Algebraic Statistics for Computational Biology: Preface

Preface Part I. Introduction to the Four Themes: 1. Statistics L. Pachter and B. Sturmfels 2. Computation L. Pachter and B. Sturmfels 3. Algebra L. Pachter and B. Sturmfels 4. Biology L. Pachter and B. Sturmfels Part II. Studies on the Four Themes: 5. Parametric inference R. Mihaescu 6. Polytope propagation on graphs M. Joswig 7. Parametric sequence alignment C. Dewey and K. Woods 8. Bounds for optimal sequence alignment S. Elizalde 9. Inference functions S. Elizalde 10. Geometry of Markov chains E. Kuo 11. Equations defining hidden Markov models N. Bray and J. Morton 12. The EM algorithm for hidden Markov models I. B. Hallgrimsdottir, A. Milowski and J. Yu 13. Homology mapping with Markov random fields A. Caspi 14. Mutagenetic tree models N. Beerenwinkel and M. Drton 15. Catalog of small trees M. Casanellas, L. Garcia and S. Sullivant 16. The strand symmetric model M. Casanellas and S. Sullivant 17. Extending statistical models from trees to splits graphs D. Bryant 18. Small trees and generalized neighbor-joining M. Contois and D. Levy 19. Tree construction using Singular Value Decomposition N. Eriksson 20. Applications of interval methods to phylogenetics R. Sainudiin and R. Yoshida 21. Analysis of point mutations in vertebrate genomes J. Al-Aidroos and S. Snir 22. Ultra-conserved elements in vertebrate genomes M. Drton, N. Eriksson and G. Leung Index.

[1]  G. D,et al.  American Naturalist , 1867, Nature.

[2]  G. G. Stokes.  "J." , 1890, The New Yale Book of Quotations.

[3]  W. Bowen,et al.  Philadelphia , 1892 .

[4]  Katherine D. Blake.  To San Francisco , 1911 .

[5]  H. W. Parker,et al.  Systematic Zoology , 1896, Nature.

[6]  M. I. Rosenberg,et al.  Naval Research Logistics Quarterly. , 1958 .

[7]  Journal of Molecular Biology , 1959, Nature.

[8]  Stephen J. Garland,et al.  Algorithm 97: Shortest path , 1962, Commun. ACM.

[9]  Verzekeren Naar Sparen,et al.  Cambridge , 1969, Humphrey Burton: In My Own Time.

[10]  Peter H. A. Sneath,et al.  Numerical Taxonomy: The Principles and Practice of Numerical Classification , 1973 .

[11]  Miss A.O. Penney.  (b) , 1974, The New Yale Book of Quotations.

[12]  B. Bainbridge,et al.  Genetics , 1981, Experientia.

[13]  V. Strassen.  Rank and optimal computation of generic tensors , 1983 .

[14]  Donald Geman,et al.  Gibbs distributions and the bayesian restoration of images , 1984 .

[15]  Takayuki Hibi,et al.  Distributive Lattices, Affine Semigroup Rings and Algebras with Straightening Laws , 1987 .

[16]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[17]  J A Lake,et al.  A rate-independent technique for analysis of nucleic acid sequences: evolutionary parsimony. , 1987, Molecular biology and evolution.

[18]  G. Gutman,et al.  Slipped-strand mispairing: a major mechanism for DNA sequence evolution. , 1987, Molecular biology and evolution.

[19]  E. Lander,et al.  Genomic mapping by fingerprinting random clones: a mathematical analysis. , 1988, Genomics.

[20]  Ina Ruck,et al.  USA , 1969, The Lancet.

[21]  David P. Mindell,et al.  Ribosomal RNA in Vertebrates: Evolution and Phylogenetic Applications , 1990 .

[22]  J. Mattick.  Genome research , 1990, Nature.

[23]  A. Neumaier.  Interval methods for systems of equations , 1990 .

[24]  B. M. Fulk.  MATH , 1992 .

[25]  Peter L. Hammer,et al.  Discrete Applied Mathematics , 1993 .

[26]  Alexander Varchenko,et al.  Critical Points of the Product of Powers of Linear Functions and Families of Bases of Singular Vectors , 1993, hep-th/9312119.

[27]  F J Ayala,et al.  Tempo and mode in evolution. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[28]  Pavel A. Pevzner,et al.  Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals , 1995, JACM.

