66. Wong Miller KM, Bachtrog D. (2014). The genomic landscape of incipient species reveals a candidate behavioral isolation gene in Drosophila athabasca. submitted.

65. Blackmon H, Ross L, Bachtrog D. (2014). Sex determination, sex chromosomes and karyotype evolution in insects, submitted.

64. Mahajan S & Bachtrog D (2014). Partial dosage compensation in Strepsiptera, a sister group of beetles. submitted.

63. Vicoso B & Bachtrog D (2014). Numerous transitions of sex chromosomes in Diptera. submitted.

62. Kaiser V & Bachtrog D (2014). Transcripts from the Y: maintenance of male genes and acquisition of transposable elements in
Drosophila pseudoobscura and Drosophila miranda. submitted

61. Assis R, Bachtrog D (2014). Gradual divergence and diversification of mammalian duplicate gene functions. submitted.

60. Zhou*, Q., Zhang*, J., Bachtrog*, D., An, N., Huang, Q., Nanda, I., Gilbert, T., Jarvis, E.D., and Zhang, G. (2014). Sex Chromosomes Demonstrate Complex Evolutionary Trajectories Across Bird Taxa.
Science, in revision.
*co-first authors

59. Bastien B, Walton Z, Delgado JA, Collantes F, Beani L, Stewart IJ, Cameron SA, Whitfield JB, Johnston S, Holland PWH, Bachtrog D, Kathirithamby J, Huelsenbeck JP (2014). Strepsiptera, phylogenomics and the long branch attraction problem.
PLoS ONE, in revision.

58. The Tree of Sex Consortium (2014). Tree of Sex: A database of sexual systems.
Scientific Data, in press.

57. Bachtrog D, Mank J, Peichel C, Otto S, Kirkpatrick M, Ashman TL, Hahn M, Kitano J, Mayrose I, Ming R, Perrin N, Ross L, Valenzuela N, Vamosi J. (2014) Sex determination: Why so many ways of doing it?
PLoS Biology, in press.

56. Kaiser V & Bachtrog D (2014) De novo transcriptome assembly reveals sex-specific selection acting on evolving neo-sex chromosomes in
Drosophila miranda. BMC Genomics, 15(1):241.

55. Brown E., and Bachtrog, D. (2014). The chromatin landscape of Drosophila miranda: comparisons between species, sexes and chromosomes.
Genome Research, in press.

54. Lott, S.E., Villalta, J.E., Zhou, Q., Bachtrog, D., and Eisen, M.B. (2014). Sex-specific embryonic gene expression in species with newly evolved sex chromosomes.
PLoS Genetics, 10(2):e1004159.

53. Assis R, Bachtrog D (2013). Neofunctionalization of young duplicates in
Drosophila. Proceeding of the National Academy of Sciences, 110: 17409-17414.

52. Ellison C, Bachtrog D (2013). Dosage compensation via transposable element mediated rewiring of a regulatory network.
Science, 342: 846-50.
see also Perspective in
Science: Transposons up the Dosage; Research Highlight in Nature Review Genetics: Transposons drive sex chromosome evolution.

51. Zhou* Q, Ellison* CE, Kaiser VB, Alekseyenko AA, Gorchakov AA, Bachtrog D (2013). The epigenome of evolving Drosophila neo-sex chromosomes: dosage compensation and heterochromatin formation,
PLoS Biology, 11:e1000711.
*co-first authors

50. Husnik F, N Nikoh, R Koga, L Ross, M Fujie, M Tanaka, N Satoh, D Bachtrog, CD von Dohlen, T Fukatsu, JP McCutcheon. Horizontal gene transfer from diverse bacteria to an insect genome enables a tripartite nested mealybug symbiosis,
Cell, 153: 1567-1578.

49. Vicoso* B, Emerson* JJ, Zekster Y, Mahajan S & Bachtrog D (2013). Comparative sex chromosome genomics in snakes: differentiation, evolutionary strata, and lack of global dosage compensation.
PLoS Biology, 11:e1001643.
*co-first authors

48. Vicoso B & Bachtrog D (2013). Reversal of an ancient sex chromosome to an autosome in Drosophila.
Nature, 499: 322-335.

