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Phylogeny

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  • Leffler, Ellen M, Kevin Bullaughey, Daniel R Matute, Wynn K Meyer, Laure Ségurel, Aarti Venkat, Peter Andolfatto, and Molly Przeworski. 2012. “Revisiting an Old Riddle: What Determines Genetic Diversity Levels Within Species?”. PLoS Biol 10 (9): e1001388.
    Reference Link
  • Aardema, Matthew L, Ying Zhen, and Peter Andolfatto. (2012) 2012. “The Evolution of Cardenolide-Resistant Forms of Na⁺,K⁺ -ATPase in Danainae Butterflies.”. Mol Ecol 21 (2): 340-9.
    Reference Link
  • Papatsenko, Dmitri, and Michael Levine. (2005) 2005. “Quantitative Analysis of Binding Motifs Mediating Diverse Spatial Readouts of the Dorsal Gradient in the Drosophila Embryo.”. Proc Natl Acad Sci U S A 102 (14): 4966-71.
    Reference Link
  • Schumer, Molly, Rongfeng Cui, Bastien Boussau, Ronald Walter, Gil Rosenthal, and Peter Andolfatto. (2013) 2013. “An Evaluation of the Hybrid Speciation Hypothesis for Xiphophorus Clemenciae Based on Whole Genome Sequences.”. Evolution 67 (4): 1155-68.
    Reference Link
  • Peifer, M, and E Wieschaus. (1993) 1993. “The Product of the Drosophila Melanogaster Segment Polarity Gene Armadillo Is Highly Conserved in Sequence and Expression in the Housefly Musca Domestica.”. J Mol Evol 36 (3): 224-33.
    Reference Link
  • Callahan, Benjamin, Richard A Neher, Doris Bachtrog, Peter Andolfatto, and Boris I Shraiman. (2011) 2011. “Correlated Evolution of Nearby Residues in Drosophilid Proteins.”. PLoS Genet 7 (2): e1001315.
    Reference Link
  • Heinicke, Sven, Michael S Livstone, Charles Lu, Rose Oughtred, Fan Kang, Samuel Angiuoli V, Owen White, David Botstein, and Kara Dolinski. 2007. “The Princeton Protein Orthology Database (P-POD): A Comparative Genomics Analysis Tool for Biologists.”. PLoS One 2 (8): e766.
    Reference Link
  • McCarroll, Steven A, Coleen T Murphy, Sige Zou, Scott D Pletcher, Chen-Shan Chin, Yuh Nung Jan, Cynthia Kenyon, Cornelia I Bargmann, and Hao Li. (2004) 2004. “Comparing Genomic Expression Patterns across Species Identifies Shared Transcriptional Profile in Aging.”. Nat Genet 36 (2): 197-204.
    Reference Link
  • Wilson, Daniel J, Ryan D Hernandez, Peter Andolfatto, and Molly Przeworski. (2011) 2011. “A Population Genetics-Phylogenetics Approach to Inferring Natural Selection in Coding Sequences.”. PLoS Genet 7 (12): e1002395.
    Reference Link
  • Kapheim, Karen M, Hailin Pan, Cai Li, Steven L Salzberg, Daniela Puiu, Tanja Magoc, Hugh M Robertson, et al. (2015) 2015. “Social Evolution. Genomic Signatures of Evolutionary Transitions from Solitary to Group Living.”. Science 348 (6239): 1139-43. doi:10.1126/science.aaa4788.
    Reference Link
  • Cui, Rongfeng, Molly Schumer, Karla Kruesi, Ronald Walter, Peter Andolfatto, and Gil G Rosenthal. (2013) 2013. “Phylogenomics Reveals Extensive Reticulate Evolution in Xiphophorus Fishes.”. Evolution 67 (8): 2166-79.
    Reference Link
  • Gibney, Patrick A, Mark J Hickman, Patrick H Bradley, John C Matese, and David Botstein. (2013) 2013. “Phylogenetic Portrait of the Saccharomyces Cerevisiae Functional Genome.”. G3 (Bethesda) 3 (8): 1335-40.
    Reference Link
  • Andolfatto, Peter, Mark Scriber, and Brian Charlesworth. (2003) 2003. “No Association Between Mitochondrial DNA Haplotypes and a Female-Limited Mimicry Phenotype in Papilio Glaucus.”. Evolution 57 (2): 305-16.
    Reference Link
  • Rowe, Kevin C, Sonal Singhal, Matthew D Macmanes, Julien Ayroles, Toni Lyn Morelli, Emily M Rubidge, Ke Bi, and Craig C Moritz. (2011) 2011. “Museum Genomics: Low-Cost and High-Accuracy Genetic Data from Historical Specimens.”. Mol Ecol Resour 11 (6): 1082-92.
    Reference Link
  • Hendrix, David, Michael Levine, and Weiyang Shi. 2010. “MiRTRAP, a Computational Method for the Systematic Identification of MiRNAs from High Throughput Sequencing Data.”. Genome Biol 11 (4): R39.
    Reference Link
  • Zhen, Ying, and Peter Andolfatto. 2012. “Methods to Detect Selection on Noncoding DNA.”. Methods Mol Biol 856: 141-59.
    Reference Link
  • Abitua, Philip Barron, Eileen Wagner, Ignacio A Navarrete, and Michael Levine. (2012) 2012. “Identification of a Rudimentary Neural Crest in a Non-Vertebrate Chordate.”. Nature 492 (7427): 104-7.
    Reference Link
  • Capra, John A, Katrin Paeschke, Mona Singh, and Virginia A Zakian. 2010. “G-Quadruplex DNA Sequences Are Evolutionarily Conserved and Associated With Distinct Genomic Features in Saccharomyces Cerevisiae.”. PLoS Comput Biol 6 (7): e1000861.
    Reference Link
  • Hong, Joung-Woo, David A Hendrix, and Michael S Levine. (2008) 2008. “Shadow Enhancers As a Source of Evolutionary Novelty.”. Science 321 (5894): 1314.
    Reference Link
  • Vrana, P B, P G Matteson, J Schmidt V, R S Ingram, A Joyce, K L Prince, M J Dewey, and S M Tilghman. (2001) 2001. “Genomic Imprinting of a Placental Lactogen Gene in Peromyscus.”. Dev Genes Evol 211 (11): 523-32.
    Reference Link
  • Hu, Tina T, Michael B Eisen, Kevin R Thornton, and Peter Andolfatto. (2013) 2013. “A Second-Generation Assembly of the Drosophila Simulans Genome Provides New Insights into Patterns of Lineage-Specific Divergence.”. Genome Res 23 (1): 89-98.
    Reference Link
  • Garrigan, Daniel, Sarah B Kingan, Anthony J Geneva, Peter Andolfatto, Andrew Clark, Kevin R Thornton, and Daven C Presgraves. (2012) 2012. “Genome Sequencing Reveals Complex Speciation in the Drosophila Simulans Clade.”. Genome Res 22 (8): 1499-511.
    Reference Link
  • Christiaen, Lionel, Eileen Wagner, Weiyang Shi, and Michael Levine. (2009) 2009. “The Sea Squirt Ciona Intestinalis.”. Cold Spring Harb Protoc 2009 (12): pdb.emo138.
    Reference Link
  • Bachtrog, Doris, Kevin Thornton, Andrew Clark, and Peter Andolfatto. (2006) 2006. “Extensive Introgression of Mitochondrial DNA Relative to Nuclear Genes in the Drosophila Yakuba Species Group.”. Evolution 60 (2): 292-302.
    Reference Link

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