BAGEL Software Papers

• Hunt B.G., L. Ometto, Y. Wurm, D. Shoemaker, S.V. Yi, L. Keller, M.A.D. Goodisman, 2011. Relaxed selection is a precursor to the evolution of phenotypic plasticity. Proceedings of the National Academy of Sciences - USA 108 (38): 15936-15941.
  
  
• Paredes S., A.T. Branco, D.L. Hartl, K.A. Maggart, B. Lemos, 2011. Ribosomal DNA deletions modulate genome-wide gene expression: “rDNA-Sensitive” genes and natural variation. PLoS Genetics 7(4): e1001376.
  
  
• Guo W., X. Wang, Z. Ma, X. Liang, J. Han, D. Yu, L. Kang, 2011. CSP and Takeout genes modulate the switch between attraction and repulsion during behavioral phase change in the migratory locust. PLoS Genetics 7(2): e1001291.
  
  
• Lemos B., A.T. Branco, and D.L. Hartl, 2010. Epigenetic effects of polymorphic Y chromosomes modulate chromatin components, immune response, and sexual conflict. Proceedings of the National Academy of Sciences – USA 107 (36) 15826-15831.
  
  
• Bachtrog D., N.R.T. Toda, and S. Lockton, 2010. Dosage compensation and demasculinization of X chromosomes in Drosophila. Current Biology 20(16): 1476-1481.
  
  
• Elango N., B.G. Hunt, M.A.D. Goodisman, S.V. Yi, 2009. DNA methylation is widespread and associated with differential gene expression in castes of the honeybee, Apis mellifera. Proceedings of the National Academy of Sciences – USA 106(27):11206-11211.
  
  
• Tian C., W.T. Beeson, A.T. Iavarone, J. Sun, M.A. Marletta, J.H.D. Cate, N.L. Glass, 2009. Systems analysis of plant cell wall degradation by the model filamentous fungus Neurospora crassa. Proceedings of the National Academy of Sciences – USA 106 (52): 22157-22162.
  
  
• Cummings M.E., J. Larkins-Ford, C.R.L. Reilly, R.Y. Wong, M. Ramsey, H. Hofmann, 2008. Sexual and social stimuli elicit rapid and contrasting genomic responses. Proceedings of the Royal Society B 275 (1633): 393-402.
  
  
• Tian C, Kasuga T, Sachs MS, Glass NL, 2007. Transcriptional profiling of cross pathway control in Neurospora crassa and comparative analysis of the Gcn4 and CPC1 regulons. Eukaryotic Cell 6(6): 1-18.
  
  
• Aubin-Horth N, Letcher BH, Hofmann HA, 2005. Interaction of rearing environment and reproductive tatic on gene expression profiles in Atlantic salmon. Journal of Heredity 96(2): 1-18.
  
  
• Salmi ML, Bushart TJ, Stout SC, Roux SJ, 2005. Profile and analysis of gene expression changes during the early development in germinating spores of Ceratopteris richardii. Plant Physiology 138: 1734-1745.
  
  
• Aubin-Horth N, Landry CR, Letcher BH, Hofmann HA, 2005. Alternative life histories shape brain gene expression profiles in males of the same population. Proceedings of the Royal Society B 272(1573): 1655-1662.
  
  
• Lemos B, Bettencourt BR, Meiklejohn CD, Hartl DL, 2005. Evolution of proteins and gene expression levels are coupled in Drosophila and are independently associated with mRNA abundance, protein length, and number of protein-protein interactions. Molecular Biology and Evolution 22(5): 1345-1354.
  
  
• Kasuga T, Townsend JP, Tian C, Gilbert LB, Mannhaupt G, Taylor JW, Glass LN, 2005. Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germination. Nucleic Acids Research 33(20): 6469-6485.
  
  
• Lemos B, Meiklejohn CD, Hartl DL, 2004. Regulatory evolution across the protein interaction network. Nature Genetics 36(10): 1059-1060.
  