47. Alekseyenko* AA, Ellison* CE, Gorchakov* AA, Zhou Q, Kaiser VB, Toda N, Walton Z, Peng S, Park PJ, Bachtrog# D, Kuroda# M (2013). Conservation and de novo acquisition of dosage compensation on newly evolved sex chromosomes in Drosophila,
Genes & Development, 27:853-858.
*co-first authors, #co-corresponding authors

46. Vicoso B, Kaiser VB & Bachtrog D (2013). Sex-biased gene expression at homomorphic sex chromosomes in emus, and its implication for sex chromosome evolution.
Proceedings of the National Academy of Sciences, 110(16): 6453-6458.

45. Bachtrog D (2013). Y chromosome evolution: emerging insights into processes of Y degeneration.
Nature Review Genetics, 14:113-124.

44. Assis R, Zhou Q & Bachtrog D (2012) Sex-biased transcriptome evolution in Drosophila.
Genome Biology and Evolution 4:1189-1200.

43. Zhou Q & Bachtrog D (2012) Sex-specific adaptation drives early sex chromosome evolution in Drosophila.
Science. 337(6092):341-5.

42. Bachtrog D (2013) Evolution of sex chromosomes. ”
Princeton Guide to Evolution”. Princeton University Press.

41. Zhou Q, Zhu HM, …, J Wang, W Wang Bachtrog D (2012) Deciphering neo-sex and B chromosome evolution by the draft genome of
Drosophila albomicans. BMC Genomics 13:109.

40. Zhou Q & Bachtrog D (2012) Chromosome-wide gene silencing initiates Y degeneration in Drosophila.
Current Biology, 22(6):522-5.

39. Kaiser V, Q Zhou & Bachtrog D (2011) Non-random gene loss from the Drosophila miranda neo-Y chromosome. Genome Biology & Evolution, 3: 1329-37.

Bachtrog D (2011) Plant sex chromosomes: a non-degenerated Y? Current Biology, 21(18): R685-8.

Bachtrog D, M Kirkpatrick, J Mank, JC Pires, W Rice & N Valenzuela (2011). Are all sex chromosomes created equal? Trends in Genetics, 27(9):350-7.

36. Andolfatto P, K Wong & Bachtrog D (2011). Population size and the efficacy of selection in two closely related Drosophila species. Genome Biology and Evolution, 3: 114-128

35. Callahan B, RA Neher, Bachtrog D, P Andolfatto, BI Shraiman (2011). Correlated evolution of nearby residues in Drosophila genomes. PLoS Genetics, 7:e1001315.

34. Vicoso B &
Bachtrog D (2011). Lack of dosage compensation in Schistosoma mansoni, a female-heterogametic parasite. Genome Biology and Evolution, 3:230-5.

33. Jensen J &
Bachtrog D (2010) Characterizing the influence of effective population size on the rate of adaptation: Gillespie’s Darwin domain. Genome Biology and Evolution,3:687-701.

32. Kaiser V & Bachtrog D (2010). Evolution of sex chromosomes in Insects. Annual Review of Genetics, 44: 91-112.

31. Jensen J &
Bachtrog D (2010). Characterizing recurrent positive selection at fast-evolving genes in Drosophila miranda and D. pseudoobcurca. Genome Biology and Evolution, 2: 371-378.

30. Bachtrog D, N Toda & S Lockton (2010) Dosage compensation and Demasculinization of X chromosomes in Drosophila,
Current Biology 20(16): 1476-81.

29. Vicoso B & Bachtrog D(2009) Progress and prospects toward our understanding of the evolution of dosage compensation.
Chromosome Research, 17(5): 585-602.

28. Bachtrog D, J Jensen & Z Zhang (2009) Accelerated adaptive evolution on a newly formed X chromosome. PLoS Biology, 7(4): e82.

Bachtrog D (2008) Similar rates of protein adaptation in Drosophila miranda and D. melanogaster, two species with different current effective population sizes. BMC Evolutionary Biology, 8:334.

26. Gurbich T & Bachtrog D (2008) Gene content evolution on the X chromosome.
Current Opinion in Genetics and Development, 18(6): 493-8.

Bachtrog D (2008) Positive selection at the binding sites of the male-specific lethal complex involved in dosage compensation in Drosophila, Genetics, 180(2): 1123-1129.

