Preprints
E. Camacho-Aguilar, S. Yoon, M. A. Ortiz-Salazar, and A. Warmflash. Combinatorial interpretation of BMP and WNT allows BMP to act as a morphogen in time but not in concentration. link
Peer-reviewed publications
43. E. Sempou, V Kostiuk, J Zhu, M. C. Guerra, L. Tyan, W. Hwant, E. Camacho-Aguilar, M. J. Caplan, D. Zenisek, A. Warmflash, N. D. L. Owens, and M. K. Khokha. Membrane potential drives the exit from pluripotency and cell fate commitment via calcium and mTOR. 2022. Nature Communications 13, 6681. link
42. L. Liu, A. Nemashkalo, L. Rezende, J. Y. Jung, S. Chhabra, M. C. Guerra, I. Heemskerk, A. Warmflash. Nodal is a short-range morphogen with activity that spreads via a relay mechanism in human gastruloids. 2022. Nature Communications. 13:497. link
41. P. Bedekar, I. Timofeyev, A. Warmflash, and M. Perepelitsa. Reaction-diffusion models for the morphological patterning of hESCs. 2021. J Math Biol. 83:55. link
40. E. Karzbrun, A. H. Khankhel, H. C. Megale, S. M. K. Glasauer, Y. Wyle, G. Britton, A. Warmflash, K. S. Kosik, E. D. Siggia, B. I. Shraiman, S. J. Streichan. Human neural tube morphogenesis in vitro by geometric constraints. 2021. Nature. 599:368-272. link
39. S. Chhabra and A. Warmflash. BMP-treated human embryonic stem cells transcriptionally resemble amnion cells in the monkey embryo. 2021. Biology Open. 10:bio.058617.link
38. E. Camacho-Aguilar, A. Warmflash, and D. A. Rand. Quantifying cell transitions in C. elegans with data-fitted landscape models. 2021. PLOS Comp Biol. 17(6):e1009034. link
37. Y. Zhu, D. Sazer, J. S. Miller, and A. Warmflash. Rapid fabrication of hydrogel micropatterns by projection stereolithography for studying self-organized developmental patterning. 2021. PLOS One. 16(6):e0245634. link
36. L. Liu and A. Warmflash. Self-organized signaling in stem cell models of embryos. 2021. Stem Cell Reports. 16(5):1065-1077. link
35. K. R. W. Matthews, D. S. Wagner, and A. Warmflash. Stem Cell-Based Models of Embryos: The Need for Improved Naming Conventions. 2021. Stem Cell Reports. S2213-6711(21)00098-9 link
34. G. Britton, S. Chhabra, J. Massey, and A. Warmflash. Fate-Patterning of 2D Gastruloids and Ectodermal Colonies Using Micropatterned Human Pluripotent Stem Cells. 2021. Methods Mol Biol 2258:119-130. pdf
33. J. Fu, A. Warmflash, and M. P. Lutolf. Stem-cell-based embryo models for fundamental research and translation. 2021. Nature Materials. 20:132-144. link
32. E. Camacho Aguilar and A. Warmflash. Insights into mammalian morphogen dynamics from embryonic stem cell systems. 2020. Curr Top Dev Biol 137:279-305. pdf
31. S. Hamiki, Y. Nakaya, H. Nagai, C. Alev, S. Chhabra, R. Lee, H. Niwa, A. Warmflash, T. Shibata, and G. Sheng. Mesenchymal-epithelial transition regulates initiation of pluripotency exit before gastrulation. 2020. Development. 147:dev184960. link
30. S. Chhabra, L. Liu, R. Goh, X. Kong, and A. Warmflash. Dissecting the dynamics of signaling events in the BMP, WNT, and NODAL cascade during self-organized fate patterning in human gastruloids. 2019. PLOS Biology 17:e300048. link
29. G. Britton, I. Heemskerk, R. Hodge, A. A. Qutub, and A. Warmflash. A novel self-organized stem cell system reveals signaling interactions underlying the patterning of human ectoderm. 2019. Development. dev.179093. link.
28. Idse Heemskerk, Kari Burt, Matthew Miller, Sapna Chabra, M. Cecilia Guerra, Lizhong Liu, Aryeh Warmflash. Rapid changes in morphogen concentration control self-organized patterning in human embryonic stem cells. 2019. eLife 8:e40526 link
27. , , , , ,
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.