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Volumn 9780521857000, Issue , 2005, Pages 1-420

Algebraic statistics for computational biology

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EID: 84926122052     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1017/CBO9780511610684     Document Type: Book
Times cited : (312)

References (280)
  • 1
    • 12744263064 scopus 로고    scopus 로고
    • Comparison of splice sites in mammals and chicken
    • Cited on p. 144 [Abril et al., 2005]
    • [Abril et al., 2005] JF Abril, R Castelo, and R Guigo. Comparison of splice sites in mammals and chicken. Genome Research, 15:111-119, 2005. Cited on p. 144
    • (2005) Genome Research , vol.15 , pp. 111-119
    • Abril, J.F.1    Castelo, R.2    Guigo, R.3
  • 2
    • 0035028769 scopus 로고    scopus 로고
    • Molecular phylogeny and divergence time estimates for major rodent groups: Evidence from multiple genes
    • Cited on p. 384 [Adkins et al., 2001]
    • [Adkins et al., 2001] RM Adkins, EL Gelke, D Rowe, and RL Honeycutt. Molecular phylogeny and divergence time estimates for major rodent groups: evidence from multiple genes. Molecular Biology and Evolution, 18(5):777-791, 2001. Cited on p. 384
    • (2001) Molecular Biology and Evolution , vol.18 , Issue.5 , pp. 777-791
    • Adkins, R.M.1    Gelke, E.L.2    Rowe, D.3    Honeycutt, R.L.4
  • 3
    • 0003535936 scopus 로고
    • Wiley Series in Probability and Mathematical Statistics: Applied Probability and Statistics. John Wiley & Sons Inc., New York, A Wiley-Interscience Publication. Cited on p. 14 [Agresti, 1990]
    • [Agresti, 1990] A Agresti. Categorical Data Analysis. Wiley Series in Probability and Mathematical Statistics: Applied Probability and Statistics. John Wiley & Sons Inc., New York, 1990. A Wiley-Interscience Publication. Cited on p. 14
    • (1990) Categorical Data Analysis
    • Agresti, A.1
  • 4
    • 0033907315 scopus 로고    scopus 로고
    • The generalized distributive law
    • Cited on p. 41 [Aji and McEliece, 2000]
    • [Aji and McEliece, 2000] SM Aji and RJ McEliece. The generalized distributive law. IEEE Transactions on Information Theory, 46(2):325-343, 2000. Cited on p. 41
    • (2000) IEEE Transactions on Information Theory , vol.46 , Issue.2 , pp. 325-343
    • Aji, S.M.1    McEliece, R.J.2
  • 6
    • 0037350957 scopus 로고    scopus 로고
    • SLAM: Crossspecies gene finding and alignment with a generalized pair hidden Markov model
    • Cited on p. 145 [Alexandersson et al., 2003]
    • [Alexandersson et al., 2003] M Alexandersson, S Cawley, and L Pachter. SLAM: crossspecies gene finding and alignment with a generalized pair hidden Markov model. Genome Research, 13(3):496-502, 2003. Cited on p. 145
    • (2003) Genome Research , vol.13 , Issue.3 , pp. 496-502
    • Alexandersson, M.1    Cawley, S.2    Pachter, L.3
  • 7
    • 0242607587 scopus 로고    scopus 로고
    • Phylogenetic invariants for the general Markov model of sequence mutation
    • Cited on p. 348 [Allman and Rhodes, 2003]
    • [Allman and Rhodes, 2003] ES Allman and JA Rhodes. Phylogenetic invariants for the general Markov model of sequence mutation. Mathematical Biosciences, 186(2):113-144, 2003. Cited on p. 348
    • (2003) Mathematical Biosciences , vol.186 , Issue.2 , pp. 113-144
    • Allman, E.S.1    Rhodes, J.A.2
  • 9
    • 55449086015 scopus 로고    scopus 로고
    • Quartets and parameter recovery for the general Markov model of sequence mutation
    • Cited on p. 102, 351 [Allman and Rhodes, 2004b]
    • [Allman and Rhodes, 2004b] ES Allman and JA Rhodes. Quartets and parameter recovery for the general Markov model of sequence mutation. AMRX Applied Mathematics Research Express, 2004(4):107-131, 2004. Cited on p. 102, 351
    • (2004) AMRX Applied Mathematics Research Express , vol.2004 , Issue.4 , pp. 107-131
    • Allman, E.S.1    Rhodes, J.A.2
  • 11
    • 0001432978 scopus 로고
    • A lower bound on the volume of strictly convex bodies with many boundary points
    • Cited on p. 174 [Andrews, 1963]
    • [Andrews, 1963] G Andrews. A lower bound on the volume of strictly convex bodies with many boundary points. Transactions of the American Mathematical Society, 106:270-279, 1963. Cited on p. 174
    • (1963) Transactions of the American Mathematical Society , vol.106 , pp. 270-279
    • Andrews, G.1
  • 12
    • 0003399969 scopus 로고
    • Springer-Verlag, New York, Undergraduate Texts in Mathematics. Cited on p. 221 [Apostol, 1976]
    • [Apostol, 1976] TM Apostol. Introduction to Analytic Number Theory. Springer-Verlag, New York, 1976. Undergraduate Texts in Mathematics. Cited on p. 221
    • (1976) Introduction to Analytic Number Theory
    • Apostol, T.M.1
  • 13
    • 84926108172 scopus 로고    scopus 로고
    • A tropical morphism related to the hyperplane arrangement of the complete bipartite graph
    • To appear. Cited on p. 116 [Ardila, 2005]
    • [Ardila, 2005] F Ardila. A tropical morphism related to the hyperplane arrangement of the complete bipartite graph. Discrete and Computational Geometry, 2005. To appear. Cited on p. 116
    • (2005) Discrete and Computational Geometry
    • Ardila, F.1
  • 14
    • 0037461032 scopus 로고    scopus 로고
    • How Bayes tests of molecular phylogenies compare with frequentist approaches
    • Cited on p. 374 [Aris-Brosou, 2003]
    • [Aris-Brosou, 2003] S Aris-Brosou. How Bayes tests of molecular phylogenies compare with frequentist approaches. Bioinformatics, 19:618-624, 2003. Cited on p. 374
    • (2003) Bioinformatics , vol.19 , pp. 618-624
    • Aris-Brosou, S.1
  • 16
    • 84889395646 scopus 로고    scopus 로고
    • editors, John Wiley & Sons, second edition, Cited on p. 126 [Balding et al., 2003]
    • [Balding et al., 2003] DJ Balding, M Bishop, and C Cannings, editors. Handbook of Statistical Genetics (2 Volume Set). John Wiley & Sons, second edition, 2003. Cited on p. 126
    • (2003) Handbook of Statistical Genetics , vol.2
    • Balding, D.J.1    Bishop, M.2    Cannings, C.3
  • 17
    • 34047267637 scopus 로고
    • A canonical decomposition theory for metrics on a finite set
    • Cited on p. 323, 326 [Bandelt and Dress, 1992]
    • [Bandelt and Dress, 1992] HJ Bandelt and AWM Dress. A canonical decomposition theory for metrics on a finite set. Advances in Mathematics, 92:47-105, 1992. Cited on p. 323, 326
    • (1992) Advances in Mathematics , vol.92 , pp. 47-105
    • Bandelt, H.J.1    Dress, A.W.M.2
  • 18
    • 0029149631 scopus 로고
    • Mitochondrial portraits of human population using median networks
    • Cited on p. 323 [Bandelt et al., 1995]
    • [Bandelt et al., 1995] HJ Bandelt, P Forster, BC Sykes, and MB Richards. Mitochondrial portraits of human population using median networks. Genetics, 141:743-753, 1995. Cited on p. 323
    • (1995) Genetics , vol.141 , pp. 743-753
    • Bandelt, H.J.1    Forster, P.2    Sykes, B.C.3    Richards, M.B.4
  • 20
    • 0002128307 scopus 로고
    • What can be computed in algebraic geometry?
    • Cambridge University Press, Cortona, Cited on p. 239 [Bayer and Mumford, 1993]
    • [Bayer and Mumford, 1993] D Bayer and D Mumford. What can be computed in algebraic geometry? In Computational Algebraic Geometry and Commutative Algebra, Sympos. Math., XXXIV, pages 1-48. Cambridge University Press, Cortona, 1991, 1993. Cited on p. 239
    • (1991) Computational Algebraic Geometry and Commutative Algebra, Sympos. Math., XXXIV , pp. 1-48
    • Bayer, D.1    Mumford, D.2
  • 23
    • 18744366364 scopus 로고    scopus 로고
    • Mtreemix: A software package for learning and using mixture models of mutagenetic trees
    • To appear. Cited on p. 278 [Beerenwinkel et al., 2005b]
    • [Beerenwinkel et al., 2005b] N Beerenwinkel, J Rahnenfiihrer, R Kaiser, D Hoffmann, J Selbig, and T Lengauer. Mtreemix: a software package for learning and using mixture models of mutagenetic trees. Bioinformatics, 2005. To appear. Cited on p. 278
    • (2005) Bioinformatics
    • Beerenwinkel, N.1    Rahnenfiihrer, J.2    Kaiser, R.3    Hoffmann, D.4    Selbig, J.5    Lengauer, T.6
  • 25
    • 0000913755 scopus 로고
    • Spatial interaction and the statistical analysis of lattice systems
    • Cited on p. 266 [Besag, 1974]
    • [Besag, 1974] J. Besag. Spatial interaction and the statistical analysis of lattice systems. Journal of the Royal Statistical Society, B,36:192-236, 1974. Cited on p. 266
    • (1974) Journal of the Royal Statistical Society , vol.36 B , pp. 192-236
    • Besag, J.1
  • 26
    • 0000013152 scopus 로고
    • On the statistical analysis of dirty pictures
    • Cited on p. 274 [Besag, 1986]
    • [Besag, 1986] J Besag. On the statistical analysis of dirty pictures. Journal of the Royal Statistical Society, B 48 No. 3:259-302, 1986. Cited on p. 274
    • (1986) Journal of the Royal Statistical Society , vol.B48 , Issue.3 , pp. 259-302
    • Besag, J.1
  • 28
    • 0035520029 scopus 로고    scopus 로고
    • Geometry of the space of phylogenetic trees
    • Cited on p. 68 [Billera et al., 2001]
    • [Billera et al., 2001] LJ Billera, SP Holmes, and K Vogtmann. Geometry of the space of phylogenetic trees. Advances in Applied Mathematics, 27(4):733-767, 2001. Cited on p. 68
    • (2001) Advances in Applied Mathematics , vol.27 , Issue.4 , pp. 733-767
    • Billera, L.J.1    Holmes, S.P.2    Vogtmann, K.3
  • 30
    • 0242418246 scopus 로고    scopus 로고
    • Phylogenetic shadowing of primate sequences to find functional regions of the human genome
    • Cited on p. 130, 157 [Boffelli et al., 2003]
    • [Boffelli et al., 2003] D Boffelli, J McAuliffe, D Ovcharenko, KD Lewis, I Ovcharenko, L Pachter, and EM Rubin. Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science, 299(5611):1391-4, 2003. Cited on p. 130, 157
    • (2003) Science , vol.299 , Issue.5611 , pp. 1391-1394
    • Boffelli, D.1    McAuliffe, J.2    Ovcharenko, D.3    Lewis, K.D.4    Ovcharenko, I.5    Pachter, L.6    Rubin, E.M.7
  • 31
    • 3042740671 scopus 로고    scopus 로고
    • Comparative genomics at the vertebrate extremes
    • Cited on p. 394, 400 [Boffelli et al., 2004]
    • [Boffelli et al., 2004] D Boffelli, MA Nobrega, and EM Rubin. Comparative genomics at the vertebrate extremes. Nature Reviews Genetics, 5:456-465, 2004. Cited on p. 394, 400
    • (2004) Nature Reviews Genetics , vol.5 , pp. 456-465
    • Boffelli, D.1    Nobrega, M.A.2    Rubin, E.M.3
  • 32
    • 0031232428 scopus 로고    scopus 로고
    • The MAGMA algebra system I: The user language
    • Cited on p. 77 [Bosma et al., 1997]
    • [Bosma et al., 1997] W Bosma, J Cannon, and C Playoust. The MAGMA algebra system I: the user language. Journal of Symbolic Computation, 24(3-4):235-265, 1997. Cited on p. 77
    • (1997) Journal of Symbolic Computation , vol.24 , Issue.3-4 , pp. 235-265
    • Bosma, W.1    Cannon, J.2    Playoust, C.3
  • 33
    • 1842768393 scopus 로고    scopus 로고
    • Reconstructing the genomic architecture of ancestral mammals: Lessons from human, mouse, and rat genomes
    • Cited on p. 131 [Bourque et al., 2004]
    • [Bourque et al., 2004] G Bourque, PA Pevzner, and G Tesler. Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes. Genome Research, 14(4):507-16, 2004. Cited on p. 131
    • (2004) Genome Research , vol.14 , Issue.4 , pp. 507-516
    • Bourque, G.1    Pevzner, P.A.2    Tesler, G.3
  • 34
    • 0033283778 scopus 로고    scopus 로고
    • Fast approximate energy minimization via graph cuts
    • Cited on p. 273, 275 [Boykov et al., 1999]
    • [Boykov et al., 1999] Y Boykov, O Veksler, and R Zabih. Fast approximate energy minimization via graph cuts. Intl. Conf. on Computer Vision, 1999. Cited on p. 273, 275
    • (1999) Intl. Conf. On Computer Vision
    • Boykov, Y.1    Veksler, O.2    Zabih, R.3
  • 35
    • 1842667852 scopus 로고    scopus 로고
    • MAVID: Constrained ancestral alignment of multiple sequences
    • Cited on p. 82, 137, 378, 387 [Bray and Pachter, 2004]
    • [Bray and Pachter, 2004] N Bray and L Pachter. MAVID: constrained ancestral alignment of multiple sequences. Genome Research, 14(4):693-9, 2004. Cited on p. 82, 137, 378, 387
