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Mapping cell migrations and fates in a gastruloid model to the human primitive streak.

Martyn I, Siggia ED, Brivanlou AH.

Development. 2019 Sep 12;146(17). pii: dev179564. doi: 10.1242/dev.179564.


A 3D model of a human epiblast reveals BMP4-driven symmetry breaking.

Simunovic M, Metzger JJ, Etoc F, Yoney A, Ruzo A, Martyn I, Croft G, You DS, Brivanlou AH, Siggia ED.

Nat Cell Biol. 2019 Jul;21(7):900-910. doi: 10.1038/s41556-019-0349-7. Epub 2019 Jul 1.


Self-organization of stem cells into embryos: A window on early mammalian development.

Shahbazi MN, Siggia ED, Zernicka-Goetz M.

Science. 2019 Jun 7;364(6444):948-951. doi: 10.1126/science.aax0164.


A wave of WNT signaling balanced by secreted inhibitors controls primitive streak formation in micropattern colonies of human embryonic stem cells.

Martyn I, Brivanlou AH, Siggia ED.

Development. 2019 Mar 25;146(6). pii: dev172791. doi: 10.1242/dev.172791.


Author Correction: Self-organization of a human organizer by combined Wnt and Nodal signalling.

Martyn I, Kanno TY, Ruzo A, Siggia ED, Brivanlou AH.

Nature. 2018 Dec;564(7735):E10. doi: 10.1038/s41586-018-0583-3.


WNT signaling memory is required for ACTIVIN to function as a morphogen in human gastruloids.

Yoney A, Etoc F, Ruzo A, Carroll T, Metzger JJ, Martyn I, Li S, Kirst C, Siggia ED, Brivanlou AH.

Elife. 2018 Oct 12;7. pii: e38279. doi: 10.7554/eLife.38279.


Modeling Mammalian Gastrulation With Embryonic Stem Cells.

Siggia ED, Warmflash A.

Curr Top Dev Biol. 2018;129:1-23. doi: 10.1016/bs.ctdb.2018.03.001. Epub 2018 Apr 12. Review.


Self-organization of a human organizer by combined Wnt and Nodal signalling.

Martyn I, Kanno TY, Ruzo A, Siggia ED, Brivanlou AH.

Nature. 2018 Jun;558(7708):132-135. doi: 10.1038/s41586-018-0150-y. Epub 2018 May 23. Erratum in: Nature. 2018 Dec;564(7735):E10.


Micropattern differentiation of mouse pluripotent stem cells recapitulates embryo regionalized cell fate patterning.

Morgani SM, Metzger JJ, Nichols J, Siggia ED, Hadjantonakis AK.

Elife. 2018 Feb 7;7. pii: e32839. doi: 10.7554/eLife.32839.


Gene-free methodology for cell fate dynamics during development.

Corson F, Siggia ED.

Elife. 2017 Dec 13;6. pii: e30743. doi: 10.7554/eLife.30743.


A Geometric Model of Stripe Refinement.

Siggia ED.

Dev Cell. 2017 May 8;41(3):225-227. doi: 10.1016/j.devcel.2017.04.016. Review.


Long-Term High-Resolution Imaging of Developing C. elegans Larvae with Microfluidics.

Keil W, Kutscher LM, Shaham S, Siggia ED.

Dev Cell. 2017 Jan 23;40(2):202-214. doi: 10.1016/j.devcel.2016.11.022. Epub 2016 Dec 29.


A Balance between Secreted Inhibitors and Edge Sensing Controls Gastruloid Self-Organization.

Etoc F, Metzger J, Ruzo A, Kirst C, Yoney A, Ozair MZ, Brivanlou AH, Siggia ED.

Dev Cell. 2016 Nov 7;39(3):302-315. doi: 10.1016/j.devcel.2016.09.016. Epub 2016 Oct 13.


Predicting Ancestral Segmentation Phenotypes from Drosophila to Anopheles Using In Silico Evolution.

Rothschild JB, Tsimiklis P, Siggia ED, François P.

PLoS Genet. 2016 May 26;12(5):e1006052. doi: 10.1371/journal.pgen.1006052. eCollection 2016 May.


Self-organization of the in vitro attached human embryo.

Deglincerti A, Croft GF, Pietila LN, Zernicka-Goetz M, Siggia ED, Brivanlou AH.

