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Diverse conditions support near-zero growth in yeast: Implications for the study of cell lifespan.

Gulli J, Cook E, Kroll E, Rosebrock A, Caudy A, Rosenzweig F.

Microb Cell. 2019 Aug 20;6(9):397-413. doi: 10.15698/mic2019.09.690. Review.


Rhodoquinone biosynthesis in C. elegans requires precursors generated by the kynurenine pathway.

Del Borrello S, Lautens M, Dolan K, Tan JH, Davie T, Schertzberg MR, Spensley MA, Caudy AA, Fraser AG.

Elife. 2019 Jun 24;8. pii: e48165. doi: 10.7554/eLife.48165.


Transposon insertional mutagenesis in Saccharomyces uvarum reveals trans-acting effects influencing species-dependent essential genes.

Sanchez MR, Payen C, Cheong F, Hovde BT, Bissonnette S, Arkin AP, Skerker JM, Brem RB, Caudy AA, Dunham MJ.

Genome Res. 2019 Mar;29(3):396-406. doi: 10.1101/gr.232330.117. Epub 2019 Jan 11.


Functional genetic discovery of enzymes using full-scan mass spectrometry metabolomics 1.

Caudy AA, Hanchard JA, Hsieh A, Shaan S, Rosebrock AP.

Biochem Cell Biol. 2019 Feb;97(1):73-84. doi: 10.1139/bcb-2018-0058. Epub 2018 Jul 12.


Systematic analysis of complex genetic interactions.

Kuzmin E, VanderSluis B, Wang W, Tan G, Deshpande R, Chen Y, Usaj M, Balint A, Mattiazzi Usaj M, van Leeuwen J, Koch EN, Pons C, Dagilis AJ, Pryszlak M, Wang JZY, Hanchard J, Riggi M, Xu K, Heydari H, San Luis BJ, Shuteriqi E, Zhu H, Van Dyk N, Sharifpoor S, Costanzo M, Loewith R, Caudy A, Bolnick D, Brown GW, Andrews BJ, Boone C, Myers CL.

Science. 2018 Apr 20;360(6386). pii: eaao1729. doi: 10.1126/science.aao1729.


Metabolomics in Yeast.

Caudy AA, Mülleder M, Ralser M.

Cold Spring Harb Protoc. 2017 Sep 1;2017(9):pdb.top083576. doi: 10.1101/pdb.top083576.


Spectrophotometric Analysis of Ethanol and Glucose Concentrations in Yeast Culture Media.

Caudy AA.

Cold Spring Harb Protoc. 2017 Sep 1;2017(9):pdb.prot089102. doi: 10.1101/pdb.prot089102.


Metabolite Extraction from Saccharomyces cerevisiae for Liquid Chromatography-Mass Spectrometry.

Rosebrock AP, Caudy AA.

Cold Spring Harb Protoc. 2017 Sep 1;2017(9):pdb.prot089086. doi: 10.1101/pdb.prot089086.


Drosophila larvae synthesize the putative oncometabolite L-2-hydroxyglutarate during normal developmental growth.

Li H, Chawla G, Hurlburt AJ, Sterrett MC, Zaslaver O, Cox J, Karty JA, Rosebrock AP, Caudy AA, Tennessen JM.

Proc Natl Acad Sci U S A. 2017 Feb 7;114(6):1353-1358. doi: 10.1073/pnas.1614102114. Epub 2017 Jan 23.


Proteomic analysis of the human KEOPS complex identifies C14ORF142 as a core subunit homologous to yeast Gon7.

Wan LC, Maisonneuve P, Szilard RK, Lambert JP, Ng TF, Manczyk N, Huang H, Laister R, Caudy AA, Gingras AC, Durocher D, Sicheri F.

Nucleic Acids Res. 2017 Jan 25;45(2):805-817. doi: 10.1093/nar/gkw1181. Epub 2016 Nov 29.


Mitochondrial control through nutritionally regulated global histone H3 lysine-4 demethylation.

Soloveychik M, Xu M, Zaslaver O, Lee K, Narula A, Jiang R, Rosebrock AP, Caudy AA, Meneghini MD.

Sci Rep. 2016 Nov 29;6:37942. doi: 10.1038/srep37942.


A global genetic interaction network maps a wiring diagram of cellular function.

