
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 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.
Accepted to Appear

Wang, L.S., Jansen, R.K., Moret, B.M.E., Raubeson, L.A., and Warnow, T.,
"Distancebased 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), 19211923.

Pattengale, N.D., and Moret, B.M.E., "A sublineartime randomized
approximation scheme for the RobinsonFoulds metric,"
Proc. 10th Int'l Conf. on Research in Comput. Molecular
Biol. RECOMB'06, Venice (2006), in
Lecture Notes
in Computer Science 3909, 221230.
PS
PDF

Williams, T.L., Bader, D.A., Yan, M., and Moret, B.M.E.,
"Highperformance phylogeny reconstruction under maximum parsimony,"
in Parallel Computing for Bioinformatics and Computational Biology,
A.Y. Zomaya, ed., John Wiley & Sons, Chap. 16, pp. 369394 (2006).
PS
PDF
2005

Bader, D.A.,
"Highperformance algorithm engineering for largescale graph problems
and computational biology,"
Proc. 4th Workshop on Efficient and Experimental Algorithms (WEA'05),
Santorini (2005),
Lecture Notes in Computer Science 3503,
1621, 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),
547556, 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,
6373, 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), 673700.
PS
PDF

Moret, B.M.E., Tang, J., and Warnow. T.,
"Reconstructing phylogenies from genecontent and geneorder data,"
in Mathematics of Evolution and
Phylogeny, O. Gascuel, ed., Oxford Univ. Press (2005), 321352.
PS
PDF

Moret, B.M.E.,
"Computational challenges from the Tree of Life,"
Proc. 7th Workshop on Algorithm Engineering & Experiments
ALENEX'05,
316, SIAM Press (2005).
PS
PDF

Swenson, K.M., Marron, M., EarnestDeYoung, J.V., and Moret, B.M.E.,
"Approximating the true evolutionary distance between two genomes,"
Proc. 7th Workshop on Algorithm Engineering & Experiments
ALENEX'05,
121129, 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,
153166, 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,
406416, Springer Verlag (2005).
PS
PDF

Yan, M., and Bader, D.A.,
"Highperformance algorithms for phylogeny reconstruction with maximum
parsimony," in Handbook of Computational Molecular Biology,
S. Aluru, ed., Chapman and Hall, Chap. 22, 119, 2005.
2004

Bader, D.A.,
"Computational biology and highperformance computing,"
Commun. ACM 47, 11 (2004), 3540.

Bader, D.A.,
"An improved, randomized algorithm for parallel selection with an
experimental study,"
J. Parallel and Distributed Computing 64, 9 (2004),
10511059.

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 sharedmemory 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 branchandbound,"
in Tutorials on Emerging Methodologies and Applications in Operations
Research, H.J. Greenberg, ed., Kluwer Academic Publ. (2004), 144.

Bader, D.A., and Madduri, K.,
"A parallel state assignment algorithm for finite state machines,"
Proc. IEEE Conf. on HighPerformance Computing (HiPC'04)
Bangalore (2004),
Lecture Notes in Computer Science 3296,
297308, Springer Verlag.

BergerWolf, T.Y.,
"Online consensus of phylogenetic trees,"
Proc. 4th Workshop on Algorithms in Bioinformatics
WABI'04,
Bergen (2004),
Lecture Notes in Computer
Science 3240,
350361, Springer Verlag.
TRCS200334

Cong, G., and Bader, D.A.,
"Lockfree parallel algorithms: An experimental study,"
Proc. IEEE Conf. on HighPerformance Computing (HiPC'04)
Bangalore (2004),
Lecture Notes in Computer Science 3296,
516527, 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),
448457.

EarnestDeYoung, J.V., Lerat, E., and Moret, B.M.E.,
"Reversing gene erosion: Reconstructing ancestral bacterial genomes from
genecontent and order data,"
Proc. 4th Workshop on Algorithms in Bioinformatics
WABI'04,
Bergen (2004),
Lecture Notes in Computer
Science 3240,
113, 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), 347360 (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), 1323.
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. BinindaEdmonds, ed., Kluwer Acad. Publ., Dordrecht, 2004, 301328.
PS
PDF

Roshan, U., Moret, B.M.E., Williams, T.L., and Warnow, T..
"RecIDCM3: A fast algorithmic technique for reconstructing large
phylogenetic trees,"
Proc. 3rd IEEE Computational Systems Bioinformatics Conf.
CSB 2004, 98109, IEEE Press (2004).
PS
PDF

Snir, M., and Bader, D.A., "A framework for measuring supercomputer
productivity,"
Int'l
J. of HighPerformance Comput. Applic. 18, 4
(2004), 417432.
PDF

Su, M.F., ElKady, I., Bader, D.A., and Lin, S.Y.,
"A novel FDTD application featuring OpenMPMPI hybrid parallelization,"
Proc. 33rd Conf. on Parallel Processing ICPP'04, Montreal (2004),
373379.