    • (2004) Genome Research , vol.14 , Issue.4 , pp. 693-699
    • Bray, N.1    Pachter, L.2
  • 36
    • 0037270315 scopus 로고    scopus 로고
    • AVID: A global alignment program
    • Cited on p. 137 [Bray et al., 2003]
    • [Bray et al., 2003] N Bray, I Dubchak, and L Pachter. AVID: A global alignment program. Genome Research, 13(1):97-102, 2003. Cited on p. 137
    • (2003) Genome Research , vol.13 , Issue.1 , pp. 97-102
    • Bray, N.1    Dubchak, I.2    Pachter, L.3
  • 37
    • 0020328686 scopus 로고
    • Mitochondrial DNA sequences of primates, tempo and mode of evolution
    • Cited on p. 371 [Brown et al., 1982]
    • [Brown et al., 1982] WM Brown, EM Prager, A Wang, and AC Wilson. Mitochondrial DNA sequences of primates, tempo and mode of evolution. Journal of Molecular Evolution, 18:225-239, 1982. Cited on p. 371
    • (1982) Journal of Molecular Evolution , vol.18 , pp. 225-239
    • Brown, W.M.1    Prager, E.M.2    Wang, A.3    Wilson, A.C.4
  • 38
    • 0037827862 scopus 로고    scopus 로고
    • John Wiley & Son, Inc., Cited on p. 2, 130 [Brown, 2002]
    • [Brown, 2002] TA Brown. Genomes 2. John Wiley & Son, Inc., 2002. Cited on p. 2, 130
    • (2002) Genomes 2
    • Brown, T.A.1
  • 39
    • 0037398368 scopus 로고    scopus 로고
    • LAGAN and Multi-LAGAN: Efficient tools for largescale multiple alignment of genomic DNA
    • Cited on p. 137 [Brudno et al., 2003a]
    • [Brudno et al., 2003a] M Brudno, C Do, G Cooper, MF Kim, E Davydov, ED Green, A Sidow, and S Batzoglou. LAGAN and Multi-LAGAN: efficient tools for largescale multiple alignment of genomic DNA. Genome Research, 13:721-731, 2003. Cited on p. 137
    • (2003) Genome Research , vol.13 , pp. 721-731
    • Brudno, M.1    Do, C.2    Cooper, G.3    Kim, M.F.4    Davydov, E.5    Green, E.D.6    Sidow, A.7    Batzoglou, S.8
  • 41
    • 1542347067 scopus 로고    scopus 로고
    • NeighborNet: An agglomerative algorithm for the construction of planar phylogenetic networks
    • Cited on p. 323 [Bryant and Moulton, 2004]
    • [Bryant and Moulton, 2004] D Bryant and V Moulton. NeighborNet: An agglomerative algorithm for the construction of planar phylogenetic networks. Molecular Biology And Evolution, 21:255-265, 2004. Cited on p. 323
    • (2004) Molecular Biology And Evolution , vol.21 , pp. 255-265
    • Bryant, D.1    Moulton, V.2
  • 43
    • 0026005922 scopus 로고
    • Use of the method of generalized least squares in reconstructing phylogenies from sequence data
    • Cited on p. 325 [Bulmer, 1991]
    • [Bulmer, 1991] D Bulmer. Use of the method of generalized least squares in reconstructing phylogenies from sequence data. Molecular Biology and Evolution, 8(6):868-883, 1991. Cited on p. 325
    • (1991) Molecular Biology and Evolution , vol.8 , Issue.6 , pp. 868-883
    • Bulmer, D.1
  • 44
    • 0031586003 scopus 로고    scopus 로고
    • Prediction of complete gene structures in human genomic DNA
    • Cited on p. 145, 236 [Burge and Karlin, 1997]
    • [Burge and Karlin, 1997] C Burge and S Karlin. Prediction of complete gene structures in human genomic DNA. Journal of Molecular Biology, 268(1): 78-94, 1997. Cited on p. 145, 236
    • (1997) Journal of Molecular Biology , vol.268 , Issue.1 , pp. 78-94
    • Burge, C.1    Karlin, S.2
  • 45
    • 0033529862 scopus 로고    scopus 로고
    • Genome signature comparisons among prokaryote, plasmid and mitochondrial DNA
    • Cited on p. 128, 129 [Campbell et al., 1999]
    • [Campbell et al., 1999] A Campbell, J Mrazek, and S Karlin. Genome signature comparisons among prokaryote, plasmid and mitochondrial DNA. Proceedings of the National Academy of Sciences USA, 96(16):9184-9189, 1999. Cited on p. 128, 129
    • (1999) Proceedings of the National Academy of Sciences USA , vol.96 , Issue.16 , pp. 9184-9189
    • Campbell, A.1    Mrazek, J.2    Karlin, S.3
  • 46
    • 0344268984 scopus 로고    scopus 로고
    • Ranks of tensors, secant varieties of Segre varieties and fat points
    • Cited on p. 288 [Catalisano et al., 2002]
    • [Catalisano et al., 2002] MV Catalisano, AV Geramita, and A Gimigliano. Ranks of tensors, secant varieties of Segre varieties and fat points. Linear Algebra Appi, 355:263-285, 2002. Cited on p. 288
    • (2002) Linear Algebra Appi , vol.355 , pp. 263-285
    • Catalisano, M.V.1    Geramita, A.V.2    Gimigliano, A.3
  • 48
    • 0000156374 scopus 로고
    • Phylogenetic analysis models and estimation procedures
    • Cited on p. 325 [Cavalli-Sforza and Edwards, 1967]
    • [Cavalli-Sforza and Edwards, 1967] L Cavalli-Sforza and A Edwards. Phylogenetic analysis models and estimation procedures. Evolution, 32:550-570, 1967. Cited on p. 325
    • (1967) Evolution , vol.32 , pp. 550-570
    • Cavalli-Sforza, L.1    Edwards, A.2
  • 49
    • 0001899693 scopus 로고
    • Invariants of phylogenies in a simple case with discrete states
    • Cited on p. 348 [Cavender and Felsenstein, 1987]
    • [Cavender and Felsenstein, 1987] J Cavender and J Felsenstein. Invariants of phylogenies in a simple case with discrete states. Journal of Classification, 4:57-71, 1987. Cited on p. 348
    • (1987) Journal of Classification , vol.4 , pp. 57-71
    • Cavender, J.1    Felsenstein, J.2
  • 50
    • 0000897884 scopus 로고
    • Chemical specificity of nucleic acids and mechanism for the enzymatic degradation
    • Cited on p. 126 [Chargaff, 1950]
    • [Chargaff, 1950] E Chargaff. Chemical specificity of nucleic acids and mechanism for the enzymatic degradation. Experientia, 6:201-209, 1950. Cited on p. 126
    • (1950) Experientia , vol.6 , pp. 201-209
    • Chargaff, E.1
  • 51
    • 51249162153 scopus 로고
    • An optimal convex hull algorithm in any fixed dimension
    • Cited on p. 177 [Chazelle, 1993]
    • [Chazelle, 1993] B Chazelle. An optimal convex hull algorithm in any fixed dimension. Discrete Computational Geometry, 10:377-409, 1993. Cited on p. 177
    • (1993) Discrete Computational Geometry , vol.10 , pp. 377-409
    • Chazelle, B.1
  • 52
    • 9244259543 scopus 로고
    • Nonnegative ranks, decompositions, and factorizations of nonnegative matrices
    • Cited on p. 116 [Cohen and Rothblum, 1993]
    • [Cohen and Rothblum, 1993] JE Cohen and UG Rothblum. Nonnegative ranks, decompositions, and factorizations of nonnegative matrices. Linear. Algebra AppL, 190:149-168, 1993. Cited on p. 116
    • (1993) Linear. Algebra AppL , vol.190 , pp. 149-168
    • Cohen, J.E.1    Rothblum, U.G.2
  • 53
    • 14044279173 scopus 로고    scopus 로고
    • Mathematics is biology's next microscope, only better; biology is mathematics' next physics, only better
    • Cited on p. 2 [Cohen, 2004]
    • [Cohen, 2004] JE Cohen. Mathematics is biology's next microscope, only better; biology is mathematics' next physics, only better. PLoS Biol, 2(12):e439, 2004. Cited on p. 2
    • (2004) PLoS Biol , vol.2 , Issue.12
    • Cohen, J.E.1
  • 54
    • 7444260846 scopus 로고    scopus 로고
    • The ENCODE (ENCyclopedia Of DNA Elements) Project
    • Cited on p. 141, 378 [Consortium, 2004]
    • [Consortium, 2004] ENCODE Project Consortium. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science, 306(5696):636-40, 2004. Cited on p. 141, 378
    • (2004) Science , vol.306 , Issue.5696 , pp. 636-640
    • ENCODE Project Consortium1
  • 56
    • 0003908675 scopus 로고    scopus 로고
    • Springer-Verlag, New York, second edition, An introduction to computational algebraic geometry and commutative algebra. Cited on p. 2, 88, 89, 91, 95, 97, 282, 283, 285 [Cox et al., 1997]
    • [Cox et al., 1997] D Cox, J Little, and D O'Shea. Ideals, Varieties, and Algorithms. Undergraduate Texts in Mathematics. Springer-Verlag, New York, second edition, 1997. An introduction to computational algebraic geometry and commutative algebra. Cited on p. 2, 88, 89, 91, 95, 97, 282, 283, 285
    • (1997) Ideals, Varieties, and Algorithms. Undergraduate Texts in Mathematics
    • Cox, D.1    Little, J.2    O'Shea, D.3
  • 57
    • 27844475135 scopus 로고    scopus 로고
    • Multiple equilibria in complex chemical reaction networks: I. The injectivity property
    • To appear. Cited on p. 94 [Craciun and Feinberg, 2005]
    • [Craciun and Feinberg, 2005] G Craciun and M Feinberg. Multiple equilibria in complex chemical reaction networks: I. the injectivity property. SIAM Journal of Applied Mathematics, 2005. To appear. Cited on p. 94
    • (2005) SIAM Journal of Applied Mathematics
    • Craciun, G.1    Feinberg, M.2
  • 58
    • 0034952666 scopus 로고    scopus 로고
    • A remarkable example of catastrophic cancellation unraveled
    • Cited on p. 360 [Cuyt et al., 2001]
    • [Cuyt et al., 2001] A Cuyt, B Verdonk, S Becuwe, and P Kuterna. A remarkable example of catastrophic cancellation unraveled. Computing, 66:309-320, 2001. Cited on p. 360
    • (2001) Computing , vol.66 , pp. 309-320
    • Cuyt, A.1    Verdonk, B.2    Becuwe, S.3    Kuterna, P.4
  • 59
    • 3543051830 scopus 로고    scopus 로고
    • Mauve: Multiple alignment of conserved genomic sequence with rearrangements
    • Cited on p. 137 [Darling et al., 2004]
    • [Darling et al., 2004] ACE Darling, B Mau, FR Blattner, and NT Perna. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Research, 14:1394-1403, 2004. Cited on p. 137
    • (2004) Genome Research , vol.14 , pp. 1394-1403
    • Darling, A.C.E.1    Mau, B.2    Blattner, F.R.3    Perna, N.T.4
  • 61
    • 84863131502 scopus 로고
    • Societe Mathematique de France, Paris, With a French summary. Cited on p. 101 [DeConcini et al., 1982]
    • [DeConcini et al., 1982] C DeConcini, D Eisenbud, and C Procesi. Hodge algebras, volume 91 of Asterisque. Societe Mathematique de France, Paris, 1982. With a French summary. Cited on p. 101
    • (1982) Hodge algebras, volume 91 of Asterisque
    • DeConcini, C.1    Eisenbud, D.2    Procesi, C.3
  • 62
    • 0003424372 scopus 로고    scopus 로고
    • Society for Industrial and Applied Mathematics (SIAM). Philadelphia, PA, Cited on p. 351, 352, 353 [Demmel, 1997]
    • [Demmel, 1997] JW Demmel. Applied Numerical Linear Algebra. Society for Industrial and Applied Mathematics (SIAM). Philadelphia, PA, 1997. Cited on p. 351, 352, 353
    • (1997) Applied Numerical Linear Algebra
    • Demmel, J.W.1
  • 63
    • 0242662461 scopus 로고    scopus 로고
    • Evolutionary discrimination of mammalian conserved non-genic sequences (CNGs)
    • Cited on p. 130 [Dermitzakis et al., 2003]
    • [Dermitzakis et al., 2003] ET Dermitzakis, A Reymond, N Scamuffa, C Ucla, E Kirkness, C Rossier, and SE Antonarakis. Evolutionary discrimination of mammalian conserved non-genic sequences (CNGs). Science, 302:1033-1035, 2003. Cited on p. 130
    • (2003) Science , vol.302 , pp. 1033-1035
    • Dermitzakis, E.T.1    Reymond, A.2    Scamuffa, N.3    Ucla, C.4    Kirkness, E.5    Rossier, C.6    Antonarakis, S.E.7
  • 65
    • 18644364808 scopus 로고    scopus 로고
    • Tropical convexity
    • (electronic), Cited on p. 116 [Develin and Sturmfels, 2004]
    • [Develin and Sturmfels, 2004] M Develin and B Sturmfels. Tropical convexity. Documenta Mathematica, 9:1-27 (electronic), 2004. Cited on p. 116
    • (2004) Documenta Mathematica , vol.9 , pp. 1-27
    • Develin, M.1    Sturmfels, B.2
  • 66
    • 84926116887 scopus 로고    scopus 로고
    • On the tropical rank of a matrix
    • To appear. Cited on p. 114, 116 [Develin et al., 2003]
    • [Develin et al., 2003] M Develin, F Santos, and B Sturmfels. On the tropical rank of a matrix. MSRI Proceedings, 2003. To appear. Cited on p. 114, 116
    • (2003) MSRI Proceedings
    • Develin, M.1    Santos, F.2    Sturmfels, B.3
  • 67
    • 1842818736 scopus 로고    scopus 로고
    • Accurate identification of novel human genes through simultaneous gene prediction in human, mouse, and rat
    • Cited on p. 129 [Dewey et al., 2004]
    • [Dewey et al., 2004] C Dewey, JQ Wu, S Cawley, M Alexandersson, R Gibbs, and L Pachter. Accurate identification of novel human genes through simultaneous gene prediction in human, mouse, and rat. Genome Research, 14(4):661-4, 2004. Cited on p. 129
    • (2004) Genome Research , vol.14 , Issue.4 , pp. 661-664
