Aryeh Warmflash

Aryeh Warmflash

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Aryeh Warmflash

Aryeh Warmflash

Publications by authors named "Aryeh Warmflash"

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

Development 2019 Oct 17;146(20). Epub 2019 Oct 17.

Department of Biosciences, Rice University Houston, Houston, TX 77005, USA

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http://dx.doi.org/10.1242/dev.179093DOI Listing
October 2019

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

PLoS Biol 2019 Oct 15;17(10):e3000498. Epub 2019 Oct 15.

Department of Biosciences, Rice University, Houston, Texas, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.3000498DOI Listing
October 2019

Modeling Mammalian Gastrulation With Embryonic Stem Cells.

Curr Top Dev Biol 2018 12;129:1-23. Epub 2018 Apr 12.

Departments of Biosciences and Bioengineering, Rice University, Houston, TX, United States. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00702153183004
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http://dx.doi.org/10.1016/bs.ctdb.2018.03.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6260823PMC
May 2019

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

Proc Natl Acad Sci U S A 2019 03 28;116(11):4989-4998. Epub 2019 Feb 28.

Department of Biosciences, Rice University, Houston, TX 77005;

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http://dx.doi.org/10.1073/pnas.1815363116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6421465PMC
March 2019

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

ACS Synth Biol 2019 01 21;8(1):25-33. Epub 2018 Dec 21.

Department of Bioengineering , Rice University , Houston , Texas 77005 , United States.

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http://pubs.acs.org/doi/10.1021/acssynbio.8b00406
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http://dx.doi.org/10.1021/acssynbio.8b00406DOI Listing
January 2019

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

Development 2017 09 31;144(17):3042-3053. Epub 2017 Jul 31.

Department of Biosciences, Rice University, Houston, TX 77005, USA

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http://dev.biologists.org/lookup/doi/10.1242/dev.153239
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http://dx.doi.org/10.1242/dev.153239DOI Listing
September 2017

Synthetic Embryos: Windows into Mammalian Development.

Authors:
Aryeh Warmflash

Cell Stem Cell 2017 05;20(5):581-582

Departments of Biosciences and Bioengineering, Rice University, Houston, TX 77005, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S19345909173012
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http://dx.doi.org/10.1016/j.stem.2017.04.001DOI Listing
May 2017

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

Dev Dyn 2016 10 25;245(10):976-90. Epub 2016 Aug 25.

Department of Biosciences, Rice University, Houston, Texas.

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http://dx.doi.org/10.1002/dvdy.24432DOI Listing
October 2016

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

Sci Signal 2016 Feb 23;9(416):ra20. Epub 2016 Feb 23.

Yale Systems Biology Institute and Department of Biomedical Engineering, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA.

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http://dx.doi.org/10.1126/scisignal.aad3188DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5301990PMC
February 2016

Coco is a dual activity modulator of TGFβ signaling.

Development 2015 Aug 26;142(15):2678-85. Epub 2015 Jun 26.

Laboratory of Stem Cell Biology and Molecular Embryology, The Rockefeller University, New York, NY 10065, USA

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http://dx.doi.org/10.1242/dev.122358DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4529031PMC
August 2015

Comment on "Controlling long-term signaling: receptor dynamics determine attenuation and refractory behavior of the TGF-β pathway"-Smad2/3 activity does not predict the dynamics of transcription.

Sci Signal 2014 Sep 23;7(344):lc1. Epub 2014 Sep 23.

Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 10065, USA.

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http://dx.doi.org/10.1126/scisignal.2005562DOI Listing
September 2014

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

Nat Methods 2014 Aug 29;11(8):847-54. Epub 2014 Jun 29.

Laboratory of Molecular Vertebrate Embryology, The Rockefeller University, New York, New York, USA.

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http://dx.doi.org/10.1038/nmeth.3016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4341966PMC
August 2014

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

Dev Cell 2014 Aug 24;30(3):334-42. Epub 2014 Jul 24.

Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 10065, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S15345807140034
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http://dx.doi.org/10.1016/j.devcel.2014.05.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4165855PMC
August 2014

The molecular circuitry underlying pluripotency in embryonic stem cells.

Wiley Interdiscip Rev Syst Biol Med 2012 Sep-Oct;4(5):443-56. Epub 2012 Jul 3.

Laboratory of Molecular Vertebrate Embryology, The Rockefeller University, New York, NY, USA.

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http://dx.doi.org/10.1002/wsbm.1182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5872147PMC
January 2013

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

Stem Cells 2013 Jan;31(1):35-47

Laboratory of Molecular Embryology, The Rockefeller University, New York, New York 10065, USA.

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http://doi.wiley.com/10.1002/stem.1246
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http://dx.doi.org/10.1002/stem.1246DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4103884PMC
January 2013

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

Phys Biol 2012 Oct 8;9(5):056001. Epub 2012 Aug 8.

Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 10065, USA.

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http://stacks.iop.org/1478-3975/9/i=5/a=056001?key=crossref.
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http://dx.doi.org/10.1088/1478-3975/9/5/056001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3609408PMC
October 2012

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

Proc Natl Acad Sci U S A 2012 Jul 11;109(28):E1947-56. Epub 2012 Jun 11.

Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 10065, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.1207607109
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http://dx.doi.org/10.1073/pnas.1207607109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3396545PMC
July 2012

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

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

James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA.

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https://link.aps.org/doi/10.1103/PhysRevE.81.011112
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http://dx.doi.org/10.1103/PhysRevE.81.011112DOI Listing
January 2010

Separating forward and backward pathways in nonequilibrium umbrella sampling.

J Chem Phys 2009 Oct;131(15):154104

James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA.

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http://aip.scitation.org/doi/10.1063/1.3244561
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http://dx.doi.org/10.1063/1.3244561DOI Listing
October 2009

Critical behavior of a model for catalyzed autoamplification.

J Chem Phys 2009 Apr;130(13):134906

James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA.

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http://dx.doi.org/10.1063/1.3101649DOI Listing
April 2009

Nonequilibrium umbrella sampling in spaces of many order parameters.

J Chem Phys 2009 Feb;130(7):074104

James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA.

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http://aip.scitation.org/doi/10.1063/1.3070677
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http://dx.doi.org/10.1063/1.3070677DOI Listing
February 2009

Signatures of combinatorial regulation in intrinsic biological noise.

Proc Natl Acad Sci U S A 2008 Nov 3;105(45):17262-7. Epub 2008 Nov 3.

James Franck Institute, University of Chicago, Chicago, IL 60637, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0809314105
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http://dx.doi.org/10.1073/pnas.0809314105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2582248PMC
November 2008

How noise statistics impact models of enzyme cycles.

J Chem Phys 2008 Jun;128(22):225101

James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA.

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http://dx.doi.org/10.1063/1.2929841DOI Listing
June 2008

Umbrella sampling for nonequilibrium processes.

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

James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA.

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http://dx.doi.org/10.1063/1.2784118DOI Listing
October 2007

A model for TCR gene segment use.

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

Department of Physics, University of Chicago, Chicago, IL 60637, USA.

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http://dx.doi.org/10.4049/jimmunol.177.6.3857DOI Listing
September 2006

Multilineage transcriptional priming and determination of alternate hematopoietic cell fates.

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

Howard Hughes Medical Institute and Department of Molecular Genetics and Cell Biology, The University of Chicago, 929 East 57th Street, GCIS W522, IL 60637, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S009286740600980
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http://dx.doi.org/10.1016/j.cell.2006.06.052DOI Listing
August 2006

Control of genotypic allelic inclusion through TCR surface expression.

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

Department of Physics, University of Chicago, IL 60637, USA.

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http://dx.doi.org/10.4049/jimmunol.175.10.6412DOI Listing
November 2005