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Angela Depace, Ph.D.

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Research
The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
  1. R01GM122928 (DEPACE, ANGELA H) Apr 10, 2017 - Mar 31, 2021
    NIH/NIGMS
    Information Integration and Energy Expenditure in Eukaryotic Gene Regulation
    Role: Principal Investigator
  2. U01GM103804 (NUZHDIN, SERGEY V) Sep 30, 2013 - Jun 30, 2017
    NIH/NIGMS
    Multi-scale modeling of genetic variation in a developmental network
    Role: Co-Principal Investigator

Bibliographic
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Wunderlich Z, Fowlkes CC, Eckenrode KB, Bragdon MDJ, Abiri A, DePace AH. Quantitative Comparison of the Anterior-Posterior Patterning System in the Embryos of Five Drosophila Species. G3 (Bethesda). 2019 07 09; 9(7):2171-2182. PMID: 31048401.
    Citations:    
  2. Park J, Estrada J, Johnson G, Vincent BJ, Ricci-Tam C, Bragdon MD, Shulgina Y, Cha A, Wunderlich Z, Gunawardena J, DePace AH. Dissecting the sharp response of a canonical developmental enhancer reveals multiple sources of cooperativity. Elife. 2019 06 21; 8. PMID: 31223115.
    Citations:    
  3. Scholes C, Biette KM, Harden TT, DePace AH. Signal Integration by Shadow Enhancers and Enhancer Duplications Varies across the Drosophila Embryo. Cell Rep. 2019 02 26; 26(9):2407-2418.e5. PMID: 30811990.
    Citations:    
  4. Vincent BJ, Staller MV, Lopez-Rivera F, Bragdon MDJ, Pym ECG, Biette KM, Wunderlich Z, Harden TT, Estrada J, DePace AH. Hunchback is counter-repressed to regulate even-skipped stripe 2 expression in Drosophila embryos. PLoS Genet. 2018 09; 14(9):e1007644. PMID: 30192762.
    Citations:    Fields:    Translation:AnimalsCells
  5. Wang X, Zhou T, Wunderlich Z, Maurano MT, DePace AH, Nuzhdin SV, Rohs R. Analysis of Genetic Variation Indicates DNA Shape Involvement in Purifying Selection. Mol Biol Evol. 2018 08 01; 35(8):1958-1967. PMID: 29850830.
    Citations:    Fields:    
  6. Bentovim L, Harden TT, DePace AH. Transcriptional precision and accuracy in development: from measurements to models and mechanisms. Development. 2017 11 01; 144(21):3855-3866. PMID: 29089359.
    Citations: 2     Fields:    Translation:AnimalsCells
  7. Samee MAH, Lydiard-Martin T, Biette KM, Vincent BJ, Bragdon MD, Eckenrode KB, Wunderlich Z, Estrada J, Sinha S, DePace AH. Quantitative Measurement and Thermodynamic Modeling of Fused Enhancers Support a Two-Tiered Mechanism for Interpreting Regulatory DNA. Cell Rep. 2017 Oct 03; 21(1):236-245. PMID: 28978476.
    Citations:    Fields:    Translation:AnimalsCells
  8. Scholes C, DePace AH, Sánchez Á. Combinatorial Gene Regulation through Kinetic Control of the Transcription Cycle. Cell Syst. 2017 01 25; 4(1):97-108.e9. PMID: 28041762.
    Citations: 2     Fields:    
  9. Estrada J, Wong F, DePace A, Gunawardena J. Information Integration and Energy Expenditure in Gene Regulation. Cell. 2016 Jun 30; 166(1):234-44. PMID: 27368104.
    Citations: 8     Fields:    
  10. Wunderlich Z, Bragdon MD, Vincent BJ, White JA, Estrada J, DePace AH. Krüppel Expression Levels Are Maintained through Compensatory Evolution of Shadow Enhancers. Cell Rep. 2016 Mar 29; 14(12):3030. PMID: 27028762.
    Citations: 1     Fields:    
  11. Estrada J, Ruiz-Herrero T, Scholes C, Wunderlich Z, DePace AH. SiteOut: An Online Tool to Design Binding Site-Free DNA Sequences. PLoS One. 2016; 11(3):e0151740. PMID: 26987123.
