The publications listed below are limited to those co-authored 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.

All Papers by Year                      Papers by Area

2012 (so far)

• Lin, Y., Rajan, V., and Moret, B.M.E., "Bootstrapping phylogenies inferred from rearrangement data," BMC Algorithms for Molecular Biology, accepted, to appear. (best papers from WABI'11)
• Christinat, Y., and Moret, B.M.E., "Inferring transcript phylogenies," BMC Bioinformatics, accepted, to appear.
• Christinat, Y., and Moret, B.M.E., ``A transcript perspective on evolution," Proc. 8th Int'l Symp. Bioinformatics Research & Appls. ISBRA'12, accepted, to appear.
• Brusslan, J.A., Alvarez-Canterbury, A.M.R., Nair, N.U., Rice, J.C., Hitchler, M.J., and Pellegrini, M., "Genome-Wide Evaluation of Histone Methylation Changes Associated with Leaf Senescence in Arabidopsis," PLoS One 7(3): e33151. doi:10.1371/journal.pone.0033151, (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, online preprint. PDF
• Zhang, X., and Moret, B.M.E., "Refining regulatory networks through phylogenetic transfer of information," IEEE/ACM Trans. on Computational Biology and Bioinformatics, online preprint. PDF

2011

• Christinat, Y., and Moret, B.M.E., "Inferring transcript phylogenies," Proc. 5th IEEE Conf. Bioinformatics & Biomedicine BIBM'11, 208-215, IEEE Press (2011) (best student paper award). 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, 1055-1064 (2011). (special issue on RECOMB-CG'10). PDF PDF
• 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). 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, 175-187, 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, 197-208, 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, 4-7, 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), 902-911. (best papers from ISBRA'10) 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, 351-363, 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. (best papers from BIBM'10) PDF
• Zhang, X., Kupiec, M., Gophna, U., and Tuller, T., "Analysis of co-evolving 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, 344-357, 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, 1059-1067. 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 RECOMB-CG'10, in Lecture Notes in Computer Science 6398, 228-239, Springer Verlag (2010). PDF
• 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). PDF
• 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. 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):763-767 (2010) PDF
• Pattengale, N.D., Alipour, M., Bininda-Edmonds, O.R.P., Moret, B.M.E., and Stamatakis, A., "How many bootstrap replicates are necessary?" J. Computational Biology, 17, 3 (2010), 337-354. (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, 128-139, 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 Asia-Pacific 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), 489-501. (special issue on RECOMB'09). PDF
• Xu, A.W., "The median problems on linear multichromosomal genomes: Graph representation and fast exact solutions", J. Computational Biology, 17, 9 (2010), 1195-1211. (special issue on RECOMB-CG'09). PDF
• Xu, A.W., "On exploring genome rearrangement phylogenetic patterns," Proc. 8th RECOMB Workshop on Comparative Genomics RECOMB-CG'10, in Lecture Notes in Computer Science 6398, 121-136, 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, 579-584 (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. (best papers from WABI'09). PDF

2009

• Pattengale, N.D., Alipour, M., Bininda-Edmonds, 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, 184-200, 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):1339-1351 (2009) (special issue on RECOMB-CG'08). PDF
• Swenson, K.M., and Moret, B.M.E., "Inversion-based genomic signatures," Proc. 7th Asia-Pacific 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, 386-399, 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 Asia-Pacific Bioinformatics Conf. APBC'09, in BMC Bioformatics 2009, 10 (Suppl. 1):S6. PDF
• Xu, A.W., "A fast and exact algorithm for the median-of-three problem: A graph decomposition approach," J. Computational Biology, 16(10):1369-1381 (2009) (special issue on RECOMB-CG'08).
• Xu, A.W., "DCJ median problems on linear multichromosomal genomes: Graph representation and fast exact solutions," Proc. 7th RECOMB Workshop on Comparative Genomics RECOMB-CG'09, in Lecture Notes in Computer Science 5817, 70-83, 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, 412-425, 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 5,4:583-593 (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):i114-i122 (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 Asia-Pacific Bioinformatics Conf. APBC'08, in Advances in Bioinformatics and Computational Biology, vol. 6, 241-250, 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 RECOMB-CG'08, in Lecture Notes in Computer Science 5267, 239-249, Springer Verlag (2008). PDF
• Swenson, K.M., Marron, M., Earnest-DeYoung, 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
• 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, 245-258, 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, 186-193 (2008). PDF

2007

• Bininda-Emonds, 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 Species-Rich Clades, T. Hodkinson and J. Parnell, eds., CRC Press, pp. 77-95 (2007).
• Blagojevic, F., Nikolopoulos, D.S, Stamatakis, A., and Antonopoulos, C.D., "RAxML-Cell: 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. 90-100 (best paper award). PDF
• Blagojevic, F., Nikolopoulos, D.S., Stamatakis, A., Antonopoulos, C.D., and Curtis-Maury, M., "Runtime scheduling of dynamic parallelism on accelerator-based multicore systems," Parallel Computing 33(10-11): 700--719 (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):1242-1258 (2007). PDF
• Kothari, M., and Moret, B.M.E., "An experimental evaluation of inversion-and transposition-based genomic distances through simulations," Proc. 3rd IEEE Symp. on Comput. Intelligence in Bioinformatics and Comput. Biol. CIBCB'07, 151-158, IEEE Press (2007). PDF
• Moret, B.M.E., "Large-scale phylogenetic reconstruction," in Comparative Genomics: Basic and Applied Research, J.R. Brown, ed., CRC Press/Taylor & Francis, pp. 29-48 (2007).
• Ott, M., Zola, J., Aluru, S., and Stamatakis, A., "Large-scale maximum likelihood-based 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 Robinson-Foulds metric," J. Computational Biology, 14(6): 724-735 (2007) (special issue on RECOMB'06). PDF
• Stamatakis, A., Auch, A., Meier-Kolthoff, J. and Goeker, M., "AxPcoords and parallel AxParafit: Statistical co-phylogenetic 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):271-286 (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 2:7-22 (2006). PDF
• Stamatakis, A., "RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models", Bioinformatics 22(21):2688-2690 (2006). PDF