Publications from the Gibson Lab

A Primer of Genome Science, Second Edition (2004)
Greg Gibson and Spencer Muse; Sinauer Associates, Sunderland MA

Adobe PDF files containing some of our recent publications can be downloaded from the following links.

In The Works

Kennerly, E.M., A. Acton S. Gregory, M. Stoskopf and G. Gibson  (2007)  A gene expression signature of stress in peripheral blood of captive and free-ranging red wolves (Canis rufus).  Submitted.

Published Manuscripts

73. Ocorr KA, T. Crawley, R. Bodmer, and G. Gibson (2007) PLoS ONE, In press.
"Genetic variation for cardiac dysfunction in Drosophila".

72. Hsieh, W.P., G. Passador-Gurgel, and G. Gibson (2007) Genome Biology. In press.
"Mixture modeling of transcription abundance classes in natural populations".

71. Moser, J.M., I. Carbone, P. Arasu, and G. Gibson (2007) Journal of Parasitology. In press.
"Genetic variation and population structure at asp-1 and cox-1 of the canine hookworm, Ancylostoma caninum".

70. Bushel, P.R., R.D. Wolfinger and G. Gibson  (2006)  BMC Systems Biology . In press. 
"Simultaneous clustering of gene expression data with clinical chemistry and pathological evaluations reveals phenotypic prototypes"

69. Passador-Gurgel, G., W-P. Hsieh, P. Hunt, N. Deighton, and G. Gibson.
(2007) Nature Genetics 39: 264-268
"Quantitative Trait Transcripts for Nicotine Resistance in Drosophila melanogaster "

65. Ayroles, J.F. and  G. Gibson (2006)  Methods Enzymol. 411: 214-233. "Analysis of variance of microarray data "

64. Dworkin, I. and G. Gibson (2006) Genetics 173: 1417-1431.
"Epidermal growth factor receptor and Transforming Growth Factor-Beta signaling contributes to variation for wing shape in Drosophila melanogaster

59. Gibson, G. and B. Weir (2005) Trends in Genetics21: 616-623.
"The quantitative genetics of transcription"

58. Palsson, A., J. Dodgson, I. Dworkin and G. Gibson (2005)
BMC Genetics, 6: 44.
“Tests for the replication of an association between Egfr and natural variation in Drosophila melanogaster wing morphology”

57. Moser, J.M, T. Freitas, P. Arasu and G. Gibson (2005) Mol & Biochem. Parasitology 143 (1): 39-48
“Gene expression profiles associated with the transition to parasitism in Ancylostoma caninum larvae”

56. Dworkin, I., A. Palsson and G. Gibson (2005) Genetics 169: 2115-2125.
“Replication of an Egfr-wing shape association in a wild-caught cohort of Drosophila melanogaster”

55. Goering, L.M. and G. Gibson (2005) Evol. Development 7: 81-88.
"Genetic variation for dorsal-ventral patterning of the Drosophila melanogaster eggshell"

53. Kennerly, E., S. Thompson, N. Olby, M. Breen, and G. Gibson. (2004)  Human Genomics 1: 435 -443.
"Comparison of Regional Gene Expression Differences in the Brains of the Domestic Dog and Human "

52. Nikoh, N., A. Duty and G. Gibson. (2004) Genetics 168: 1963-1974.
"Effects of population structure and sex on association between serotonin receptors and Drosophila heart rate"

51. Gibson, G., R. Riley, L. Harshman, A. Kopp, S. Vacha, S. Nuzhdin and M. Wayne (2004) Genetics 167: 1791-1799.
"Extensive sex-specific non-additivity of gene expression in Drosophila melanogaster"

50. Yu, X., T-M. Chu, G. Gibson, and R.D. Wolfinger (2004) SAGMB 3(1): Article 22.   (Revised June 28, 2005)
"A mixed model approach to identify yeast transcriptional regulatory motifs via microarray experiments"
The original published version is available here.

49. Gibson, G. and I. Dworkin (2004) Nature Reviews Genetics 5: 681-691.
“Uncovering Cryptic Genetic Variation”

48. Honeycutt, E. and G. Gibson (2004) Genetical Research 83: 177-188.
"Use of regression methods to identify motifs that modulate germline transcription in Drosophila melanogaster"

47. Palsson, A., A. Rouse, R. Riley-Berger, I. Dworkin, and G. Gibson. (2004) Genetics 167: 1199-1212.
"Nucleotide variation in the Egfr locus of Drosophila melanogaster"

46. Palsson, A., and G. Gibson. (2004) Genetics 167: 1187-1198.
"Association between nucleotide variation in Egfr and wing shape in Drosophila melanogaster"

45. McGraw, L.A., G. Gibson, A.G. Clark, M.F. Wolfner  (2004)
Current Biology 14: 1509-1514. 
"Genes regulated by mating, sperm, or seminal proteins in mated female Drosophila melanogaster>"

