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Laboratory for Computational
Biology and Bioinformatics
Copyright Notice:
The documents accessible through these links are included by the authors
as a means to ensure convenient electronic dissemination of technical
work on a noncommercial basis. Copyright and all rights therein are
maintained by the copyright holders (the authors or the publishers),
notwithstanding that they have offered their works here electronically.
It is understood that all persons copying this information will adhere
to the terms and constraints invoked by each author's and publisher's
copyright. In particular, these works may not be reposted without
permission of the copyright holders.
The publications listed below are limited to those coauthored by
members of the Laboratory for Computational Biology and Bioinformatics on work
carried out at least in part during their association with the laboratory since
its start in late 2006 to its closure at the end of 2016.
All Papers by Year
Papers by Area
2017 (so far)

Doerr, D., and B.M.E. Moret,
"Sequencebased synteny analysis of multiple large genomes,"
accepted, to appear as a chapter in
Comparative Genomics, J.C. Setubal, J. Stoye, and P.F. Stadler, eds.,
Methods in Molecular Biology xx, Springer (2017).

Doerr, D., Kowada, L., de Araujo, F., Deshpande, Sh., Dantas, S., Moret, B.M.E., and J. Stoye,
"New genome similarity measures based on conserved gene adjacencies,"
accepted, to appear in
J. of Comput. Biol. (2017).

Ye, M., Racz, G., Jiang, Q., Zhang, X., and Moret, B.M.E.,
"NEMo, an evolutionary model with modularity for PPI networks,"
accepted, to appear in IEEE Trans. on NanoBioscience (2017).

Ye, M, Zhang, X., and Moret, B.M.E.,
"Modularity in PPI networks: Characteristics of existing networks and models of evolution,"
Proc. 9th Conf. on Bioinformatics and Computational Biology BiCoB'17, 155163 (2017).
PDF
2016

Moret, B.M.E., "Limites des Algorithmes,", chap. 3 in "Découvrir le
Numérique," A. Schiper, ed., Presses Polytechniques et Universitaires Romandes, 5180 (2016).

Doerr, D., Feijao, P., Balaban, M., and Chauve, C.,
"The gene familyfree median of three,"
Proc. 16th Workshop on Algs. in Bioinformatics
WABI'16, in
Lecture Notes in Computer Science 9838, 102120 (2016).
PDF

Ye, M., Racz, G., Jiang, Q., Zhang, X., and Moret, B.M.E.,
"NEMo, an evolutionary model with modularity for PPI networks,"
Proc. 12th Int'l Symp. Bioinformatics Research & Appls. ISBRA'16, in Lecture Notes in Computer Science 9683, 224236 (2016).
PDF

Shao, M., and Moret, B.M.E.,
``On computing pairwise breakpoint distances under duplication and loss,"
Proc. 20th Int'l Conf. on Research in Comput. Molecular
Bio. RECOMB'16, in Lecture Notes in Computer Science 9649, 189203 (2016).
PDF

Shao, M., and Moret, B.M.E.,
"A fast and exact algorithm for the exemplar breakpoint distance,"
J. Computational Biology 23, 5 337346 (2016).
PDF

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,
in BMC Genomics 17, 1, 14 (2016).
PDF
2015

Shao, M., and Moret, B.M.E.,
"Comparing genomes with rearrangements and segmental duplications,"
Proc. 23rd Symp. on Intelligent Systems for Mol. Bio.
ISMB'15,
in Bioinformatics
31, 12, i329i338 (2015).
PDF

Shao, M., and Moret, B.M.E.,
"A fast and exact algorithm for the exemplar breakpoint distance,"
Proc. 19th Int'l Conf. on Research in Comput. Molecular
Bio. RECOMB'15,
in Lecture Notes in Computer Science 9029, 309322, Springer Verlag (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.
2014

Zhang, X., Ye, M., and Moret B.M.E.,
"Phylogenetic transfer of knowledge for biological networks,"
PeerJ PrePrints 2:e401v1 (2014).
PDF

Ghiurcuta, C.G., and Moret, B.M.E.,
"Evaluating synteny for improved comparative studies,"
Proc. 22nd Symp. on Intelligent Systems for Mol. Bio.
ISMB'14,
in Bioinformatics
30, 12, i9i18 (2014).
PDF

Nair, N.U., Kumar, S., Moret, B.M.E., and Bucher, P.,
"Probabilistic partitioning methods to find significant patterns in ChIPSeq data,"
Bioinformatics 30, 17,
24062413 (2014).
PDF

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).
PDF

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).
PDF

Shao, M., and Moret, B.M.E.,
"On the DCJ median problem,"
Proc. 25th Symp. on Combinatorial Pattern Matching
CPM'14,
in Lecture Notes in Computer Science 8486, 273282,
Springer Verlag (2014).
PDF
2013

