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Reavey, CT, Hickman, MJ, Dobi, KC, Botstein, D, Winston, F. (2015) Analysis of polygenic mutants suggests a role for mediator in regulating transcriptional activation distance in Saccharomyces cerevisiae. Genetics, 201(2): 599-612 [PMCID: PMC4596672]

Moller, HD, Parsons, L, Jorgensen, TS, Botstein, D, Regenberg, B. (2015) Extrachromosomal circular DNA is common in yeast. Proc. Natl. Acad. Sci. USA, pii: 201508825.

Gibney, PA, Schieler, A, Chen, JC, Rabinowitz, JD, Botstein, D. (2015) Characterizing the in vivo role of trehalose in Saccharomyces cerevisiae using the AGT1 transporter. Proc. Natl. Acad. Sci. USA, 112(9): 6116-21. [PMCID: PMC4434743]


Botstein, D. (2014) Lasker~Koshland to genetics pioneer. Cell, 158(6): 1230-2. doi: 10.1016/j.cell.2014.08.020

McIsaac, RS, Gibney, P A, Chandran, SS, Benjamin, KR, Botstein, D. (2014) Synthetic biology tools for programming gene expression without nutritional perturbations in Saccharomyces cerevisiae. Nucleic Acids Res., 42(6): e48. [PMCID: PMC3973312]


McIsaac, RS, Oakes, BL, Botstein, D, Noyes, MB. (2013) Rapid synthesis and screening of chemically activated transcription factors with GFP-based reporters. J. Vis. Exp. 2013 Nov 26; (81): e51153. [PMCID: PMC3992113]

Gibney, PA, Lu, C, Caudy, AA, Hess, DC, Botstein D. (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. USA. 110(46): e4393-402. [PMCID: PMC3831991]

Lang, G, Rice, DP, Hickman, MJ, Sodergren, E, Weinstock, GM, Botstein, D, Desai, MM. (2013) Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations. Nature. 500(7464): 571-4. [PMCID: PMC3758440]

Caudy, AA, Guan, Y, Jia Y, Hansen C, Desevo C, Hayes AP, Agee, J, Alvarez-Dominguez, JR, Arellano H, Barrett, D, Bauerle C, Bradley, PH, Breunig, JS, Bush EC, Cappel DA, Capra E, ChenW, 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, SJ, Singer, C, Sinha, S, Staller, M, Stern, P, Tang, H, Weeks, S, Weidmann, M, Wolf, A, Young, C, Yuan, J, Crutchfield, C, McClean, MN, Murphy, CT, Llinás, M, Botstein, D, Troyanskaya, OG, Dunham, MJ. (2013) A new system for comparative functional genomics of Saccharomyces yeasts. Genetics. 195(1): 275-87. [PMCID: PMC3761308] 

McIsaac, RS, Silverman, SJ, Parsons, L, Xu, P, Briehof, R, McClean, MN, Botstein, D. (2013) Visualization and analysis of mRNA molecules using fluorescence in situ hybridization in Saccharomyces cerevisiae. J. Vis. Exp. (76), e50382. [PMCID: PMC37274560]

Gibney, PA, Hickman, MJ, Bradley, PH, Matese, JC, Botstein D. (2013) Phylogenetic portrait of the Saccharomyces cerevisiae functional genome. G3 pii: g3.113.006585v1. [PMCID: PMC3737173]

Reisser, C, Dick, C, Kruglyak, L, Botstein, D, Schacherer, J, Hess, D. (2013) Genetic basis of ammonium toxicity resistance in a sake strain of yeast: a Mendelian case. G3 pii: g3.113.005884v1. [PMCID: PMC3618360]

Dolinski, K, Botstein, D. (2013) Automating the construction of gene ontologies. Nat Biotechnol. 31(1): 34-5.

McIsaac, RS, Oakes, BL, Wang, X, Dummit, KA, Botstein, D, Noyes, MB. (2013) Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast. Nucleic Acids Res. 41(4): e57. Epub 2012 Dec 28. [PMCID: PMC3575806]

Welch, AZ, Gibney, PA, Botstein, D, Koshland, DE. (2013) TOR and RAS pathways regulate desiccation tolerance in Saccharomyces cerevisiae. Mol Biol Cell. 24(2): 115-28. Epub 2012 Nov 21. [PMCID: PMC3541959]

Slavov, N, Botstein, D. (2013) Decoupling nutrient signaling from growth rate causes aerobic glycolysis and deregulation of cell size and gene expression. Mol Biol Cell. 24(2): 157-68. Epub 2012 Nov 7.  [PMCID: PMC3541962]


Botstein, D. (2012) Why we need more basic biology research, not less. Mol Biol Cell. Nov; 23(21): 4160-1. [PMCID: PMC3484092]

Doherty, KM, Pride, LD, Lukose, J, Snydsman, BE, Charles, R, Pramanik, A, Muller, EG, Botstein, D, Moore, CW. (2012)  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. G3: Genes, Genomes, Genetics Mission. Aug; 2(8): 943-59. Epub 2012 Aug. [PMCID: PMC3411250]

McIsaac, RS, Petti, AA, Bussemaker, HJ, Botstein, D. (2012) Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway. Mol Biol Cell. Aug; 23(15): 2993-3007. Epub 2012 Jun 13. [PMCID: PMC3408425]

Petti, AA, McIsaac, RS, Ho-Shing, O, Bussemaker, HJ, Botstein, D. (2012) Combinatorial control of diverse metabolic and physiological functions by transcriptional regulators of the yeast sulfur assimilation pathway. Mol Biol Cell. Aug; 23(15): 3008-24. Epub2012 Jun 13. [PMCID: PMC3408426]

Slavov N, Airoldi EM, van Oudenaarden A, Botstein D. (2012) A conserved cell growth cycle can account for the environmental stress responses of divergent eukaryotes. Mol Biol Cell. May; 23(10): 1986-97.Epub 2012 Mar 28. [PMCID: PMC3350561] 


Botstein D, Fink GR. (2011) Yeast: an experimental organism for 21st century biology.  Genetics. 2011 Nov;189(3):695-704. [PMCID:PMC3213361] 

Slavov N, Macinskas J, Caudy A, Botstein D. (2011) Metabolic cycling without cell division cycling in respiring yeast. Proc Natl Acad Sci U S A. 2011 Nov 22;108(47):19090-5. Epub 2011 Nov 7. [PMCID: PMC3223432] 

Lang GI, Botstein D. (2011) A test of the coordinated expression hypothesis for the origin and maintenance of the GAL cluster in yeast. PLoS One. 2011;6(9):e25290. Epub 2011 Sep 22.  [PMCID: PMC3178652] 

McIsaac RS, Silverman SJ, McClean MN, Gibney PA, Macinskas J, Hickman MJ, Petti AA, Botstein D.(2011) Fast-acting and nearly gratuitous induction of gene expression and protein depletion in Saccharomyces cerevisiae.  Mol Biol Cell. 2011 Nov;22(22):4447-59. Epub 2011 Sep 30. [PMCID: PMC3216669]

Hickman MJ, Petti AA, Ho-Shing O, Silverman SJ, McIsaac RS, Lee TA, Botstein D. (2011) Coordinated regulation of sulfur and phospholipid metabolism reflects the importance of methylation in the growth of yeast.  Mol Biol Cell. 2011 Nov;22(21):4192-204. Epub 2011 Sep 7.
[PMCID: PMC3204079]

Petti AA, Crutchfield CA, Rabinowitz JD, Botstein D. (2011) Survival of starving yeast is correlated with oxidative stress response and nonrespiratory mitochondrial function. Proc Natl Acad Sci U S A. 2011 Jul 6. [PMCID: PMC3215077]

Lang GI, Botstein D, and Desai MM. (2011) Genetic Variation and the Fate of Beneficial Mutations in Asexual Populations. Genetics. 2011 May 5. [PMCID:PMC3176544]

Slavov N, Botstein D. (2011) Coupling among Growth Rate Response, Metabolic Cycle and Cell Division Cycle in Yeast. Mol Biol Cell. 2011 Apr 27. [PMCID: PMC3113766]

Botstein D. (2011) Genome-sequencing anniversary. Fruits of genome sequences for biology. Science. 2011 Feb 25;331(6020):1025. [PMID:21350164[PubMed - indexed for MEDLINE]



Wyart M, Botstein D, Wingreen NS. (2010) Evaluating gene expression dynamics using pairwise RNA FISH data. PLoS Comput Biol. 2010 Nov 4;6(11):e1000979. [PMCID: PMC2973809]

Botstein D. (2010) Technological innovation leads to fundamental understanding in cell biology. Mol Biol Cell. 2010 Nov;21(22):3791-2. No abstract available. [PMCID: PMC2982132]

Gresham D, Usaite R, Germann SM, Lisby M, Botstein D, Regenberg B. (2010) Adaptation to diverse nitrogen-limited environments by deletion or extrachromosomal element formation of the GAP1 locus. Proc Natl Acad Sci U S A. 2010 Oct 26;107(43):18551-6. Epub 2010 Oct 11. [PMCID: PMC2972935]

Gresham D, Boer V, Caudy A, Ziv N, Brandt NJ, Storey JD, Botstein D. (2010) System-Level Analysis of Genes and Functions Affecting Survival During Nutrient Starvation in Saccharomyces cerevisiae. Genetics. 2010 Oct 13. Epub ahead of print. [PMCID: PMC3018308]

Silverman SJ, Petti AA, Slavov N, Parsons L, Briehof R, Thiberge SY, Zenklusen D, Gandhi SJ, Larson DR, Singer RH, Botstein D. (2010) Metabolic cycling in single yeast cells from unsynchronized steady-state populations limited on glucose or phosphate.Proc Natl Acad Sci U S A. 2010 Apr 13;107(15):6946-51. Epub 2010 Mar 24. [PMCID: PMC2872461]

Gresham D, Curry B, Ward A, Gordon DB, Brizuela L, Kruglyak L, Botstein D. (2010) Optimized detection of sequence variation in heterozygous genomes using DNA microarrays with isothermal-melting probes. Proc Natl Acad Sci U S A. 2010 Jan 26;107(4):1482-7. Epub 2010 Jan 8. [PMCID: PMC2824413]

Botstein D. (2010) It's the data! Mol Biol Cell. 2010 Jan 1;21(1):4-6. [PMCID: PMC2801718]


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. (2009) Recurated protein interaction datasets. Nat Methods. Dec;6(12):860-1. [PMCID: PMC2683745]

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. (2009) Saccharomyces Genome Database provides mutant phenotype data.  Nucleic Acids Res. 2010 Jan;38(Database issue):D433-6. Epub 2009 Nov 11. [PMCID: PMC2808950]

Boer, VM, Crutchfield, CA, Bradley PH, Botstein D, Rabinowitz JD. (2009) Growth-limiting Intracellular Metabolites in Yeast Growing Under Diverse Nutrient Limitations. Mol Biol Cell. Nov 4. Mol Biol Cell. 2010 Jan;21(1):198-211. Epub 2009 Nov 4. [PMCID: PMC2801714]

Ho CH, Magtanong L, Barker SL, Gresham D, Nishimura S, Natarajan P, Koh JL, Porter J, Gray CA, Andersen RJ, Giaever G, Nislow C, Andrews B, Botstein D, Graham TR, Yoshida M, Boone C. (2009) A molecular barcoded yeast ORF library enables mode-of-action analysis of bioactive compounds. Nat Biotechnol. 2009 Apr;27(4):369-77. PMID:19349972[PubMed - indexed for MEDLINE]

Lang GI, Murray AW, Botstein D. (2009) The cost of gene expression underlies a fitness trade-off in yeast. Proc Natl Acad Sci U S A. Apr 7;106(14):5755-60. [PMCID: PMC2658138]

Airoldi, E.M., Huttenhower, C., Gresham, D., Lu, C., Caudy, A., Dunham, M., Broach, J., Botstein, D., and Troyanskaya, O.G. (2009). Predicting cellular growth from gene expression signatures. PLoS Computational Biology. Jan;5(1):e1000257. [PMCID: PMC2599889]

Lu, C., Brauer, M., Botstein D. (2009) Slow Growth Induces Heat Shock Resistance in Normal and Respiratory-deficient Yeast. Molecular Biology of the Cell. Feb;20(3):891-903. [PMCID: PMC2633392]


Gresham, D., Desai, M.M., Tucker, C.M., Jenq, H.T., Pai, D.A., Ward, A., DeSevo, C.G., Botstein, D., and Dunham, M.J. (2008).  The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast. PLoS Genetics. Dec;4(12):e1000303. [PMCID: PMC2586090]

Boer VM, Amini S, Botstein D. (2008) Influence of genotype and nutrition on survival and metabolism of starving yeast. Proc Natl Acad Sci U S A. May 13;105(19):6930-5.  [PMCID: PMC2383937] 

