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
Lily Li
PhD Student
BS, Bioengineering, Caltech
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
Oluchi Ofoegbu
Undergraduate Student
Biological Sciences Major
Duncan Hoard
Undergraduate Student
Biological Sciences Major
Vinay Kumar
Research Assistant
BS, Biology, UCLA
Ariana Lee
Junior Specialist
BS, Biology, UC Irvine
Lianne Cohen
Post-doctoral Fellow
PhD, Biology, UCSD
BS, Biological Sciences, Carnegie Mellon University
Aman Burji
Undergraduate Student
Biological Sciences Major
Sima Tahmouresie
Undergraduate Student
Biological Sciences Major
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
