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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.

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