Our main projects and selected publications are listed below. For a complete publication list go to Publications.
Our group has mapped the interactomes of 4 different microbial species, more than any other lab in the world. These interactomes have provided insights into the molecular organization of unicellular systems and the functions of their proteins.
• Rajagopala, SV et al. (2014) The binary protein-protein interaction landscape of Escherichia coli. Nature Biotechnology, 32, 285–290
• Häuser, R. et al. (2014) A Second-generation Protein-Protein Interaction Network of Helicobacter pylori. Mol Cell Proteomics 13(5):1318-29
Titz, B. et al. (2008) The Binary Protein Interactome of Treponema pallidum - the Syphilis Spirochete. PloS ONE 3(5): e2292.
Uetz, P. et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403: 623-627
Protein function, protein complexes, and protein domains
We are interested in protein function, especially the functions of uncharacterized and poorly understood proteins. We use protein-protein interaction studies and other methods to elucidate their function.
• Caufield JH, Wimble C, Abreu M & Uetz P (2015) Protein complexes in bacteria. Plos. Comp. Biol., 27;11(2):e1004107.
• Goodacre, N.F., Gerloff, D.L. & Uetz, P. (2013) Protein domains of unknown function (DUFs) are essential in bacteria. mBio 5 (1): e00744-13.
• Blasche, S. et al. (2013) The E. coli effector protein NleF is a caspase inhibitor. Plos One, 8(3): e58937.
Häuser, R. et al. (2012) RsfA (YbeB) proteins are conserved ribosomal silencing factors. Plos Genetics 8(7): e1002815.
Virus and phage interactomics
Viruses and phage are excellent models to study protein interaction networksand 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. We have recently started to study bacteriophage of Bacillus in collaboration with Drs. Margarita Salas and Allison Johnson.
• Osterman A. et al. (2015) The Hepatitis E virus intraviral interactome. Scientific Reports 5: 13872.
• Blasche S. et al. (2013) The Protein Interaction Network of Bacteriophage Lambda with Its Host, Escherichia coli. J Virol. 2013 Dec;87(23):12745-55
Häuser, R., Sabri, M., Moineau, S. & Uetz, P. (2011) The proteome and interactome of Streptococcus pneumoniae phage Cp1. J. Bact. 193 (12): 3135–3138.
Fossum E. et al. (2009) Evolution and divergence of herpesviral protein interaction networks. PloS Pathogens 5 (9): 00570
Bioinformatics of protein networks
In addition to generating interactome data, we also analyze the resulting networks with a variety of bioinformatics methods. Eventually the goal is to understand both the organisms but also individual proteins and protein domains.
• Mariano R., Khuri S., Uetz P. & Wuchty S. (2016) Local Action with Global Impact: Highly Similar Infection Patterns of Human Viruses and Bacteriophages. mSystems 1 (2): e00030-15.
Uetz, P. et al. (2006) Herpesviral Protein Networks and Their Interaction with the Human Proteome. Science 311: 239-242
Schwikowski,B., Uetz, P. & Fields,S. (2000) A network of interacting proteins in yeast. Nature Biotechnology 18 (12): 1257-1261
Biodiversity: Reptile taxonomy and genomics
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.
• Feldman, A . et al. (2015) The geography of snake reproductive mode. Global Ecology and Biogeography 24 (12): 1433–1442
• Castoe, T. A. et al. (2013) The Burmese python genome reveals the molecular basis for extreme adaptation in snakes. PNAS, Dec 2, 2013.
Rasmussen, A.R., Murphy, J.C., Ompi, M., Gibbons, J.W. & Uetz, P. (2011) Marine Reptiles. PLoS ONE 6(11): e27373
See also Lab Members