Student Publications

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Lin MS, Cherny JJ, Fournier CT, Roth SJ, Krizanc D, Weir MP. "Assessment of MS/MS search algorithms with parent-protein profiling." J. Proteome Res.. 2014;13(4):1823-32.
Anandasabapathy N, Feder R, Mollah S, et al. "Classical Flt3L-dependent dendritic cells control immunity to protein vaccine." J. Exp. Med.. 2014;211(9):1875-91.
Prlić A, Yates A, Bliven SE, et al. "BioJava: an open-source framework for bioinformatics in 2012." Bioinformatics. 2012;28(20):2693-5.
Bliven S, Prlić A. "Circular permutation in proteins." PLoS Comput. Biol.. 2012;8(3):e1002445.
Grubisic I, Shokhirev MN, Orzechowski M, Miyashita O, Tama F. "Biased coarse-grained molecular dynamics simulation approach for flexible fitting of X-ray structure into cryo electron microscopy maps." J. Struct. Biol.. 2010;169(1):95-105.
Prlic A, Bliven S, Rose PW, et al. "Pre-calculated protein structure alignments at the RCSB PDB website." Bioinformatics. 2010;26(23):2983-5.
Tanner S, Payne SH, Dasari S, et al. "Accurate annotation of peptide modifications through unrestrictive database search." J. Proteome Res.. 2008;7(1):170-81.
Briedis KM, Starr A, Bourne PE. "Analysis of the human kinome using methods including fold recognition reveals two novel kinases." PLoS ONE. 2008;3(2):e1597.
Suthram S, Beyer A, Karp RM, Eldar Y, Ideker T. "eQED: an efficient method for interpreting eQTL associations using protein networks." Mol. Syst. Biol.. 2008;4:162.
König R, Zhou Y, Elleder D, et al. "Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication." Cell. 2008;135(1):49-60.
Chen OY-C, Chen G-W, Chen WY-C. "A novel strategy for the structure-based drug design of heat shock protein 90 inhibitors.". In: Neural Networks, 2008. IJCNN 2008. (IEEE World Congress on Computational Intelligence). IEEE International Joint Conference on.; 2008.
Lee K, Chuang H-Y, Beyer A, et al. "Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species." Nucleic Acids Res.. 2008;36(20):e136.
Dost B, Shlomi T, Gupta N, Ruppin E, Bafna V, Sharan R. "QNet: a tool for querying protein interaction networks." J. Comput. Biol.. 2008;15(7):913-25.
Kim T H, Barrera LO, Ren B. "ChIP-chip for genome-wide analysis of protein binding in mammalian cells." Curr Protoc Mol Biol. 2007;Chapter 21:Unit 21.13.
Hawkins T, Luban S, Kihara D. "Enhanced automated function prediction using distantly related sequences and contextual association by PFP." Protein Sci.. 2006;15(6):1550-6.
Joyce AR, Palsson BØ. "The model organism as a system: integrating 'omics' data sets." Nat. Rev. Mol. Cell Biol.. 2006;7(3):198-210.
Zhi D, Krishna SS, Cao H, Pevzner P, Godzik A. "Representing and comparing protein structures as paths in three-dimensional space." BMC Bioinformatics. 2006;7:460.
Fong SS, Joyce AR, Palsson BØ. "The econometrics of evolution." Nat. Chem. Biol.. 2005;1(4):191-2.
Tsur D, Tanner S, Zandi E, Bafna V, Pevzner PA. "Identification of post-translational modifications via blind search of mass-spectra." Proc IEEE Comput Syst Bioinform Conf. 2005:157-66.
Chandonia J-M, Hon G, Walker NS, et al. "The ASTRAL Compendium in 2004." Nucleic Acids Res.. 2004;32(Database issue):D189-92.
Papin JA, Reed JL, Palsson BO. "Hierarchical thinking in network biology: the unbiased modularization of biochemical networks." Trends Biochem. Sci.. 2004;29(12):641-7.