Lin He

I am a Ph.D. student in Bioinformatics Research Group in David R. Cheriton School of Computer Science, University of Waterloo. My supervisor is Professor Bin Ma. I concentrate on the algorithm design and implementation to assist the identification of protein sequences using Mass Spectrometry technology.

Refereed Papers:

L. He, X. Han and B. Ma. De Novo Sequencing with Limited Number of Post-Translational Modifications per Peptide. Accepted by APBC 2012
X. Han, L. He, L. Xin, B. Shan and B. Ma. PeaksPTM: Mass Spectrometry Based Identification of Peptides with Unspecified Modifications. Journal of Proteomics Research, 2011, 10(7): 2930-2936. (Also appeared in RECOMB-CP'2011)
L. He and B. Ma. ADEPTS: Advanced Peptide De Novo Sequencing with a Pair of Tandem Mass Spectra. Journal of Bioinformatics and Computational Biology, 2010, 8(6): 981-94. (Download PDF)

Posters:

L. He, X. Han, L. Xin, B. Shan and B. Ma. New Computational Method for Identifying Peptides with Unspecified Modifications. ASMS Conference on Mass Spectrometry and Allied Topics 2011, Denver, CO, US.
L. He, X. Han and B. Ma. An Efficient De Novo Sequencing Algorithm for the Identification of Modified Peptides from MS/MS spectra. RECOMB 2011, Vancouver, BC, Canada
L. He and B. Ma. No News Is Good News: De Novo Determination of Amino Acids When Peaks Are Missing. ASMS Conference on Mass Spectrometry and Allied Topics 2010, Salt Lake City, UT, US.

Software:

DeNovoPTM - DeNovoPTM is a MS-based peptide identification software tool, which is the first available tool to do de novo sequencing with limited number of PTM occurances per peptide while considering many types of PTMs. The software can be downloaded here.

PeaksPTM - PeaksPTM is a MS-based peptide identification software tool, which is designed for unrestricted post-translational modification (PTM) search. An online web server is provided for PeaksPTM.

ADEPTS - ADEPTS (Advanced Peptide De Novo Sequencing with a Pair of Tandem Mass Spectra) is a software package for peptide identification using two different types of MS/MS spectra. Click here to download the runable program. A sample is also provided here to test the software. Please follow README to run the program.

Awards:

TAs:

Useful Links:

It is my first time to read this How To Read A Paper, and I would like to share it with all the grad students who did not read it before. You can also download it here.