Costanzo M, VanderSluis B, Koch EN, Baryshnikova A, Pons C, Tan G, Wang W, Usaj M, Hanchard J, Lee SD, Pelechano V, Styles EB, Billmann M, van Leeuwen J, van Dyk N, Lin ZY, Kuzmin E, Nelson J, Piotrowski JS, Srikumar T, Bahr S, Chen Y, Deshpande R, Kurat CF, Li SC, Li Z, Usaj MM, Okada H, Pascoe N, San Luis BJ, Sharifpoor S, Shuteriqi E, Simpkins SW, Snider J, Suresh HG, Tan Y, Zhu H, Malod-Dognin N, Janjic V, Przulj N, Troyanskaya OG, Stagljar I, Xia T, Ohya Y, Gingras AC, Raught B, Boutros M, Steinmetz LM, Moore CL, Rosebrock AP, Caudy AA, Myers CL, Andrews B, Boone C.

Science. 2016 Sep 23;353(6306). pii: aaf1420.


Challenges of analyzing different classes of metabolites by a single analytical method.

Mirnaghi FS, Caudy AA.

Bioanalysis. 2014;6(24):3393-416. doi: 10.4155/bio.14.236. Review.


Targeted metabolomics in cultured cells and tissues by mass spectrometry: method development and validation.

Abdel Rahman AM, Pawling J, Ryczko M, Caudy AA, Dennis JW.

Anal Chim Acta. 2014 Oct 3;845:53-61. doi: 10.1016/j.aca.2014.06.012. Epub 2014 Jun 12.


Heritability and genetic basis of protein level variation in an outbred population.

Parts L, Liu YC, Tekkedil MM, Steinmetz LM, Caudy AA, Fraser AG, Boone C, Andrews BJ, Rosebrock AP.

Genome Res. 2014 Aug;24(8):1363-70. doi: 10.1101/gr.170506.113. Epub 2014 May 13.


Broad metabolic sensitivity profiling of a prototrophic yeast deletion collection.

VanderSluis B, Hess DC, Pesyna C, Krumholz EW, Syed T, Szappanos B, Nislow C, Papp B, Troyanskaya OG, Myers CL, Caudy AA.

Genome Biol. 2014 Apr 10;15(4):R64. doi: 10.1186/gb-2014-15-4-r64.


Uniform nomenclature for the mitochondrial contact site and cristae organizing system.

Pfanner N, van der Laan M, Amati P, Capaldi RA, Caudy AA, Chacinska A, Darshi M, Deckers M, Hoppins S, Icho T, Jakobs S, Ji J, Kozjak-Pavlovic V, Meisinger C, Odgren PR, Park SK, Rehling P, Reichert AS, Sheikh MS, Taylor SS, Tsuchida N, van der Bliek AM, van der Klei IJ, Weissman JS, Westermann B, Zha J, Neupert W, Nunnari J.

J Cell Biol. 2014 Mar 31;204(7):1083-6. doi: 10.1083/jcb.201401006.


Interspecies Systems Biology Uncovers Metabolites Affecting C. elegans Gene Expression and Life History Traits.

Watson E, MacNeil LT, Ritter AD, Yilmaz LS, Rosebrock AP, Caudy AA, Walhout AJM.

Cell. 2014 Mar 13;156(6):1336-1337. doi: 10.1016/j.cell.2014.02.036. Epub 2014 Mar 13. No abstract available.


Interspecies systems biology uncovers metabolites affecting C. elegans gene expression and life history traits.

Watson E, MacNeil LT, Ritter AD, Yilmaz LS, Rosebrock AP, Caudy AA, Walhout AJ.

Cell. 2014 Feb 13;156(4):759-70. doi: 10.1016/j.cell.2014.01.047. Erratum in: Cell. 2014 Mar 13;156(6):1336-7.


Biochemical and structural studies of conserved Maf proteins revealed nucleotide pyrophosphatases with a preference for modified nucleotides.

Tchigvintsev A, Tchigvintsev D, Flick R, Popovic A, Dong A, Xu X, Brown G, Lu W, Wu H, Cui H, Dombrowski L, Joo JC, Beloglazova N, Min J, Savchenko A, Caudy AA, Rabinowitz JD, Murzin AG, Yakunin AF.

Chem Biol. 2013 Nov 21;20(11):1386-98. doi: 10.1016/j.chembiol.2013.09.011. Epub 2013 Oct 24.


Yeast metabolic and signaling genes are required for heat-shock survival and have little overlap with the heat-induced genes.

Gibney PA, Lu C, Caudy AA, Hess DC, Botstein D.

Proc Natl Acad Sci U S A. 2013 Nov 12;110(46):E4393-402. doi: 10.1073/pnas.1318100110. Epub 2013 Oct 28.


A new system for comparative functional genomics of Saccharomyces yeasts.

