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Databases

This page provides links to various Databases developed by members of the Nei laboratory as well as links to the journal abstracts.  Feel free to contact the laboratory of Masatoshi Nei with questions regarding the database information.

      Lin, Z., Kong, H., Nei, M., & Ma, H. (2006) Origins and evolution of the recA/RAD51 gene family: Evidence for ancient gene duplication and endosymbiotic gene transfer. Proc. Natl. Acad. Sci USA.
  Data:      

Supplementary material-Amino acid sequences

Supplementary material-Nucleotide sequences

      Hao, L., Klein, J. & Nei, M. (2006) Heterogeneous but conserved natural killer receptor gene complexes in four major orders of mammals. Proc. Natl. Acad. Sci. USA.
  Data:       Supplementary material

Niimura, Y. & Nei, M. (2005) Comparative evolutionary analysis of olfactory receptor gene clusters between humans and mice. Gene 346:13-21

  Data: Supplementary material  

Piontkivska H. (2004) Efficiencies of maximum likelihood method of phylogenetic inferences when different substitution models are used. Mol. Phylogenet. Evol. 31:865-873.

       
  Data: Supplementary material  

Piontkivska H. and M. Nei. Molecular evolution of the histones gene family in two sibling nematode species, Caenorhabditis elegans and C. briggsae. (submitted)

       
  Data: Supplementary material  

Hao, L and M. Nei (2004) Genomic organization and evolutionary analysis of Ly49 genes encoding the rodent natural killer cell receptors: rapid evolution by repeated gene duplication. Immunogenetics. 56:343:354.


  Data: Ly49 Dataset  

N. Nikolaidis and M. Nei (2003) Evolution of the Hsp70 Gene Superfamily in Two Sibling Species of Nematodes Caenorhabditis elegans and C. briggsae. Mol. Biol. Evol.


  Data: Supplemental Material  

Y. Niimura and M. Nei (2003) Evolution of olfactory receptor genes in the human genome. Proc. Natl. Acad. Sci. USA. 21:12235-12240.


  Data: Supplemental Material PubMed

Glazko, G. and M. Nei (2003) Estimation of divergence times for major lineages of primate species. Mol. Biol. Evol. 20:424-434.


  Data: Supplemental Table 1-10-09-023+  (last modified November 19, 2002)
Supplemental Table S3mt  (last modified November 19, 2002)
Supplemental Table 6  (last modified October 2, 2002)

H. Piontkivska, A. P. Rooney, and M. Nei (2002) Purifying selection and birth-and-death evolution in the histone H4 gene family. Mol. Biol. Evol. 19:689-97.


  Data: Appendix
Histone fold alignment (pdf file)
PubMed

Rooney, A.P., H. Piontkivska and M. Nei (2001) Molecular evolution of the non-tandemly repeated genes of the histone 3 multigene family. Mol. Biol. Evol. 19:68-75.


  Data: Appendix PubMed

Su, C., V. K. Nguyen, and M. Nei (2002) Adaptive evolution of the variable region genes of an unusual type of immunoglobulins in camelids. Mol. Biol. Evol. 19:205-15.


  Data: Text PubMed

Nei, M., P. Xu, and G. Glazko (2001) Estimation of divergence times from multiprotein sequences for a few mammalian species and several distantly related organisms. Proc. Natl. Acad. Sci. USA 98:2497-2502.


  Data: Table 3
Table 4
PubMed abstract

Su, C. and M. Nei (2001) Evolutionary dynamics of the T-cell receptor VB gene family as inferred from the human and mouse genomic sequences. Mol. Biol. Evol. 18:503-513.


  Data: Figure 2
Figure 3
Figure 4
Figure 5
Figure 7A
Figure 7B
PubMed abstract
 
PNAS online

Nei, M., I. B. Rogozin, and H. Piontkivska (2000) Purifying selection and birth-and-death evolution in the ubiquitin gene family. Proc. Natl. Acad. Sci. USA 97:10866-10871.


  Data: Table 7
Table 8
Figures
PubMed abstract
 
PNAS online

Takahashi, K. and M. Nei (2000) Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used. Mol. Biol. Evol. 17:1251-1258.


  Data: Figure 1
Tree Files (names correspond to the
     Fig. 1 notations)
PubMed abstract
 

MBE online

Takahashi, K., A. P. Rooney, and M. Nei (2000) Origins and divergence times of mammalian class II MHC gene clusters. J. Hered. 91:198-204.


  Data: MHC Class II alfa genes dataset
     (in MEGA format)
MHC Class II beta genes dataset
     (in MEGA format)
PubMed abstract

Su, C., I. Jakobsen, X. Gu, and M. Nei (1999) Diversity and evolution of T-cell receptor variable region genes in mammals and birds. Immunogenetics 50:301-308.


  Data: Figure 1 dataset
Figure 2 dataset
Figure 3 dataset
PubMed abstract
 
MBE online

Piontkivska H. (2004) Efficiencies of maximum likelihood method of phylogenetic inferences when different substitution models are used. Mol. Phylogenet. Evol. 31:865-873.



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| Department of Biology | Eberly College of Science |
| Institute of Molecular Evolutionary Genetics | Penn State |
2003 The Pennsylvania State University
This page was last updated 08/13/12 by T. Kushner.