Log on / register
Feedback | Support | My details
Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes.
Mirkin BG, Fenner TI, Galperin MY, Koonin EV
BMC Evol Biol 2003 Jan 6, 3:2
[Full text] [PubMed] [Related articles] [Cited on BioMed Central]


printer friendly 
to  [Help]

PubMed Central articles that cite the above article:

1.
Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysis.
Wolf YI, Rogozin IB, Koonin EV
Genome Res 2004 Jan, 14:29-36
[PubMed Central] [PubMed] [Related articles]

2.
Imprint of evolution on protein structures.
Tiana G, Shakhnovich BE, Dokholyan NV, Shakhnovich EI
Proc Natl Acad Sci U S A 2004 Mar 2, 101:2846-51
[PubMed Central] [PubMed] [Related articles]

3.
Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution.
Krylov DM, Wolf YI, Rogozin IB, Koonin EV
Genome Res 2003 Oct, 13:2229-35
[PubMed Central] [PubMed] [Related articles]

4.
Computational inference of scenarios for alpha-proteobacterial genome evolution.
Boussau B, Karlberg EO, Frank AC, Legault BA, Andersson SG
Proc Natl Acad Sci U S A 2004 Jun 29, 101:9722-7
[PubMed Central] [PubMed] [Related articles]

5.
Computing prokaryotic gene ubiquity: rescuing the core from extinction.
Charlebois RL, Doolittle WF
Genome Res 2004 Dec, 14:2469-77
[PubMed Central] [PubMed] [Related articles]

6.
Protein structure and evolutionary history determine sequence space topology.
Shakhnovich BE, Deeds E, Delisi C, Shakhnovich E
Genome Res 2005 Mar, 15:385-92
[PubMed Central] [PubMed] [Related articles]

7.
Prokaryotic phylogenies inferred from protein structural domains.
Deeds EJ, Hennessey H, Shakhnovich EI
Genome Res 2005 Mar, 15:393-402
[PubMed Central] [PubMed] [Related articles]

8.
Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell.
Makarova KS, Wolf YI, Mekhedov SL, Mirkin BG, Koonin EV
Nucleic Acids Res 2005, 33:4626-38
[PubMed Central] [PubMed] [Related articles]

9.
Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance.
Omelchenko MV, Wolf YI, Gaidamakova EK, Matrosova VY, Vasilenko A, Zhai M, Daly MJ, Koonin EV, Makarova KS
BMC Evol Biol 2005, 5:57
[PubMed Central] [PubMed] [Related articles]

10.
Genome trees from conservation profiles.
Tekaia F, Yeramian E
PLoS Comput Biol 2005 Dec, 1:e75
[PubMed Central] [PubMed] [Related articles]

11.
*** Unable to retrieve article 16362074 ***

[PubMed Central] [PubMed] [Related articles]

12.
Protein content of minimal and ancestral ribosome.
Mushegian A
RNA 2005 Sep, 11:1400-6
[PubMed Central] [PubMed] [Related articles]

13.
Identification and analysis of evolutionarily cohesive functional modules in protein networks.
Campillos M, von Mering C, Jensen LJ, Bork P
Genome Res 2006 Mar, 16:374-82
[PubMed Central] [PubMed] [Related articles]

14.
Stochastic models for horizontal gene transfer: taking a random walk through tree space.
Suchard MA
Genetics 2005 May, 170:419-31
[PubMed Central] [PubMed] [Related articles]

15.
The fate of laterally transferred genes: life in the fast lane to adaptation or death.
Hao W, Golding GB
Genome Res 2006 May, 16:636-43
[PubMed Central] [PubMed] [Related articles]

