? Mishler, B. D. 20055 The logic of the data matrix in phylogenetic analysis 57 - 70" Parsimony, Phylogeny, and Genomics
Albert, V. A. Oxford Oxford University Press;D? B Milch, B.
Marthi, B.
Sontag, D.
Russell, S.
Ong, D. L.
Kolobov, A. 2005? Approximate inference for infinite contingent Bayesian networksM Proc. Tenth International Workshop on Artificial Intelligence and Statistics
BarbadosB http://www.cs.berkeley.edu/~russell/papers/aistats05-inference.pdf D? ! Milch, B.
Marthi, B.
Russell, S. 2004. BLOG: Relational modeling with unknown objects9 Proc. ICML-04 Workshop on Statistical Relational Learning
Banff, Canada9 http://www.cs.berkeley.edu/~russell/papers/srl04-blog.pdf, ?
Bader, D. A. 2004S An improved, randomized algorithm for parallel selection with an experimental study 1051-1059- Journal of Parallel and Distributed Computing 64 95 www.eece.unm.edu/~dbader/papers/ALENEX00-select.pdf 4 www.eece.unm.edu/~dbader/papers/ALENEX00-select.pdf s? Bader, D. A. 20045 Computational biology and high-performance computing
34-41: Communications of the ACM, Special Issue on Bioinformatics 47 11 Stewart, C. http://portal.acm.org/citation.cfm?id=1029496.1029523&coll=ACM&dl=ACM&idx=1029496&part=periodical&WantType=periodical&title=Communications%20of%20the%20ACM&CFID=30617240&CFTOKEN=22560579 D ? Cong, G.
Bader, D. A. 2004: The Euler tour technique and parallel rooted spanning tree 448-457; 33rd International Conference on Parallel Processing (ICPP) Montreal, Canada= http://www.eece.unm.edu/~dbader/papers/RootedSpanningTree.pdf= http://www.eece.unm.edu/~dbader/papers/RootedSpanningTree.pdf F?
Tang, J
Moret, B. M. E. 2004: Distance correction for large pairwise genomic distances,
Technical Report
TR-CS-2004-26 U. New Mexico B http://www.cs.unm.edu/colloq-bin/tech_reports.cgi?ID=TR-CS-2004-26 D? Berger-Wolf, T.Y. 2004E Properties of compatibility and consensus sets of phylogenetic trees
Technical Report
TR-CS-2004-24
U. New MexicoB http://www.cs.unm.edu/colloq-bin/tech_reports.cgi?ID=TR-CS-2004-24 D? = Nakhleh, L.
Clement, A.
Warnow, T.
Linder, C.R.
Moret, B.M.E. 2004* Quality measures for phylogenetic networks Technical Report
TR-CS-2004-06 U. New Mexico B http://www.cs.unm.edu/colloq-bin/tech_reports.cgi?ID=TR-CS-2004-06 +D? G Williams, T. L.
Berger-Wolf, T.Y.
Moret, B. M. E.
Roshan, U.
Warnow, T. 2004R The relationship between maximum parsimony scores and phylogenetic tree topologies Technical Report
TR-CS-2004-04
U. New MexicoB http://www.cs.unm.edu/colloq-bin/tech_reports.cgi?ID=TR-CS-2004-04 ? V " Moret, B. M. E.
Tang, J
Warnow, T. 2005@ Reconstructing phylogenies from gene-content and gene-order data 321-352& Mathematics of Evolution and Phylogeny 2005 O. Gascuel, Oxford Univ. Press< http://www.lirmm.fr/w3ifa/MAAS/IHP-BOOK/Math-Phylo-Book.html0 http://www.cs.unm.edu/~moret/poincare_survey.pdf D? Moret, B. M. E. 2005. Computational challenges from the Tree of LifeG Proc. 7th Workshop on Algorithm Engineering & Experiments (ALENEX '05) Vancouver
SIAM Press& http://www.siam.org/meetings/alenex05/ eD? Bader, D. A.
Cong, G. 2004X Fast shared memory algorithms for computing the minimum spanning forest of sparse graphsK Proc. 18th IEEE Int'l Parallel and Distributed Processing Symp. (IPDPS'04) Santa Fe, NM
IEEE Press7 www.ece.unm.edu/~dbader/papers/MST-IPDPS2004-BC04b.pdf 7 www.ece.unm.edu/~dbader/papers/MST-IPDPS2004-BC04b.pdf L F? Berger-Wolf, T.Y.
Warnow, T. 2004& Online consensus of phylogenetic trees
3240, 350-361< Proc. 4th Workshop on Algorithms in Bioinformatics (WABI'04) 3240 Kim, J.
Jonassen, I. Bergen, Norway Springer-Verlag TR-CS-2003-34 ' http://www.ii.uib.no/algo2004/wabi2004/" Lecture Notes in Computer Science Ο? 0 Earnest-DeYoung, J. V.
Lerat, E.
