1.       Soule, M. and B Baker (1968).  Phenetics of natural populations.  IV.  The population asymmetry parameter in the butterfly Ceononympha tullia . Heredity 23:  611-614.

2.       Markovitz, A. and B. Baker (1967).  Supression of radiation sensitivity and capsular polysaccharide synthesis in Escherichia coli  K-12 by Ochre suppressors.  J. Bact. 94 : 383-395.

3.       Markovitz, A., N Rosenbaum, and B. Baker (1968).  P1-mediated transduction of a gene that controls radiation sensitivity and capsular polysaccharide synthesis from Shigella dysenteriae  to  Escherichia coli.  J. Bact. 96 221-226.

4.       Lindsley, D.L., and L. Sandler and B. Baker, A. T. C. Carpenter, R. E. Denell, J. C. Hall, P.A. Jacobs and G. L. G. Miklos and B. K. Davis, R. C. Gethmann, R. W. Hartdy, A. Hessler, S. M. Miller, H. Nozawa, D. M. Parry and M. Gould-Somero (1972).  Segmental aneuploidy and the genetic gross structure of the Drosophila genome.  Genetics 71: 157-184.

5.       Baker, B. S. and A. T. C. Carpenter (1972).  Genetic analysis of sex chromosomal meiotic mutants in Drosophila melanogaster.   Genetics 71: 255-286.

6.       Baker, B. S. (1973).  The maternal and zygotic control of development by cinnamon, a new mutant in Drosophila melanogaster.  Devel. Biol. 33 :  429-440.

7.       Carpenter, A. T. C. and B. S. Baker (1974).  Genic control of meiosis and some observations on the synaptonemal complex in  Drosophila melanogaster.  In: Mechanisms in Recombination,  Gatlinberg Symposium, R. F. Grell, Ed.,Plenum, New York, pp.365-375.

8.       Baker, B. S. and J. Hall (1976).  Meiotic mutants:  genic control of meiotic recombination and chromosome segregation.  In: The Genetics and Biology of Drosophila, Vol. 1, E. Novitski and M. Ashburner, eds.  Academic Press, pp. 352-434.

9.       Baker, B. S. (1975).  Paternal loss (pal) : a mutant in D. melanogaster  causing loss of paternal chromosomes.  Genetics 80: 267-296.

10.   Huang, S. L. and B. S. Baker (1976).  The mutability of the Minute  loci in Drosophila melanogaster  with ethyl methanesulfonate.  Mutat. Res. 34:407-444.

11.   Baker, B. S., A. T. C. Carpenter, M. S. Esposito, R. E. Esposito and L. Sandler (1976). The genetic control of meiosis.  Ann. Rev. Genetics 10: 53-134.

12.   Baker, B. S., J. B. Boyd, A. T. C. Carpenter, M. M. Green, T. D. Nguyen, P. Ripoll, and P. D.Smith  (1976).  Genetic controls of meiotic recombination and somatic DNA metabolism in Drosophila melanogaster.  Proc. Natl. Acad. Sci. (USA) 73:  4140-4144.

13.   Baker, B. S., A. T. C. Carpenter, and P. Ropoll  (1978).  The utilization during mitotic cell division of loci controlling meiotic recombination and disjunction in Drosophila melanogaster.  Genetics 90:  531-578.

14.   Baker, B. S., and D. A. Smith  (1979)  The effects of mutagen-sensitive mutants of  Drosophila melanogaster  in non-mutagenized cells.  Genetics 92: 833-847.

15.   Lutken, T. and B. S. Baker  (1979).  The effects of recombination-defective meiotic mutants in Drosophila melanogaster  on gonial recombination in males.  Mutation Res.  61:  221-227.

16.   Baker, B. S. and K. Ridge  (1980).  Sex and the single cell:  I.  On the action of major loci affecting sex determination in Drosophila melanogaster.  Genetics  92:  383-423.

17.   Baker, B. S., M. Gatti, A. T. C. Carpenter, S. Pimpinelli, and D. A. Smith  (1980).  Effects of recombination-deficient and repair-deficient loci on meiotic and mitotic chromosome behavior in Drosophila melanogaster .  In:  DNA Repair and Mutagenesis in Eukaryotes.   Generoso, W. M., M. D. Shelby and F. D. deSerres, eds. Plenum Press, pp. 189-208.