16.
Comparative genomics of the lactic acid bacteria.
Makarova K, Slesarev A, Wolf Y, Sorokin A, Mirkin B, Koonin E, Pavlov A, Pavlova N, Karamychev V, Polouchine N, Shakhova V, Grigoriev I, Lou Y, Rohksar D, Lucas S, Huang K, Goodstein DM, Hawkins T, Plengvidhya V, Welker D, Hughes J, Goh Y, Benson A, Baldwin K, Lee JH, Díaz-Muñiz I, Dosti B, Smeianov V, Wechter W, Barabote R, Lorca G, Altermann E, Barrangou R, Ganesan B, Xie Y, Rawsthorne H, Tamir D, Parker C, Breidt F, Broadbent J, Hutkins R, O'Sullivan D, Steele J, Unlu G, Saier M, Klaenhammer T, Richardson P, Kozyavkin S, Weimer B, Mills D
Proc Natl Acad Sci U S A 2006 Oct 17, 103:15611-6
[PubMed Central] [PubMed] [Related articles]

17.
Data mining for proteins characteristic of clades.
Bern M, Goldberg D, Lyashenko E
Nucleic Acids Res 2006, 34:4342-53
[PubMed Central] [PubMed] [Related articles]

18.
Using phylogeny to improve genome-wide distant homology recognition.
Abeln S, Teubner C, Deane CM
PLoS Comput Biol 2007 Jan 19, 3:e3
[PubMed Central] [PubMed] [Related articles]

19.
*** Unable to retrieve article 17238281 ***

[PubMed Central] [PubMed] [Related articles]

20.
Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution.
Dagan T, Martin W
Proc Natl Acad Sci U S A 2007 Jan 16, 104:870-5
[PubMed Central] [PubMed] [Related articles]

21.
Evolutionary genomics of lactic acid bacteria.
Makarova KS, Koonin EV
J Bacteriol 2007 Feb, 189:1199-208
[PubMed Central] [PubMed] [Related articles]

22.
Global extent of horizontal gene transfer.
Choi IG, Kim SH
Proc Natl Acad Sci U S A 2007 Mar 13, 104:4489-94
[PubMed Central] [PubMed] [Related articles]

23.
A first-principles model of early evolution: emergence of gene families, species, and preferred protein folds.
Zeldovich KB, Chen P, Shakhnovich BE, Shakhnovich EI
PLoS Comput Biol 2007 Jul, 3:e139
[PubMed Central] [PubMed] [Related articles]

24.
*** Unable to retrieve article 17630830 ***

[PubMed Central] [PubMed] [Related articles]

25.
Orthologous transcription factors in bacteria have different functions and regulate different genes.
Price MN, Dehal PS, Arkin AP
PLoS Comput Biol 2007 Sep, 3:1739-50
[PubMed Central] [PubMed] [Related articles]

26.
*** Unable to retrieve article 17845071 ***

[PubMed Central] [PubMed] [Related articles]

27.
Patterns and implications of gene gain and loss in the evolution of Prochlorococcus.
Kettler GC, Martiny AC, Huang K, Zucker J, Coleman ML, Rodrigue S, Chen F, Lapidus A, Ferriera S, Johnson J, Steglich C, Church GM, Richardson P, Chisholm SW
PLoS Genet 2007 Dec, 3:e231
[PubMed Central] [PubMed] [Related articles]

28.
Reconstruction of ancestral protein interaction networks for the bZIP transcription factors.
Pinney JW, Amoutzias GD, Rattray M, Robertson DL
Proc Natl Acad Sci U S A 2007 Dec 18, 104:20449-53
[PubMed Central] [PubMed] [Related articles]

29.
Coevolution of gene families in prokaryotes.
Cordero OX, Snel B, Hogeweg P
Genome Res 2008 Mar, 18:462-8
[PubMed Central] [PubMed] [Related articles]

30.
*** Unable to retrieve article 18159947 ***

[PubMed Central] [PubMed] [Related articles]


This article is also cited by 19 articles in BioMed Central


You can also check ISI Web of Science for additional citations (subscription required)
  
printer friendly 
to  [Help]

© 1999-2008 BioMed Central Ltd unless otherwise stated