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Yu Lin
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Doctoral Program in Computer, Communication and Information Sciences
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BIOGRAPHY
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I was born in Jiangsu Province, P.R. China.
In 2000, I became an undergraduate student in University of Science and Technology (USTC) and specialized in Computer Science and Technology.
In 2004, I entered Institute of Computing Technology (ICT), Chinese Academy of Sciences (CAS) for Master degree under Dr. Dongbo Bu. Also I spent nine months to work as a research assistant in City University of Hong Kong (CityU) under Prof. Lusheng Wang.
At present, I am a research assistant and PhD candidate under the supervision of Prof. Bernard Moret at EPFL.
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MAIN PUBLICATIONS
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Bootstrapping phylogenies inferred from rearrangement data, Yu Lin, Vaibhav Rajan, Bernard M.E. Moret, Proc. 11th Workshop on Algorithms in Bioinformatics WABI'11, Lecture Notes in Computer Science.
A metric for phylogenetic trees based on matching , Yu Lin, Vaibhav Rajan, Bernard M.E. Moret, Proc. 7th Int'l Symp. Bioinformatics Research & Appls. ISBRA'11, Lecture Notes in Computer Science 6674, 197-208, Springer Verlag (2011)
Fast and accurate phylogenetic reconstruction from high-resolution whole-genome data and a novel robustness estimator, Yu Lin, Vaibhav Rajan, Bernard M.E. Moret, J. Computational Biology (2011). (special issue on RECOMB-CG'10)
A new genomic evolutionary model for rearrangements, duplications, and losses that applies across eukaryotes and prokaryotes, Yu Lin, Bernard M.E. Moret, J. Computational Biology (2011). (special issue on RECOMB-CG'10)
Estimating true evolutionary distances under rearrangements, duplications, and losses, Yu Lin, Vaibhav Rajan, Krister M. Swenson, Bernard M.E. Moret, Proc. 8th Asia-Pacific Bioinformatics Conf. APBC'10, in BMC Bioinformatics 2010, 11 (Suppl. 1):S54.
Heuristics for the inversion median problem, Vaibhav Rajan, Andrew W. Xu, Yu Lin, Krister M. Swenson, Bernard M.E. Moret, Proc. 8th Asia-Pacific Bioinformatics Conf. APBC'10, in BMC Bioinformatics 2010, 11 (Suppl. 1):S30.
Sorting signed permutations by inversions in O(nlogn) time, Krister M. Swenson, Vaibhav Rajan, Yu Lin, Bernard M.E. Moret, J. Computational Biology, 17, 3 (2010), 489-501. (special issue on best papers from RECOMB'09).
Hurdles and sorting by inversions: Combinatorial, statistical, and experimental results, Krister M. Swenson, Yu Lin, Vaibhav Rajan, Bernard M.E. Moret, J. Computational Biology, 16(10):1339-1351 (2009) (special issue on best papers from RECOMB-CG'08).
Estimating True Evolutionary Distances under the DCJ Model, Yu Lin, Bernard M.E. Moret, 16th International Conference on Intelligent Systems for Molecular Biology (ISMB) 2008, in Bioinformatics 24, 13
(2008), i114–i122.
A Fragmentation Event Model for Peptide Identification by Mass Spectrometry, Yu Lin, Yantao Qiao, Shiwei Sun, Chungong Yu, Gongjin Dong, Dongbo Bu, 12th Annual International Conference Research in Computational Molecular Biology (RECOMB) 2008, 154-166.
Approximation Algorithms for Biclustering Problems., Lusheng Wang, Yu Lin, Xiaowen Liu , SIAM J. Comput. 38(4): 1504-1518 (2008) (previous version from WABI'06)
Deriving the probabilities of water loss and ammonia loss for amino acids from tandem mass spectra, Shiwei Sun, Chungong Yu, Yantao Qiao, Yu Lin,Gongjin Dong,Changning Liu, Jingfen Zhang, Zhuo Zhang, Jinjin Cai, Hong Zhang, Dongbo Bu, J. Proteome Res., 7 (01), 202–208, 2008. 10.1021
An Iterative Algorithm to Quantify Factors Influencing peptide Fragmentation during Tandem Mass Spectrometry, Chungong Yu, Yu Lin, Shiwei Sun, Jinjin Cai, Jingfen Zhang, Dongbo Bu, Zhuo Zhang, Runsheng Chen, J. Bioinformatics and Computational Biology 5(2a): 297-311 (2007) (previous version from CSB'06)
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Student