    Citations:    Fields:    Translation:Cells
  12. Vincent BJ, Estrada J, DePace AH. The appeasement of Doug: a synthetic approach to enhancer biology. Integr Biol (Camb). 2016 Apr 18; 8(4):475-84. PMID: 26936291.
    Citations: 2     Fields:    Translation:HumansAnimalsCells
  13. Wunderlich Z, Bragdon MD, Vincent BJ, White JA, Estrada J, DePace AH. Krüppel Expression Levels Are Maintained through Compensatory Evolution of Shadow Enhancers. Cell Rep. 2015 Sep 22; 12(11):1740-7. PMID: 26344774.
    Citations: 10     Fields:    Translation:AnimalsCells
  14. Vincent BJ, Scholes C, Staller MV, Wunderlich Z, Estrada J, Park J, Bragdon MD, Lopez Rivera F, Biette KM, DePace AH. Yearly planning meetings: individualized development plans aren't just more paperwork. Mol Cell. 2015 Jun 04; 58(5):718-21. PMID: 26046646.
    Citations:    Fields:    Translation:Humans
  15. Staller MV, Fowlkes CC, Bragdon MD, Wunderlich Z, Estrada J, DePace AH. A gene expression atlas of a bicoid-depleted Drosophila embryo reveals early canalization of cell fate. Development. 2015 Feb 01; 142(3):587-96. PMID: 25605785.
    Citations: 6     Fields:    Translation:AnimalsCells
  16. Staller MV, Vincent BJ, Bragdon MD, Lydiard-Martin T, Wunderlich Z, Estrada J, DePace AH. Shadow enhancers enable Hunchback bifunctionality in the Drosophila embryo. Proc Natl Acad Sci U S A. 2015 Jan 20; 112(3):785-90. PMID: 25564665.
    Citations: 15     Fields:    Translation:AnimalsCells
  17. 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. PMID: 24434507.
    Citations: 4     Fields:    Translation:AnimalsCells
  18. 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. PMID: 23105012.
    Citations: 20     Fields:    Translation:AnimalsCells
  19. 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. PMID: 22893002.
    Citations: 14     Fields:    Translation:AnimalsCells
  20. 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. PMID: 22046143.
    Citations: 17     Fields:    Translation:Animals
  21. Wunderlich Z, DePace AH. Modeling transcriptional networks in Drosophila development at multiple scales. Curr Opin Genet Dev. 2011 Dec; 21(6):711-8. PMID: 21889888.
    Citations: 12     Fields:    Translation:AnimalsCells
  22. 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. PMID: 20975127.
    Citations: 6     Fields:    Translation:Animals
  23. Rübel O, Ahern S, Bethel EW, Biggin MD, Childs H, Cormier-Michel E, Depace A, Eisen MB, Fowlkes CC, Geddes CG, Hagen H, Hamann B, Huang MY, Keränen SV, Knowles DW, Hendriks CL, Malik J, Meredith J, Messmer P, Ushizima D, Weber GH, Wu K. Coupling visualization and data analysis for knowledge discovery from multi-dimensional scientific data. Procedia Comput Sci. 2010 May; 1(1):1757-1764. PMID: 23762211.
    Citations: 2     
  24. 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. PMID: 19407353.
    Citations: 9     Fields:    Translation:Animals
  25. 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. PMID: 18423206.
    Citations: 92     Fields:    Translation:Animals
  26. 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. PMID: 17184546.
    Citations: 52     Fields:    Translation:AnimalsCells
  27. Chien P, Weissman JS, DePace AH. Emerging principles of conformation-based prion inheritance. Annu Rev Biochem. 2004; 73:617-56. PMID: 15189155.
    Citations: 111     Fields:    Translation:HumansAnimalsCells
  28. 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. PMID: 12931190.
    Citations: 30     Fields:    Translation:Cells
  29. DePace AH, Weissman JS. Origins and kinetic consequences of diversity in Sup35 yeast prion fibers. Nat Struct Biol. 2002 May; 9(5):389-96. PMID: 11938354.
    Citations: 34     Fields:    Translation:AnimalsCells
  30. 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. PMID: 9657156.
    Citations: 141     Fields:    Translation:AnimalsCells
  31. 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. PMID: 9475737.
    Citations: 77     Fields:    Translation:AnimalsCells
  32. 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. PMID: 9230079.
    Citations: 145     Fields:    Translation:HumansAnimalsCells
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.