18.   Gatti, M., S. Pimpinelli, and B. S. Baker (1980).  Relationships among chromatid interchanges, sister chromastid exchanges, and meiotic recombination in Drosophila  melanogaster.  Proc. Natl. Acad. Sci. (USA) 77:  1575-1579.

19.   Baker, B. S.,  and  D. L. Lindsley (1982).  The genetic control of sex determination and male fertility in Drosophila melanogaster.  In:  Genetic Control of Gamete Production and Function, No. 3  P. G. Crosignani and B. L. Rubin, eds., Academic Press, pp. 152-170.

20.   Carpenter, A. T. C. and B. S. Baker  (1982).  On the control of the distribution of meiotic exchange in  Drosophila melanogaster.   Genetics 101:  80-89.

21.    Belote, J. M., and B. S. Baker  (1982).  Sex determination in Drosophila melanogaster:   analysis of trasnsformer-2 , a sex-transforming locus.  Proc. Natl. Acad. Sci.  (USA).  79:  1568-1572.

22.   Baker, B. S., D. A. Smith, and M. Gatti  (1982).  Region-specific effects on chromosome integrity of mutations at essential loci in Drosophila melanogaster.  Proc.Natl. Acad. Sci. (USA).  79:  1205-1209.

23.   Gatti, M., D. A. Smith, and B. S. Baker  (1983).  A gene controlling condensation of heterochromatin in Drosophila melanogaster.  Science 221:  83-85.

24.   Belote, J. M., and B. S. Baker  (1983).  The dual functions of a sex determination gene in Drosophila melanogaster.  Devel. Biol. 95:  512-517.

25.   Baker, B. S., and J. M. Belote  (1983).  Sex determination and dosage compensation in melanogaster.  Ann. Rev. Genet. 17:  345-393.

26.   Gatti, M., S. Pimpinelli, C. Bove, B. S. Baker, D. A. Smith, A T. C. Carpenter and P. Ripoll  (1984).  Genetic control of mitotic cell division in  Drosophila melanogaster.  Proc. XV Int. Cong. Genetics, New Delhi, pp. 193-204.

27.   Baker, B. S., M. Wolfner, and J. Belote  (1984).  Sex determination in Drosophila melanogaster.  Proc XV Int. Cong. Genetics, New Delhi,  pp.223-232.

28.   Belote, J. M., M. B. McKeown, D. J. Andrew, T. N. Scott, M. F. Wolfner, and B. S. Baker (1985).  Control of sexual diferentiation in  Drosophila melanogaster.  CSHSQB 50:  605-614.

29.   Belote, J. M., A. M. Handler, M. F. Wolfner, K. J. Livak, and B. S. Baker (1985).  Sex-specific regulation of yolk protein gene expression in Drosophila.  Cell  40:  339-348.

30.   Smith, D. A., B. S. Baker, M. Gatti  (1985).  Genes controlling essential mitotic functions  in Drosophila melanogaster.  Genetics 110: 647-670.

31.   McKeown, M. B., J.M. Belote, D. J. Andrew, T. N. Scott, M. Wolfner, and B. S. Baker  (1986).  Molecular genetics of sex determination in Drosophila.   In: Gametogenesis and the early embryo ( 44th  Symp. Soc. for Devel. Biol.),  Alan R. Liss, Inc. pp3-17

32.   Baker, B. S., A. T. C. Carpenter, and M. Gatti  (1987).  On the biological effects of mutants producing aneuploidy in Drosophila.  In: Aneuploidy-Incidence and Etiology, A. Sandberg  and B. Vig, eds., Alan R. Liss, New York, 273-296.

33.   DiBenedetto, A. J., Lakich, D. M., Kruger, W. D., Belote, J.M., Baker, B. S., and M.F.  Wolfner  (1987)  Sequences expressed sex-specifically in D. melanogaster adults.  Devel. Biol,.   119:242-251.

34.   McKeown, M., Belote, J. M., and  B. S. Baker (1987)  A molecular analysis of transformer, a gene in Drosophila that controls female sexual differentiation.  Cell, 48: 489-499.

35.   Baker, B. S., Nagoshi, R. N., and K. C. Burtis  (1987)  Molecular genetic aspects of sex determination in Drosophila.  BioEssays,  6: 66-70.

36.   Belote, J. M. and B. S. Baker (1987).  On the establishment and maintenance of an inate action pattern by genes regulating sex determination in Drosophila.  Proc. Natl. Acad. Sci. USA, 84:  8026-8030.

