The evolution of gene expression levels in mammalian organs

[1]  Jianzhi Zhang,et al.  Evolutionary conservation of expression profiles between human and mouse orthologous genes. , 2006, Molecular biology and evolution.

[2]  Henrik Kaessmann,et al.  Origins, evolution, and phenotypic impact of new genes. , 2010, Genome research.

[3]  N. Vinckenbosch,et al.  The emergence of new genes on the young therian X. , 2010, Trends in genetics : TIG.

[4]  S. Pääbo,et al.  Intra- and Interspecific Variation in Primate Gene Expression Patterns , 2002, Science.

[5]  J. Daudin,et al.  A Segmentation/Clustering Model for the Analysis of Array CGH Data , 2007, Biometrics.

[6]  R. Guigó,et al.  Transcriptome genetics using second generation sequencing in a Caucasian population , 2010, Nature.

[7]  S. Pääbo,et al.  Parallel Patterns of Evolution in the Genomes and Transcriptomes of Humans and Chimpanzees , 2005, Science.

[8]  N. Vinckenbosch,et al.  RNA-based gene duplication: mechanistic and evolutionary insights , 2009, Nature Reviews Genetics.

[9]  M. Long,et al.  Chromosomal Redistribution of Male-Biased Genes in Mammalian Evolution with Two Bursts of Gene Gain on the X Chromosome , 2010, PLoS biology.

[10]  Eric T. Wang,et al.  Alternative Isoform Regulation in Human Tissue Transcriptomes , 2008, Nature.

[11]  Miriam K. Konkel,et al.  Genome analysis of the platypus reveals unique signatures of evolution , 2008, Nature.

[12]  P. Schoenemann,et al.  Prefrontal white matter volume is disproportionately larger in humans than in other primates , 2005, Nature Neuroscience.

[13]  Jianzhi Zhang,et al.  RNA sequencing shows no dosage compensation of the active X-chromosome , 2010, Nature Genetics.

[14]  M. King,et al.  Evolution at two levels in humans and chimpanzees. , 1975, Science.

[15]  D. Frayer.  SEXUAL DIMORPHISM , 2005 .

[16]  D. Reich,et al.  Analysis of Chimpanzee History Based on Genome Sequence Alignments , 2008, PLoS genetics.

[17]  Matthew A. Zapala,et al.  Elevated gene expression levels distinguish human from non-human primate brains , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[18]  M. Lercher,et al.  Explorer Evidence for Widespread Degradation of Gene Control Regions in Hominid Genomes , 2015 .

[19]  Albert J. Vilella,et al.  EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. , 2009, Genome research.

[20]  K. Scearce-Levie,et al.  COL25A1 triggers and promotes Alzheimer’s disease-like pathology in vivo , 2009, neurogenetics.

[21]  Wenbo Xu,et al.  Sister grouping of chimpanzees and humans as revealed by genome-wide phylogenetic analysis of brain gene expression profiles. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[22]  Michael Lachmann,et al.  Evolution of primate gene expression , 2006, Nature Reviews Genetics.

[23]  Terrence S. Furey,et al.  Both Noncoding and Protein-Coding RNAs Contribute to Gene Expression Evolution in the Primate Brain , 2010, Genome biology and evolution.

[24]  Gary F. Marcus,et al.  The Birth of the Mind , 2003 .

[25]  M. Stephens,et al.  Sex-specific and lineage-specific alternative splicing in primates. , 2010, Genome research.

[26]  C. Kemkemer,et al.  Enrichment of brain-related genes on the mammalian X chromosome is ancient and predates the divergence of synapsid and sauropsid lineages , 2009, Chromosome Research.

[27]  J. Jensen,et al.  Accelerated Adaptive Evolution on a Newly Formed X Chromosome , 2009, PLoS biology.

[28]  N. Vinckenbosch,et al.  Chromosomal Gene Movements Reflect the Recent Origin and Biology of Therian Sex Chromosomes , 2008, PLoS biology.