Gresham D, Dunham MJ, Botstein D. (2008) Comparing whole genomes using DNA microarrays. Nat Rev Genet. Apr;9(4):291-302. Review. PMID:18347592[PubMed - indexed for MEDLINE]

Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, Binkley G, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Krieger CJ, Livstone MS, Miyasato SR, Nash RS, Oughtred R, Skrzypek MS, Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, Cherry JM. (2008) Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 2008 Jan;36(Database issue):D577-81. [PMCID: PMC2238894]
Brauer MF, Huttenhower C, Airoldi EM, Rosenstein R, Matese JC, Gresham D, Boer VM, Troyanskaya OG, Botstein D. (2008) Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast. Mol Biol Cell. Jan;19(1):352-67. [PMCID: PMC2174172] 


Heinicke S, Livstone MS, Lu C, Oughtred R, Kang F, Angiuoli SV, White O, Botstein D, Dolinski K. (2007) The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists. PLoS ONE. Aug 22;2(1):e766. [PMCID: PMC1942082]

Schacherer J, Ruderfer DM, Gresham D, Dolinski K, Botstein D, Kruglyak L. (2007) Genome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strains. PLoS ONE. Mar 28;2(3):e322. [PMCID: PMC1829191]

Dolinski K, Botstein D. (2007) Orthology and functional conservation in eukaryotes. Annu Rev Genet. 41:564-507. Review. PMID:17678444[PubMed - indexed for MEDLINE]


Pelham RJ, Rodgers L, Hall I, Lucito R, Nguyen KC, Navin N, Hicks J, Mu D, Powers S, Wigler M, Botstein D. (2006) Identification of alterations in DNA copy number in host stromal cells during tumor progression. Proc Natl Acad Sci U S A. Dec 26;109(52): 19848-53. [PMCID: PMC1698871]

Brauer MJ, Yuan J, Bennett BD, Lu W, Kimball E, Botstein D, Rabinowitz JD. (2006) Conservation of the metabolomic response to starvation across two divergent microbes. Proc Natl Acad Sci U S A. Dec 19;103(51):19302-7. [PMCID: PMC1697828]

Nash R, Weng S, Hitz B, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Livstone MS, Oughtred R, Park J, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Dolinski K, Botstein D, Cherry JM. (2006) Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res. 2007 Jan; 35 (Database issue): D468-71. [PMCID: PMC1669759]

Sorlie T, Perou CM, Fan C, Geisler S, Aas T, Nobel A, Anker G, Akslen LA, Botstein D, Borresen-Dale AL, Lonning PE. (2006) Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer. Mol Cancer Ther. Nov; 5(11):2914-8.

Hess DC, Lu W, Rabinowitz JD, Botstein D. (2006) Ammonium toxicity and potassium limitation in yeast. PLoS Biol. Oct 17;4(11). [PMCID: PMC1609136]

Fisk DG, Ball CA, Dolinski K, Engel SR, Hong EL, Issel-Tarver L, Schwartz K, Sethuraman A, Botstein D, Cherry JM. (2006)  The Saccharomyces Genome Database Project. Saccharomyces cerevisiae S288C genome annotation: a working hypothesis. Yeast. Sep;23(12):857-65.

Wingreen N, Botstein D. (2006) Back to the future: education for systems-level biologists. Nat Rev Mol Cell Biol. Nov; 7(11):829-32. [PMCID: PMC1950154]

Heck JA, Gresham D, Botstein D, Alani E. (2006) Accumulation of recessive lethal mutations in Saccharomyces cerevisiae mlh1 mismatch repair mutants is not associated with gross chromosomal rearrangements. Genetics. Sep; 174(1):519-23. [PMCID: PMC1569777]

Reguly T, Breitkreutz A, Boucher L, Breitkreutz BJ, Hon GC, Myers CL, Parsons A, Friesen H, Oughtred R, Tong A, Stark C, Ho Y, Botstein D, Andrews B, Boone C, Troyanskya OG, Ideker T, Dolinski K, Batada NN, Tyers M. (2006) Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. J Biol. June;5(4):11. [PMCID: PMC1561585]

Botstein, D. (2006) Willing to do the math: an interview with David Botstein. Inverview by Jane Gitschier. PLoS. May;2(5):e79. [PMCID: PMC1464829]

Gresham D, Ruderfer DM, Pratt SC, Schacherer J, Dunham M, Botstein D, Kruglyak L. (2006) Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray. Science. Mar 31;311(5769):1932-6.

Diehn M, Bhattacharya R, Botstein D, Brown PO. (2006) Genome-scale identification of membrane-associated human mRNAs. PLoS Genet. Jan 13;2(1):e11. [PMCID: PMC1326219]

Hirschman JE, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hong EL, Livstone MS, Nash R, Park J, Oughtred R, Skrzypek M, Starr B, Theesfeld CL, Williams J, Andrada R, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Thanawala MK, Weng S, Dolinski K, Botstein D, Cherry JM. (2006) Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome. Nucleic Acids Res. Jan 1;34(Database issue):D442-5. [PMCID: PMC1347479]
Ronen M, Botstein D. (2006) Transcriptional response of steady-state yeast cultures to transient perturbations in carbon source. Proc Natl Acad Sci U S A. Jan 10;103(2):389-94. [PMCID: PMC1326188]


Dolinski K, Botstein D. (2005) Changing perspectives in yeast research nearly a decade after the genome sequence. Genome Res. Dec;15(12):1611-9. Review.

Liang Y, Diehn M, Watson N, Bollen AW, Aldape KD, Nicholas MK, Lamborn KR, Berger MS, Botstein D, Brown PO, Israel MA. (2005) Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme. Proc Natl Acad Sci (USA). Apr 19;102(16): 5814-9. [PMCID: PMC556127]

Shyamsundar R, Kim YH, Higgins JP, Montgomery K, Jorden M, Sethuraman A, van de Rijn M, Botstein D, Brown PO, Pollack JR. (2005) A DNA microarray survey of gene expression in normal human tissues. Genome Biol. 6(3): R22. [PMCID: PMC1088941]

Brauer MJ, Saldanha AJ, Dolinski K, Botstein D. (2005) Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures. Mol Biol Cell. May;16(5): 2503-17. [PMCID: PMC1087253]

Wang W, Cherry JM, Nochomovitz Y, Jolly E, Botstein D, Li H. (2005) Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation. Proc Natl Acad Sci (USA). Feb 8;102(6): 1998-2003. [PMCID: PMC548531]

Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Nash R, Oughtred R, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Sethuraman A, Weng S, Botstein D, Cherry JM. (2005) Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD). Nucleic Acids Res. 33: D374-7. [PMCID: PMC539977]


Trinklein ND, Murray JI, Hartman SJ, Botstein D, Myers RM. (2004) The role of heat shock transcription factor 1 in the genome-wide regulation of the mammalian heat shock response. Mol Biol Cell. Mar;15(3):1254-61. [PMCID: PMC363119]

Shakoury-Elizeh M, Tiedeman J, Rashford J, Ferea T, Demeter J, Garcia E, Rolfes R, Brown PO, Botstein D, Philpott CC. (2004) Transcriptional remodeling in response to iron deprivation in Saccharomyces cerevisiae. Mol Biol Cell. 15: 1233-43. [PMCID: PMC363115]

Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, de la Cruz N, Tonellato P, Jaiswal P, Seigfried T, White R; (2004) Gene Ontology Consortium. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D258-61. [PMCID: PMC308770]

Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM. (2004) Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res. Jan 1;32(Database issue):D311-4. [PMCID: PMC308767]

Lapointe J, Li C, Higgins JP, van de Rijn M, Bair E, Montgomery K, Ferrari M, Egevad L, Rayford W, Bergerheim U, Ekman P, DeMarzo AM, Tibshirani R, Botstein D, Brown PO, Brooks JD, Pollack JR. (2004) Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Proc Natl Acad Sci (USA) 101: 811-6. [PMCID: PMC321763]

Chang HY, Sneddon JB, Alizadeh AA, Sood R, West RB, Montgomery K, Chi JT, Rijn Mv M, Botstein D, Brown PO. (2004) Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds. PLoS Biol. 2004; 2: E7. [PMCID: PMC314300]

Murray JI, Whitfield ML, Trinklein ND, Myers RM, Brown PO, Botstein D. (2004) Diverse and specific gene expression responses to stresses in cultured human cells. Mol Biol Cell. 15: 2361-74. [PMCID: PMC404029]

Lossos IS, Czerwinski DK, Alizadeh AA, Wechser MA, Tibshirani R, Botstein D, Levy R. (2004) Prediction of survival in diffuse large-B-cell lymphoma based on the expression of six genes. N Engl J Med. 2004 Apr 29;350(18):1828-37.

Zhao H, Langerod A, Ji Y, Nowels KW, Nesland JM, Tibshirani R, Bukholm IK, Karesen R, Botstein D, Borresen-Dale AL, Jeffrey SS.. (2004) Different gene expression patterns in invasive lobular and ductal carcinomas of the breast. Mol Biol Cell. 15: 2523-36. [PMCID: PMC420079]

Saldanha AJ, Brauer MJ, Botstein D. (2004) Nutritional homeostasis in batch and steady-state culture of yeast. Mol Biol Cell. 15: 4089-104. [PMCID: PMC515343]

Shapira M, Segal E, Botstein D. (2004) Disruption of Yeast Forkhead-associated Cell Cycle Transcription by Oxidative Stress. Mol Biol Cell. 15: 5659-69. [PMCID: PMC532044]

Rees CA, Demeter J, Matese JC, Botstein D, Sherlock G. (2004) GeneXplorer: an interactive web application for microarray data visualization and analysis. BMC Bioinformatics. Oct 1;5:141. [PMCID: PMC523853]

Tu IP, Schaner M, Diehn M, Sikic BI, Brown PO, Botstein D, Fero MJ. (2004) A method for detecting and correcting feature misidentification on expression microarrays. BMC Genomics. Sep 9;5(1):64. [PMCID: PMC521069]

Bialek W, Botstein D. (2004) Introductory science and mathematics education for 21st-Century biologists. Science. Feb 6;303(5659):788-90.

Botstein, D., (2004) Ira Herskowitz: 1946-2003. Genetics 166:653-60. [PMCID: PMC1470729]

Boyle E, Weng S, Gollub J, Jin H, Botstein D, Cherry JM, Sherlock G. (2004) GO:: TermFinder-open source software for accessing gene ontology information and finding significantly enriched gene ontology terms associated with a list of genes. Bioinformatics. Dec 12;20(18): 3710-3715. [PMCID: PMC3037731]


Botstein, D., (2003) Genomic perspective and cancer. Cold Spring Harb Symp Quant Biol.;68:417-24.

Diehn M, Sherlock G, Binkley G, Jin H, Matese JC, Hernandez-Boussard T, Rees CA, Cherry JM, Botstein D, Brown PO, Alizadeh AA. (2003) SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. Nucleic Acids Res.; 31: 219-23.  [PMCID: PMC165461]

Ranade K, Hinds D, Hsiung CA, Chuang LM, Chang MS, Chen YT, Pesich R, Hebert J, Chen YD, Dzau V, Olshen R, Curb D, Botstein D, Cox DR, Risch N. (2003). A genome scan for hypertension susceptibility loci in populations of Chinese and Japanese origins. Am J Hypertens. 16: 158-62. 

Bohen SP, Troyanskaya OG, Alter O, Warnke R, Botstein D, Brown PO, Levy R. (2003) Variation in gene expression patterns in follicular lymphoma and the response to rituximab. Proc Natl Acad Sci (USA) 100:1926-30. [PMCID: PMC149935]

Alter O, Brown PO, Botstein D. (2003). Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms. Proc Natl Acad Sci (USA). 100: 3351-6. [PMCID: PMC152296]

McInnis MG, Lan TH, Willour VL, McMahon FJ, Simpson SG, Addington AM, MacKinnon DF, Potash JB, Mahoney AT, Chellis J, Huo Y, Swift-Scanlan T, Chen H, Koskela R, Colin Stine O, Jamison KR, Holmans P, Folstein SE, Ranade K, Friddle C, Botstein D, Marr T, Beaty TH, Zandi P, Raymond DePaulo J. (2003) Genome-wide scan of bipolar disorder in 65 pedigrees: supportive evidence for linkage at 8q24, 18q22, 4q32, 2p12, and 13q12. Mol Psychiatry. 8: 288-98.

Segal E, Shapira M, Regev A, Pe'er D, Botstein D, Koller D, Friedman N. (2003) Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet. 34: 166-76.

