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Aryeh Warmflash, Ph.D. - Publications

Affiliations: 
2008 University of Chicago, Chicago, IL 
Area:
theoretical studies of cellular behavior
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35 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Camacho-Aguilar E, Warmflash A. Insights into mammalian morphogen dynamics from embryonic stem cell systems. Current Topics in Developmental Biology. 137: 279-305. PMID 32143746 DOI: 10.1016/Bs.Ctdb.2019.11.010  0.358
2020 Hamidi S, Nakaya Y, Nagai H, Alev C, Kasukawa T, Chhabra S, Lee R, Niwa H, Warmflash A, Shibata T, Sheng G. Mesenchymal-epithelial transition regulates initiation of pluripotency exit before gastrulation. Development (Cambridge, England). 147. PMID 32014865 DOI: 10.1242/Dev.184960  0.323
2019 Chhabra S, Liu L, Goh R, Kong X, Warmflash A. Dissecting the dynamics of signaling events in the BMP, WNT, and NODAL cascade during self-organized fate patterning in human gastruloids. Plos Biology. 17: e3000498. PMID 31613879 DOI: 10.1371/Journal.Pbio.3000498  0.355
2019 Britton G, Heemskerk I, Hodge R, Qutub AA, Warmflash A. A novel self-organizing embryonic stem cell system reveals signaling logic underlying the patterning of human ectoderm. Development (Cambridge, England). PMID 31519692 DOI: 10.1242/Dev.179093  0.349
2019 Heemskerk I, Burt K, Miller M, Chhabra S, Guerra MC, Liu L, Warmflash A. Rapid changes in morphogen concentration control self-organized patterning in human embryonic stem cells. Elife. 8. PMID 30829572 DOI: 10.7554/Elife.40526  0.358
2019 Massey J, Liu Y, Alvarenga O, Saez T, Schmerer M, Warmflash A. Synergy with TGFβ ligands switches WNT pathway dynamics from transient to sustained during human pluripotent cell differentiation. Proceedings of the National Academy of Sciences of the United States of America. PMID 30819898 DOI: 10.1073/Pnas.1815363116  0.328
2018 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. Acs Synthetic Biology. PMID 30550267 DOI: 10.1021/Acssynbio.8B00406  0.328
2018 Siggia ED, Warmflash A. Modeling Mammalian Gastrulation With Embryonic Stem Cells. Current Topics in Developmental Biology. 129: 1-23. PMID 29801527 DOI: 10.1016/Bs.Ctdb.2018.03.001  0.342
2017 Nemashkalo A, Ruzo A, Heemskerk I, Warmflash A. Morphogen and community effects determine cell fates in response to BMP4 signaling in human embryonic stem cells. Development (Cambridge, England). PMID 28760810 DOI: 10.1242/Dev.153239  0.353
2016 Deglincerti A, Etoc F, Guerra MC, Martyn I, Metzger J, Ruzo A, Simunovic M, Yoney A, Brivanlou AH, Siggia E, Warmflash A. Self-organization of human embryonic stem cells on micropatterns. Nature Protocols. 11: 2223-2232. PMID 27735934 DOI: 10.1038/Nprot.2016.131  0.317
2016 Heemskerk I, Warmflash A. Pluripotent stem cells as a model for embryonic patterning: From signaling dynamics to spatial organization in a dish. Developmental Dynamics : An Official Publication of the American Association of Anatomists. PMID 27404482 DOI: 10.1002/Dvdy.24432  0.358
2016 Noren DP, Chou WH, Lee SH, Qutub AA, Warmflash A, Wagner DS, Popel AS, Levchenko A. Endothelial cells decode VEGF-mediated Ca2+ signaling patterns to produce distinct functional responses. Science Signaling. 9: ra20. PMID 26905425 DOI: 10.1126/Scisignal.Aad3188  0.306
2014 Warmflash A, Zhang Q, Brivanlou AH, Siggia ED. 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. Science Signaling. 7: lc1. PMID 25249655 DOI: 10.1126/Scisignal.2005562  0.319
2014 Sorre B, Warmflash A, Brivanlou AH, Siggia ED. Encoding of temporal signals by the TGF-β pathway and implications for embryonic patterning. Developmental Cell. 30: 334-42. PMID 25065773 DOI: 10.1016/J.Devcel.2014.05.022  0.314
2014 Warmflash A, Sorre B, Etoc F, Siggia ED, Brivanlou AH. A method to recapitulate early embryonic spatial patterning in human embryonic stem cells. Nature Methods. 11: 847-54. PMID 24973948 DOI: 10.1038/Nmeth.3016  0.335
2013 Ozair MZ, Noggle S, Warmflash A, Krzyspiak JE, Brivanlou AH. SMAD7 directly converts human embryonic stem cells to telencephalic fate by a default mechanism. Stem Cells (Dayton, Ohio). 31: 35-47. PMID 23034881 DOI: 10.1002/Stem.1246  0.354
