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Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species.

Künstner A, Wolf JB, Backström N, Whitney O, Balakrishnan CN, Day L, Edwards SV, Janes DE, Schlinger BA, Wilson RK, Jarvis ED, Warren WC, Ellegren H.

Mol Ecol. 2010 Mar;19 Suppl 1:266-76. doi: 10.1111/j.1365-294X.2009.04487.x. Erratum in: Mol Ecol. 2011 Jul;20(13):2871.


Molecular evolutionary genomics of birds.

Ellegren H.

Cytogenet Genome Res. 2007;117(1-4):120-30. Review.


Sex bias and dosage compensation in the zebra finch versus chicken genomes: general and specialized patterns among birds.

Itoh Y, Replogle K, Kim YH, Wade J, Clayton DF, Arnold AP.

Genome Res. 2010 Apr;20(4):512-8. doi: 10.1101/gr.102343.109. Epub 2010 Mar 31.


Temporal genomic evolution of bird sex chromosomes.

Wang Z, Zhang J, Yang W, An N, Zhang P, Zhang G, Zhou Q.

BMC Evol Biol. 2014 Dec 12;14:250. doi: 10.1186/s12862-014-0250-8.


Benchmarking next-generation transcriptome sequencing for functional and evolutionary genomics.

Gibbons JG, Janson EM, Hittinger CT, Johnston M, Abbot P, Rokas A.

Mol Biol Evol. 2009 Dec;26(12):2731-44. doi: 10.1093/molbev/msp188. Epub 2009 Aug 25.


Genome-wide SNP detection in the great tit Parus major using high throughput sequencing.

van Bers NE, van Oers K, Kerstens HH, Dibbits BW, Crooijmans RP, Visser ME, Groenen MA.

Mol Ecol. 2010 Mar;19 Suppl 1:89-99. doi: 10.1111/j.1365-294X.2009.04486.x.


Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery.

Parchman TL, Geist KS, Grahnen JA, Benkman CW, Buerkle CA.

BMC Genomics. 2010 Mar 16;11:180. doi: 10.1186/1471-2164-11-180.


Genomics of natural bird populations: a gene-based set of reference markers evenly spread across the avian genome.

Backström N, Fagerberg S, Ellegren H.

Mol Ecol. 2008 Feb;17(4):964-80. Epub 2007 Oct 8.


A comparative physical map reveals the pattern of chromosomal evolution between the turkey (Meleagris gallopavo) and chicken (Gallus gallus) genomes.

Zhang Y, Zhang X, O'Hare TH, Payne WS, Dong JJ, Scheuring CF, Zhang M, Huang JJ, Lee MK, Delany ME, Zhang HB, Dodgson JB.

BMC Genomics. 2011 Sep 9;12:447. doi: 10.1186/1471-2164-12-447.


General lack of global dosage compensation in ZZ/ZW systems? Broadening the perspective with RNA-seq.

Wolf JB, Bryk J.

BMC Genomics. 2011 Feb 1;12:91. doi: 10.1186/1471-2164-12-91.


Genomic evidence for a large-Z effect.

Ellegren H.

Proc Biol Sci. 2009 Jan 22;276(1655):361-6. doi: 10.1098/rspb.2008.1135.


Genome-wide annotation and analysis of zebra finch microRNA repertoire reveal sex-biased expression.

Luo GZ, Hafner M, Shi Z, Brown M, Feng GH, Tuschl T, Wang XJ, Li X.

BMC Genomics. 2012 Dec 26;13:727. doi: 10.1186/1471-2164-13-727.


A comparison of reptilian and avian olfactory receptor gene repertoires: species-specific expansion of group gamma genes in birds.

Steiger SS, Kuryshev VY, Stensmyr MC, Kempenaers B, Mueller JC.

BMC Genomics. 2009 Sep 21;10:446. doi: 10.1186/1471-2164-10-446.


Cross-species overgo hybridization and comparative physical mapping within avian genomes.

Romanov MN, Dodgson JB.

Anim Genet. 2006 Aug;37(4):397-9.


Dynamic evolution of base composition: causes and consequences in avian phylogenomics.

Nabholz B, Künstner A, Wang R, Jarvis ED, Ellegren H.

Mol Biol Evol. 2011 Aug;28(8):2197-210. doi: 10.1093/molbev/msr047. Epub 2011 Apr 4.


Transcriptome sequencing reveals the character of incomplete dosage compensation across multiple tissues in flycatchers.

Uebbing S, Künstner A, Mäkinen H, Ellegren H.

Genome Biol Evol. 2013;5(8):1555-66. doi: 10.1093/gbe/evt114.


Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes.

Elmer KR, Fan S, Gunter HM, Jones JC, Boekhoff S, Kuraku S, Meyer A.

Mol Ecol. 2010 Mar;19 Suppl 1:197-211. doi: 10.1111/j.1365-294X.2009.04488.x.


Combining next-generation sequencing and microarray technology into a transcriptomics approach for the non-model organism Chironomus riparius.

Marinković M, de Leeuw WC, de Jong M, Kraak MH, Admiraal W, Breit TM, Jonker MJ.

PLoS One. 2012;7(10):e48096. doi: 10.1371/journal.pone.0048096. Epub 2012 Oct 25.

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