37.   Baker, B. S. and M. A. Wolfner (1988).  A molecular analysis of doublesex, a bifunctional gene that controls both male and female sexual differentiation in Drosophila melanogaster.  Genes and Develop.  2:  477-489.

38.   Nagoshi, R., McKeown, M., Burtis, K., Belote, J. M., and Baker, B. S. (1988).  The Control of alternative splicing at the genes regulating sexual differentiation in D. melanogaster.  Cell, 53:  229-236.

39.   Baker, B. S., K. Burtis, T. Goralski, W. Mattox and R. Nagoshi (1988).  Molecular geneitc aspects of sex determination in Drosophila melanogaster.  In:  Proceedings of the XVI international congress of genetics.  Genome 31:  638-645.

40.   Goralski, T. J., J.-E. Edstrom, and B. S. Baker  (1989). The sex determination locus transformer-2 of Drosophila encodes a polypeptide with similarity to RNA binding proteins.  Cell, 56:  1011-1018.

41.   Burtis, K. C. and B. S. Baker  (1989).  Drosophila doublesex gene controls somatic sexual differentiation by producing alternatively spliced mRNAs encoding related sex-specific polypeptides.  Cell 56:  997-1010.

42.   Gatti, M. and B. S. Baker (1989).  Genes controlling essential cell cycle functions in Drosophila melanogaster.  Genes and Develop.  3:  438-453.

43.   Tearle, R. G., J. M. Belote, M. McKeown, B. S. Baker, and A. J. Howells.  (1989).  Cloning and characterization of the scarlet gene of  Drosophila melanogaster.  Genetics. 122:  595-606.

44.   Baker, B. S., (1989).  Sex in flies: the splice of life.  Nature.  340:  521-524.

45.   Nagoshi, R. N., and Baker, B. S. (1990) The regulation of sex-specific RNA splicing at the Drosophila doublesex gene: Cis-acting mutations in exon sequences alter sex-specific RNA splicing patterns.  Genes and Develop.,  4:  89-97.

46.   Mattox, W., Palmer, M. J., Baker, B. S., (1990).   Alternative splicing of the sex determination gene transformer-2 is sex-specific in the germ line but not in the Soma.  Genes and Develop., 4:  789-805.

47.   Belote, J. m., F. M. Hoffmann, M. McKeown, R. Chorsky,  and B. S. Baker.  (1990). Cytogenetic analysis of chromosome region 73AD of Drosophila melanlgaster.  Genetics 125:  783-793.

48.   Baker, B. S., Hoff, G., Kaufman, T. C., Wolfner, M. W., and Hazelrigg, T. (1991).  A cytopgenetic analysis of the doublesex locus and its flanking regions. Genetics 127:  125-138.

49.   K. C. Burtis, K. T. Coshigano, B. S. Baker and P. C. Wensink  (1991).  Drosophila doublesex proteins bind to a sex-specific yolk protein gene enhancer.  EMBO J, 10:  2577-2582.

50.   Mattox, W. and B. S. Baker (1991).  Autoregulation of the splicing of transcripts from the transformer-2 gene of Drosophila.  Genes and Dev., 5: 786-796.

51.   Kuroda, M. I., Kernan, M. J., Kreber, R., Ganetzky, B. and Baker, B. S., 1991.  The maleless protein associates with the X chromosome to regulate dosage compensation in Drosophila.  Cell 66: 935-948.

52.   Kernan, M. J., Kuroda, M. I., Kreber, R., Baker, B. S., and Ganetzky, B. 1991.  napts, a mutation affecting sodium channel activity in Drosophila, is an allele of mle, a regulator of X chromosome transcription.  Cell 66: 949-961.

53.   Ryner, Lisa, and Baker, B. S. 1991.  Regulation of doublesex  pre-mRNA splicing occurs by 3' splice site activation.  Genes and Dev.  5: 2071-2085.

54.   Mattox, W., Ryner, L. and Baker, B. S. 1992.  Autoregulation and multifunctionality among trans-acting factors that regulate alternative pre-mRNA processing.  J. Biol. Chem., 267:19023-19026.

55.   Kim, Young-Yoon, P. Zuo, J. L. Manley, and Baker, B. S. 1992.  The Drosophila RNA binding protein RBP1 is localized to transcriptionally active sites of chromosomes and shows a functional similarity to human splicing factor ASF/ SF2.  Genes and Dev., 6:2569-2579.

56.   Kim, Young-Yoon, and Baker, B. S. 1993.  Studies on the RRM-type RNA binding protein gene family in Drosophila melanogaster using PCR with degenerate primers.  Mol. Cell Bio., 13:  174-183.

