Thornton, Kevin, Doris Bachtrog, and Peter Andolfatto. (2006) 2006. “X Chromosomes and Autosomes Evolve at Similar Rates in Drosophila: No Evidence for Faster-X Protein Evolution.”. Genome Res 16 (4): 498-504.

Ahmed, Yashi, Ali Nouri, and Eric Wieschaus. (2002) 2002. “Drosophila Apc1 and Apc2 Regulate Wingless Transduction Throughout Development.”. Development 129 (7): 1751-62.

Edwards, Alexis C, Julien Ayroles, Eric A Stone, Mary Anna Carbone, Richard F Lyman, and Trudy F C Mackay. 2009. “A Transcriptional Network Associated With Natural Variation in Drosophila Aggressive Behavior.”. Genome Biol 10 (7): R76.

Putnam, Andrea S, Mark Scriber, and Peter Andolfatto. (2007) 2007. “Discordant Divergence Times Among Z-Chromosome Regions Between Two Ecologically Distinct Swallowtail Butterfly Species.”. Evolution 61 (4): 912-27.

Guan, Yuanfang, Maitreya Dunham, Amy A Caudy, and Olga Troyanskaya. (2010) 2010. “Systematic Planning of Genome-Scale Experiments in Poorly Studied Species.”. PLoS Comput Biol 6 (3): e1000698.

Brauer, Matthew J, Jie Yuan, Bryson D Bennett, Wenyun Lu, Elizabeth Kimball, David Botstein, and Joshua D Rabinowitz. (2006) 2006. “Conservation of the Metabolomic Response to Starvation across Two Divergent Microbes.”. Proc Natl Acad Sci U S A 103 (51): 19302-7.

Gregor, Thomas, Alistair P McGregor, and Eric F Wieschaus. (2008) 2008. “Shape and Function of the Bicoid Morphogen Gradient in Dipteran Species With Different Sized Embryos.”. Dev Biol 316 (2): 350-8.

Cande, Jessica Doran, Yury Goltsev, and Michael S Levine. (2009) 2009. “Conservation of Enhancer Location in Divergent Insects.”. Proc Natl Acad Sci U S A 106 (34): 14414-9.

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.

Guan, Yuanfang, Maitreya Dunham, Olga G Troyanskaya, and Amy A Caudy. 2013. “Comparative Gene Expression Between Two Yeast Species.”. BMC Genomics 14: 33.

Khan, Zia, Joshua S Bloom, Sasan Amini, Mona Singh, David H Perlman, Amy A Caudy, and Leonid Kruglyak. 2012. “Quantitative Measurement of Allele-Specific Protein Expression in a Diploid Yeast Hybrid by LC-MS.”. Mol Syst Biol 8: 602.

Papatsenko, Dmitri, Michael Levine, and Yury Goltsev. 2011. “Clusters of Temporal Discordances Reveal Distinct Embryonic Patterning Mechanisms in Drosophila and Anopheles.”. PLoS Biol 9 (1): e1000584.

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.

Zartman, Jeremiah J, Nir Yakoby, Christopher A Bristow, Xiaofeng Zhou, Karin Schlichting, Christian Dahmann, and Stanislav Y Shvartsman. (2008) 2008. “Cad74A Is Regulated by BR and Is Required for Robust Dorsal Appendage Formation in Drosophila Oogenesis.”. Dev Biol 322 (2): 289-301.

Dolinski, Kara, and David Botstein. 2007. “Orthology and Functional Conservation in Eukaryotes.”. Annu Rev Genet 41: 465-507.

Chikina, Maria D, and Olga G Troyanskaya. 2011. “Accurate Quantification of Functional Analogy Among Close Homologs.”. PLoS Comput Biol 7 (2): e1001074.

Guan, Yuanfang, Victoria Yao, Kyle Tsui, Marinella Gebbia, Maitreya Dunham, Corey Nislow, and Olga G Troyanskaya. 2011. “Nucleosome-Coupled Expression Differences in Closely-Related Species.”. BMC Genomics 12: 466.

Nuttle, Xander, Giuliana Giannuzzi, Michael H Duyzend, Joshua G Schraiber, Iñigo Narvaiza, Peter H Sudmant, Osnat Penn, et al. (2016) 2016. “Emergence of a Homo Sapiens-Specific Gene Family and Chromosome 16p11.2 CNV Susceptibility.”. Nature 536 (7615): 205-9. doi:10.1038/nature19075.

Marsh, J L, E B van Deusen, E Wieschaus, and W J Gehring. (1977) 1977. “Germ Line Dependence of the Deep Orange Maternal Effect in Drosophila.”. Dev Biol 56 (1): 195-9.

Vrana, P B, X J Guan, R S Ingram, and S M Tilghman. (1998) 1998. “Genomic Imprinting Is Disrupted in Interspecific Peromyscus Hybrids.”. Nat Genet 20 (4): 362-5.

Guan, Yuanfang, Chad L Myers, Rong Lu, Ihor R Lemischka, Carol J Bult, and Olga G Troyanskaya. 2008. “A Genomewide Functional Network for the Laboratory Mouse.”. PLoS Comput Biol 4 (9): e1000165.

Schacherer, Joseph, Douglas M Ruderfer, David Gresham, Kara Dolinski, David Botstein, and Leonid Kruglyak. 2007. “Genome-Wide Analysis of Nucleotide-Level Variation in Commonly Used Saccharomyces Cerevisiae Strains.”. PLoS One 2 (3): e322.

Rebeiz, Mark, Margarita Ramos-Womack, Sangyun Jeong, Peter Andolfatto, Thomas Werner, John True, David L Stern, and Sean B Carroll. (2009) 2009. “Evolution of the Tan Locus Contributed to Pigment Loss in Drosophila Santomea: A Response to Matute Et Al.”. Cell 139 (6): 1189-96.

Cande, Jessica Doran, Peter Andolfatto, Benjamin Prud’homme, David L Stern, and Nicolas Gompel. 2012. “Evolution of Multiple Additive Loci Caused Divergence Between Drosophila Yakuba and D. Santomea in Wing Rowing During Male Courtship.”. PLoS One 7 (8): e43888.

Jeong, Sangyun, Mark Rebeiz, Peter Andolfatto, Thomas Werner, John True, and Sean B Carroll. (2008) 2008. “The Evolution of Gene Regulation Underlies a Morphological Difference Between Two Drosophila Sister Species.”. Cell 132 (5): 783-93.