Publications
(Google Scholar)

Lin, Y., Yuan, J., Shen, M.W., Kolmogorova, M., Chaissonb, M. and Pevzner, P.A.,"Assembly of long errorprone reads using de Bruijn graphs," Proc Natl Acad Sci (2016).
 Zhou, L., Lin, Y., Feng, B., Zhao, J., and Tang, J., "Phylogeny Reconstruction from WholeGenome Data Using Variable Length Binary Encoding", Proc. 12th Int'l Symp.Bioinformatics Research & Appls. ISBRA16, 345346, (2016)

Zhou, J., Lin, Y., Rajan, V., Hoskins, W., Feng, B., and Tang, J., "Analysis of gene copy number changes in tumor phylogenetics", Algorithms for Molecular Biology 11(1) 26, (2016)

Lin, Y., Shen, M.W., Yuan, J., and Pevzner, P.A., "Assembly of long errorprone reads using de Bruijn graphs," Proc. 20th Int'l Conf. on Research in Comput. Molecular Bio. RECOMB'16 (2016).

Nair, N.U., Hunter, L., Shao, M., Grnarova, P., Lin, Y., Bucher, P., and Moret, B.M.E.,
"A maximumlikelihood approach for building celltype trees by lifting,"
Proc. 14th AsiaPacific Bioinf. Conf.
APBC'16,
Best Paper Award, in BMC Genomics, 17, 1, 14 (2016).

Zhou, J., Lin, Y., Rajan, V., Hoskins, W., and Tang. J.,
"Maximum parsimony analysis of gene copy number changes in tumor phylogenetics,"
Proc. 15th Workshop on Algorithms in Bioinformatics
WABI'15,
Lecture Notes in Computer Science
9289, 108120, Springer Berlin Heidelberg, (2015).

Zhou, J., Lin, Y., Hoskins, W., and Tang. J.,
"An iterative approach for phylogenetic analysis of tumor progression using FISH copy number,"
Int'l Symp.Bioinformatics Research & Appls. ISBRA'15,
Lecture Notes in Computer Science
9096, 402412. Springer International Publishing (2015).

Shao, M., Lin, Y., and Moret, B.M.E.,
"An exact algorithm to compute the DCJ distance for genomes with
duplicate genes,"
J. Computational Biology
22, 5 (2015), 425435.

Lin, Y. and Pevzner, P.A.,
"Manifold de Bruijn Graphs,"
Proc. 14th Workshop on Algorithms in Bioinformatics
WABI'14,
Lecture Notes in Computer Science
8701, 296310, Springer Berlin Heidelberg, (2014).

Lin, Y., Nurk, S., and Pevzner, P.A.,
"
What is the difference between the breakpoint graph and the de Bruijn graph?"
BMC Genomics 15(Suppl 6), S6, (2014).

Hu, F., Lin, Y., and Tang, J.,
"
MLGO: phylogeny reconstruction and ancestral inference from geneorder data,
"
BMC
Bioinformatics, 15:354, (2014).

Nair, N.U., Lin, Y., Manasovska, A., Antic, J., Grnarova, P., Sahu, A.D.,
Bucher, P., and Moret, B.M.E.,
"Study of
cell differentiation by phylogenetic analysis using histone modification
data,"
BMC
Bioinformatics, 15:269 (2014).

Shao, M., and Lin, Y., and Moret, B.M.E.,
"An exact algorithm to compute the DCJ distance for genomes with duplicate genes,"
Proc. 18th Int'l Conf. on Research in Comput. Molecular
Bio. RECOMB'14,
in Lecture Notes in Computer Science 8394, 280292, Springer Verlag (2014).

Moret, B.M.E., Lin, Y., and Tang, J.,
"Rearrangements in phylogenetic inference: Compare, model, or encode?",
in Models and Algorithms for Genome Evolution,
vol. 19 of Computational Biology series,
Chauve, C., et al., eds, Springer Verlag (2013), 147172.