Moret, B. M. E. 2004c Reversing gene erosion: Reconstructing ancestral bacterial genomes from gene-content and order data 1-13< Proc. 4th Workshop on Algorithms in Bioinformatics (WABI'04) 3240 Bergen, Norway Springer-Verlag& compbio.unm.edu/~joeled/Ancestral.pdf ! Lecture Notes in Computer Science& compbio.unm.edu/~joeled/Ancestral.pdf ? & Marron, M.
Swenson, K.M.
Moret, B.M.E. 20040 Genomic distances under deletions and insertions 347-360 Theoretical Computer Science 325 3" www.cs.unm.edu/~moret/cocoon03.pdf" www.cs.unm.edu/~moret/cocoon03.pdf_? 5 Roshan, U.
Moret, B. M. E.
Warnow, T.
Williams, T. L. 2004B Performance of supertree methods on various dataset decompositions 301-328I Phylogenetic Supertrees: Combining information to reveal the Tree of Life Bininda-Edmonds, O. R. P. Dordrecht Kluwer Academic PublishersL http://www.cs.utexas.edu/users/usman/research/phylogenetics/book_chapter.pdf
Andreas DressL http://www.cs.utexas.edu/users/usman/research/phylogenetics/book_chapter.pdf +? 2 Tang, J
Moret, B. M. E.
Cui, L.
dePamphilis, C. W. 2004: Phylogenetic reconstruction from arbitrary gene-order data 592-599C Proc. 4th IEEE Conf. on Bioinformatics and Bioengineering (BIBE'04)
IEEE Press! www.cs.unm.edu/~moret/bibe04.pdf ! www.cs.unm.edu/~moret/bibe04.pdf JD? 5 Roshan, U.
Moret, B. M. E.
Williams, T. L.
Warnow, T. 2004N Rec-I-DCM3: A fast algorithmic technique for reconstructing phylogenetic trees@ Proc. IEEE Compter Society Bioinformatics Conference (CSB 2004) 98-109
IEEE Press' http://www.cs.rice.edu/~nakhleh/pdf.gif' http://www.cs.rice.edu/~nakhleh/pdf.gif I?" 2 St. John, K.
Warnow, T.
Moret, B. M. E.
Vawter, L. 2003\ Performance study of phylogenetic methods: (unweighted) quartet methods and neighbor-joining 173 - 193
J. Algorithms 48 1& http://www.cs.unm.edu/~moret/jalgs.pdf) Special issue on best papers from SODA'01& http://www.cs.unm.edu/~moret/jalgs.pdf://000230201100006 ISI Document Delivery No.: 941FQ 1439-6092 Org. Divers. Evol. ISI:000230201100006 Yale Univ, Dept Ecol & Evolutionary Biol, New Haven, CT 06521 USA.
Bell, CD, Yale Univ, Dept Ecol & Evolutionary Biol, New Haven, CT 06521 USA.
cbell3@xula.edu q ?% U Wang, L.-S.
Warnow, T. 2005- Distance-based genome rearrangement phylogeny in press) In Mathematics of Evolution and Phylogeny Gascuel, O. Oxford Oxford University Press' http://kim.bio.upenn.edu/~lisan/ihp.pdf' http://kim.bio.upenn.edu/~lisan/ihp.pdfF?* - Warnow, T.
Evans, S. N.
Ringe, D.
Nakhleh, L. 2005R A stochastic model of language evolution that incorporates homoplasy and borrowingI a special volume on Phylogenetic Methods and the Prehistory of Languages. Cambridge University Press> http://www.cs.rice.edu/~nakhleh/PAPERS/WarnowRevComplete.pdf > http://www.cs.rice.edu/~nakhleh/PAPERS/WarnowRevComplete.pdf Rƿ?+ ) Kelch, D. G.
Driskell, A.
Mishler, B. D. 2004W Inferring phylogeny using genomic characters: a case study using land plant plastomes 3-12# Molecular Systematics of Bryophytes 982 In B. Goffinet, V. Hollowell, and R. Magill (eds.) St. Louis Missouri Botanical Garden Press Monographs in Systematic Botany ://000230260800015 ISI Document Delivery No.: 942CP 0002-9122 Am. J. Bot. ISI:000230260800015- Yale Univ, Dept Ecol & Evolutionary Biol, New Haven, CT 06520 USA. Yale Univ, Peabody Museum Nat Hist, New Haven, CT 06520 USA. Univ Zurich, Inst Systemat Bot, CH-8008 Zurich, Switzerland.
Erika, JE, Yale Univ, Dept Ecol & Evolutionary Biol, POB 208105, New Haven, CT 06520 USA.
erika.edwards@yale.edu ?2 Bader, D. A.
Madduri, K. 2004@ A parallel state assignment algorithm for finite state machines 297-308K The 11th International Conference on High Performance Computing (HiPC 2004) 3296 Bangalore, India Springer-Verlag: http://www.ece.unm.edu/~dbader/papers/parjedi-HiPC2004.pdf! Lecture Notes in Computer Science Bougé, L.
Prasanna, V.K. : http://www.ece.unm.edu/~dbader/papers/parjedi-HiPC2004.pdf Ɵ?3 Cong, G.
