80 Publications (Page 3 of 4)
2014
A new scoring function for top-down spectral deconvolution
Kou, Qiang⋅Kou, Qiang⋅Wu, Si⋅Wu, Si⋅Liu, Xiaowen and Liu, Xiaowen
BMC Genomics, vol. 15, 2014. | Journal Article
 
De novo protein sequencing by combining top-down and bottom-up tandem mass spectra.
Liu, Xiaowen⋅Dekker, Lennard J M⋅Wu, Si⋅Vanduijn, Martijn M⋅Luider, Theo M⋅Tolić, Nikola⋅Kou, Qiang⋅Dvorkin, Mikhail⋅Alexandrova, Sonya⋅Vyatkina, Kira⋅Paša-Tolić, Ljiljana and Pevzner, Pavel A
Journal of proteome research, vol. 13, (no. 7), pp. 3241-3248, July 3, 2014. | Journal Article
 
Improving protein order-disorder classification using charge-hydropathy plots
Huang, Fei⋅Oldfield, Christopher⋅Xue, Bin⋅Hsu, Wei-Lun⋅Meng, Jingwei⋅Liu, Xiaowen⋅Shen, Li⋅Romero, Pedro⋅Uversky, Vladimir and Dunker, A
BMC Bioinformatics , vol. 15, 2014. | Journal Article
 
Quantitative analysis of human salivary gland‐derived intact proteome using top‐down mass spectrometry
Wu, Si⋅Wu, Si⋅Brown, Joseph N⋅Brown, Joseph N⋅Tolić, Nikola⋅Tolić, Nikola⋅Meng, Da⋅Meng, Da⋅Liu, Xiaowen⋅Liu, Xiaowen⋅Zhang, Haizhen⋅Zhang, Haizhen⋅Zhao, Rui⋅Zhao, Rui⋅Moore, Ronald J⋅Moore, Ronald J⋅Pevzner, Pavel⋅Pevzner, Pavel⋅Smith, Richard D⋅Smith, Richard D⋅Paša‐Tolić, Ljiljana and Paša-Tolić, Ljiljana
PROTEOMICS, vol. 14, (no. 10), pp. 1222, May 2014. | Journal Article
 
Spectral probabilities of top-down tandem mass spectra
Liu, Xiaowen⋅Segar, Matthew⋅Li, Shuai Cheng and Kim, Sangtae
BMC Genomics, vol. 15, 2014. | Journal Article
 
Top-down proteomics reveals concerted reductions in myofilament and Z-disc protein phosphorylation after acute myocardial infarction.
Peng, Ying⋅Gregorich, Zachery R⋅Valeja, Santosh G⋅Zhang, Han⋅Cai, Wenxuan⋅Chen, Yi-Chen⋅Guner, Huseyin⋅Chen, Albert J⋅Schwahn, Denise J⋅Hacker, Timothy A⋅Liu, Xiaowen and Ge, Ying
Molecular & cellular proteomics : MCP, vol. 13, (no. 10), pp. 2752-2764, October 2014. | Journal Article
2013
Identification of ultramodified proteins using top-down spectra
Liu, X.⋅Hengel, S.⋅Wu, S.⋅Toli?, N.⋅Pasa-Toli?, L. and Pevzner, P.A.
2013
 
Identification of ultramodified proteins using top-down tandem mass spectra.
Liu, Xiaowen⋅Liu, Xiaowen⋅Hengel, Shawna⋅Hengel, Shawna⋅Wu, Si⋅Wu, Si⋅Tolić, Nikola⋅Tolić, Nikola⋅Pasa-Tolić, Ljiljana⋅Pasa-Tolić, Ljiljana⋅Pevzner, Pavel A and Pevzner, Pavel A
Journal of proteome research, vol. 12, (no. 12), pp. 5830-8, 2013/Dec/6. | Journal Article
 
Top-down proteomics reveals a unique protein S-thiolation switch in Salmonella Typhimurium in response to infection-like conditions.
Ansong, Charles⋅Ansong, Charles⋅Wu, Si⋅Wu, Si⋅Meng, Da⋅Meng, Da⋅Liu, Xiaowen⋅Liu, Xiaowen⋅Brewer, Heather M⋅Brewer, Heather M⋅Deatherage Kaiser, Brooke L⋅Deatherage Kaiser, Brooke L⋅Nakayasu, Ernesto S⋅Nakayasu, Ernesto S⋅Cort, John R⋅Cort, John R⋅Pevzner, Pavel⋅Pevzner, Pavel⋅Smith, Richard D⋅Smith, Richard D⋅Heffron, Fred⋅Heffron, Fred⋅Adkins, Joshua N⋅Adkins, Joshua N⋅Pasa-Tolic, Ljiljana and Pasa-Tolic, Ljiljana
Proceedings of the National Academy of Sciences of the United States of America, vol. 110, (no. 25), pp. 10153-8, 2013/Jun/18. | Journal Article
2012
Dereplicating nonribosomal peptides using an informatic search algorithm for natural products (iSNAP) discovery
Ibrahim, Ashraf⋅Yang, Lian⋅Johnston, Chad⋅Liu, Xiaowen⋅Ma, Bin and Magarvey, Nathan A
Proceedings of the National Academy of Sciences of the United States of America, vol. 109, (no. 47), Nov 20, 2012. | Journal Article
 
