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Items: 33


Mesenchymal-epithelial transition regulates initiation of pluripotency exit before gastrulation.

Hamidi S, Nakaya Y, Nagai H, Alev C, Kasukawa T, Chhabra S, Lee R, Niwa H, Warmflash A, Shibata T, Sheng G.

Development. 2020 Feb 3;147(3). pii: dev184960. doi: 10.1242/dev.184960.


Dissecting the dynamics of signaling events in the BMP, WNT, and NODAL cascade during self-organized fate patterning in human gastruloids.

Chhabra S, Liu L, Goh R, Kong X, Warmflash A.

PLoS Biol. 2019 Oct 15;17(10):e3000498. doi: 10.1371/journal.pbio.3000498. eCollection 2019 Oct.


A novel self-organizing embryonic stem cell system reveals signaling logic underlying the patterning of human ectoderm.

Britton G, Heemskerk I, Hodge R, Qutub AA, Warmflash A.

Development. 2019 Oct 17;146(20). pii: dev179093. doi: 10.1242/dev.179093.


Rapid changes in morphogen concentration control self-organized patterning in human embryonic stem cells.

Heemskerk I, Burt K, Miller M, Chhabra S, Guerra MC, Liu L, Warmflash A.

Elife. 2019 Mar 4;8. pii: e40526. doi: 10.7554/eLife.40526.


Synergy with TGFβ ligands switches WNT pathway dynamics from transient to sustained during human pluripotent cell differentiation.

Massey J, Liu Y, Alvarenga O, Saez T, Schmerer M, Warmflash A.

Proc Natl Acad Sci U S A. 2019 Mar 12;116(11):4989-4998. doi: 10.1073/pnas.1815363116. Epub 2019 Feb 28.


S-MiRAGE: A Quantitative, Secreted RNA-Based Reporter of Gene Expression and Cell Persistence.

Mitra K, Feist WN, Anfossi S, Fuentes-Mattei E, Almeida MI, Kim JJ, Calin GA, Warmflash A.

ACS Synth Biol. 2019 Jan 18;8(1):25-33. doi: 10.1021/acssynbio.8b00406. Epub 2018 Dec 21.


Modeling Mammalian Gastrulation With Embryonic Stem Cells.

Siggia ED, Warmflash A.

Curr Top Dev Biol. 2018;129:1-23. doi: 10.1016/bs.ctdb.2018.03.001. Epub 2018 Apr 12. Review.


Morphogen and community effects determine cell fates in response to BMP4 signaling in human embryonic stem cells.

Nemashkalo A, Ruzo A, Heemskerk I, Warmflash A.

Development. 2017 Sep 1;144(17):3042-3053. doi: 10.1242/dev.153239. Epub 2017 Jul 31.


Synthetic Embryos: Windows into Mammalian Development.

Warmflash A.

Cell Stem Cell. 2017 May 4;20(5):581-582. doi: 10.1016/j.stem.2017.04.001.


Self-organization of human embryonic stem cells on micropatterns.

Deglincerti A, Etoc F, Guerra MC, Martyn I, Metzger J, Ruzo A, Simunovic M, Yoney A, Brivanlou AH, Siggia E, Warmflash A.

Nat Protoc. 2016 Nov;11(11):2223-2232. doi: 10.1038/nprot.2016.131. Epub 2016 Oct 13.


Pluripotent stem cells as a model for embryonic patterning: From signaling dynamics to spatial organization in a dish.

Heemskerk I, Warmflash A.

Dev Dyn. 2016 Oct;245(10):976-90. doi: 10.1002/dvdy.24432. Epub 2016 Aug 25. Review.


Endothelial cells decode VEGF-mediated Ca2+ signaling patterns to produce distinct functional responses.

Noren DP, Chou WH, Lee SH, Qutub AA, Warmflash A, Wagner DS, Popel AS, Levchenko A.

Sci Signal. 2016 Feb 23;9(416):ra20. doi: 10.1126/scisignal.aad3188.


Coco is a dual activity modulator of TGFβ signaling.

Deglincerti A, Haremaki T, Warmflash A, Sorre B, Brivanlou AH.

Development. 2015 Aug 1;142(15):2678-85. doi: 10.1242/dev.122358. Epub 2015 Jun 26.


Encoding of temporal signals by the TGF-β pathway and implications for embryonic patterning.

Sorre B, Warmflash A, Brivanlou AH, Siggia ED.

Dev Cell. 2014 Aug 11;30(3):334-42. doi: 10.1016/j.devcel.2014.05.022. Epub 2014 Jul 24.


A method to recapitulate early embryonic spatial patterning in human embryonic stem cells.

