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Internal Use
Publications by Laboratory Members

This list includes only papers on research performed in the laboratory and published or written since 2000. For earlier or other publications by laboratory members, consult their individual web pages.

Papers are listed in alphabetical order by authors within each year. All papers are available in Postscript, denoted PS; some are also available in Portable Document Format, denoted PDF.



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 non-commercial 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 re-posted without permission of the copyright holders.

Accepted to Appear

  • Wang, L.-S., Jansen, R.K., Moret, B.M.E., Raubeson, L.A., and Warnow, T., "Distance-based genome rearrangement phylogeny," J. Molecular Evolution (accepted, to appear, 2006). PDF

2006 (so far)

  • Morin, M.M. and Moret, B.M.E., "NETGEN: generating phylogenetic networks with diploid hybrids," Bioinformatics 22 (2006), 1921-1923.
  • Pattengale, N.D., and Moret, B.M.E., "A sublinear-time randomized approximation scheme for the Robinson-Foulds metric," Proc. 10th Int'l Conf. on Research in Comput. Molecular Biol. RECOMB'06, Venice (2006), in Lecture Notes in Computer Science 3909, 221-230. PS PDF
  • Williams, T.L., Bader, D.A., Yan, M., and Moret, B.M.E., "High-performance phylogeny reconstruction under maximum parsimony," in Parallel Computing for Bioinformatics and Computational Biology, A.Y. Zomaya, ed., John Wiley & Sons, Chap. 16, pp. 369-394 (2006). PS PDF

2005

  • Bader, D.A., "High-performance algorithm engineering for large-scale graph problems and computational biology," Proc. 4th Workshop on Efficient and Experimental Algorithms (WEA'05), Santorini (2005), Lecture Notes in Computer Science 3503, 16-21, Springer Verlag.
  • Bader, D.A., Cong, G., and Feo, J., "On the architectural requirements for efficient execution of graph algorithms," Proc. 34th Conf. on Parallel Processing ICPP'05, Oslo (2005), 547-556, IEEE Press.
  • Cong, G., and Bader, D.A., "An experimental study of parallel biconnected components algorithms on symmetric multiprocessors (SMPs)," Proc. 19th IEEE Int'l Parallel and Distributed Processing Symp. IPDPS'05, IEEE Press (2005), 10pp.
  • Liu, T., Tang, J., and Moret, B.M.E., "Quartet methods for phylogeny reconstruction from gene orders," Proc. 11th Computing and Combinatorics Conference (COCOON'05), Kunming (China), in Lecture Notes in Computer Science 3595, 63-73, Springer Verlag (2005). PS PDF
  • Moret, B.M.E., and Warnow, T., "Advances in phylogeny reconstruction from gene order and content data," in Molecular Evolution: Producing the Biochemical Data, Part B, E.A. Zimmer and E.H. Roalson, eds., Vol. 395 of Methods in Enzymology, Elsevier (2005), 673-700. PS PDF
  • Moret, B.M.E., Tang, J., and Warnow. T., "Reconstructing phylogenies from gene-content and gene-order data," in Mathematics of Evolution and Phylogeny, O. Gascuel, ed., Oxford Univ. Press (2005), 321-352. PS PDF
  • Moret, B.M.E., "Computational challenges from the Tree of Life," Proc. 7th Workshop on Algorithm Engineering & Experiments ALENEX'05, 3-16, SIAM Press (2005). PS PDF
  • Swenson, K.M., Marron, M., Earnest-DeYoung, J.V., and Moret, B.M.E., "Approximating the true evolutionary distance between two genomes," Proc. 7th Workshop on Algorithm Engineering & Experiments ALENEX'05, 121-129, SIAM Press (2005). PS PDF
  • Swenson, K.M., Pattengale, N.D., and Moret, B.M.E., "A framework for orthology assignment from gene rearrangement data," Proc. 3rd RECOMB Workshop on Comparative Genomics RECOMBCG'05, Dublin (Ireland). Lecture Notes in Computer Science 3678, 153-166, Springer Verlag (2005). PS PDF
  • Tang, J., and Moret, B.M.E., "Linear programming for phylogenetic reconstruction based on gene rearrangements," Proc. 16th Symp. on Combinatorial Pattern Matching CPM'05, Jeju Island (Korea), in Lecture Notes in Computer Science 3537, 406-416, Springer Verlag (2005). PS PDF
  • Yan, M., and Bader, D.A., "High-performance algorithms for phylogeny reconstruction with maximum parsimony," in Handbook of Computational Molecular Biology, S. Aluru, ed., Chapman and Hall, Chap. 22, 1-19, 2005.