Troyanskaya OG, Dolinski K, Owen AB, Altman RB, Botstein D. (2003) A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Proc Natl Acad Sci (USA). 100: 8348-53. [PMCID: PMC166232]

Sorlie T, Tibshirani R, Parker J, Hastie T, Marron JS, Nobel A, Deng S, Johnsen H, Pesich R, Geisler S, Demeter J, Perou CM, Lonning PE, Brown PO, Borresen-Dale AL, Botstein D. (2003) Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci (USA); 100: 8418-8423. [PMCID: PMC166244]

Chen X, Leung SY, Yuen ST, Chu KM, Ji J, Li R, Chan AS, Law S, Troyanskaya OG, Wong J, So S, Botstein D, Brown PO. (2003) Variation in gene expression patterns in human gastric cancers. Mol Biol Cell. 14: 3208-15.

Linn SC, West RB, Pollack JR, Zhu S, Hernandez-Boussard T, Nielsen TO, Rubin BP, Patel R, Goldblum JR, Siegmund D, Botstein D, Brown PO, Gilks CB, Van De Rijn M. (2003) Gene expression patterns and gene copy number changes in dermatofibrosarcoma protuberans. Am J Pathol. 163: 2383-95.

Roose JP, Diehn M, Tomlinson MG, Lin J, Alizadeh AA, Botstein D, Brown PO, Weiss A. (2003) T Cell Receptor-Independent Basal Signaling via Erk and Abl Kinases Suppresses RAG Gene Expression. PLoS Biol. Nov;1(2):E53.

Zhao H, Whitfield ML, Xu T, Botstein D, Brooks JD. (2003) Diverse effects of methylseleninic acid on the transcriptional program of human prostate cancer cells. Mol Biol Cell. 15: 506-19.

Smith KS, Chanda SK, Lingbeek M, Ross DT, Botstein D, van Lohuizen M, Cleary ML. (2003) Bmi-1 regulation of INK4A-ARF is a downstream requirement for transformation of hematopoietic progenitors by E2a-Pbx1. Mol Cell. 12: 393-400.

Whitfield ML, Finlay DR, Murray JI, Troyanskaya OG, Chi JT, Pergamenschikov A, McCalmont TH, Brown PO, Botstein D, Connolly MK. (2003) Systemic and cell type-specific gene expression patterns in scleroderma skin. Proc Natl Acad Sci (USA). 100: 12319-24. 
Nielsen TO, Hsu FD, O'Connell JX, Gilks CB, Sorensen PH, Linn S, West RB, Liu CL, Botstein D, Brown PO, van de Rijn M. (2003) Tissue microarray validation of epidermal growth factor receptor and SALL2 in synovial sarcoma with comparison to tumors of similar histology. Am J Pathol. 163: 1449-56.

Chi JT, Chang HY, Haraldsen G, Jahnsen FL, Troyanskaya OG, Chang DS, Wang Z, Rockson SG, van de Rijn M, Botstein D, Brown PO.(2003) Endothelial cell diversity revealed by global expression profiling. Proc Natl Acad Sci (USA) 100: 10623-8.

Schaner ME, Ross DT, Ciaravino G, Sorlie T, Troyanskaya O, Diehn M, Wang YC, Duran GE, Sikic TL, Caldeira S, Skomedal H, Tu IP, Hernandez-Boussard T, Johnson SW, O'Dwyer PJ, Fero MJ, Kristensen GB, Borresen-Dale AL, Hastie T, Tibshirani R, Van De Rijn M, Teng NN, Longacre TA, Botstein D, Brown PO, Sikic BI. (2003) Gene expression patterns in ovarian carcinomas. Mol Biol Cell. 14: 4376-86.

Gollub J, Ball CA, Binkley G, Demeter J, Finkelstein DB, Hebert JM, Hernandez-Boussard T, Jin H, Kaloper M, Matese JC, Schroeder M, Brown PO, Botstein D, Sherlock G. The Stanford Microarray Database: data access and quality assessment tools. Nucleic Acids Res. (2003) Jan 1;31(1):94-6.

Weng S, Dong Q, Balakrishnan R, Christie K, Costanzo M, Dolinski K, Dwight SS, Engel S, Fisk DG, Hong E, Issel-Tarver L, Sethuraman A, Theesfeld C, Andrada R, Binkley G, Lane C, Schroeder M, Botstein D, Michael Cherry J. (2003) Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res. Jan 1;31(1):216-8. 

Botstein D, Risch N. (2003) Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease. Nat Genet. Mar;33 Suppl:228-37. Review.

Uhlmann WR, Bennett R, Botkin JR, Botstein D, Boughman JA, Chakravarti A, Clayton EW, Kahn J, Koenig B, Murray TH, Olson MV, Rowley J, Terry S, Valle D. (2003) Planning the genome institute's future. Science. Mar 7;299 5612:1515.


Boldrick, J.C., Alizadeh, A.A., Diehn, M., Dudoit, S., Liu, C.L., Belcher, C. E., Botstein, D., Staudt, L.M., Brown, P.O., Relman, D. A., (2002) Stereotyped and specific gene expression programs in human innate immune responses to bacteria. Proc. Natl. Acad.Sci. USA 99: 972-977.
Ranade, K., Jorgenson, E., Shew, W.H. , Pei, D., Hsiung, C.A., Chiang, F., Chen,Y.I., Pratt, R., Olshen, R. A., Curb, D., Cox, D. R., Botstein, D., Risch, N. (2002) A Polymorphism in the beta1 Adrenergic Receptor Is Associated with Resting Heart Rate. Am. J. Hum. Genet 70: 935-42.

Click, E.S., Stearns, T and Botstein, D. (2002) Systematic Structure-Function Analysis of the Small GTPase Arf1 in Yeast. Mol. Biol. Cell. 13: 1652-64.

Nielsen, T.O., West, R.B., Linn, S.C., Alter, O., Knowling, M.A., O'Connell, J.X., Zhu, S., Fero, M., Sherlock, G., Pollack, J.R., Brown, P.O., Botstein, D., van de Rijn, M. (2002) Molecular characterisation of soft tissue tumours: a gene expression study. Lancet 359: 1301-7.

Yoshimoto H, Saltsman K, Gasch AP, Li HX, Ogawa N, Botstein D, Brown PO, Cyert MS. (2002) Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae. J Biol Chem. 277: 31079-88.

Chen X, Cheung ST, So S, Fan ST, Barry C, Higgins J, Lai KM, Ji J, Dudoit S, Ng IO, Van De Rijn M, Botstein D, Brown PO. (2002) Gene expression patterns in human liver cancers. Mol Biol Cell. 3: 1929-39.

Whitfield ML, Sherlock G, Saldanha AJ, Murray JI, Ball CA, Alexander KE, Matese JC, Perou CM, Hurt MM, Brown PO, Botstein D. (2002) Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol Biol Cell. 13: 1977-2000.

Lossos IS, Alizadeh AA, Diehn M, Warnke R, Thorstenson Y, Oefner PJ, Brown PO, Botstein D, Levy R. (2002) Transformation of follicular lymphoma to diffuse large-cell lymphoma: alternative patterns with increased or decreased expression of c-myc and its regulated genes. Proc Natl Acad Sci (USA) 99:8886-91.

Sayama K, Diehn M, Matsuda K, Lunderius C, Tsai M, Tam SY, Botstein D, Brown PO, Galli SJ. (2002) Transcriptional response of human mast cells stimulated via the FcεRI; RI and identification of mast cells as a source of IL-11. BMC Immunol. 3:5.

Diehn M, Alizadeh AA, Rando OJ, Liu CL, Stankunas K, Botstein D, Crabtree GR, Brown PO. (2002) Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation. Proc Natl Acad Sci U S A.;99: 11796-801. Erratum in: Proc Natl Acad Sci U S A; 99:15245.

Trotter EW, Kao CM, Berenfeld L, Botstein D, Petsko GA, Gray JV. (2002) Misfolded proteins are competent to mediate a subset of the responses to heat shock in Saccharomyces cerevisiae. J Biol Chem. ; 277: 44817-25.

Pollack JR, Sorlie T, Perou CM, Rees CA, Jeffrey SS, Lonning PE, Tibshirani R, Botstein D, Borresen-Dale AL, Brown PO. (2002) Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc Natl Acad Sci (USA) 99: 12963-8.

Chang HY, Chi JT, Dudoit S, Bondre C, van de Rijn M, Botstein D, Brown PO. (2002) Diversity, topographic differentiation, and positional memory in human fibroblasts. Proc Natl Acad Sci (USA) 99:12877-82.

Troyanskaya OG, Garber ME, Brown PO, Botstein D, Altman RB. (2002) Nonparametric methods for identifying differentially expressed genes in microarray data. Bioinformatics 18:1454-61.

Dunham MJ, Badrane H, Ferea T, Adams J, Brown PO, Rosenzweig F, Botstein D. (2002) Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae. Proc Natl Acad Sci (USA) 99: 16144-9.

Leung SY, Chen X, Chu KM, Yuen ST, Mathy J, Ji J, Chan AS, Li R, Law S, Troyanskaya OG, Tu IP, Wong J, So S, Botstein D, Brown PO. (2002) Phospholipase A2 group IIA expression in gastric adenocarcinoma is associated with prolonged survival and less frequent metastasis. Proc Natl Acad Sci U S A.; 99: 16203-8.

van de Rijn M, Perou CM, Tibshirani R, Haas P, Kallioniemi O, Kononen J, Torhorst J, Sauter G, Zuber M, Kochli OR, Mross F, Dieterich H, Seitz R, Ross D, Botstein D, Brown P. (2002) Expression of cytokeratins 17 and 5 identifies a group of breast carcinomas with poor clinical outcome. J Pathol. 161: 1991-6.

Wang W, Cherry JM, Botstein D, Li H. (2002) A systematic approach to reconstructing transcription networks in Saccharomyces cerevisiae. Proc Natl Acad Sci (USA) 99: 16893-8.

Dwight, S.S., Harris, M.A., Dolinski, K., Ball, C.A., Binkley, G., Christie, K.R., Fisk, D. G., Issel-Tarver, L., Schroeder, M., Sherlock, G., Sethuraman, A., Weng, S., Botstein, D, Cherry, J. M. (2002) Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 30:69-72.

Pollack JR, Van de Rijn M, Botstein D. (2002) Challenges in developing a molecular characterization of cancer. Semin Oncol. Jun;29(3):280-5. Review.

Issel-Tarver L, Christie KR, Dolinski K, Andrada R, Balakrishnan R, Ball CA, Binkley G, Dong S, Dwight SS, Fisk DG, Harris M, Schroeder M, Sethuraman A, Tse K, Weng S, Botstein D, Cherry JM. (2002) Saccharomyces Genome Database. Methods Enzymol. 350:329-46.

Mulholland J, Botstein D. (2002) Immunoelectron microscopy of aldehyde-fixed yeast cells. Methods Enzymol. 351:50-81.

Gilman AG, Simon MI, Bourne HR, Harris BA, Long R, Ross EM, Stull JT, Taussig R, Bourne HR, Arkin AP, Cobb MH, Cyster JG, Devreotes PN, Ferrell JE, Fruman D, Gold M, Weiss A, Stull JT, Berridge MJ, Cantley LC, Catterall WA, Coughlin SR, Olson EN, Smith TF, Brugge JS, Botstein D, Dixon JE, Hunter T, Lefkowitz RJ, Pawson AJ, Sternberg PW, Varmus H, Subramaniam S, Sinkovits RS, Li J, Mock D, Ning Y, Saunders B, Sternweis PC, Hilgemann D, Scheuermann RH, DeCamp D, Hsueh R, Lin KM, Ni Y, Seaman WE, Simpson PC, O'Connell TD, Roach T, Simon MI, Choi S, Eversole-Cire P, Fraser I, Mumby MC, Zhao Y, Brekken D, Shu H, Meyer T, Chandy G, Heo WD, Liou J, O'Rourke N, Verghese M, Mumby SM, Han H, Brown HA, Forrester JS, Ivanova P, Milne SB, Casey PJ, Harden TK, Arkin AP, Doyle J, Gray ML, Meyer T, Michnick S, Schmidt MA, Toner M, Tsien RY, Natarajan M, Ranganathan R, Sambrano GR. (2002) Participating investigators and scientists of the Alliance for Cellular Signaling. Overview of the Alliance for Cellular Signaling. Nature. Dec 12; 420: 703-6.


Carmel-Harel, O., R. Stearman, A. P. Gasch, D. Botstein, P. O. Brown, and G. Storz (2001). Role of thioredoxin reductase in the Yap1p-dependent response to oxidative stress in Saccharomyces cerevisiae. Mol. Microbiol. 39: 595-605.

Hastie, T., R. Tibshirani, D. Botstein, and P. Brown (2001). Supervised harvesting of expression trees. Genome Biol. 2. [PMCID: PMC17599]

Iyer, V. R., C. E. Horak, C. S. Scafe, D. Botstein, M. Snyder, and P. O. Brown (2001). Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature. 409: 533-8.