Caudy AA, Guan Y, Jia Y, Hansen C, DeSevo C, Hayes AP, Agee J, Alvarez-Dominguez JR, Arellano H, Barrett D, Bauerle C, Bisaria N, Bradley PH, Breunig JS, Bush E, Cappel D, Capra E, Chen W, Clore J, Combs PA, Doucette C, Demuren O, Fellowes P, Freeman S, Frenkel E, Gadala-Maria D, Gawande R, Glass D, Grossberg S, Gupta A, Hammonds-Odie L, Hoisos A, Hsi J, Hsu YH, Inukai S, Karczewski KJ, Ke X, Kojima M, Leachman S, Lieber D, Liebowitz A, Liu J, Liu Y, Martin T, Mena J, Mendoza R, Myhrvold C, Millian C, Pfau S, Raj S, Rich M, Rokicki J, Rounds W, Salazar M, Salesi M, Sharma R, Silverman S, Singer C, Sinha S, Staller M, Stern P, Tang H, Weeks S, Weidmann M, Wolf A, Young C, Yuan J, Crutchfield C, McClean M, Murphy CT, Llinás M, Botstein D, Troyanskaya OG, Dunham MJ.

Genetics. 2013 Sep;195(1):275-87. doi: 10.1534/genetics.113.152918. Epub 2013 Jul 12.


Nucleotide degradation and ribose salvage in yeast.

Xu YF, Létisse F, Absalan F, Lu W, Kuznetsova E, Brown G, Caudy AA, Yakunin AF, Broach JR, Rabinowitz JD.

Mol Syst Biol. 2013 May 14;9:665. doi: 10.1038/msb.2013.21.


Reconstitution and characterization of eukaryotic N6-threonylcarbamoylation of tRNA using a minimal enzyme system.

Wan LC, Mao DY, Neculai D, Strecker J, Chiovitti D, Kurinov I, Poda G, Thevakumaran N, Yuan F, Szilard RK, Lissina E, Nislow C, Caudy AA, Durocher D, Sicheri F.

Nucleic Acids Res. 2013 Jul;41(12):6332-46. doi: 10.1093/nar/gkt322. Epub 2013 Apr 25.


Comparative gene expression between two yeast species.

Guan Y, Dunham MJ, Troyanskaya OG, Caudy AA.

BMC Genomics. 2013 Jan 16;14:33. doi: 10.1186/1471-2164-14-33.


The future of deciphering personal genomes? The flies (and yeast and worms) still have it.

Rosebrock AP, Caudy AA.

Genome Med. 2012 Sep 27;4(9):74. doi: 10.1186/gm375. eCollection 2012.


Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS.

Khan Z, Bloom JS, Amini S, Singh M, Perlman DH, Caudy AA, Kruglyak L.

Mol Syst Biol. 2012;8:602. doi: 10.1038/msb.2012.34.


Mapping the pericentric heterochromatin by comparative genomic hybridization analysis and chromosome deletions in Drosophila melanogaster.

He B, Caudy A, Parsons L, Rosebrock A, Pane A, Raj S, Wieschaus E.

Genome Res. 2012 Dec;22(12):2507-19. doi: 10.1101/gr.137406.112. Epub 2012 Jun 28.


Accurate proteome-wide protein quantification from high-resolution 15N mass spectra.

Khan Z, Amini S, Bloom JS, Ruse C, Caudy AA, Kruglyak L, Singh M, Perlman DH, Tavazoie S.

Genome Biol. 2011 Dec 19;12(12):R122. doi: 10.1186/gb-2011-12-12-r122.


Metabolic cycling without cell division cycling in respiring yeast.

Slavov N, Macinskas J, Caudy A, Botstein D.

Proc Natl Acad Sci U S A. 2011 Nov 22;108(47):19090-5. doi: 10.1073/pnas.1116998108. Epub 2011 Nov 7.


Design of custom oligonucleotide microarrays for single species or interspecies hybrids using Array Oligo Selector.

Caudy AA.

Methods Mol Biol. 2011;772:233-41. doi: 10.1007/978-1-61779-228-1_13.


Riboneogenesis in yeast.

Clasquin MF, Melamud E, Singer A, Gooding JR, Xu X, Dong A, Cui H, Campagna SR, Savchenko A, Yakunin AF, Rabinowitz JD, Caudy AA.

Cell. 2011 Jun 10;145(6):969-80. doi: 10.1016/j.cell.2011.05.022.


System-level analysis of genes and functions affecting survival during nutrient starvation in Saccharomyces cerevisiae.

Gresham D, Boer VM, Caudy A, Ziv N, Brandt NJ, Storey JD, Botstein D.

Genetics. 2011 Jan;187(1):299-317. doi: 10.1534/genetics.110.120766. Epub 2010 Oct 13.


Dissection of genetically complex traits with extremely large pools of yeast segregants.