[29]  M. Ziegler.  Volume 152 of Graduate Texts in Mathematics , 1995 .

[30]  F. Maytag.  Evolution , 1996, Arch. Mus. Informatics.

[31]  Ross Ihaka,et al.  Gentleman R: R: A language for data analysis and graphics , 1996 .

[32]  Ziheng Yang,et al.  PAML: a program package for phylogenetic analysis by maximum likelihood , 1997, Comput. Appl. Biosci..

[33]  Andrew Rambaut,et al.  Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees , 1997, Comput. Appl. Biosci..

[34]  John J. Cannon,et al.  The Magma Algebra System I: The User Language , 1997, J. Symb. Comput..

[35]  Axthonv G. Oettinger,et al.  IEEE Transactions on Information Theory , 1998 .

[36]  Sean R. Eddy,et al.  Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids , 1998 .

[37]  M. Gouy,et al.  Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis. , 1998, Molecular biology and evolution.

[38]  Michael Joswig,et al.  polymake: a Framework for Analyzing Convex Polytopes , 2000 .

[39]  A. Schäffer,et al.  Chromosome abnormalities in ovarian adenocarcinoma: III. Using breakpoint data to infer and test mathematical models for oncogenesis , 2000, Genes, chromosomes & cancer.

[40]  Wen-Hsiung Li,et al.  NJML: a hybrid algorithm for the neighbor-joining and maximum-likelihood methods. , 2000, Molecular biology and evolution.

[41]  김삼묘,et al.  “Bioinformatics” 특집을 내면서 , 2000 .

[42]  A. R. Wagner.  Molecular Biology and Evolution , 2001 .

[43]  K. Zang,et al.  Meningioma: a cytogenetic model of a complex benign human tumor, including data on 394 karyotyped cases , 2001, Cytogenetic and Genome Research.

[44]  D. Geiger,et al.  Stratified exponential families: Graphical models and model selection , 2001 .

[45]  Michael Joswig,et al.  Polymake: an approach to modular software design in computational geometry , 2001, SCG '01.

[46]  Tandy J. Warnow,et al.  Performance study of phylogenetic methods: (unweighted) quartet methods and neighbor-joining , 2001, SODA '01.

[47]  M. Stanhope,et al.  Molecular systematics of armadillos (Xenarthra, Dasypodidae): contribution of maximum likelihood and Bayesian analyses of mitochondrial and nuclear genes. , 2003, Molecular phylogenetics and evolution.

[48]  A. Geramita,et al.  Ranks of tensors, secant varieties of Segre varieties and fat points , 2002 .

[49]  Vladimir Kolmogorov,et al.  Multi-camera Scene Reconstruction via Graph Cuts , 2002, ECCV.

[50]  A. Oliphant,et al.  A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). , 2002, Science.

[51]  Mouse Genome Sequencing Consortium.  Initial sequencing and comparative analysis of the mouse genome , 2002, Nature.

[52]  Arieh Iserles,et al.  On the Foundations of Computational Mathematics , 2001 .

[53]  Vincent Moulton,et al.  Spectronet: a package for computing spectra and median networks. , 2002, Applied bioinformatics.

[54]  G. William Walster,et al.  Rump's Example Revisited , 2002, Reliab. Comput..

[55]  Oper , 2002 .

[56]  Peter Deuflhard,et al.  Numerische Mathematik. I , 2002 .

[57]  R. Salakhutdinov,et al.  Relationship between gradient and EM steps in latent variable models , 2003 .

[58]  E. Susko.  Confidence regions and hypothesis tests for topologies using generalized least squares. , 2003, Molecular biology and evolution.

[59]  Inna Dubchak,et al.  Glocal alignment: finding rearrangements during alignment , 2003, ISMB.

[60]  J. van Leeuwen,et al.  Theoretical Computer Science , 2003, Lecture Notes in Computer Science.

[61]  Constance de Koning,et al.  Editors , 2003, Annals of Emergency Medicine.

[62]  David Mond,et al.  Stochastic factorizations, sandwiched simplices and the topology of the space of explanations , 2003, Proceedings of the Royal Society of London. Series A: Mathematical, Physical and Engineering Sciences.

[63]  Zoubin Ghahramani,et al.  Optimization with EM and Expectation-Conjugate-Gradient , 2003, ICML.

