Yu Lin Ph.D Candidate Laboratory for Computational Biology and Bioinformatics (LCBB) School of Computer and Communication Sciences (IC) École Polytechnique Fédérale de Lausanne (EPFL) E-Mail: yu.lin AT epfl.ch Address: INJ 211, Station 14, EPFL, CH-1015, Lausanne, Switzerland ---> Curriculum Vitae

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I am a fifth year Ph.D student at School of Computer and Communication Sciences (IC), EPFL.

My thesis advisor is Prof. Bernard M.E. Moret.

Research Interests

1. Models of genome evolution and algorithms
2. Phylogenetic reconstruction and comparative genomics

Education

1. Aug. 2007 - present, Ph.D Candidate at IC, EPFL, Lausanne, Switzerland.
2. Sep. 2004 - Jul. 2007, M.E. in Computer Science, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China.
3. Sep. 2000 - Jul. 2004, B.E. in Computer Science, University of Science and Technology of China, Heifei, China.

Publications

• Lin, Y., Rajan, V., and Moret, B.M.E., "Bootstrapping phylogenies inferred from rearrangement data," Proc. 11th Workshop on Algorithms in Bioinformatics WABI'11, Lecture Notes in Computer Science 6833, 175-187, Springer Verlag (2011).
• Lin, Y., and Moret, B.M.E., "A new genomic evolutionary model for rearrangements, duplications, and losses that applies across eukaryotes and prokaryotes," J. Computational Biology 18(9): 1055-1064 (2011). (special issue on RECOMB-CG'10).
• Lin, Y., Rajan, V., and Moret, B.M.E., "Fast and accurate phylogenetic reconstruction from high-resolution whole-genome data and a novel robustness estimator," J. Computational Biology 18(9): 1131-1139 (2011). (special issue on RECOMB-CG'10).
• Lin, Y., Rajan, V., and Moret, B.M.E., "A metric for phylogenetic trees based on matching," Proc. 7th Int'l Symp. Bioinformatics Research & Appls. ISBRA'11, Lecture Notes in Computer Science 6674, 197-208, Springer Verlag (2011).
• Lin, Y., and Moret, B.M.E., "A new genomic evolutionary model for rearrangements, duplications, and losses that applies across eukaryotes and prokaryotes," Proc. 8th RECOMB Workshop on Comparative Genomics RECOMB-CG'10, in Lecture Notes in Computer Science 6398, 228-239, Springer Verlag (2010).
• Lin, Y., Rajan, V., and Moret, B.M.E., "Fast and accurate phylogenetic reconstruction from high-resolution whole-genome data and a novel robustness estimator," Proc. 8th RECOMB Workshop on Comparative Genomics RECOMB-CG'10, in Lecture Notes in Computer Science 6398, 137-148, Springer Verlag (2010).
• Lin, Y., Rajan, V., Swenson, K.M., and Moret, B.M.E., "Estimating true evolutionary distances under rearrangements, duplications, and losses," Proc. 8th Asia-Pacific Bioinformatics Conf. APBC'10, in BMC Bioinformatics 2010, 11 (Suppl. 1):S54.
• Rajan, V., Xu, A.W., Lin, Y., Swenson, K.M., and Moret, B.M.E., "Heuristics for the inversion median problem," Proc. 8th Asia-Pacific Bioinformatics Conf. APBC'10, in BMC Bioinformatics 2010, 11 (Suppl. 1):S30.
• Swenson, K.M., Rajan, V., Lin, Y., and Moret, B.M.E., "Sorting signed permutations by inversions in O(nlogn) time," J. Computational Biology, 17(3): 489-501 (2010) (special issue on RECOMB'09).
• Swenson, K.M., Lin, Y., Rajan, V., and Moret, B.M.E., "Hurdles and sorting by inversions: Combinatorial, statistical, and experimental results," J. Computational Biology, 16(10):1339-1351 (2009) (special issue on RECOMB-CG'08).
• Swenson, K.M., Rajan, V., Lin, Y., and Moret, B.M.E., "Sorting signed permutations by inversions in O(nlogn) time," Proc. 13th Int'l Conf. on Research in Comput. Molecular Biol. RECOMB'09, in Lecture Notes in Computer Science 5541, 386-399, Springer Verlag (2009).
• Lin, Y., and Moret, B.M.E., "Estimating true evolutionary distances under the DCJ model", Proc. 16th Conf. on Intelligent Systems for Molecular Biology ISMB'08, in Bioinformatics 24(13):i114-i122 (2008).
• Lin, Y., Qiao, Y., Sun, S., Yu, C, Dong G., and Bu, D. "A fragmentation event model for peptide identification by mass spectrometry," Proc. 12th Int'l Conf. on Research in Comput. Molecular Biol. RECOMB'08, in Lecture Notes in Computer Science 4955, 154-166, Springer Verlag (2008).
• Swenson, K.M., Lin, Y., Rajan, V., and Moret, B.M.E., "Hurdles hardly have to be heeded," Proc. 6th RECOMB Workshop on Comparative Genomics RECOMB-CG'08, in Lecture Notes in Computer Science5267, 239-249, Springer Verlag (2008).
• Wang, L., Lin, Y., and Liu, X., "Approximation algorithms for Biclustering problems," SIAM J. Comput. 38(4): 1504-1518 (2008).
• Sun, S., Yu, C., Qiao, Y., Lin, Y., Dong, G., Liu, C., Zhang, J., Zhang, Z., Cai, J., Zhang, H., and Bu, D., "Deriving the probabilities of water loss and ammonia loss for amino acids from tandem mass spectra," J. Proteome Res., 7(01): 202-208 (2008).
• Yu, C., Lin, Y., Sun, S., Cai, J., Zhang, J., Bu, D., Zhang, Z., and Chen, R., "An iterative algorithm to quantify factors influencing peptide fragmentation during tandem mass spectrometry,"J Bioinform Comput Biol., 5(2a):297-311 (2007) (special issue on CSB'06).
• Wang, L., Lin, Y., andn Liu, X., "Approximation algorithms for Bi-clustering problems," Proc. 6th Workshop on Algorithms in Bioinformatics WABI'06, in Lecture Notes in Computer Science 4175, 310-320, Springer Verlag (2006).
• Yu, C., Lin, Y., Sun, S., Cai, J., Zhang, J., Bu, D., Zhang, Z., and Chen, R., "An iterative algorithm to quantify the factors influencing peptide fragmentation for MS/MS spectrum", Proc. 2006 LSS Computational Systems Bioinformatics Conference CSB'06, 353-360, Imperial College Press (2006)

Softwares and Webservers

• TIBA: Tree Inference with Bootstrap Analysis