Publications

Preprints

4. George Britton, Idse Heemskerk, Rachel Hodge, Amina A Qutub, Aryeh Warmflash. A novel self-organizing embryonic stem cell system reveals signaling logic underlying the patterning of human ectoderm.  

3. Sapna Chhabra, Lizhong Liu, Ryan Goh, Aryeh Warmflash. Dissecting the dynamics of signaling events in the BMP, WNT, and NODAL cascade during self-organized fate patterning in human gastruloids. 

2. Joseph Massey, Yida Liu, Omar Alvarenga, Teresa Saez, Matthew Schmerer, Aryeh Warmflash. Synergy with TGFβ ligands switches WNT pathway dynamics from transient to sustained during human pluripotent cell differentiation. 

1. Idse Heemskerk, Kari Burt, Matthew Miller, Sapna Chabra, M. Cecilia Guerra, Aryeh Warmflash. Morphogen dynamics control patterning in a stem cell model of the human embryo. 

Peer-reviewed publications

26. Mitra K, Feist W, Anfossi S, Fuentes-Mattei E, Almeida MI, Kim JJ, Calin G, Warmflash A. S-MiRAGE: A quantitative, secreted RNA-based reporter of gene expression and cell persistence. 2019. ACS Synthetic Biology 8:25-33. doi: 10.1021/acssynbio.8b00406. PDF.

25. Nemashkalo, A., Ruzo, A., Heemskerk, I., and Warmflash A. (2017). Morphogen and community effects determine cell fates in response to BMP4 signaling in human embryonic stem cells. Development 144:3042-3053. PDF

24. Deglincerti, A., Etoc, F., Guerra, M. C., Martyn, I., Metzger, J., Ruzo, A.,   Simunovic, M. , Yoney, A., Brivanlou, A. H., Siggia, E., and Warmflash, A. (2016). Self-organization of human embryonic stem cells on micropatterns. Nature Protocols, 11(11), 2223–2232. PDF

23. Heemskerk, I., & Warmflash, A. (2016). Pluripotent stem cells as a model for embryonic patterning: From signaling dynamics to spatial organization in a dish. Developmental Dynamics. PDF

22. D. P. Noren, W. H. Chou, S. H. Lee, A. A. Qutub,  A. Warmflash, D. S. Wagner,  et al. (2016). Endothelial cells decode VEGF-mediated Ca2+ signaling patterns to produce distinct functional responses. 2016. Science Signaling, 9(416), ra20. PDF

21. A. Deglincerti*, T. Haremaki*, A. Warmflash*, B. Sorre, and A. H. Brivanlou. Coco is a dual-activity modulator of TGFb signaling. 2015. Development. 142:2678-2685. *equal contributions PDF

20. A. Warmflash, Q. Zhang, A. H. Brivanlou, and E. D. Siggia. Smad2/3 activity does not predict the dynamics of transcription. 2014. Science Signaling. 7:lc1. PDF

19. 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. PDF.

18. 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. *equal contributions. PDF.

17. 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. 2013. Stem Cells 31:35-47. PDF.

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

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

14. 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. 2011. Mol. Syst. Biol. 7:495. *equal contributions. PDF.

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

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

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

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

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

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

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

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

5. 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. 2006. Cell. 126:755-766. *equal contributions. PDF.

4. A. Warmflash and A. R. Dinner. A model for TCR gene segment use. 2006. J. Immunol. 177:3857-3864. PDF.

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

2. M. Machacek, A. Doasaj, W. Forman C. Jones, M. Markevitch, A. Vikhlinin, A. Warmflash, R. Kraft. Infall of the elliptical galaxy NGC 1404 into the Fornax cluster. 2005. Astrophys. J. 621:663-672. PDF.

1. C. Jones, W. Forman, A. Vikhlinin, M. Markevitch, L. David, A. Warmflash, S. Murray, P.E.J. Nulsen. Chandra Observations of NGC 4636 – An elliptical galaxy in turmoil. 2002. Astrophys. J. Lett.  567:L115-118. PDF.

Review articles/News and Views

6. E. D. Siggia, A. Warmflash. Modeling Mammalian Gastrulation With Embryonic Stem Cells. 2018. Curr Top. Dev Biol. 129:1-23. PDF.

5. A. Warmflash. Synthetic embryos: Windows into Mammalian development. 2017. Cell Stem Cell. 20:581-582. PDF.

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

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

2. D. Reynaud, D. W. Lancki, J. M. R. Pongubala, A. Warmflash, A. R. Dinner, and H. Singh.  2009. Gene regulatory networks directing cell fates within the hematopoietic system. in Cell Determination during Hematopoiesis, R. Ceredig and G. Brown, eds. Nova Science Publishers. Link.

1. A. Warmflash and A. R. Dinner. Modeling gene regulatory networks for cell fate specification. 2009. in Statistical Mechanics of Cellular Systems, edited by M. Zaman. Cambridge University Press. Link.