[back]
 
 

Journals (by topic)


 

Computational Proteomics

  • Yong Fuga Li, Randy Arnold, Predrag Radivojac, Haixu Tang (2011). Protein identification problem from a Bayesian point of view. Statistics and Its Interface. (Invited paper, Accept). PDF
  • Xiaohui Liu, Yong Fuga Li, Brian C. Bohrer, Randy J. Arnold, Predrag Radivojac, Haixu Tang, James P. Reilly (2011). Investigation of VUV Photodissociation Propensities Using Peptide Libraries. International Journal of Mass Spectrometry and Ion Processes (In press). PDF
  • Yong Fuga Li, Randy J. Arnold, Haixu Tang, and Predrag Radivojac (2010). The importance of peptide detectability for protein identification, quantification, and experiment design in MS/MS proteomics. Journal of Proteome Research.  9(12): 6288–6297. PDF, PPT
    - Software: DQmodel
    - The dataset is available upon request.
  • Brian C. Bohrer, Yong Fuga Li, James P. Reilly, David E. Clemmer, Richard D. DiMarchi, Predrag Radivojac, Haixu Tang, and Randy J. Arnold (2010) Combinatorial Libraries of Synthetic Peptides as a Model for Shotgun Proteomics. Anal. Chem. 82 (15): 6559–6568. PDF
    - Also presented at Pittsburgh Conference 2010.
  • Yong Fuga Li, Randy Arnold, Yixue Li, Predrag Radivojac, Quanhu Sheng and Haixu Tang (2009). A Bayesian approach to protein inference problem in shotgun proteomics. Journal of Computational Biology. 16(8): 1183-1193.  PDF
    - Software: MSBayesPro
    - First presented at  RECOMB 2008

Computational Molecular & Developmental Biology

  • Fuxiao Xin, Steven Myers, Yong Fuga Li, David N. Cooper, Sean D. Mooney, Predrag Radivojac (2010). Structure-based kernels for the prediction of catalytic residues and their involvement in human inherited disease. Bioinformatics. 26(16):1975-82 PDF

Genomics and Molecular Evolution

  • Yong Fuga Li, James C. Costello, Alisha K. Holloway, and Matthew W. Hahn (2008). "Reverse ecology" and the power of population genomics. Evolution. 62: 2984–2994. PDF

Machine Learning Models and Algorithms

 

Refereed conferences (by discipline)


Computational Biology

  • Yong Fuga Li, Randy Arnold, Yixue Li, Predrag Radivojac, Quanhu Sheng and Haixu Tang (2008). A Bayesian approach to protein inference problem in shotgun proteomics. RECOMB 2008;  LNBI 4955, pp. 167 - 180, 2008. (Acceptance rate 18%) PDF
    - Full paper published in  Journal of Computational Biology. 16(8): 1183-1193. 

Computer Science

  • Xiaoyong Zhou, Bo Peng, Yong Fuga Li, Yangyi Chen, Haixu Tang, XiaoFeng Wang (2011). To Release Or Not To Release: Evaluating Information Leaks in Aggregate Human-Genome Data. ESORICS 2011. (Acceptance rate 23%) PDF
  • Rui Wang*, Yong Fuga Li*, Xiaofeng Wang, Haixu Tang and Xiaoyong Zhou (2009) Learning Your Identity and Disease from Research Papers: Information Leaks in Genome Wide Association Study. Presented at CCS (Annual ACM Computer and Communications Security) 2009: 534-544.  (Acceptance rate 18%) PDF
    * equal contribution.
    - The dataset and code is available upon request.

Book Chapters


  • Yong Fuga Li and Predrag Radivojac (2011) Computational approaches to protein inference in shotgun proteomics. In Methods in Molecular Biology: Statistical mass spectrometry-based proteomics. Springer (Invited) Submitted.

Posters and Talks


  • Yong Fuga Li, Randy J. Arnold, Predrag Radivojac, Haixu Tang. Feature Decomposition from LC-MS Data using Non-negative Matrix Factorization. Poster, 59th ASMS Conference on Mass Spectrometry and Allied Topics, 2011, Reprint
  • Yong Fuga Li, Randy J. Arnold, Predrag Radivojac, Haixu Tang. The Importance of Peptide Detectability for Protein Identification, Quantification, and Experiment Design in MS/MS Proteomics. Poster-flash Oral Presentation (PPT) and Poster (Reprint), RECOMB-CP, 2011.
  • Fuxiao Xin, Steven Myers, Yong Fuga Li, David N. Cooper, Sean D. Mooney, Predrag Radivojac. Structure-based kernels for the prediction of catalytic residues and their involvement in human inherited disease. Talk, 6th ISCB Student Council Symposium, 2010.
  • Yong Fuga Li, Randy J. Arnold, Haixu Tang, Predrag Radivojac. Accurate Prediction of Repeatability of Peptide Identification from a Single Shotgun Proteomics Experiment. Poster TP016, 58th ASMS Conference on Mass Spectrometry and Allied Topics, 2010, Reprint
  • Randy J. Arnold, Katharine Witkin, Brian Bohrer, Yong Li, David E. Clemmer, Predrag Radivojac,  Haixu Tang. Synthetic Peptide Libraries as Internal Standards for Label-Free Quantitative Proteomics. Poster TP148, 58th ASMS Conference on Mass Spectrometry and Allied Topics, 2010
  • Randy J Arnold, Brian Bohrer, David E Clemmer, Xiaohui Liu, Sujun Li, Yong F Li, Predrag Radivojac, James Reilly, Haixu Tang. Modeling Complex Proteomic Sample Analysis Using a Combinatorial Synthetic Approach. Oral session of the Technical Program, Pittcon 2010
  • Yong Fuga Li, Randy J. Arnold, Predrag Radivojac, Haixu Tang. Assessment of peptide-spectrum matches without using a decoy database. Poster TP045, 57th ASMS Conference on Mass Spectrometry and Allied Topics, 2009, Reprint
  • Yong Fuga Li, Randy J. Arnold, Predrag Radivojac, Haixu Tang. Bayesian approach for protein inference in shotgun proteomics. Poster TP618, 56th ASMS Conference on Mass Spectrometry and Allied Topics, 2008, Reprint
  • Haixu Tang, Yong Fuga Li, Randy J. Arnold, Predrag Radivojac. Posterior peptide identification for proteomics data analysis. Poster TP620, 56th ASMS Conference on Mass Spectrometry and Allied Topics, 2008, Reprint
  • Randy J. Arnold, Yong Fuga Li, Haixu Tang, Predrag Radivojac. Towards cross sample and platform prediction of peptide detectability. Poster TP612, 56th ASMS Conference on Mass Spectrometry and Allied Topics, 2008, Reprint
  • Yong Fuga Li. A Bayesian approach for protein inference problem in shotgun proteomics. Talk, Bioinformatics Workshop, CGB, Mar.17, 2008

    Note: Underlined are presenters

To Publish or Not to Publish?



 
Email: yonli(at)umail.iu.edu