    • Dewey, C.1    Wu, J.Q.2    Cawley, S.3    Alexandersson, M.4    Gibbs, R.5    Pachter, L.6
  • 70
    • 0344756485 scopus 로고    scopus 로고
    • Local molecular clocks in three nuclear genes: Divergence ages of rodents and other mammals, and incompatibility between fossil calibrations
    • Cited on p. 386 [Douzery et al., 2003]
    • [Douzery et al., 2003] EJP Douzery, F Delsuc, MJ Stanhope, and D Huchon. Local molecular clocks in three nuclear genes: divergence ages of rodents and other mammals, and incompatibility between fossil calibrations. Molecular Biology and Evolution, 57:201-213, 2003. Cited on p. 386
    • (2003) Molecular Biology and Evolution , vol.57 , pp. 201-213
    • Douzery, E.J.P.1    Delsuc, F.2    Stanhope, M.J.3    Huchon, D.4
  • 72
    • 15844426559 scopus 로고    scopus 로고
    • The tree of life and other affine buildings
    • number Extra in Vol. III (Berlin, 1998), (electronic), Cited on p. 117 [Dress and Terhalle, 1998]
    • [Dress and Terhalle, 1998] A Dress and W Terhalle. The tree of life and other affine buildings. In Proceedings of the International Congress of Mathematicians, number Extra Vol. III in Vol. III (Berlin, 1998), pages 565-574 (electronic), 1998. Cited on p. 117
    • (1998) Proceedings of the International Congress of Mathematicians , vol.3 , pp. 565-574
    • Dress, A.1    Terhalle, W.2
  • 73
    • 0036382989 scopus 로고    scopus 로고
    • On line arrangements in the hyperbolic plane
    • Cited on p. 101 [Dress et al., 2002]
    • [Dress et al., 2002] A Dress, JH Koolen, and V Moulton. On line arrangements in the hyperbolic plane. European Journal of Combinatorics, 23(5):549-557, 2002. Cited on p. 101
    • (2002) European Journal of Combinatorics , vol.23 , Issue.5 , pp. 549-557
    • Dress, A.1    Koolen, J.H.2    Moulton, V.3
  • 75
    • 0042027896 scopus 로고    scopus 로고
    • Structural dynamics of eukaryotic chromosome evolution
    • Cited on p. 130 [Eichler and Sankoff, 2003]
    • [Eichler and Sankoff, 2003] EE Eichler and D Sankoff. Structural dynamics of eukaryotic chromosome evolution. Science, 301:793-797, 2003. Cited on p. 130
    • (2003) Science , vol.301 , pp. 793-797
    • Eichler, E.E.1    Sankoff, D.2
  • 76
    • 21144483732 scopus 로고
    • Invariants of some probability models used in phylogenetic inference
    • Cited on p. 152, 296, 306, 309 [Evans and Speed, 1993]
    • [Evans and Speed, 1993] S Evans and T Speed. Invariants of some probability models used in phylogenetic inference. The Annals of Statistics, 21:355-377, 1993. Cited on p. 152, 296, 306, 309
    • (1993) The Annals of Statistics , vol.21 , pp. 355-377
    • Evans, S.1    Speed, T.2
  • 77
    • 0003650063 scopus 로고    scopus 로고
    • Statistics for Biology and Health. Springer-Verlag, New York, second edition, Cited on p. 2 [Ewens and Grant, 2005]
    • [Ewens and Grant, 2005] WJ Ewens and GR Grant. Statistical Methods in Bioinformatics: An Introduction. Statistics for Biology and Health. Springer-Verlag, New York, second edition, 2005. Cited on p. 2
    • (2005) Statistical Methods in Bioinformatics: An Introduction
    • Ewens, W.J.1    Grant, G.R.2
  • 78
    • 0026499429 scopus 로고
    • Conservation evaluation and phylogenetic diversity
    • Cited on p. 336 [Faith, 1992]
    • [Faith, 1992] DP Faith. Conservation evaluation and phylogenetic diversity. Biological Conservation, 61:1-10, 1992. Cited on p. 336
    • (1992) Biological Conservation , vol.61 , pp. 1-10
    • Faith, D.P.1
  • 79
    • 0000472542 scopus 로고
    • Estimating phylogenetic trees from distance matrices
    • Cited on p. 325 [Farris, 1972]
    • [Farris, 1972] JS Farris. Estimating phylogenetic trees from distance matrices. American Naturalist, 106:645-668, 1972. Cited on p. 325
    • (1972) American Naturalist , vol.106 , pp. 645-668
    • Farris, J.S.1
  • 80
    • 0001767194 scopus 로고
    • Cases in which parsimony or compatibility methods will be positively misleading
    • Cited on p. 385 [Felsenstein, 1978]
    • [Felsenstein, 1978] J. Felsenstein. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool., 22:240-249, 1978. Cited on p. 385
    • (1978) Syst. Zool , vol.22 , pp. 240-249
    • Felsenstein, J.1
  • 81
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: A maximum likelihood approach
    • Cited on p. 57, 155, 325, 366 [Felsenstein, 1981]
    • [Felsenstein, 1981] J Felsenstein. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution, 17:368-376, 1981. Cited on p. 57, 155, 325, 366
    • (1981) Journal of Molecular Evolution , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 82
    • 0000122573 scopus 로고
    • PHYLIP-Phylogeny Inference Package (Version 3.2)
    • Cited on p. 155 [Felsenstein, 1989]
    • [Felsenstein, 1989] J Felsenstein. PHYLIP-Phylogeny Inference Package (Version 3.2). Cladistics, 5:164-166, 1989. Cited on p. 155
    • (1989) Cladistics , vol.5 , pp. 164-166
    • Felsenstein, J.1
  • 83
    • 0003991673 scopus 로고    scopus 로고
    • Sinauer Associates, Inc., Cited on p. ix, 67, 147, 152, 326, 334 [Felsenstein, 2003]
    • [Felsenstein, 2003] J Felsenstein. Inferring Phylogenies. Sinauer Associates, Inc., 2003. Cited on p. ix, 67, 147, 152, 326, 334
    • (2003) Inferring Phylogenies
    • Felsenstein, J.1
  • 84
    • 0003437302 scopus 로고    scopus 로고
    • Distributed by the author, Department of Genome Sciences, University of Washington, Seattle, Cited on p. 83, 155, 291, 374, 375 [Felsenstein, 2004]
    • [Felsenstein, 2004] J Felsenstein. PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author, Department of Genome Sciences, University of Washington, Seattle, 2004. Cited on p. 83, 155, 291, 374, 375
    • (2004) PHYLIP (Phylogeny Inference Package) version 3.6
    • Felsenstein, J.1
  • 85
    • 84867998955 scopus 로고    scopus 로고
    • Bounds for parametric sequence comparison
    • Cited on p. 211, 212, 213 [Fernandez-Baca et al., 2002]
    • [Fernandez-Baca et al., 2002] D Fernandez-Baca, T Seppalainen, and G Slutzki. Bounds for parametric sequence comparison. Discrete Applied Mathematics, 118:181-198, 2002. Cited on p. 211, 212, 213
    • (2002) Discrete Applied Mathematics , vol.118 , pp. 181-198
    • Fernandez-Baca, D.1    Seppalainen, T.2    Slutzki, G.3
  • 86
    • 10644231132 scopus 로고    scopus 로고
    • Parametric multiple sequence alignment and phylogeny construction
    • Cited on p. 211 [Fernandez-Baca et al., 2004]
    • [Fernandez-Baca et al., 2004] D Fernandez-Baca, T Seppalainen, and G Slutzki. Parametric multiple sequence alignment and phylogeny construction. Journal of Discrete Algorithms, 2(2):271-287, 2004. Cited on p. 211
    • (2004) Journal of Discrete Algorithms , vol.2 , Issue.2 , pp. 271-287
    • Fernandez-Baca, D.1    Seppalainen, T.2    Slutzki, G.3
  • 87
    • 0000394952 scopus 로고
    • Fast approximate maximum a posteriori restoration of multi-color images
    • Cited on p. 275 [Ferrari et al., 1995]
    • [Ferrari et al., 1995] P Ferrari, A Frigessi, and P de Sa. Fast approximate maximum a posteriori restoration of multi-color images. Journal of the Royal Statistical Society, B,57, 1995. Cited on p. 275
    • (1995) Journal of the Royal Statistical Society , vol.B , pp. 57
    • Ferrari, P.1    Frigessi, A.2    de Sa, P.3
  • 88
    • 0001605074 scopus 로고
    • Optimal sequence alignments
    • Cited on p. 202, 203, 204 [Fitch and Smith, 1983]
    • [Fitch and Smith, 1983] WM Fitch and TF Smith. Optimal sequence alignments. PNAS, 80(5):1382-1386, 1983. Cited on p. 202, 203, 204
    • (1983) PNAS , vol.80 , Issue.5 , pp. 1382-1386
    • Fitch, W.M.1    Smith, T.F.2
  • 90
    • 84945709831 scopus 로고
    • Algorithm 97: Shortest path
    • [Floyd, 1962]
    • [Floyd, 1962] RW Floyd. Algorithm 97: shortest path. Communications of ACM, 5(6):345, 1962.
    • (1962) Communications of ACM , vol.5 , Issue.6 , pp. 345
    • Floyd, R.W.1
  • 91
    • 0015600423 scopus 로고
    • The Viterbi algorithm
    • Cited on p. 46 Cited on p. 227 [Forney, 1973]
    • [Forney, 1973] GD Forney. The Viterbi algorithm. Procedings of the IEEE, 61(3):268-278, 1973. Cited on p. 46 Cited on p. 227
    • (1973) Procedings of the IEEE , vol.61 , Issue.3 , pp. 268-278
    • Forney, G.D.1
  • 92
    • 0032308232 scopus 로고    scopus 로고
    • Fast Monte Carlo algorithms for low rank approximation
    • Cited on p. 353 [Frieze et al., 1998]
    • [Frieze et al., 1998] A Frieze, R Kannan, and S Vempala. Fast Monte Carlo algorithms for low rank approximation. In 39th Symposium on Foundations of Computing, pages 370-378, 1998. Cited on p. 353
    • (1998) 39th Symposium on Foundations of Computing , pp. 370-378
    • Frieze, A.1    Kannan, R.2    Vempala, S.3
  • 93
    • 84926098860 scopus 로고    scopus 로고
    • Cited on p. 190 [Fukuda, 2003]
    • [Fukuda, 2003] K Fukuda. cddlib 0.39d. Available at http://www.ifor.math.ethz. ch/-fukuda/cdd_home/cdd.html, 2003. Cited on p. 190
    • (2003) Cddlib 0.39d
    • Fukuda, K.1
  • 94
    • 4344711578 scopus 로고    scopus 로고
    • From the zonotope construction to the Minkowski addition of convex polytopes
    • Cited on p. 186 [Fukuda, 2004]
    • [Fukuda, 2004] K Fukuda. From the zonotope construction to the Minkowski addition of convex polytopes. Journal of Symbolic Computation, 38(4): 1261-1272, 2004. Cited on p. 186
    • (2004) Journal of Symbolic Computation , vol.38 , Issue.4 , pp. 1261-1272
    • Fukuda, K.1
  • 95
    • 0031829758 scopus 로고    scopus 로고
    • Inferring pattern and process: Maximum likelihood implementation of a non-homogeneous model of DNA sequence evolution for phylogenetic analysis
    • Cited on p. 385, 386 [Galtier and Gouy, 1998]
    • [Galtier and Gouy, 1998] N Galtier and M Gouy. Inferring pattern and process: maximum likelihood implementation of a non-homogeneous model of DNA sequence evolution for phylogenetic analysis. Molecular Biology and Evolution, 154(4):871-879, 1998. Cited on p. 385, 386
    • (1998) Molecular Biology and Evolution , vol.154 , Issue.4 , pp. 871-879
    • Galtier, N.1    Gouy, M.2
  • 96
    • 14944385892 scopus 로고    scopus 로고
    • Algebraic geometry of Bayesian networks
    • Special issue on the occasion of MEGA 2003. Cited on p. 40, 102, 284, 351 [Garcia et al., 2004]
    • [Garcia et al., 2004] L. D. Garcia, M. Stillman, and B. Sturmfels. Algebraic geometry of Bayesian networks. Journal of Symbolic Computation, 39/3-4:331-355, 2004. Special issue on the occasion of MEGA 2003. Cited on p. 40, 102, 284, 351
    • (2004) Journal of Symbolic Computation , vol.39 , Issue.3-4 , pp. 331-355
    • Garcia, L.D.1    Stillman, M.2    Sturmfels, B.3
  • 97
    • 55649103656 scopus 로고    scopus 로고
    • Algebraic statistics in model selection
    • M Chickering and J Halpern, editors, AUAI Press, Arlington, VA, Cited on p. 288 [Garcia, 2004]
    • th Conference on Uncertainty in Artificial Intelligence, pages 177-184. AUAI Press, Arlington, VA, 2004. Cited on p. 288
    • (2004) th Conference on Uncertainty in Artificial Intelligence , pp. 177-184
    • Garcia, L.D.1
  • 98
    • 11244271554 scopus 로고    scopus 로고
    • Bernstein's second theorem and Viro's method for sparse polynomial systems in chemistry
    • Cited on p. 94 [Gatermann and Wolfrum, 2005]
    • [Gatermann and Wolfrum, 2005] K Gatermann and M Wolfrum. Bernstein's second theorem and Viro's method for sparse polynomial systems in chemistry. Advances in Applied Mathematics, 34(2):252-294, 2005. Cited on p. 94
    • (2005) Advances in Applied Mathematics , vol.34 , Issue.2 , pp. 252-294
    • Gatermann, K.1    Wolfrum, M.2
  • 99
    • 0002529940 scopus 로고    scopus 로고
    • Polymake: A framework for analyzing convex polytopes
    • G Kalai and GM Ziegler, editors, Birkhauser, Cited on p. 79, 186 [Gawrilow and Joswig, 2000]
    • [Gawrilow and Joswig, 2000] E Gawrilow and M Joswig. Polymake: a framework for analyzing convex polytopes. In G Kalai and GM Ziegler, editors, Polytopes-Combinatorics and Computation, pages 43-74. Birkhauser, 2000. Cited on p. 79, 186
    • (2000) Polytopes-Combinatorics and Computation , pp. 43-74
    • Gawrilow, E.1    Joswig, M.2