Lieb, J. D., X. Liu, D. Botstein, and P. O. Brown (2001). Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat Genet. 28: 327-334.

Ranade, K., M. S. Chang, C. T. Ting, D. Pei, C. F. Hsiao, M. Olivier, R. Pesich, J. Hebert, Y. D. Chen, V. J. Dzau, D. Curb, R. Olshen, N. Risch, D. R. Cox, and D. Botstein (2001). High-throughput genotyping with single nucleotide polymorphisms. Genome Res. 11: 1262-8. [PMCID: PMC311112]

Sherlock, G., T. Hernandez-Boussard, A. Kasarskis, G. Binkley, J. C. Matese, S. S. Dwight, M. Kaloper, S. Weng, H. Jin, C. A. Ball, M. B. Eisen, P. T. Spellman, P. O. Brown, D. Botstein, and J. M. Cherry (2001). The Stanford Microarray Database. Nucleic Acids Res. 29: 152-5. [PMCID: PMC29818]

Troyanskaya, O., M. Cantor, G. Sherlock, P. Brown, T. Hastie, R. Tibshirani, D. Botstein, and R. B. Altman (2001). Missing value estimation methods for DNA microarrays. Bioinformatics 17: 520-5.

Sorlie, T., Perou, C.M., Tibshirani, R., Aas, T., Geisler, D., Johnsen, H., Hastie, T., Eisen, M.B., van de Rijn, M., Jeffrey, S.S., Thorsen, T., Quist, H., Matese, J.C., Brown, P.O. Botstein, D., L_nning, P.E., B_rresen-Dale, A.-L. (2001). Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc. Natl. Acad.Sci. USA 98: 10869-74. [PMCID: PMC58566]

Finlin, B.S., Gau, C.L., Murphy, G.A., Shao, H., Kimel, T., Seitz, R.S., Chiu, Y.F., Botstein, D., Brown, P.O., Der, C.J., Tamanoi, F., Andres, D.A., Perou, C.M. (2001) RERG is a Novel ras-related, Estrogen-regulated and Growth-inhibitory Gene in Breast Cancer. J. Biol. Chem. 52: 49244-50.

Ranade K., Wu K.D., Hwu, C.M., Ting, C.T., Pei, D., Pesich, R., Hebert, J., Chen, Y.D., Pratt, R., Olshen, R., Masaki, K., Risch, N., Cox, D.R., Botstein, D. (2001). Genetic variation in the human urea transporter-2 is associated with variation in blood pressure. Hum Mol Genet. 10: 2157-2164.

Ranade ,K., Wu, K.D., Risch, N., Olivier, M., Pei D., Hsiao, C.F., Chuang, L.M, Ho, L.T., Jorgenson, E., Pesich, R., Chen, Y.D., Dzau, V., Lin, A., Olshen, R.A., Curb, D., Cox, D.R., and Botstein D. (2001) Genetic variation in aldosterone synthase predicts plasma glucose levels. Proc. Natl. Acad.Sci. (USA) 98: 13219-24. [PMCID: PMC60851]

Anders KR, Botstein D. Dominant-lethal alpha-tubulin mutants defective in microtubule depolymerization in yeast. (2001) Mol Biol Cell. 12: 3973-86. [PMCID: PMC60769]

Ranade K, Shue WH, Hung YJ, Hsuing CA, Chiang FT, Pesich R, Hebert J, Olivier M, Chen YD, Pratt R, Olshen R, Curb D, Botstein D, Risch N, Cox DR. The glycine allele of a glycine/arginine polymorphism in the beta2-adrenergic receptor gene is associated with essential hypertension in a population of Chinese origin. (2001) Am J Hypertens. 14: 1196-200.

Garber, M. E., Troyanskaya, O. G., Schluens, K., Petersen, S., Thasler, Z., Pacyna-Gengelbach, M., van de Rijn, M., Rosen,G. D., Perou, C.M. Whyte, R. I., Altman, R.B., Brown, P.O., Botstein, D., Petersen, I., (2001) Diversity of gene expression in adenocarcinoma of the lung. Proc. Natl. Acad.Sci. (USA) 98: 13784-13789. [PMCID: PMC61119]

Rosenwald, A., Alizadeh, A.A., Widhopf, G., Simon, R., Davis, R. E., Yu, X., Yang, L., Pickeral, O. K., Rassenti, L. Z., Powell, J., Botstein, D., Byrd, J. C., Grever, M. R., Cheson, B. D., Chiorazzi, N., Wilson, W. H., Kipps, T. J., Brown, P. O., Staudt, L. M. (2001) Relation of gene expression phenotype to immunoglobulin mutation genotype in B cell chronic lymphocytic leukemia. J. Exp. Med. 194 :1639-47. [PMCID: PMC2193523]

Protchenko, O., Ferea, T., Rashford, J., Tiedeman, J., Brown, P. O., Botstein, D., Philpott, C. C., (2001) Three cell wall mannoproteins facilitate the uptake of iron in Saccharomyces cerevisiae. J. Biol. Chem. 52: 49244-50.

Gasch, A.P., Huang, M., Metzner, S., Botstein, D., Elledge, S.J., Brown, P.O.,m (2001) Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1p. Mol Biol. Cell 10: 2987-3003. [PMCID: PMC60150]

Lonning P.E ., Sorlie T., Perou, C.M., Brown, P.O., Botstein, D, Borresen-Dale, A.L. (2001) Microarrays in primary breast cancer - lessons from chemotherapy studies. Endocr . Relat. Cancer 8:259-63.


Richards, K.L., Anders, K.R., Nogales, E., Schwartz, K., Downing, K.H., Botstein, D. (2000) Structure-Function Relationships in Yeast Tubulins. Mol. Biol. Cell 11: 1887-1903. [PMCID: PMC14891]

Ball, C.A., Dolinski, K., Dwight, S.S., Harris, M.A., Issel-Traver, L., Kasarskis, A., Scafe, C.R., Sherlock, G., Binkley, G., Jin, H., Kaloper, M., Orr, S.D., Schroeder, M., Wend, S., Zhu, Y., Botstein, D., Cherry, J.M. (2000) Integrating Functional Genomic Information into the Saccharomyces Genome Database. Nucleic Acids Res. 28: 77-80. [PMCID: PMC102447]

Ross, D.T., Scherf, U., Eisen, M.B., Perou, C.M., Spellman, P., Iyer, V., Jeffrey, S.S., Van de Rijn, M., Waltham, M., Pergamenschikov, A., Lee, J.C.F., Lashkari, D., Shalon, D., Myers, T.G., Weinstein, J.N., Botstein, D., Brown, P.O. (2000) Systematic variation in gene expression patterns in human cancer cell lines. Nat. Genet 24: 227-235.

Scherf, U., Ross, D.T., Waltham, M., Smith, L.H., Lee, J.K., Kohn, K.W., Reinhold, W.C., Myers, T.G., Andrews, D.T., Scudiero, D.A., Eisen, M.B., Sausville, E.A., Pommier, Y., Botstein, D., Brown, P.O., Weinstein, J.N. (2000) A gene expression database for the molecular pharmacology of cancer. Nat. Genet. 24: 236-244.

Alizadeh, A.A., Eisen, M.B., Davis, R.E., Ma, C., Lossos, I.S., Rosenwald, A., Boldrick, J.C., Sabet, H., Tran, T., Powell, J.I., Yang, L., Marti, G.E., Moore, T., Hudson, J., Lu, L., Lewis, D.B., Tibshirani, R., Sherlock, G., Chan, W.C., Greiner, T.C., Weisenburger, D.D., Armitage, J.O., Warnke, R., Levy, R., Wilson,W., Grever, M.R., Byrd, J.C., Botstein, D., Brown, P.O., Staudt, L.M. (2000) Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403: 503-511.

Perou, C.M., Sorlie, T., Eisen, M.B., van de Rijn, M., Jeffrey, S.S., Rees, C.A., Pollack, J.R., Ross, D.T., Johnzsen, H., Akslen, L.A., Fluge, O., Pergamenschikov, A., Williams, C., Zhu, S.X., Lonning, P.E., Borrensen-Dale, A-L., Brown, P.O., Botstein, D. (2000) Molecular portraits of human breast tumours. Nature 406: 747-752.

Zhu, G., Spellman, P.T., Volpe, T., Brown, P.O., Botstein, D., Davis, T.N., Futcher, B. (2000) Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth. Nature 406: 90-94.

Alter, O., Brown, P.O., Botstein, D. (2000) Singular value decomposition for genome-wide expression data processing and modeling. Proc. Natl. Acad.Sci. USA 97: 10101-6. [PMCID: PMC27718]

Khodursky, A.B., Peter, B.J., Schmid, M.B., DeRisi, J., Botstein, D., Brown, P.O., Cozzarelli, N.R. (2000) Analysis of topoisomerase function in bacterial replication fork movement: Use of DNA microarrays. Proc. Natl. Acad.Sci. USA 97: 9419-9424. [PMCID: PMC16879]

Ranade, K., Hsuing, A.C., Wu, K.D., Chang, M.S., Chen, Y.T., Hebert, J., Chen, Y.I., Olshen, R., Curb, D., Dzau, V., Botstein, D., Cox, D., Risch, N. (2000) Lack of evidence for an association between alpha-adducin and blood pressure regulation in Asian populations. Am. J. Hypertens. 6: 704-709.

Lyons, T.J., Gasch, A.P., Gaither, L.A., Botstein, D., Brown,P.O., Eide, D.J. (2000) Genome-wide characterization of the Zap 1p zinc-responsive regulon in yeast. Proc. Natl. Acad.Sci. USA 97: 7957-7962. [PMCID: PMC16652]

Yun, C.W., Ferea, T., Rashford, J., Ardon, O., Brown, P.O., Botstein, D., Kaplan, J., Philpott, C.C. (2000) Desferrioxamine-mediated Iron Uptake in Saccharomyces cerevisiae. Evidence for two pathways of iron uptake. J. Biol. Chem. 275: 10709-10715.

Friddle, C. Koskela R., Ranade, K., Hebert, J., Cargill, M., Clark, C.D., McInnis, M., Simpson, S, McMahon, F., Stine, O.C., Meyers, D., Xu, J., MacKinnon, D., Swift-Scanlan, T., Jamison, K., Folstein, S., Daly, M., Kruglyak, L., Marr, T., DePaulo, J.R., Botstein, D. (2000) Full-Genome Scan for Linkage in 50 Families Segregating the Bipolar Affective Disease Phenotype. Am. J. Hum. Genet. 66: 205-215. [PMCID: PMC1288327]

Gasch, A.P., Spellman, P.T., Kao, C. M., Carmel-Harel, O., Storz, G., Botstein, D., Brown, P.O. (2000) Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes. Mol. Biol. Cell 11: 4241-57. [PMCID: PMC15070]

Khodursky, A.B., Peter, B.J., Cozzarelli, N.R., Botstein, D., Brown, P.O., Yanofsky, C. (2000). DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli. Proc. Natl. Acad.Sci. USA 97: 9419-24. [PMCID: PMC17313]

Ashburner, M., C. A. Ball, J. A. Blake, D. Botstein, H. Butler, J. M. Cherry, A. P. Davis, K. Dolinski, S. S. Dwight, J. T. Eppig, M. A. Harris, D. P. Hill, L. Issel-Tarver, A. Kasarskis, S. Lewis, J. C. Matese, J. E. Richardson, M. Ringwald, G. M. Rubin, and G. Sherlock (2000). Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25: 25-9.

Diehn, M., M. B. Eisen, D. Botstein, and P. O. Brown (2000). Large-scale identification of secreted and membrane-associated gene products using DNA microarrays. Nat Genet. 25: 58-62.

Hastie, T., R. Tibshirani, M. B. Eisen, A. Alizadeh, R. Levy, L. Staudt, W. C. Chan, D. Botstein, and P. Brown (2000). 'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns. Genome Biol. 1. [PMCID: PMC15015]

Lossos, I. S., A. A. Alizadeh, M. B. Eisen, W. C. Chan, P. O. Brown, D. Botstein, L. M. Staudt, and R. Levy (2000). Ongoing Immunoglobulin Somatic Mutation in Germinal Center B Cell-Like but Not in Activated B Cell-Like Diffuse Large Cell Lymphomas. Proc. Natl. Acad.Sci. USA 97: 10209-13. [PMCID: PMC27813]

Ross, D. T., U. Scherf, M. B. Eisen, C. M. Perou, C. Rees, P. Spellman, V. Iyer, S. S. Jeffrey, M. Van de Rijn, M. Waltham, A. Pergamenschikov, J. C. Lee, D. Lashkari, D. Shalon, T. G. Myers, J. N. Weinstein, D. Botstein, and P. O. Brown (2000). Systematic variation in gene expression patterns in human cancer cell lines. Nat Genet. 24: 227-35.

