Student Publications

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Nguyen D D, Wu C-H, Moree WJ, et al. "MS/MS networking guided analysis of molecule and gene cluster families." Proc. Natl. Acad. Sci. U.S.A.. 2013;110(28):E2611-20.
Gendron JM, Pruneda-Paz JL, Doherty CJ, Gross AM, S Kang E, Kay SA. "Arabidopsis circadian clock protein, TOC1, is a DNA-binding transcription factor." Proc. Natl. Acad. Sci. U.S.A.. 2012;109(8):3167-72.
Bliven S, Prlić A. "Circular permutation in proteins." PLoS Comput. Biol.. 2012;8(3):e1002445.
Kim D, Hong J S-J, Qiu Y, et al. "Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling." PLoS Genet.. 2012;8(8):e1002867.
Johnson DBF, Xu J, Shen Z, et al. "RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites." Nat. Chem. Biol.. 2011;7(11):779-86.
Gay SC, Shah MB, Talakad JC, et al. "Crystal structure of a cytochrome P450 2B6 genetic variant in complex with the inhibitor 4-(4-chlorophenyl)imidazole at 2.0-A resolution." Mol. Pharmacol.. 2010;77(4):529-38.
Prlic A, Bliven S, Rose PW, et al. "Pre-calculated protein structure alignments at the RCSB PDB website." Bioinformatics. 2010;26(23):2983-5.
Ng J, Bandeira N, Liu W-T, et al. "Dereplication and de novo sequencing of nonribosomal peptides." Nat. Methods. 2009;6(8):596-9.
Kim S, Gupta N, Bandeira N, Pevzner PA. "Spectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra." Mol. Cell Proteomics. 2009;8(1):53-69.
Valas RE, Bourne PE. "Structural analysis of polarizing indels: an emerging consensus on the root of the tree of life." Biol. Direct. 2009;4:30.
Ng J, Pevzner PA. "Algorithm for identification of fusion proteins via mass spectrometry." J. Proteome Res.. 2008;7(1):89-95.
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.
Frank AM, Bandeira N, Shen Z, et al. "Clustering millions of tandem mass spectra." J. Proteome Res.. 2008;7(1):113-22.
Gupta N, Benhamida J, Bhargava V, et al. "Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes." Genome Res.. 2008;18(7):1133-42.
Sharan R, Suthram S, Kelley RM, et al. "Conserved patterns of protein interaction in multiple species." Proc. Natl. Acad. Sci. U.S.A.. 2005;102(6):1974-9.