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.
The Wunderlich lab is looking for enthusiastic students and post docs to join the lab.
Graduate students must be part of one of UCI's graduate programs, e.g. the Mathematical, Computational, & Systems Biology program or the Cellular & Molecular Biosciences program. The Wunderlich lab is actively recruiting rotation students for the 2020-2021 academic year. Please email Zeba if you are interested.
We are accepting applications for a postdoc position in the lab and welcome candidates who are interested in understanding the function of regulatory DNA using a combination of experimental and computational approaches. Applicants can send a CV and cover letter describing your previous research experience and future research interests, including why you are interested in the lab, to Zeba.
Undergraduates interested in studies of gene regulation should contact Zeba to discuss possible projects.
PhD, Harvard University, Biophysics
BA, Molecular Biology & Biochemistry, Statistics, Rutgers University
BS, Bioengineering, Caltech
BS, Genetics, UC Davis
BS, Neuroscience, College of William & Mary
BS, Biology, BA Chemistry, Florida International University
Biological Sciences Major
BS, Biological Sciences, UC Irvine
Biological Sciences Major
BS, Biology, UCLA
High School Student, Summer 2019
Undergraduate Student, Public Health Sciences, 2017-2019
Research Assistant, 2017-2018, now at Western University of Health Sciences
Undergraduate Student, Biomedical Engineering, 2016-2017, now in UCI MD/PhD program
Undergraduate Student, Genetics and Anthropology, 2015-2016, now at Sangamo Theraputics
Masters Student, Biotechnology Management, 2016-2017, now at BD Biosciences
Masters Student, Developmental and Cell Biology, 2015-2017
F Lopez-Rivera, OK Foster, BJ Vincent, ECG Pym, MDJ Bragdon, J Estrada, AH DePace, Z Wunderlich. bioRxiv. (Pre-print).
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).
BJ Vincent, MV Staller, F Lopez-Rivera, MDJ Bragdon, ECG Pym, KM Biette, Z Wunderlich, TT Harden, J Estrada, AH DePace. PLOS Genetics. (2018).
NM Osman, S Vlaho, TH Kitapci, Z Wunderlich, SV Nuzhdin. Biophysics. (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).
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).