Alberts, B.M., Ayala, F.J., Botstein, D., Frank, E., Holmes, E.W., Lee, R.D., Macagno, E.R., Marrack, P., Oparil, S., Orkin, S.H., Ribenstein, A.H., Slayman, C.W., Sparling, P.F., Squire, L.R., von Hippel, P.H., Yamamoto, K.R. (2000) Proposed Changes for NIH's Center for Scientific Review. Panel of Scientific Boundaries for Review. Center for Scientific Review Advisory Committee, National Institutes of Health. Science 285: 666-667.

Lee SE, Pellicioli A, Demeter J, Vaze MP, Gasch AP, Malkova A, Brown PO, Botstein D, Stearns T, Foiani M, Haber JE. Arrest, Adaptation, and Recovery following a Chromosome Double-strand Break in Saccharomyces cerevisiae. Cold Spring Harb Symp Quant Biol. (2000);65:303-14. Review. No abstract available. 


Chervitz, S.A., Hester, E.T., Ball, C.A., Dolinski, K., Dwight, S.S., Harris M.A., Juvik, G., Malekian, A., Roberts, S., Roe, T.Y., Scafe, C., Schroeder, M., Sherlock, G., Weng, S., Zhu, Y., Cherry, J.M., Botstein, D. (1999) Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure. Nucleic Acids Res. 27: 74-78. [PMCID: PMC148101]

Mulholland, J., Konopka, J., Singer-Kruger, B., Zerial, M. Botstein, D. (1999) Visualization of Receptor-mediated Endocytosis in Yeast. Mol. Biol. Cell 10: 799-817. [PMCID: PMC25203]

Iyer, V.R., Eisen, M.B., Ross, D.T., Schuler, G., Moore, T., Lee, J.C.F., Trent, J.M., Staudt, L.M., Hudson, J., Boguski, M.S., Lashkari, D., Shalon, D., Botstein, D., Brown, P.O. (1999) The Transcriptional Program in the Response of Human Fibroblasts to Serum. Science 283: 83-87.
Pollack, J.R., Perou, C.M., Alizadeh, A., Eisen, M.B., Pergamenschikov, A., Williams, C.F., Jeffrey, S.S., Botstein, D., Brown, P.O. (1999) Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat. Genet. 23 :41-6.

Ferea, T.L., Botstein, D., Brown, P.O., Rosenzweig, R.F. (1999) Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc. Natl. Acad. Sci. (USA) 96: 9721-9726. [PMCID: PMC22277]

Perou, C.M., Jeffrey, S.S., van de Rijn, M., Rees, C.A., Eisen, M.B., Ross, D.T., Pergamenshikov, A., Williams, C.F., Zhu, S.X., Lee, J.C.F., Lashkari, D., Shalon, D., Brown, P.O., Botstein, D. (1999) Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. Proc. Natl. Acad.Sci. USA 96: 9212-9217. [PMCID: PMC17759]

Brown, P.O., Botstein, D. (1999) Exploring the new world of the genome with DNA microarrays. Nature Genet. 21: 33-37.

Ferea, T., Dunn, B., Botstein, D., Brown, P.O. (1999) Genetic Footprinting and Functional Maps of the yeast Genome. In: PCR Applications: Protocols for Functional Genomics. Michael A. Innis, David H. Gelfand and John J. Sninsky, eds. Academic Press.

Botstein, D. (1999) Of Genes and Genomes. In: Great Issues for Medicine in the Twenty-first Century. Dana Cook Grossman and Heinz Valtin eds. Ann. NY Acad. Sci. 882: 32-41.


Cali, B.M., Doyle, T.C., Botstein, D., Fink, G.R. (1998) Multiple Functions for Actin during Filamentous Growth of Saccharomyces cerevisiae. Mol. Biol. Cell 9: 1873-1889. [PMCID: PMC25429]

Cherry, J.M., Adler, C., Ball, C., Chervitz, S.A., Dwight, S.S., Hester,E.T., Jia, Y., Juvik, G., Roe, T., Schroeder, M., Weng, S., Botstein, D. (1998) SGD: Saccharomyces Genome Database. Nucleic Acids Res. 26: 73-79. [PMCID: PMC147204]

Sekiya-Kawasaki, M., Botstein, D., Ohya, Y. (1998) Identification of Functional Connections Between Calmodulin and the Yeast Actin Cytoskeleton. Genetics 150: 43-58. [PMCID: PMC1460329]

Spellman, P.T., Sherlock, G., Zhang, M.Q., Iyer, V.R., Anders, K., Eisen, M.B., Brown, P.O., Botstein, D., Futcher, B. (1998) Comprehensive Identification of Cell Cycle-regulated Genes of the Yeast Saccharomyces cerevisiae by Microarray Hybridization. Mol. Biol. Cell 9: 3273-3297. [PMCID: PMC25624]

Pitti, R.M., Marsters, S.A., Lawrence, D.A., Roy, M., Kischkel, F., Dowd, P., Huang, A., Donahue, C.J., Sherwood, S.W., Baldwin D., Godowski, P., Wood, W.I., Gurney, A., Hillan, K.J., Cohen, R.L., Goddard, A.D., Botstein, D., Ashkenazi, A. (1998) Genomic amplification of a decoy receptor for Fas ligand in lung and colon cancer. Nature 396: 699-702.

Dolinski, K., Ball, C.A., Chervitz, S.A., Dwight, S.S., Harris, M.A., Roberts, S., Roe, T., Cherry, M., Botstein, D. (1998) Expanding Yeast Knowledge Online. Yeast 14: 1453-1469.

Eisen, M., Spellman, P., Brown, P.O., Botstein, D. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad.Sci. USA 95: 14863-14868. [PMCID: PMC24541]

Chervitz, S.A., Koonin, E.V., Aravind, L., Ball, C.A., Dwight, S.S., Harris, M.A., Dolinski, K., Sherlock, G., Mohr, S., Smith, T., Cherry, J.M., Botstein, D. (1998) Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence. Science 282: 2022-2028.

Chu, S., DeRisi, J., Eisen, M., Mulholland, J., Botstein, D., Brown, P.O., Herskowitz, I. (1998) The Transcriptional Program of Sporulation in Budding Yeast. Science 282: 699-705.

Pennica, D., Swanson, T.A., Welsh, J.W., Roy, M.A., Lawrence, D.A., Lee, J., Brush, J., Taneyhill, L.A.m Deuel, B., Lew, M., Watanabe, C., Cohen, R.L., Melham, M.F., Finley, G.G., Quirke, P., Goddard, A.D., Hillan, K.J., Gurney, A.L., Botstein, D., Levine, A.J. (1998) WISP genes are new members of the connective tissue growth factor family that are up-regulated in Wnt-1 transformed cells and aberrantly expressed in human colon tumors. Proc. Natl. Acad.Sci. USA 95: 14717-14722. [PMCID: PMC24515]

Alizadeh, A., Eisen, M., Botstein, D., Brown, P.O., Staudt, L.M (1998) Probing Lymphocyte Biology by Genomic-Scale Gene Expression Analysis. J. Clin. Immunol. 18: 373-379.


Cherry, J.M., Ball, C., Weng, S., Juvik, G., Schmidt, R., Adler, C., Dunn, B., Dwight, S., Riles, L., Mortimore, R.K., Botstein, D. (1997) Genetic and Physical Maps of Saccharomyces cerevisiae. Nature 387: 67-73.

Amberg, D.C., Zahner, J.E., Mulholland, J.M., Pringle J.R., Botstein, D. (1997) Aip3p/Bud6p, a Yeast Actin-interacting Protein That Is Involved in Morphogenesis and the Selection of Bipolar Budding Sites. Mol. Biol. Cell 8: 729-753. [PMCID: PMC276122]

Mulholland, J.M., Wesp, A., Riezma, H., Botstein, D. (1997) Yeast Actin Cytoskeleton Mutants Accumulate a New Class of Golgi-Derived Secretory Vesicle. Mol. Biol. Cell 8: 1481-1499. [PMCID: PMC276171]

Schwartz, K., Richards, K., Botstein, D. (1997) BIM1 Encodes a Microtubule-binding Protein in Yeast. Mol. Biol. Cell 8: 2677-2691. [PMCID: PMC25736]
Dietrich, F. S., Mulligan, J., Hennessay, K., Yelton, M.A., Allen, E., Araujo, R., Aviles, E., Berno, A., Brennan, T., Carpenter, J., Chen, E., Cherry, J.M., Chung, E., Duncan, M., Guzman, E., Hartzell, G., Hunicke-Smith, S., Hyman, R.W., Kayser, A., Komp, C.., Lashkari, D., Lew, H., Lin, D., Mosedale, D., Nakahara, K., Namath, A., Norgren, R., Oefner, P., Oh, C., Petel, F.X., Roberts, D., Sehl, P., Schramm, S., Shogren, T., Smith, V., Taylor, P., Wei, Y., Botstein, D., Davis, R.W. (1997) The nucleotide sequence of Saccharomyces cerevisiae chromosome V. Nature 387 (Suppl.): 78-81.

Bussey, H., Storms, R.K., Ahmed, A., Albermann, K., Allen, E., Ansorge, W., Aruajo, R., Aparicio, A., Barrell, B., Badcock, K., Benes, V., Botstein, D., Bowman, S., Brückner, M., Carpenter, J., Cherry, J.M., Chung, E., Churcher, C., Coster, F., Davis, K., Davis, R.W., Dietrich, F.S., Delius,H., DiPaolo, T., Dubois, E., Düsterhöft, A., Duncan, M., Floeth, M., Fortin, N., Friesen, J.D., Fritz, C., Goffeau, A., Hall, J., Hebling, U., Heumann, K., Hilbert, H., Hillier, L., and other member sof the Genome Sequencing Center, Hunicke-Smith, S., Hyman, R., Johnston, M., Kalman, S., Kleine, K., Komp, C., Kurdi, O., Lashkari, D., Lew, H., Lin, A., Lin, D., Louis, E.J., Marathe, R., Messenguy, F., Mewes, H.W., Mirtipati, S., Moestl, D., Müller-Auer, S., Namath, A., Nentwich, U., Oefner, P., Pearson, D., Petel, F.X., Pohl, T.M., Purnelle, B., Rajandream, M.A., Rechmann, S., Rieger, M., Riles, L., Roberts, D., Schäfer, M., Scharfe, M., Scherens, B., Schramm, S., Schröder, M., Sdicu, A.M., Tettelin, H., Urrestarazu, L.A., Ushinsky, S., Vierendeels, F., Vissers, S., Voss, H., Walsh, S.V., Wambutt, R., Wang, Y., Wedler, H., Wedler, H., Winnett, E., Zhong, W-W, Zollner, A., Vo, D.H., Hani, J. (1997) The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI. Nature 387 (Suppl.): 103-105.

Jacq C., Alt-Mörbe, J., Andre, B., Arnold, W., Bahr, A., Ballesta, J.P.G., Bargues, M., Baron, L., Becker, A., Biteau, N., Blöcker, H., Blugeon, C., Boskovic, J., Brandt, P., Brückner, M., Buitttrago, M.J., Coster, F., Delaveau, T., del rey, F., Dujon, B., Eide, L.G., Garcia-Cantalejo, J.M., Goffeau, A., Gomez-Peris, A., Granotier, C., Hanemann, V., Hankeln, T., Hoheisel, J.D., Jäger, W., Jimenez, A., Jonniaux, J.-L., Krämer, C., Küster, H., Laamanen, P., Legros, Y., Louis, E., Möller-Rieker, S., Monnet, A., Moro, M., Müller-Auer, S., Nußbaumer, B., Paricio, N., Paulin, L., Perea, J., Perez-Alonso, M., Perez-Ortin, J.E., Pohl, T.M., Prydz, H., Purnelle, B., Rasmussen, S.W., Remacha, M., Revuelta, J.L., Rieger, M., Salom, D., Saluz, H.P., Saiz, J.E., Saren, A.- M., Schäfer, M., Scharfe, M., Schmidt, E.R., Schneider, C., Scholler, P., Schwarz, S., Soler-Mira, A., Urrestarazu, L.A., Verhasselt, P., Vissers, S., Voet, M., Volckaert, G., Wagner, G., Wambutt, R., Wedler, E., Wedler, H., Wölfl, S., Harris, D.E., Bowman, S., Brown, D., Churcher, C.M., Connor, R., Dedman, K., Gentles, S., Hamlin, N., Hunt, S., Jones, L., McDonald, S., Murphy, L., Niblett, D., Odell, C., Oliver, K., Rajandream, M.A., Richards, C., Shore, L., Walsh, S.V., Barrell, B.G., Dietrich, F.S., Mulligan, J., Allen, E., Araujo, R., Aviles, E., Berno, A., Carpenter, J., Chen, E., Cherry, J.M., Chung, E., Duncan, M., Hunicke-Smith, S., Hyman, R., Komp, C., Lashkari, D., Lew, H., Lin, D., Mosedale, D., Nakahara, K., Namath, A., Oefner, P., Oh, C., Petel, F.X., Roberts, D., Schramm, S., Schroeder, M., Shogren, T., Shroff, N., Winant, A., Yelton, M., Botstein, D., Davis, R.W., Johnston, M., Hiller, L., Riles, L. and other members of the Genome Sequencing Center, Albermann, K., Hani, J., Heumann, K., Kleine, K., Mewes, H.W., Zollner, A., Zaccaria, P. (1997) The nucleotide sequence of Saccharomyces cerevisiae chromosome IV. Nature 387 (Suppl.): 75-78.