Bader, D. A. 20045 Lock-free parallel algorithms: an experimental study 516-527K The 11th International Conference on High Performance Computing (HiPC 2004) 3296 Bougé, L.
Prasanna, V.K. Bangalore, India Springer-Verlag LNCS < http://www.eece.unm.edu/~dbader/papers/lockfree-HiPC2004.pdf! Lecture Notes in Computer Science< http://www.eece.unm.edu/~dbader/papers/lockfree-HiPC2004.pdfs?4 ( Bader, D. A.
Hart, W. E.
Phillips, C. A. 2004. Parallel algorithm design for branch and bound 1-44K Tutorials on Emerging Methodologies and Applications in Operations Research Greenberg, H. J. Kluwer Academic Press? http://www.eece.unm.edu/~dbader/papers/ParallelBranchBound.pdf > http://www.eece.unm.edu/~dbader/papers/ParallelBranchBound.pdf ://000230302500010 ISI Document Delivery No.: 942SL 1063-5157 Syst. Biol. ISI:0002303025000100 Univ Texas, Sect Integrat Biol, Austin, TX 78712 USA. Univ Texas, Ctr Computat Biol & Bioinformat, Austin, TX 78712 USA. CUNY Herbert H Lehman Coll, Dept Math & Comp Sci, Bronx, NY 10468 USA.
Hillis, DM, Univ Texas, Sect Integrat Biol, Austin, TX 78712 USA.
dhillis@mail.utexas.edu stjohn@lehman.cuny.edu 3|?T Tang, J. J.
Moret, B. M. E. 2005O Linear programming for phylogenetic reconstruction based on gene rearrangements 406-416+ Combinatorial Pattern Matching, Proceedings 3537= GENOME REARRANGEMENT; ORDER DATA; INSERTIONS/DELETIONS; TREES Phylogenetic reconstruction from gene rearrangements has attracted increasing attention from biologists and computer scientists over the last few years. Methods used in reconstruction include distance-based methods, parsimony methods using sequence-based encodings, and direct optimization. The latter, pioneered by Sankoff and extended by us with the software suite GRAPPA, is the most accurate approach, but has been limited to small genomes because the running time of its scoring algorithm grows exponentially with the number of genes in the genome. We report here on a new method to compute a tight lower bound on the score of a given tree, using a set of linear constraints generated through selective applications of the triangle inequality (in the spirit of GESTALT). Our method generates an integer linear program with a carefully limited number of constraints, rapidly solves its relaxed version, and uses the result to provide a tight lower bound. Since this bound is very close to the optimal tree score, it can be used directly as a selection criterion, thereby enabling us to bypass entirely the expensive scoring procedure. We have implemented this method within our GRAPPA software and run several series of experiments on both biological and simulated datasets to assess its accuracy. Our results show that using the bound as a selection criterion yields excellent trees, with error rates below 5% up to very large evolutionary distances, consistently beating the baseline Neighbor-Joining. Our new method enables us to extend the range of applicability of the direct optimization method to chromosomes of size comparable to those of bacteria, as well as to datasets with complex combinations of evolutionary events. ://000230459400035 ! Lecture Notes in Computer Science( ISI Document Delivery No.: BCO99
Article 0302-9743 ISI:000230459400035 Univ S Carolina, Dept Comp Sci & Engn, Columbia, SC 29208 USA. Univ New Mexico, Dept Comp Sci, Albuquerque, NM 87131 USA.
Tang, JJ, Univ S Carolina, Dept Comp Sci & Engn, Columbia, SC 29208 USA.
jtang@cse.sc.edu +D?= E Swenson, K.M., Marron, M., Earnest-DeYoung, J.V., and Moret, B.M.E., 2005A Approximating the true evolutionary distance between two genomes
E Proc. 7th Workshop on Algorithm Engineering & Experiments (ALENEX'05) Vancouver SIAM Press.& http://www.siam.org/meetings/alenex05/ S://000229973800007 ) ISI Document Delivery No.: 938BB
Suppl. S 0094-8373 Paleobiology ISI:000229973800007 Yale Univ, Dept Ecol & Evolutionary Biol, New Haven, CT 06520 USA. Yale Univ, Peabody Museum Natl Hist, New Haven, CT 06520 USA.
Donoghue, MJ, Yale Univ, Dept Ecol & Evolutionary Biol, New Haven, CT 06520 USA.
michael.donoghue@yale.edu T ?A [ Moret, B.M.E.
Nakhleh, L.
Warnow, T.
Linder, C.R.
Tholse, A.
Padolina, A.
Sun, J.
Timme, R. 2004A Phylogenetic networks: modeling, reconstructibility, and accuracy 13-239 IEEE/ACM Trans. on Computational Biology and Biocomputing 1 1' http://www.cs.unm.edu/~moret/tcbb04.pdf' http://www.cs.unm.edu/~moret/tcbb04.pdftg T|?U Moret, B. M. E.
