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Scholarly Interest Report
Aryeh Warmflash
Assistant Professor
Assistant Professor of BioSciences
  • Ph.D. Physics (2008) University of Chicago
  • B.A. Physics and Mathematics (2003) University of Pennsylvania
Primary Department
   Department of BioSciences
Department Affiliations
  • Department of Bioengineering
    Other Affiliations
  • Baylor College of Medicine
     Warmflash Lab Home Page
    Research Areas
     Signaling dynamics and spatial pattern formation during embryonic development and in the cancer microenvironment

    Research Statement


    Warmflash's Research

    My research focuses on quantitative studies of signaling dynamics and spatial pattern formation during embryonic development and in the cancer microenvironment. My previous work has used live-cell signaling assays to show that the dynamics of the TGF-beta signaling pathway are adaptive and to explore the consequences of this discovery for the function of TGFbeta as a patterning signal. I have also used micropatterning technology to develop in vitro systems for studying pattern formation. In particular, I have demonstrated that human embryonic stem cells (hESCs) confined to micropatterns during differentiation form self-organized patterns containing all three germ layers and reminiscent of those in mammalian embryos.

    Current projects include: using live-cell reporters of both signaling and fate in micropatterned culture to dissect the mechanisms of pattern formation, manipulating the shape of the micropatterned constraint to understand the relationship between geometry and cell fate, and developing three-dimensional culture systems that more completely mimic embryonic development. Ideas and tools developed for the study of embryonic development are also being deployed to understand the role of signaling dynamics and the relationship between healthy and diseased cells in the cancer microenvironment.

    Selected Publications
     Refereed articles

    D. P. Noren, W. H. Chou, S. H. Lee, A. A. Qutub, A. Warmflash, D. S. Wagner, A. S. Popel, A. Levchenko. VEGF-Mediated Ca2+ Signaling Steers Endothelial Cell Phenotypes by a Combination of Stochastic and Deterministic Decoding. 2016. Science Signaling (in press).


    A. Deglincerti, T. Haremaki, A. Warmflash, B. Sorre, and A. H. Brivanlou. Coco is a dual-activity modulator of TGFβ signaling. 2015. Development. 142:2678-2685.  PMCID: PMC4529031 [Available on 2016-08-01]


    A. Warmflash, B. Sorre, F. Etoc, E. D. Siggia, and A. H. Brivanlou. A method to recapitulate early embryonic spatial patterning in human embryonic stem cells. 2014. Nature Methods. 11:847-854. PMCID: PMC4341966 


    A. Warmflash, Q. Zhang, A. H. Brivanlou, and E. D. Siggia. "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. 2014. Science Signaling. 7:lc1


    B. Sorre, A. Warmflash, A. H. Brivanlou, and E. D. Siggia. Encoding of temporal signals by the TGF-β pathway and implications for embryonic patterning. 2014. Developmental Cell. 30:334-342.  PMCID: PMC4165855 


    M. Z. Ozair, S. Noggle, A. Warmflash, J. E. Krzyspiak, A. H. Brivanlou "Smad7 directly converts human embryonic stem cells to telencephalic fate by a default mechanism." Stem Cells , 31 (2013) : 35-47.


    A. Warmflash, B. L. Arduini, and A. H. Brivanlou "The molecular circuitry underlying pluripotency in embryonic stem cells." Wiley Interdiscip. Rev. Syst. Biol. Med., 4 (2012) : 443-456.


    A. Warmflash, E. D. Siggia and A. H. Brivanlou "Signaling dynamics and embryonic development." Cell Cycle, 11:2 (2012)


    A. Warmflash, P. Francois, and E. D. Siggia "Pareto evolution of gene networks: an algorithm to optimize multiple fitness objectives ." Phys. Biol. , 9 (2012) : 056001.


    A. Warmflash, Q. Zhang, B. Sorre, A. Vonica, E. D. Siggia, and A. H. Brivanlou "Dynamics of TGF-β signaling reveal adaptive and pulsatile behaviors reflected in the nuclear localization of transcription factor Smad4." Proc. Natl. Acad. Sci. , 109 (2012) : E1947-E1956.


    R. Sciammas*, Y. Li*, A. Warmflash*, Y Song, A. R. Dinner, and H. Singh "An incoherent regulatory network architecture that orchestrates B cell diversification in response to antigen signaling." Mol. Syst. Biol., 7 (2011) : 495.


