Wunderlich, Zeba B

TitleAssistant Professor
InstitutionUniversity of California, Irvine
DepartmentDevelopmental & Cell Biology
Address4107 Natural Sciences II
Zot 2305
Irvine CA 92697
Phone(949) 824-5959
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    Collapse Research 
    Collapse Research Activities and Funding
    Mechanisms of shadow enhancer robustness during development
    NIH/NICHD R01HD095246Jul 1, 2018 - May 31, 2023
    Role: Principal Investigator
    Dissecting expression divergence in developmental networks across Drosophilids
    NIH/NICHD R00HD073191Apr 1, 2015 - Mar 31, 2018
    Role: Principal Investigator
    Dissecting expression divergence in developmental networks across Drosophilids
    NIH/NICHD K99HD073191Sep 1, 2012 - Aug 31, 2014
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. 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 Sep 07; 14(9):e1007644. PMID: 30192762.
      View in: PubMed
    2. 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 May 29. PMID: 29850830.
      View in: PubMed
    3. 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.
      View in: PubMed
    4. Li L, Wunderlich Z. An Enhancer's Length and Composition Are Shaped by Its Regulatory Task. Front Genet. 2017; 8:63. PMID: 28588608.
      View in: PubMed
    5. 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.
      View in: PubMed
    6. 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; PMCID: PMC4795680.
    7. 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; PMCID: PMC4581983 [Available on 09/22/16].
    8. 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.
      View in: PubMed
    9. 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; PMCID: PMC4302997.
    10. 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; PMCID: PMC4311800.
    11. 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; PMCID: PMC4048779.
    12. 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; PMCID: PMC3527254.
    13. 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; PMCID: PMC3435502.
    14. 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; PMCID: PMC3203197.
    15. 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.
      View in: PubMed
    16. Wunderlich Z, Mirny LA. Different gene regulation strategies revealed by analysis of binding motifs. Trends Genet. 2009 Oct; 25(10):434-40. PMID: 19815308; PMCID: PMC3697852.
    17. Wunderlich Z, Mirny LA. Using genome-wide measurements for computational prediction of SH2-peptide interactions. Nucleic Acids Res. 2009 Aug; 37(14):4629-41. PMID: 19502496; PMCID: PMC2724268.
    18. Tian W, Zhang LV, Tasan M, Gibbons FD, King OD, Park J, Wunderlich Z, Cherry JM, Roth FP. Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function. Genome Biol. 2008; 9 Suppl 1:S7. PMID: 18613951; PMCID: PMC2447541.
    19. Wunderlich Z, Mirny LA. Spatial effects on the speed and reliability of protein-DNA search. Nucleic Acids Res. 2008 Jun; 36(11):3570-8. PMID: 18453629; PMCID: PMC2441786.
    20. Wunderlich Z, Kuchibhotla K. Non-traditional publishing choices can enrich science. Nature. 2008 Feb 21; 451(7181):887. PMID: 18288164.
      View in: PubMed
    21. Bhattacharya A, Wunderlich Z, Monleon D, Tejero R, Montelione GT. Assessing model accuracy using the homology modeling automatically software. Proteins. 2008 Jan 01; 70(1):105-18. PMID: 17640066.
      View in: PubMed
    22. Kolesov G, Wunderlich Z, Laikova ON, Gelfand MS, Mirny LA. How gene order is influenced by the biophysics of transcription regulation. Proc Natl Acad Sci U S A. 2007 Aug 28; 104(35):13948-53. PMID: 17709750; PMCID: PMC1955771.
    23. Wunderlich Z, Mirny LA. Using the topology of metabolic networks to predict viability of mutant strains. Biophys J. 2006 Sep 15; 91(6):2304-11. PMID: 16782788; PMCID: PMC1557581.
    24. Wunderlich Z, Acton TB, Liu J, Kornhaber G, Everett J, Carter P, Lan N, Echols N, Gerstein M, Rost B, Montelione GT. The protein target list of the Northeast Structural Genomics Consortium. Proteins. 2004 Aug 01; 56(2):181-7. PMID: 15211503.
      View in: PubMed
    25. Goh CS, Lan N, Echols N, Douglas SM, Milburn D, Bertone P, Xiao R, Ma LC, Zheng D, Wunderlich Z, Acton T, Montelione GT, Gerstein M. SPINE 2: a system for collaborative structural proteomics within a federated database framework. Nucleic Acids Res. 2003 Jun 01; 31(11):2833-8. PMID: 12771210; PMCID: PMC156730.
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