila eggshell patterning.

Pyrowolakis G, Veikkolainen V, Yakoby N, Shvartsman SY.

Proc Natl Acad Sci U S A. 2017 Jun 6;114(23):5808-5813. doi: 10.1073/pnas.1610619114.

13.

Epithelial Patterning, Morphogenesis, and Evolution: Drosophila Eggshell as a Model.

Osterfield M, Berg CA, Shvartsman SY.

Dev Cell. 2017 May 22;41(4):337-348. doi: 10.1016/j.devcel.2017.02.018. Review.

14.

Parallel imaging of Drosophila embryos for quantitative analysis of genetic perturbations of the Ras pathway.

Goyal Y, Levario TJ, Mattingly HH, Holmes S, Shvartsman SY, Lu H.

Dis Model Mech. 2017 Jul 1;10(7):923-929. doi: 10.1242/dmm.030163. Epub 2017 May 11.

15.

Uncoupling neurogenic gene networks in the Drosophila embryo.

Rogers WA, Goyal Y, Yamaya K, Shvartsman SY, Levine MS.

Genes Dev. 2017 Apr 1;31(7):634-638. doi: 10.1101/gad.297150.117. Epub 2017 Apr 20.

16.

Complex structures from patterned cell sheets.

Misra M, Audoly B, Shvartsman SY.

Philos Trans R Soc Lond B Biol Sci. 2017 May 19;372(1720). pii: 20150515. doi: 10.1098/rstb.2015.0515. Review.

17.

A process engineering approach to increase organoid yield.

Arora N, Imran Alsous J, Guggenheim JW, Mak M, Munera J, Wells JM, Kamm RD, Asada HH, Shvartsman SY, Griffith LG.

Development. 2017 Mar 15;144(6):1128-1136. doi: 10.1242/dev.142919. Epub 2017 Feb 7.

18.

Divergent effects of intrinsically active MEK variants on developmental Ras signaling.

Goyal Y, Jindal GA, Pelliccia JL, Yamaya K, Yeung E, Futran AS, Burdine RD, Schüpbach T, Shvartsman SY.

Nat Genet. 2017 Mar;49(3):465-469. doi: 10.1038/ng.3780. Epub 2017 Feb 6.

19.

The Spatiotemporal Limits of Developmental Erk Signaling.

Johnson HE, Goyal Y, Pannucci NL, Schüpbach T, Shvartsman SY, Toettcher JE.

Dev Cell. 2017 Jan 23;40(2):185-192. doi: 10.1016/j.devcel.2016.12.002.

20.

In vivo severity ranking of Ras pathway mutations associated with developmental disorders.

Jindal GA, Goyal Y, Yamaya K, Futran AS, Kountouridis I, Balgobin CA, Schüpbach T, Burdine RD, Shvartsman SY.

Proc Natl Acad Sci U S A. 2017 Jan 17;114(3):510-515. doi: 10.1073/pnas.1615651114. Epub 2017 Jan 3.

21.

Reconstructing ERK Signaling in the Drosophila Embryo from Fixed Images.

Lim B, Dsilva CJ, Kevrekidis IG, Shvartsman SY.

Methods Mol Biol. 2017;1487:337-351.

PMID:
27924579
22.

Minibrain and Wings apart control organ growth and tissue patterning through down-regulation of Capicua.

Yang L, Paul S, Trieu KG, Dent LG, Froldi F, Forés M, Webster K, Siegfried KR, Kondo S, Harvey K, Cheng L, Jiménez G, Shvartsman SY, Veraksa A.

Proc Natl Acad Sci U S A. 2016 Sep 20;113(38):10583-8. doi: 10.1073/pnas.1609417113. Epub 2016 Sep 6.

23.

Diffusive flux in a model of stochastically gated oxygen transport in insect respiration.

Berezhkovskii AM, Shvartsman SY.

J Chem Phys. 2016 May 28;144(20):204101. doi: 10.1063/1.4950769.

24.

Long-term dynamics of multisite phosphorylation.

Rubinstein BY, Mattingly HH, Berezhkovskii AM, Shvartsman SY.