Warnow, T. 2005E Advances in phylogeny reconstruction from gene order and content data 673 - 700; Molecular Evolution: Producing the Biochemical Data, Part B 395 MAXIMUM-LIKELIHOOD; COMPUTATIONAL PHYLOGENETICS; 1.5-APPROXIMATION
ALGORITHM; GENOME REARRANGEMENT; RECONCILED TREES; DNA-SEQUENCES;
SPECIES TREES; EVOLUTION; DISTANCE; TOOL Genomes can be viewed in terms of their gene content and the order in which the genes appear along each chromosome. Evolutionary events that affect the gene order or content are "rare genomic events" (rarer than events that affect the composition of the nucleotide sequences) and have been advocated by systernatists for inferring deep evolutionary histories. This chapter surveys recent developments in the reconstruction of phylogenies from gene order and content, focusing on their performance under various stochastic models of evolution. Because such methods are quite restricted in the type of data they can analyze, we also present research aimed at handling the full range of whole-genome data. ://000230001100035 Methods in Enzymology' ISI Document Delivery No.: BCM61
Review 0076-6879 ISI:000230001100035 Univ New Mexico, Dept Comp Sci, Albuquerque, NM 87131 USA. Univ Texas, Dept Comp Sci, Austin, TX 78712 USA.
Moret, BME, Univ New Mexico, Dept Comp Sci, Albuquerque, }?C P Snir, M.
Bader, D. A. 20044 A framework for measuring supercomputer productivity 417-432+ Int'l J. of High-Performance Comput. Applic 18 4A http://www-faculty.cs.uiuc.edu/~snir/PDF/productivity%20final.pdfA http://www-faculty.cs.uiuc.edu/~snir/PDF/productivity%20final.pdfG?H * Ganapathy, G.
Ramachandran, V.
Warnow, T. 2003* Better Hill-Climbing Seaches for Parsimony 245-258C Third International Workshop on Algorithms in Bioinformatics (WABI)
WABI 2003: Budapest, Hungary1 http://www.cs.utexas.edu/~gsgk/papers/bn-ver7.pdf1 http://www.cs.utexas.edu/~gsgk/papers/bn-ver7.pdf ?J ) Ganapathy, G.
Ramachandran, V.
Warnow, T. 2004A On Contract-and-Refine-Transformations Between Phylogenetic Trees 900-909M Proceedings of the Fifteenth ACM-SIAM Symposium on Discrete Algorithms (SODA)
SODA 2004: J. Ian Munro New Orleans, LA January 11-14, 2004/ http://www.cs.utexas.edu/~vlr/papers/soda04.pdf/ http://www.cs.utexas.edu/~vlr/papers/soda04.pdf VF?M Nakhleh, L.
Ringe, D.
Warnow, T. 2005r Perfect Phylogenetic Networks: A New Methodology for Reconstructing the Evolutionary History of Natural Languages.7 Language (Journal of the Linguistic Society of America)6 http://www.cs.rice.edu/~nakhleh/PAPERS/NWRlanguage.pdf6 http://www.cs.rice.edu/~nakhleh/PAPERS/NWRlanguage.pdf #?N Evans, S. N.
Warnow, T. 2005< Unidentifiable divergence times in rates-across-sites models 130-134A IEEE/ACM Transactions on Computational Biology and Bioinformatics 10 http://www.stat.berkeley.edu/users/evans/668.pdf0 http://www.stat.berkeley.edu/users/evans/668.pdf 2?O - Nakhleh, L.
Warnow, T.
Ringe, D.
Evans, S. N. 2005D A Comparison of Phylogenetic Reconstruction Methods on an IE Dataset in press, The Transactions of the Philological Society5 http://www.cs.rice.edu/~nakhleh/PAPERS/NWREpaper.pdf 4 http://www.cs.rice.edu/~nakhleh/PAPERS/NWREpaper.pdf {://000226721400391 ISI Document Delivery No.: 893LU 1540-7063 Integr. Comp. Biol. ISI:000226721400391K Univ Calif Berkeley, Berkeley, CA 94720 USA.
bmishler@socrates.Berkeley.edu
://000229279100003 ISI Document Delivery No.: 928NS 0737-4038 Mol. Biol. Evol. ISI:000229279100003r Univ Idaho, Dept Biol Sci, Moscow, ID 83843 USA. Univ Idaho, Program Bioinformat & Computat Biol, Moscow, ID 83843 USA. Univ Idaho, Dept Math, Moscow, ID 83843 USA. Florida State Univ, Sch Computat Sci, Tallahassee, FL 32306 USA. Florida State Univ, Dept Biol Sci, Tallahassee, FL 32306 USA.
Sullivan, J, Univ Idaho, Dept Biol Sci, Moscow, ID 83843 USA.
jacks@uidaho.edu ://000228805100005 ISI Document Delivery No.: 921ZP 1063-5157 Syst. Biol. ISI:000228805100005, Univ Connecticut, Dept Ecol & Evolut Biol, Storrs, CT 06269 USA. Florida State Univ, Sch Computat Sci & Informat Technol CSIT, Dirac Sci Lib 150F, Tallahassee, FL 32306 USA.
