Parsch, John, Sergey Novozhilov, Sarah S Saminadin-Peter, Karen M Wong, and Peter Andolfatto. (2010) 2010. “On the Utility of Short Intron Sequences As a Reference for the Detection of Positive and Negative Selection in Drosophila.”. Mol Biol Evol 27 (6): 1226-34.

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.

Ober, Ulrike, Julien Ayroles, Eric A Stone, Stephen Richards, Dianhui Zhu, Richard A Gibbs, Christian Stricker, et al. 2012. “Using Whole-Genome Sequence Data to Predict Quantitative Trait Phenotypes in Drosophila Melanogaster.”. PLoS Genet 8 (5): e1002685.

Andolfatto, Peter, Karen M Wong, and Doris Bachtrog. 2011. “Effective Population Size and the Efficacy of Selection on the X Chromosomes of Two Closely Related Drosophila Species.”. Genome Biol Evol 3: 114-28.

Wall, Jeffrey D, Peter Andolfatto, and Molly Przeworski. (2002) 2002. “Testing Models of Selection and Demography in Drosophila Simulans.”. Genetics 162 (1): 203-16.

Mackay, Trudy F C, Stephen Richards, Eric A Stone, Antonio Barbadilla, Julien Ayroles, Dianhui Zhu, Sònia Casillas, et al. (2012) 2012. “The Drosophila Melanogaster Genetic Reference Panel.”. Nature 482 (7384): 173-8.

Bachtrog, Doris, and Peter Andolfatto. (2006) 2006. “Selection, Recombination and Demographic History in Drosophila Miranda.”. Genetics 174 (4): 2045-59.

Lang, Gregory I, Andrew W Murray, and David Botstein. (2009) 2009. “The Cost of Gene Expression Underlies a Fitness Trade-off in Yeast.”. Proc Natl Acad Sci U S A 106 (14): 5755-60.

Wingreen, Ned S, Jonathan Miller, and Edward C Cox. (2003) 2003. “Scaling of Mutational Effects in Models for Pleiotropy.”. Genetics 164 (3): 1221-8.

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.

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.

Andolfatto, Peter. (2008) 2008. “Controlling Type-I Error of the McDonald-Kreitman Test in Genomewide Scans for Selection on Noncoding DNA.”. Genetics 180 (3): 1767-71.

Gresham, David, Michael M Desai, Cheryl M Tucker, Harry T Jenq, Dave A Pai, Alexandra Ward, Christopher G DeSevo, David Botstein, and Maitreya Dunham. (2008) 2008. “The Repertoire and Dynamics of Evolutionary Adaptations to Controlled Nutrient-Limited Environments in Yeast.”. PLoS Genet 4 (12): e1000303.

Dunham, Maitreya, Hassan Badrane, Tracy Ferea, Julian Adams, Patrick O Brown, Frank Rosenzweig, and David Botstein. (2002) 2002. “Characteristic Genome Rearrangements in Experimental Evolution of Saccharomyces Cerevisiae.”. Proc Natl Acad Sci U S A 99 (25): 16144-9.

Haddrill, Penelope R, Doris Bachtrog, and Peter Andolfatto. (2008) 2008. “Positive and Negative Selection on Noncoding DNA in Drosophila Simulans.”. Mol Biol Evol 25 (9): 1825-34.

Jensen, Jeffrey D, Kevin R Thornton, and Peter Andolfatto. 2008. “An Approximate Bayesian Estimator Suggests Strong, Recurrent Selective Sweeps in Drosophila.”. PLoS Genet 4 (9): e1000198.

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.

Andolfatto, Peter. (2005) 2005. “Adaptive Evolution of Non-Coding DNA in Drosophila.”. Nature 437 (7062): 1149-52.

Sella, Guy, Dmitri A Petrov, Molly Przeworski, and Peter Andolfatto. (2009) 2009. “Pervasive Natural Selection in the Drosophila Genome?”. PLoS Genet 5 (6): e1000495.

Gresham, David, Renata Usaite, Susanne Manuela Germann, Michael Lisby, David Botstein, and Birgitte Regenberg. (2010) 2010. “Adaptation to Diverse Nitrogen-Limited Environments by Deletion or Extrachromosomal Element Formation of the GAP1 Locus.”. Proc Natl Acad Sci U S A 107 (43): 18551-6.

Haddrill, Penelope R, Kevin R Thornton, Brian Charlesworth, and Peter Andolfatto. (2005) 2005. “Multilocus Patterns of Nucleotide Variability and the Demographic and Selection History of Drosophila Melanogaster Populations.”. Genome Res 15 (6): 790-9.

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.

Zhen, Ying, and Peter Andolfatto. 2012. “Methods to Detect Selection on Noncoding DNA.”. Methods Mol Biol 856: 141-59.

Browning, Sharon R, Brian L Browning, Ying Zhou, Serena Tucci, and Joshua Akey. (2018) 2018. “Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture.”. Cell 173 (1): 53-61.e9. doi:10.1016/j.cell.2018.02.031.

Andolfatto, Peter. (2007) 2007. “Hitchhiking Effects of Recurrent Beneficial Amino Acid Substitutions in the Drosophila Melanogaster Genome.”. Genome Res 17 (12): 1755-62.

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.

Lang, Gregory I, David Botstein, and Michael M Desai. (2011) 2011. “Genetic Variation and the Fate of Beneficial Mutations in Asexual Populations.”. Genetics 188 (3): 647-61.

Slotte, Tanja, Khaled M Hazzouri, David Stern, Peter Andolfatto, and Stephen I Wright. (2012) 2012. “Genetic Architecture and Adaptive Significance of the Selfing Syndrome in Capsella.”. Evolution 66 (5): 1360-74.