[29]  Franz Vauti,et al.  The mouse Trm1-like gene is expressed in neural tissues and plays a role in motor coordination and exploratory behaviour. , 2007, Gene.

[30]  J. Graves,et al.  In the platypus a meiotic chain of ten sex chromosomes shares genes with the bird Z and mammal X chromosomes , 2004, Nature.

[31]  Chris P. Ponting,et al.  The functional repertoires of metazoan genomes , 2008, Nature Reviews Genetics.

[32]  Kateryna D. Makova,et al.  Evolution and Survival on Eutherian Sex Chromosomes , 2009, PLoS genetics.

[33]  Laurent Duret,et al.  Biased gene conversion and the evolution of mammalian genomic landscapes. , 2009, Annual review of genomics and human genetics.

[34]  G. Wray,et al.  Contrasts between adaptive coding and noncoding changes during human evolution , 2010, Proceedings of the National Academy of Sciences.

[35]  T. Kemp.  The Origin and Evolution of Mammals , 2005 .

[36]  Andrew M. Jenkinson,et al.  Ensembl 2009 , 2008, Nucleic Acids Res..

[37]  B. Charlesworth.  Model for evolution of Y chromosomes and dosage compensation. , 1978, Proceedings of the National Academy of Sciences of the United States of America.

[38]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

[39]  Joseph K. Pickrell,et al.  Understanding mechanisms underlying human gene expression variation with RNA sequencing , 2010, Nature.

[40]  T. Graves,et al.  Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes. , 2008, Genome research.

[41]  Timothy B Sackton,et al.  A Scan for Positively Selected Genes in the Genomes of Humans and Chimpanzees , 2005, PLoS biology.

[42]  Martin Kircher,et al.  Improved base calling for the Illumina Genome Analyzer using machine learning strategies , 2009, Genome Biology.

[43]  R. Agarwala,et al.  An ~140-kb deletion associated with feline spinal muscular atrophy implies an essential LIX1 function for motor neuron survival , 2006 .

[44]  Paulo P. Amaral,et al.  The Reality of Pervasive Transcription , 2011, PLoS biology.

[45]  Korbinian Strimmer,et al.  APE: Analyses of Phylogenetics and Evolution in R language , 2004, Bioinform..

[46]  M. Gerstein,et al.  RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.

[47]  R. Agarwala,et al.  An approximately 140-kb deletion associated with feline spinal muscular atrophy implies an essential LIX1 function for motor neuron survival. , 2006, Genome research.

[48]  Jean L. Chang,et al.  Initial sequence of the chimpanzee genome and comparison with the human genome , 2005, Nature.

[49]  M. Goodman,et al.  The genomic record of Humankind's evolutionary roots. , 1999, American journal of human genetics.

[50]  Terence P. Speed,et al.  Expression profiling in primates reveals a rapid evolution of human transcription factors , 2006, Nature.

[51]  J Krushkal,et al.  Rates of nucleotide substitution in primates and rodents and the generation-time effect hypothesis. , 1996, Molecular phylogenetics and evolution.

[52]  W. Rice.  SEX CHROMOSOMES AND THE EVOLUTION OF SEXUAL DIMORPHISM , 1984, Evolution; international journal of organic evolution.

[53]  Sven Bergmann,et al.  Defining transcription modules using large-scale gene expression data , 2004, Bioinform..

[54]  C. Ponting,et al.  Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes , 2010, Genome Biology.

[55]  D. Haussler,et al.  Aligning multiple genomic sequences with the threaded blockset aligner. , 2004, Genome research.

[56]  Esther T. Chan,et al.  Conservation of core gene expression in vertebrate tissues , 2009, Journal of biology.

[57]  S. Larson,et al.  Testis weight, body weight and breeding system in primates , 1981, Nature.

[58]  David L. Steffen,et al.  The DNA sequence of the human X chromosome , 2005, Nature.

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

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