De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis): genomic tools for an ecological model system

[1]  Jeong-Hyeon Choi,et al.  De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis): genomic tools for an ecological model system , 2012, BMC Genomics.

[2]  James M. Maley,et al.  Next-generation sequencing reveals phylogeographic structure and a species tree for recent bird divergences. , 2009, Molecular phylogenetics and evolution.

[3]  P. Parker,et al.  Promiscuous mating produces offspring with higher lifetime fitness , 2012, Proceedings of the Royal Society B: Biological Sciences.

[4]  Monica F. Poelchau,et al.  A de novo transcriptome of the Asian tiger mosquito, Aedes albopictus, to identify candidate transcripts for diapause preparation , 2011, BMC Genomics.

[5]  M. Carling,et al.  Effects of Postmortem Interval and Preservation Method on RNA Isolated from Field-Preserved Avian Tissues , 2011 .

[6]  J. Colbourne,et al.  Dual Labeled Expression Microarray Protocol for High-Throughput Genomic Investigations , 2011 .

[7]  D. Haussler,et al.  Three Periods of Regulatory Innovation During Vertebrate Evolution , 2011, Science.

[8]  J. Slate,et al.  Characterisation of the transcriptome of a wild great tit Parus major population by next generation sequencing , 2011, BMC Genomics.

[9]  Emese Meglécz,et al.  Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing , 2011, BMC Genomics.

[10]  Todd H. Oakley,et al.  The Ecoresponsive Genome of Daphnia pulex , 2011, Science.

[11]  Daniel Rios,et al.  Ensembl 2011 , 2010, Nucleic Acids Res..

[12]  Evgeny M. Zdobnov,et al.  OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011 , 2010, Nucleic Acids Res..

[13]  J. Atwell,et al.  ANIMAL MIGRATION AS A MOVING TARGET FOR CONSERVATION: INTRA-SPECIES VARIATION AND RESPONSES TO ENVIRONMENTAL CHANGE, AS ILLUSTRATED IN A SOMETIMES MIGRATORY SONGBIRD. , 2011, Environmental law.

[14]  N. Karrow,et al.  Mesenteric lymph node transcriptome profiles in BALB/c mice sensitized to three common food allergens , 2011, BMC Genomics.

[15]  C. Millar,et al.  Next generation sequencing and analysis of a conserved transcriptome of New Zealand's kiwi , 2010, BMC Evolutionary Biology.

[16]  E. Snell-Rood,et al.  Gene discovery in the horned beetle Onthophagus taurus , 2010, BMC Genomics.

[17]  Jeong-Hyeon Choi,et al.  A garter snake transcriptome: pyrosequencing, de novo assembly, and sex-specific differences , 2010, BMC Genomics.

[18]  H. Hofmann,et al.  Parallel evolution of opsin gene expression in African cichlid fishes. , 2010, Molecular biology and evolution.

[19]  Arne Elofsson,et al.  Nebulin: a study of protein repeat evolution. , 2010, Journal of molecular biology.

[20]  E. Ketterson,et al.  Natural Selection on Testosterone Production in a Wild Songbird Population , 2010, The American Naturalist.

[21]  Albert J. Vilella,et al.  The genome of a songbird , 2010, Nature.

[22]  R. Wilson,et al.  Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species , 2010, Molecular ecology.

[23]  Markus Schilhabel,et al.  Nucleotide divergence vs. gene expression differentiation: comparative transcriptome sequencing in natural isolates from the carrion crow and its hybrid zone with the hooded crow , 2010, Molecular ecology.

[24]  Jeremy Schmutz,et al.  Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer , 2010, Science.

[25]  Susumu Goto,et al.  KEGG for representation and analysis of molecular networks involving diseases and drugs , 2009, Nucleic Acids Res..

[26]  W. Wüster,et al.  Comparative venom gland transcriptome surveys of the saw-scaled vipers (Viperidae: Echis) reveal substantial intra-family gene diversity and novel venom transcripts , 2009, BMC Genomics.

[27]  D. Guo,et al.  Global characterization of Artemisia annua glandular trichome transcriptome using 454 pyrosequencing , 2009, BMC Genomics.

[28]  J. Atwell,et al.  Phenotypic integration and independence: Hormones, performance, and response to environmental change. , 2009, Integrative and comparative biology.

[29]  Jade Buchanan-Carter,et al.  Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx , 2009, BMC Genomics.

[30]  Junjun Zhang,et al.  BioMart Central Portal—unified access to biological data , 2009, Nucleic Acids Res..

[31]  K. Kubokawa,et al.  Characterization of amphioxus nebulin and its similarity to human nebulin , 2009, Journal of Experimental Biology.

[32]  Tatiana A. Tatusova,et al.  NCBI Reference Sequences: current status, policy and new initiatives , 2008, Nucleic Acids Res..

[33]  Jian-Qun Chen,et al.  Patterns of exon-intron architecture variation of genes in eukaryotic genomes , 2009, BMC Genomics.

[34]  Damian Smedley,et al.  BioMart – biological queries made easy , 2009, BMC Genomics.

[35]  H. Ellegren Sequencing goes 454 and takes large‐scale genomics into the wild , 2008, Molecular ecology.

