The genome sequence and insights into the immunogenetics of the bananaquit (Passeriformes: Coereba flaveola)

[1]  J. DeWoody,et al.  Genomic Landscape of Long Terminal Repeat Retrotransposons (LTR-RTs) and Solo LTRs as Shaped by Ectopic Recombination in Chicken and Zebra Finch , 2016, Journal of Molecular Evolution.

[2]  R. Jia,et al.  CpG oligodeoxynucleotide-specific goose TLR21 initiates an anti-viral immune response against NGVEV but not AIV strain H9N2 infection. , 2016, Immunobiology.

[3]  M. Grabherr,et al.  Evolution of Darwin’s finches and their beaks revealed by genome sequencing , 2015, Nature.

[4]  I. Jamieson,et al.  Toll-like receptor diversity in 10 threatened bird species: relationship with microsatellite heterozygosity , 2015, Conservation Genetics.

[5]  Andreas R. Pfenning,et al.  Comparative genomics reveals insights into avian genome evolution and adaptation , 2014, Science.

[6]  Yanzhu Ji,et al.  The Genome Sequence of a Widespread Apex Predator, the Golden Eagle (Aquila chrysaetos) , 2014, PloS one.

[7]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[8]  C. Witt,et al.  Metabolic ‘engines’ of flight drive genome size reduction in birds , 2014, Proceedings of the Royal Society B: Biological Sciences.

[9]  Matthew Fraser,et al.  InterProScan 5: genome-scale protein function classification , 2014, Bioinform..

[10]  J. DeWoody,et al.  Hosts, parasites, and horizontal gene transfer. , 2013, Trends in parasitology.

[11]  Bhagya K. Wijayawardena,et al.  Of contigs and quagmires: next‐generation sequencing pitfalls associated with transcriptomic studies , 2013, Molecular ecology resources.

[12]  Gordon Gremme,et al.  GenomeTools: A Comprehensive Software Library for Efficient Processing of Structured Genome Annotations , 2013, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[13]  Alberto Policriti,et al.  GAM-NGS: genomic assemblies merger for next generation sequencing , 2013, BMC Bioinformatics.

[14]  Alexey A. Gurevich,et al.  QUAST: quality assessment tool for genome assemblies , 2013, Bioinform..

[15]  Jun Wang,et al.  Genomic Diversity and Evolution of the Head Crest in the Rock Pigeon , 2013, Science.

[16]  Jian Wang,et al.  SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler , 2012, GigaScience.

[17]  W. Pirovano,et al.  Toward almost closed genomes with GapFiller , 2012, Genome Biology.

[18]  Pablo Cingolani,et al.  © 2012 Landes Bioscience. Do not distribute. , 2022 .

[19]  Mark Yandell,et al.  MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects , 2011, BMC Bioinformatics.

[20]  Ioannis Xenarios,et al.  T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension , 2011, Nucleic Acids Res..

[21]  S. Edwards,et al.  Molecular evolution of the toll-like receptor multigene family in birds. , 2011, Molecular biology and evolution.

[22]  D. Golenbock,et al.  Toll-Like Receptors Participate in Macrophage Activation and Intracellular Control of Leishmania (Viannia) panamensis , 2011, Infection and Immunity.

[23]  Carl Kingsford,et al.  A fast, lock-free approach for efficient parallel counting of occurrences of k-mers , 2011, Bioinform..

[24]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer , 2011, Nature Biotechnology.

[25]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[26]  R. Brownlie,et al.  Avian toll-like receptors , 2010, Cell and Tissue Research.

[27]  T. Graves,et al.  Gene duplication and fragmentation in the zebra finch major histocompatibility complex , 2010, BMC Biology.

[28]  Patricia C. Babbitt,et al.  Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies , 2009, PLoS Comput. Biol..

[29]  A. T. Lloyd,et al.  The avian Toll-Like receptor pathway--subtle differences amidst general conformity. , 2009, Developmental and comparative immunology.

[30]  Jeanette C Papp,et al.  The value of avian genomics to the conservation of wildlife , 2009, BMC Genomics.

[31]  Steven J. M. Jones,et al.  Abyss: a Parallel Assembler for Short Read Sequence Data Material Supplemental Open Access , 2022 .

[32]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[33]  C. Hughes,et al.  Support for the minimal essential MHC hypothesis: a parrot with a single, highly polymorphic MHC class II B gene , 2008, Immunogenetics.

[34]  K. Magor,et al.  The duck toll like receptor 7: genomic organization, expression and function. , 2008, Molecular immunology.

[35]  Sofia M. C. Robb,et al.  MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. , 2007, Genome research.

[36]  R. Ricklefs,et al.  The dynamic evolutionary history of the bananaquit (Coereba flaveola) in the Caribbean revealed by a multigene analysis , 2008, BMC Evolutionary Biology.

