Literature DB >> 18787111

The infinite sites model of genome evolution.

Jian Ma1, Aakrosh Ratan, Brian J Raney, Bernard B Suh, Webb Miller, David Haussler.   

Abstract

We formalize the problem of recovering the evolutionary history of a set of genomes that are related to an unseen common ancestor genome by operations of speciation, deletion, insertion, duplication, and rearrangement of segments of bases. The problem is examined in the limit as the number of bases in each genome goes to infinity. In this limit, the chromosomes are represented by continuous circles or line segments. For such an infinite-sites model, we present a polynomial-time algorithm to find the most parsimonious evolutionary history of any set of related present-day genomes.

Mesh：

Year:  2008        PMID： 18787111      PMCID： PMC2533685          DOI： 10.1073/pnas.0805217105

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN： 0027-8424            Impact factor:   11.205


  28 in total

Review 1.  Structural dynamics of eukaryotic chromosome evolution.

Authors:  Evan E Eichler; David Sankoff
Journal:  Science       Date:  2003-08-08       Impact factor: 47.728

Review 2.  Genetic analyses from ancient DNA.

Authors:  Svante Pääbo; Hendrik Poinar; David Serre; Viviane Jaenicke-Despres; Juliane Hebler; Nadin Rohland; Melanie Kuch; Johannes Krause; Linda Vigilant; Michael Hofreiter
Journal:  Annu Rev Genet       Date:  2004       Impact factor: 16.830

3.  Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps.

Authors:  William J Murphy; Denis M Larkin; Annelie Everts-van der Wind; Guillaume Bourque; Glenn Tesler; Loretta Auvil; Jonathan E Beever; Bhanu P Chowdhary; Francis Galibert; Lisa Gatzke; Christophe Hitte; Stacey N Meyers; Denis Milan; Elaine A Ostrander; Greg Pape; Heidi G Parker; Terje Raudsepp; Margarita B Rogatcheva; Lawrence B Schook; Loren C Skow; Michael Welge; James E Womack; Stephen J O'brien; Pavel A Pevzner; Harris A Lewin
Journal:  Science       Date:  2005-07-22       Impact factor: 47.728

4.  Cell cycle and genetic requirements of two pathways of nonhomologous end-joining repair of double-strand breaks in Saccharomyces cerevisiae.

Authors:  J K Moore; J E Haber
Journal:  Mol Cell Biol       Date:  1996-05       Impact factor: 4.272

5.  Nonhomologous recombination in mammalian cells: role for short sequence homologies in the joining reaction.

Authors:  D B Roth; J H Wilson
Journal:  Mol Cell Biol       Date:  1986-12       Impact factor: 4.272

6.  Additive evolutionary trees.

Authors:  M S Waterman; T F Smith; M Singh; W A Beyer
Journal:  J Theor Biol       Date:  1977-01-21       Impact factor: 2.691

7.  Properties of a neutral allele model with intragenic recombination.

Authors:  R R Hudson
Journal:  Theor Popul Biol       Date:  1983-04       Impact factor: 1.570

8.  Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages.

Authors:  Guillaume Bourque; Evgeny M Zdobnov; Peer Bork; Pavel A Pevzner; Glenn Tesler
Journal:  Genome Res       Date:  2004-12-08       Impact factor: 9.043

Review 9.  The leptotene-zygotene transition of meiosis.

Authors:  D Zickler; N Kleckner
Journal:  Annu Rev Genet       Date:  1998       Impact factor: 16.830

10.  Dating of the human-ape splitting by a molecular clock of mitochondrial DNA.

Authors:  M Hasegawa; H Kishino; T Yano
Journal:  J Mol Evol       Date:  1985       Impact factor: 2.395
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  28 in total

1.  Accelerated evolution and coevolution drove the evolutionary history of AGPase sub-units during angiosperm radiation.

Authors:  Jonathan Corbi; Julien Y Dutheil; Catherine Damerval; Maud I Tenaillon; Domenica Manicacci
Journal:  Ann Bot       Date:  2012-02-02       Impact factor: 4.357

2.  CAGE: Combinatorial Analysis of Gene-cluster Evolution.

Authors:  Giltae Song; Louxin Zhang; Tomas Vinar; Webb Miller
Journal:  J Comput Biol       Date:  2010-09       Impact factor: 1.479

3.  Toward Recovering Allele-specific Cancer Genome Graphs.

Authors:  Ashok Rajaraman; Jian Ma
Journal:  J Comput Biol       Date:  2018-04-16       Impact factor: 1.479

4.  Phylogenetic Copy-Number Factorization of Multiple Tumor Samples.

Authors:  Simone Zaccaria; Mohammed El-Kebir; Gunnar W Klau; Benjamin J Raphael
Journal:  J Comput Biol       Date:  2018-04-16       Impact factor: 1.479

5.  Profile of David Haussler.

Authors:  Philip Downey
Journal:  Proc Natl Acad Sci U S A       Date:  2008-09-17       Impact factor: 11.205

6.  Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs.

Authors:  Benedict Paten; Javier Herrero; Kathryn Beal; Stephen Fitzgerald; Ewan Birney
Journal:  Genome Res       Date:  2008-10-10       Impact factor: 9.043

7.  Fast computation of a string duplication history under no-breakpoint-reuse.

Authors:  Broňa Brejová; Martin Kravec; Gad M Landau; Tomaš Vinař
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2014-04-21       Impact factor: 4.226

8.  Breakpoint graphs and ancestral genome reconstructions.

Authors:  Max A Alekseyev; Pavel A Pevzner
Journal:  Genome Res       Date:  2009-02-13       Impact factor: 9.043

9.  progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement.

Authors:  Aaron E Darling; Bob Mau; Nicole T Perna
Journal:  PLoS One       Date:  2010-06-25       Impact factor: 3.240

10.  Frequency-dependent selection predicts patterns of radiations and biodiversity.

Authors:  Carlos J Melián; David Alonso; Diego P Vázquez; James Regetz; Stefano Allesina
Journal:  PLoS Comput Biol       Date:  2010-08-26       Impact factor: 4.475
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