  • 100
    • 0034826991 scopus 로고    scopus 로고
    • Polymake: An approach to modular software design in computational geometry
    • ACM, 2001. June 3-5, Medford, MA. Cited on p. 79, 186 [Gawrilow and Joswig, 2001]
    • [Gawrilow and Joswig, 2001] E Gawrilow and M Joswig. Polymake: an approach to modular software design in computational geometry. In Proceedings of the 17th Annual Symposium on Computational Geometry, pages 222-231. ACM, 2001. June 3-5, 2001, Medford, MA. Cited on p. 79, 186
    • (2001) Proceedings of the 17th Annual Symposium on Computational Geometry , pp. 222-231
    • Gawrilow, E.1    Joswig, M.2
  • 101
    • 0035612908 scopus 로고    scopus 로고
    • Stratified exponential families: Graphical models and model selection
    • Cited on p. 290 [Geiger et al., 2001]
    • [Geiger et al., 2001] D Geiger, D Heckerman, H King, and C Meek. Stratified exponential families: graphical models and model selection. The Annals of Statist., 29(2):505-529, 2001. Cited on p. 290
    • (2001) The Annals of Statist , vol.29 , Issue.2 , pp. 505-529
    • Geiger, D.1    Heckerman, D.2    King, H.3    Meek, C.4
  • 102
    • 29744451810 scopus 로고    scopus 로고
    • On the toric algebra of graphical models
    • To appear. Cited on p. 38, 267, 283 [Geiger et al., 2005]
    • [Geiger et al., 2005] D Geiger, C Meek, and B Sturmfels. On the toric algebra of graphical models. The Annals of Statistics, 2005. To appear. Cited on p. 38, 267, 283
    • (2005) The Annals of Statistics
    • Geiger, D.1    Meek, C.2    Sturmfels, B.3
  • 104
    • 0035049521 scopus 로고    scopus 로고
    • Genome-scale compositional comparisons in eukaryotes
    • Cited on p. 128 [Gentles and Karlin, 2001]
    • [Gentles and Karlin, 2001] AJ Gentles and S Karlin. Genome-scale compositional comparisons in eukaryotes. Genome Research, 4:540-546, 2001. Cited on p. 128
    • (2001) Genome Research , vol.4 , pp. 540-546
    • Gentles, A.J.1    Karlin, S.2
  • 111
    • 0001734192 scopus 로고
    • Minkowski addition of polytopes: Computational complexity and applications to Grobner bases
    • Cited on p. 217 [Gritzmann and Sturmfels, 1993]
    • [Gritzmann and Sturmfels, 1993] P Gritzmann and B Sturmfels. Minkowski addition of polytopes: Computational complexity and applications to Grobner bases. SIAM Journal of Discrete Mathematics, 6:246-269, 1993. Cited on p. 217
    • (1993) SIAM Journal of Discrete Mathematics , vol.6 , pp. 246-269
    • Gritzmann, P.1    Sturmfels, B.2
  • 113
    • 38849143845 scopus 로고    scopus 로고
    • Springer-Verlag, New York, second edition, Prepared and with a preface by Volker Kaibel, Victor Klee and Giinter M. Ziegler. Cited on p. 60 [Griinbaum, 2003]
    • [Griinbaum, 2003] B Griinbaum. Convex polytopes, volume 221 of Graduate Texts in Mathematics. Springer-Verlag, New York, second edition, 2003. Prepared and with a preface by Volker Kaibel, Victor Klee and Giinter M. Ziegler. Cited on p. 60
    • (2003) Convex polytopes, volume 221 of Graduate Texts in Mathematics
    • Griinbaum, B.1
  • 115
    • 0028517367 scopus 로고
    • Parametric optimization of sequence alignment
    • Cited on p. 55, 194, 209, 211 [Gusfield et al., 1994]
    • [Gusfield et al., 1994] D Gusfield, K Balasubramanian, and D Naor. Parametric optimization of sequence alignment. Algorithmica, 12:312-326, 1994. Cited on p. 55, 194, 209, 211
    • (1994) Algorithmica , vol.12 , pp. 312-326
    • Gusfield, D.1    Balasubramanian, K.2    Naor, D.3
  • 116
    • 0004137004 scopus 로고    scopus 로고
    • Cambridge University Press, Cited on p. 49, 55, 194, 206 [Gusfield, 1997]
    • [Gusfield, 1997] D Gusfield. Algorithms on Strings, Trees, and Sequences. Cambridge University Press, 1997. Cited on p. 49, 55, 194, 206
    • (1997) Algorithms on Strings, Trees, and Sequences
    • Gusfield, D.1
  • 117
    • 84926107949 scopus 로고    scopus 로고
    • Resultants in genetic linkage analysis
    • To appear. Cited on p. 126 [Hallgrimsdottir and Sturmfels, 2005]
    • [Hallgrimsdottir and Sturmfels, 2005] I Hallgrimsdottir and B Sturmfels. Resultants in genetic linkage analysis. Journal of Symbolic Computation, 2005. To appear. Cited on p. 126
    • (2005) Journal of Symbolic Computation
    • Hallgrimsdottir, I.1    Sturmfels, B.2
  • 119
    • 0002856077 scopus 로고    scopus 로고
    • Transforming cabbage into turnip: Polynomial algorithm for sorting signed permutations by reversals
    • Cited on p. 130 [Hannenhalli and Pevzner, 1999]
    • [Hannenhalli and Pevzner, 1999] S Hannenhalli and PA Pevzner. Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals. Journal of the ACM, 46(1):1-27, 1999. Cited on p. 130
    • (1999) Journal of the ACM , vol.46 , Issue.1 , pp. 1-27
    • Hannenhalli, S.1    Pevzner, P.A.2
  • 120
    • 0019690663 scopus 로고
    • Bounding solutions of systems of equations using interval analysis
    • Cited on p. 364 [Hansen and Sengupta, 1981]
    • [Hansen and Sengupta, 1981] E Hansen and S Sengupta. Bounding solutions of systems of equations using interval analysis. BIT, 21:203-211, 1981. Cited on p. 364
    • (1981) BIT , vol.21 , pp. 203-211
    • Hansen, E.1    Sengupta, S.2
  • 121
    • 33751433220 scopus 로고
    • Global optimization using interval analysis-the multidimensional case
    • Cited on p. 360 [Hansen, 1980]
    • [Hansen, 1980] E Hansen. Global optimization using interval analysis-the multidimensional case. Numerische Mathematik, 34:247-270, 1980. Cited on p. 360
    • (1980) Numerische Mathematik , vol.34 , pp. 247-270
    • Hansen, E.1
  • 124
    • 0022376704 scopus 로고
    • Dating of the humanape splitting by a molecular clock of mitochondrial DNA
    • Cited on p. 155 [Hasegawa et al., 1985]
    • [Hasegawa et al., 1985] M Hasegawa, H Kishino, and T Yano. Dating of the humanape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution, 22:160-174, 1985. Cited on p. 155
    • (1985) Journal of Molecular Evolution , vol.22 , pp. 160-174
    • Hasegawa, M.1    Kishino, H.2    Yano, T.3
  • 125
    • 0000084234 scopus 로고
    • A framework for the quantitative study of evolutionary trees
    • Cited on p. 332, 334, 385 [Hendy and Penny, 1989]
    • [Hendy and Penny, 1989] M Hendy and D Penny. A framework for the quantitative study of evolutionary trees. Systematic Zoology, 38(4), 1989. Cited on p. 332, 334, 385
    • (1989) Systematic Zoology , vol.38 , Issue.4
    • Hendy, M.1    Penny, D.2
  • 126
    • 21144475766 scopus 로고
    • Spectral analysis of phylogenetic data
    • Cited on p. 152 [Hendy and Penny, 1993]
    • [Hendy and Penny, 1993] MD Hendy and D Penny. Spectral analysis of phylogenetic data. Journal of Classification, 10:5-24, 1993. Cited on p. 152
    • (1993) Journal of Classification , vol.10 , pp. 5-24
    • Hendy, M.D.1    Penny, D.2
  • 127
    • 0040355010 scopus 로고
    • Distributive lattices, affine semigroup rings and algebras with straightening laws
    • Cited on p. 283 [Hibi, 1987]
    • [Hibi, 1987] T Hibi. Distributive lattices, affine semigroup rings and algebras with straightening laws. Advanced Studies in Pure Mathematics, 11:93-109, 1987. Cited on p. 283
    • (1987) Advanced Studies in Pure Mathematics , vol.11 , pp. 93-109
    • Hibi, T.1
  • 128
    • 10644283823 scopus 로고    scopus 로고
    • Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
    • Cited on p. 130, 384 [Hillier et al., 2004]
    • [Hillier et al., 2004] LW Hillier, W Miller, E Birney, W Warren, RC Hardison, CP Ponting, P Bork, DW Burt, MAM Groenen, ME Delany, et al. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature, 432(7018):695-716, 2004. Cited on p. 130, 384
    • (2004) Nature , vol.432 , Issue.7018 , pp. 695-716
    • Hillier, L.W.1    Miller, W.2    Birney, E.3    Warren, W.4    Hardison, R.C.5    Ponting, C.P.6    Bork, P.7    Burt, D.W.8    Groenen, M.A.M.9    Delany, M.E.10
  • 129
    • 0038632308 scopus 로고    scopus 로고
    • Outgroup misplacement and phylogenetic inaccuracy under a molecular clock-a simulation study
    • Cited on p. 385 [Holland et al., 2003]
    • [Holland et al., 2003] BR Holland. D Penny, and MD Hendy. Outgroup misplacement and phylogenetic inaccuracy under a molecular clock-a simulation study. Systematic Biology, 52(2):229-238, 2003. Cited on p. 385
    • (2003) Systematic Biology , vol.52 , Issue.2 , pp. 229-238
    • Holland, B.R.1    Penny, D.2    Hendy, M.D.3
  • 130
    • 3042637206 scopus 로고    scopus 로고
    • Using consensus networks to visualize contradictory evidence for species phylogeny
    • Cited on p. 323 [Holland et al., 2004]
    • [Holland et al., 2004] B Holland, KT Huber, V Moulton, and P Lockhart. Using consensus networks to visualize contradictory evidence for species phylogeny. Molecular Biology and Evolution, 21 (7): 1459-1461, 2004. Cited on p. 323
    • (2004) Molecular Biology and Evolution , vol.21 , Issue.7 , pp. 1459-1461
    • Holland, B.1    Huber, K.T.2    Moulton, V.3    Lockhart, P.4
  • 131
    • 31844444234 scopus 로고    scopus 로고
    • Solving the likelihood equations
    • To appear. Cited on p. 108, 335, 343, 344 [Ho§ten et al., 2005]
    • [Ho§ten et al., 2005] S Ho§ten, A Khetan, and B Sturmfels. Solving the likelihood equations. Foundations of Computational Mathematics, 2005. To appear. Cited on p. 108, 335, 343, 344
    • (2005) Foundations of Computational Mathematics
    • Ho§ten, S.1    Khetan, A.2    Sturmfels, B.3
  • 132
    • 1342347024 scopus 로고    scopus 로고
    • Spectronet: A package for computing spectra and median networks
    • Cited on p. 323 [Huber et al., 2002]
    • [Huber et al., 2002] KT Huber, M Langton, D Penny, V Moulton, and M Hendy. Spectronet: A package for computing spectra and median networks. Applied Bioinformatics, 1(3):2041-2059, 2002. Cited on p. 323
    • (2002) Applied Bioinformatics , vol.1 , Issue.3 , pp. 2041-2059
    • Huber, K.T.1    Langton, M.2    Penny, D.3    Moulton, V.4    Hendy, M.5
  • 133
    • 0034077901 scopus 로고    scopus 로고
    • A compound poisson process for relaxing the molecular clock
    • Cited on p. 385 [Huelsenbeck et al., 2000]
    • [Huelsenbeck et al., 2000] JP Huelsenbeck, B Larget, and DL Swofford. A compound poisson process for relaxing the molecular clock. Genetics, 154(4):1879-1892, 2000. Cited on p. 385
    • (2000) Genetics , vol.154 , Issue.4 , pp. 1879-1892
    • Huelsenbeck, J.P.1    Larget, B.2    Swofford, D.L.3
  • 134
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • February, Cited on p. 384 [Human Genome Sequencing Consortium, 2001]
    • [Human Genome Sequencing Consortium, 2001] Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature, 409(6822):860-921, February 2001. Cited on p. 384
    • (2001) Nature , vol.409 , Issue.6822 , pp. 860-921
    • Human Genome Sequencing Consortium1
  • 135
    • 7244245762 scopus 로고    scopus 로고
    • Finishing the euchromatic sequence of the human genome
    • Cited on p. 125, 126, 129, 135 [Human Genome Sequencing Consortium, 2004]
    • [Human Genome Sequencing Consortium, 2004] International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature, 431(7011):931-945, 2004. Cited on p. 125, 126, 129, 135
    • (2004) Nature , vol.431 , Issue.7011 , pp. 931-945
    • International Human Genome Sequencing Consortium1
  • 138
    • 84926131824 scopus 로고
    • A preliminary draft was published in the January, issue of IEEE Computer, together with several companion articles. from the IEEE Service Center, Piscataway, NJ, USA. Cited on p. 359 [IEEE Task P754, 1985]
    • [IEEE Task P754, 1985] IEEE, New York. ANSI/IEEE 754-1985, Standard for Binary Floating-Point Arithmetic, 1985. A preliminary draft was published in the January 1980 issue of IEEE Computer, together with several companion articles. Available from the IEEE Service Center, Piscataway, NJ, USA. Cited on p. 359
    • (1980) ANSI/IEEE 754-1985, Standard for Binary Floating-Point Arithmetic, 1985
    • IEEE, New York,1
  • 139
    • 0242458540 scopus 로고    scopus 로고
    • Wiley-Interscience Series in Discrete Mathematics and Optimization. Wiley-Interscience, New York, Structure and recognition, With a foreword by Peter Winkler. Cited on p. 323 [Imrich and Klavzar, 2000]