2004

  • Bader, D.A., "Computational biology and high-performance computing," Commun. ACM 47, 11 (2004), 35-40.
  • Bader, D.A., "An improved, randomized algorithm for parallel selection with an experimental study," J. Parallel and Distributed Computing 64, 9 (2004), 1051-1059.
  • Bader, D.A., and Cong, G., "A fast, parallel spanning tree algorithm for symmetric multiprocessors (SMPs)," Proc. 18th IEEE Int'l Parallel and Distributed Processing Symp. IPDPS'04, IEEE Press (2004), 10pp.
  • Bader, D.A., and Cong, G., "Fast shared-memory algorithms for computing the minimum spanning forest of sparse graphs," Proc. 18th IEEE Int'l Parallel and Distributed Processing Symp. IPDPS'04, IEEE Press (2004), 10pp.
  • Bader, D.A., Hart, W.E., and Phillips, C.A., "Parallel algorithm design for branch-and-bound," in Tutorials on Emerging Methodologies and Applications in Operations Research, H.J. Greenberg, ed., Kluwer Academic Publ. (2004), 1-44.
  • Bader, D.A., and Madduri, K., "A parallel state assignment algorithm for finite state machines," Proc. IEEE Conf. on High-Performance Computing (HiPC'04) Bangalore (2004), Lecture Notes in Computer Science 3296, 297-308, Springer Verlag.
  • Berger-Wolf, T.Y., "Online consensus of phylogenetic trees," Proc. 4th Workshop on Algorithms in Bioinformatics WABI'04, Bergen (2004), Lecture Notes in Computer Science 3240, 350-361, Springer Verlag. TR-CS-2003-34
  • Cong, G., and Bader, D.A., "Lock-free parallel algorithms: An experimental study," Proc. IEEE Conf. on High-Performance Computing (HiPC'04) Bangalore (2004), Lecture Notes in Computer Science 3296, 516-527, Springer Verlag.
  • Cong, G., and Bader, D.A., "The Euler tour technique and parallel rooted spanning trees," Proc. 33rd Conf. on Parallel Processing ICPP'04, Montreal (2004), 448-457.
  • Earnest-DeYoung, J.V., Lerat, E., and Moret, B.M.E., "Reversing gene erosion: Reconstructing ancestral bacterial genomes from gene-content and order data," Proc. 4th Workshop on Algorithms in Bioinformatics WABI'04, Bergen (2004), Lecture Notes in Computer Science 3240, 1-13, Springer Verlag. PS PDF
  • Marron, M., Swenson, K.M., and Moret, B.M.E., "Genomic distances under deletions and insertions," Theoretical Computer Science 325, 3 (2004), 347-360 (special issue devoted to the best papers from COCOON'03). PS PDF
  • Moret, B.M.E., Nakhleh, L., Warnow, T., Linder, C.R., Tholse, A., Padolina, A., Sun, J., and Timme, R., "Phylogenetic networks: modeling, reconstructibility, and accuracy," IEEE/ACM Trans. on Computational Biology and Bioinformatics 1, 1 (2004), 13-23. PS PDF
  • Roshan, U., Moret, B.M.E., Warnow, T., and Williams, T.L., "Performance of supertree methods on various dataset decompositions," in Phylogenetic Supertrees: Combining information to reveal the Tree of Life, O.R.P. Bininda-Edmonds, ed., Kluwer Acad. Publ., Dordrecht, 2004, 301-328. PS PDF
  • Roshan, U., Moret, B.M.E., Williams, T.L., and Warnow, T.. "Rec-I-DCM3: A fast algorithmic technique for reconstructing large phylogenetic trees," Proc. 3rd IEEE Computational Systems Bioinformatics Conf. CSB 2004, 98-109, IEEE Press (2004). PS PDF
  • Snir, M., and Bader, D.A., "A framework for measuring supercomputer productivity," Int'l J. of High-Performance Comput. Applic. 18, 4 (2004), 417-432. PDF
  • Su, M.F., El-Kady, I., Bader, D.A., and Lin, S.-Y., "A novel FDTD application featuring OpenMP-MPI hybrid parallelization," Proc. 33rd Conf. on Parallel Processing ICPP'04, Montreal (2004), 373-379.
  • Tang, J., Moret, B.M.E., Cui, L., and dePamphilis, C.W., "Phylogenetic reconstruction from arbitrary gene-order data" Proc. 4th IEEE Conf. on Bioinformatics and Bioengineering BIBE'04, 592-599, IEEE Press (2004). PS PDF