[37]  Keith Bradnam,et al.  CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes , 2007, Bioinform..

[38]  Af Smit,et al.  RepeatMasker software program (computer program), ver. 3.1.8. Seattle: Institute for Systems Biology. , 2007 .

[39]  S. Akira,et al.  Toll-like receptors and innate immunity , 2006, Journal of Molecular Medicine.

[40]  Ronald E. Bontrop,et al.  Immunogenetics , 2005, Genes and Immunity.

[41]  S. Bensch,et al.  Associations between malaria and MHC genes in a migratory songbird , 2005, Proceedings of the Royal Society B: Biological Sciences.

[42]  N. Bumstead,et al.  Identification and characterization of a functional, alternatively spliced Toll‐like receptor 7 (TLR7) and genomic disruption of TLR8 in chickens , 2005, Immunology.

[43]  S. Akira,et al.  Induction of Proinflammatory Responses in Macrophages by the Glycosylphosphatidylinositols of Plasmodium falciparum , 2005, Journal of Biological Chemistry.

[44]  D. Gowda,et al.  Induction of Proinflammatory Responses in Macrophages by the Glycosylphosphatidylinositols of Plasmodium falciparum , 2005, Journal of Biological Chemistry.

[45]  Daniel G Peterson,et al.  The repetitive landscape of the chicken genome. , 2004, Genome research.

[46]  G. Valkiūnas Avian Malaria Parasites and other Haemosporidia , 2004 .

[47]  Eldredge Bermingham,et al.  Evolutionary relationships, cospeciation, and host switching in avian malaria parasites. , 2004, Systematic biology.

[48]  Peter Parham,et al.  Nomenclature for the major histocompatibility complexes of different species: a proposal , 2004, Immunogenetics.

[49]  Mario Stanke,et al.  Gene prediction with a hidden Markov model and a new intron submodel , 2003, ECCB.

[50]  David A. Hume,et al.  A Guide to the Mammalian Genome , 2003 .

[51]  J. Doležel,et al.  Nuclear DNA content and genome size of trout and human. , 2003, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[52]  S. Edwards,et al.  Evolutionary Dynamics of Intron Size, Genome Size, and Physiological Correlates in Archosaurs , 2002, The American Naturalist.

[53]  P. Gros,et al.  Susceptibility to malaria as a complex trait: big pressure from a tiny creature. , 2002, Human molecular genetics.

[54]  C. Hess,et al.  The Evolution of the Major Histocompatibility Complex in Birds , 2002 .

[55]  S. Gandon,et al.  Local adaptation, evolutionary potential and host–parasite coevolution: interactions between migration, mutation, population size and generation time , 2002 .

[56]  B. Kobe,et al.  The leucine-rich repeat as a protein recognition motif. , 2001, Current opinion in structural biology.

[57]  H. Wittzell,et al.  Mhc diversity in two passerine birds: no evidence for a minimal essential Mhc , 2000, Immunogenetics.

[58]  B. Grant,et al.  Mhc class II genes of Darwin’s Finches: divergence by point mutations and reciprocal recombination , 2000 .

[59]  G. Benson,et al.  Tandem repeats finder: a program to analyze DNA sequences. , 1999, Nucleic acids research.

[60]  R. Griffiths,et al.  A DNA test to sex most birds , 1998, Molecular ecology.

[61]  R. Cann,et al.  Mhc Allelic Diversity and Modern Human Origins , 1997, Journal of Molecular Evolution.

[62]  T Gojobori,et al.  Large-scale search for genes on which positive selection may operate. , 1996, Molecular biology and evolution.

[63]  A. Hughes,et al.  Natural selection on Plasmodium surface proteins. , 1995, Molecular and biochemical parasitology.

[64]  J. Kaufman,et al.  A “Minimal Essential Mhc” and an “Unrecognized Mhc”: Two Extremes in Selection for Polymorphism , 1995, Immunological reviews.

[65]  A. Hughes Positive selection and interallelic recombination at the merozoite surface antigen-1 (MSA-1) locus of Plasmodium falciparum. , 1992, Molecular biology and evolution.

[66]  Andrew J. McMichael,et al.  Common West African HLA antigens are associated with protection from severe malaria , 1991, Nature.

[67]  C. Auffray,et al.  Isolation of chicken major histocompatibility complex class II (B‐L) beta chain sequences: comparison with mammalian beta chains and expression in lymphoid organs. , 1988, The EMBO journal.

[68]  M. A. Saper,et al.  The foreign antigen binding site and T cell recognition regions of class I histocompatibility antigens , 1987, Nature.

[69]  R M May,et al.  Epidemiology and genetics in the coevolution of parasites and hosts , 1983, Proceedings of the Royal Society of London. Series B. Biological Sciences.