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Hess, David C, Chad L Myers, Curtis Huttenhower, Matthew A Hibbs, Alicia P Hayes, Jadine Paw, John J Clore, et al. (2009) 2009. “Computationally Driven, Quantitative Experiments Discover Genes Required for Mitochondrial Biogenesis.”. PLoS Genet 5 (3): e1000407.

Gibney, Patrick A, Charles Lu, Amy A Caudy, David C Hess, and David Botstein. (2013) 2013. “Yeast Metabolic and Signaling Genes Are Required for Heat-Shock Survival and Have Little Overlap With the Heat-Induced Genes.”. Proc Natl Acad Sci U S A 110 (46).

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

Gresham, David, Viktor M Boer, Amy A Caudy, Naomi Ziv, Nathan J Brandt, John D Storey, and David Botstein. (2011) 2011. “System-Level Analysis of Genes and Functions Affecting Survival During Nutrient Starvation in Saccharomyces Cerevisiae.”. Genetics 187 (1): 299-317.

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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.

Khan, Zia, Sasan Amini, Joshua S Bloom, Cristian Ruse, Amy A Caudy, Leonid Kruglyak, Mona Singh, David H Perlman, and Saeed Tavazoie. 2011. “Accurate Proteome-Wide Protein Quantification from High-Resolution 15N Mass Spectra.”. Genome Biol 12 (12): R122.

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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.

Guan, Yuanfang, Chad L Myers, David C Hess, Zafer Barutcuoglu, Amy A Caudy, and Olga G Troyanskaya. 2008. “Predicting Gene Function in a Hierarchical Context With an Ensemble of Classifiers.”. Genome Biol 9 Suppl 1: S3.

Airoldi, Edoardo M, Curtis Huttenhower, David Gresham, Charles Lu, Amy A Caudy, Maitreya Dunham, James R Broach, David Botstein, and Olga G Troyanskaya. (2009) 2009. “Predicting Cellular Growth from Gene Expression Signatures.”. PLoS Comput Biol 5 (1): e1000257.

Xu, Yi-Fan, Fabien Létisse, Farnaz Absalan, Wenyun Lu, Ekaterina Kuznetsova, Greg Brown, Amy A Caudy, Alexander F Yakunin, James R Broach, and Joshua D Rabinowitz. 2013. “Nucleotide Degradation and Ribose Salvage in Yeast.”. Mol Syst Biol 9: 665.

Caudy, Amy A, Yuanfang Guan, Yue Jia, Christina Hansen, Chris DeSevo, Alicia P Hayes, Joy Agee, et al. (2013) 2013. “A New System for Comparative Functional Genomics of Saccharomyces Yeasts.”. Genetics 195 (1): 275-87.

Lu, Wenyun, Michelle F Clasquin, Eugene Melamud, Daniel Amador-Noguez, Amy A Caudy, and Joshua D Rabinowitz. (2010) 2010. “Metabolomic Analysis via Reversed-Phase Ion-Pairing Liquid Chromatography Coupled to a Stand Alone Orbitrap Mass Spectrometer.”. Anal Chem 82 (8): 3212-21.

Slavov, Nikolai, Joanna Macinskas, Amy A Caudy, and David Botstein. (2011) 2011. “Metabolic Cycling Without Cell Division Cycling in Respiring Yeast.”. Proc Natl Acad Sci U S A 108 (47): 19090-5.

Bloom, Joshua S, Zia Khan, Leonid Kruglyak, Mona Singh, and Amy A Caudy. 2009. “Measuring Differential Gene Expression by Short Read Sequencing: Quantitative Comparison to 2-Channel Gene Expression Microarrays.”. BMC Genomics 10: 221.

He, Bing, Amy A Caudy, Lance Parsons, Adam Rosebrock, Attilio Pane, Sandeep Raj, and Eric Wieschaus. (2012) 2012. “Mapping the Pericentric Heterochromatin by Comparative Genomic Hybridization Analysis and Chromosome Deletions in Drosophila Melanogaster.”. Genome Res 22 (12): 2507-19.

Huttenhower, Curtis, Matthew A Hibbs, Chad L Myers, Amy A Caudy, David C Hess, and Olga G Troyanskaya. (2009) 2009. “The Impact of Incomplete Knowledge on Evaluation: An Experimental Benchmark for Protein Function Prediction.”. Bioinformatics 25 (18): 2404-10.