RESEARCH
Regulatory DNA encodes the gene regulatory networks that are required for virtually every process in an a nimal, 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-occuring sequence variation between individuals and species as a tool to measure how changes in regulatory DNA affect transcriptional regulation.
PEOPLE
Zeba Wunderlich
Assistant Professor
PhD, Harvard University, Biophysics
BA, Molecular Biology & Biochemistry, Statistics, Rutgers University
Bryan Ramirez
PhD Student
BS, Genetics, UC Davis
Rachel Waymack
PhD Student
BS, Neuroscience, College of William & Mary
Kevin Cabrera
PhD Student
BS, Biology, BA Chemistry, Florida International University
Lianne Cohen
Post-doctoral Fellow
PhD, Biology, UCSD
BS, Biological Sciences, Carnegie Mellon University
Jillian Ness
PhD Student
BS, MS, Perdue University
PUBLICATIONS
L Li, R Waymack, M Gad, Z Wunderlich. bioRxiv. (Pre-print).
BA Ramirez-Corona, SM Fruth, O Ofoegbu, Z Wunderlich. Genome Research. (2021).
EZ Kvon, R Waymack, M Gad, Z Wunderlich. Nature Reviews Genetics. (2021).
F Lopez-Rivera, OK Foster, BJ Vincent, ECG Pym, MDJ Bragdon, J Estrada, AH DePace, Z Wunderlich. G3. (2020).
R Waymack, A Fletcher, G Enciso, Z Wunderlich. eLife. (2020).
Z Wunderlich, CC Fowlkes, KB Eckenrode, MDJ Bragdon, A Abiri, AH DePace. G3. (2019).
J Park, J Estrada, G Johnson, BJ Vincent, C Ricci-Tam, MDJ Bragdon, Y Shulgina, A Cha, Z Wunderlich, J Gunawardena, AH DePace. eLife. (2019).
NM Osman, S Vlaho, TH Kitapci, Z Wunderlich, SV Nuzhdin. Biophysics. (2018).
BJ Vincent, MV Staller, F Lopez-Rivera, MDJ Bragdon, ECG Pym, KM Biette, Z Wunderlich, TT Harden, J Estrada, AH DePace. PLOS Genetics. (2018).
X Wang, T Zhou, Z Wunderlich, MT Maurano, AH DePace, SV Nuzhdin, R Rohs. Molecular Biology and Evolution. (2018).
Samee MAH, Lydiard-Martin T, Biette KM, Vincent BJ, Bragdon MD, Eckenrode KB, Wunderlich Z, Estrada J, Sinha S, DePace AH. Cell Reports. (2017).
L Li, Z Wunderlich. Frontiers in Genetics. (2017).
J Estrada, T Ruiz-Herrero, C Scholes, Z Wunderlich , DePace AH. PLoS ONE. (2016).
Z Wunderlich, M DJ Bragdon, BJ Vincent, JA White, J Estrada, AH DePace. Cell Reports. (2015).
Older works:
BJ Vincent*, C Scholes*, MV Staller*, Z Wunderlich*, J Estrada*, J Park*, MD Bragdon*, F Lopez Rivera*, KM Biette*, AH DePace*. Yearly Planning Meetings: Individualized Development Plans Aren't Just More Paperwork. Molecular Cell. (2015).
MV Staller, CC Fowlkes, MD Bragdon, Z Wunderlich, J Estrada, AH DePace. A gene expression atlas of a bicoid-depleted Drosophila embryo reveals early canalization of cell fate. Development. (2015).
MV Staller, BJ Vincent, MD Bragdon, T Lydiard-Martin, Z Wunderlich, J Estrada, AH DePace. Shadow enhancers enable Hunchback bifunctionality in the Drosophila embryo. PNAS. (2015).
Z Wunderlich, MD Bragdon, and AH DePace. Comparing mRNA levels using in situ hybridization of a target gene and co-stain. Methods. (2014)
MV Staller, D Yan, S Randklev, MD Bragdon, Z Wunderlich, R Tao, LA Perkins, AH DePace, N Perrimon. Depleting gene Activities in Early Drosophila Embryos with the "maternal-Gal4 - shRNA" system. Genetics. (2013).
Z Wunderlich, MD Bragdon, K Eckenrode, T Martin, S Pearl, and AH DePace. Dissecting sources of quantitative gene expression pattern divergence between Drosophila species. Molecular Systems Biology. (2012).
CC Fowlkes*, K Eckenrode*, MD Bragdon*, M Meyer, Z Wunderlich, L Simirenko, CL Luengo Hendriks, SVE Keränen, C Henriquez, DW Knowles, MD Biggin, MB Eisen, AH DePace. A conserved developmental patterning network produces quantitatively different output in multiple species of Drosophila. PLoS Genetics. (2011).
Z Wunderlich, AH DePace. Modeling transcriptional networks in Drosophila development at multiple scales. Current Opinion in Genetics and Development. (2011).
L Mirny, M Slutsky, Z Wunderlich, A Tafvizi, J Leith, A Kosmrlj. How a protein searches for its site on DNA: the mechanism of facilitated diffusion. Journal of Physics A. (2009).
Z Wunderlich, LA Mirny. Different gene regulation strategies revealed by analysis of binding motifs. Trends in Genetics. (2009).
Z Wunderlich, LA Mirny. Using genome-wide measurements for computational prediction of SH2-peptide interactions. Nucleic Acids Research. (2009).
Z Wunderlich, LA Mirny. Spatial effects on the speed and reliability of protein-DNA search. Nucleic Acids Research. (2008).
W Tian, LV Zhang, M Tasan, FD Gibbons, OD King, J Park, Z Wunderlich, JM Cherry, FP Roth. Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function. Genome Biology. (2008).
A Bhattacharya, Z Wunderlich, D Monleon, R Tejero, GT Montelione. Assessing model accuracy using the Homology Modeling Automatically (HOMA) Software. Proteins: Structure, Function, Bioinformatics. (2007).
G Kolesov*, Z Wunderlich*, ON Laikova, MS Gelfand, LA Mirny. How gene order is influenced by the biophysics of transcription regulation. PNAS. (2007).
Z Wunderlich and LA Mirny. Using topology of the metabolic network to predict viability of mutant strains. Biophysical Journal. (2006).
Z Wunderlich, TB Acton, J Liu, G Kornhaber, J Everett, P Carter, N Lan, N Echols, M Gerstein, B Rost, and GT Montelione. The protein target list of the Northeast Structural Genomics Consortium. Proteins: Structure, Function, Bioinformatics. (2004).
C-S Goh, N Lan, N Echols, S Douglas, D Milburn, P Bertone, R Xiao, L-C Ma, D Zheng, Z Wunderlich, TB Acton, GT Montelione, and Mark Gerstein. SPINE 2: A system for collaborative structural proteomics within a federated database framework. Nucleic Acids Research. (2003).
CONTACT US
Email
zeba[at]uci[dot]edu
Call
Lab: 949-824-5498
Office: 949-824-5959