Lewis, PO, Univ Connecticut, Dept Ecol & Evolut Biol, 75 N Eagleville Rd,Unit 3043, Storrs, CT 06269 USA.
paul.lewis@uconn.edu , ://000228384100001 ISI Document Delivery No.: 916KP 1058-5893 Int. J. Plant Sci. ISI:000228384100001 Yale Univ, Dept Ecol & Evolutionary Biol, New Haven, CT 06520 USA.
Howarth, DG, Yale Univ, Dept Ecol & Evolutionary Biol, New Haven, CT 06520 USA.
dianella.howarth@yale.edu://000228259300005 ISI Document Delivery No.: 914WR 0362-2525 J. Morphol. ISI:000228259300005R Univ Calif Berkeley, ESPM, Div Insect Biol, Berkeley, CA 94720 USA. Cornell Univ, Dept Entomol, Ithaca, NY 14853 USA. Univ Arizona, Dept Entomol, Tucson, AZ 85721 USA. Fac Vet, Dept Biol Anim, Murcia 30071, Spain.
Will, KW, Univ Calif Berkeley, ESPM, Div Insect Biol, 201 Wellman Hall, Berkeley, CA 94720 USA.
kiplingw@nature.berkeley.edu ` ://000228126800009 ISI Document Delivery No.: 913CB 0002-9122 Am. J. Bot. ISI:000228126800009 Yale Univ, Dept Ecol & Evolutionary Biol, New Haven, CT 06520 USA.
Winkworth, RC, Yale Univ, Dept Ecol & Evolutionary Biol, POB 208106, New Haven, CT 06520 USA.
Richard.Winkworth@yale.edu ://000228126800017 ISI Document Delivery No.: 913CB 0002-9122 Am. J. Bot. ISI:000228126800017L Bowdoin Coll, Dept Biol, Brunswick, ME 04011 USA. Univ New Mexico, Dept Biol, Albuquerque, NM 87131 USA. Valles Caldera Natl Preserve, Los Alamos, NM 87544 USA. Univ Connecticut, Dept Ecol & Evolutionary Biol, Storrs, CT 06269 USA.
Duran, KL, Bowdoin Coll, Dept Biol, 6500 Coll Stn, Brunswick, ME 04011 USA.
kristy.duran@bowdoin.edu*://000227598500058 ISI Document Delivery No.: 905VJ 1471-8278 Mol. Ecol. Notes ISI:000227598500058 Yale Univ, Dept Ecol & Evolutionary Biol, New Haven, CT 06520 USA.
Webb, CO, Yale Univ, Dept Ecol & Evolutionary Biol, Box 208106, New Haven, CT 06520 USA.
campbell.webb@yale.edu
://000227516600001 ISI Document Delivery No.: 904RY 0003-0147 Am. Nat. ISI:000227516600001L Univ Michigan, Herbarium, Dept Ecol & Evolutionary Biol, Ann Arbor, MI 48108 USA. Yale Univ, Dept Ecol & Evolutionary Biol, New Haven, CT 06520 USA. Natl Museum Nat Hist, Smithsonian Inst, Dept Bot, Washington, DC 20013 USA. Natl Museum Nat Hist, Smithsonian Inst, Labs Analyt Biol, Washington, DC 20013 USA. Inst Colombiano Petroleo, Biostratig Team, Bucaramanga, Colombia.
Davis, CC, Univ Michigan, Herbarium, Dept Ecol & Evolutionary Biol, Ann Arbor, MI 48108 USA.
chdavis@umich.edu campbell.webb@yale.edu kwurdack@lms.si.edu carlos.jaramillo@ecopetrol.com.co michael.donoghue@yale.edu|?b ' Moret, B. M. E.
Bader, D. A.
Warnow, T. 2001F High-performance algorithm engineering for computational phylogenetics 1012-10214 Computational Science -- ICCS 2001, Proceedings Pt 2 2074 Phylogeny reconstruction from molecular data poses complex optimization problems: almost all optimization models are NP-hard and thus computationally intractable. Yet approximations must be of very high quality in order to avoid outright biological nonsense. Thus many biologists have been willing to run farms of processors for many months in order to analyze just one dataset. High-performance algorithm engineering offers a battery of tools that can reduce, sometimes spectacularly, the running time of existing phylogenetic algorithms. We present an overview of algorithm engineering techniques, illustrating them with an application to the "breakpoint analysis" method of Sankoff et al., which resulted in the GRAPPA software suite. GRAPPA demonstrated a million-fold speedup in running time (on a variety of real and simulated datasets) over the original implementation. We show how algorithmic engineering techniques are directly applicable to a large variety of challenging combinatorial problems in computational biology. ://000227039400107 ! Lecture Notes in Computer Science( ISI Document Delivery No.: BBQ28
Article 0302-9743 ISI:000227039400107/ Univ New Mexico, Dept Comp Sci, Albuquerque, NM 87131 USA. Univ New Mexico, Dept Elect & Comp Engn, Albuquerque, NM 87131 USA. Univ Texas, Dept Comp Sci, Austin, TX 78712 USA.
