Angela H DePace
Scholes C, Biette K, Harden T, DePace A. Signal Integration by Shadow Enhancers and Enhancer Duplications Varies across the Drosophila Embryo. Cell Rep. 2019;26:2407-2418.e5 pubmed publisher
..Characterizing signal integration by multiple enhancers is a critical step in developing conceptual and computational models of gene expression at the locus level, where multiple enhancers control transcription together. ..
Staller M, Vincent B, Bragdon M, Lydiard Martin T, Wunderlich Z, Estrada J, et al
. Shadow enhancers enable Hunchback bifunctionality in the Drosophila embryo. Proc Natl Acad Sci U S A. 2015;112:785-90 pubmed publisher
..These two "shadow enhancers" use different regulatory logic to create the same pattern. ..
Vincent B, Scholes C, Staller M, Wunderlich Z, Estrada J, Park J, et al
. Yearly planning meetings: individualized development plans aren't just more paperwork. Mol Cell. 2015;58:718-21 pubmed publisher
..We describe our approach to building an Individualized Development Plan, the reasons we find them useful and empowering for both PIs and trainees, and resources to help other labs implement them constructively. ..
Vincent B, Estrada J, DePace A. The appeasement of Doug: a synthetic approach to enhancer biology. Integr Biol (Camb). 2016;8:475-84 pubmed publisher
..We believe that with a communal effort in open data sharing, we can make substantial progress toward a complete understanding of enhancer function. ..
Wunderlich Z, Bragdon M, Vincent B, White J, Estrada J, DePace A. KrÃ¼ppel Expression Levels Are Maintained through Compensatory Evolution of Shadow Enhancers. Cell Rep. 2015;12:1740-7 pubmed publisher
..These results support the hypothesis that compensatory evolution can occur between shadow enhancers, which has implications for mechanistic and evolutionary studies of gene regulation. ..
Wunderlich Z, Bragdon M, DePace A. Comparing mRNA levels using in situ hybridization of a target gene and co-stain. Methods. 2014;68:233-41 pubmed publisher
..This strategy can be broadly applied to detect quantitative, spatially resolved changes in mRNA levels. ..
Staller M, Fowlkes C, Bragdon M, Wunderlich Z, Estrada J, DePace A. A gene expression atlas of a bicoid-depleted Drosophila embryo reveals early canalization of cell fate. Development. 2015;142:587-96 pubmed publisher
..Our gene expression atlas provides a high resolution picture of a classic perturbation and will enable further computational modeling of canalization and gene regulation in this transcriptional network. ..
Scholes C, DePace A, Sanchez A. Combinatorial Gene Regulation through Kinetic Control of the Transcription Cycle. Cell Syst. 2017;4:97-108.e9 pubmed publisher
..We propose experiments that will illuminate the role of kinetic control in transcription and discuss implications for deciphering the cis-regulatory "code." ..
Samee M, Lydiard Martin T, Biette K, Vincent B, Bragdon M, Eckenrode K, et al
. Quantitative Measurement and Thermodynamic Modeling of Fused Enhancers Support a Two-Tiered Mechanism for Interpreting Regulatory DNA. Cell Rep. 2017;21:236-245 pubmed publisher
..Our results underscore that mechanisms of how modules are defined and how their outputs are combined remain to be elucidated. ..