2003

  • Marron, M., Swenson, K.M., and Moret, B.M.E., "Genomic distances under deletions and insertions," Proc. 9th Combinatorics and Computing Conf. COCOON'03, in Lecture Notes in Computer Science 2697, 2003, 537-547. PS PDF
  • Nakhleh, L., Sun, J., Warnow, T., Linder, R., Moret, B.M.E., and Tholse, A., "Towards the development of computational tools for evaluating phylogenetic network reconstruction methods," Proc. 8th Pacific Symp. on Biocomputing PSB'03, Hawaii, World Scientific Pub. (2003), 315-326. PS PDF
  • St. John, K., Warnow, T., Moret, B.M.E., and Vawter, L., "Performance study of phylogenetic methods: (unweighted) quartet methods and neighbor-joining," J. Algorithms 48, 1 (2003), 173-193 (special issue on best papers from SODA'01). PS PDF
  • Tang, J., and Moret, B.M.E., "Scaling up accurate phylogenetic reconstruction from gene-order data," Proc. 11th Conf. on Intelligent Systems for Molecular Biology ISMB'03, in Bioinformatics 19 (Suppl. 1) (2003), i305-i312. PS PDF
  • Tang, J., and Moret, B.M.E., "Phylogenetic reconstruction from gene rearrangement data with unequal gene contents," Proc. 8th Workshop on Algorithms and Data Structures WADS'03, in Lecture Notes in Computer Science 2748, 2003, 37-46. PS PDF
  • Williams, T., and Moret, B.M.E., "An investigation of phylogenetic likelihood methods," Proc. 3rd IEEE Symp. on Bioinformatics and Bioengineering BIBE'03, IEEE Press (2003), 79-86. PS PDF

2002

  • Bader, D.A., Moret, B.M.E., and Sanders, P., "Algorithm engineering for parallel computation," Lecture Notes in Computer Science 2547, 2002, 1-23. PS PDF
  • Bader, D.A., Sreshta, S., and Weisse-Bernstein, N.R., "Evaluating arithmetic expressions using tree contraction: A fast and scalable parallel implementation for symmetric multiprocessors (SMPs)," Proc. 9th IEEE Conf. High-Performance Computing (HiPC'02), Bangalore (India), Lecture Notes in Computer Science, 2552, 63-75, Springer Verlag, 2002. PS PDF
  • Moret, B.M.E., "Towards a discipline of experimental algorithmics," in Data Structures, Near Neighbor Searches, and Methodology: Fifth and Sixth DIMACS Implementation Challenges, M.H. Goldwasser, D.S. Johnson, and C.C. McGeoch, eds, DIMACS Monographs 59, 197-213, American Mathematical Society, Providence, 2002. PS PDF
  • Moret, B.M.E., Bader, D.A., and Warnow, T., "High-performance algorithm engineering for computational phylogenetics,'' J. Supercomputing 22 (2002), 99-111 (special issue on best papers from ICCS'01). PS PDF
  • Moret, B.M.E., Roshan, U., and Warnow, T., "Sequence length requirements for phylogenetic methods," Proc. 2nd Workshop on Algorithms in Bioinformatics (WABI'02), Rome (2002), Lecture Notes in Computer Science 2452, 343-356, Springer Verlag. PS PDF
  • Moret, B.M.E., Siepel, A.C., Tang, J., and Liu, T., "Inversion medians outperform breakpoint medians in phylogeny reconstruction from gene-order data," Proc. 2nd Workshop on Algorithms in Bioinformatics (WABI'02), Rome (2002), Lecture Notes in Computer Science 2452, 521-536, Springer Verlag. PS PDF
  • Moret, B.M.E., Tang, J., Wang, L.S., and Warnow, T., "Steps toward accurate reconstruction of phylogenies from gene-order data'' (invited, special issue on computational biology), J. Comput. Syst. Sci. 65, 3 (2002), 508-525. PS PDF
  • Moret, B.M.E., Wang, L.-S., and Warnow, T., "Towards new software for computational phylogenetics," IEEE Computer 35, 7 (July 2002), special issue on Bioinformatics, 55-64. PS PDF
  • Moret, B.M.E., and Warnow, T., "Reconstructing optimal phylogenetic trees: A challenge in experimental algorithmics," Lecture Notes in Computer Science 2547, 2002, 163-180. PS PDF
  • Nakhleh, L., Moret, B.M.E., Roshan, U., St. John, K., Sun, J., and Warnow, T., "The accuracy of fast phylogenetic methods for large datasets," Proc. 7th Pacific Symp. on Biocomputing PSB 2002, Hawaii, World Scientific Pub. (2002), 211-222. PS PDF
  • Sun, Y., Lin, X., Pan, Y., Lau, R.W.H., Bader, D.A., and Chang, P.Y.S., "Generalized block shift network for clusters," IEEE Trans. Circuits and Systems I 49, 4 (2002), 543-546. PS PDF
  • Wang, L.S., Jansen, R.K., Moret, B.M.E., Raubeson, L., and Warnow, T., "Fast phylogenetic methods for the analysis of genome rearrangement data: an empirical study," Proc. 7th Pacific Symp. on Biocomputing PSB 2002, Hawaii, World Scientific Pub. (2002), 524-535. PS PDF