Moret, BME, Univ New Mexico, Dept Comp Sci, Albuquerque, NM 87131 USA.
moret@cs.unm.edu dbader@eece.unm.edu tandy@cs.utexas.edu < ://000227293200001 ISI Document Delivery No.: 901PA 0363-6445
Syst. Bot. ISI:000227293200001 Iowa State Univ, Dept Ecol Evolut & Organismal Biol, Ames, IA 50011 USA. Yale Univ, Dept Ecol & Evolutionary Biol, New Haven, CT 06520 USA. Yale Univ, Peabody Museum Nat Hist, New Haven, CT 06520 USA.
Clark, LG, Iowa State Univ, Dept Ecol Evolut & Organismal Biol, Ames, IA 50011 USA.
://000227021400010 ISI Document Delivery No.: 897RB 0002-9122 Am. J. Bot. ISI:000227021400010 Yale Univ, Dept Ecol & Evolutionary Biol, New Haven, CT 06520 USA.
Bell, CD, Xavier Univ, Dept Biol, New Orleans, LA 70125 USA.
cbell3@xula.edu
://000226378400003 ISI Document Delivery No.: 888ML 0307-6970 Syst. Entomol. ISI:000226378400003] Univ Jena, Inst Spezielle Zool & Evolut Biol, Phyletischem Museum, D-07743 Jena, Germany. Univ Pretoria, Dept Zool & Entomol, ZA-0002 Pretoria, South Africa. Univ Arizona, Dept Entomol, Tucson, AZ 85721 USA.
Grebennikov, VV, Univ Jena, Inst Spezielle Zool & Evolut Biol, Phyletischem Museum, Erbertstr 1, D-07743 Jena, Germany.
v_grebennikov@mail.ru @ ://000226306600003 ISI Document Delivery No.: 887LC 1063-5157 Syst. Biol. ISI:000226306600003 Univ Texas, Sect Integrate Biol, Austin, TX 78712 USA. Univ Connecticut, Dept Ecol & Evolutionary Biol, Storrs, CT 06269 USA.
Zwickl, DJ, Univ Texas, Sect Integrate Biol, 1 Univ Stn C0930, Austin, TX 78712 USA.
zwickl@mail.utexas.edu "://000226258600005 ISI Document Delivery No.: 886UQ 1055-7903 Mol. Phylogenet. Evol. ISI:000226258600005 Univ Texas, Sect Integrat Biol, Austin, TX 78712 USA. Univ Texas, Ctr Computat Biol & Bioinformat, Austin, TX 78712 USA.
Hillis, DM, Univ Texas, Sect Integrat Biol, Austin, TX 78712 USA.
dhillis@mail.utexas.edu H ://000225778100010 ISI Document Delivery No.: 880GX 0169-5347 Trends Ecol. Evol. ISI:000225778100010' SUNY Stony Brook, Dept Ecol & Evolut, Stony Brook, NY 11794 USA. Yale Univ, Dept Ecol & Evolutionary Biol, New Haven, CT 06511 USA. Yale Univ, Peabody Museum Nat Hist, New Haven, CT 06511 USA.
Wiens, JJ, SUNY Stony Brook, Dept Ecol & Evolut, Stony Brook, NY 11794 USA.
wiensj@life.bio.sunysb.eduZ|?i . Cohen-Boulakia, S.
Davidson, S.
Froidevaux, C. 2005C A user-centric framework for accessing biological sources and tools 3-182 Data Integration in the Life Sciences, Proceedings 3615 CLASSIFICATION Biologists face two problems in interpreting their experiments: the integration of their data with information from multiple heterogeneous sources and data analysis with bioinformatics tools. It is difficult for scientists to choose between the numerous sources and tools without assistance. Following a thorough analysis of scientists' needs during the querying process, we found that biologists express preferences concerning the sources to be queried and the tools to be used. Interviews also showed that the querying process itself - the strategy followed - differs between scientists. In response to these findings, we have introduced a user-centric framework allowing to specify various querying processes. Then we have developed the BioGuide system which helps the scientists to choose suitable sources and tools, find complementary information in sources, and deal with divergent data. It is generic in that it can be adapted by each user to provide answers respecting his/her preferences, and obtained following his/her strategies. ://000231195100001 ! Lecture Notes in Computer Science( ISI Document Delivery No.: BCT88
Article 0302-9743 ISI:000231195100001 Univ Paris 11, CNRS, UMR 8023, LRI, Orsay, France. Univ Penn, Dept Comp & Informat Sci, Philadelphia, PA 19104 USA.
Cohen-Boulakia, S, Univ Paris 11, CNRS, UMR 8023, LRI, Orsay, France.
cohen@lri.fr chris@lri.fr p(2)). As the spanning tree problem is notoriously hard for any parallel implementation to achieve reasonable speedup, our study may shed new light on implementing PRAM algorithms for shared-memory parallel computers. The main results of this paper are 1. A new and practical spanning tree algorithm for symmetric multiprocessors that exhibits parallel speedups on graphs with regular and irregular topologies; and 2. an experimental study of parallel spanning tree algorithms that reveals the superior performance of our new approach compared with the previous algorithms. The source code for these algorithms is freely-available from our web site. (c) 2005 Elsevier Inc. All rights reserved. ://000231516400002 ISI Document Delivery No.: 959KK 0743-7315 J. Parallel Distrib. Comput. ISI:000231516400002 Georgia Inst Technol, Coll Comp, Atlanta, GA 30332 USA. IBM Corp, TJ Watson Res Ctr, Yorktown Hts, NY USA.