Christinat, Y., and Moret, B.M.E.,
"A transcript perspective on evolution,"
IEEE/ACM Trans.
on Computational Biology and Bioinformatics
10, 6 (2013), 14031411.
PDF

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,
PDF

Moret, B.M.E.,
"Extending the reach of phylogenetic inference,"
Proc. 13th Workshop on Algorithms in Bioinformatics
WABI'13,
in Lecture Notes in Computer Science 8126,
12, Springer Verlag (2013)
(keynote address).
PDF

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.
PDF

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).
PDF

Rajan, V.,
"A method of alignment masking for refining the phylogenetic signal of multiple sequence alignments,"
Molecular Biology and Evolution, 30, 3 (2013), 689712.
PDF

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).
PDF
2012

Brusslan, J.A., AlvarezCanterbury, A.M.R., Nair, N.U., Rice, J.C., Hitchler, M.J., and Pellegrini, M.,
"GenomeWide
Evaluation of Histone Methylation Changes Associated with Leaf Senescence in Arabidopsis,"
PLoS ONE 7(3): e33151, 2012. doi:10.1371/journal.pone.0033151.
PDF

Christinat, Y., and Moret, B.M.E.,
"
Inferring transcript phylogenies,"
BMC Bioinformatics 13 (Suppl. 9):S1, 2012.
PDF

Christinat, Y., and Moret, B.M.E.,
"A transcript perspective on evolution,"
Proc. 8th Int'l Symp. Bioinformatics Research & Appls.
ISBRA'12, in
Lecture Notes in Computer Science 7292, 4859, Springer Verlag (2012).
PDF

Lin, Y., Rajan, V., and Moret, B.M.E.,
"Bootstrapping phylogenies inferred from rearrangement data,"
BMC Algorithms for Molecular Biology 7:21, 2012.
PDF

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.
PDF

Lin, Y. and Shao, M.,
"
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.
PDF

Nair, N.U., Sahu, A.D., Bucher, P., and Moret, B.M.E., "ChIPnorm: a statistical method for normalizing and identifying differential regions in histone modification ChIPseq libraries ,"
PLoS ONE, 7(8): e39573, 2012.
PDF

Rajan, V., Lin, Y., and Moret, B.M.E.,
"TIBA: A tool for phylogeny inference from rearrangement data with bootstrap analysis,"
Bioinformatics 28, 24 (2012), 33243325. doi: 10.1093/bioinformatics/bts603
PDF

Zhang, X., and Moret, B.M.E.,
"Refining
regulatory networks through phylogenetic transfer of information,"
IEEE/ACM Trans.
on Computational Biology and Bioinformatics,
9, 4 (2012), 10321045.
PDF
2011

Christinat, Y., and Moret, B.M.E.,
"Inferring transcript phylogenies,"
Proc. 5th IEEE Conf. Bioinformatics & Biomedicine
BIBM'11, 208215,
IEEE Press (2011)
PDF

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).
PDF
PDF

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).
PDF
PDF

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).
PDF

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).
PDF

Moret, B.M.E.,
"Phylogenetic analysis of whole genomes,"
Proc. 7th Int'l Symp. Bioinformatics Research & Appls.
ISBRA'11,
Lecture Notes in Computer Science 6674,
47, Springer Verlag (2011).
(keynote address).
PDF

Pattengale, N.D., Aberer, A., Swenson, K.D., Stamatakis, A., and Moret, B.M.E.,
"Uncovering hidden phylogenetic consensus in large datasets,"
IEEE/ACM Trans. on Computational Biology and Bioinformatics 8, 4 (2011), 902911.
PDF

Xu, A.W., and Moret. B.M.E.,
"GASTS: parsimony scoring under rearrangements,"
Proc. 11th Workshop on Algorithms in Bioinformatics WABI'11,
Lecture Notes in Computer Science
6833, 351363, Springer Verlag (2011).
PDF

Yurovski, A., and Moret, B.M.E.,
"FluReF, an automated flu virus reassortment finder based on phylogenetic trees",
BMC Genomics 12 (Suppl. 2):S3, 2011.
PDF

Zhang, X., Kupiec, M., Gophna, U., and Tuller, T.,
"Analysis of coevolving gene families using mutually exclusive orthologous
modules,"
Genome Biology and Evolution
3 (2011), 413423.
PDF

Zhang, X., and Moret, B.M.E.,
"ProPhyC: a probabilistic phylogenetic model for refining regulatory networks,"
Proc. 7th Int'l Symp. Bioinformatics Research & Appls.
ISBRA'11,
Lecture Notes in Computer Science 6674,
344357, Springer Verlag (2011).
PDF
2010