2001

  • Bader, D.A., Ilendula, A.K., Moret, B.M.E., and Weisse-Bernstein, N.R., "Using PRAM algorithms on a uniform-memory-access shared-memory architecture" Proc. 5th Workshop on Algorithm Engineering (WAE 01), Aarhus (2001), Lecture Notes in Computer Science 2141, 129-144, Springer Verlag. PS PDF
  • Bader, D.A., Moret, B.M.E., and Vawter, L., "Industrial applications of high-performance computing for phylogeny reconstruction," Proc. SPIE Conf. on Commercial Appls. for High-Perf. Comput. ITComm 2001, Denver (2001), 159-168. PS PDF
  • Bader, D.A., Moret, B.M.E., and Yan, M., "A linear-time algorithm for computing inversion distances between signed permutations with an experimental study,'' J. Comput. Biol. 8, 5 (2001), 483-491. PS (2MB) PDF
  • Bader, D.A., Moret, B.M.E., and Yan, M., "A linear-time algorithm for computing inversion distances between signed permutations with an experimental study,'' Proc. 7th Workshop on Algorithms and Data Structures WADS'01, Providence (2001), Lecture Notes in Computer Science 2125, 365-376, Springer Verlag. PS PDF
  • Bader, D.A, and Pennington, R., "Cluster computing: applications," The International Journal of High Performance Computing 15, 2 (2001), 181-185. PS PDF
  • Moret, B.M.E., Bader, D.A., and Warnow, T., "High-performance algorithmic engineering for computational phylogenetics,'' Proc. 2001 Int'l Conf. Computational Science ICCS'01, San Francisco (2001), Lecture Notes in Computer Science 2074, 1012-1021, Springer Verlag. PS PDF
  • Moret, B.M.E., and Shapiro, H.D., "Algorithms and experiments: the new (and the old) methodology," J. Univ. Computer Sci. 7, 5 (2001), 434-446. PS
  • Moret, B.M.E., Wang, L., Warnow, T., and Wyman, S.K., "New approaches to phylogeny reconstruction from gene order data,'' 9th Conf. on Intelligent Systems for Molecular Biology (ISMB 2001), Copenhagen, in Bioinformatics 17 (2001), S165-S173; chosen as one of the 5 best papers at the conference. PS PDF
  • Moret, B.M.E., Wyman, S., Bader, D.A., Warnow, T., and Yan, M., "A new implementation and detailed study of breakpoint analysis," Proc. 6th Pacific Symp. on Biocomputing PSB 2001, Hawaii, World Scientific Pub. (2001), 583-594. PS PDF
  • St. John, K., Warnow, T., Moret, B.M.E., and Vawter, L., "Performance study of phylogenetic methods: (unweighted) quartet methods and neighbor-joining," Proc. 12th Ann. Symp. Discrete Algs. SODA 01, Washington DC, SIAM Press (2001), 196-205. PS
  • Siepel, A., and Moret. B.M.E., "Finding an optimal inversion median: experimental results," Proc. 1st Workshop on Algorithms in Bioinformatics WABI 01, Aarhus (2001), Lecture Notes in Computer Science 2149, 189-203, Springer Verlag. PS PDF
  • Warnow, T., Moret, B.M.E., and St. John, K., "Absolute convergence: true trees from short sequences," Proc. 12th Ann. Symp. Discrete Algs. SODA 01, Washington DC, SIAM Press (2001), 186-195. PS

