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    Strikingly
    • 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.

       

    • OPPORTUNITIES

      The Wunderlich lab is looking for enthusiastic students and post docs to join the lab.

       

      Graduate Students

      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.

       

      Postdoctoral Fellows

      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.

       

      Undergraduate Students

      Undergraduates interested in studies of gene regulation should contact Zeba to discuss possible projects.

    • 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

    • ALUMNI

      Mario Elabd

      Junior Specialist, 2019-2020, now at UCSF School of Dentistry

      Phoebe Cao

      High School Student, Summer 2019, now an undergraduate at Emory University

      Stephanie Fruth

      Undergraduate Student, Public Health Sciences, 2017-2019, now at Thermo Fisher Scientific

      Subhapradha Rangarajan

      Research Assistant, 2017-2018, now at Western University of Health Sciences

      Arash Abiri

      Undergraduate Student, Biomedical Engineering, 2016-2017, now in UCI MD/PhD program

      Flo Ramirez

      Undergraduate Student, Genetics and Anthropology, 2015-2016, now at the Vincent J Coates Genomics Sequencing Lab at UC Berkeley

      Punya Narayan

      Masters Student, Biotechnology Management, 2016-2017, now at BD Biosciences

      Marley Hilleger

      Masters Student, Developmental and Cell Biology, 2015-2017

    • PUBLICATIONS

      Enhancer redundancy in development and disease

      EZ Kvon, R Waymack, MG Elabd, Z Wunderlich. Nature Reviews Genetics. (2021).

      The mode of expression divergence in Drosophila fat body is infection-specific

      BA Ramirez-Corona, SM Fruth, O Ofoegbu, Z Wunderlich. bioRxiv. (Pre-print).

       

       

      A mutation in the Drosophila melanogaster eve stripe 2 minimal enhancer is buffered by flanking sequences

      F Lopez-Rivera, OK Foster, BJ Vincent, ECG Pym, MDJ Bragdon, J Estrada, AH DePace, Z Wunderlich. G3. (2020).

      Shadow enhancers can suppress input transcription factor noise through distinct regulatory logic

      R Waymack, A Fletcher, G Enciso, Z Wunderlich. eLife. (2020).

      Quantitative comparison of the anterior-posterior patterning system in the embryos of five Drosophila species.

      Z Wunderlich, CC Fowlkes, KB Eckenrode, MDJ Bragdon, A Abiri, AH DePace. G3. (2019).

      Dissecting the sharp response of a canonical developmental enhancer reveals multiple sources of cooperativity.

      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).

      Inference of transcription factor regulation patterns using gene expression covariation in natural populations of Drosophila melanogaster.

      NM Osman, S Vlaho, TH Kitapci, Z Wunderlich, SV Nuzhdin. Biophysics. (2018).

      Hunchback is counter-repressed to regulate even-skipped stripe 2 expression in Drosophila embryos.

      BJ Vincent, MV Staller, F Lopez-Rivera, MDJ Bragdon, ECG Pym, KM Biette, Z Wunderlich, TT Harden, J Estrada, AH DePace. PLOS Genetics. (2018).

      Analysis of Genetic Variation Indicates DNA Shape Involvement in Purifying Selection.

      X Wang, T Zhou, Z Wunderlich, MT Maurano, AH DePace, SV Nuzhdin, R Rohs. Molecular Biology and Evolution. (2018).

      Quantitative Measurement and Thermodynamic Modeling of Fused Enhancers Support a Two-Tiered Mechanism for Interpreting Regulatory DNA.

      Samee MAH, Lydiard-Martin T, Biette KM, Vincent BJ, Bragdon MD, Eckenrode KB, Wunderlich Z, Estrada J, Sinha S, DePace AH. Cell Reports. (2017).

      An enhancer's length and composition are shaped by its regulatory task.

      L Li, Z Wunderlich. Frontiers in Genetics. (2017).

      Site Out: An online tool to design binding-site free DNA sequences.

      J Estrada, T Ruiz-Herrero, C Scholes, Z Wunderlich , DePace AH. PLoS ONE. (2016).

      Krüppel Expression Levels Are Maintained through Compensatory Evolution of Shadow Enhancers

      Z Wunderlich, M DJ Bragdon, BJ Vincent, JA White, J Estrada, AH DePace. Cell Reports. (2015).

       

      Pre-UCI:

      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

      Write

       

      Lab: Room 4432

       

      Office: Room 4107

       

      Natural Sciences II

      Irvine, CA 92697

      Visit

       

      Directions to campus are here.

       

      If you are driving, the closest parking lot is Lot 16, which was a permit vending station.

       

      Tweet

       

      @zebabw

    UC Irvine / Department of Developmental and Cell Biology / Center for Complex Biological Systems / Center for Multiscale Cell Fate Research / Institute for Immunology

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