Botstein, D., Amberg, D., Huffaker, T., Mulholland, J., Adams, A., Drubin, D., Stearns, T. (1997) The Yeast Cytoskeleton. In: Molecular and Cellular Biology of the Yeast Saccharomyces, vol.3. J.R. Broach, J.R. Pringle and E.W. Jones, eds. Cold Spring Harbor Press.

Botstein, D., Cherry, J.M. (1997) Molecular linguistics: Extracting information from gene and protein sequences. Proc. Natl. Acad.Sci. USA 94: 5506-5507. [PMCID: PMC34160]

Botstein, D., Chervitz, S.A., Cherry, J.M. (1997) Yeast as a Model Organism. Science 277: 1259-1260.

Amberg D. C., Botstein, D. (1997) Obtaining Structural Information about Protein Complexes with the Two-Hybrid System. In: The Yeast Two-Hybrid System. Paul L. Bartel and Stanley Fields, eds. Oxford University Press.


Gschwend, M., Levran, O., Kruglyak, L., Ranade, K., Verlander, P.C., Shen, S., Faure, S., Weissenbach, J., Altay, C., Lander, E.S., Auerbach, A.D., Botstein, D. (1996) A Locus for Fanconi Anemia on 16q Determined by Homozygosity Mapping. Am. J. Hum. Genet. 59: 377-384.  [PMCID: PMC1914713]

Doyle, T., Botstein, D. (1996) Movement of yeast cortical actin cytoskeleton visualized in vivo. Proc. Natl. Acad. Sci. USA 93: 3886-3891. [PMCID: PMC39454]

Miller, C.J., Doyle, T.C., Bobkova, E., Botstein, D., Reisler, E. (1996) Mutational Analysis of the Role of Hydrophobic Residues in the 338-348 Helix on Actin in Actomyosin Interactions. Biochemistry 35: 3670-3676.

Smith, V., Chou, K.N., Lashkari, D., Botstein, D., Brown, P.O. (1996) Functional Analysis of the Genes of Yeast Chromosome V by Genetic Footprinting. Science 274: 2069-2074.

Risch, N. and Botstein, D. (1996) A manic depressive history. Nature Genet. 12: 351-353.


Amberg, D., Basart, E., Botstein, D. (1995) Defining protein interactions with yeast actin in vivo. Nat. Struct. Biol. 2: 28-35.

Stine, O.C., Xu, J., Koskela, R., McMahon, F.J., Clark, C.D., Friddle, C., Gschwend, M., Breschel, T., Simpson, S.G., Botstein, D., Marr, T.G., McInnis, M.G., Meyers, D.A., DePaulo, J.R. (1995) Evidence for Linkage of Bipolar Disorder to Chromosome 18 with a Parent-of-Origin Effect. Am. J. Hum. Genet. 57: 1384-1394. [PMCID: PMC1801428]

Smith, V., Botstein, D., Brown, P.O. (1995) Genetic footprinting: A genomic strategy for determining a gene's function given its sequence. Proc. Natl. Acad. Sci. USA 92: 6479-6483. [PMCID: PMC41541]

Amberg, D.C., Beasley, E.M., Botstein, D. (1995) Precise Gene Disruption in Saccharomyces cerevisiae by Double Fusion Polymerase Chain Reaction. Yeast 11: 1275-1280.

Botstein, D. (1995) Structure and Function of the Gene. In: Clinical Oncology. Martin D. Abeloff, James O. Armitage, Allen S. Lichter, John E. Niederhuber, eds. Churchill Livingstone, Inc.


Ohya, Y., Botstein, D. (1994) Diverse Essential Functions Revealed by Complementing Yeast Calmodulin Mutants. Science 263: 963-966.

Clark, C., Palzkill, T., Botstein, D. (1994) Systematic Mutagenesis of the Yeast Mating Pheromone Receptor Third Intracellular Loop. J. Biol. Chem. 269: 8831-8841.

Keyt, B., Paoni, N., Refino, C., Berleau, L, Nguyen, H., Pater, C., Ogez, J., Etcheverry, T., Botstein, D., Bennett, W. (1994) A faster-acting and more potent form of tissue plasminogen activator. Proc. Natl. Acad. Sci. USA 91: 3670-3674. [PMCID: PMC43643]

Ziman, M., Preuss, D., Mulholland, J., O'Brien, J. M. , Botstein, D., Johnson, D. I. (1994) Subcellular Localization of Cdc42p, a Saccharomyces cerevisiae GTP-binding Protein Involved in the Control of Cell Polarity. Mol. Biol. Cell 4: 1307-1316. [PMCID: PMC275766]
Mulholland, J., Preuss, D., Moon, A., Wong, A., Drubin, D., Botstein, D. (1994) Ultrastructure of the Yeast Actin Cytoskeleton and Its Association with the Plasma Membrane. J. Cell Biol. 125: 381-391. [PMCID: PMC2120025]

Palzkill, T., Quyen-Quyen L., Wong, A., Botstein, D. (1994) Selection of Functional Signal Peptide Cleavage Sites from a Library of Random Sequences. J. Bacteriol. 176: 563-568. [PMCID: PMC205091]

Ohya, Y., Botstein, D. (1994) Structure-Based Systematic Isolation of Conditional-Lethal Mutations in the Single Yeast Calmodulin Gene. Genetics 138: 1041-1054. [PMCID: PMC1206246]

Qadota, H., Anraku, Y., Botstein, D., Ohya, Y. (1994) Conditional lethality of a yeast strain expressing human RHOA in place of RHO1. Proc. Natl. Acad. Sci. USA 91: 9317-9321. [PMCID: PMC44803]

Kolling, R., Lee, A., Chen, E.Y., Botstein, D. (1994) Nucleotide Sequence of the SAC2 Gene of Saccharomyces cerevisiae. Yeast 10: 1211-1216.


Kolling, R., Nguyen, T., Chen, E. Y., Botstein, D. (1993) A new yeast gene with a myosin-like heptad repeat stucture. Mol. Gen. Genet. 237: 359-369.

Dunn, B., Stearns, T., Botstein, D. (1993) Specificity domains distinguish the Ras-related GTPases Ypt1 and Sec4. Nature 362: 563-565.

Winey, M., Hoyt, M. A., Chan, C., Goetsch, L., Botstein, D., Byers, B. (1993) NDC1: A Nuclear Periphery Component Required for Yeast Spindle Pole Body Duplication. J. Cell Biol. 122: 743-752. [PMCID: PMC2119589]

Ohya, Y., Qadota, H., Anraku, Y., Pringle, J. R., Botstein, D. (1993) Suppression of Yeast Geranylgeranyl Transferase I Defect by Alternative Prenylation of Two Target GTPases, Rho1p, and Cdc42p. Mol. Biol. Cell 4: 1017-1025. [PMCID: PMC275735]

Chan, C. S. M., Botstein, D. (1993) Isolation and Characterization of Chromosome-Gain and Increase-in-Ploidy Mutants in Yeast. Genetics 135: 667-691. [PMCID: PMC1205712]

Botstein, D. (1993) Genetics in the post-sequence era. Trends in Genetics April, p. 101.
Botstein, D. (1993) A Phage Geneticist Turns to Yeast. In: The Early Days of Yeast Genetics. Michael N. Hall and Patrick Linder, eds. Cold Spring Harbor Laboratory Press, Publishers.


Barnes, G., Louie, K.A. and Botstein, D. (1992). Yeast Proteins Associated with Microtubules In Vitro and In Vivo. Mol. Biol. Cell 3: 29-47. [PMCID: PMC275500]

Kron, S.J., Drubin, D.G., Botstein, D. and Spudich, J.A. (1992). Yeast actin filaments display ATP-dependent sliding movement over surfaces coated with rabbit muscle myosin. Proc. Natl. Acad. Sci. USA 89 4466-4470. [PMCID: PMC49103]

Palzkill, T. and Botstein, D. (1992). Probing  b-Lactamase Structure and Function Using Random Replacement Mutagenesis. Proteins: 14 29-44.

Preuss, D., Mulholland, J., Franzusoff, A., Segev, N., Botstein, D.(1992) Characterization of the Saccharomyces Golgi Complex Through the Cell Cycle by Immunoelectron Microscopy. Mol. Biol. Cell 3 789-803. [PMCID: PMC275635]

Paoni, N.F., Refino, C.J., Brady, K., Pena, L.C., Nguyen, H.V., Kerr, E.M., Johnson, A.C., Wurm, F.M., van Reis, R., Botstein, D. and Bennett, W.F.(1992) Involvement of residues 296-299 in the enzymatic activity of tissue-type plasminogen activator. Protein Eng. 5 259-266.
Wertman, K.F., Drubin, D.G., and Botstein, D. (1992) Systematic Mutational Analysis of the Yeast ACT1 Gene. Genetics 132 337-350. [PMCID: PMC1205140]

Palzkill, T., Botstein, D. (1992) Identification of Amino Acid Substitutions that Alter the Substrate Specificity of TEM-1 b-Lactamase. J. Bacteriol. 174 5237-5243. [PMCID: PMC206357]

Manolson, M.F., Proteau, D., Preston, R.A., Stenbit, A., Roberts, B.T., Hoyt, M.A., Preuss, D., Mulholland, J., Botstein, D., Jones, E.W. (1992) The VPH1 Gene Encodes a 95-kDA Integral Membrane Polypeptide Required for in Vivo Assembly and Activity of the Yeast Vacuolar H+-ATPase. J. Biol. Chem. 267: 14294-303.

Chen, Y, Hennessy, K. M., Botstein, D., Tye, B. (1992) CDC46/MCM5, a yeast protein whose subcellular localization is cell cycle-regulated, is involved in DNA replication at autonomously replicating sequences. Proc. Natl. Acad. Sci. USA 89: 10459-10463. [PMCID: PMC50358]
Botstein, D 1992 Genetics Society of America Medal: Maynard V. Olson. Genetics 131: (supplement) S11-12.


Bennett, W.F., Paoni, N.F., Keyt, B.A., Botstein, D., Jones, A.J.S., Presta, L., Wurm, F.M. and Zoller, M.J. (1991). High Resolution Analysis of Functional Determinants on Human Tissue-type Plasminogen Activator. J. Biol. Chem 266: 5191-5201.

Hennessy, K.M., Lee, A., Chen, E. and Botstein, D. (1991). A group of interacting yeast DNA replication genes. Genes Dev. 5: 958-969.

States, D.J. and Botstein, D. (1991). Molecular sequence accuracy and the analysis of protein coding regions. Proc. Natl. Acad. Sci. USA 88: 5518-5522. [PMCID: PMC51908]

Fröhlich, K.U., Fries, H.W., Rudiger, M., Erdmann, R., Botstein, D. and Mecke, D. (1991). Yeast Cell Cycle Protein CDC48p Shows Full-Length Homology to the Mammalian Protein VCP and is a Member of a Protein Family Involved in Secretion, Peroxisome Formation, and Gene Expression. J. Cell Biol. 114: 443-453. [PMCID: PMC2289087]

Adams, A.E.M., Botstein, D.and Drubin, D.G. (1991). Requirement of yeast fimbrin for actin organization and morphogenesis in vivo. Nature 354: 404-408.

Preuss, D., Mulholland, J., Kaiser, C.A., Orlean, P., Albright, C., Rose, M.D., Robbins, P.W. and Botstein, D. (1991). Structure of the Yeast Endoplasmic Reticulum: Localization of ER proteins using Immunofluorescence and Immunoelectron Microscopy. Yeast 7: 891-911.

Botstein, D. (1991) Why yeast? Hospital Practice (Office Edition) 26: 157-61, 164.

Botstein, D. (1991). Linkage Genetics in Humans: Origins and Prospects. In: Etiology of Human Disease at the DNA Level. Jan Lindsten and Ulf Pettersson, eds. Raven Press, Ltd.