    • [Imrich and Klavzar, 2000] W Imrich and S Klavzar. Product Graphs. Wiley-Interscience Series in Discrete Mathematics and Optimization. Wiley-Interscience, New York, 2000. Structure and recognition, With a foreword by Peter Winkler. Cited on p. 323
    • (2000) Product Graphs
    • Imrich, W.1    Klavzar, S.2
  • 140
    • 0041928191 scopus 로고    scopus 로고
    • Performance study of phylogenetic methods: (unweighted) quartet methods and neighbor joining
    • Cited on p. 303 [John et al., 2003]
    • [John et al., 2003] K St. John, T Warnow, B Moret, and L Vawter. Performance study of phylogenetic methods: (unweighted) quartet methods and neighbor joining. Journal of Algorithms, 48:174-193, 2003. Cited on p. 303
    • (2003) Journal of Algorithms , vol.48 , pp. 174-193
    • St. John, K.1    Warnow, T.2    Moret, B.3    Vawter, L.4
  • 142
    • 0000732090 scopus 로고
    • Evolution of protein molecules
    • HN Munro, editor, New York Academic Press, Cited on p. 153, 366 [Jukes and Cantor, 1969]
    • [Jukes and Cantor, 1969] TH Jukes and C Cantor. Evolution of protein molecules. In HN Munro, editor, Mammalian Protein Metabolism, pages 21-32. New York Academic Press, 1969. Cited on p. 153, 366
    • (1969) Mammalian Protein Metabolism , pp. 21-32
    • Jukes, T.H.1    Cantor, C.2
  • 143
    • 0025259313 scopus 로고
    • Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes
    • Cited on p. 80 [Karlin and Altschul, 1990]
    • [Karlin and Altschul, 1990] S Karlin and SF Altschul. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proceedings of the National Academy of Sciences, USA, 87:2264-2268, 1990. Cited on p. 80
    • (1990) Proceedings of the National Academy of Sciences, USA , vol.87 , pp. 2264-2268
    • Karlin, S.1    Altschul, S.F.2
  • 144
    • 1942452749 scopus 로고    scopus 로고
    • Proof and evolutionary analysis of ancient genome duplication in the yeast saccharomyces cerevisae
    • Cited on p. 130 [Kellis et al., 2004]
    • [Kellis et al., 2004] M Kellis, B Birren, and E Lander. Proof and evolutionary analysis of ancient genome duplication in the yeast saccharomyces cerevisae. Nature, 8:617-624, 2004. Cited on p. 130
    • (2004) Nature , vol.8 , pp. 617-624
    • Kellis, M.1    Birren, B.2    Lander, E.3
  • 146
    • 0036226603 scopus 로고    scopus 로고
    • Blat-the blast like alignment tool
    • Cited on p. 81, 276 [Kent, 2002]
    • [Kent, 2002] WJ Kent. Blat-the blast like alignment tool. Genome Biology, 12(4):656-664, 2002. Cited on p. 81, 276
    • (2002) Genome Biology , vol.12 , Issue.4 , pp. 656-664
    • Kent, W.J.1
  • 147
    • 45949127443 scopus 로고
    • Polynomial algorithms in linear programming
    • Cited on p. 176, 184 [Khachiyan, 1980]
    • [Khachiyan, 1980] LG Khachiyan. Polynomial algorithms in linear programming. USSR. Computational Mathematics and Mathematical Physics, 20:53-72, 1980. Cited on p. 176, 184
    • (1980) USSR. Computational Mathematics and Mathematical Physics , vol.20 , pp. 53-72
    • Khachiyan, L.G.1
  • 148
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rates of base substitution through comparative studies of nucleotide sequences
    • Cited on p. 154 [Kimura, 1980]
    • [Kimura, 1980] M Kimura. A simple method for estimating evolutionary rates of base substitution through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16:111-120, 1980. Cited on p. 154
    • (1980) Journal of Molecular Evolution , vol.16 , pp. 111-120
    • Kimura, M.1
  • 149
    • 0001464973 scopus 로고
    • Estimation of evolutionary sequences between homologous nucleotide sequences
    • Cited on p. 154, 329 [Kimura, 1981]
    • [Kimura, 1981] M Kimura. Estimation of evolutionary sequences between homologous nucleotide sequences. Proceedings of the National Academy of Sciences, USA, 78:454-458, 1981. Cited on p. 154, 329
    • (1981) Proceedings of the National Academy of Sciences, USA , vol.78 , pp. 454-458
    • Kimura, M.1
  • 150
    • 0042782730 scopus 로고    scopus 로고
    • Multi-camera scenere construction viagraph cuts
    • Cited on p. 274, 276 [Kolmogorov and Zabih, 2003]
    • [Kolmogorov and Zabih, 2003] V Kolmogorov and R Zabih. Multi-camera scene re-. construction via graph cuts. European Conference on Computer Vision (ECCV), 2003. Cited on p. 274, 276
    • (2003) European Conference on Computer Vision (ECCV)
    • Kolmogorov, V.1    Zabih, R.2
  • 151
    • 17444437765 scopus 로고    scopus 로고
    • Integrating genomic homology into gene structure prediction
    • Cited on p. 129 [Korf et al., 2001]
    • [Korf et al., 2001] I Korf, P Flicek, D Duan, and MR Brent. Integrating genomic homology into gene structure prediction. Bioinformatics, 17 Suppl l:S140-8, 2001. Cited on p. 129
    • (2001) Bioinformatics , vol.17 , pp. S140-S148
    • Korf, I.1    Flicek, P.2    Duan, D.3    Brent, M.R.4
  • 152
    • 10044259013 scopus 로고    scopus 로고
    • O'Reilly & Associates, Sebastopol, CA, Cited on p. 81 [Korf et al., 2003]
    • [Korf et al., 2003] I Korf, M Yandell, and J Bedell. BLAST. O'Reilly & Associates, Sebastopol, CA, 2003. Cited on p. 81
    • (2003) BLAST
    • Korf, I.1    Yandell, M.2    Bedell, J.3
  • 153
    • 0003967444 scopus 로고
    • Cambridge University Press, Cambridge, second edition, Cited on p. 328, 333 [Korner, 1989]
    • [Korner, 1989] TW Korner. Fourier Analysis. Cambridge University Press, Cambridge, second edition, 1989. Cited on p. 328, 333
    • (1989) Fourier Analysis
    • Korner, T.W.1
  • 154
    • 0035246564 scopus 로고    scopus 로고
    • Factor graphs and the sum-product algorithm
    • February, Cited on p. 41 [Kschischang et al., 2001]
    • [Kschischang et al., 2001] F Kschischang, H Loeliger, and B Frey. Factor graphs and the sum-product algorithm. IEEE Transactions on Information Theory, 47(2), February 2001. Cited on p. 41
    • (2001) IEEE Transactions on Information Theory , vol.47 , Issue.2
    • Kschischang, F.1    Loeliger, H.2    Frey, B.3
  • 155
    • 0002719797 scopus 로고
    • The Hungarian method for the assignment problem
    • Cited on p. 49 [Kuhn, 1955]
    • [Kuhn, 1955] HW Kuhn. The Hungarian method for the assignment problem. Naval Research Logistics Quarterly, 2:83-97, 1955. Cited on p. 49
    • (1955) Naval Research Logistics Quarterly , vol.2 , pp. 83-97
    • Kuhn, H.W.1
  • 158
    • 84926106224 scopus 로고    scopus 로고
    • Viterbi sequences and polytopes
    • To appear. Cited on p. 229, 230, 235 [Kuo, 2005]
    • [Kuo, 2005] E Kuo. Viterbi sequences and polytopes. Journal of Symbolic Computation, 2005. To appear. Cited on p. 229, 230, 235
    • (2005) Journal of Symbolic Computation
    • Kuo, E.1
  • 159
    • 0023150708 scopus 로고
    • A rate-independent technique for analysis of nucleaic acid sequences: Evolutionary parsimony
    • Cited on p. 348 [Lake, 1987]
    • [Lake, 1987] JA Lake. A rate-independent technique for analysis of nucleaic acid sequences: evolutionary parsimony. Molecular Biology and Evolution, 4:167-191, 1987. Cited on p. 348
    • (1987) Molecular Biology and Evolution , vol.4 , pp. 167-191
    • Lake, J.A.1
  • 160
    • 0021277009 scopus 로고
    • A new method for calculating evolutionary substitution rates
    • Cited on p. 155 [Lanave et al., 1984]
    • [Lanave et al., 1984] CG Lanave, G Preparata, C Saccone, and G Serio. A new method for calculating evolutionary substitution rates. Journal of Molecular Evolution, 20:86-93, 1984. Cited on p. 155
    • (1984) Journal of Molecular Evolution , vol.20 , pp. 86-93
    • Lanave, C.G.1    Preparata, G.2    Saccone, C.3    Serio, G.4
  • 161
    • 0023988195 scopus 로고
    • Genomic mapping by fingerprinting random clones: A mathematical analysis
    • Cited on p. 134 [Lander and Waterman, 1988]
    • [Lander and Waterman, 1988] ES Lander and MS Waterman. Genomic mapping by fingerprinting random clones: a mathematical analysis. Genomics, 2:231-239, 1988. Cited on p. 134
    • (1988) Genomics , vol.2 , pp. 231-239
    • Lander, E.S.1    Waterman, M.S.2
  • 162
    • 10844229441 scopus 로고    scopus 로고
    • On the ideals of secant varieties of Segre varieties
    • Cited on p. 351 [Landsberg and Manivel, 2004]
    • [Landsberg and Manivel, 2004] JM Landsberg and L Manivel. On the ideals of secant varieties of Segre varieties. Foundations of Computational Mathematics, 4(4):397-422, 2004. Cited on p. 351
    • (2004) Foundations of Computational Mathematics , vol.4 , Issue.4 , pp. 397-422
    • Landsberg, J.M.1    Manivel, L.2
  • 163
    • 3042799574 scopus 로고    scopus 로고
    • A computational algebra approach to the reverse engineering of gene regulatory networks
    • Cited on p. 94 [Laubenbacher and Stigler, 2004]
    • [Laubenbacher and Stigler, 2004] R Laubenbacher and B Stigler. A computational algebra approach to the reverse engineering of gene regulatory networks. Journal of Theoretical Biology, 229:523-537, 2004. Cited on p. 94
    • (2004) Journal of Theoretical Biology , vol.229 , pp. 523-537
    • Laubenbacher, R.1    Stigler, B.2
  • 164
    • 0039429807 scopus 로고    scopus 로고
    • The Clarendon Press Oxford University Press, New York, Oxford Science Publications. Cited on p. 36, 38, 40, 281, 283 [Lauritzen, 1996]
    • [Lauritzen, 1996] SL Lauritzen. Graphical models, volume 17 of Oxford Statistical Science Series. The Clarendon Press Oxford University Press, New York, 1996. Oxford Science Publications. Cited on p. 36, 38, 40, 281, 283
    • (1996) Graphical models volume 17 of Oxford Statistical Science Series
    • Lauritzen, S.L.1
  • 165
    • 0020845921 scopus 로고
    • Integer programming with a fixed number of variables
    • Cited on p. 48 [Lenstra, 1983]
    • [Lenstra, 1983] HW Lenstra. Integer programming with a fixed number of variables. Mathematics of Operations Research, 8(4):538-548, 1983. Cited on p. 48
    • (1983) Mathematics of Operations Research , vol.8 , Issue.4 , pp. 538-548
    • Lenstra, H.W.1
  • 166
    • 0023256559 scopus 로고
    • Slipped-strand rnispairing: A major mechanism for DNA sequence evolution
    • Cited on p. 157 [Levinson and Gutman, 1987]
    • [Levinson and Gutman, 1987] G Levinson and GA Gutman. Slipped-strand rnispairing: a major mechanism for DNA sequence evolution. Molecular Biology and Evolution, 4:203-221, 1987. Cited on p. 157
    • (1987) Molecular Biology and Evolution , vol.4 , pp. 203-221
    • Levinson, G.1    Gutman, G.A.2
  • 168
    • 0036897677 scopus 로고    scopus 로고
    • Four new mitochondrial genomes and the increased stability of evolutionary trees of mammals from improved taxon sampling
    • Cited on p. 382 [Lin et al., 2002]
    • [Lin et al., 2002] YH Lin, PA McLenachan, AR Gore, MJ Phillips, R Ota, MD Hendy, and D Penny. Four new mitochondrial genomes and the increased stability of evolutionary trees of mammals from improved taxon sampling. Molecular Phylogenetics and Evolution, 19:2060-2070, 2002. Cited on p. 382
    • (2002) Molecular Phylogenetics and Evolution , vol.19 , pp. 2060-2070
    • Lin, Y.H.1    McLenachan, P.A.2    Gore, A.R.3    Phillips, M.J.4    Ota, R.5    Hendy, M.D.6    Penny, D.7
  • 170
    • 0036605359 scopus 로고    scopus 로고
    • Rump's example revisited
    • Cited on p. 360 [Loh and Walster, 2002]
    • [Loh and Walster, 2002] E Loh and GW Walster. Rump's example revisited. Reliable Computing, 8:245-248, 2002. Cited on p. 360
    • (2002) Reliable Computing , vol.8 , pp. 245-248
    • Loh, E.1    Walster, G.W.2
  • 172
    • 0033523854 scopus 로고    scopus 로고
    • A combined algorithm for genome-wide prediction of protein function
    • Cited on p. 265 [Marcotte et al., 1999]
    • [Marcotte et al., 1999] EM Marcotte, M Pellegrini, MJ Thompson, T Yeates, and D Eisenberg. A combined algorithm for genome-wide prediction of protein function. Nature, 402:83-86, 1999. Cited on p. 265
    • (1999) Nature , vol.402 , pp. 83-86
    • Marcotte, E.M.1    Pellegrini, M.2    Thompson, M.J.3    Yeates, T.4    Eisenberg, D.5
  • 173
    • 4444311171 scopus 로고    scopus 로고