Ehrenreich IM, Torabi N, Jia Y, Kent J, Martis S, Shapiro JA, Gresham D, Caudy AA, Kruglyak L.

Nature. 2010 Apr 15;464(7291):1039-42. doi: 10.1038/nature08923.


Metabolomic analysis via reversed-phase ion-pairing liquid chromatography coupled to a stand alone orbitrap mass spectrometer.

Lu W, Clasquin MF, Melamud E, Amador-Noguez D, Caudy AA, Rabinowitz JD.

Anal Chem. 2010 Apr 15;82(8):3212-21. doi: 10.1021/ac902837x.


Systematic planning of genome-scale experiments in poorly studied species.

Guan Y, Dunham M, Caudy A, Troyanskaya O.

PLoS Comput Biol. 2010 Mar 5;6(3):e1000698. doi: 10.1371/journal.pcbi.1000698.


The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction.

Huttenhower C, Hibbs MA, Myers CL, Caudy AA, Hess DC, Troyanskaya OG.

Bioinformatics. 2009 Sep 15;25(18):2404-10. doi: 10.1093/bioinformatics/btp397. Epub 2009 Jun 26.


Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays.

Bloom JS, Khan Z, Kruglyak L, Singh M, Caudy AA.

BMC Genomics. 2009 May 12;10:221. doi: 10.1186/1471-2164-10-221.


Directing experimental biology: a case study in mitochondrial biogenesis.

Hibbs MA, Myers CL, Huttenhower C, Hess DC, Li K, Caudy AA, Troyanskaya OG.

PLoS Comput Biol. 2009 Mar;5(3):e1000322. doi: 10.1371/journal.pcbi.1000322. Epub 2009 Mar 20.


Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis.

Hess DC, Myers CL, Huttenhower C, Hibbs MA, Hayes AP, Paw J, Clore JJ, Mendoza RM, Luis BS, Nislow C, Giaever G, Costanzo M, Troyanskaya OG, Caudy AA.

PLoS Genet. 2009 Mar;5(3):e1000407. doi: 10.1371/journal.pgen.1000407. Epub 2009 Mar 20.


Predicting cellular growth from gene expression signatures.

Airoldi EM, Huttenhower C, Gresham D, Lu C, Caudy AA, Dunham MJ, Broach JR, Botstein D, Troyanskaya OG.

PLoS Comput Biol. 2009 Jan;5(1):e1000257. doi: 10.1371/journal.pcbi.1000257. Epub 2009 Jan 2.


Predicting gene function in a hierarchical context with an ensemble of classifiers.

Guan Y, Myers CL, Hess DC, Barutcuoglu Z, Caudy AA, Troyanskaya OG.

Genome Biol. 2008;9 Suppl 1:S3. doi: 10.1186/gb-2008-9-s1-s3. Epub 2008 Jun 27.


CD25 deficiency causes an immune dysregulation, polyendocrinopathy, enteropathy, X-linked-like syndrome, and defective IL-10 expression from CD4 lymphocytes.

Caudy AA, Reddy ST, Chatila T, Atkinson JP, Verbsky JW.

J Allergy Clin Immunol. 2007 Feb;119(2):482-7. Epub 2006 Dec 27.


Element 1360 and RNAi components contribute to HP1-dependent silencing of a pericentric reporter.

Haynes KA, Caudy AA, Collins L, Elgin SC.

Curr Biol. 2006 Nov 21;16(22):2222-7.


Genetic and functional analyses of membrane cofactor protein (CD46) mutations in atypical hemolytic uremic syndrome.

Fremeaux-Bacchi V, Moulton EA, Kavanagh D, Dragon-Durey MA, Blouin J, Caudy A, Arzouk N, Cleper R, Francois M, Guest G, Pourrat J, Seligman R, Fridman WH, Loirat C, Atkinson JP.

J Am Soc Nephrol. 2006 Jul;17(7):2017-25. Epub 2006 Jun 8.


Short hairpin activated gene silencing in mammalian cells.

Paddison PJ, Caudy AA, Sachidanandam R, Hannon GJ.

Methods Mol Biol. 2004;265:85-100.


A micrococcal nuclease homologue in RNAi effector complexes.

Caudy AA, Ketting RF, Hammond SM, Denli AM, Bathoorn AM, Tops BB, Silva JM, Myers MM, Hannon GJ, Plasterk RH.

Nature. 2003 Sep 25;425(6956):411-4.


Fragile X-related protein and VIG associate with the RNA interference machinery.

Caudy AA, Myers M, Hannon GJ, Hammond SM.

Genes Dev. 2002 Oct 1;16(19):2491-6.


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