Aberer, A., Pattengale, N.D., and Stamatakis, A.,
"Parallel computation of phylogenetic consensus trees",
Proc. 10th Int'l Conf. Computational Science
ICCS'10, in
Procedia Computer Science 1(1):2010, 10591067.
PDF

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).
PDF

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).
PDF

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.
PDF

Miklós, I., Mélykúti, B., and Swenson, K.M.,
``The Metropolized Partial Importance Sampling MCMC mixes slowly on minimal reversal rearrangement paths,"
IEEE/ACM Trans. on Computational Biology and Bioinformatics, 7(4):763767 (2010)
PDF

Pattengale, N.D., Alipour, M., BinindaEdmonds, O.R.P., Moret, B.M.E., and Stamatakis, A.,
"How
many bootstrap replicates are necessary?"
J. Computational Biology, 17, 3 (2010), 337354.
PDF

Pattengale, N.D., Swenson, K.M., and Moret, B.M.E.,
"Uncovering hidden phylogenetic consensus,"
Proc. 6th Int'l Symp. Bioinformatics Research & Appls.
ISBRA'10, in
Lecture Notes in Computer Science 6053,
128139, Springer Verlag (2010).
PDF

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.
PDF

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 (2010), 489501.
PDF

Xu, A.W.,
"The median problems on linear multichromosomal genomes: Graph representation and fast exact solutions",
J. Computational Biology, 17, 9 (2010), 11951211.
PDF

Xu, A.W.,
"On exploring genome rearrangement phylogenetic patterns,"
Proc. 8th RECOMB Workshop on Comparative Genomics
RECOMBCG'10,
in
Lecture Notes in Computer Science
6398, 121136, Springer Verlag (2010).
PDF

Yurovski, A., and Moret, B.M.E.,
"FluRF, an automated flu virus reassortment finder based on phylogenetic trees",
Proc. 4th IEEE Conf. Bioinformatics & Biomedicine
BIBM'10,
IEEE Press, 579584 (2010).

Zhang, X., and Moret, B.M.E.,
"Refining transcriptional
regulatory networks using network evolutionary models and gene histories,"
BMC Algorithms in Molecular
Biology 2010, 5(1):1.
PDF
2009

Pattengale, N.D., Alipour, M., BinindaEdmonds, O.R.P., Moret, B.M.E., and Stamatakis, A.,
"How many bootstrap replicates are necessary?"
Proc. 13th Int'l Conf. on Research in Comput. Molecular Biol.
RECOMB'09, in
Lecture Notes in Computer Science
5541, 184200, Springer Verlag (2009).
PDF
PDF

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)
PDF

Swenson, K.M., and Moret, B.M.E.,
"Inversionbased genomic signatures,"
Proc. 7th AsiaPacific Bioinformatics Conf.
APBC'09, in
BMC
Bioformatics 2009, 10 (Suppl. 1):S7.
PDF

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).
PDF
PDF

Swenson, K.M., To, Y., Tang, J., and Moret, B.M.E.,
"Maximum independent sets of commuting and noninterfering inversions,"
Proc. 7th AsiaPacific Bioinformatics Conf.
APBC'09, in
BMC
Bioformatics 2009, 10 (Suppl. 1):S6.
PDF

Xu, A.W.,
"A fast and exact algorithm for the medianofthree problem:
A graph decomposition approach,"
J. Computational Biology, 16(10):13691381 (2009)

Xu, A.W.,
"DCJ median problems on linear multichromosomal genomes:
Graph representation and fast exact solutions,"
Proc. 7th RECOMB Workshop on Comparative Genomics
RECOMBCG'09,
in Lecture Notes in Computer Science
5817, 7083, Springer Verlag (2009).
PDF

Zhang, X., and Moret, B.M.E.,
"Improving inference of transcriptional regulatory networks based on network evolutionary models,"
Proc. 9th Workshop on Algs. in Bioinformatics
WABI'09,
Lecture Notes in Computer Science 5724,
412425, Springer Verlag (2009).
PDF
2008

Christinat, Y., Wachmann, B., and Zhang, L.,
"Gene expression data analysis using a novel approach to biclustering combining discrete and continuous data,"
IEEE/ACM Trans. on Computational Biology and Bioinformatics 5,4:583593 (2008).