Bader, DA, Georgia Inst Technol, Coll Comp, Atlanta, GA 30332 USA.
bader@cc.gatech.edu gcong@us.ibm.comZ://000231374200015 ISI Document Delivery No.: 957MP 1066-5277 J. Comput. Biol. ISI:000231374200015R Rice Univ, Dept Comp Sci, Houston, TX 77005 USA. Univ Texas, Dept Comp Sci, Austin, TX 78712 USA. Univ Texas, Sch Biol Sci, Sect Integrat Biol, Austin, TX 78712 USA. CUNY Herbert H Lehman Coll, Dept Math & Comp Sci, Bronx, NY 10468 USA.
Nakhleh, L, Rice Univ, Dept Comp Sci, 6100 Main St,MS 132, Houston, TX 77005 USA.
nakhleh@cs.rice.edu p ://000231333000002 ISI Document Delivery No.: 956XI 1476-9271 Comput. Biol. Chem. ISI:000231333000002 Nanyang Technol Univ, BioInformat Res Ctr, Singapore 639798, Singapore. New Jersey Inst Technol, Dept Comp Sci, Coll Comp Sci, Newark, NJ 07102 USA.
Du, ZH, Nanyang Technol Univ, BioInformat Res Ctr, Nanyang Ave, Singapore 639798, Singapore.
duzhihua@pmail.ntu.edu.sg |?m Nakhleh, L.
Wang, L. S. 2005* Phylogenetic networks, trees, and clusters 919-926' Computational Science - ICCS 2005, Pt 2 3515% Phylogenetic networks model evolutionary histories in the presence of non-treelike events such as hybrid speciation and horizontal gene transfer. In spite of their widely acknowledged importance, very little is known about phylogenetic networks, which have so far been studied mostly for specific datasets. Even when the evolutionary history of a set of species is non-treelike, individual genes in these species usually evolve in a treelike fashion. An important question, then, is whether a gene tree is "contained" inside a species network. This information is used to detect the presence of events such as horizontal gene transfer and hybrid speciation. Another question of interest for biologists is whether a group of taxa forms a clade based on a given phylogeny. This can be efficiently answered when the phylogeny is a tree simply by inspecting the edges of the tree, whereas no efficient solution currently exists for the problem when the phylogeny is a network. In this paper, we give polynomial-time algorithms for answering the above two questions. ://000230023800117 ! Lecture Notes in Computer Science( ISI Document Delivery No.: BCM76
Article 0302-9743 ISI:000230023800117 Rice Univ, Dept Comp Sci, Houston, TX 77005 USA. Univ Penn, Dept Biol, Philadelphia, PA 19104 USA.
Nakhleh, L, Rice Univ, Dept Comp Sci, Houston, TX 77005 USA.
nakhleh@cs.rice.edu lswang@mail.med.upenn.edu#|?n Bader, D. A. 2005_ High-performance algorithm engineering for large-scale graph problems and computational biology 16-212 Experimental and Efficient Algorithms, Proceedings 3503 PHYLOGENY; TREES Many large-scale optimization problems rely on graph theoretic solutions; yet high-performance computing has traditionally focused on regular applications with high degrees of locality. We describe our novel methodology for designing and implementing irregular parallel algorithms that attain significant performance on high-end computer systems. Our results for several fundamental graph theory problems are the first ever to achieve parallel speedups. Specifically, we have demonstrated for the first time that significant parallel speedups are attainable for arbitrary instances of a variety of graph problems and are developing a library of fundamental routines for discrete optimization (especially in computational biology) on shared-memory systems. Phylogenies derived from gene order data may prove crucial in answering some fundamental questions in biomolecular evolution. High-performance algorithm engineering offers a battery of tools that can reduce, sometimes spectacularly, the running time of existing approaches. We discuss one such such application, GRAPPA, that demonstrated over a billion-fold speedup in running time (on a variety of real and simulated datasets), by combining low-level algorithmic improvements, cache-aware programming, careful performance tuning, and massive parallelism. We show how these techniques are directly applicable to a large variety of problems in computational biology.! Lecture Notes in Computer Science( ISI Document Delivery No.: BCL08
Article 0302-9743 ISI:000229801300003 Univ New Mexico, Dept Elect & Comp Engn, Albuquerque, NM 87131 USA.
Bader, DA, Univ New Mexico, Dept Elect & Comp Engn, Albuquerque, NM 87131 USA.
dbader@ece.unm.edu ?o Alfaro, M. E.
Holder, M. T. 20065 The prior and the posterior in Bayesian phylogenetics 19-424 Annual Review of Ecology, Evolution, and Systematics 37 ?p ! Alfaro, M. E.
Huelsenbeck, J. P. 2006\ Comparative performance of Bayesian and AIC-based measures of phylogenetic model uncertainty 89 – 96 Systematic Biology 55 ?q ; Altekar, G.
