I am a member of Phil Bourne’s lab at UCSD. I have broad interests in proteomics and structural biology, but am currently focusing on
- Improving the CE algorithm for comparing protein structures. This includes the CE-CP algorithm for detecting circular permutations [poster] and CE-symm for detecting pseudo-symmetry in proteins.
- Investigating and quantifying protein fold space. [ISMB 2012 poster] [ISMB 2011 poster] [Qual Exam]
- Predicting hydrogen-deuterium exchange rates from protein 3D structures. Virgil Woods and Tong Liu. Fall 2010 Rotation.
- Identifying crosslinked peptides using mass spectrometry. Mike MacCoss, Pavel Pevzner, and Nuno Bandeira. Summer 2010 Rotation.
- Structure and dynamics of IL-1β binding. Pat Jennings, José Onuchic, and Alex Schlug. Spring 2010 Rotation.
- Comparing circularly permuted structures with CE. Phil Bourne and Andreas Prlić. Winter 2010 Rotation. [Report]
- Mass spectral database searches using locality-sensitive hashing. Pavel Pevzner and Sangtae Kim. Fall 2009 Rotation.[Report]
- Modeling disulfide bonds for protein folding and design with ROSETTA. David Baker and Jacob Corn. Fall 2008-Summer 2009.[Senior Thesis]
Publications & Conferences
- Andreas Prlić, Spencer Bliven, Peter Rose, Julius Jacobsen, Peter V. Troshin, Mark Chapman, Jianjiong Gao, Chuan Hock Koh, Sylvain Foisy, Richard Holland, Gediminas Rimša, Michael L. Heuer, H. Brandstätter–Müller, Philip E. Bourne, and Scooter Willis. BioJava: an open-source framework for bioinformatics in 2012. Bioinformatics (2012). doi:10.1093/bioinformatics/bts494
- Spencer Bliven, Andreas Prlić, and Philip Bourne. Why Scientists Should Contribute to Wikipedia. Bioinformatics Open Source Conference 2012. [Slides] [Poster]
- Spencer Bliven and Andreas Prlić. Circular Permutation in Proteins. PLoS Comput Biol (2012) 8(3): e1002445. doi:10.1371/journal.pcbi.1002445
- Spencer Bliven, Andreas Prlić, Philip Bourne. A comprehensive review of protein fold space and the correlation of structure with function. ISMB/ECCB 2011. F1000 Posters 2011, 2: 1292 [Poster]
- Andreas Prlić, Spencer Bliven, Peter W Rose, Wolfgang F. Bluhm, Chris Bizon, Adam Godzik, Philip E. Bourne. “Precalculated Protein Structure Alignments at the RCSB PDB website.” Bioinformatics (2010) vol. 26 (23) pp. 2983-2985 [PMID 20937596]