Publications

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BOOKS

Gibson, G. and Muse, S. (2009)  A Primer of Genome Science   Sinauer Associates, Sunderland MA.  3rd edition

Gibson, G.  (2008)  It Takes a Genome: How a genetic culture clash with modernity is making us sick. Pearson/Zôon, New York NY.  To be published January 16th, 2009.  


PUBLISHED RESEARCH PAPERS  

Gibson, G (2009)  Decanalization and the origin of complex disease.  Nature Review Genetics 10(2):134-40.  February 2009 publication.

Gibson, G (2008) The environmental contribution to gene expression profiles.  Nature Reviews Genetics 9: 575 - 581 

Dworkin, I. Kennerly, E. Tack, D. Hutchinson, J. Brown, J. Mahaffey, J and Gibson, G. (2008) Genomic consequences of background effects on scalloped mutant expressivity in the wing of  Drosophila melanogaster. Genetics.

Idaghdour, Y., J.D. Storey, S. Jadallah, and G. Gibson  (2008)   A genome-wide gene expression signature of environmental geography in leukocytes of Moroccan Amazighs.  PLoS Genetics  4: e1000052.

Kennerly, E.M., A. Acton, S. Martin, S. Gregory, R. Wolfinger, M. Stoskopf and G. Gibson  (2008)  A gene expression signature of stress in peripheral blood of captive and free-ranging red wolves (Canis rufus).  Molecular Ecology.

Passador-Gurgel, G., W-P. Hsieh, P.K. Hunt, N. Deighton, and G. Gibson  (2007)  Quantitative trait transcripts for nicotine resistance in Drosophila melanogaster.  Nature Genetics 39: 264-268 

Ocorr, K.A., T. Crawley, G. Gibson and R. Bodmer  (2007)  Genetic variation for cardiac dysfunction in Drosophila.  PLoS ONE 2: e601

Hsieh, W.P., G.Passador-Gurgel, E.A. Stone and G. Gibson (2007)  Mixture modeling of transcript abundance classes in natural populations.   Genome Biol. 8(6): R98 

Moser, J.M., I. Carbone, P. Arasu, and G. Gibson  (2007)  Genetic variation and population structure at asp-1 and cox-1 of the canine hookworm, Ancylostoma caninum.  J. Parasitol., 93: 796-805

Need, A.C., D. Attix, J. McEvoy, E. Cirulli, K. Linney, A.P. Wagoner, C. Gumbs, I. Giegling, H.J. Möller,  C. Francks, P. Muglia, A. Roses, G. Gibson, M.E. Weale, D. Rujescu and D.B. Goldstein. (2008)  Failure to replicate effect of Kibra on human memory in two large cohorts of European origin.  Neuropsychiatric Genetics.

Bushel, P.R., R.D. Wolfinger and G. Gibson  (2007)  Simultaneous clustering of gene expression data with clinical chemistry and pathological evaluations reveals phenotypic prototypes.
BMC Syst Biol. 1: 15.

Dworkin, I.D. and G. Gibson  (2006)  Epidermal Growth Factor Receptor and Transforming Growth Factor- Signaling Contributes to Variation for Wing Shape in Drosophila melanogaster.  Genetics, 173: 1417-1431.

Ayroles, J.F. and   G. Gibson (2006)  Analysis of Variance of Microarray Data.  Methods Enzymol. 411: 214-233.

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

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

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

Thomson, S., E. Kennerly, N. Olby, J. Mickelson, D. Hoffmann, P. Dickinson, G. Gibson, and M. Breen.  (2005)  Microarray analysis of differentially expressed genes of primary tumors in the canine central nervous system.  Veterinary Pathology 42: 550-558.

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

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

Kennerly, E., S. Thomson, N. Olby, M. Breen, and G. Gibson.  (2004)  Comparison of regional gene expression differences in the brains of the domestic dog and human.  Human Genomics, 1: 435-443.

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

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

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

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

Goering, L.M. and G. Gibson  (2004)  Quantitative genetic variation for dorsal appendage spacing during embryogenesis of Drosophila melanogaster.  Evolution and Development 7: 81-88.

Yu, X., T-M. Chu, G. Gibson, and R.D. Wolfinger (2004)  A mixed model approach to identify yeast transcriptional regulatory motifs via microarray experiments.  SAGMB 3(1): Article 22.

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

Ranz, J., K. Namgyal, G. Gibson, and D. Hartl  (2003)  Anomalies in the Expression Profile of Interspecific Hybrids of Drosophila melanogaster and Drosophila simulan.  Genome Research 14: 373-379.

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

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

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

Carrillo, R., and Gibson, G.  (2002)  Unusual genetic architecture of natural variation affecting drug resistance in Drosophila melanogaster.  Genet. Res. 80: 205-213.

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

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

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

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

Teeter, K, Naeemuddin, M, Gasperini, R, Zimmerman E, White, KP, Hoskins R, & Gibson, G. (2000) Haplotype Dimorphism in a SNP Collection from Drosophila melanogaster.  J. Exp. Zool. 288: 63-75

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

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

Gasperini, R. and Gibson, G.  (1999)  Absence of protein polymorphism in the Ras genes of Drosophila.     J. Mol. Evol. 49: 583-590.