Dwarkadas, S.
Huelsenbeck, J. P.
Ronquist, F. 2004X Parallel Metropolis-coupled Markov chain Monte Carlo for Bayesian phylogenetic inference 407 – 415 Bioinformatics 20 ?r 5 Angelov, S.
Harb, B.
Kannan, S.
Khanna, S.
Kim, J. 2006A Efficient enumeration of phylogenetically informative substrings 248-264" Lecture Notes in Computer Science 3909 Q 3909 of Lecture Notes in Computer Science, pages 248-264. Springer-Verlag, 2006. ?s > Angelov, S.
Harb, B.
Khanna, S.
Khanna, S.
Kim, J.
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Chandu, V.
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Reif, J.
CRC Press ?x Bader, D.A.
Cong, G. 2006: Fast shared-memory algorithms for graph theoretic problems
1366 -1378- Journal of Parallel and Distributed Computing 66 11?y Bader, D.A.
Cong, G.
Feo, J. 2005M On the Architectural Requirements for Efficient Execution of Graph Algorithms 547-556 D The 34th International Conference on Parallel Processing (ICPP 2005) University of Oslo, Norway June 14-17, 2005 ?z Bader, D.A.
Madduri, K. 2005\ Design and implementation of the HPCS graph analysis benchmark on symmetric multiprocessors. 465-4762 12th Conf. on High Performance Computing HiPC’05 3769! Lecture Notes in D?{ Bader, D.A.
Madduri, K. 2006a Designing Multithreaded Algorithms for Breadth-First Search and st-connectivity on the Cray MTA-2@ 35th International Conference on Parallel Processing (ICPP 2006)
Columbus, OH August 14-18, 2006 D?| Bader, D.A.
Madduri, K. 2006L Parallel Algorithms for Evaluating Centrality Indices in Real-world NetworksE The 35th International Conference on Parallel Processing (ICPP 2006) Columbus, OH August 14-18, 2006 D?} ( Bader, D.A.
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Stamatakis, A. 2006S Computational Grand Challenges in Assembling the Tree of Life: Problems & Solutions 127 -176( Computational Biology and Bioinformatics 68
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Nielesen, S. M. 2005] A compressed format for collections of phylogenetic trees and improved consensus performance. 353 -364^ Proc. 5th Workshop Algorithms in Bioinformatics (WABI’05), Lecture Notes in Computer Science 3692 Springer-Verlag ? Bray, N.
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Rao, S. 2006E On the tandem duplication-random loss model of genome rearrangement. 564–5704 17th ACM-SIAM Symp. on Discrete Algorithms SODA’06
SIAM Press ? 8 Chen, B.
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? Donoghue, M.J. 2005. Comparisons, phylogeny, and teaching evolution 69-77< Evolutionary Science and Society: Educating a New Generation Cracraft, J.
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Gauthier, J. A. 2004 Implementing the PhyloCode 281–282 Trends"? B Coarfa, C.
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dePamphilis, C.W. 20064 Adaptive evolution of chloroplast genome structure. 13 BMC Evolutionary Biology 6 ? A Daskalakis, C.
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281 - 295 8 10th Ann. Int’l Conf. Comput. Mol. Biol. (RECOMB’06) 3909 Springer-Verlag! Lecture Notes in Computer Science ? " Daskalakis, C.
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Roch, S. 2006# Optimal Phylogenetic Reconstruction 159 - 168 D Thirty-eighth annual ACM Symposium on Theory of Computing (STOC '06) Seattle, WA- http://portal.acm.org/citation.cfm?id=1132540 ? ! Davidson, S. B.
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188–198
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Snir, S. 2005U The homology kernel: A biologically motivated sequence embedding into Euclidean space 179–186e 3rd IEEE Symp. on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB’05)
IEEE Press ? Eskin, E.
Snir, S. 2006G Incorporating homologues into sequence embeddings for protein analysis. 717-38( J. of Bioinformatics and Comput. Biology 5 3 ? Evans, S.N.
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Altintas, I. 20069 Authentication framework in the Kepler workflow system. 1st TeraGrid Conf., ? 5 Guindon, S.
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12957–12962 Proc. Nat’l Acad. Sci., USA 101 35 ? Harb, B.
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McGregor, A. 2005/ Approximating the best-fit tree under Lp norms
123–133 ^ 8th Workshop on Approximation Algorithms for Combinatorial Optimization Problems (APPROX’05) ? = Herbert, K.G.
Gehani, N. J.
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Wu, C.H. 2004@ BIO-AJAX: An extensible framework for biological data cleaning. 51–57 SIGMOD Record, 33 2 ? 3 Herbert, K.G.
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117 - 120 K 17th Int’l Conf. Scientific & Statistical Database Management SSDBM’05 ? 5 Holder, M. T.
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Ronquist, F. 20056 Bayesian analysis of molecular evolution using MrBayes* Statistical Methods in Molecular Evolution XII
Nielsen, R. Springer-Verlag" Statistics for Biology and Health ? Janson, S.
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