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Minor Isozymes Tailor Yeast Metabolism to Carbon Availability.

Bradley PH, Gibney PA, Botstein D, Troyanskaya OG, Rabinowitz JD.

mSystems. 2019 Feb 26;4(1). pii: e00170-18. doi: 10.1128/mSystems.00170-18. eCollection 2019 Jan-Feb.


Simultaneous Profiling of DNA Accessibility and Gene Expression Dynamics with ATAC-Seq and RNA-Seq.

Hendrickson DG, Soifer I, Wranik BJ, Botstein D, Scott McIsaac R.

Methods Mol Biol. 2018;1819:317-333. doi: 10.1007/978-1-4939-8618-7_15.


Discovery and Functional Characterization of a Yeast Sugar Alcohol Phosphatase.

Xu YF, Lu W, Chen JC, Johnson SA, Gibney PA, Thomas DG, Brown G, May AL, Campagna SR, Yakunin AF, Botstein D, Rabinowitz JD.

ACS Chem Biol. 2018 Oct 19;13(10):3011-3020. doi: 10.1021/acschembio.8b00804. Epub 2018 Oct 4.


The future of humans as model organisms.

FitzGerald G, Botstein D, Califf R, Collins R, Peters K, Van Bruggen N, Rader D.

Science. 2018 Aug 10;361(6402):552-553. doi: 10.1126/science.aau7779. No abstract available.


Common and divergent features of galactose-1-phosphate and fructose-1-phosphate toxicity in yeast.

Gibney PA, Schieler A, Chen JC, Bacha-Hummel JM, Botstein M, Volpe M, Silverman SJ, Xu Y, Bennett BD, Rabinowitz JD, Botstein D.

Mol Biol Cell. 2018 Apr 15;29(8):897-910. doi: 10.1091/mbc.E17-11-0666. Epub 2018 Mar 30.


Systems-level analysis of mechanisms regulating yeast metabolic flux.

Hackett SR, Zanotelli VR, Xu W, Goya J, Park JO, Perlman DH, Gibney PA, Botstein D, Storey JD, Rabinowitz JD.

Science. 2016 Oct 28;354(6311). pii: aaf2786. Epub 2016 Oct 27.


Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells.

Møller HD, Bojsen RK, Tachibana C, Parsons L, Botstein D, Regenberg B.

J Vis Exp. 2016 Apr 4;(110):e54239 |. doi: 10.3791/54239.


Analysis of Polygenic Mutants Suggests a Role for Mediator in Regulating Transcriptional Activation Distance in Saccharomyces cerevisiae.

Reavey CT, Hickman MJ, Dobi KC, Botstein D, Winston F.

Genetics. 2015 Oct;201(2):599-612. doi: 10.1534/genetics.115.181164. Epub 2015 Aug 17.


Extrachromosomal circular DNA is common in yeast.

Møller HD, Parsons L, Jørgensen TS, Botstein D, Regenberg B.

Proc Natl Acad Sci U S A. 2015 Jun 16;112(24):E3114-22. doi: 10.1073/pnas.1508825112. Epub 2015 Jun 2.


Characterizing the in vivo role of trehalose in Saccharomyces cerevisiae using the AGT1 transporter.

Gibney PA, Schieler A, Chen JC, Rabinowitz JD, Botstein D.

Proc Natl Acad Sci U S A. 2015 May 12;112(19):6116-21. doi: 10.1073/pnas.1506289112. Epub 2015 Apr 27.


Lasker∼Koshland to genetics pioneer.

Botstein D.

Cell. 2014 Sep 11;158(6):1230-1232. doi: 10.1016/j.cell.2014.08.020.


Synthetic biology tools for programming gene expression without nutritional perturbations in Saccharomyces cerevisiae.

McIsaac RS, Gibney PA, Chandran SS, Benjamin KR, Botstein D.

Nucleic Acids Res. 2014 Apr;42(6):e48. doi: 10.1093/nar/gkt1402. Epub 2014 Jan 20.


Rapid synthesis and screening of chemically activated transcription factors with GFP-based reporters.

McIsaac RS, Oakes BL, Botstein D, Noyes MB.

J Vis Exp. 2013 Nov 26;(81):e51153. doi: 10.3791/51153.


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.


Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations.

Lang GI, Rice DP, Hickman MJ, Sodergren E, Weinstock GM, Botstein D, Desai MM.

Nature. 2013 Aug 29;500(7464):571-4. doi: 10.1038/nature12344. Epub 2013 Jul 21.


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.


Visualization and analysis of mRNA molecules using fluorescence in situ hybridization in Saccharomyces cerevisiae.

McIsaac RS, Silverman SJ, Parsons L, Xu P, Briehof R, McClean MN, Botstein D.

J Vis Exp. 2013 Jun 14;(76):e50382. doi: 10.3791/50382.


