Zeba Wunderlich

Associate Professor

Boston University Graduate School of Arts and Sciences

Biology

PhD, Harvard University
BA, Rutgers University

Websites

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ORCID : 0000-0003-4491-5715

Regulatory DNA encodes the gene regulatory networks that are required for virtually every process in an animal, from development to immunity. The Wunderlich lab is interested in understanding how a gene regulatory network’s tasks influence its architecture, robustness, and evolvability. To probe these questions, we use two model systems: the Drosophila early embryonic patterning system and the Drosophila innate immune response. In both systems, we pair imaging-based and genomic measurements of gene expression with statistical and physically based computational models to explore questions of gene regulatory network function. We exploit naturally occurring sequence variation between individuals and species as a tool to measure how changes in regulatory DNA affect transcriptional regulation.

Associate Professor
Boston University Graduate School of Arts and Sciences
Biomedical Engineering

BU Research

Mechanisms of shadow enhancer robustness during development
04/01/2025 - 12/31/2029 (PI)
NIH/National Institute of Child Health & Human Development
2R01HD095246-07A1

Collaborative Research: OSIB: Uncovering drivers of infection resistance, survival, and tolerance using non-invasive real-time imaging
08/01/2025 - 07/31/2028 (PI)
National Science Foundation
IOS-2426656

Uncovering the regulatory DNA logic of the Drosophila innate immune response
03/01/2022 - 04/30/2025 (PI)
National Science Foundation
MCB-2223888

Mechanisms of shadow enhancer robustness during development
09/03/2021 - 03/31/2025 (PI)
NIH/National Institute of Child Health & Human Development
5R01HD095246-06

Title

Yr	Title	Project-Sub Proj	Pubs

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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Nawar N, Rits E, Cohen L, Wunderlich Z. Heterogeneous NF-?B activation and enhancer features shape transcription in Drosophila immunity. bioRxiv. 2025 May 19. PMID: 40475619; DOI: 10.1101/2025.05.19.654881;

Zhu Y, Wunderlich Z, Lander AD. Epithelial cell competition is promoted by signaling from immune cells. Nat Commun. 2025 Apr 19; 16(1):3710. PMID: 40251197; DOI: 10.1038/s41467-025-59130-5;

Gibbs JR, Mei C, Wunderlich Z. Beyond the heat shock pathway: Heat stress responses in Drosophila development. Dev Biol. 2025 Feb; 518:53-60. PMID: 39557149; DOI: 10.1016/j.ydbio.2024.11.003;

Cabrera K, Hoard DS, Gibson O, Martinez DI, Wunderlich Z. Drosophila immune priming to Enterococcus faecalis relies on immune tolerance rather than resistance. PLoS Pathog. 2023 Aug; 19(8):e1011567. PMID: 37566589; DOI: 10.1371/journal.ppat.1011567;

Fletcher A, Wunderlich Z, Enciso G. Shadow enhancers mediate trade-offs between transcriptional noise and fidelity. PLoS Comput Biol. 2023 May; 19(5):e1011071. PMID: 37205714; DOI: 10.1371/journal.pcbi.1011071;

Ramirez-Corona BA, Love AC, Chandrasekaran S, Prescher JA, Wunderlich Z. Longitudinal monitoring of individual infection progression in Drosophila melanogaster. iScience. 2022 Nov 18; 25(11):105378. PMID: 36345341; DOI: 10.1016/j.isci.2022.105378;

Li L, Waymack R, Gad M, Wunderlich Z. Two promoters integrate multiple enhancer inputs to drive wild-type knirps expression in the Drosophila melanogaster embryo. Genetics. 2021 Dec 10; 219(4). PMID: 34849867; DOI: 10.1093/genetics/iyab154;

Han J, Perera S, Wunderlich Z, Periwal V. Mechanistic gene networks inferred from single-cell data with an outlier-insensitive method. Math Biosci. 2021 Dec; 342:108722. PMID: 34688607; DOI: 10.1016/j.mbs.2021.108722;

Waymack R, Gad M, Wunderlich Z. Molecular competition can shape enhancer activity in the Drosophila embryo. iScience. 2021 Sep 24; 24(9):103034. PMID: 34568782; DOI: 10.1016/j.isci.2021.103034;

Waymack R, Wunderlich Z. Embryonic development across space and time. Nat Comput Sci. 2021 Aug; 1(8):507-508. PMID: 38217246

Showing 10 of 43 results. Show More

Kvon EZ, Waymack R, Gad M, Wunderlich Z. Author Correction: Enhancer redundancy in development and disease. Nat Rev Genet. 2021 May; 22(5):337. PMID: 33850330

Ramirez-Corona BA, Fruth S, Ofoegbu O, Wunderlich Z. The mode of expression divergence in Drosophila fat body is infection-specific. Genome Res. 2021 Jun; 31(6):1024-1034. PMID: 33858842; DOI: 10.1101/gr.269597.120;

Kvon EZ, Waymack R, Gad M, Wunderlich Z. Enhancer redundancy in development and disease. Nat Rev Genet. 2021 May; 22(5):324-336. PMID: 33442000; DOI: 10.1038/s41576-020-00311-x;

López-Rivera F, Foster Rhoades OK, Vincent BJ, Pym ECG, Bragdon MDJ, Estrada J, DePace AH, Wunderlich Z. A Mutation in the Drosophila melanogaster eve Stripe 2 Minimal Enhancer Is Buffered by Flanking Sequences. G3 (Bethesda). 2020 Dec 03; 10(12):4473-4482. PMID: 33037064; DOI: 10.1534/g3.120.401777;

Waymack R, Fletcher A, Enciso G, Wunderlich Z. Shadow enhancers can suppress input transcription factor noise through distinct regulatory logic. Elife. 2020 Aug 17; 9. PMID: 32804082; DOI: 10.7554/eLife.59351;

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 Jul 09; 9(7):2171-2182. PMID: 31048401

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 Jun 21; 8. PMID: 31223115

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; 14(9):e1007644. PMID: 30192762

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 Aug 01; 35(8):1958-1967. PMID: 29850830

Osman NM, Kitapci TH, Vlaho S, Wunderlich Z, Nuzhdin SV. Inference of Transcription Factor Regulation Patterns Using Gene Expression Covariation in Natural Populations of Drosophila melanogaster. Biophysics (Oxf). 2018 Jan; 63(1):43-51. PMID: 30739944

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

Li L, Wunderlich Z. An Enhancer's Length and Composition Are Shaped by Its Regulatory Task. Front Genet. 2017; 8:63. PMID: 28588608; DOI: 10.3389/fgene.2017.00063;

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

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

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

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

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

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

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

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

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

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

Wunderlich Z, Mirny LA. Different gene regulation strategies revealed by analysis of binding motifs. Trends Genet. 2009 Oct; 25(10):434-40. PMID: 19815308

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

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(Suppl 1):S7. PMID: 18613951

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

Wunderlich Z, Kuchibhotla K. Non-traditional publishing choices can enrich science. Nature. 2008 Feb 21; 451(7181):887. PMID: 18288164

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

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

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

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

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

This graph shows the total number of publications by year, by first, middle/unknown, or last author.

Bar chart showing 43 publications over 20 distinct years, with a maximum of 7 publications in 2021