Jgu Denmarkboat Name: Gu, Jenny

Status: Postdoc

Email:

Tel.: +49-(0)251-83-

Room:


Jenny Gu at PACBIO

Experience
  • 2009 - 2011  :    Alexander Humboldt Postdoctoral Fellow (University of Muenster)
  • 2008 - 2011  :    Postdoctoral Project Leader (University of Muenster)
  • 2007-2008    :    Jeanne Kempner Postdoctoral Fellow (University of Texas, Medical Branch)
  • 2000-2006    :    Ph.D. Biomedical Sciences (University of California, San Diego)
  • 1996-1999    :    B.A. Molecular and Cell Biology, Biochemistry Emphasis (University of California, Berkeley)
Research Interest
Understand the systemic molecular evolution of plants to abiotic stress with a particular focus on marine seagrasses.  What are the quickest and fastest biochemical strategies for plants to adapt and respond to environmental stress? Evolutionary changes impacting DNA, RNA, and proteins will be investigated.  Changes in the metabolism of plants are of special interest due to the potential interactions between the metabolome and proteome through secondary metabolic pathways.

Previous Research Interest
Proteins are amongst the quickest and fastest biological processors known, sometimes catalyzing reactions close to the speed of light. Understand how the intrinsic flexibility required for these proteins to carry out these functions is encoded in the sequence. How do changes in the amino acid impact the energetic properties of the proteins?  Sequence-based predictors were constructed which now enables us to understand the proteomic energy landscape of protein sequences that are rapidly churned out with new next generation sequencing technology.  The changes in the energy landscape of proteomes resulting from evolution and adaptation to new environments can now be quickly investigated using real biological data in silico.

Publications
*=corresponding author
  1. Franssen SU*, Gu J*, Winters G, Huylmans AK, Wienpahl I, Sparwel M, Coyer JA, Olsen JL, Reusch TL and Bornberg-Bauer E. Genome-wide transcriptomic responses of the seagrasses Zostera marina and Nanozostera noltii under a simulated heatwave confirm functional types
    Marine Genomics 15:65 - 73., 2014
    [Online access]
  2. Gu, J*; Weber, KL; Kemp, E; Winters, G; Franssen, SU; Weinpahl, I; Huylmans, A; Zecher, K.; Reusch, TBH; Bornberg-Bauer, E; Weber, APM. Identifying core features of adaptive metabolic mechanisms for chronic heat stress attenuation as a feature for systems robustness. Integrative Biology (2012 Mar 8, Epub ahead of print).
  3. Franssen, S; Gu, J; Bergmann, N; Winters, G; Klostermeier, UC; Rosenstiel, P; Bornberg-Bauer, E; Reusch, TBH*. Transcriptomic resilience to global warming in the seagrass Zostera marina, a marine foundation species. Proc Natl Acad Sci U S A. 2011 108(48):19276-81.
  4. Reineke AR; Bornberg-Bauer E; Gu J*.  Evolutionary divergence and limits of conserved non-coding sequence detection in plant genomes.  Nucleic Acids Research, 2011 Aug 1;39(14):6029-43. **Selected as Featured Article & Cover Art
  5. Wissler, L; Codoner, FM; Gu, J; Reusch, TBH; Olsen, JL; Procaccini, G*; Bornberg-Bauer, E*. Back to the Sea twice: identifying candidate plant genes for molecular evolution to marine life. BMC Evol. Biology, 2011 Jan 12;11:8. 
  6. Bergmann N; Winters G; Rauch G; Eizaguirre C; Gu J; Nelle P; Fricke B; Reusch TBH*. Population-specificity of heat stress gene induction in northern and southern eelgrass Zostera marina populations under simulated global warming.  Molecular Ecology, 2010(19), 2870-2883. 
  7. Gu J*; Hilser VJ*.  Sequence-based Analysis of Protein Energy Landscapes Reveals Non-uniform Thermal Adaptation within the Proteome.  Molecular Biology and Evolution, 2009 Oct:26(10):2217-27.
  8. Gu J; Hilser VJ*.  Predicting the Energetics of Conformational Fluctuations in Proteins from Sequence: A Strategy for Profiling the Proteome. Structure, 2008 Nov 12;16(11):1627-37.
  9. Wang S; Gu J; Larson SA; Whitten ST; Hilser VJ*.  Denatured state energy landscapes of a protein structural database reveal the energetic determinants of a framework model for folding.  Journal of Molecular Biology, 2008 Sep 19;381(5):1184-201. 
  10. Gu, J*; Bourne P.  Identifying allosteric fluctuation transitions between different protein conformational states as applied to Cyclin Dependent Kinase 2.  BMC Bioinformatics, 2007 8:45  
  11. Gu, J*; Gribskov, M; Bourne, P.  Wiggle – Predicting Functionally Flexible Regions from Primary Sequence.  PLoS Computational Biology, 2006 Jul 14:2(7):e90.
  12. Arndt, JW; Gu J; Jaroszewski L; Schwarzenbacher R; Hanson MA; Lebeda FJ; Stevens RC*.  The structure of the neurotoxin-associated protein HA33/A from Clostridium botulinum suggests a reoccurring beta-trefoil fold in the progenitor toxin complex.  Journal of Molecular Biology, 2005 Mar 346(4): 1083-1093
  13. Santarsiero, BD; Yegian, DT; Lee, CC; Spraggon, G; Gu, J; Scheibe, D; Uber, DC; Cornell, EW; Nordmeyer, RA; Kolbe, WF; Jin, J; Jones, AL; Jaklevic, JM; Schultz, PG; Stevens, RC*.  An approach to rapid protein crystallization using nanodroplets.  Journal of Applied Crystallography, 2002 Apr, 35(2):278-281.

Books
  • Gu, J. and Bourne PE.  Structural Bioinformatics (Second Edition). Wiley-Blackwell Publishing, Mar 2009.
 
Book Chapters
  1. Gu, J., Hilser V.J.. Protein Disorder and Conformational Variants. Structural Bioinformatics (Second Edition). Wiley-Blackwell Publishing. (March 2009)
  2. Gu, J; Bourne, P; CASP and Other Community-wide Assessments to Advance the Field of Structure Prediction. Structural Bioinformatics (Second Edition). Wiley-Blackwell Publishing. (March 2009)
  3. Samish, I; Gu, J; Klein, ML. Protein Motion: Simulation. Structural Bioinformatics (Second Edition). Wiley-Blackwell Publishing. (March 2009)
  4. Veretnik, S; Gu, J; Wodak, S. Identifying structural domains in proteins. Structural Bioinformatics (Second Edition). Wiley-Blackwell Publishing. (March 2009)
  5. Community Contributions
    Gu, J; Bourne P. Ten simple rules for graduate students. PLoS Computational Biology, 2007 3(11): e229. 10.1371/journal.pcbi.0030229
  6. Teaching
    Bioinformatics: Protein Structures and Evolution
Students Proudly Supervised - Thank you!
BSc: Philipp Bayer, Ina Huylman, Torben Pinnow, Thaddaeus Slawicki, Isabell Wienpahl, Florian Wuennemann, Karsten Zecher

PhD: Anna Reineke