Phylogenetic portrait of the Saccharomyces cerevisiae functional genome.

Gibney PA, Hickman MJ, Bradley PH, Matese JC, Botstein D.

G3 (Bethesda). 2013 Aug 7;3(8):1335-40. doi: 10.1534/g3.113.006585.


Genetic Basis of Ammonium Toxicity Resistance in a Sake Strain of Yeast: A Mendelian Case.

Reisser C, Dick C, Kruglyak L, Botstein D, Schacherer J, Hess DC.

G3 (Bethesda). 2013 Apr 9;3(4):733-740. doi: 10.1534/g3.113.005884.


Automating the construction of gene ontologies.

Dolinski K, Botstein D.

Nat Biotechnol. 2013 Jan;31(1):34-5. doi: 10.1038/nbt.2476. No abstract available.


Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast.

McIsaac RS, Oakes BL, Wang X, Dummit KA, Botstein D, Noyes MB.

Nucleic Acids Res. 2013 Feb 1;41(4):e57. doi: 10.1093/nar/gks1313. Epub 2012 Dec 28.


TOR and RAS pathways regulate desiccation tolerance in Saccharomyces cerevisiae.

Welch AZ, Gibney PA, Botstein D, Koshland DE.

Mol Biol Cell. 2013 Jan;24(2):115-28. doi: 10.1091/mbc.E12-07-0524. Epub 2012 Nov 21.


Decoupling nutrient signaling from growth rate causes aerobic glycolysis and deregulation of cell size and gene expression.

Slavov N, Botstein D.

Mol Biol Cell. 2013 Jan;24(2):157-68. doi: 10.1091/mbc.E12-09-0670. Epub 2012 Nov 7.


Why we need more basic biology research, not less.

Botstein D.

Mol Biol Cell. 2012 Nov;23(21):4160-1. doi: 10.1091/mbc.E12-05-0406.


Loss of a 20S proteasome activator in Saccharomyces cerevisiae downregulates genes important for genomic integrity, increases DNA damage, and selectively sensitizes cells to agents with diverse mechanisms of action.

Doherty KM, Pride LD, Lukose J, Snydsman BE, Charles R, Pramanik A, Muller EG, Botstein D, Moore CW.

G3 (Bethesda). 2012 Aug;2(8):943-59. doi: 10.1534/g3.112.003376. Epub 2012 Aug 1.


Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway.

McIsaac RS, Petti AA, Bussemaker HJ, Botstein D.

Mol Biol Cell. 2012 Aug;23(15):2993-3007. doi: 10.1091/mbc.E12-03-0232. Epub 2012 Jun 13.


Combinatorial control of diverse metabolic and physiological functions by transcriptional regulators of the yeast sulfur assimilation pathway.

Petti AA, McIsaac RS, Ho-Shing O, Bussemaker HJ, Botstein D.

Mol Biol Cell. 2012 Aug;23(15):3008-24. doi: 10.1091/mbc.E12-03-0233. Epub 2012 Jun 13. Erratum in: Mol Biol Cell. 2014 Apr;25(8):1409.


A conserved cell growth cycle can account for the environmental stress responses of divergent eukaryotes.

Slavov N, Airoldi EM, van Oudenaarden A, Botstein D.

Mol Biol Cell. 2012 May;23(10):1986-97. doi: 10.1091/mbc.E11-11-0961. Epub 2012 Mar 28.


Yeast: an experimental organism for 21st Century biology.

Botstein D, Fink GR.

Genetics. 2011 Nov;189(3):695-704. doi: 10.1534/genetics.111.130765. Review.


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.


A test of the coordinated expression hypothesis for the origin and maintenance of the GAL cluster in yeast.

Lang GI, Botstein D.

PLoS One. 2011;6(9):e25290. doi: 10.1371/journal.pone.0025290. Epub 2011 Sep 22.


Fast-acting and nearly gratuitous induction of gene expression and protein depletion in Saccharomyces cerevisiae.

McIsaac RS, Silverman SJ, McClean MN, Gibney PA, Macinskas J, Hickman MJ, Petti AA, Botstein D.

Mol Biol Cell. 2011 Nov;22(22):4447-59. doi: 10.1091/mbc.E11-05-0466. Epub 2011 Sep 30.


Coordinated regulation of sulfur and phospholipid metabolism reflects the importance of methylation in the growth of yeast.

Hickman MJ, Petti AA, Ho-Shing O, Silverman SJ, McIsaac RS, Lee TA, Botstein D.

Mol Biol Cell. 2011 Nov;22(21):4192-204. doi: 10.1091/mbc.E11-05-0467. Epub 2011 Sep 7.


Survival of starving yeast is correlated with oxidative stress response and nonrespiratory mitochondrial function.

Petti AA, Crutchfield CA, Rabinowitz JD, Botstein D.