[64]  Mario Marchese,et al.  Techniques and applications , 2003 .

[65]  P. Pevzner,et al.  Genome rearrangements in mammalian evolution: lessons from human and mouse genomes. , 2003, Genome research.

[66]  David Sankoff,et al.  Chromosome rearrangements in evolution: From gene order to genome sequence and back , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[67]  R. Nielsen,et al.  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 , 2005, Journal of Molecular Evolution.

[68]  N. Turner.  PLOS Biology , 2004, BMJ : British Medical Journal.

[69]  D. Steinley.  Journal of Classification , 2004, Vegetatio.

[70]  Daniel H. Huson,et al.  Constructing splits graphs , 2004, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[71]  Lior Pachter,et al.  Needed for completion of the human genome: hypothesis driven experiments and biologically realistic mathematical models , 2004, q-bio/0410008.

[72]  Paul T. Groth,et al.  The ENCODE (ENCyclopedia Of DNA Elements) Project , 2004, Science.

[73]  A. Karimi,et al.  Master‟s thesis , 2011 .

[74]  Bernd Sturmfels,et al.  The maximum likelihood degree , 2004, math/0406533.

[75]  Lisa M. D'Souza,et al.  Genome sequence of the Brown Norway rat yields insights into mammalian evolution , 2004, Nature.

[76]  Daniel H. Huson,et al.  Estimating phylogenetic trees and networks using SplitsTree 4 , 2004 .

[77]  P. Pevzner,et al.  Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes. , 2004, Genome research.

[78]  Lior Pachter,et al.  MAVID: constrained ancestral alignment of multiple sequences. , 2003, Genome research.

[79]  Raazesh Sainudiin,et al.  Enclosing the Maximum Likelihood of the Simplest DNA Model Evolving on Fixed Topologies: Towards a Rigorous Framework for Phylogenetic Inference , 2004 .

[80]  Lior Pachter,et al.  Neighbor Joining with Subtree Weights , 2004 .

[81]  Joel E. Cohen,et al.  Mathematics Is Biology's Next Microscope, Only Better; Biology Is Mathematics' Next Physics, Only Better , 2004, PLoS biology.

[82]  Jean YH Yang,et al.  Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.

[83]  Bernd Sturmfels,et al.  Solving the Likelihood Equations , 2005, Found. Comput. Math..

[84]  Matthias Wolfrum,et al.  Bernstein's second theorem and Viro's method for sparse polynomial systems in chemistry , 2005, Adv. Appl. Math..

[85]  Thomas Lengauer,et al.  Estimating cancer survival and clinical outcome based on genetic tumor progression scores , 2005, Bioinform..

[86]  Ericka Stricklin-Parker,et al.  Ann , 2005 .

[87]  刘金明,et al.  IL-13受体α2降低血吸虫病肉芽肿的炎症反应并延长宿主存活时间[英]/Mentink-Kane MM,Cheever AW，Thompson RW，et al//Proc Natl Acad Sci U S A , 2005 .

[88]  Martin Feinberg,et al.  Multiple Equilibria in Complex Chemical Reaction Networks: I. the Injectivity Property * , 2006 .

[89]  Thomas Lengauer,et al.  Mtreemix: a software package for learning and using mixture models of mutagenetic trees , 2005, Bioinform..

[90]  Tommy Färnqvist.  Number Theory Meets Cache Locality – Efficient Implementation of a Small Prime FFT for the GNU Multiple Precision Arithmetic Library , 2005 .

[91]  Seth Sullivant,et al.  Toric Ideals of Phylogenetic Invariants , 2004, J. Comput. Biol..

[92]  J. Cavanaugh.  Biostatistics , 2005, Definitions.

[93]  J. Quadrat,et al.  The Maslov Dequantization, Idempotent and Tropical Mathematics: a Very Brief Introduction , 2005 .

[94]  J. Felsenstein.  Evolutionary trees from DNA sequences: A maximum likelihood approach , 2005, Journal of Molecular Evolution.

[95]  D. Hinkley.  Annals of Statistics , 2006 .

[96]  Dan Suciu,et al.  Journal of the ACM , 2006 .

[97]  D. Geiger,et al.  On the toric algebra of graphical models , 2006, math/0608054.

[98]  Lior Pachter,et al.  The Mathematics of Phylogenomics , 2004, SIAM Rev..