Publications

References and links to our papers

Estrada J, Wong F, DePace AH, Gunawardena J (2016) Information Integration and Energy Expenditure in Gene Regulation Cell 166: 234-244 Link to .pdf
*Note that the online .html version currently has errors in the equations. These errors are not present in the .pdf.

Estrada J, Ruiz-Herrara T, Scholes C, Wunderlich Z, DePace AH (2016) SiteOut: An Online Tool to Design Binding Site Free DNA Sequences PLoS One 11(3) e0151740 Link to PLoS One

Vincent BJ, Estrada J, DePace AH (2015) The Appeasement of Doug: A Synthetic Approach to Enhancer Biology Intgr. Biol. 8:475-484 Link to Integrative Biology

Wunderlich Z, Bragdon MD, Vincent BJ, White JA, Estrada J, DePace AH. (2015) Krüppel Expression Levels Are Maintained through Compensatory Evolution of Shadow Enhancers. Cell Rep. Sep 22;12(11):1740-7 Link to Cell Reports

Vincent BJ, Scholes C, Staller MV, Wunderlich Z, Estrada J, Park J, Bragdon MD, Lopez Rivera F, Biette KM, DePace AH (2015) Yearly Planning Meetings: Individualized Development Plans Aren’t Just More Paperwork. Mol CellJun 4;58(5):718-21 Link to Mol Cell

Staller MV, Vincent BJ, Bragdon MDJ, Lydiard-Martin T, Wunderlich Z, Estrada J, DePace AH (2015) Shadow Enhancers enable Hunchback bifunctionality in the Drosophila embryo. PNAS, early edition
Link to PNASLink to BioRXiV

Staller MV, Fowlkes CC, Bragdon MDJ, Wunderlich Z, Estrada J, DePace AH (2015) A gene expression atlas of a bicoid-depleted Drosophila embryo reveals early canalization of cell fate. Development.
Link to DevelopmentLink to BioRXiV

Lydiard-Martin T, Bragdon MDJ, Eckenrode KB, Wunderlich Z, DePace AH (2014) Locus architecture affects mRNA expression levels in Drosophila embryos.
Link to BioRXiV

Wunderlich Z, Bragdon MD, DePace AH. Comparing mRNA levels using in situ hybridization of a target gene and co-stain. Methods. 2014 Jun 15;68(1):233-41.
Link to Methods; Download .pdf

Staller MV, Yan D, Randklev S, Bragdon MD, Wunderlich ZB, Tao R, Perkins LA, DePace AH, Perrimon N. Depleting gene activities in early Drosophila embryos with the “maternal-Gal4-shRNA” system. Genetics. 2013 Jan;193(1):51-61.
Link to GeneticsLink to PubMedCentral

Ilsley GR, Fisher J, Apweiler R, DePace AH*, Luscombe NM* (2013) Cellular resolution 
models of even-skipped regulation in the entire Drosophila embryo eLife 2:e00522
Link to eLife

Wunderlich Z, Bragdon MD, Eckenrode KB, Lydiard-Martin T, Pearl-Waserman S, DePace AH. Dissecting sources of quantitative gene expression pattern divergence between Drosophila species. Mol Syst Biol. 2012;8:604.
Link to Mol Systems Biol

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.  A conserved developmental patterning network produces quantitatively different output in multiple species of Drosophila. PLoS Genet. 2011 Oct;7(10):e1002346.
Link to PLoS Genetics

Wunderlich Z, DePace AH. Modeling transcriptional networks in Drosophila development at multiple scales.Curr Opin Genet Dev. 2011 Dec;21(6):711-8.
Link to Curr Opin in Genet Dev

Meyer M, Munzner T, DePace A, Pfister H. MulteeSum: a tool for comparative spatial and temporal gene expression data. IEEE Trans Vis Comput Graph. 2010 Nov-Dec;16(6):908-17.
Link to IEEE 

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. Visual exploration of three-dimensional gene expression using physical views and linked abstract views. IEEE/ACM Trans Comput Biol Bioinform. 2009 Apr-Jun;6(2):296-309.
Link to IEEE/ACM

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. A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm. Cell. 2008 Apr 18;133(2):364-74.
Link to Cell

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. Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution I: data acquisition pipeline. Genome Biol. 2006;7(12):R123.
Link to Genome Biology

Graduate and Undergraduate Work

Chien P, Weissman JS, DePace AH. Emerging principles of conformation-based prion inheritance. Annu Rev Biochem. 2004;73:617-56.
Link to Annual Reviews

Chien P, DePace AH, Collins SR, Weissman JS. Generation of prion transmission barriers by mutational control of amyloid conformations. Nature. 2003 Aug 21;424(6951):948-51.
Link to Nature; Download .pdf

DePace AH, Weissman JS. Origins and kinetic consequences of diversity in Sup35 yeast prion fibers. Nat Struct Biol. 2002 May;9(5):389-96.
Link to Nat Struct Biol

DePace AH*, Santoso A*, Hillner P, Weissman JS.A critical role for amino-terminal glutamine/asparagine repeats in the formation and propagation of a yeast prion. Cell. 1998 Jun 26;93(7):1241-52.
Link to Cell

Dempsey LA, Li MJ, DePace A, Bray-Ward P, Maizels N. The human HNRPD locus maps to 4q21 and encodes a highly conserved protein. Genomics. 1998 May 1;49(3):378-84.
Link to Genomics; Download .pdf

Elfring LK, Daniel C, Papoulas O, Deuring R, Sarte M, Moseley S, Beek SJ, Waldrip WR, Daubresse G, DePace A, Kennison JA, Tamkun JW. Genetic analysis of brahma: the Drosophila homolog of the yeast chromatin remodeling factor SWI2/SNF2. Genetics. 1998 Jan;148(1):251-65.
Link to Genetics

Welch MD, DePace AH, Verma S, Iwamatsu A, Mitchison TJ. The human Arp2/3 complex is composed of evolutionarily conserved subunits and is localized to cellular regions of dynamic actin filament assembly. J Cell Biol. 1997 Jul 28;138(2):375-84.
Link to JCB