Proc Natl Acad Sci U S A. 2011 Nov 8;108(45):E1089-98. doi: 10.1073/pnas.1101494108. Epub 2011 Jul 6.


Genetic variation and the fate of beneficial mutations in asexual populations.

Lang GI, Botstein D, Desai MM.

Genetics. 2011 Jul;188(3):647-61. doi: 10.1534/genetics.111.128942. Epub 2011 May 5.


Coupling among growth rate response, metabolic cycle, and cell division cycle in yeast.

Slavov N, Botstein D.

Mol Biol Cell. 2011 Jun 15;22(12):1997-2009. doi: 10.1091/mbc.E11-02-0132. Epub 2011 Apr 27.


Genome-sequencing anniversary. Fruits of genome sequences for biology.

Botstein D.

Science. 2011 Feb 25;331(6020):1025. doi: 10.1126/science.1204038. No abstract available.


Evaluating gene expression dynamics using pairwise RNA FISH data.

Wyart M, Botstein D, Wingreen NS.

PLoS Comput Biol. 2010 Nov 4;6(11):e1000979. doi: 10.1371/journal.pcbi.1000979.


Technological innovation leads to fundamental understanding in cell biology.

Botstein D.

Mol Biol Cell. 2010 Nov 15;21(22):3791-2. doi: 10.1091/mbc.E10-04-0366. No abstract available.


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.


Adaptation to diverse nitrogen-limited environments by deletion or extrachromosomal element formation of the GAP1 locus.

Gresham D, Usaite R, Germann SM, Lisby M, Botstein D, Regenberg B.

Proc Natl Acad Sci U S A. 2010 Oct 26;107(43):18551-6. doi: 10.1073/pnas.1014023107. Epub 2010 Oct 11.


Metabolic cycling in single yeast cells from unsynchronized steady-state populations limited on glucose or phosphate.

Silverman SJ, Petti AA, Slavov N, Parsons L, Briehof R, Thiberge SY, Zenklusen D, Gandhi SJ, Larson DR, Singer RH, Botstein D.

Proc Natl Acad Sci U S A. 2010 Apr 13;107(15):6946-51. doi: 10.1073/pnas.1002422107. Epub 2010 Mar 24. Erratum in: Proc Natl Acad Sci U S A. 2011 Jul 19;108(29):12185.


Optimized detection of sequence variation in heterozygous genomes using DNA microarrays with isothermal-melting probes.

Gresham D, Curry B, Ward A, Gordon DB, Brizuela L, Kruglyak L, Botstein D.

Proc Natl Acad Sci U S A. 2010 Jan 26;107(4):1482-7. doi: 10.1073/pnas.0913883107. Epub 2010 Jan 8.


It's the data!

Botstein D.

Mol Biol Cell. 2010 Jan 1;21(1):4-6. doi: 10.1091/mbc.E09-07-0575.


Recurated protein interaction datasets.

Salwinski L, Licata L, Winter A, Thorneycroft D, Khadake J, Ceol A, Aryamontri AC, Oughtred R, Livstone M, Boucher L, Botstein D, Dolinski K, Berardini T, Huala E, Tyers M, Eisenberg D, Cesareni G, Hermjakob H.

Nat Methods. 2009 Dec;6(12):860-1. doi: 10.1038/nmeth1209-860. No abstract available.


Saccharomyces Genome Database provides mutant phenotype data.

Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Livstone MS, Miyasato SR, Nash R, Oughtred R, Park J, Skrzypek MS, Weng S, Wong ED, Dolinski K, Botstein D, Cherry JM.

Nucleic Acids Res. 2010 Jan;38(Database issue):D433-6. doi: 10.1093/nar/gkp917. Epub 2009 Nov 11.


Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations.

Boer VM, Crutchfield CA, Bradley PH, Botstein D, Rabinowitz JD.

Mol Biol Cell. 2010 Jan 1;21(1):198-211. doi: 10.1091/mbc.E09-07-0597. Epub 2009 Nov 4.


A molecular barcoded yeast ORF library enables mode-of-action analysis of bioactive compounds.

Ho CH, Magtanong L, Barker SL, Gresham D, Nishimura S, Natarajan P, Koh JLY, Porter J, Gray CA, Andersen RJ, Giaever G, Nislow C, Andrews B, Botstein D, Graham TR, Yoshida M, Boone C.

Nat Biotechnol. 2009 Apr;27(4):369-77. doi: 10.1038/nbt.1534. Epub 2009 Apr 6.


The cost of gene expression underlies a fitness trade-off in yeast.

Lang GI, Murray AW, Botstein D.

Proc Natl Acad Sci U S A. 2009 Apr 7;106(14):5755-60. doi: 10.1073/pnas.0901620106. Epub 2009 Mar 19.


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.

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