    M. Maienschein-Cline, A. Warmflash, and A. R. Dinner "Defining cooperativity in gene regulation locally through intrinsic noise." IET Syst. Biol., 4 (2010) : 379-392.


    M. Tchernookov, A. Warmflash, and A. R. Dinner "Field theoretic treatment of an effective action for a model of catalyzed autoamplification." Phys. Rev. E., 81 (2010) : 011112.


    A. Dickson, A. Warmflash, and A. R. Dinner " Separating forward and backward pathways in nonequilibrium umbrella sampling." J. Chem. Phys., 131 (2009) : 154104.


    A. Dickson, A. Warmflash, and A. R. Dinner "Nonequilibrium umbrella sampling in spaces of many order parameters."  J. Chem. Phys., 130 (2009) : 074104.


    M. Tchernookov, A. Warmflash, and A. R. Dinner "Critical behavior of a model for catalyzed autoamplification." J. Chem. Phys. , 130 (2009) : 134936.


    A. Warmflash and A. R. Dinner "Signatures of combinatorial regulation in intrinsic biological noise." Proc. Natl. Acad. Sci., 105 (2008) : 17262-17267.


    A. Warmflash, D. N. Adamson, and A. R. Dinner " The impact of the choice of noise statistics on models of enzyme kinetics."  J. Chem. Phys., 128 (2008) : 225101.


    A. Warmflash, P. Bhimalapuram, and A. R. Dinner "Umbrella sampling for nonequilibrium processes." J. Chem. Phys., 127 (2007) : 154112.


    A. Warmflash and A. R. Dinner "A model for TCR gene segment use." J. Immunol., 177 (2006) : 3857-3864.


    P. Laslo, C. Spooner*, A. Warmflash*, D. W. Lancki, H.-J. Lee, R. Sciammas, B. N. Gantner, A. R. Dinner and H. Singh "Multilineage transcriptional priming and determination of alternate hematopoietic cell fates." Cell, 126 (2006) : 755-766.


    A. Warmflash, M. Weigert and A. R. Dinner "Control of genotypic allelic inclusion through TCR surface expression." J. Immunol. , 175 (2005) : 6412-6419.

     Book chapters

    A. Warmflash and A. R. Dinner "Modeling gene regulatory networks for cell fate specification." Statistical Mechanics of Cellular Systems (2009)


    D. Reynaud, D. W. Lancki, J. M. R. Pongubala, A. Warmflash, A. R. Dinner, and H. Singh. "Gene regulatory networks directing cell fates within the hematopoietic system." Cell Determination during Hematopoiesis (2009)

     Invited Talks

    "Embryonic patterning in space and time." Rice University, Department of Biochemistry and Cell Biology, (January 2014)


    "Embryonic patterning in space and time." University of California, Santa Barbara, Department of Physics, (February 2014)


    "Embryonic patterning in space and time." The University of Chicago, Institute for Genomics and Systems Biology, (January 2014)


    "Embryonic patterning in space and time." Rockefeller University, Center for Studies in Physics and Biology, (May 2014)


    "Embryonic patterning in space and time." Memorial Sloan Kettering Cancer Center, (February 2014)


    "Embryonic patterning in space and time." University of California, San Diego, Department of Physics, (January 2014)


    "Embryonic patterning in space and time." New York University, Department of Biology, (January 2014)


    "Embryonic patterning in space and time." University of Georgia, Institute for Bioinformatics , (January 2014)


    "Embryonic patterning in space and time." California Institute of Technology, Division of Biology, (February 2014)


    "Stem cell systems for studying self-organized embryonic patterning." Rice University, Center for Theoretical Biological Physics, Houston, TX. (October 2014)

     Keynote Speaker

    "2015 BioSciences Keynote." Gulf Coast Undergraduate Research Symposium, Rice University. (Oct 17, 2015)

     Seminar Speaker

    Rice University, Department of Bioengineering Colloquuia, March 2015

    Supervised Theses & Dissertations
     Joseph Massey, PhD TBD. (Thesis Director)

     Sapna Chhabra, PhD TBD. (Thesis Director)

     George Britton, PhD TBD. (Thesis Co-Director)

     Lindsey Sablatura, PhD TBD. (Thesis Committee Member)

     Kinshuk Mitra, PhD TBD. (Thesis Director)

    Awards, Prizes, & Fellowships
     Scholar in Cancer Research, CPRIT Scholar in Cancer Research (2014-2018)