Lin, Y., Hu, F., Tang, J., and Moret, B.M.E.,
"
Maximum likelihood phylogenetic reconstruction from highresolution wholegenome data and a tree of 68 eukaryotes,"
Proc. 18th Pacific Symp. on Biocomputing PSB'13, pp. 285296, 2013,

Nair, N.U., Lin, Y., Bucher, P., and Moret, B.M.E.,
"Phylogenetic analysis of cell types using histone modifications,"
Proc. 13th Workshop on Algorithms in Bioinformatics WABI'13, in
Lecture Notes in Computer Science 8126,
326337, Springer Verlag (2013).

Shao, M., and Lin, Y., and Moret, B.M.E.,
"Sorting genomes with rearrangements and segmental duplications through trajectory graphs,"
Proc. 11th RECOMB Workshop on Comparative Genomics
RECOMBCG'13,
in BMC Bioinformatics 14, Suppl. 15, S9 (2013).

Lin, Y., Rajan, V., and Moret, B.M.E.,
"A
metric for phylogenetic trees based on matching,"
IEEE/ACM Trans.
on Computational Biology and Bioinformatics,
9, 4 (2012), 10141022.

Lin, Y., Rajan, V., and Moret, B.M.E.,
"TIBA: A tool for phylogeny inference from rearrangement data with bootstrap analysis,"
Bioinformatics 28, 24 (2012), 33243325.

Lin, Y., Rajan, V., and Moret, B.M.E.,
"Bootstrapping phylogenies inferred from rearrangement data,"
BMC Algorithms for Molecular Biology 7:21, 2012.
(best papers from WABI'11)

Shao, M., and Lin, Y.,
"
Approximating the edit distance for genomes under DCJ, insertion
and deletion,"
Proc. 10th RECOMB Workshop on Comparative Genomics
RECOMBCG'12,
in BMC Bioinformatics 13 (Suppl 19):S13, 2012.

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, 175187, 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): 10551064 (2011).
(special issue on RECOMBCG'10).

Lin, Y., Rajan, V., and Moret, B.M.E.,
"Fast and accurate phylogenetic reconstruction from highresolution
wholegenome data and a novel robustness estimator,"
J. Computational Biology 18(9): 11311139 (2011).
(special issue on RECOMBCG'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,
197208, 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
RECOMBCG'10,
in
Lecture Notes in Computer Science 6398, 228239, Springer Verlag (2010).

Lin, Y., Rajan, V., and Moret, B.M.E.,
"Fast and accurate phylogenetic reconstruction from
highresolution wholegenome data and a novel robustness estimator,"
Proc. 8th RECOMB Workshop on Comparative Genomics
RECOMBCG'10,
in
Lecture Notes in Computer Science
6398, 137148, 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 AsiaPacific 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 AsiaPacific 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): 489501 (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):13391351 (2009)
(special issue on RECOMBCG'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, 386399, 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):i114i122 (2008).

Lin, Y., Qiao, Y., Sun, S., Yu, C, Dong G., and Bu, D. "A fragmentation event model for peptide identiļ¬cation by mass spectrometry," Proc. 12th Int'l Conf. on Research in Comput. Molecular Biol. RECOMB'08, in Lecture Notes in Computer Science 4955, 154166, 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
RECOMBCG'08, in
Lecture Notes in Computer Science5267, 239249, Springer Verlag (2008).

Wang, L., Lin, Y., and Liu, X., "Approximation algorithms for Biclustering problems," SIAM J. Comput. 38(4): 15041518 (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): 202208 (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):297311 (2007) (special issue on CSB'06).

Wang, L., Lin, Y., andn Liu, X., "Approximation algorithms for Biclustering problems," Proc. 6th Workshop on Algorithms in Bioinformatics WABI'06, in Lecture Notes in Computer Science 4175, 310320, 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, 353360, Imperial College Press (2006)