24. Haddrill P, Bachtrog D, P Andolfatto (2008) Positive and negative selection on noncoding DNA in Drosophila simulans. Molecular Biology & Evolution, 25(9): 1825-1834.

23. Bachtrog D (2008) The temporal dynamics of processes underlying Y-chromosome degeneration, Genetics, 179(3): 1513-1525.

Bachtrog D (2008) Evidence for male-driven evolution in Drosophila. Molecular Biology & Evolution, 25(4): 617-619.

Bachtrog D, E Hom, K Wong, X Maside & P de Jong (2008) Genomic degradation of a young Y chromosome in Drosophila miranda. Genome Biology, 9(2): R30.

20. Bachtrog D (2007) Reduced selection for codon usage bias in Drosophila miranda. Journal of Molecular Evolution, 64(5): 586-590.

19. Bachtrog D & Andolfatto P (2006) Selection, recombination and the demographic history of Drosophila miranda. Genetics, 174(4): 2045-2059.

18. Bachtrog D (2006) A dynamical view of sex chromosome evolution. Current Opinion in Genetics and Development, 16(6): 578-585.

17. Bachtrog D (2006) Expression profile of a degenerating neo-Y chromosome in Drosophila. Current Biology, 16(17): 1694-1699. [see comment in Nature Reviews Genetics].

16. Bachtrog D (2006) The speciation history of the Drosophila nasuta complex. Genetical Research, 88(1): 13-26.

15. Bachtrog D, Thornton K, Clark AG & Andolfatto P (2006) Extensive introgression of mitochondrial DNA relative to nuclear gene flow in the Drosophila yakuba species group. Evolution, 60 (2): 292-302.

14. Thornton K, Bachtrog D & Andolfatto P (2006) X-chromosomes and autosomes evolve at similar rates in Drosophila - no evidence for faster-X protein evolution. Genome Research, 16 (4): 498-504.

13. Bachtrog D (2005)  Sex chromosome evolution: Molecular aspects of Y chromosome degeneration in Drosophila. Genome Research, 15(10): 1393-1401.

12. Bachtrog D & I Gordo (2004) Adaptive evolution of asexual populations under Muller’s ratchet. Evolution, 58 (7): 1403-1413.

11. Bachtrog D (2004) Evidence that positive selection drives Y chromosome degeneration in Drosophila miranda.
Nature Genetics, 36 (5): 518-522.

10. Bachtrog D (2003) Protein evolution and codon usage bias on the neo-sex chromosomes of Drosophila miranda.
Genetics, 165: 1221-1232.

9. Bachtrog D (2003) Adaptation shapes patterns of genome evolution on sexual and asexual chromosomes in Drosophila.
Nature Genetics, 34 (2): 215-219. [see comment by Carvalho].

8. Bachtrog D (2003) Accumulation of spock and worf, two novel retrotransposons, on the neo-Y chromosome of Drosophila miranda.
Molecular Biology and Evolution, 20 (2): 173-181.

7. Bachtrog D & B Charlesworth (2003) On the genomic location of the exuperantia1 gene in Drosophila miranda – the limits of in situ hybridization experiments.
Genetics, 164 (3): 1237-1240.

6. Yi S, Bachtrog D & B Charlesworth (2003) A survey of chromosomal and nucleotide sequence variation in Drosophila miranda.
Genetics, 164 (4): 1369-1381.

5. Bachtrog D & B Charlesworth (2002) Reduced adaptation on a non-recombining neo-Y chromosome.
Nature, 416 (6878): 323-326.

4. Bachtrog D & B Charlesworth (2001) Towards a complete sequence of the human Y chromosome.
Genome Biology, 2 (5):1016.1-1016.5.

3. Bachtrog D & B Charlesworth (2000) Reduced levels of microsatellite variability on the neo-Y chromosome of Drosophila miranda.
Current Biology, 10 (17): 1025-1031.

2. Bachtrog D, M Imhof, M Agis & C Schlötterer (2000) Microsatellite variability differs between dinucleotide repeat motifs - evidence from Drosophila melanogaster.
Molecular Biology and Evolution, 17 (9): 1277-1285.

1. Bachtrog D, S Weiss, B Zangerl, G Brem & C Schlötterer (1999) Distribution of microsatellites in the Drosophila melanogaster genome.
Molecular Biology and Evolution,16 (5): 602-610.