[36]  J. Marden,et al.  Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing , 2008, Molecular ecology.

[37]  Evgeny M. Zdobnov,et al.  OrthoDB: the hierarchical catalog of eukaryotic orthologs , 2007, Nucleic Acids Res..

[38]  E. Ketterson,et al.  Hormone-mediated suites as adaptations and evolutionary constraints , 2008, Philosophical Transactions of the Royal Society B: Biological Sciences.

[39]  R. Wayne,et al.  Recent postglacial range expansion drives the rapid diversification of a songbird lineage in the genus Junco , 2007, Proceedings of the Royal Society B: Biological Sciences.

[40]  W. Goymann,et al.  Sex‐role reversal is reflected in the brain of African black coucals (Centropus grillii) , 2007, Developmental neurobiology.

[41]  P. Yeh,et al.  Alternative nesting behaviours following colonisation of a novel environment by a passerine bird , 2007 .

[42]  M. Mulanax,et al.  Dark-eyed Junco : Junco hyemalis , 2007 .

[43]  G. Wray The evolutionary significance of cis-regulatory mutations , 2007, Nature Reviews Genetics.

[44]  B. Schlinger,et al.  Low sex steroids, high steroid receptors: Increasing the sensitivity of the nonreproductive brain , 2007, Developmental neurobiology.

[45]  Trupti Joshi,et al.  Quantitative assessment of relationship between sequence similarity and function similarity , 2007, BMC Genomics.

[46]  P. Parker,et al.  Physiological Effects on Demography: A Long‐Term Experimental Study of Testosterone’s Effects on Fitness , 2006, The American Naturalist.

[47]  P. Yeh,et al.  Reduced territorial responses in dark-eyed juncos following population establishment in a climatically mild environment , 2006, Animal Behaviour.

[48]  Kiyoko F. Aoki-Kinoshita,et al.  From genomics to chemical genomics: new developments in KEGG , 2005, Nucleic Acids Res..

[49]  Juan Miguel García-Gómez,et al.  BIOINFORMATICS APPLICATIONS NOTE Sequence analysis Manipulation of FASTQ data with Galaxy , 2005 .

[50]  Jun Lu,et al.  Pathway level analysis of gene expression using singular value decomposition , 2005, BMC Bioinformatics.

[51]  Thomas D. Wu,et al.  GMAP: a genomic mapping and alignment program for mRNA and EST sequence , 2005, Bioinform..

[52]  Gordon K. Smyth,et al.  limma: Linear Models for Microarray Data , 2005 .

[53]  P. Yeh,et al.  Adaptive Phenotypic Plasticity and the Successful Colonization of a Novel Environment , 2004, The American Naturalist.

[54]  K. Pelin,et al.  Complete genomic structure of the human nebulin gene and identification of alternatively spliced transcripts , 2004, European Journal of Human Genetics.

[55]  Joel Cracraft,et al.  Phylogeny and diversification of the largest avian radiation. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[56]  P. Yeh,et al.  Genetic and morphological evolution following a founder event in the dark‐eyed junco, Junco hyemalis thurberi , 2004, Molecular ecology.

[57]  P. Yeh RAPID EVOLUTION OF A SEXUALLY SELECTED TRAIT FOLLOWING POPULATION ESTABLISHMENT IN A NOVEL HABITAT , 2004, Evolution; international journal of organic evolution.

[58]  C. Gregorio,et al.  Nebulin: the nebulous, multifunctional giant of striated muscle. , 2003, Trends in cardiovascular medicine.

[59]  C. Buerkle,et al.  Testosterone , phenotype and fitness : a research program in evolutionary behavioral endocrinology , 2002 .

[60]  A. Valencia,et al.  Intrinsic errors in genome annotation. , 2001, Trends in genetics : TIG.

[61]  Donna R. Maglott,et al.  RefSeq and LocusLink: NCBI gene-centered resources , 2001, Nucleic Acids Res..

[62]  Michael Y. Galperin,et al.  The COG database: new developments in phylogenetic classification of proteins from complete genomes , 2001, Nucleic Acids Res..

[63]  A. Valencia,et al.  Practical limits of function prediction , 2000, Proteins.

[64]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[65]  J. Wingfield,et al.  Androgen-metabolizing enzymes show region-specific changes across the breeding season in the brain of a wild songbird. , 1999, Journal of neurobiology.

[66]  Hiroyuki Ogata,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..

[67]  Michael G. Ruscio,et al.  Role of the Archistriatal Nucleus taeniae in the Sexual Behavior of Male Japanese Quail (Coturnix japonica): A Comparison of Function with the Medial Nucleus of the Amygdala in Mammals , 1998, Brain, Behavior and Evolution.

[68]  D. Lipman,et al.  A genomic perspective on protein families. , 1997, Science.

[69]  G. Ball,et al.  Testosterone and avian life histories: The effect of experimentally elevated testosterone on corticosterone and body mass in dark-eyed juncos , 1991, Hormones and Behavior.

[70]  P. Chomczyński,et al.  Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. , 1987, Analytical biochemistry.

[71]  W. Rowan Relation of Light to Bird Migration and Developmental Changes , 1925, Nature.