  
• Ranz JM, Namgyal K, Gibson G, Hartl DL, 2004. Anomalies in the expression profile of interspecific hybrids of Drosophila melanogaster and Drosophila simulans. Genome Research 14: 373-379.
  
  
• Townsend JP, 2004. Resolution of large and small differences in gene expression using models for the Bayesian analysis of gene expression levels and spotted DNA microarrays. BMC Bioinformatics 5: 54.
  
  
• Grozinger CM, Sharabash NM, Whitfield CW, Robinson, GE, 2003. Pheromone-mediated gene expression in the honey bee brain. PNAS 100 (suppl 2):14519-14525.
  
  
• Whitfield CW, Cziko A, Robinson, GE, 2003. Gene expression profiles in the brain predict behavior in individual bees. Science 302:296-299.
  
  
• Silverman N, Zhou R, Erlich RL, Hunter M, Bernstein E, Schneider D, Maniatis T, 2003. Immune activation of NF-kappaB and JNK requires Drosophila TAK1. J. Biol. Chem. 278(49):48928-48934.
  
  
• Townsend JP, 2003. Multifactorial experimental design and the transitivity of ratios with spotted DNA microarrays. BMC Genomics 4:41.
  
  
• Ranz JM, Castillo-Davis CI, Meiklejohn CD, Hartl DL, 2003. Sex-dependent gene expression and evolution of the Drosophila transcriptome. Science 300(5626):1742-5.
  
  
• Meiklejohn CD, Parsch J, Ranz JM, Hartl DL, 2003. Rapid evolution of male-biased gene expression in Drosophila. PNAS 100(17):9894-9899.
  
  
• Townsend JP, Cavalieri D, Hartl DL, 2003. Population genetic variation in genome-wide gene expression. Mol. Biol. Evol. 20(6):955-63.
  
  
• Townsend JP, Hartl DL, 2002. Bayesian analysis of gene expression levels: statistical quantification of relative mRNA level across multiple strains or treatments. Genome Biol. 3(12):RESEARCH0071.
  

Additions? email Jeffrey.Townsend@yale.edu

Some Papers That Use the Bayesian Analysis of Gene Expression Levels

• Hunt B.G., L. Ometto, Y. Wurm, D. Shoemaker, S.V. Yi, L. Keller, M.A.D. Goodisman, 2011. Relaxed selection is a precursor to the evolution of phenotypic plasticity. Proceedings of the National Academy of Sciences - USA 108 (38): 15936-15941.
  
  
• Paredes S., A.T. Branco, D.L. Hartl, K.A. Maggart, B. Lemos, 2011. Ribosomal DNA deletions modulate genome-wide gene expression: “rDNA-Sensitive” genes and natural variation. PLoS Genetics 7(4): e1001376.
  
  
• Guo W., X. Wang, Z. Ma, X. Liang, J. Han, D. Yu, L. Kang, 2011. CSP and Takeout genes modulate the switch between attraction and repulsion during behavioral phase change in the migratory locust. PLoS Genetics 7(2): e1001291.
  
  
• Lemos B., A.T. Branco, and D.L. Hartl, 2010. Epigenetic effects of polymorphic Y chromosomes modulate chromatin components, immune response, and sexual conflict. Proceedings of the National Academy of Sciences – USA 107 (36) 15826-15831.
  
  
• Bachtrog D., N.R.T. Toda, and S. Lockton, 2010. Dosage compensation and demasculinization of X chromosomes in Drosophila. Current Biology 20(16): 1476-1481.
  
  
• Elango N., B.G. Hunt, M.A.D. Goodisman, S.V. Yi, 2009. DNA methylation is widespread and associated with differential gene expression in castes of the honeybee, Apis mellifera. Proceedings of the National Academy of Sciences – USA 106(27):11206-11211.
  
  
• Tian C., W.T. Beeson, A.T. Iavarone, J. Sun, M.A. Marletta, J.H.D. Cate, N.L. Glass, 2009. Systems analysis of plant cell wall degradation by the model filamentous fungus Neurospora crassa. Proceedings of the National Academy of Sciences – USA 106 (52): 22157-22162.
  
