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Items: 28


Dissecting the sharp response of a canonical developmental enhancer reveals multiple sources of cooperativity.

Park J, Estrada J, Johnson G, Vincent BJ, Ricci-Tam C, Bragdon MD, Shulgina Y, Cha A, Wunderlich Z, Gunawardena J, DePace AH.

Elife. 2019 Jun 21;8. pii: e41266. doi: 10.7554/eLife.41266.


Quantitative Comparison of the Anterior-Posterior Patterning System in the Embryos of Five Drosophila Species.

Wunderlich Z, Fowlkes CC, Eckenrode KB, Bragdon MDJ, Abiri A, DePace AH.

G3 (Bethesda). 2019 Jul 9;9(7):2171-2182. doi: 10.1534/g3.118.200953.


Signal Integration by Shadow Enhancers and Enhancer Duplications Varies across the Drosophila Embryo.

Scholes C, Biette KM, Harden TT, DePace AH.

Cell Rep. 2019 Feb 26;26(9):2407-2418.e5. doi: 10.1016/j.celrep.2019.01.115.


Hunchback is counter-repressed to regulate even-skipped stripe 2 expression in Drosophila embryos.

Vincent BJ, Staller MV, Lopez-Rivera F, Bragdon MDJ, Pym ECG, Biette KM, Wunderlich Z, Harden TT, Estrada J, DePace AH.

PLoS Genet. 2018 Sep 7;14(9):e1007644. doi: 10.1371/journal.pgen.1007644. eCollection 2018 Sep.


Analysis of Genetic Variation Indicates DNA Shape Involvement in Purifying Selection.

Wang X, Zhou T, Wunderlich Z, Maurano MT, DePace AH, Nuzhdin SV, Rohs R.

Mol Biol Evol. 2018 Aug 1;35(8):1958-1967. doi: 10.1093/molbev/msy099.


Transcriptional precision and accuracy in development: from measurements to models and mechanisms.

Bentovim L, Harden TT, DePace AH.

Development. 2017 Nov 1;144(21):3855-3866. doi: 10.1242/dev.146563. Review.


Quantitative Measurement and Thermodynamic Modeling of Fused Enhancers Support a Two-Tiered Mechanism for Interpreting Regulatory DNA.

Samee MAH, Lydiard-Martin T, Biette KM, Vincent BJ, Bragdon MD, Eckenrode KB, Wunderlich Z, Estrada J, Sinha S, DePace AH.

Cell Rep. 2017 Oct 3;21(1):236-245. doi: 10.1016/j.celrep.2017.09.033.


Combinatorial Gene Regulation through Kinetic Control of the Transcription Cycle.

Scholes C, DePace AH, Sánchez Á.

Cell Syst. 2017 Jan 25;4(1):97-108.e9. doi: 10.1016/j.cels.2016.11.012. Epub 2016 Dec 29.


Krüppel Expression Levels Are Maintained through Compensatory Evolution of Shadow Enhancers.

Wunderlich Z, Bragdon MD, Vincent BJ, White JA, Estrada J, DePace AH.

Cell Rep. 2016 Mar 29;14(12):3030. doi: 10.1016/j.celrep.2016.03.032. No abstract available.


SiteOut: An Online Tool to Design Binding Site-Free DNA Sequences.

Estrada J, Ruiz-Herrero T, Scholes C, Wunderlich Z, DePace AH.

PLoS One. 2016 Mar 17;11(3):e0151740. doi: 10.1371/journal.pone.0151740. eCollection 2016.


The appeasement of Doug: a synthetic approach to enhancer biology.

Vincent BJ, Estrada J, DePace AH.

Integr Biol (Camb). 2016 Apr 18;8(4):475-84. doi: 10.1039/c5ib00321k. Epub 2016 Mar 3. Review.


Krüppel Expression Levels Are Maintained through Compensatory Evolution of Shadow Enhancers.

Wunderlich Z, Bragdon MD, Vincent BJ, White JA, Estrada J, DePace AH.

Cell Rep. 2015 Sep 22;12(11):1740-7. doi: 10.1016/j.celrep.2015.08.021. Epub 2015 Sep 3. Erratum in: Cell Rep. 2016 Mar 29;14(12):3030.


Yearly planning meetings: individualized development plans aren't just more paperwork.

Vincent BJ, Scholes C, Staller MV, Wunderlich Z, Estrada J, Park J, Bragdon MD, Lopez Rivera F, Biette KM, DePace AH.

