Publications

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Selected Publications

  • Abdul Rehman Basharat, Yong Zang, Liangliang Sun, and Xiaowen Liu (2023), TopFD: A proteoform feature detection tool for top–down proteomics, Analytical Chemistry, DOI: 10.1021/acs.analchem.2c05244
  • Elijah N. McCool, Tian Xu, Wenrong Chen, Nicole C. Beller, Scott M. Nolan, Amanda B. Hummon, Xiaowen Liu, and Liangliang Sun (2022). Deep top-down proteomics revealed significant proteoform-level differences between metastatic and nonmetastatic colorectal cancer cells. Science Advances, 8: eabq6348.
  • Wenrong Chen and Xiaowen Liu (2021). Proteoform identification by combining RNA-seq and top-down mass spectrometry. Journal of Proteome Research, 20: 261–269.
  • Abdul Rehman Basharat, Xia Ning, and Xiaowen Liu (2020). EnvCNN: A convolutional neural network model for evaluating isotopic envelopes in top-down mass-spectral deconvolution. Analytical Chemistry, 92: 7778–7785.
  • Qiang Kou, Zhe Wang, Rachele A. Lubeckyj, Si Wu, Liangliang Sun, and Xiaowen Liu (2019). A Markov chain Monte Carlo method for estimating the statistical significance of proteoform identifications by top-down mass spectrometry. Journal of Proteome Research 18:878-889.
  • Qiang Kou, Si Wu, Nikola Tolić, Ljiljana Paša-Tolić, Yunlong Liu, and Xiaowen Liu (2017). A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra. Bioinformatics, 33:1309-1316.
  • Qiang Kou, Likun Xun, and Xiaowen Liu (2016). TopPIC: a software tool for top-down mass spectrometry-based proteoform identification and characterization. Bioinformatics, 32:3495-97.
  • Xiaowen Liu, Lennard Dekker, Si Wu, Martijn M. Vanduijn, Theo M. Luider, Nikola Tolić, Qiang Kou, Mikhail Dvorkin, Sonya Alexandrova, Kira Vyatkina, Ljiljana Paša-Tolić, and Pavel A. Pevzner (2014). De novo protein sequencing by combining top-down and bottom-up tandem mass spectra. Journal of Proteome Research, 13: 3241-3248.
  • Xiaowen Liu, Yakov Sirotkin, Yufeng Shen, Gordon Anderson, Yihsuan S. Ting, Ying S. Ting, David R. Goodlett, Richard D. Smith, Vineet Bafna and Pavel A. Pevzner (2012). Protein identification using top-down spectra. Molecular & Cellular Proteomics, 11:M111.008524.
  • Xiaowen Liu, Yuval Inbar, Pieter C. Dorrestein, Colin Wynne, Nathan Edwards, Puneet Souda, Julian P. Whitelegge, Vineet Bafna and Pavel A. Pevzner (2010). Deconvolution and database search of complex tandem mass spectra of intact proteins: a combinatorial approach. Molecular & Cellular Proteomics, 9:2772-2782.
  • Xiaowen Liu and Lusheng Wang (2007). Computing the maximum similarity bi-clusters of gene expression data. Bioinformatics, 23:50-56.
  • Lusheng Wang, Daming Zhu, Xiaowen Liu and Shaohan Ma (2005). An O(n2) algorithm for signed translocation. Journal of Computer and System Sciences, 70:284-299.