  
• Cummings M.E., J. Larkins-Ford, C.R.L. Reilly, R.Y. Wong, M. Ramsey, H. Hofmann, 2008. Sexual and social stimuli elicit rapid and contrasting genomic responses. Proceedings of the Royal Society B 275 (1633): 393-402.
  
  
• Tian C, Kasuga T, Sachs MS, Glass NL, 2007. Transcriptional profiling of cross pathway control in Neurospora crassa and comparative analysis of the Gcn4 and CPC1 regulons. Eukaryotic Cell 6(6): 1-18.
  
  
• Aubin-Horth N, Letcher BH, Hofmann HA, 2005. Interaction of rearing environment and reproductive tatic on gene expression profiles in Atlantic salmon. Journal of Heredity 96(2): 1-18.
  
  
• Salmi ML, Bushart TJ, Stout SC, Roux SJ, 2005. Profile and analysis of gene expression changes during the early development in germinating spores of Ceratopteris richardii. Plant Physiology 138: 1734-1745.
  
  
• Aubin-Horth N, Landry CR, Letcher BH, Hofmann HA, 2005. Alternative life histories shape brain gene expression profiles in males of the same population. Proceedings of the Royal Society B 272(1573): 1655-1662.
  
  
• Lemos B, Bettencourt BR, Meiklejohn CD, Hartl DL, 2005. Evolution of proteins and gene expression levels are coupled in Drosophila and are independently associated with mRNA abundance, protein length, and number of protein-protein interactions. Molecular Biology and Evolution 22(5): 1345-1354.
  
  
• Kasuga T, Townsend JP, Tian C, Gilbert LB, Mannhaupt G, Taylor JW, Glass LN, 2005. Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germination. Nucleic Acids Research 33(20): 6469-6485.
  
  
• Lemos B, Meiklejohn CD, Hartl DL, 2004. Regulatory evolution across the protein interaction network. Nature Genetics 36(10): 1059-1060.
  
  
• Ranz JM, Namgyal K, Gibson G, Hartl DL, 2004. Anomalies in the expression profile of interspecific hybrids of Drosophila melanogaster and Drosophila simulans. Genome Research 14: 373-379.
  
  
• Townsend JP, 2004. Resolution of large and small differences in gene expression using models for the Bayesian analysis of gene expression levels and spotted DNA microarrays. BMC Bioinformatics 5: 54.
  
  
• Grozinger CM, Sharabash NM, Whitfield CW, Robinson, GE, 2003. Pheromone-mediated gene expression in the honey bee brain. PNAS 100 (suppl 2):14519-14525.
  
  
• Whitfield CW, Cziko A, Robinson, GE, 2003. Gene expression profiles in the brain predict behavior in individual bees. Science 302:296-299.
  
  
• Silverman N, Zhou R, Erlich RL, Hunter M, Bernstein E, Schneider D, Maniatis T, 2003. Immune activation of NF-kappaB and JNK requires Drosophila TAK1. J. Biol. Chem. 278(49):48928-48934.
  
  
• Townsend JP, 2003. Multifactorial experimental design and the transitivity of ratios with spotted DNA microarrays. BMC Genomics 4:41.
  
  
• Ranz JM, Castillo-Davis CI, Meiklejohn CD, Hartl DL, 2003. Sex-dependent gene expression and evolution of the Drosophila transcriptome. Science 300(5626):1742-5.
  
  
• Meiklejohn CD, Parsch J, Ranz JM, Hartl DL, 2003. Rapid evolution of male-biased gene expression in Drosophila. PNAS 100(17):9894-9899.
  
  
• Townsend JP, Cavalieri D, Hartl DL, 2003. Population genetic variation in genome-wide gene expression. Mol. Biol. Evol. 20(6):955-63.
  
  
• Townsend JP, Hartl DL, 2002. Bayesian analysis of gene expression levels: statistical quantification of relative mRNA level across multiple strains or treatments. Genome Biol. 3(12):RESEARCH0071.
  

Additions? email Jeffrey.Townsend@yale.edu