… at the Center for Biological Data Science at Virginia Commonwealth University

The Uetz lab is working on proteins, protein function, bioinformatics and reptile taxonomy. Some of our recent projects and publications include:

Microbial interactomics. Our group has mapped the interactomes of 5 different microbes, more than any other lab in the world. These interactomes continue to provide insights into the molecular organization of unicellular systems and the functions of their proteins:

• Streptococcus pneumoniae / Meta-interactomes. Wuchty, S et al. (2017) mSystems 2(3): e00019-17
• Escherichia coli: Rajagopala, SV et al. (2014) Nature Biotechnology, 32, 285–290
• Helicobacter pylori: Häuser, R. et al. (2014) Mol Cell Proteomics 13(5):1318-29
• Saccharomyces cerevisiae: Uetz, P. et al. (2000) Nature 403: 623-627

Bioinformatics of protein networks. We also analyze the networks we have produced experimentally with a variety of bioinformatics methods. We strive to understand complex networks but also individual proteins and protein domains (see Protein function … below):

• Mariano R. et al. (2016) Infection Patterns of Human Viruses and Bacteriophages. mSystems 1 (2): e00030-15.
• Uetz, P. et al. (2006) Herpesviral Protein Networks and the Human Proteome. Science 311: 239-242
• Schwikowski, B. et al. (2000) A network of interacting proteins in yeast. Nature Biotech. 18 (12): 1257-1261

Protein function, protein complexes, and protein domains. We study protein function, especially the functions of uncharacterized and poorly understood proteins using both computational and experimental approaches. Our group has solved the function of half a dozen uncharacterized proteins and domains:

• Blasche, S. et al. (2013) The E. coli effector protein NleF is a caspase inhibitor. Plos One, 8(3): e58937.
• Caufield JH et al. (2015) Protein complexes in bacteria. Plos. Comp. Biol., 27;11(2):e1004107.
• Goodacre, N.F. et al. (2014) Protein domains of unknown function are essential in bacteria. mBio 5 (1): e00744-13.
• Häuser, R. et al. (2012) RsfA (YbeB) proteins are ribosomal silencing factors. Plos Genetics 8(7): e1002815.

Virus and phage interactomics. Viruses and phage are excellent models to study protein interaction networks and protein function because they are small and have loads of uncharacterized proteins. We have studied both human viruses and phage of various bacteria, including E. coli, Mycobacteria, and Streptococcus:

• Osterman A. et al. (2015) The Hepatitis E virus intraviral interactome. Scientific Reports 5: 13872.
• Blasche S. et al. (2013) Interactions of Bacteriophage Lambda with E. coli. J Virol. 87 (23): 12745-55
• Häuser, R. et al. (2011) The interactome of Streptococcus pneumoniae phage Cp1. J. Bact. 193 (12): 3135–3138.
• Fossum E. et al. (2009) Herpesviral protein interaction networks. PloS Pathogens 5 (9): 00570

Reptile taxonomy and biodiversity informatics. There are not only millions of proteins but also millions of species. Our contribution to biodiversity research is the Reptile Database and its integration with other data sources, including genomics and ecological data:

• Roll U et al. (2017) Global distribution of tetrapods and reptile conservation. Nature Ecol. Evol. 1: 1677–1682
• Castoe, T. A. et al. (2013) The Burmese python genome. PNAS, Dec 2, 2013.
• Uetz P et al. (2019) A global catalog of reptile type specimens. Zootaxa 4695 (5): 438–450
• Garg, A. et al. (2019) DNA and species names in the NCBI taxonomy database. Zootaxa 4706 (3): 401–407

See also Lab Members