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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 whose work was carried out during their association
with the laboratory since its start in late 2006.
Papers by Area
All Papers by Year
Papers on Genome Rearrangements

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., 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

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

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. 23rd Int'l Conf. on Research in Comput. Molecular
Bio. RECOMB'15,
in Lecture Notes in Computer Science 9029, 309322, Springer Verlag (2015).

Shao, M., and 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.

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

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

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

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

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

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

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)
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

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

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).
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).
(special issue on RECOMBCG'10).
PDF
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.
(best papers from BIBM'10)
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

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).

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).

Xu, A.W.,
"The
median problems on linear multichromosomal genomes: Graph representation and
fast exact solutions",
J. Computational Biology, 17, 9 (2010), 11951211.
(special issue on RECOMBCG'09).
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

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

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.
(special issue on RECOMB'09).
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

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., 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).
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)
(special issue on RECOMBCG'08).

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

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, 241251, 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)
(best papers from ALENEX'05).
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
Papers on Phylogeny Reconstruction

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

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

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

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

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

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

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 (2011).
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

Christinat, Y., and Moret, B.M.E.,
"Inferring transcript
phylogenies," Proc. 5th IEEE Conf. Bioinformatics & Biomedicine
BIBM'11, 208215,
IEEE Press (2011)
(best student paper award).
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).
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.
(best papers from ISBRA'10)
PDF

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

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.
(special issue on RECOMB'09).
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

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

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).
PDF

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).

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).
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
(best paper finalist).
PDF

Pattengale, N.D., Gottlieb, E.J., and Moret, B.M.E.,
"Efficiently Computing the RobinsonFoulds metric,"
J. Computational Biology,
14(6): 724735 (2007).
(special issue on RECOMB'06).
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).
PDF

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
Papers on Biological Networks and Gene Families

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.

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

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

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

Zhang, X., Kupiec, M., Gophna, U., and Tuller, T.,
"Analysis of coevolving gene families using mutually exclusive orthologous
modules,"
Genome Biology and Evolution,
2011 (10.1093/gbe/evr030).
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

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.
(best papers from WABI'09).
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

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).

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
Papers on HighThroughput Genomics and Epigenomics

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

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).

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

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

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

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
Papers on HighPerformance Computing

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

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
(best paper award).
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).
PDF

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
(best paper finalist).
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).
PDF
