Jenny Gu at PACBIO
- 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)
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.
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
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).
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.
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
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
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.
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.
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.
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.
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
Gu, J*; Gribskov, M; Bourne, P. Wiggle – Predicting Functionally
Flexible Regions from Primary Sequence. PLoS Computational Biology,
2006 Jul 14:2(7):e90.
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
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.
Gu, J. and Bourne PE. Structural Bioinformatics (Second Edition). Wiley-Blackwell Publishing, Mar 2009.
Students Proudly Supervised - Thank you!
Gu, J., Hilser V.J.. Protein Disorder and Conformational Variants.
Structural Bioinformatics (Second Edition). Wiley-Blackwell Publishing.
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)
Samish, I; Gu, J; Klein, ML. Protein Motion: Simulation. Structural
Bioinformatics (Second Edition). Wiley-Blackwell Publishing. (March
Veretnik, S; Gu, J; Wodak, S. Identifying structural domains in
proteins. Structural Bioinformatics (Second Edition). Wiley-Blackwell
Publishing. (March 2009)
Gu, J; Bourne P. Ten simple rules for graduate students. PLoS
Computational Biology, 2007 3(11): e229. 10.1371/journal.pcbi.0030229
Bioinformatics: Protein Structures and Evolution
BSc: Philipp Bayer, Ina Huylman, Torben Pinnow, Thaddaeus Slawicki, Isabell Wienpahl, Florian Wuennemann, Karsten Zecher
PhD: Anna Reineke