Hennessy, K.M. and Botstein, D. (1991). Regulation of DNA Replication during the Yeast Cell Cycle. Cold Spring Harbor Symp. Quant. Biol. 56: 279-284.

Stearns, T., Ma, H. and Botstein, D. (1991) Manipulating Yeast Genome Using Plasmid Vectors. In: Gene Expression Technology. David V. Goeddel, Editor. Academic Press, Inc. Harcourt Brace Jovanovich, Publishers.


Drubin, D.G., Mulholland, J., Zhu, Z. and Botstein, D. (1990). Homology of a yeast actin-binding protein to signal transduction proteins and myosin-I. Nature 343: 288-290.

Baker, D., Wuestehube, L., Schekman, R., Botstein, D. and Segev, N. (1990). GTP-binding Ypt1 protein and Ca2+ function independently in a cell-free protein transport reaction. Proc. Natl. Acad. Sci. USA 87: 355-359. [PMCID: PMC53262]

Stearns, T., Hoyt, M.A. and Botstein, D. (1990). Yeast Mutants Sensitive to Antimicrotubule Drugs Define Three Genes That Affect Microtubule Function. Genetics 124: 251-262. [PMCID: PMC1203918]

Kaiser, C.A. and Botstein, D. (1990). Efficiency and Diversity of Protein Localization by Random Signal Sequences. Mol. Cell. Biol. 10: 3163-3173.

Stearns, T., Willingham, M.C., Botstein, D. and Kahn, R. (1990). ADP-ribosylation factor is functionally and physically associated with the Golgi complex. Proc. Natl. Acad. Sci. USA 87: 1238-1242. [PMCID: PMC53446]

Hoyt, M.A., Stearns, T. and Botstein, D. (1990). Chromosome Instability Mutants of Saccharomyces cerevisiae That Are Defective in Microtubule-Mediated Processes. Mol. Cell. Biol. 10: 223-234. [PMCID: PMC360730]

Kunes, S., Botstein, D. and Fox, M.S. (1990). Synapsis-Mediated Fusion of Free DNA Ends Forms Inverted Dimer Plasmids in Yeast. Genetics 124: 67-80. [PMCID: PMC1203910]

Hennessy, K.M., Clark, C.D. and Botstein, D. (1990). Subcellular localization of yeast CDC46 varies with the cell cycle. Genes Dev. 4: 2252-2263.

Stearns T., Kahn R.A. Botstein, D. and Hoyt M.A. (1990). ADP Ribosylation Factor is an Essential Protein in Saccharomyces cerevisiae and is Encoded by Two Genes. Mol. Cell. Biol. 10: 6690-6699. [PMCID: PMC362947]

Botstein, D. (1990). 1989 Allen Award Address: The American Society of Human Genetics Annual Meeting, Baltimore. Am. J. Hum. Genet. 47: 887-891. [PMCID: PMC1683888]


Lander, E.S. and Botstein, D. (1989) Mapping Mendelian Factors Underlying Quantitative Traits Using RFLP Linkage Maps. Genetics 121: 185-194. [PMCID: PMC1203601]

Preuss, D. and Botstein, D. (1989) Intragenic Revertants of Yeast Invertase Variants with Secretion-Defective Leader Sequences. Mol. Cell. Biol. 9: 1452-1464. [PMCID: PMC362562]

Novick, P., Osmond, B.C. and Botstein, D. (1989) Suppressors of Yeast Actin Mutations. Genetics 121: 659-674. [PMCID: PMC1203651]

Adams, A.E.M. and Botstein (1989). Dominant Suppressors of Yeast Actin Mutations That Are Reciprocally Suppressed. Genetics 121: 675-683. [PMCID: PMC1203652]

Adams, A.E.M., Botstein, D. and Drubin, D.G. (1989) A Yeast Actin-Binding Protein is Encoded by SAC6, a Gene Found by Suppression of an Actin Mutation. Science 243: 231-233.

Ma, H., Bloom, L.M., Dakin, S.E., Walsh, C.T. and Botstein, D. (1989) The 15 N-Terminal Amino Acids of Hexokinase II Are Not Required for In Vivo Function: Analysis of a Truncated Form of Hexokinase II in Saccharomyces cerevisiae. Proteins 5: 218-223.

Ma, H., Bloom, L.M., Zhu, Z., Walsh, C.T. and Botstein, D. (1989). Isolation and Characterization of Mutations in the HXK2 Gene of Saccharomyces cerevisiae. Mol. Cell. Biol. 9: 5630-5642. [PMCID: PMC363734]

Ma, H., Bloom, L.M., Walsh, C.T. and Botstein, D. (1989). The Residual Enzymatic Phosphorylation Activity of Hexokinase II Mutants is Correlated with Glucose Repression in Saccharomyces cerevisiae. Mol. Cell. Biol. 9: 5643-5649. [PMCID: PMC363735]

Holm, C., Stearns, T. and Botstein, D. (1989) DNA Topoisomerase II Must Act at Mitosis to Prevent Nondisjunction and Chromosome Breakage. Mol. Cell. Biol. 9: 159-168. [PMCID: PMC362157]

Lander, E.S. and Botstein, D. (1989) Accurate and Efficient Mapping of Quantitative Trait Loci in Development and Application of Molecular Markers to Problems in Plant Genetics. In: Plant RFLPs (T. Helentjaris and B. Burr, eds.) Cold Spring Harbor Press, pp. 89-96.

Olson, M., Hood, L., Cantor, C., and Botstein, D. (1989). A Common Language for Physical Mapping of the Human Genome. Science 245: 1434-1435.


Schumm, J.W., Knowlton, R.G., Braman, J.C., Barker, D.F., Botstein, D., Akots, G, Brown, V.A., Gravius, T.C., Helms, C., Hsiao, K. et al. (1988) Identification of More Than 500 RFLPs by Screening Random Genomic Clones. Am. J. Hum. Genet. 42: 143-159. [PMCID: PMC1715337]

Segev, N., Mulholland, J. and Botstein, D. (1988) The Yeast GTP-Binding YPT1 Protein and a Mammalian Counterpart Are Associated with the Secretion Machinery. Cell 52: 915-924.

Stearns, T. and Botstein, D. (1988) Unlinked Noncomplementation: Isolation of New Conditional-Lethal Mutations in Each of the Tubulin Genes of Saccharomyces cerevisiae. Genetics 119: 249-260. [PMCID: PMC1203409]

Daub, E., Zawadzke, L.E., Botstein, D. and Walsh, C.T. (1988) Isolation, Cloning, and Sequencing of the Salmonella typhimurium dd1A Gene with Purification and Characterization of its Product, D-Alanine:D-Alanine Ligase (ADP Forming). Biochemistry 27: 3701-3708.

Huffaker, T.C., Thomas, J.H. and Botstein, D. (1988) Diverse Effects of beta-Tubulin Mutations on Microtubule Formation and Function. J. Cell Biol. 106: 1997-2010. [PMCID: PMC2115142]

Schatz, P.J., Solomon, F. and Botstein, D. (1988) Isolation and Characterization of Conditional-Lethal Mutations in the TUB1 alpha-Tubulin Gene of the Yeast Saccharomyces cerevisiae. Genetics 120: 681-695. [PMCID: PMC1203547]

Drubin, D.G., Miller, K.G. and Botstein, D. (1988). Yeast Actin-binding Proteins: Evidence for a Role in Morphogenesis. J. Cell Biol. 107: 2551-2561.

Botstein, D. and Fink, G. (1988) Yeast: An Experimental Organism for Modern Biology. Science 240: 1439-1443.

Donis-Keller, H. and Botstein, D. (1988) Recombinant DNA Methods: Applications to Human Genetics. Prog. Med. Genet. 7: 17-42.

Drubin, D. and Botstein, D. (1988) Molecular Genetic Analysis of the Yeast Actin Cytoskeleton. Gene Expression and Regulation: The Legacy of Luigi Gorini.

Botstein, D. (1988) Why Study the Cytoskeleton in Yeast? Harvey Lectures.87: 157-167.

Botstein, D., Segev, N., Stearns, T., Hoyt, M.A., Holden, J. and Kahn, R.A. (1988) Diverse Biological Functions of Small GTP-Binding Proteins in Yeast. Cold Spring Harbor Symp. Quant. Biol. 53: 629-636.
Alberts, B.M., Botstein, D., Brenner, S., Cantor, C.R., Doolittle, R.F., Hood, L., McKusick, V.A., Nathans, D., Olson, M.V., Orkin, S., Rosenberg, L.E., Ruddle, F.H., Tilghman, S., Tooze, J., & Watson, J.D. (1988) Report of the Committee on Mapping and Sequencing the Human Genome. Board on Basic Biology, Commission on Life Sciences, National Research Council. National Academy Press, Washington, D.C.


Kunes, S., Ma, H., Overbye, K., Fox, M.S. and Botstein, D. (1987) Fine Structure Recombinational Analysis of Cloned Genes Using Yeast Transformation. Genetics 115: 73-81. [PMCID: PMC1203065]

Thomas, James H. and Botstein, David (1987) Ordered Linear Tetrads Are Produced by the Sporulation of Newly Formed Zygotes of Saccharomyces cerivisiae. Genetics 115: 229-232. [PMCID: PMC1203070]

Kaiser, C.A., Preuss, D., Grisafi, P. and Botstein, D. (1987) Many Random Sequences Functionally Replace the Secretion Signal Sequence of Yeast Invertase. Science 235: 312-317.

Huisman, O., Raymond, W., Froehlich, K., Errada, P., Kleckner, N., Botstein, D. and Hoyt, M.A. (1987) A Tn10-lacZ-kanR-URA3 Gene Fusion Transposon for Insertion Mutagenesis and Fusion Analysis of Yeast and Bacterial Genes. Genetics 116: 191-199. [PMCID: PMC1203129]

Donis-Keller, H., Green, P., Helms, Cartinhour, S., Weiffenbach, B., Stephens, K., Keith, T.P., Bowden, D.W., Smith, D.R., Lander, E.S., Botstein, D., et al. (1987) A Genetic Linkage Map of the Human Genome. Cell 51: 319-337.

Riggs, P.D. and Botstein, D. (1987) Bacteriophage P22 Gene 23 Product Acts Preferentially in cis. J. Virology 61: 2316-2318. [PMCID: PMC283699]

Segev, N. and Botstein, D. (1987) The ras-Like Yeast YPT1 Gene Is Itself Essential for Growth, Sporulation, and Starvation Response. Mol. Cell. Biol. 7: 2367-2377. [PMCID: PMC365368]

Fitts, R., Reuveny, Z., Van Amsterdam, J., Mulholland, J. and Botstein, D. (1987) Substitution of tyrosine for either cysteine in b-lactamase prevents release from the membrane during secretion. Proc. Nat. Acad. Sci. USA 84: 8540-8543. [PMCID: PMC299580]

Rose, M.D., Novick, P., Thomas, J.H., Botstein, D. and Fink, G.R. (1987) A Saccharomyces cerevisiae genomic plasmid bank based on a centromere-containing shuttle vector. Gene 60: 237-243.

Ma, H., Kunes, S., Schatz, P.J. and Botstein, D. (1987) Plasmid construction by homologous recombination in yeast. Gene 58: 201-216.

Schatz, P.J., Georges, G.E.; Solomon, F. and Botstein, D. (1987) Insertions of up to 17 Amino Acids into a Region of a-Tubulin Do Not Disrupt Function In Vivo. Mol. Cell. Biol. 7: 3799-3805. [PMCID: PMC368037]

Riggs, P.D. and Botstein, D. (1987) Fusions of Bacteriophage P22 Late Genes to the Escherichia coli lacZ Gene. J.Virology 61: 3621-3624. [PMCID: PMC255965]

Lander, E.S. and Botstein, D. (1987) Homozygosity Mapping: A Way to Map Human Recessive Traits with the DNA of Inbred Children. Science 236: 1567-1570.

Huffaker, T.C., Hoyt, M.A. and Botstein, D. (1987) Genetic Analysis of the Yeast Cytoskeleton. Ann. Rev. Genet. 21: 259-284.


Thomas, J.H. and Botstein, D. (1986) A Gene Required for the Separation of Chromosomes on the Spindle Apparatus in Yeast. Cell 44: 65-76.

Vergnaud, G., Page, D.C., Simmler, M., Brown, L., Rouyer, F., Noel, B., Botstein, D., de la Chapelle, A. and Weissenbach, J. (1986) A Deletion Map of the Human Y Chromosome Based on DNA Hybridization. Am. J. Hum. Genet. 38: 109-124. [PMCID: PMC1684749]

Holm, C., Wagner, D.W., Fangman, W.L. and Botstein, D. (1986) A rapid, efficient method for isolating DNA from yeast. Gene 42: 169-173.