57.   Kim, Young-Yoon, and Baker, B. S. 1993.  The Drosophila gene rbp9 encodes a protein that is a member of a conserved group of putative RNA binding proteins that are nervous system-specific in both flies and humans.  J. Neurosci., 13(3):  1045-1056.

58.   Gorman, M., Kuroda, M. and Baker, B.S., 1993. Regulation of the sex-specific binding of the maleless dosage compensation protein to the male X chromosome in Drosophila.  Cell, 72: 39-49.

59.   Oliver, B., Kim, Y.-J., and Baker, B. S. (1993) Sex-lethal, master and slave: The hierarchy of germline sex determination in Drosophila. Development,119:  897-908.

60.   Pultz, M. A., Carson, G., and Baker, B. S. (1994) A genetic analysis of hermaphrodite, a pleiotropic sex determination gene in Drosophila.  Genetics, 136:  195-207.

61.   Gorman, M., and Baker, B. S. (1994) How flies make one equal two:  dosage compensation in Drosophila. TIGS 10:  376-380.

62.   Taylor, B. J., Villella, A., Ryner, L. C., Baker, B. S., and Hall, J. C. (1994).  Behavioral and Neurobiological implications of sex-determining factors in Drosophila. Devel. Genetics 15:  275-296.

63.   Baker, B. S., Marin, I., and Gorman, M. (1994) Dosage compensation in Drosophila.  Annu. Rev. Genetics, 28:  491-521.

64.   Pultz, M. A., and Baker, B. S. (1995).  The dual role of hermaphrodite in the Drosophila sex determination hierarchy.  Development 121:  99-111.

65.   Gorman, M., Franke, A., and Baker, B. S., (1995) Molecular characterization of the male-specific lethal-3 gene and investigations of the regulation of dosage compensation in Drosophila. Development, 121:  463-475.

66.   Chase, B. A., and Baker, B. S., (1995)  A genetic analysis of intersex, a gene regulating sexual differentiation in Drosophila melanogaster females. Genetics, 139:1649-1661.

67.   Heinrichs, V., and Baker, B. S. (1995).  The Drosophila SR protein RBP1 contributes to the regulation of doublesex alternative splicing by recognizing RBP1 RNA target sequences.  EMBO, 14:  3987-4000.

68.   Bashaw, G. J., and Baker, B. S. (1995).  The msl-2 dosage compensation gene of Drosophila encodes a putative DNA-binding protein whose expression is sex-specifically regulated by Sex-lethal.  Development, 121:  3245-3258.

69.   Mattox, M., McGuffin, M. E., and Baker, B. S., (1996).  A negative feedback mechanism revealed by functional analysis of the alternative isoforms of the Drosophila splicing regulator transformer-2.   Genetics 143:  303-314.

70.   Bashaw, G. J., and Baker, B. S. (1996).  Dosage Compensation and chromatin structure in Drosophila.  Curr. Opinions in Genet. and Dev. 496-501.

71.   Franke, A., Dernberg, A., Bashaw, G. J., and Baker, B. S. (1996).  Evidence that MSL mediated dosage compensation in Drosophila begins at blastoderm.  Development 122: 2751-2760.

72.   Marín, I., Franke, A., Bashaw, G. J., and Baker, B. S. (1996).  Dosage compensation in flies:  a regulatory system adapting to chromosome evolution.. Nature, 383:  160-163.

73.   Ryner, L. C., Goodwin, S. F., Castrillon, D. H., Anand, A., Villella, A., Baker, B., Hall, J. C., Taylor, B. J., and Wasserman, S. A. (1996).  Control of male sexual behavior and sexual orientation in Drosophila by the fruitless gene.  Cell, 87:1079-1089.

74.   Chen, E. H., and Baker, B. S., (1997). Compartmental organization of the Drosophila genital imaginal disks.  Development, 124:  205-218.

75.   Heinrichs, V., and Baker, B. S., (1997). In vivo analysis of functional domains of the Drosophila alternative splicing factor RBP1.  Proc. Natl. Acad. Sci., 94: 115-120.

76.   Chandler, D., McGuffiin, M. E., Piskur, J., Yao, J., Baker, B. S., and Mattox, W., (1997) Evolutionary conservation of regulatory strategies for the sex determining factor transformer-2. Mol. Cell. Biol.,17:  2908-2919.

