Publications

Ma, B. ., & Johnson, R. . (2012). De Novo Sequencing and Homology Searching. Molecular \& Cellular Proteomics 11. DOI 10.1074 Mcp.O111.014902.

Gidvani, R. ., Sudmant, P. ., Li, G. ., DaSilva, L. ., McConkey, B. ., Duncker, B. ., & Ingalls, B. . (2012). A quantitative model of the initiation of DNA replication in Saccharomyces cerevisiae predicts the effects of system perturbations. BMC Systems Biology, 6:78.

Brown, D. ., & Truszkowski, J. . (2012). Fast phylogeny algorithms using locality-sensitive hashing.

Whelan, F. ., Meehan, C. ., Golding, G. ., McConkey, B. ., & Bowdish, D. . (2012). The evolution of the class A scavenger receptors. BMC Evolutionary Biology, 12:227.

Ackerman, M. ., Brown, D. ., & Loker, D. . (2012). Effects of rooting via outgroups on ingroup topology in phylogeny. Proceedings of the International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), 7 Pages. Presented at the.

Masella, A. ., Bartram, A. ., Truszkowski, J. ., Brown, D. ., & Neufeld, J. . (2012). PANDAseq: paired-end assembler for illumina sequences. BMC Bioinformatics Volume 13, Article Number: 31.

He, L. ., Han, X. ., & Ma, B. . (2012). De Novo Sequencing with Limited Number of Post-Translational Modifications per Peptide.

Bu, D. ., Li, S. ., & Li, M. . (2012). Clustering 100,000 potein structure decoys in minutes. IEEE/ACM/Trans./Comput./Biol./Bioinf./9:3,/765-773.

Zhang, J. ., Xin, L. ., Shan, B. ., Chen, W. ., Xie, M. ., Yuen, D. ., Zhang, W. ., Zhang, Z. ., Lajoie, G. ., & Ma, B. . (2012). PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification. Molecular & Cellular Proteomics 11. DOI, 10.1074 Mcp.M111.010587.

Alipanahi, B. ., Krislock, N. ., Wolkowicz, H. ., Ghodsi, A. ., Donaldson, L. ., & Li, M. . (2012). Protein Structure by Semidefinite Facial Reduction. RECOMB 2012. Pp. 1-11, Barcelona, Spain. Presented at the.