Nature. 2016 May 12;533(7602):251-4. doi: 10.1038/nature17948. Epub 2016 May 4.


Temperature compensation and temperature sensation in the circadian clock.

Kidd PB, Young MW, Siggia ED.

Proc Natl Acad Sci U S A. 2015 Nov 17;112(46):E6284-92. doi: 10.1073/pnas.1511215112. Epub 2015 Nov 2.


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

Sorre B, Warmflash A, Brivanlou AH, Siggia ED.

Dev Cell. 2014 Aug 11;30(3):334-42. doi: 10.1016/j.devcel.2014.05.022. Epub 2014 Jul 24.


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

Warmflash A, Sorre B, Etoc F, Siggia ED, Brivanlou AH.

Nat Methods. 2014 Aug;11(8):847-54. doi: 10.1038/nmeth.3016. Epub 2014 Jun 29.


Decisions on the fly in cellular sensory systems.

Siggia ED, Vergassola M.

Proc Natl Acad Sci U S A. 2013 Sep 24;110(39):E3704-12. doi: 10.1073/pnas.1314081110. Epub 2013 Sep 9.


Phenotypic model for early T-cell activation displaying sensitivity, specificity, and antagonism.

François P, Voisinne G, Siggia ED, Altan-Bonnet G, Vergassola M.

Proc Natl Acad Sci U S A. 2013 Mar 5;110(10):E888-97. doi: 10.1073/pnas.1300752110. Epub 2013 Feb 19.


Phenotypic models of evolution and development: geometry as destiny.

François P, Siggia ED.

Curr Opin Genet Dev. 2012 Dec;22(6):627-33. doi: 10.1016/j.gde.2012.09.001. Epub 2012 Sep 28.


Signaling dynamics and embryonic development.

Warmflash A, Siggia ED, Brivanlou AH.

Cell Cycle. 2012 Oct 1;11(19):3529-30. doi: 10.4161/cc.21964. Epub 2012 Aug 30. No abstract available.


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

Warmflash A, Francois P, Siggia ED.

Phys Biol. 2012 Oct;9(5):056001. doi: 10.1088/1478-3975/9/5/056001. Epub 2012 Aug 8.


Adaptive temperature compensation in circadian oscillations.

François P, Despierre N, Siggia ED.

PLoS Comput Biol. 2012;8(7):e1002585. doi: 10.1371/journal.pcbi.1002585. Epub 2012 Jul 12.


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

Warmflash A, Zhang Q, Sorre B, Vonica A, Siggia ED, Brivanlou AH.

Proc Natl Acad Sci U S A. 2012 Jul 10;109(28):E1947-56. doi: 10.1073/pnas.1207607109. Epub 2012 Jun 11.


Profile of Eric D. Siggia. Interview by Farooq Ahmed.

Siggia ED.

Proc Natl Acad Sci U S A. 2012 Apr 10;109(15):5551-2. doi: 10.1073/pnas.1204149109. Epub 2012 Apr 2. No abstract available.


Geometry, epistasis, and developmental patterning.

Corson F, Siggia ED.

Proc Natl Acad Sci U S A. 2012 Apr 10;109(15):5568-75. doi: 10.1073/pnas.1201505109. Epub 2012 Mar 20.


Predicting embryonic patterning using mutual entropy fitness and in silico evolution.

François P, Siggia ED.

Development. 2010 Jul;137(14):2385-95. doi: 10.1242/dev.048033.


Nucleosome-depleted regions in cell-cycle-regulated promoters ensure reliable gene expression in every cell cycle.

Bai L, Charvin G, Siggia ED, Cross FR.

Dev Cell. 2010 Apr 20;18(4):544-55. doi: 10.1016/j.devcel.2010.02.007.


Origin of irreversibility of cell cycle start in budding yeast.

Charvin G, Oikonomou C, Siggia ED, Cross FR.

PLoS Biol. 2010 Jan 19;8(1):e1000284. doi: 10.1371/journal.pbio.1000284. Erratum in: PLoS Biol. 2011 Jul;9(7). doi:10.1371/annotation/90916531-1b34-4eb5-92a9-a7f8c5d72318.


Scaling of BMP gradients in Xenopus embryos.

Francois P, Vonica A, Brivanlou AH, Siggia ED.

