Ancient hybridization and strong adaptation to viruses across African vervet monkey populations

[1]  R. Wilson,et al.  Publisher Correction: Ancient hybridization and strong adaptation to viruses across African vervet monkey populations , 2018, Nature Genetics.

[2]  S. Pfeifer,et al.  The demographic and adaptive history of the African green monkey , 2017, bioRxiv.

[3]  André L. Martins,et al.  Natural Selection has Shaped Coding and Non-coding Transcription in Primate CD4+ T-cells , 2016, bioRxiv.

[4]  J. Kelso,et al.  Genetic Adaptation and Neandertal Admixture Shaped the Immune System of Human Populations , 2016, Cell.

[5]  J. Sese,et al.  Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism , 2016, Nature Genetics.

[6]  K. Dewar,et al.  Envelope-specific B-cell populations in African green monkeys chronically infected with simian immunodeficiency virus , 2016, Nature Communications.

[7]  Shu-wen Liu,et al.  Heat Shock Factor 1 Mediates Latent HIV Reactivation , 2016, Scientific Reports.

[8]  J. Lifson,et al.  Rapid Inflammasome Activation following Mucosal SIV Infection of Rhesus Monkeys , 2016, Cell.

[9]  Brian L Browning,et al.  Genotype Imputation with Millions of Reference Samples. , 2016, American journal of human genetics.

[10]  James Mallet,et al.  How reticulated are species? , 2015, BioEssays : news and reviews in molecular, cellular and developmental biology.

[11]  D. Petrov,et al.  Viruses are a dominant driver of protein adaptation in mammals , 2015, bioRxiv.

[12]  K. Zeng,et al.  Investigation Title : The effects of background and interference selection on patterns of genetic variation in subdivided populations , 2015 .

[13]  R. Wilson,et al.  Sequencing strategies and characterization of 721 vervet monkey genomes for future genetic analyses of medically relevant traits , 2015, BMC Biology.

[14]  N. Freimer,et al.  Local Virus Extinctions following a Host Population Bottleneck , 2015, Journal of Virology.

[15]  Guangfeng Song,et al.  HIV-1, human interaction database: current status and new features , 2014, Nucleic Acids Res..

[16]  L. Duret,et al.  Comparative population genomics in animals uncovers the determinants of genetic diversity , 2014, Nature.

[17]  F. Barré-Sinoussi,et al.  Innate Immune Responses and Rapid Control of Inflammation in African Green Monkeys Treated or Not with Interferon-Alpha during Primary SIVagm Infection , 2014, PLoS pathogens.

[18]  R. Durbin,et al.  Inferring human population size and separation history from multiple genome sequences , 2014, Nature Genetics.

[19]  H. Feldmann,et al.  African Green Monkeys Recapitulate the Clinical Experience with Replication of Live Attenuated Pandemic Influenza Virus Vaccine Candidates , 2014, Journal of Virology.

[20]  D. Douek,et al.  Pathogenic Features Associated with Increased Virulence upon Simian Immunodeficiency Virus Cross-Species Transmission from Natural Hosts , 2014, Journal of Virology.

[21]  R. Hernandez,et al.  Live Attenuated Tetravalent Dengue Virus Host Range Vaccine Is Immunogenic in African Green Monkeys following a Single Vaccination , 2014, Journal of Virology.

[22]  N. Freimer,et al.  Factors Associated with Siman Immunodeficiency Virus Transmission in a Natural African Nonhuman Primate Host in the Wild , 2014, Journal of Virology.

[23]  Nicolas Duforet-Frebourg,et al.  Genome Scans for Detecting Footprints of Local Adaptation Using a Bayesian Factor Model , 2014, Molecular biology and evolution.

[24]  K. Mansfield,et al.  Frequent infection of neurons by SV40 virus in SIV-infected macaque monkeys with progressive multifocal leukoencephalopathy and meningoencephalitis. , 2013, The American journal of pathology.