Feng, Y., Cui, L., dePamphilis, C.W., Moret, B.M.E., and Tang, J.,
"Inferring ancestral chloroplast genomes with inverted repeat,"
Proc. Int'l Conf. on Bioinformatics and Comput. Biol. BIOCOMP'07, in BMC Genomics 2008, 9 (Suppl. 1):S25.
PDF

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).
PDF
PDF

Swenson, K.M., Arndt, W., Tang, J., and Moret, B.M.E.,
"Phylogenetic reconstruction from complete gene orders of whole genomes,"
Proc. 6th AsiaPacific Bioinformatics Conf.
APBC'08,
in Advances in Bioinformatics and Computational
Biology, vol. 6, 241250, Imperial Press (2008).
PDF

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 Science
5267, 239249, Springer Verlag (2008).
PDF

Swenson, K.M., Marron, M., EarnestDeYoung, J.V., and Moret, B.M.E.,
"Approximating the true evolutionary distance between two genomes,"
ACM J. Experimental Algorithmics
12, 3.5 (2008)
PDF

Zhang, X., and Moret, B.M.E.,
"Boosting the performance of inference algorithms for transcriptional
regulatory networks using a phylogenetic approach,"
Proc. 8th Workshop on Algs. in Bioinformatics
WABI'08, in
Lecture Notes in Computer Science
5251, 245258, Springer Verlag (2008).
PDF

Zhang, X., Zaheri, M., and Moret, B.M.E.,
"Using phylogenetic relationships to improve the inference of transcriptional regulatory networks,"
Proc. 1st Conf. on Biomedical Eng. and Informatics
BMEI'08,
IEEE Computer Society Press, 186193 (2008).
PDF
2007

BinindaEmonds, O.R.P., and Stamatakis, A.,
"Taxon sampling versus computational complexity and their impact on obtaining
the Tree of Life," in
Towards the Tree of Life: Taxonomy and Systematics of Large and SpeciesRich Clades, T. Hodkinson and J. Parnell, eds.,
CRC Press, pp. 7795 (2007).

Blagojevic, F., Nikolopoulos, D.S, Stamatakis, A., and Antonopoulos, C.D.,
"RAxMLCell: Parallel phylogenetic tree inference on the Cell broadband engine",
Proc. 21st IEEE Int'l Parallel and Distributed Processing Symp.
IPDPS'07 (2007).

Blagojevic, F., Nikolopoulos, D.S., Stamatakis, A., and Antonopoulos, C.D.,
"Dynamic multigrain parallelization on the Cell broadband engine",
Proc. ACM SIGPLAN Symp. on Principles and Practice of Parallel
Programming PPoPP'07, pp. 90100
PDF

Blagojevic, F., Nikolopoulos, D.S., Stamatakis, A., Antonopoulos, C.D., and
CurtisMaury, M.,
"Runtime scheduling of dynamic parallelism on acceleratorbased multicore
systems,"
Parallel Computing 33(1011): 700719 (2007).

Gottschling, M., Stamatakis, A., Nindl, I., Stockfleth, I., Alonso, A.,
Gissmann, L., and Bravo, I.G.,
"Multiple evolutionary mechanisms drive papillomavirus diversification",
Molecular Biology and Evolution 24(5):12421258 (2007).
doi:10.1093/molbev/msm039 PDF

Kothari, M., and Moret, B.M.E.,
"An experimental evaluation of inversionand transpositionbased genomic
distances through simulations,"
Proc. 3rd IEEE Symp. on Comput. Intelligence in Bioinformatics and Comput.
Biol. CIBCB'07,
151158, IEEE Press (2007).
PDF

Moret, B.M.E.,
"Largescale phylogenetic reconstruction,"
in Comparative Genomics:
Basic and Applied Research, J.R. Brown, ed.,
CRC Press/Taylor & Francis, pp. 2948 (2007).

Ott, M., Zola, J., Aluru, S., and Stamatakis, A.,
"Largescale maximum likelihoodbased phylogenetic analysis on the IBM
BlueGene/L",
Proc. IEEE/ACM Supercomputing Conf. SC'07
PDF

Pattengale, N.D., Gottlieb, E.J., and Moret, B.M.E.,
"Efficiently Computing the RobinsonFoulds metric,"
J. Computational Biology,
14(6): 724735 (2007)
PDF

Stamatakis, A., Auch, A., MeierKolthoff, J. and Goeker, M.,
"AxPcoords and parallel AxParafit: Statistical cophylogenetic analyses on
thousands of taxa",
BMC Bioinformatics 2007, 8:405.
PDF

Stamatakis, A., Blagojevic, F., Antonopoulos, C.D., and Nikolopoulos, D.S.,
"Exploring new search algorithms and hardware for phylogenetics: RAxML meets
the IBM Cell,"
Journal of VLSI Signal Processing Systems 48(3):271286 (2007).
2006

Grimm, G., Renner, S., Stamatakis, A., and Hemleben, V.,
"A nuclear ribosomal DNA phylogeny of Acer inferred with maximum likelihood,
splits graphs, and motif analysis of 606 sequences",
Evolutionary Bioinformatics 2:722 (2006).
PDF

Stamatakis, A.,
"RAxMLVIHPC: Maximum likelihoodbased phylogenetic analyses with thousands
of taxa and mixed models",
Bioinformatics 22(21):26882690 (2006).
PDF