44. Gibson, G., and R.D. Wolfinger (2004)  Ch 11, pp 251-278 in AM Saxton, ed. Genetic Analysis of Complex Traits using SAS, SAS Users Presss, Cary NC. “Genetic analysis of complex traits using SAS”

You may also find the following two papers by T-M. Chu, B. Weir and R. Wolfinger on analysis of Affymetrix GeneChip data interesting:

"A systematic statistical linear modeling approach to oligonucleotide array experiments."  Mathematical Biosciences 176: 35-51. (2002)

"Comparison of Li-Wong and Loglinear Mixed Models for the Statistical Analysis of Oligonucleotide Arrays."  Bioinformatics 20: 500-506 (2004).

40. Hsieh, W-P., T-M. Chu, R.D. Wolfinger, and G. Gibson. (2003) Genetics 165: 747-757.
"Mixed model reanalysis of primate data suggests tissue and species biases in oligonucleotide-based gene expression profiles"

39. Dworkin, I., A. Palsson, K. Birdsall, and G. Gibson. (2003) Current Biology 13: 1888-1893.
"Evidence that EGFR contributes to cryptic genetic variation for photoreceptor determination in natural populations of Drosophila melanogaster"

38. Ranz, J., K. Namgyal, G. Gibson, and D. Hartl  (2003)  Genome Research 14: 373-379.
"Meltdown of the gene expression network in interspecific hybrids of Drosophila" 

37. Riley, R., W. Jin and G. Gibson. (2003) Molecular Ecology 12: 1315-1323. "Contrasting selection pressures on components of Ras-mediated signal transduction in Drosophila"

36. Purugganan, M. and G. Gibson. (2003) Molecular Ecology 12: 1109-1112. "Merging ecology, molecular evolution, and functional genetics"

35. Arjan, J. et al. (2003) Evolution 57: 1959-1972.
"Perspective: Evolution and detection of genetic robustness"

31. Gibson, G. (2002) Molecular Ecology 11: 17-24.
"Microarrays in Ecology and Evolution: A Preview"

30. Gibson, G., and T.F.C. Mackay (2002)
“Enabling Population and Quantitative Genomics”
Genetical Research 80: 1-6.

29. Carrillo, R.J., and G. Gibson (2002)
“Unusual genetic architecture of natural variation affecting drug responses in Drosophila melanogaster” Genetical Research 80: 205-213.

26. Jin, W., R. Riley, R.D. Wolfinger, K.P. White, G. Passador-Gurgel, and G. Gibson (2001)   "Contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster"
Nature Genetics 29: 389-395

25. Wolfinger, R.D., G. Gibson, E. Wolfinger, L. Bennett, H. Hamadeh, P. Bushel, C. Afshari, and R.S. Paules (2001)   
"Assessing gene significance from cDNA microarray expression data via mixed models"  J. Compu. Biol. 8: 625-637

24. Ashton, K., A. P. Wagoner, R. Carrillo and G. Gibson (2001)
"Quantitative trait loci for the monamine-related traits heart rate and headless behavior in Drosophila melanogaster"
Genetics 157: 283-294.

22. Palsson, A. and G. Gibson (2000)
"Quantitative developmental genetic analysis reveals that the ancestral dipteran wing vein prepattern is conserved in Drosophila melanogaster"
Development, Genes and Evolution 210: 617-622.

21. Teeter, K., M. Naeemuddin, R. Gasperini, E. Zimmerman, K.P. White, R. Hoskins and G. Gibson (2000)
"Haplotype dimorphism in a SNP collection from Drosophila melanogaster"
Journal of Experimental Zoology (Mol. Dev. Evol) 288: 63-75.

20. Zimmerman, E., A. Palsson and G. Gibson (2000)
"Quantitative trait loci affecting components of wing shape in Drosophila melanogaster"
Genetics 155: 671-683.

19. Birdsall, K., E. Zimmerman, K. Teeter and G. Gibson (2000)
"Genetic variation for the positioning of wing veins in Drosophila melanogaster"
Evolution and Development 2: 16-24.

18. Gibson, G. and G. Wagner (2000)
"Canalization in evolutionary genetics: a stabilizing theory ?"
 BioEssays 22: 372-380.

15. Ahn, D. and Gibson, G.  (1999) Expression patterns of Hox genes in threespine sticklebacks and insights into the evolution of the vertebrate body axis.  Dev Genes Evol 209:482-494.

14. Ahn, D. and Gibson, G.  (1999) Axial variation in the threespine stickleback: relationship to Hox gene expression.
Dev Genes Evol 209:473-481.

13. Ahn, D. and Gibson, G.  (1999) "Axial variation in the threespine stickleback: genetic and environmental factors" Evol Dev. 1:100-112. 