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

Robbins, J., Aggarwal, R., Nichols, R. and Gibson, G.  (1999)   Quantitative genetic analysis of heart rate in Drosophila melanogaster.  Genetical Research, 74:121-128.

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

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

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

Polaczyk, P., Gasperini, R. & Gibson, G.  (1998)  Naturally occurring genetic variation affects Drosophila photoreceptor determination.  Dev. Genes Evol.  207:462-470

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

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.

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

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

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.

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.

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

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


SUBMITTED and MANUSCRIPTS IN PREPARATION


Goering, L.M., P.K. Hunt, C.S. Heighington, S. Kumar and G. Gibson  (2008)  A selected regulatory polymorphism affecting embryonic patterning in Drosophila.  In prep.

Dworkin, I.D., E. Kennerly, J. Hutchinson, J. Mahaffey and G. Gibson  (2008)  Genomic consequences of background effects on scalloped mutant expressivity in the wing of Drosophila melanogaster.  Genetics, submitted.


REVIEW PAPERS and COMMENTARIES

Gibson, G.  (2008)  Environmental contributions to gene expression variation.  Nature Reviews Genetics, In press.

Gibson, G.  (2008)  Putting the environment back into genetic analysis by way of gene expression profiling.  Nature Reviews Genetics In revision

Gibson, G. and Goldstein, D.  (2007)  Human genetics: the hidden text of genome-wide associations.  Curr Biol. 17: R929-R932.

Gibson, G.  (2007)  Human evolution: thrifty genes and the dairy queen.  Curr Biol. 17: R295-R296.

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

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

Gibson, G. and B.S. Weir  (2005)  The quantitative genetics of transcription. Trends Genet. 21: 616-623.

Gibson, G.  (2005)  The origins of stability  Science 310: 237.

Gibson G. (2005)  Greg Gibson.  Curr Biol. 15: R531-R532. 

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

Gibson, G. (2005)  Mutational accumulation of the transcriptome.  Nature Genetics 37: 458-460.

Gibson, G.  (2005)  Population genomics: patterns of genetic variation within populations.  Chapter 99 in Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics.  L. Jorde, P. Little, M. Dunn and S. Subramaniam, eds.  Wiley and Sons, London.. 

Gibson, G., and Dworkin, I.D. (2004) Uncovering cryptic genetic variation.  Nat. Rev. Genet. 5: 681-691. 

Zhou, X.J., and Gibson, G.  (2004)  Cross-species comparison of genome-wide expression patterns.  Genome Biology 5(7): 232.

Gibson, G., and Wolfinger, R.D.  (2004)  Gene expression profiling using mixed models.  A. Saxton, Ed.  Quantitative Genetic Analysis with SAS Software.  SAS Institute.

Gibson, G.  (2003)  Microarray analysis: Genome-Scale hypothesis testing.  PLoS Biol 1: 28-29.

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

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

Purugganan, M. and Gibson, G.  (2003)  Merging Ecology, Molecular Evolution, and Functional Genetics.  Molecular Ecology 12: 1109-1112.

Gibson, G. and Mackay, T.F.C.  (2002)  Enabling population and quantitative genomics.  Genetical Res. 80: 1-6.

Gibson, G. and Honeycutt, E.  (2002)  Evolution of developmental regulatory systems. 
Curr. Op. Gen. Devt. 12: 695-700.

Greg Gibson  (2002)  Current Biology 12:R347-R349  Getting robust about robustness

Greg Gibson  (2002)  Bioessays 24:487-489  A genetic attack on the defense complex

Gibson, G. (2001)  Microarrays in ecology and evolution: a preview.  Molecular Ecology 11: 17-24.

Greg Gibson  (2001)  Current Biology 11:R345-R348  The unbearable likeness of beings

Greg Gibson and Arnar Palsson (2001)  Curr Biol 11:R74-R76  A complement for evolutionary genetics

Gibson, G. and Wagner, G.  (2000)  Canalization in Evolutionary Genetics: A stabilizing theory?  BioEssays 22: 372-380

Greg Gibson  (2000)  Current Biology 10:R452-R455  Hox genes and the cellared wine principle

Greg Gibson  (1999)  Current Biology 9:R942-945  Going beyond the 'just so'

Greg Gibson  (1999)  Current Biology 9:R86-R89  Redesigning the fruitfly 


Gasperini, R. and Gibson, G.  (1999)  Absence of protein polymorphism in the Ras genes of Drosophila.     J. Mol. Evol. 49: 583-590.

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

Robbins, J., Aggarwal, R., Nichols, R. and Gibson, G.  (1999)   Quantitative genetic analysis of heart rate in Drosophila melanogaster.  Genetical Research, 74:121-128.

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

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

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

Polaczyk, P., Gasperini, R. & Gibson, G.  (1998)  Naturally occurring genetic variation affects Drosophila photoreceptor determination.  Dev. Genes Evol.  207:462-470

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

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.

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

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

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.

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.

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

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