Protein identification using top-down.
Liu, Xiaowen⋅Sirotkin, Yakov⋅Shen, Yufeng⋅Anderson, Gordon A⋅Tsai, Yihsuan S⋅Ting, Ying S⋅Goodlett, David R⋅Smith, Richard D⋅Bafna, Vineet and Pevzner, Pavel A
Molecular & cellular proteomics : MCP, vol. 11, (no. 6), pp. M111.008524, 2012/Jun. | Journal Article
 
Speeding up tandem mass spectral identification using indexes.
Liu, Xiaowen⋅Mammana, Alessandro and Bafna, Vineet
Bioinformatics (Oxford, England), vol. 28, (no. 13), pp. 1692-7, 2012/Jul/1. | Journal Article
2010
Better score function for peptide identification with ETD MS/MS spectra
Liu, Xiaowen⋅Shan, Baozhen⋅Xin, Lei and Ma, Bin
BMC Bioinformatics, vol. 11, (no. Suppl 1), pp. S4, 2010. | Journal Article
 
Better score function for peptide identification with ETD MS/MS spectra.
Liu, Xiaowen⋅Shan, Baozhen⋅Xin, Lei and Ma, Bin
BMC bioinformatics, vol. 11 Suppl 1, pp. S4, 2010. | Journal Article
 
Deconvolution and database search of complex tandem mass spectra of intact proteins: a combinatorial approach.
Liu, Xiaowen⋅Inbar, Yuval⋅Dorrestein, Pieter C⋅Wynne, Colin⋅Edwards, Nathan⋅Souda, Puneet⋅Whitelegge, Julian⋅Bafna, Vineet and Pevzner, Pavel A
Molecular & cellular proteomics : MCP, vol. 9, (no. 12), pp. 2772-82, 2010/Dec. | Journal Article
 
Modeling protein interacting groups by quasi-bicliques: complexity, algorithm, and application.
Liu, Xiaowen⋅Li, Jinyan and Wang, Lusheng
IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM, vol. 7, (no. 2), pp. 354-64, 2010 Apr-Jun. | Journal Article
2009
Automated protein (re)sequencing with MS/MS and a homologous database yields almost full coverage and accuracy
Liu, Xiaowen⋅Han, Yonghua⋅Yuen, Denis and Ma, Bin
Bioinformatics, vol. 25, (no. 17), pp. 2174-2180, 2009. | Journal Article
2008
A (1.5 + epsilon)-approximation algorithm for unsigned translocation distance.
Cui, Yun⋅Wang, Lusheng⋅Zhu, Daming and Liu, Xiaowen
IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM, vol. 5, (no. 1), pp. 56-66, 2008 Jan-Mar. | Journal Article
 
A (1.5 + Im)-Approximation Algorithm for Unsigned Translocation Distance
Cui, Yun⋅Wang, Lusheng⋅Zhu, Darning and Liu, Xiaowen
IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 5, (no. 1), pp. 56-66, 2008. | Journal Article
 
An Efficient Voting Algorithm for Finding Additive Biclusters with Random Background
Xiao, J.⋅Wang, Lusheng⋅Liu, Xiaowen and Jiang, Tao
Journal of Computational Biology, vol. 15, (no. 10), pp. 1275-1293, 2008. | Journal Article
 
Approximation algorithms for biclustering problems
Wang, L.⋅Lin, Y. and Liu, X.
SIAM Journal on Computing, vol. 38, pp. 1504-1518. | Journal Article
 
Finding additive biclusters with random background
Xiao, J.⋅Wang, L.⋅Liu, X. and Jiang, T.
2008
 
Quasi-bicliques: Complexity and binding pairs
Liu, X.⋅Li, J. and Wang, L.
2008
 
Voting algorithms for the motif finding problem.
Liu, Xiaowen⋅Ma, Bin and Wang, Lusheng
Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference, vol. 7, pp. 37-47, 2008. | Journal Article
 
Voting algorithms for the motif finding problem.
Liu, X.⋅Ma, B. and Wang, L.
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