    • Multiple-sequence functional annotation and the generalized hidden Markov phylogeny
    • Cited on p. 157, 402 [McAuliffe et al., 2004]
    • [McAuliffe et al., 2004] JD McAuliffe, L Pachter, and MI Jordan. Multiple-sequence functional annotation and the generalized hidden Markov phylogeny. Bioinformatics, 20(12):1850-60, 2004. Cited on p. 157, 402
    • (2004) Bioinformatics , vol.20 , Issue.12 , pp. 1850-1860
    • McAuliffe, J.D.1    Pachter, L.2    Jordan, M.I.3
  • 174
    • 0020845843 scopus 로고
    • Linear programming in linear time when the dimension is fixed
    • Cited on p. 176, 177, 184 [Megiddo, 1984]
    • [Megiddo, 1984] N Megiddo. Linear programming in linear time when the dimension is fixed. Journal of the Association for Computing Machinery, 31(1):114-127, 1984. Cited on p. 176, 177, 184
    • (1984) Journal of the Association for Computing Machinery , vol.31 , Issue.1 , pp. 114-127
    • Megiddo, N.1
  • 176
    • 0000028316 scopus 로고
    • Ribosomal RNA in vertebrates: Evolution and phylogenetic applications
    • Cited on p. 386 [Mindell and Honeycutt, 1990]
    • [Mindell and Honeycutt, 1990] DP Mindell and RL Honeycutt. Ribosomal RNA in vertebrates: evolution and phylogenetic applications. Annual Review of Ecology and Systematics, 21:541-566, 1990. Cited on p. 386
    • (1990) Annual Review of Ecology and Systematics , vol.21 , pp. 541-566
    • Mindell, D.P.1    Honeycutt, R.L.2
  • 177
    • 1542407746 scopus 로고    scopus 로고
    • Stochastic factorisations, sandwiched simplices and the topology of the space of explanations
    • Cited on p. 24 [Mond et al., 2003]
    • [Mond et al., 2003] DMQ Mond, JQ Smith, and D Van Straten. Stochastic factorisations, sandwiched simplices and the topology of the space of explanations. Proceedings of the Royal Society of London, Series A, 459:2821-2845, 2003. Cited on p. 24
    • (2003) Proceedings of the Royal Society of London, Series A , vol.459 , pp. 2821-2845
    • Mond, D.M.Q.1    Smith, J.Q.2    Van Straten, D.3
  • 178
    • 0004293209 scopus 로고
    • Prentice-Hall, Englewood Cliffs, New Jersey, Cited on p. 360, 363 [Moore, 1967]
    • [Moore, 1967] RE Moore. Interval Analysis. Prentice-Hall, Englewood Cliffs, New Jersey, 1967. Cited on p. 360, 363
    • (1967) Interval Analysis
    • Moore, R.E.1
  • 180
    • 0020050314 scopus 로고
    • A catalogue of splice junction sequence
    • Cited on p. 144 [Mount, 1982]
    • [Mount, 1982] SM Mount. A catalogue of splice junction sequence. Nucleic Acids Research, 10(2):459-472, 1982. Cited on p. 144
    • (1982) Nucleic Acids Research , vol.10 , Issue.2 , pp. 459-472
    • Mount, S.M.1
  • 181
    • 0035252080 scopus 로고    scopus 로고
    • Molecular phylogenetics and the origins of placental mammals
    • Cited on p. 382 [Murphy et al., 2001]
    • [Murphy et al., 2001] WJ Murphy, E Eizirik, WE Johnson, YP Zhang, OA Ryder, and SJ O'Brien. Molecular phylogenetics and the origins of placental mammals. Nature, 409:614-618, 2001. Cited on p. 382
    • (2001) Nature , vol.409 , pp. 614-618
    • Murphy, W.J.1    Eizirik, E.2    Johnson, W.E.3    Zhang, Y.P.4    Ryder, O.A.5    O'Brien, S.J.6
  • 182
    • 0346388742 scopus 로고    scopus 로고
    • Whole-genome DNA sequencing
    • Cited on p. 127 [Myers, 1999]
    • [Myers, 1999] E Myers. Whole-genome DNA sequencing. IEEE Computational Engineering and Science, 3(1):33-43, 1999. Cited on p. 127
    • (1999) IEEE Computational Engineering and Science , vol.3 , Issue.1 , pp. 33-43
    • Myers, E.1
  • 183
    • 0037066461 scopus 로고    scopus 로고
    • Recognition and rejection of self in plant reproduction
    • Cited on p. 374 [Nasrallah, 2002]
    • [Nasrallah, 2002] JB Nasrallah. Recognition and rejection of self in plant reproduction. Science, 296:305-308, 2002. Cited on p. 374
    • (2002) Science , vol.296 , pp. 305-308
    • Nasrallah, J.B.1
  • 184
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • Cited on p. 50 [Needleman and Wunsch, 1970]
    • [Needleman and Wunsch, 1970] SB Needleman and CD Wunsch. A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal of Molecular Biology, 48:443-445, 1970. Cited on p. 50
    • (1970) Journal of Molecular Biology , vol.48 , pp. 443-445
    • Needleman, S.B.1    Wunsch, C.D.2
  • 186
    • 0001879933 scopus 로고
    • Molecular studies of evolution: A source of novel statistical problems
    • S Gupta and Y Jackel, editors, Academic Press, New York, Cited on p. 298 [Neyman, 1971]
    • [Neyman, 1971] J Neyman. Molecular studies of evolution: A source of novel statistical problems. In S Gupta and Y Jackel, editors, Statistical Decision Theory and Related Topics, pages 1-27. Academic Press, New York, 1971. Cited on p. 298
    • (1971) Statistical Decision Theory and Related Topics , pp. 1-27
    • Neyman, J.1
  • 187
    • 0022261138 scopus 로고
    • Evolution of the functional human beta-actin gene and its multipseudogene family: Conservation of noncoding regions and chromosomal dispersion of pseudogenes
    • Cited on p. 396 [Ng et al., 1985]
    • [Ng et al., 1985] SY Ng, P Gunning, R Eddy, P Ponte, J Leavitt, T Shows, and L Kedes. Evolution of the functional human beta-actin gene and its multipseudogene family: conservation of noncoding regions and chromosomal dispersion of pseudogenes. Molecular and Cellular Biology, 5:2720-2732, 1985. Cited on p. 396
    • (1985) Molecular and Cellular Biology , vol.5 , pp. 2720-2732
    • Ng, S.Y.1    Gunning, P.2    Eddy, R.3    Ponte, P.4    Leavitt, J.5    Shows, T.6    Kedes, L.7
  • 188
    • 0142084743 scopus 로고    scopus 로고
    • Scanning human gene deserts for long-range enhancers
    • Cited on p. 393 [Nobrega et al., 2003]
    • [Nobrega et al., 2003] MA Nobrega, I Ovcharenko, V Afzal, and EM Rubin. Scanning human gene deserts for long-range enhancers. Science, 302(5644):413-, 2003. Cited on p. 393
    • (2003) Science , vol.302 , Issue.5644 , pp. 413
    • Nobrega, M.A.1    Ovcharenko, I.2    Afzal, V.3    Rubin, E.M.4
  • 189
    • 0033857959 scopus 로고    scopus 로고
    • Njml: A hybrid algorithm for the neighborjoining and maximum likelihood methods
    • Cited on p. 356 [Ota and Li, 2000]
    • [Ota and Li, 2000] S Ota and WH Li. Njml: A hybrid algorithm for the neighborjoining and maximum likelihood methods. Molecular Biology and Evolution, 17(9):1401-1409, 2000. Cited on p. 356
    • (2000) Molecular Biology and Evolution , vol.17 , Issue.9 , pp. 1401-1409
    • Ota, S.1    Li, W.H.2
  • 190
    • 25144492428 scopus 로고    scopus 로고
    • Reconstructing trees from subtree weights
    • Cited on p. 335 [Pachter and Speyer, 2004]
    • [Pachter and Speyer, 2004] L Pachter and D Speyer. Reconstructing trees from subtree weights. Applied Mathematics Letters, 17(6):615-621, 2004. Cited on p. 335
    • (2004) Applied Mathematics Letters , vol.17 , Issue.6 , pp. 615-621
    • Pachter, L.1    Speyer, D.2
  • 191
    • 9244264948 scopus 로고    scopus 로고
    • Parametric inference for biological sequence analysis
    • Cited on p. 165, 181, 194 [Pachter and Sturmfels, 2004a]
    • [Pachter and Sturmfels, 2004a] L Pachter and B Sturmfels. Parametric inference for biological sequence analysis. Proc Natl Acad Sci USA, 101(46):16138-43, 2004. Cited on p. 165, 181, 194
    • (2004) Proc Natl Acad Sci USA , vol.101 , Issue.46 , pp. 16138-16143
    • Pachter, L.1    Sturmfels, B.2
  • 192
    • 9244251033 scopus 로고    scopus 로고
    • Tropical geometry of statistical models
    • Cited on p. 115, 239 [Pachter and Sturmfels, 2004b]
    • [Pachter and Sturmfels, 2004b] L Pachter and B Sturmfels. Tropical geometry of statistical models. Proceedings of the National Academy of Sciences, USA, 101(46):16132-7, 2004. Cited on p. 115, 239
    • (2004) Proceedings of the National Academy of Sciences, USA , vol.101 , Issue.46 , pp. 16132-16137
    • Pachter, L.1    Sturmfels, B.2
  • 193
    • 84926128263 scopus 로고    scopus 로고
    • The mathematics of phylogenomics
    • Cited on p. 215, 345, 390, 400 [Pachter and Sturmfels, 2005]
    • [Pachter and Sturmfels, 2005] L Pachter and B Sturmfels. The mathematics of phylogenomics. Submitted, 2005. Cited on p. 215, 345, 390, 400
    • (2005) Submitted
    • Pachter, L.1    Sturmfels, B.2
  • 194
    • 0036112213 scopus 로고    scopus 로고
    • Applications of generalized pair hidden Markov models to alignment and gene finding problems
    • Cited on p. 145 [Pachter et al., 2002]
    • [Pachter et al., 2002] L Pachter, M Alexandersson, and S Cawley. Applications of generalized pair hidden Markov models to alignment and gene finding problems. J Comput Biol, 9(2):389-99, 2002. Cited on p. 145
    • (2002) J Comput Biol , vol.9 , Issue.2 , pp. 389-399
    • Pachter, L.1    Alexandersson, M.2    Cawley, S.3
  • 195
    • 0034061137 scopus 로고    scopus 로고
    • GENEID in drosophila
    • Cited on p. 236 [Parra et al., 2000]
    • [Parra et al., 2000] G Parra, E Blanco, and R Guigo. GENEID in drosophila. Genome Research, 10(4):511-515, 2000. Cited on p. 236
    • (2000) Genome Research , vol.10 , Issue.4 , pp. 511-515
    • Parra, G.1    Blanco, E.2    Guigo, R.3
  • 197
    • 0033782832 scopus 로고    scopus 로고
    • Organization of mouse iroquois homeobox genes in two clusters suggests a conserved regulation and function in vertebrate development
    • Cited on p. 395 [Peters et al., 2000]
    • [Peters et al., 2000] T Peters, R Dildrop, K Ausmeier, and U Ruther. Organization of mouse iroquois homeobox genes in two clusters suggests a conserved regulation and function in vertebrate development. Genome Research, 10:1453-1462, 2000. Cited on p. 395
    • (2000) Genome Research , vol.10 , pp. 1453-1462
    • Peters, T.1    Dildrop, R.2    Ausmeier, K.3    Ruther, U.4
  • 198
    • 0037264074 scopus 로고    scopus 로고
    • Genome rearrangements in mammalian evolution: Lessons from human and mouse genomes
    • Cited on p. 265 [Pevzner and Tesler, 2003]
    • [Pevzner and Tesler, 2003] P Pevzner and G Tesler. Genome rearrangements in mammalian evolution: lessons from human and mouse genomes. Genome Research, 13(1):37-45, 2003. Cited on p. 265
    • (2003) Genome Research , vol.13 , Issue.1 , pp. 37-45
    • Pevzner, P.1    Tesler, G.2
  • 199
    • 0141721426 scopus 로고    scopus 로고
    • The root of the mammalian tree inferred from whole mitochondrial genomes
    • Cited on p. 382 [Phillips and Penny, 2003]
    • [Phillips and Penny, 2003] MJ Phillips and D Penny. The root of the mammalian tree inferred from whole mitochondrial genomes. Molecular Phylogenetics and Evolution, 28:171-185, 2003. Cited on p. 382
    • (2003) Molecular Phylogenetics and Evolution , vol.28 , pp. 171-185
    • Phillips, M.J.1    Penny, D.2
  • 200
    • 0003388502 scopus 로고    scopus 로고
    • Tropical semirings
    • Publ. Newton Inst., Cambridge Univ. Press, Cambridge, Cited on p. 49 [Pin, 1998]
    • [Pin, 1998] Jean-Eric Pin. Tropical semirings. In Idempotency (Bristol, 1994), volume 11 of Publ. Newton Inst., pages 50-69. Cambridge Univ. Press, Cambridge, 1998. Cited on p. 49
    • (1998) Idempotency (Bristol, 1994) , vol.11 , pp. 50-69
    • Pin, J.-E.1
  • 202
    • 0035865464 scopus 로고    scopus 로고
    • Genomics, the cytoskeleton and motility
    • Cited on p. 396 [Pollard, 2001]
    • [Pollard, 2001] TD Pollard. Genomics, the cytoskeleton and motility. Nature, 409:842-843, 2001. Cited on p. 396
    • (2001) Nature , vol.409 , pp. 842-843
    • Pollard, T.D.1
  • 203
    • 0003487647 scopus 로고
    • Texts and Monographs in Computer Science. Springer Verlag, New York, Cited on p. 176 [Preparata and Shamos, 1985]
    • [Preparata and Shamos, 1985] F Preparata and MI Shamos. Computational Geometry: An Introduction. Texts and Monographs in Computer Science. Springer Verlag, New York, 1985. Cited on p. 176
    • (1985) Computational Geometry: An Introduction
    • Preparata, F.1    Shamos, M.I.2
  • 205
    • 19544368188 scopus 로고    scopus 로고
    • Estimating cancer survival and clinical outcome based on genetic tumor progression scores
    • To appear. Cited on p. 278 [Rahnenfiihrer et al., 2005]