2012 Warmflash A, Siggia ED, Brivanlou AH. Signaling dynamics and embryonic development. Cell Cycle (Georgetown, Tex.). 11: 3529-30. PMID 22935712 DOI: 10.4161/Cc.21964  0.356
2012 Warmflash A, Francois P, Siggia ED. Pareto evolution of gene networks: an algorithm to optimize multiple fitness objectives. Physical Biology. 9: 056001. PMID 22874123 DOI: 10.1088/1478-3975/9/5/056001  0.301
2012 Warmflash A, Arduini BL, Brivanlou AH. The molecular circuitry underlying pluripotency in embryonic stem cells. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 4: 443-56. PMID 22761038 DOI: 10.1002/Wsbm.1182  0.361
2012 Dickson A, Warmflash A, Dinner AR. Erratum: “Separating forward and backward pathways in nonequilibrium umbrella sampling” [J. Chem. Phys. 131, 154104 (2009)] The Journal of Chemical Physics. 136: 239901. DOI: 10.1063/1.4730937  0.612
2012 Dickson A, Warmflash A, Dinner AR. Erratum: “Nonequilibrium umbrella sampling in spaces of many order parameters” [J. Chem. Phys. 130, 074104 (2009)] The Journal of Chemical Physics. 136: 229901. DOI: 10.1063/1.4729744  0.622
2011 Sciammas R, Li Y, Warmflash A, Song Y, Dinner AR, Singh H. An incoherent regulatory network architecture that orchestrates B cell diversification in response to antigen signaling. Molecular Systems Biology. 7: 495. PMID 21613984 DOI: 10.1038/Msb.2011.25  0.574
2010 Maienschein-Cline M, Warmflash A, Dinner AR. Defining cooperativity in gene regulation locally through intrinsic noise. Iet Systems Biology. 4: 379-92. PMID 21073237 DOI: 10.1049/Iet-Syb.2009.0070  0.666
2010 Tchernookov M, Warmflash A, Dinner AR. Field theoretic treatment of an effective action for a model of catalyzed autoamplification. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 81: 011112. PMID 20365328 DOI: 10.1103/Physreve.81.011112  0.546
2009 Dickson A, Warmflash A, Dinner AR. Separating forward and backward pathways in nonequilibrium umbrella sampling. The Journal of Chemical Physics. 131: 154104. PMID 20568844 DOI: 10.1063/1.3244561  0.651
2009 Tchernookov M, Warmflash A, Dinner AR. Critical behavior of a model for catalyzed autoamplification. The Journal of Chemical Physics. 130: 134906. PMID 19355779 DOI: 10.1063/1.3101649  0.548
2009 Dickson A, Warmflash A, Dinner AR. Nonequilibrium umbrella sampling in spaces of many order parameters. The Journal of Chemical Physics. 130: 074104. PMID 19239281 DOI: 10.1063/1.3070677  0.649
2009 Warmflash A, Dinner AR. Modeling gene regulatory networks for cell fate specification Statistical Mechanics of Cellular Systems and Processes. 121-154. DOI: 10.1017/CBO9780511576768.006  0.529
2009 Reynaud D, Lancki DW, Pongubala JMR, Warmflash A, Dinner AR, Singh H. Gene regulatory networks directing cell fates within the hematopoietic system Cell Determination During Hematopoiesis. 1-23.  0.52
2008 Warmflash A, Dinner AR. Signatures of combinatorial regulation in intrinsic biological noise. Proceedings of the National Academy of Sciences of the United States of America. 105: 17262-7. PMID 18981421 DOI: 10.1073/Pnas.0809314105  0.568
2008 Warmflash A, Adamson DN, Dinner AR. How noise statistics impact models of enzyme cycles. The Journal of Chemical Physics. 128: 225101. PMID 18554058 DOI: 10.1063/1.2929841  0.511
2007 Warmflash A, Bhimalapuram P, Dinner AR. Umbrella sampling for nonequilibrium processes. The Journal of Chemical Physics. 127: 154112. PMID 17949137 DOI: 10.1063/1.2784118  0.562
2006 Warmflash A, Dinner AR. A model for TCR gene segment use. Journal of Immunology (Baltimore, Md. : 1950). 177: 3857-64. PMID 16951348 DOI: 10.4049/Jimmunol.177.6.3857  0.53
2006 Laslo P, Spooner CJ, Warmflash A, Lancki DW, Lee HJ, Sciammas R, Gantner BN, Dinner AR, Singh H. Multilineage transcriptional priming and determination of alternate hematopoietic cell fates. Cell. 126: 755-66. PMID 16923394 DOI: 10.1016/J.Cell.2006.06.052  0.58
2005 Warmflash A, Weigert M, Dinner AR. Control of genotypic allelic inclusion through TCR surface expression. Journal of Immunology (Baltimore, Md. : 1950). 175: 6412-9. PMID 16272293 DOI: 10.4049/Jimmunol.175.10.6412  0.531
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