[25]  Jean-François Zagury,et al.  Haplotype estimation using sequencing reads. , 2013, American journal of human genetics.

[26]  Mauricio O. Carneiro,et al.  From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline , 2013, Current protocols in bioinformatics.

[27]  Arcadi Navarro,et al.  Great ape genetic diversity and population history , 2013, Nature.

[28]  Yan Zhou,et al.  The role of Ran-binding protein 3 during influenza A virus replication. , 2013, The Journal of general virology.

[29]  Laurent Excoffier,et al.  Evidence for polygenic adaptation to pathogens in the human genome. , 2013, Molecular biology and evolution.

[30]  L. Kozlovskaya,et al.  Exploring of Primate Models of Tick-Borne Flaviviruses Infection for Evaluation of Vaccines and Drugs Efficacy , 2013, PloS one.

[31]  Tongqing Zhou,et al.  Somatic Mutations of the Immunoglobulin Framework Are Generally Required for Broad and Potent HIV-1 Neutralization , 2013, Cell.

[32]  Heng Li Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM , 2013, 1303.3997.

[33]  M. Hofreiter,et al.  Mitochondrial Diversity and Distribution of African Green Monkeys (Chlorocebus Gray, 1870) , 2013, American journal of primatology.

[34]  N. Freimer,et al.  SIVagm Infection in Wild African Green Monkeys from South Africa: Epidemiology, Natural History, and Evolutionary Considerations , 2013, PLoS pathogens.

[35]  J. Lifson,et al.  Differential infection patterns of CD4+ T cells and lymphoid tissue viral burden distinguish progressive and nonprogressive lentiviral infections. , 2012, Blood.

[36]  Swapan Mallick,et al.  Ancient Admixture in Human History , 2012, Genetics.

[37]  Kenny Q. Ye,et al.  An integrated map of genetic variation from 1,092 human genomes , 2012, Nature.

[38]  P. Andolfatto,et al.  Revisiting an Old Riddle: What Determines Genetic Diversity Levels within Species? , 2012, PLoS biology.

[39]  E. Major,et al.  Molecular Biology, Epidemiology, and Pathogenesis of Progressive Multifocal Leukoencephalopathy, the JC Virus-Induced Demyelinating Disease of the Human Brain , 2012, Clinical Microbiology Reviews.

[40]  H. Shida Role of Nucleocytoplasmic RNA Transport during the Life Cycle of Retroviruses , 2012, Front. Microbio..

[41]  Páll Melsted,et al.  Comparative RNA sequencing reveals substantial genetic variation in endangered primates. , 2012, Genome research.

[42]  David Reich,et al.  Testing for ancient admixture between closely related populations. , 2011, Molecular biology and evolution.

[43]  Gonçalo R. Abecasis,et al.  The variant call format and VCFtools , 2011, Bioinform..

[44]  S. Pryputniewicz,et al.  Early Induction of Polyfunctional Simian Immunodeficiency Virus (SIV)-Specific T Lymphocytes and Rapid Disappearance of SIV from Lymph Nodes of Sooty Mangabeys during Primary Infection , 2011, The Journal of Immunology.

[45]  M. DePristo,et al.  A framework for variation discovery and genotyping using next-generation DNA sequencing data , 2011, Nature Genetics.

[46]  V. Rybin,et al.  Insights into the Function of the CRM1 Cofactor RanBP3 from the Structure of Its Ran-Binding Domain , 2011, PloS one.

[47]  T. Butynski,et al.  Three Sykes's Monkey Cercopithecus mitis × Vervet Monkey Chlorocebus pygerythrus Hybrids in Kenya , 2010 .

[48]  David Reich,et al.  Population differentiation as a test for selective sweeps. , 2010, Genome research.

[49]  F. Barré-Sinoussi,et al.  Nonpathogenic SIV infection of African green monkeys induces a strong but rapidly controlled type I IFN response. , 2009, The Journal of clinical investigation.