    • [Rahnenfiihrer et al., 2005] J Rahnenfuhrer, N Beerenwinkel, WA Schulz, C Hartmann, A von Deimling, B Wullich, and T Lengauer. Estimating cancer survival and clinical outcome based on genetic tumor progression scores. Bioinformatics, 2005. To appear. Cited on p. 278
    • (2005) Bioinformatics
    • Rahnenfuhrer, J.1    Beerenwinkel, N.2    Schulz, W.A.3    Hartmann, C.4    von Deimling, A.5    Wullich, B.6    Lengauer, T.7
  • 207
    • 0030928378 scopus 로고    scopus 로고
    • Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
    • Cited on p. 343, 355 [Rambaut and Grassly, 1997]
    • [Rambaut and Grassly, 1997] A Rambaut and NC Grassly. Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci., 13:235-238, 1997. Cited on p. 343, 355
    • (1997) Comput. Appl. Biosci , vol.13 , pp. 235-238
    • Rambaut, A.1    Grassly, N.C.2
  • 208
    • 24044529257 scopus 로고    scopus 로고
    • Reconstructing tumor amplisomes
    • Special ISMB/ECCB, issue:I265-I273, 2004. Cited on p. 131 [Raphael and Pevzner, 2004]
    • [Raphael and Pevzner, 2004] B Raphael and P Pevzner. Reconstructing tumor amplisomes. Bioinformatics, 20 Suppl 1, Special ISMB/ECCB 2004 issue:I265-I273, 2004. Cited on p. 131
    • (2004) Bioinformatics , vol.20
    • Raphael, B.1    Pevzner, P.2
  • 211
    • 0030305457 scopus 로고    scopus 로고
    • R: A language for data analysis and graphics
    • Cited on p. 79, 303 [Ross and Gentleman, 1996]
    • [Ross and Gentleman, 1996] I Ross and R Gentleman. R: A language for data analysis and graphics. Journal of Computational and Graphical Statistics, 5(3):299-314, 1996. Cited on p. 79, 303
    • (1996) Journal of Computational and Graphical Statistics , vol.5 , Issue.3 , pp. 299-314
    • Ross, I.1    Gentleman, R.2
  • 212
    • 18844420035 scopus 로고    scopus 로고
    • Detecting site-specific physicochemical selective pressures: Applications to the class-I HLA of the human major histocompatibility complex and the SRK of the plant sporophytic self-incompatibility system
    • press, Cited on p. 374 [Sainudiin et al., 2005]
    • [Sainudiin et al., 2005] R Sainudiin, SW Wong, K Yogeeswaran, J Nasrallah, Z Yang, and R Nielsen. Detecting site-specific physicochemical selective pressures: applications to the class-I HLA of the human major histocompatibility complex and the SRK of the plant sporophytic self-incompatibility system. Journal of Molecular Evolution, in press, 2005. Cited on p. 374
    • (2005) Journal of Molecular Evolution
    • Sainudiin, R.1    Wong, S.W.2    Yogeeswaran, K.3    Nasrallah, J.4    Yang, Z.5    Nielsen, R.6
  • 214
    • 0023375195 scopus 로고
    • The neighbor joining method: A new method for reconstructing phylogenetic trees
    • Cited on p. 72, 335, 374 [Saitou and Nei, 1987]
    • [Saitou and Nei, 1987] N Saitou and M Nei. The neighbor joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4(4):406-425, 1987. Cited on p. 72, 335, 374
    • (1987) Molecular Biology and Evolution , vol.4 , Issue.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 217
    • 22144473057 scopus 로고    scopus 로고
    • Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes
    • Cited on p. 394, 395, 400 [Sandelin et al., 2004]
    • [Sandelin et al., 2004] A Sandelin, P Bailey, S Bruce, PG Engstrom, JM Klos, WW Wasserman, J Ericson, and B Lenhard. Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes. BMC Genomics, 5:99, 2004. Cited on p. 394, 395, 400
    • (2004) BMC Genomics , vol.5 , pp. 99
    • Sandelin, A.1    Bailey, P.2    Bruce, S.3    Engstrom, P.G.4    Klos, J.M.5    Wasserman, W.W.6    Ericson, J.7    Lenhard, B.8
  • 219
    • 0141817723 scopus 로고    scopus 로고
    • Chromosome rearrangements in evolution: From gene order to genome sequence and back
    • Cited on p. 130 [Sankoff and Nadeau, 2003]
    • [Sankoff and Nadeau, 2003] D Sankoff and JH Nadeau. Chromosome rearrangements in evolution: from gene order to genome sequence and back. Proceedings of the National Academy of Sciences, USA, 100:11188-11189, 2003. Cited on p. 130
    • (2003) Proceedings of the National Academy of Sciences, USA , vol.100 , pp. 11188-11189
    • Sankoff, D.1    Nadeau, J.H.2
  • 220
    • 11344254316 scopus 로고    scopus 로고
    • London Mathematical Society Student Texts. Cambridge University Press, Cited on p. 89 [Schenck, 2003]
    • [Schenck, 2003] H Schenck. Computational Algebraic Geometry. London Mathematical Society Student Texts. Cambridge University Press, 2003. Cited on p. 89
    • (2003) Computational Algebraic Geometry
    • Schenck, H.1
  • 221
    • 0141721394 scopus 로고    scopus 로고
    • A novel family of trna-derived sines in the colugo and two new retrotransposable markers separating dermopterans from primates
    • Cited on p. 382 [Schmitz and Zischler, 2003]
    • [Schmitz and Zischler, 2003] J Schmitz and H Zischler. A novel family of trna-derived sines in the colugo and two new retrotransposable markers separating dermopterans from primates. Molecular Phylogenetics and Evolution, 28:341-349, 2003. Cited on p. 382
    • (2003) Molecular Phylogenetics and Evolution , vol.28 , pp. 341-349
    • Schmitz, J.1    Zischler, H.2
  • 222
    • 0003690189 scopus 로고
    • Wiley-Interscience Series in Discrete Mathematics. John Wiley & Sons Ltd., Chichester, A Wiley-Interscience Publication. Cited on p. 48 [Schrijver, 1986]
    • [Schrijver, 1986] A Schrijver. Theory of Linear and Integer Programming. Wiley-Interscience Series in Discrete Mathematics. John Wiley & Sons Ltd., Chichester, 1986. A Wiley-Interscience Publication. Cited on p. 48
    • (1986) Theory of Linear and Integer Programming
    • Schrijver, A.1
  • 224
    • 34347382891 scopus 로고    scopus 로고
    • Convex hull computations
    • Jacob E. Goodman and Joseph O'Rourke, editors, Discrete Mathematics and its Applications (Boca Raton), chapter 22. Chapman & Hall/CRC, Boca Raton, FL, second edition, Cited on p. 185 [Seidel, 2004]
    • [Seidel, 2004] R Seidel. Convex hull computations. In Jacob E. Goodman and Joseph O'Rourke, editors, Handbook of Discrete and Computational Geometry, Discrete Mathematics and its Applications (Boca Raton), chapter 22. Chapman & Hall/CRC, Boca Raton, FL, second edition, 2004. Cited on p. 185
    • (2004) Handbook of Discrete and Computational Geometry
    • Seidel, R.1
  • 227
    • 1542537849 scopus 로고    scopus 로고
    • Combining phylogenetic and hidden markov models in biosequence analysis
    • Cited on p. 157, 402 [Siepel and Haussler, 2004]
    • [Siepel and Haussler, 2004] A Siepel and D Haussler. Combining phylogenetic and hidden markov models in biosequence analysis. Journal of Computational Biology, 11:413-428, 2004. Cited on p. 157, 402
    • (2004) Journal of Computational Biology , vol.11 , pp. 413-428
    • Siepel, A.1    Haussler, D.2
  • 228
    • 0034110066 scopus 로고    scopus 로고
    • Chromosome abnormalities in ovarian adenocarcinoma: III. Using breakpoint data to infer and test mathematical models for oncogenesis
    • Cited on p. 278 [Simon et al., 2000]
    • [Simon et al., 2000] R Simon, R Desper, CH Papadimitriou, A Peng, DS Alberts, R Taetle, JM Trent, and AA Schaffer. Chromosome abnormalities in ovarian adenocarcinoma: III. Using breakpoint data to infer and test mathematical models for oncogenesis. Genes, Chromosomes & Cancer, 28:106-120, 2000. Cited on p. 278
    • (2000) Genes, Chromosomes & Cancer , vol.28 , pp. 106-120
    • Simon, R.1    Desper, R.2    Papadimitriou, C.H.3    Peng, A.4    Alberts, D.S.5    Taetle, R.6    Trent, J.M.7    Schaffer, A.A.8
  • 229
    • 0004124452 scopus 로고    scopus 로고
    • Oxford University Press, second edition, March, Cited on p. ii [Smith, 1998]
    • [Smith, 1998] JM Smith. Evolutionary Genetics. Oxford University Press, second edition, March 1998. Cited on p. ii
    • (1998) Evolutionary Genetics
    • Smith, J.M.1
  • 231
    • 21144449316 scopus 로고    scopus 로고
    • The tropical Grassmannian
    • Cited on p. 118, 122 [Speyer and Sturmfels, 2004]
    • [Speyer and Sturmfels, 2004] D Speyer and B Sturmfels. The tropical Grassmannian. Adv. Geom., 4(3):389-411, 2004. Cited on p. 118, 122
    • (2004) Adv. Geom , vol.4 , Issue.3 , pp. 389-411
    • Speyer, D.1    Sturmfels, B.2
  • 232
    • 84926078236 scopus 로고    scopus 로고
    • The tropical totally positive Grassmanian
    • Cited on p. 115 [Speyer and Williams, 2004]
    • [Speyer and Williams, 2004] D Speyer and L Williams. The tropical totally positive Grassmanian. Journal of Algebraic Combinatorics, in press, 2004. Cited on p. 115
    • (2004) Journal of Algebraic Combinatorics, in press
    • Speyer, D.1    Williams, L.2
  • 233
    • 84926111279 scopus 로고    scopus 로고
    • Tropical linear spaces
    • Cited on p. 121 [Speyer, 2004]
    • [Speyer, 2004] D Speyer. Tropical linear spaces. Submitted, 2004. Cited on p. 121
    • (2004) Submitted
    • Speyer, D.1
  • 234
    • 0004882650 scopus 로고    scopus 로고
    • Cambridge University Press, Cambridge, With a foreword by Gian-Carlo Rota and appendix 1 by Sergey Fomin. Cited on p. 51, 100, 279 [Stanley, 1999]
    • [Stanley, 1999] RP Stanley. Enumerative combinatorics. Vol. 2, volume 62 of Cambridge Studies in Advanced Mathematics. Cambridge University Press, Cambridge, 1999. With a foreword by Gian-Carlo Rota and appendix 1 by Sergey Fomin. Cited on p. 51, 100, 279
    • (1999) Enumerative combinatorics. Vol. 2, volume 62 of Cambridge Studies in Advanced Mathematics
    • Stanley, R.P.1
  • 235
    • 38249008297 scopus 로고
    • Spectral analysis and a closest tree method for genetic sequences
    • Cited on p. 332, 334 [Steel et al., 1992]
    • [Steel et al., 1992] MA Steel, MD Hendy, LA Szekely, and PL Erdos. Spectral analysis and a closest tree method for genetic sequences. Applied Mathematics Letters, 5(6):63-67, 1992. Cited on p. 332, 334
    • (1992) Applied Mathematics Letters , vol.5 , Issue.6 , pp. 63-67
    • Steel, M.A.1    Hendy, M.D.2    Szekely, L.A.3    Erdos, P.L.4
  • 236
    • 0004045702 scopus 로고    scopus 로고
    • Garland Press, third edition, June, Cited on p. 131 [Strachan and Read, 2004]
    • [Strachan and Read, 2004] T Strachan and AP Read. Human Molecular Genetics. Garland Press, third edition, June 2004. Cited on p. 131
    • (2004) Human Molecular Genetics
    • Strachan, T.1    Read, A.P.2
  • 237
    • 0039957423 scopus 로고
    • Rank and optimal computation of generic tensors
    • Cited on p. 351 [Strassen, 1983]
    • [Strassen, 1983] V Strassen. Rank and optimal computation of generic tensors. Linear Algebra Appl., 52/53:645-685, 1983. Cited on p. 351
    • (1983) Linear Algebra Appl , vol.52-53 , pp. 645-685
    • Strassen, V.1
  • 238
    • 0034088330 scopus 로고    scopus 로고
    • Likelihood analysis of phylogenetic networks using directed graphical models
    • Cited on p. 326 [Strimmer and Moulton, 2000]
    • [Strimmer and Moulton, 2000] K Strimmer and V Moulton. Likelihood analysis of phylogenetic networks using directed graphical models. Molecular Biology and Evolution, 17:875-881, 2000. Cited on p. 326
    • (2000) Molecular Biology and Evolution , vol.17 , pp. 875-881
    • Strimmer, K.1    Moulton, V.2
  • 239
    • 0029836454 scopus 로고    scopus 로고
    • Quartet puzzling: A quartet maximum likelihood method for reconstructing tree topologies
    • Cited on p. 356 [Strimmer and von Haeseler, 1996]
    • [Strimmer and von Haeseler, 1996] K Strimmer and A von Haeseler. Quartet puzzling: A quartet maximum likelihood method for reconstructing tree topologies. Molecular Biology and Evolution, 13:964-969, 1996. Cited on p. 356
    • (1996) Molecular Biology and Evolution , vol.13 , pp. 964-969
    • Strimmer, K.1    von Haeseler, A.2
  • 240
    • 0035151371 scopus 로고    scopus 로고
    • Recombination analysis using directed graphical models
    • Cited on p. 326, 327 [Strimmer et al., 2001]
    • [Strimmer et al., 2001] K Strimmer, C Wiuf, and V Moulton. Recombination analysis using directed graphical models. Molecular Biology and Evolution, 18:97-99, 2001. Cited on p. 326, 327
    • (2001) Molecular Biology and Evolution , vol.18 , pp. 97-99
    • Strimmer, K.1    Wiuf, C.2    Moulton, V.3