Mol Biol Cell. 2016 Jul 15;27(14):2331-40. doi: 10.1091/mbc.E16-03-0137. Epub 2016 May 25.

25.

A Systematic Ensemble Approach to Thermodynamic Modeling of Gene Expression from Sequence Data.

Samee MA, Lim B, Samper N, Lu H, Rushlow CA, Jiménez G, Shvartsman SY, Sinha S.

Cell Syst. 2015 Dec 23;1(6):396-407. doi: 10.1016/j.cels.2015.12.002. Epub 2015 Dec 23.

26.

Shape Transformations of Epithelial Shells.

Misra M, Audoly B, Kevrekidis IG, Shvartsman SY.

Biophys J. 2016 Apr 12;110(7):1670-1678. doi: 10.1016/j.bpj.2016.03.009.

27.

Microfluidics for High-Throughput Quantitative Studies of Early Development.

Levario TJ, Lim B, Shvartsman SY, Lu H.

Annu Rev Biomed Eng. 2016 Jul 11;18:285-309. doi: 10.1146/annurev-bioeng-100515-013926. Epub 2016 Feb 29. Review.

PMID:
26928208
28.

An integrated platform for large-scale data collection and precise perturbation of live Drosophila embryos.

Levario TJ, Zhao C, Rouse T, Shvartsman SY, Lu H.

Sci Rep. 2016 Feb 11;6:21366. doi: 10.1038/srep21366.

29.

Structural Basis of Neurohormone Perception by the Receptor Tyrosine Kinase Torso.

Jenni S, Goyal Y, von Grotthuss M, Shvartsman SY, Klein DE.

Mol Cell. 2015 Dec 17;60(6):941-52. doi: 10.1016/j.molcel.2015.10.026. Epub 2015 Nov 19.

30.

A Transport Model for Estimating the Time Course of ERK Activation in the C. elegans Germline.

Mattingly HH, Chen JJ, Arur S, Shvartsman SY.

Biophys J. 2015 Dec 1;109(11):2436-45. doi: 10.1016/j.bpj.2015.10.021.

31.

RASopathies: unraveling mechanisms with animal models.

Jindal GA, Goyal Y, Burdine RD, Rauen KA, Shvartsman SY.

Dis Model Mech. 2015 Sep;8(9):1167. doi: 10.1242/dmm.022442. No abstract available.

32.

Dynamics of gradient formation by intracellular shuttling.

Berezhkovskii AM, Shvartsman SY.

J Chem Phys. 2015 Aug 21;143(7):074116. doi: 10.1063/1.4928858.

33.

RASopathies: unraveling mechanisms with animal models.

Jindal GA, Goyal Y, Burdine RD, Rauen KA, Shvartsman SY.

Dis Model Mech. 2015 Aug 1;8(8):769-82. doi: 10.1242/dmm.020339. Review. Erratum in: Dis Model Mech. 2015 Sep;8(9):1167.

34.

From discrete to continuum models of three-dimensional deformations in epithelial sheets.

Murisic N, Hakim V, Kevrekidis IG, Shvartsman SY, Audoly B.

Biophys J. 2015 Jul 7;109(1):154-63. doi: 10.1016/j.bpj.2015.05.019.

35.

Mapping the binding interface of ERK and transcriptional repressor Capicua using photocrosslinking.

Futran AS, Kyin S, Shvartsman SY, Link AJ.

Proc Natl Acad Sci U S A. 2015 Jul 14;112(28):8590-5. doi: 10.1073/pnas.1501373112. Epub 2015 Jun 29.

36.

Dynamics of Inductive ERK Signaling in the Drosophila Embryo.

Lim B, Dsilva CJ, Levario TJ, Lu H, Schüpbach T, Kevrekidis IG, Shvartsman SY.

Curr Biol. 2015 Jun 29;25(13):1784-90. doi: 10.1016/j.cub.2015.05.039. Epub 2015 Jun 18.

37.

Diversity of epithelial morphogenesis during eggshell formation in drosophilids.

Osterfield M, Schüpbach T, Wieschaus E, Shvartsman SY.