12. Gasperini, R. and G. Gibson (1999)
"Absence of Protein Polymorphism in the Ras Genes of Drosophila melanogaster"
Journal of Molecular Evolution 49: 583-590.

11.Gibson, G., M. Wemple and S. van Helden (1999)
"Potential variance affecting homeotic Ultrabithorax and Antennapedia phenotypes in Drosophila melanogaster"
Genetics 151: 1081-1091.

10. Robbins, J., R. Aggarwal, R. Nichols and G. Gibson (1999)
"Genetic variation affecting heart rate in Drosophila melanogaster"
Genetical Research 74: 121-128.

9. Polaczyk, P., R. Gasperini and G. Gibson (1998)
"Naturally occurring genetic variation affects Drosophila photoreceptor determination" Genes, Development, and Evolution 207: 462-470.

8. Gibson, G. and S. van Helden (1997)
"Is function of the Drosophila homeotic gene Ultrabithorax canalized?"
Genetics 147: 1155-1168.

7. Liu, J., J. Mercer, L. Stam, G. Gibson, Z-B. Zeng, and C.C. Laurie  (1996)  Genetic analysis of a morphological shape difference in the male genitalia of Drosophila simulans and D. mauritiana.  Genetics 142:1129-1145.

6. Gibson, G.  (1996)  Epistasis and pleiotropy as natural properties of transcriptional regulation.  Theor. Popul Biol. 49: 58-89.

5. Gibson, G. and D. Hogness (1996)
"Effect of polymorphism in the Drosophila regulatory gene Ultrabithorax on homeotic stability"Science 271: 200-203.

4. Wagner-Bernholz, J.T., C. Wilson, G. Gibson, R. Schuh, and W.J. Gehring  (1991) "Identification of target genes of the homeotic gene Antennapedia by enhancer detection" Genes Dev. 5:2467-480.

3. Gibson, G., A. Schier, P. LeMotte, and W.J. Gehring  (1990) "The specificities of Sex combs reduced and Antennapedia are defined by a distinct portion of each protein that includes the homeodomain"
Cell 62:1087-1103.

2. Mlodzik, M., G. Gibson, and W.J. Gehring  (1990)  "Effects of ectopic expression of caudal during Drosophila development" 
Development 109:271-277.

1. Gibson, G. and W.J. Gehring (1988)  "Head and thoracic transformations caused by ectopic expression of Antennapedia during Drosophila development"  Development 102:657-675.

Commentaries

68. Gibson, G. (2007) Curr Biol. In press.
"Thrifty genes and the dairy queen"

67. Gibson, G.  (2006)  "Making use of evolution": book review of David Mindell’s “This Evolving World” Evolution, in press.

66. Gibson, G.  (2006)  Curr Biol. 16: R285-287.
"The plastic transcriptome"

63. Gibson G. (2005) Curr Biol.15: R531-R532.
"Q&A: Greg Gibson"

62. Gibson G. (2005) Science 310: 237.
"The Origins of Stability"

61. Gibson G. (2005) Science 307: 1890-1891.
"The synthesis and evolution of a supermodel"

60. Gibson G. (2005) Nature Genetics 37: 458-460.
"Mutation accumulation of the transcriptome"

54. Zhou, J. and G. Gibson  (2004) Genome Biology 5: 232
“Cross-species comparison of genome-wide expression patterns”

43. Gibson, G.  (2003) Curr Biol 13:R901-903
"Population Genomics: Finding the variants of mass disruption"

42. Gibson, G.  (2003)  Heredity 90: 1-2.
"Population Genomics: Celebrating Individual Expression"

41. Gibson, G. (2003) PLoS Biology 1: 28-29
“Microarray Analysis: Genome scale hypothesis scanning” 

34. Gibson, G. and E. Honeycutt (2002) Curr Op Gen Devt 12: 695-700
"The evolution of developmental regulatory pathways"  

33. Gibson, G. (2002) Current Biology 12(10):R347-R349
"Developmental Evolution: Getting robust about robustness"

32. Gibson, G. (2002) BioEssays 24(6): 487-489
"A genetic attack on the defense complex"

28. Gibson, G. (2001) Current Biology 11(9):R345-R348
"Developmental Evolution: The Unbearable Likeness of Beings"

27. Gibson, G. and A. Palsson (2001) Current Biology 11(2):R74-R76
"Evolution: A Complement for Evolutionary Genetics"

23. Gibson, G. (2000) Current Biology 10:R452-R455
"Evolution: Hox genes and the Cellared Wine Principle"

17. Gibson, G. (1999) Current Biology 9:R942-R945
"Developmental Evolution: Going Beyond the Just-so"

16. Gibson, G. (1999) Current Biology 9:R86-R89
"Insect Evolution: Redesigning the Fruitfly"