Warmflash A, Sorre B, Etoc F, Siggia ED, Brivanlou AH.

Nat Methods. 2014 Aug;11(8):847-54. doi: 10.1038/nmeth.3016. Epub 2014 Jun 29.


SMAD7 directly converts human embryonic stem cells to telencephalic fate by a default mechanism.

Ozair MZ, Noggle S, Warmflash A, Krzyspiak JE, Brivanlou AH.

Stem Cells. 2013 Jan;31(1):35-47. doi: 10.1002/stem.1246.


Signaling dynamics and embryonic development.

Warmflash A, Siggia ED, Brivanlou AH.

Cell Cycle. 2012 Oct 1;11(19):3529-30. doi: 10.4161/cc.21964. Epub 2012 Aug 30. No abstract available.


Pareto evolution of gene networks: an algorithm to optimize multiple fitness objectives.

Warmflash A, Francois P, Siggia ED.

Phys Biol. 2012 Oct;9(5):056001. doi: 10.1088/1478-3975/9/5/056001. Epub 2012 Aug 8.


The molecular circuitry underlying pluripotency in embryonic stem cells.

Warmflash A, Arduini BL, Brivanlou AH.

Wiley Interdiscip Rev Syst Biol Med. 2012 Sep-Oct;4(5):443-56. doi: 10.1002/wsbm.1182. Epub 2012 Jul 3. Review.


Dynamics of TGF-β signaling reveal adaptive and pulsatile behaviors reflected in the nuclear localization of transcription factor Smad4.

Warmflash A, Zhang Q, Sorre B, Vonica A, Siggia ED, Brivanlou AH.

Proc Natl Acad Sci U S A. 2012 Jul 10;109(28):E1947-56. doi: 10.1073/pnas.1207607109. Epub 2012 Jun 11.


An incoherent regulatory network architecture that orchestrates B cell diversification in response to antigen signaling.

Sciammas R, Li Y, Warmflash A, Song Y, Dinner AR, Singh H.

Mol Syst Biol. 2011 May 24;7:495. doi: 10.1038/msb.2011.25.


Defining cooperativity in gene regulation locally through intrinsic noise.

Maienschein-Cline M, Warmflash A, Dinner AR.

IET Syst Biol. 2010 Nov;4(6):379-92. doi: 10.1049/iet-syb.2009.0070.


Separating forward and backward pathways in nonequilibrium umbrella sampling.

Dickson A, Warmflash A, Dinner AR.

J Chem Phys. 2009 Oct 21;131(15):154104. doi: 10.1063/1.3244561. Erratum in: J Chem Phys. 2012 Jun 21;136(23):239901.


Field theoretic treatment of an effective action for a model of catalyzed autoamplification.

Tchernookov M, Warmflash A, Dinner AR.

Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Jan;81(1 Pt 1):011112. Epub 2010 Jan 8.


Critical behavior of a model for catalyzed autoamplification.

Tchernookov M, Warmflash A, Dinner AR.

J Chem Phys. 2009 Apr 7;130(13):134906. doi: 10.1063/1.3101649.


Nonequilibrium umbrella sampling in spaces of many order parameters.

Dickson A, Warmflash A, Dinner AR.

J Chem Phys. 2009 Feb 21;130(7):074104. doi: 10.1063/1.3070677. Erratum in: J Chem Phys. 2012 Jun 14;136(22):229901.


Signatures of combinatorial regulation in intrinsic biological noise.

Warmflash A, Dinner AR.

Proc Natl Acad Sci U S A. 2008 Nov 11;105(45):17262-7. doi: 10.1073/pnas.0809314105. Epub 2008 Nov 3.


How noise statistics impact models of enzyme cycles.

Warmflash A, Adamson DN, Dinner AR.

J Chem Phys. 2008 Jun 14;128(22):225101. doi: 10.1063/1.2929841.


Umbrella sampling for nonequilibrium processes.

Warmflash A, Bhimalapuram P, Dinner AR.

J Chem Phys. 2007 Oct 21;127(15):154112.


A model for TCR gene segment use.

Warmflash A, Dinner AR.

J Immunol. 2006 Sep 15;177(6):3857-64.


Multilineage transcriptional priming and determination of alternate hematopoietic cell fates.

Laslo P, Spooner CJ, Warmflash A, Lancki DW, Lee HJ, Sciammas R, Gantner BN, Dinner AR, Singh H.

Cell. 2006 Aug 25;126(4):755-66.


Control of genotypic allelic inclusion through TCR surface expression.

Warmflash A, Weigert M, Dinner AR.

J Immunol. 2005 Nov 15;175(10):6412-9.

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