2000

  • Bader, D.A., "High-performance algorithms and applications for SMP clusters," Proc. NASA High-Performance Computing and Communications Computational Aerosciences Workshop (CAS 2000). PS PDF
  • Bader, D.A., "An improved randomized selection algorithm with an experimental study," Proc. 2nd Workshop on Algorithm Engineering and Experiments ALENEX'00, San Francisco (2000), 115-130. PS PDF
  • Cosner, M.E., Jansen, R.K., Moret, B.M.E., Raubeson, L.A., Wang, L.S., Warnow, T., and Wyman, S., "An empirical comparison of phylogenetic methods on chloroplast gene order data in Campanulaceae," in Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment, and the Evolution of Gene Families, D. Sankoff and J. Nadeau, eds., Kluwer Academic Publishers, Dordrecht, 2000, 99-121. PS
  • Cosner, M.E., Jansen, R.K., Moret, B.M.E., Raubeson, L.A., Wang, L.S., Warnow, T., and Wyman, S., "A new fast heuristic for computing the breakpoint phylogeny and experimental phylogenetic analyses of real and synthetic data," Proc. 8th Conf. on Intelligent Systems for Molecular Biology (ISMB 2000), San Diego (2000), 104-115. PS
  • Kalluri, S.N.V., JáJá, J., Bader, D.A., Zhang, Z., Townshend, J.R.G., and Fallah-Adl, H., "High performance computing algorithms for land cover dynamics using remote sensing data," International Journal of Remote Sensing 21, 6 (2000), 1513-1536. PDF
  • Zhang, Z., JáJá, J., Bader, D.A., Kalluri, S.N.V., Song, H., El Saleous, N., Vermote, E., and Townshend, J.R.G., "Kronos: A Software System for the Processing and Retrieval of Large Scale AVHRR Data Sets," Photogrammetric Engineering & Remote Sensing 66, 9 (2000), 1073-1082. PS (large, 28MB) PDF

Edited Volumes and Proceedings

  • D.A. Bader, A.Y. Zomaya, et al., eds.
    Handbook of Innovative Computing, Springer-Verlag USA, to appear 2005.
  • D.A. Bader and S. Aluru, guest eds.
    in Concurrency and Computation: Practice and Experience, John Wiley & Sons, to appear 2005.
  • D.A. Bader and S. Aluru, guest eds.
    Special Issue on High-Performance Computational Biology, in J. Parallel and Distributed Computing 63, 7-8, 2003 (102pp)
  • D.A. Bader and S. Aluru, eds.
    Proc. 2nd Workshop on High-Performance Computational Biology HiCOMB 2003, IEEE Computer Society Press, 2003 (99 pp.)
  • D.A. Bader and S. Aluru, eds,
    Proc. 1st Workshop on High-Performance Computational Biology HiCOMB 2002, 2002 (85 pp.)
  • Fleischer, R., Moret, B.M.E., and Schmidt, E.M., eds.
    Experimental Algorithmics, LNCS 2547, Springer Verlag, 2002 (296pp.)
  • Gascuel, O., and Moret, B.M.E., eds.
    Proc. 1st Workshop on Algorithms in Bioinformatics WABI'01, LNCS 2149, Springer Verlag, 2001 (310pp.)
  • Moret, B.M.E., guest ed.
    10th ACM-SIAM Symp. on Discrete Algorithms SODA'99 in J. of Algorithms 38, 1, 2001 (333pp.)
  • Goldberg, A., and Moret, B.M.E., eds.
    Proc. 2nd Workshop on Algorithm Engineering and Experiments ALENEX'00, 2000 (300pp.)

Publications about our Work



Last updated April 15, 2005.