[50]  David H. Alexander,et al.  Fast model-based estimation of ancestry in unrelated individuals. , 2009, Genome research.

[51]  G. Melikyan,et al.  HIV Enters Cells via Endocytosis and Dynamin-Dependent Fusion with Endosomes , 2009, Cell.

[52]  Steve Horvath,et al.  WGCNA: an R package for weighted correlation network analysis , 2008, BMC Bioinformatics.

[53]  Ryan D. Hernandez,et al.  Demographic Histories and Patterns of Linkage Disequilibrium in Chinese and Indian Rhesus Macaques , 2007, Science.

[54]  S. Horvath,et al.  A General Framework for Weighted Gene Co-Expression Network Analysis , 2005, Statistical applications in genetics and molecular biology.

[55]  D. Haussler,et al.  Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. , 2005, Genome research.

[56]  Charles R. Brown,et al.  Plateau Levels of Viremia Correlate with the Degree of CD4+-T-Cell Loss in Simian Immunodeficiency Virus SIVagm-Infected Pigtailed Macaques: Variable Pathogenicity of Natural SIVagm Isolates , 2005, Journal of Virology.

[57]  Robert C. Edgar,et al.  MUSCLE: a multiple sequence alignment method with reduced time and space complexity , 2004, BMC Bioinformatics.

[58]  S. Salzberg,et al.  Versatile and open software for comparing large genomes , 2004, Genome Biology.

[59]  Y. Hakata,et al.  A Multifunctional Domain in Human CRM1 (Exportin 1) Mediates RanBP3 Binding and Multimerization of Human T-Cell Leukemia Virus Type 1 Rex Protein , 2003, Molecular and Cellular Biology.

[60]  E. Major,et al.  Lineage pathway of human brain progenitor cells identified by JC virus susceptability , 2003, Annals of neurology.

[61]  T. Rana,et al.  A bimolecular mechanism of HIV-1 Tat protein interaction with RNA polymerase II transcription elongation complexes. , 2002, Journal of molecular biology.

[62]  Carsten Schwarz,et al.  Genomewide comparison of DNA sequences between humans and chimpanzees. , 2002, American journal of human genetics.

[63]  K. Crandall,et al.  Selecting the best-fit model of nucleotide substitution. , 2001, Systematic biology.

[64]  C. Chappey,et al.  Simian immunodeficiency viruses from central and western Africa: evidence for a new species-specific lentivirus in tantalus monkeys , 1993, Journal of virology.

[65]  A. Koff,et al.  Sequence-specific interactions between a cellular DNA-binding protein and the simian virus 40 origin of DNA replication , 1988, Molecular and cellular biology.

[66]  Robert M. Seyfarth,et al.  The recognition of social alliances by vervet monkeys , 1986, Animal Behaviour.

[67]  B. Weir,et al.  ESTIMATING F‐STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE , 1984, Evolution; international journal of organic evolution.

[68]  P. Marler,et al.  Vervet monkey alarm calls: Semantic communication in a free-ranging primate , 1980, Animal Behaviour.

[69]  M. Hirai,et al.  A case of patas-vervet hybrid in captivity , 1978, Primates.

[70]  Christine B. Peterson,et al.  Genetic variation and gene expression across multiple tissues and developmental stages in a nonhuman primate. , 2016 .

[71]  Trey Ideker,et al.  Cytoscape: the network visualization tool for GenomeSpace workflows , 2014, F1000Research.

[72]  N. Freimer,et al.  Systems biology of the vervet monkey. , 2013, ILAR journal.

[73]  R. Johnson,et al.  Sooty mangabeys and rhesus macaques exhibit significant divergent natural killer cell responses during both acute and chronic phases of SIV infection. , 2008, Cellular immunology.

[74]  H. Kishino,et al.  Dating of the human-ape splitting by a molecular clock of mitochondrial DNA , 2005, Journal of Molecular Evolution.