Convergent Evolution of Rumen Microbiomes in High-Altitude Mammals

[1]  Dongwan D. Kang,et al.  Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome , 2014, Genome research.

[2]  R. E. Everts,et al.  Ruminal epithelium transcriptome dynamics in response to plane of nutrition and age in young Holstein calves , 2014, Functional & Integrative Genomics.

[3]  J. Qi,et al.  Metagenomic sequencing reveals microbiota and its functional potential associated with periodontal disease , 2013, Scientific Reports.

[4]  Loretta Auvil,et al.  Draft genome sequence of the Tibetan antelope , 2013, Nature Communications.

[5]  A. Spang,et al.  Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen , 2013, Nature Communications.

[6]  L. Pachter,et al.  Streaming fragment assignment for real-time analysis of sequencing experiments , 2012, Nature Methods.

[7]  H. Tan,et al.  Comparison of methanogen diversity of yak (Bos grunniens) and cattle (Bos taurus) from the Qinghai-Tibetan plateau, China , 2012, BMC Microbiology.

[8]  Loretta Auvil,et al.  The yak genome and adaptation to life at high altitude , 2012, Nature Genetics.

[9]  Siu-Ming Yiu,et al.  IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth , 2012, Bioinform..

[10]  Robert W. Li,et al.  Quantification of Transcriptome Responses of the Rumen Epithelium to Butyrate Infusion using RNA-seq Technology , 2012, Gene regulation and systems biology.

[11]  William A. Walters,et al.  Experimental and analytical tools for studying the human microbiome , 2011, Nature Reviews Genetics.

[12]  Qi Wu,et al.  Evidence of cellulose metabolism by the giant panda gut microbiome , 2011, Proceedings of the National Academy of Sciences.

[13]  G. Fuchs.  Alternative pathways of carbon dioxide fixation: insights into the early evolution of life? , 2011, Annual review of microbiology.

[14]  J. Clemente,et al.  Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans , 2011, Science.

[15]  F. Stumpff,et al.  Ruminant Nutrition Symposium: Role of fermentation acid absorption in the regulation of ruminal pH. , 2011, Journal of animal science.

[16]  M. Steele,et al.  Ruminant Nutrition Symposium: Molecular adaptation of ruminal epithelia to highly fermentable diets. , 2011, Journal of animal science.

[17]  S. Tringe,et al.  Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen , 2011, Science.

[18]  M. Kreuzer,et al.  Methane emissions from yak (Bos grunniens) steers grazing or kept indoors and fed diets with varying forage:concentrate ratio during the cold season on the Qinghai-Tibetan Plateau , 2010 .

[19]  C. Martin,et al.  Microbial ecosystem and methanogenesis in ruminants. , 2010, Animal : an international journal of animal bioscience.

[20]  P. Bork,et al.  A human gut microbial gene catalogue established by metagenomic sequencing , 2010, Nature.

[21]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[22]  K. Nelson,et al.  Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases , 2009, Proceedings of the National Academy of Sciences.

[23]  Brad T. Sherman,et al.  Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists , 2008, Nucleic acids research.

[24]  B. Williams,et al.  Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.

[25]  Zhanhuan Shang,et al.  The yak grazing system on the Qinghai-Tibetan plateau and its status , 2008 .

[26]  R. Knight,et al.  Evolution of Mammals and Their Gut Microbes , 2008, Science.

[27]  Yoshihiro Yamanishi,et al.  KEGG for linking genomes to life and the environment , 2007, Nucleic Acids Res..

[28]  L. Tong,et al.  Acetyl-coenzyme A carboxylase: crucial metabolic enzyme and attractive target for drug discovery , 2005, Cellular and Molecular Life Sciences CMLS.

[29]  Terence P. Speed,et al.  A comparison of normalization methods for high density oligonucleotide array data based on variance and bias , 2003, Bioinform..

[30]  J. Russell,et al.  Factors That Alter Rumen Microbial Ecology , 2001, Science.

[31]  M. Borodovsky,et al.  Heuristic approach to deriving models for gene finding. , 1999, Nucleic acids research.

[32]  H. Strobel.  Vitamin B12-dependent propionate production by the ruminal bacterium Prevotella ruminicola 23 , 1992, Applied and environmental microbiology.

[33]  L. Raab,et al.  The estimation of the digestibility and metabolizable energy content of ruminant feedingstuffs from the gas production when they are incubated with rumen liquor in vitro , 1979, The Journal of Agricultural Science.

[34]  P. C. Thomas.  Microbial protein synthesis , 1973, Proceedings of the Nutrition Society.

[35]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.