Transcriptome sequencing and phylogenomic resolution within Spalacidae (Rodentia)

[1]  E. Nevo,et al.  Transcriptome sequencing and phylogenomic resolution within Spalacidae (Rodentia) , 2014, BMC Genomics.

[2]  A. Munshi.  Dna Sequencing: Methods And Applications , 2014 .

[3]  X. Xia.  DAMBE5: A Comprehensive Software Package for Data Analysis in Molecular Biology and Evolution , 2013, Molecular biology and evolution.

[4]  Ramón Doallo,et al.  CircadiOmics: integrating circadian genomics, transcriptomics, proteomics and metabolomics , 2012, Nature Methods.

[5]  L. Granjon,et al.  The Input of DNA Sequences to Animal Systematics: Rodents as Study Cases , 2012 .

[6]  Zhong Wang,et al.  Next-generation transcriptome assembly , 2011, Nature Reviews Genetics.

[7]  M. Nei,et al.  MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. , 2011, Molecular biology and evolution.

[8]  Frédéric Delsuc,et al.  MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons , 2011, PloS one.

[9]  Alvaro G. Hernandez,et al.  Transcriptome Sequencing of the Blind Subterranean Mole Rat, Spalax galili: Utility and Potential for the Discovery of Novel Evolutionary Patterns , 2011, PloS one.

[10]  N. Friedman,et al.  Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.

[11]  N. Veniaminova,et al.  Nucleotide sequences of B1 SINE and 4.5S(I) RNA support a close relationship of zokors to blind mole rats (Spalacinae) and bamboo rats (Rhizomyinae). , 2010, Gene.

[12]  Jinchuan Xing,et al.  Genetic Evidence for High-Altitude Adaptation in Tibet , 2010, Science.

[13]  O. Gascuel,et al.  New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. , 2010, Systematic biology.

[14]  L. J. Flynn,et al.  Chapter 4. The Antiquity of Rhizomys and Independent Acquisition of Fossorial Traits in Subterranean Muroids , 2009 .

[15]  S. Jansa,et al.  The Phylogenetic Position of the Rodent Genus Typhlomys and the Geographic Origin of Muroidea , 2009 .

[16]  S. Pongor,et al.  The quest for orthologs: finding the corresponding gene across genomes. , 2008, Trends in genetics : TIG.

[17]  A. Oskooi.  Molecular Evolution and Phylogenetics , 2008 .

[18]  Ziheng Yang.  PAML 4: phylogenetic analysis by maximum likelihood. , 2007, Molecular biology and evolution.

[19]  E. Nevo.  Mosaic Evolution of Subterranean Mammals: Tinkering, Regression, Progression, and Global Convergence , 2007 .

[20]  Alexandros Stamatakis,et al.  RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models , 2006, Bioinform..

[21]  Gang Liu,et al.  Automatic clustering of orthologs and inparalogs shared by multiple proteomes , 2006, ISMB.

[22]  Adam Godzik,et al.  Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences , 2006, Bioinform..

[23]  F. Delsuc,et al.  Phylogenomics: the beginning of incongruence? , 2006, Trends in genetics : TIG.

[24]  Ari Löytynoja,et al.  An algorithm for progressive multiple alignment of sequences with insertions. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[25]  Fredrik Dahl,et al.  Multiplex amplification enabled by selective circularization of large sets of genomic DNA fragments , 2005, Nucleic acids research.

[26]  John Quackenbush,et al.  The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes , 2004, Nucleic Acids Res..

[27]  J. Taubenberger,et al.  Evidence of an absence: the genetic origins of the 1918 pandemic influenza virus , 2004, Nature Reviews Microbiology.

[28]  D. Posada,et al.  Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests. , 2004, Systematic biology.

[29]  R. Adkins,et al.  Phylogeny and divergence-date estimates of rapid radiations in muroid rodents based on multiple nuclear genes. , 2004, Systematic biology.

[30]  K. Zhou,et al.  The phylogenetic position of the zokors (Myospalacinae) and comments on the families of muroids (Rodentia). , 2004, Molecular phylogenetics and evolution.

[31]  S. Jansa,et al.  Phylogeny of muroid rodents: relationships within and among major lineages as determined by IRBP gene sequences. , 2004, Molecular phylogenetics and evolution.

[32]  Christian E. V. Storm,et al.  Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. , 2001, Journal of molecular biology.

[33]  F. Catzeflis,et al.  Evolutionary history of the most speciose mammals: molecular phylogeny of muroid rodents. , 2001, Molecular biology and evolution.

[34]  John P. Huelsenbeck,et al.  MRBAYES: Bayesian inference of phylogenetic trees , 2001, Bioinform..

[35]  X. Xia,et al.  DAMBE: software package for data analysis in molecular biology and evolution. , 2001, The Journal of heredity.

[36]  R. Debry,et al.  Phylogeny of rodentia (Mammalia) inferred from the nuclear-encoded gene IRBP. , 2001, Molecular phylogenetics and evolution.

[37]  F. Catzeflis,et al.  The bushlike radiation of muroid rodents is exemplified by the molecular phylogeny of the LCAT nuclear gene. , 2000, Molecular phylogenetics and evolution.

[38]  C. G. Faulkes.  Mosaic Evolution of Subterranean Mammals — Regression, Progression and Global Convergence , 2000, Heredity.

[39]  D. Mouchiroud,et al.  Molecular phylogeny of rodents, with special emphasis on murids: evidence from nuclear gene LCAT. , 1997, Molecular phylogenetics and evolution.

[40]  J. Honacki,et al.  Mammal species of the world : a taxonomic and geographic reference , 1982 .

[41]  E. Nevo.  Adaptive Convergence and Divergence of Subterranean Mammals , 1979 .