Nature. 2009 Sep 3;461(7260):E1; discussion E2.


Using DNA mechanics to predict in vitro nucleosome positions and formation energies.

Morozov AV, Fortney K, Gaykalova DA, Studitsky VM, Widom J, Siggia ED.

Nucleic Acids Res. 2009 Aug;37(14):4707-22. doi: 10.1093/nar/gkp475. Epub 2009 Jun 9.


Forced periodic expression of G1 cyclins phase-locks the budding yeast cell cycle.

Charvin G, Cross FR, Siggia ED.

Proc Natl Acad Sci U S A. 2009 Apr 21;106(16):6632-7. doi: 10.1073/pnas.0809227106. Epub 2009 Apr 3.


Analysis of combinatorial cis-regulation in synthetic and genomic promoters.

Gertz J, Siggia ED, Cohen BA.

Nature. 2009 Jan 8;457(7226):215-8. doi: 10.1038/nature07521. Epub 2008 Nov 23.


Developmental regulatory bits.

Siggia ED.

Mol Syst Biol. 2008;4:226. doi: 10.1038/msb.2008.64. Epub 2008 Nov 4. No abstract available.


Positive feedback of G1 cyclins ensures coherent cell cycle entry.

Skotheim JM, Di Talia S, Siggia ED, Cross FR.

Nature. 2008 Jul 17;454(7202):291-6. doi: 10.1038/nature07118.


A case study of evolutionary computation of biochemical adaptation.

François P, Siggia ED.

Phys Biol. 2008 Jun 24;5(2):026009. doi: 10.1088/1478-3975/5/2/026009.


Sequence context affects the rate of short insertions and deletions in flies and primates.

Tanay A, Siggia ED.

Genome Biol. 2008;9(2):R37. doi: 10.1186/gb-2008-9-2-r37. Epub 2008 Feb 21.


A microfluidic device for temporally controlled gene expression and long-term fluorescent imaging in unperturbed dividing yeast cells.

Charvin G, Cross FR, Siggia ED.

PLoS One. 2008 Jan 23;3(1):e1468. doi: 10.1371/journal.pone.0001468.


Deriving structure from evolution: metazoan segmentation.

François P, Hakim V, Siggia ED.

Mol Syst Biol. 2007;3:154. Epub 2007 Dec 18.


The effects of molecular noise and size control on variability in the budding yeast cell cycle.

Di Talia S, Skotheim JM, Bean JM, Siggia ED, Cross FR.

Nature. 2007 Aug 23;448(7156):947-51. Erratum in: Nature. 2007 Dec 20;450(7173):1272.


Tracking the in vivo evolution of multidrug resistance in Staphylococcus aureus by whole-genome sequencing.

Mwangi MM, Wu SW, Zhou Y, Sieradzki K, de Lencastre H, Richardson P, Bruce D, Rubin E, Myers E, Siggia ED, Tomasz A.

Proc Natl Acad Sci U S A. 2007 May 29;104(22):9451-6. Epub 2007 May 21.


Connecting protein structure with predictions of regulatory sites.

Morozov AV, Siggia ED.

Proc Natl Acad Sci U S A. 2007 Apr 24;104(17):7068-73. Epub 2007 Apr 16.


PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny.

Siddharthan R, Siggia ED, van Nimwegen E.

PLoS Comput Biol. 2005 Dec;1(7):e67. Epub 2005 Dec 9.


Gene expression from random libraries of yeast promoters.

Ligr M, Siddharthan R, Cross FR, Siggia ED.

Genetics. 2006 Apr;172(4):2113-22. Epub 2006 Jan 16.


Coherence and timing of cell cycle start examined at single-cell resolution.

Bean JM, Siggia ED, Cross FR.

Mol Cell. 2006 Jan 6;21(1):3-14.


Protein-DNA binding specificity predictions with structural models.

Morozov AV, Havranek JJ, Baker D, Siggia ED.

Nucleic Acids Res. 2005 Oct 24;33(18):5781-98. Print 2005.


Mode locking the cell cycle.

Cross FR, Siggia ED.

Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Aug;72(2 Pt 1):021910. Epub 2005 Aug 24.


Shake it, don't break it: positive feedback and the evolution of oscillator design.

Cross FR, Siggia ED.

Dev Cell. 2005 Sep;9(3):309-10. Review.

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