77.   Bashaw, G. J., and Baker, B. S., (1997) The regulation of the Drosophila msl-2 gene reveals a function for Sex-lethal in translational control.  Cell, 89:  789-798.

78.   Li, H., and Baker, B. S., (1998). her, a sex differentiation gene of Drosophila, encodes a zinc finger protein with characteristics of ZFY-like proteins and is expressed independently of the sex determination hierarchy.  Development, 125:  225-235.

79.   Heinrichs, V., Ryner, L., and Baker, B. S., (1998).  Regulation of fruitless sex-specific 5' splice site selection by transformer and transformer-2. Mol. Cell. Biol.,18: 450-458.

80.   Li, H., and Baker, B., (1998).  her and dsx iact both dependently and independently to control various aspects of sexual differentiation in Drosophila.  Development, 125:  2641-2651.

81.   Marin, I., and Baker, B. S., 1998 The evolutionary dynamics of sex determination.  Science, 281:  1990-1994.

82.   Franke, A. and Baker, B. S., (1999)  The rox1 and rox2 RNAs are essential components of the Compensasome, which mediates dosage compensation in Drosophila.  Molec. Cell 4: 117-122.

83.   Franke, A. and Baker, B. S., (2000). Dosage compensation rox!  Curr. Opinion in Cell Biol. 12:351-354.

84.   Goodwin S.F., Taylor, B.J., Villella, A., Foss, M., Ryner, L. C., Baker, B. S., and Hall, J. C.,  (2000)  Aberrant splicing and altered spatial expression patterns in fruitless mutants of Drosophila melanogaster. Genetics 154:  725-45.

85.   Marin, I., and Baker, B. S. (2000).  Origin and evolution of the regulatory gene male-specific lethal 3. Mol. Biol. Evol.17: 1240-1250.

86.   Marin, I., Siegal, M. L. and Baker, B. S.,  (2000).  The evolution of dosage compensation mechanisms.  BioEssays, 22:  1106-1114.

87. Anand, A., Villella, A., Ryner, L. C., Carlo, T., Goodwin, S. F., Song, H.-J., Gailey, D. A., Hall, J. C., Baker, B. S., and Taylor, B. J.,  (2001).  The sex determination gene fruitless , in addition to controlling male sexual behaviors, has sex-nonspecific vital functions.  Genetics, 158: 1569-1595.

88.   Keisman, E. L., and Baker, B. S.,  (2001).  The Drosophila sex determination hierarchy modulates wingless and decapentaplegic signaling to sex-specifically deploy dachsund in the genital imaginal disc. Development 128:  1643-1656.

89.   Baker, B. S., Taylor, B. T., and Hall, J. C., (2001) Are complex behaviors specified by dedicated regulatory genes? Reasoning from Drosophila.  Cell 105:  13-24.

91.   Keisman, E. L., Christiansen, A. E., and Baker, B. S., (2001) The sex determination gene doublesex (dsx) regulates the A/P organizer to direct sex-specific patterns of growth in the Drosophila genital imaginal disc.  Developmental Cell, 1:  215-225.

92. Ahmad, S. M. and Baker, B. S., (2002). Sex-Specific deployment of FGF signaling in Drosophila recruits mesodermal cells into the male genital imaginal disc. Cell, 109, 651-661.

93.   Song, H.-J.,. Goodwin , S. F., Reynaud, E., Carlo, T., Billeter, J.-C., Eric P. Spana, E. P., Perrimon, N., Baker, B. S., and Taylor, B. J., (2002).  The fruitless gene is required for the proper formation of axonal tracts in the embryonic CNS of Drosophila.  Genetics, 162, 1703-1724.

94.   Garrett-Engele C. M., Siegal, M. L., Manoli, D. S., Williams, B. C., Li. H., and Baker, B. S., (2002). intersex, a gene required for female sexual development in Drosophila, is expressed in both sexes and functions together with doublesex to regulate terminal differentiation. Development, 129:  4661-4675.

95.   Christiansen, A. E., Keisman, E. L., Ahmad, S. M., and Baker, B. S., (2002).  Sex comes in from the cold: the integration of sex and pattern. Trends in Genetics, 18:  510-516.

96.   Arbeitman, M.*, Furlong, E.*, Imam, F.*, Johnson, E.*, Null, B.*, Baker, B. S., Davis, R., Krasnow, M., Scott, M., White, K.P..(2002).  A genomic analysis of gene expression during the Drosophila life cycle.  Science, 297: 2270-75. (*Co-first authors).