Development. 2015 Jun 1;142(11):1971-7. doi: 10.1242/dev.119404. Epub 2015 May 7.

38.

Temporal ordering and registration of images in studies of developmental dynamics.

Dsilva CJ, Lim B, Lu H, Singer A, Kevrekidis IG, Shvartsman SY.

Development. 2015 May 1;142(9):1717-24. doi: 10.1242/dev.119396. Epub 2015 Apr 1.

39.

BMP-dependent gene repression cascade in Drosophila eggshell patterning.

Charbonnier E, Fuchs A, Cheung LS, Chayengia M, Veikkolainen V, Seyfferth J, Shvartsman SY, Pyrowolakis G.

Dev Biol. 2015 Apr 15;400(2):258-65. doi: 10.1016/j.ydbio.2015.02.004. Epub 2015 Feb 20. Erratum in: Dev Biol. 2015 Jun 15;402(2):263.

40.

Computational analysis of three-dimensional epithelial morphogenesis using vertex models.

Du X, Osterfield M, Shvartsman SY.

Phys Biol. 2014 Nov 20;11(6):066007. doi: 10.1088/1478-3975/11/6/066007.

41.

Zelda potentiates morphogen activity by increasing chromatin accessibility.

Foo SM, Sun Y, Lim B, Ziukaite R, O'Brien K, Nien CY, Kirov N, Shvartsman SY, Rushlow CA.

Curr Biol. 2014 Jun 16;24(12):1341-1346. doi: 10.1016/j.cub.2014.04.032. Epub 2014 Jun 5.

42.

Vertex models of epithelial morphogenesis.

Fletcher AG, Osterfield M, Baker RE, Shvartsman SY.

Biophys J. 2014 Jun 3;106(11):2291-304. doi: 10.1016/j.bpj.2013.11.4498. Review.

43.

On the GFP-based analysis of dynamic concentration profiles.

Berezhkovskii AM, Shvartsman SY.

Biophys J. 2014 Feb 4;106(3):L13-5. doi: 10.1016/j.bpj.2013.12.007.

44.

ERK as a model for systems biology of enzyme kinetics in cells.

Futran AS, Link AJ, Seger R, Shvartsman SY.

Curr Biol. 2013 Nov 4;23(21):R972-9. doi: 10.1016/j.cub.2013.09.033. Review.

45.

Dynamic model for the coordination of two enhancers of broad by EGFR signaling.

Cheung LS, Simakov DS, Fuchs A, Pyrowolakis G, Shvartsman SY.

Proc Natl Acad Sci U S A. 2013 Oct 29;110(44):17939-44. doi: 10.1073/pnas.1304753110. Epub 2013 Oct 14.

46.

Context-dependent transcriptional interpretation of mitogen activated protein kinase signaling in the Drosophila embryo.

Kim Y, Iagovitina A, Ishihara K, Fitzgerald KM, Deplancke B, Papatsenko D, Shvartsman SY.

Chaos. 2013 Jun;23(2):025105. doi: 10.1063/1.4808157.

47.

Kinetics of receptor occupancy during morphogen gradient formation.

Berezhkovskii AM, Shvartsman SY.

J Chem Phys. 2013 Jun 28;138(24):244105. doi: 10.1063/1.4811654.

48.

Mathematical models of morphogen gradients and their effects on gene expression.

Shvartsman SY, Baker RE.

Wiley Interdiscip Rev Dev Biol. 2012 Sep-Oct;1(5):715-30. doi: 10.1002/wdev.55. Epub 2012 Apr 12.

PMID:
23799569
49.

Kinetics of gene derepression by ERK signaling.

Lim B, Samper N, Lu H, Rushlow C, Jiménez G, Shvartsman SY.

Proc Natl Acad Sci U S A. 2013 Jun 18;110(25):10330-5. doi: 10.1073/pnas.1303635110. Epub 2013 Jun 3.

50.

Local accumulation times for source, diffusion, and degradation models in two and three dimensions.

Gordon PV, Muratov CB, Shvartsman SY.

J Chem Phys. 2013 Mar 14;138(10):104121. doi: 10.1063/1.4793985.

PMID:
23514479

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