Mol Cell. 2015 Jun 4;58(5):718-21. doi: 10.1016/j.molcel.2015.04.025.


A gene expression atlas of a bicoid-depleted Drosophila embryo reveals early canalization of cell fate.

Staller MV, Fowlkes CC, Bragdon MD, Wunderlich Z, Estrada J, DePace AH.

Development. 2015 Feb 1;142(3):587-96. doi: 10.1242/dev.117796.


Shadow enhancers enable Hunchback bifunctionality in the Drosophila embryo.

Staller MV, Vincent BJ, Bragdon MD, Lydiard-Martin T, Wunderlich Z, Estrada J, DePace AH.

Proc Natl Acad Sci U S A. 2015 Jan 20;112(3):785-90. doi: 10.1073/pnas.1413877112. Epub 2015 Jan 6.


Comparing mRNA levels using in situ hybridization of a target gene and co-stain.

Wunderlich Z, Bragdon MD, DePace AH.

Methods. 2014 Jun 15;68(1):233-41. doi: 10.1016/j.ymeth.2014.01.003. Epub 2014 Jan 13.


Depleting gene activities in early Drosophila embryos with the "maternal-Gal4-shRNA" system.

Staller MV, Yan D, Randklev S, Bragdon MD, Wunderlich ZB, Tao R, Perkins LA, Depace AH, Perrimon N.

Genetics. 2013 Jan;193(1):51-61. doi: 10.1534/genetics.112.144915. Epub 2012 Oct 26.


Dissecting sources of quantitative gene expression pattern divergence between Drosophila species.

Wunderlich Z, Bragdon MD, Eckenrode KB, Lydiard-Martin T, Pearl-Waserman S, DePace AH.

Mol Syst Biol. 2012;8:604. doi: 10.1038/msb.2012.35.


A conserved developmental patterning network produces quantitatively different output in multiple species of Drosophila.

Fowlkes CC, Eckenrode KB, Bragdon MD, Meyer M, Wunderlich Z, Simirenko L, Luengo Hendriks CL, Keränen SV, Henriquez C, Knowles DW, Biggin MD, Eisen MB, DePace AH.

PLoS Genet. 2011 Oct;7(10):e1002346. doi: 10.1371/journal.pgen.1002346. Epub 2011 Oct 27.


Modeling transcriptional networks in Drosophila development at multiple scales.

Wunderlich Z, DePace AH.

Curr Opin Genet Dev. 2011 Dec;21(6):711-8. doi: 10.1016/j.gde.2011.07.005. Epub 2011 Sep 1. Review.


Visual exploration of three-dimensional gene expression using physical views and linked abstract views.

Weber GH, Rübel O, Huang MY, DePace AH, Fowlkes CC, Keränen SV, Luengo Hendriks CL, Hagen H, Knowles DW, Malik J, Biggin MD, Hamann B.

IEEE/ACM Trans Comput Biol Bioinform. 2009 Apr-Jun;6(2):296-309. doi: 10.1109/TCBB.2007.70249.


A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm.

Fowlkes CC, Hendriks CL, Keränen SV, Weber GH, Rübel O, Huang MY, Chatoor S, DePace AH, Simirenko L, Henriquez C, Beaton A, Weiszmann R, Celniker S, Hamann B, Knowles DW, Biggin MD, Eisen MB, Malik J.

Cell. 2008 Apr 18;133(2):364-74. doi: 10.1016/j.cell.2008.01.053.


Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution I: data acquisition pipeline.

Luengo Hendriks CL, Keränen SV, Fowlkes CC, Simirenko L, Weber GH, DePace AH, Henriquez C, Kaszuba DW, Hamann B, Eisen MB, Malik J, Sudar D, Biggin MD, Knowles DW.

Genome Biol. 2006;7(12):R123.


Emerging principles of conformation-based prion inheritance.

Chien P, Weissman JS, DePace AH.

Annu Rev Biochem. 2004;73:617-56. Review.


Generation of prion transmission barriers by mutational control of amyloid conformations.

Chien P, DePace AH, Collins SR, Weissman JS.

Nature. 2003 Aug 21;424(6951):948-51.


Origins and kinetic consequences of diversity in Sup35 yeast prion fibers.

DePace AH, Weissman JS.

Nat Struct Biol. 2002 May;9(5):389-96.


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