  • 241
    • 0024114801 scopus 로고
    • A note on the neighborjoining method of saitou and nei
    • Cited on p. 72 [Studier and Keppler, 1988]
    • [Studier and Keppler, 1988] JA Studier and KJ Keppler. A note on the neighborjoining method of saitou and nei. Molecular Biology and Evolution, 5:729-731, 1988. Cited on p. 72
    • (1988) Molecular Biology and Evolution , vol.5 , pp. 729-731
    • Studier, J.A.1    Keppler, K.J.2
  • 242
    • 15944419142 scopus 로고    scopus 로고
    • Toric ideals of phylogenetic invariants
    • Cited on p. 152, 153, 296, 302, 303, 306, 348 [Sturmfels and Sullivant, 2005]
    • [Sturmfels and Sullivant, 2005] B Sturmfels and S Sullivant. Toric ideals of phylogenetic invariants. Journal of Computational Biology, 12:204-228, 2005. Cited on p. 152, 153, 296, 302, 303, 306, 348
    • (2005) Journal of Computational Biology , vol.12 , pp. 204-228
    • Sturmfels, B.1    Sullivant, S.2
  • 243
    • 51249172372 scopus 로고
    • Grobner bases and Stanley decompositions of determinantal rings
    • Cited on p. 92 [Sturmfels, 1990]
    • [Sturmfels, 1990] B Sturmfels. Grobner bases and Stanley decompositions of determinantal rings. Mathematische Zeitschrift, 205(1):137-144, 1990. Cited on p. 92
    • (1990) Mathematische Zeitschrift , vol.205 , Issue.1 , pp. 137-144
    • Sturmfels, B.1
  • 244
    • 0003834321 scopus 로고
    • Texts and Monographs in Symbolic Computation. Springer-Verlag, Vienna, Cited on p. 99 [Sturmfels, 1993]
    • [Sturmfels, 1993] B Sturmfels. Algorithms in Invariant Theory. Texts and Monographs in Symbolic Computation. Springer-Verlag, Vienna, 1993. Cited on p. 99
    • (1993) Algorithms in Invariant Theory
    • Sturmfels, B.1
  • 246
    • 0038586502 scopus 로고    scopus 로고
    • Confidence regions and hypothesis tests for topologies using generalized least squares
    • Cited on p. 325, 326 [Susko, 2003]
    • [Susko, 2003] E Susko. Confidence regions and hypothesis tests for topologies using generalized least squares. Molecular Biology and Evolution, 2003. Cited on p. 325, 326
    • (2003) Molecular Biology and Evolution
    • Susko, E.1
  • 249
    • 0036224045 scopus 로고    scopus 로고
    • Estimating an oncogenetic tree when false negatives and positives are present
    • Cited on p. 289 [Szabo and Boucher, 2002]
    • [Szabo and Boucher, 2002] A Szabo and K Boucher. Estimating an oncogenetic tree when false negatives and positives are present. Mathematical Biosciences, 176:219-240, 2002. Cited on p. 289
    • (2002) Mathematical Biosciences , vol.176 , pp. 219-240
    • Szabo, A.1    Boucher, K.2
  • 250
    • 0040454585 scopus 로고
    • Fourier calculus on evolutionary trees
    • Cited on p. 296, 306, 309, 332, 334 [Szekely et al., 1993]
    • [Szekely et al., 1993] LA Szekely, MA Steel, and PL Erdos. Fourier calculus on evolutionary trees. Advances in Applied Mathematics, 14(2):200-210, 1993. Cited on p. 296, 306, 309, 332, 334
    • (1993) Advances in Applied Mathematics , vol.14 , Issue.2 , pp. 200-210
    • Szekely, L.A.1    Steel, M.A.2    Erdos, P.L.3
  • 251
    • 0027157960 scopus 로고
    • Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees
    • Cited on p. 155 [Tamura and Nei, 1993]
    • [Tamura and Nei, 1993] K Tamura and M Nei. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution, 10:512-526, 1993. Cited on p. 155
    • (1993) Molecular Biology and Evolution , vol.10 , pp. 512-526
    • Tamura, K.1    Nei, M.2
  • 252
    • 0002671410 scopus 로고
    • Some probabilistic and statistical problems in the analysis of DNA sequences
    • Cited on p. 155 [Tavare, 1986]
    • [Tavare, 1986] S Tavare. Some probabilistic and statistical problems in the analysis of DNA sequences. Lectures on the Mathematics in the Life Sciences, 17:57-86, 1986. Cited on p. 155
    • (1986) Lectures on the Mathematics in the Life Sciences , vol.17 , pp. 57-86
    • Tavare, S.1
  • 253
    • 0038658640 scopus 로고    scopus 로고
    • Efficient algorithms for multichromosomal genome rearrangements
    • Cited on p. 130, 131 [Tesler, 2002]
    • [Tesler, 2002] G Tesler. Efficient algorithms for multichromosomal genome rearrangements. Journal of Computer and System Sciences, 65(3):587-609, 2002. Cited on p. 130, 131
    • (2002) Journal of Computer and System Sciences , vol.65 , Issue.3 , pp. 587-609
    • Tesler, G.1
  • 256
    • 49249151236 scopus 로고
    • The complexity of computing the permanent
    • Cited on p. 49 [Valiant, 1979]
    • [Valiant, 1979] L Valiant. The complexity of computing the permanent. Theoretical Computer Science, 8:189-201, 1979. Cited on p. 49
    • (1979) Theoretical Computer Science , vol.8 , pp. 189-201
    • Valiant, L.1
  • 257
    • 0000024868 scopus 로고
    • Critical points of the product of powers of linear functions and families of bases of singular vectors
    • Cited on p. 10 [Varchenko, 1995]
    • [Varchenko, 1995] A Varchenko. Critical points of the product of powers of linear functions and families of bases of singular vectors. Compositio Mathematica, 97(3):385-401, 1995. Cited on p. 10
    • (1995) Compositio Mathematica , vol.97 , Issue.3 , pp. 385-401
    • Varchenko, A.1
  • 259
    • 84935113569 scopus 로고
    • Error bounds for convolutional codes and an asymptotically optimum decoding algorithm
    • Cited on p. 57, 227 [Viterbi, 1967]
    • [Viterbi, 1967] AJ Viterbi. Error bounds for convolutional codes and an asymptotically optimum decoding algorithm. IEEE Transactions on Information Theory, 13:260-269, 1967. Cited on p. 57, 227
    • (1967) IEEE Transactions on Information Theory , vol.13 , pp. 260-269
    • Viterbi, A.J.1
  • 260
    • 0023748414 scopus 로고
    • Genetic alterations during colorectal-tumor development
    • Cited on p. 278 [Vogelstein et al., 1988]
    • [Vogelstein et al., 1988] B Vogelstein, E Fearon, and S Hamilton. Genetic alterations during colorectal-tumor development. New England Journal of Medicine, 319:525-532, 1988. Cited on p. 278
    • (1988) New England Journal of Medicine , vol.319 , pp. 525-532
    • Vogelstein, B.1    Fearon, E.2    Hamilton, S.3
  • 261
    • 14844354380 scopus 로고    scopus 로고
    • Maximum likelihood estimation of oncogenetic tree models
    • Cited on p. 278 [von Heydebreck et al., 2004]
    • [von Heydebreck et al., 2004] A von Heydebreck, B Gunawan, and L Fiizesi. Maximum likelihood estimation of oncogenetic tree models. Bio statistics, 5(4):545-556, 2004. Cited on p. 278
    • (2004) Bio statistics , vol.5 , Issue.4 , pp. 545-556
    • von Heydebreck, A.1    Gunawan, B.2    Fiizesi, L.3
  • 262
    • 84945708259 scopus 로고
    • A theorem on boolean matrices
    • Cited on p. 46 [Warshall, 1962]
    • [Warshall, 1962] S Warshall. A theorem on boolean matrices. Journal of the ACM, 9(1):18, 1962. Cited on p. 46
    • (1962) Journal of the ACM , vol.9 , Issue.1 , pp. 18
    • Warshall, S.1
  • 266
    • 33749048664 scopus 로고
    • A structure for deoxyribose nucleic acid
    • Cited on p. 126 [Watson and Crick, 1953]
    • [Watson and Crick, 1953] J Watson and F Crick. A structure for deoxyribose nucleic acid. Nature, 171:964-967, 1953. Cited on p. 126
    • (1953) Nature , vol.171 , pp. 964-967
    • Watson, J.1    Crick, F.2
  • 267
    • 0002915858 scopus 로고
    • Master's thesis, Fakultat Mathematik, Universitat Bielefeld, Cited on p. 323, 324 [Wetzel, 1995]
    • [Wetzel, 1995] R Wetzel. Zur Visualisierung abstrakter Ahnlichkeitsbeziehungen. Master's thesis, Fakultat Mathematik, Universitat Bielefeld, 1995. Cited on p. 323, 324
    • (1995) Zur Visualisierung abstrakter Ahnlichkeitsbeziehungen
    • Wetzel, R.1
  • 268
    • 0021372972 scopus 로고
    • Isometric embeddings in products of complete graphs
    • Cited on p. 323 [Winkler, 1984]
    • [Winkler, 1984] P Winkler. Isometric embeddings in products of complete graphs. Discrete Applied Mathematics, 7:221-225, 1984. Cited on p. 323
    • (1984) Discrete Applied Mathematics , vol.7 , pp. 221-225
    • Winkler, P.1
  • 269
    • 0034123820 scopus 로고    scopus 로고
    • Trexml: A maximum likelihood program for extensive tree-space exploration
    • Cited on p. 374 [Wolf et al., 2000]
    • [Wolf et al., 2000] MJ Wolf, S Easteal, M Kahn, BD McKay, and LS Jermiin. Trexml: A maximum likelihood program for extensive tree-space exploration. Bioinformatics, 16:383-394, 2000. Cited on p. 374
    • (2000) Bioinformatics , vol.16 , pp. 383-394
    • Wolf, M.J.1    Easteal, S.2    Kahn, M.3    McKay, B.D.4    Jermiin, L.S.5
  • 271
    • 0000378875 scopus 로고
    • Evidence for higher rates of nucleotide substitution in rodents than in man
    • Cited on p. 384 [Wu and Li, 1985]
    • [Wu and Li, 1985] CI Wu and WH Li. Evidence for higher rates of nucleotide substitution in rodents than in man. PNAS, 82(6):1741-1745, 1985. Cited on p. 384
    • (1985) PNAS , vol.82 , Issue.6 , pp. 1741-1745
    • Wu, C.I.1    Li, W.H.2
  • 272
    • 0028961933 scopus 로고
    • On the use of nucleic acid sequences to infer early branchings in the tree of life
    • Cited on p. 385 [Yang and Roberts, 1995]
    • [Yang and Roberts, 1995] Z Yang and D Roberts. On the use of nucleic acid sequences to infer early branchings in the tree of life. Molecular Biology and Evolution, 12:451-458, 1995. Cited on p. 385
    • (1995) Molecular Biology and Evolution , vol.12 , pp. 451-458
    • Yang, Z.1    Roberts, D.2
  • 273
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program package for phylogenetic analysis by maximum likelihood
    • Cited on p. 303, 375, 400 [Yang, 1997]
    • [Yang, 1997] Z Yang. PAML: A program package for phylogenetic analysis by maximum likelihood. CABIOS, 15:555-556, 1997. Cited on p. 303, 375, 400
    • (1997) CABIOS , vol.15 , pp. 555-556
    • Yang, Z.1
  • 274
    • 1842667853 scopus 로고    scopus 로고
    • Identification of evolutionary hotspots in the rodent genomes
    • Cited on p. 154, 305 [Yap and Pachter, 2004]
    • [Yap and Pachter, 2004] VB Yap and L Pachter. Identification of evolutionary hotspots in the rodent genomes. Genome Research, 14(4):574-9, 2004. Cited on p. 154, 305
    • (2004) Genome Research , vol.14 , Issue.4 , pp. 574-579
    • Yap, V.B.1    Pachter, L.2
  • 275
    • 0033933640 scopus 로고    scopus 로고
    • Estimation of primate speciation dates using local molecular clocks
    • Cited on p. 386 [Yoder and Yang, 2000]
    • [Yoder and Yang, 2000] AD Yoder and Z Yang. Estimation of primate speciation dates using local molecular clocks. Molecular Biology and Evolution, 17:1081-1090, 2000. Cited on p. 386
    • (2000) Molecular Biology and Evolution , vol.17 , pp. 1081-1090
    • Yoder, A.D.1    Yang, Z.2
  • 276
    • 0037023384 scopus 로고    scopus 로고
    • A draft sequence of the rice genome (Oryza sativa L. Ssp. Indica)
    • Cited on p. 134 [Yu et al., 2002]
    • [Yu et al., 2002] J Yu, S Hu, J Wang, GKS Wong, S Li, B Liu, Y Deng, L Dai, Y Zhou, X Zhang, et al. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science, 296(5565).:79-92, 2002. Cited on p. 134
    • (2002) Science , vol.296 , Issue.5565 , pp. 79-92
    • Yu, J.1    Hu, S.2    Wang, J.3    Wong, G.K.S.4    Li, S.5    Liu, B.6    Deng, Y.7    Dai, L.8    Zhou, Y.9    Zhang, X.10
  • 278
    • 0034867374 scopus 로고    scopus 로고
    • Meningioma: A cytogenetic model of a complex benign human tumor, including data on 394 karyotyped cases
    • Cited on p. 278 [Zang, 2001]
    • [Zang, 2001] KD Zang. Meningioma: a cytogenetic model of a complex benign human tumor, including data on 394 karyotyped cases. Cytogenet. Cell Genet., 93:207-220, 2001. Cited on p. 278
    • (2001) Cytogenet. Cell Genet , vol.93 , pp. 207-220
    • Zang, K.D.1
  • 279
    • 0028108336 scopus 로고
    • Estimation of evolutionary distances between nucleotide sequences
    • Cited on p. 155 [Zharkikh, 1994]
    • [Zharkikh, 1994] A Zharkikh. Estimation of evolutionary distances between nucleotide sequences. Journal of Molecular Evolution, 39:315-329, 1994. Cited on p. 155
    • (1994) Journal of Molecular Evolution , vol.39 , pp. 315-329
    • Zharkikh, A.1


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