Tang, J., Moret, B.M.E., Cui, L., and dePamphilis, C.W.,
"Phylogenetic reconstruction from arbitrary geneorder data"
Proc. 4th IEEE Conf. on Bioinformatics and Bioengineering
BIBE'04, 592599, 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, 537547.
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), 315326.
PS
PDF

St. John, K., Warnow, T., Moret, B.M.E., and Vawter, L.,
"Performance study of phylogenetic methods: (unweighted) quartet methods
and neighborjoining,"
J. Algorithms 48, 1
(2003), 173193 (special issue on best papers from SODA'01).
PS
PDF

Tang, J., and Moret, B.M.E.,
"Scaling up accurate phylogenetic reconstruction from geneorder data,"
Proc. 11th Conf. on Intelligent Systems for Molecular Biology
ISMB'03,
in Bioinformatics 19 (Suppl. 1) (2003), i305i312.
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, 3746.
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), 7986.
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, 123.
PS
PDF

Bader, D.A., Sreshta, S., and WeisseBernstein, N.R.,
"Evaluating arithmetic expressions using tree contraction: A
fast and scalable parallel implementation for symmetric
multiprocessors (SMPs),"
Proc. 9th IEEE Conf. HighPerformance Computing
(HiPC'02), Bangalore (India),
Lecture Notes in Computer Science, 2552, 6375, 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, 197213,
American Mathematical Society, Providence, 2002.
PS
PDF

Moret, B.M.E., Bader, D.A., and Warnow, T.,
"Highperformance algorithm engineering for computational phylogenetics,''
J. Supercomputing 22 (2002), 99111
(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, 343356, 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 geneorder data,"
Proc. 2nd Workshop on Algorithms in Bioinformatics
(WABI'02),
Rome (2002),
Lecture Notes in Computer
Science 2452, 521536, Springer Verlag.
PS
PDF

Moret, B.M.E., Tang, J., Wang, L.S., and Warnow, T.,
"Steps toward accurate reconstruction of phylogenies from geneorder data''
(invited, special issue on computational biology),
J. Comput. Syst. Sci. 65, 3 (2002), 508525.
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, 5564.
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, 163180.
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), 211222.
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), 543546.
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), 524535.
PS
PDF
2001

Bader, D.A., Ilendula, A.K., Moret, B.M.E., and WeisseBernstein, N.R.,
"Using PRAM algorithms on a uniformmemoryaccess sharedmemory architecture"
Proc. 5th Workshop on Algorithm Engineering (WAE 01), Aarhus (2001),
Lecture Notes in Computer Science 2141, 129144, Springer Verlag.
PS
PDF

Bader, D.A., Moret, B.M.E., and Vawter, L.,
"Industrial applications of highperformance computing for phylogeny reconstruction,"
Proc. SPIE Conf. on Commercial Appls. for HighPerf. Comput. ITComm 2001, Denver (2001), 159168.
PS
PDF

Bader, D.A., Moret, B.M.E., and Yan, M.,
"A lineartime algorithm for computing inversion distances between signed
permutations with an experimental study,''
J. Comput. Biol. 8, 5 (2001), 483491.
PS (2MB)
PDF

Bader, D.A., Moret, B.M.E., and Yan, M.,
"A lineartime 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, 365376,
Springer Verlag.
PS
PDF

Bader, D.A, and Pennington, R.,
"Cluster computing: applications,"
The International Journal of High
Performance Computing 15, 2 (2001), 181185.
PS
PDF

Moret, B.M.E., Bader, D.A., and Warnow, T.,
"Highperformance algorithmic engineering for computational phylogenetics,''
Proc. 2001 Int'l Conf. Computational Science ICCS'01,
San Francisco (2001),
Lecture Notes in Computer Science 2074, 10121021,
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), 434446.
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), S165S173; 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), 583594.
PS
PDF

St. John, K., Warnow, T., Moret, B.M.E., and Vawter, L.,
"Performance study of phylogenetic methods: (unweighted) quartet methods
and neighborjoining,"
Proc. 12th Ann. Symp. Discrete Algs.
SODA 01, Washington DC,
SIAM Press (2001), 196205.
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, 189203,
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), 186195.
PS
2000

Bader, D.A.,
"Highperformance algorithms and applications for SMP clusters,"
Proc. NASA HighPerformance 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), 115130.
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, 99121.
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), 104115.
PS

Kalluri, S.N.V., JáJá, J., Bader, D.A., Zhang, Z.,
Townshend, J.R.G., and FallahAdl, H.,
"High performance computing algorithms for land cover dynamics
using remote sensing data,"
International Journal of Remote Sensing 21,
6 (2000), 15131536.
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), 10731082.
PS (large, 28MB)
PDF
Edited Volumes and Proceedings

D.A. Bader, A.Y. Zomaya, et al., eds.
Handbook of Innovative Computing,
SpringerVerlag 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 HighPerformance Computational Biology,
in J.
Parallel and Distributed Computing 63, 78, 2003 (102pp)

D.A. Bader and S. Aluru, eds.
Proc. 2nd Workshop on HighPerformance Computational Biology
HiCOMB 2003,
IEEE Computer Society Press, 2003 (99 pp.)

D.A. Bader and S. Aluru, eds,
Proc. 1st Workshop on HighPerformance 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 ACMSIAM 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.