Kaiser, C. and Botstein, D. (1986) Secretion-Defective Mutations in the Signal Sequence for Saccharomyces cerevisiae Invertase. Mol. Cell. Biol. 6: 2382-2391. [PMCID: PMC367791]

Stachelek, C., Stachelek, J., Swan, J., Botstein, D.and Konigsberg, W. (1986) Identification, cloning and sequence determination of genes specifying hexokinase A and B from yeast. Nucleic Acids Res. 14: 945-963. [PMCID: PMC339475]

Schatz, P.J., Pillus, L., Grisafi, P., Solomon, F. and Botstein, D. (1986) Two Functional a-Tubulin Genes of the Yeast Saccharomyces cerevisiae Encode Divergent Proteins. Mol. Cell. Biol. 6: 3711-3721. [PMCID: PMC367132]

Schatz, P.J., Solomon, F. and Botstein, D. (1986) Genetically Essential and Nonessential a-Tubulin Genes Specify Functionally Interchangeable Proteins. Mol. Cell. Biol. 6: 3722-3733. [PMCID: PMC367133]
Ma, H. and Botstein, D. (1986) Effects of Null Mutations in the Hexokinase Genes of Saccharomyces cerevisiae on Catabolite Repression. Mol. Cell. Biol. 6: 4046-4052. [PMCID: PMC367170]

Wertman, K.F., Wyman, A.R. and Botstein, D. (1986) Host/vector interactions which affect the viability of recombinant phage lambda clones. Gene 49: 253-262.

Galakatos, N.G., Daub, E., Botstein, D. and Walsh, C.T. (1986) Biosynthetic alr Alanine Racemase from Salmonella typhimurium: DNA and Protein Sequence Determination. Biochemistry 25: 3255-3260.

Brissenden, D.C., Page, D.C., de Martinville, J., Trowsdale, J., Botstein, D.and Francke, U. (1986) Regional Assignments of Three Polymorphic DNA Segments on Human Chromosome 15. Genet. Epidemiol. 3: 231-239.

Lander, Eric S. and Botstein, David (1986) Strategies for studying heterogeneous genetic traits in humans by using a linkage map of restriction fragment length polymorphisms. Proc. Nat. Acad. Sci. USA 83: 7353-7357. [PMCID: PMC386715]

Thomas, J.H., Novick, P. and Botstein, D. (1984) Genetics of the Yeast Cytoskeleton. In: Molecular Biology of the Cytoskeleton (G.G. Bomsy, D.W. Cleveland and D.B. Murphy, eds.), Cold Spring Harbor Laboratory Press, New York, pp. 153-174. Also republished (1986) as Genetics of the Yeast Cytoskeleton. Yeast Cell Biology (J. Hicks, ed.), Alan R. Liss, New York, pp. 13-44.

Botstein, D. (1986) The Molecular Biology of Color Vision. Science 232: 142-143.

Lander, E. and Botstein, D. (1986) Mapping Complex Genetic Traits in Humans: New Methods Using A Complete RFLP Linkage Map. Cold Spring Harbor Laboratory Symp. Quant. Biol. 51: 49-62.

Lander, E. and Botstein, D. (1986) Consanguinity and Heterogeneity: Cystic Fibrosis Need Not be Homogeneous in Italy. Am. J. Hum. Genet. 39: 282-283. [PMCID: PMC1683934]


Kunes, S., Botstein, D. and Fox, M.S. (1985) Transformation of Yeast With Linearized Plasmid DNA: Formation of Inverted Dimers and Recombinant Plasmid Products. J.Mol.Biol. 184: 375-387.

Wyman, A.R., Wolfe, L. and Botstein, D. (1985) Propagation of some human DNA sequences in bacteriophage l vectors requires mutant Escherichia coli hosts. Proc. Natl. Acad. Sci. USA 82: 2880-2884. [PMCID: PMC397670]

Novick, P. and Botstein, D. (1985) Phenotypic Analysis of Temperature-Sensitive Yeast Actin Mutants. Cell 40: 405-416.

Holm, C., Goto, T., Wang, J.C. and Botstein, D. (1985) DNA Topoisomerase II Is Required at the Time of Mitosis in Yeast. Cell 41: 553-563.

Thomas, J.H., Neff, N. and Botstein, D. (1985) Isolation and Characterization of Mutations in the b-Tubulin Gene of Saccharomyces cerevisiae. Genetics 112: 715-734. [PMCID: PMC1202667]

Botstein, D. (1985) Considerations Affecting the Feasibility of Mapping a Single-Gene Disorder Using Restriction Fragment Polymorphisms, With Special Reference to Ataxia Telangiectasia. Ataxia-Telangiectasia, pp. 125-131.

Botstein, D. and Shortle, D. (1985) Strategies and Applications of in Vitro Mutagenesis. Science 229:4719, 1193-1201.

Botstein, D. (1985) Mapping the Human Genome Using Restriction Fragment Length Polymorphisms. Genetics and the Law, pp. 97-105.


Carlson, M., Osmond, B.C., Neigeborn, L. and Botstein, D. (1984) A Suppressor of SNF1 Mutations Causes Constitutive High-Level Invertase Synthesis in Yeast. Genetics 107: 19-32. [PMCID: PMC1202312]

Maurer, R., Osmond, B.C., Shekhtman, E., Wong, A. and Botstein, D. (1984) Functional Interchangeability of DNA Replication Genes in Salmonella typhimurium and Escherichia coli Demonstrated by a General Complementation Procedure. Genetics 108: 1-23. [PMCID: PMC1202388]

Maurer, R., Osmond, B.C. and Botstein, D. (1984) Genetic Analysis of DNA Replication in Bacteria: DNAB mutants that suppress DNAC Mutations and DNAQ Mutations That Suppress DNAE Mutations in Salmonella typhimurium. Genetics 108: 25-38. [PMCID: PMC1202398]

Rose, M., Grisafi, P. and Botstein, D. (1984) Structure and function of the yeast URA3 gene: expression in Escherichia coli. Gene 29: 113-124.

Shortle, D., Novick, P. and Botstein, D. (1984) Construction and genetic characterization of temperature-sensitive mutant alleles of the yeast actin gene. Proc. Natl. Acad. Sci. USA 81: 4889-4893. [PMCID: PMC391597]

Page, D.C., Harper, M.E., Love, J. and Botstein, D. (1984) Occurrence of a transposition from the X-chromosome long arm to the Y-chromosome short arm during human evolution. Nature 311: 119-123.

Wasserman, S., Daub, E., Grisafi, P., Botstein, D. and Walsh, C. (1984) Catabolic Alanine Racemase from Salmonella typhimurium: DNA Sequence, Enzyme Purification, and Characterization. Biochemistry 23: 5182-5187.

Novick, P., Thomas, J.H. and Botstein, D. (1984) Genetic Analysis of Cytoskeletal Protein Function in Yeast. In Genetic Engineering, Principles and Methods, Vol. 6, (A. Hollaender and J.K. Setlow, eds.), pp. 211-231.

Botstein, D. and Donis-Keller, H. (1984) A Molecular Approach to Defining the Inherited Components in Epilepsy and Other Diseases of Uncertain Etiology. Epilepsia 25 (suppl. 2): S150-S155.

Kunes, S., Botstein, D. and Fox, M.S. (1984) Formation of Inverted Dimer Plasmids After Transformation of Yeast With Linearized Plasmid DNA. Cold Spring Harbor Symp. Quant. Biology 49: 617-628.


Wasserman, S.Z., Walsh, C.T. and Botstein, D. (1983) Two Alanine Racemase Genes in Salmonella typhimurium That Differ in Structure and Function. J. Bacteriol. 153: 1439-1450.
Carlson, M. and Botstein, D. (1983) Organization of the SUC Gene Family in Saccharomyces. Mol. Cell. Biol. 3: 351-359.

Carlson, M., Taussig, R., Kustu, S. and Botstein, D. (1983) The Secreted Form of Invertase in Saccharomyces cerevisiae is Synthesized From mRNA Encoding a Signal Sequence. Mol. Cell. Biol. 3: 439-447.

Neff, N., Thomas, J. and Botstein, D. (1983) Isolation of the b-tubulin Gene From Yeast and Demonstration of its Essential Function in vivo. Cell 33: 211-219.

Falco, C., Rose, M. and Botstein, D. (1983) Homologous Recombination Between Episomal Plasmids and Chromosomes in Yeast. Genetics 105: 843-856.

Falco, C. and Botstein, D. (1983) A Rapid Chromosome Mapping Method for Cloned Fragments of Yeast DNA. Genetics 105: 857-872.

Rose, M. and Botstein, D. (1983) Structure and Function of the Yeast URA3 Gene: Differentially Regulated Expression of Hybrid b-Galactosidase From Overlapping Coding Sequences in Yeast. J. Mol. Biol. 170: 883-904.

Shortle, D. and Botstein, D. (1983) Directed Mutagenesis With Sodium Bisulfite. Meth.Enzymol. 100: 457-468.

Rose, M. and Botstein, D. (1983) Construction and Use of Gene Fusions to lacZ (b-galactosidase) Which Are Expressed in Yeast. Meth.Enzymol. 101: 167-180.

Campbell, A. and Botstein, D. (1983) Evolution of the Lambdoid Phages. In Lambda II (R.W. Hendrix, J.W. Roberts, F.W. Stahl and R.A. Weisberg, eds.), Cold Spring Harbor Laboratory Press, N.Y., pp. 365-380.

Page, D., Wyman, A. and Botstein, D. (1983) Homologous Single-Copy Sequences on the Human X and Y Chromosomes. In Banbury Report 14: Recombinant DNA Applications to Human Disease. Cold Spring Harbor Laboratory Press, N.Y., pp. 267-273.


Carlson, M. and Botstein, D. (1982) Two Differentially Regulated mRNAs with Different 5' Ends Encode Secreted and Intracellular Forms of Yeast Invertase. Cell 28: 145-154.

Moir, D., Stewart, S.E., Osmond, B.C. and Botstein, D. (1982) Cold-Sensitive Cell-Division-Cycle Mutants of Yeast: Isolation, Properties and Pseudoreversion Studies. Genetics 100: 565-577.

Moir, D. and Botstein, D. (1982) Determination of the Order of Gene Function in Yeast Nuclear Division Pathway Using cs and ts Mutants. Genetics 100: 547-563.

Shortle, D., Grisafi, P., Benkovic, S.J. and Botstein, D. (1982) Gap Misrepair Mutagenesis: Efficient Site-Directed Induction of Transition, Transversion and Frameshift Mutations in vitro. Proc. Natl. Acad. Sci. USA 79: 1588-1592.

Falco, S.C., Li, Y., Broach, J.R. and Botstein, D. (1982) Genetic Properties of Chromosomally Integrated 2m Plasmid DNA in Yeast. Cell 29: 573-584.

Shortle, D., Haber, J.E. and Botstein, D. (1982) Lethal Disruption of the Yeast Actin Gene by Integrative DNA Transformation. Science 217: 371-373.

Koshland, D. and Botstein, D. (1982) Evidence for Post-Translational Translocation of b-lactamase Across the Bacterial Inner Membrane. Cell 30: 893-902.

Koshland, D., Sauer, R.T. and Botstein, D. (1982) Diverse Effects of Mutations in the Signal Sequence on the Secretion of b-lactamase in Salmonella typhimurium. Cell 30: 903-914.

Page, D., de Martinville, B., Barker, D., Wyman, A., White, R., Francke, U. and Botstein, D. (1982) Single-Copy Sequence Hybridizes to Polymorphic and Homologous Loci on the Human X and Y Chromosomes. Proc. Natl. Acad. Sci.USA 79: 5352-5357.

Silverman, S., Rose, M., Botstein, D. and Fink, G.R. (1982) Regulation of a HIS4-lacZ Fusions in Saccharomyces cerevisiae. Mol. Cell. Biol. 2: 1212-1219.

Ibe, S.N., Sinskey, A.J. and Botstein, D. (1982) Genetic Mapping of Mutations in a Highly Radiation-Resistant Mutant of Salmonella typhimurium LT2. J. Bacteriol. 152: 260-268.

Macaluso, A., Midthun, K., Bender, R.A. and Botstein, D. (1982) Nonsense Suppressor Mutants of Bacteriophage T5. Virology 117: 275-279. 
Botstein, D. and Davis, R.W. (1982) Principles and Practice of Recombinant DNA Research With Yeast. In Molecular Genetics of Yeast Saccharomyces: Metabolism and Gene Expression (E.W. Jones, J. Broach and J.N. Strathern, eds.), Cold Spring Harbor Laboratory Press, N.Y., pp. 607-636.

Botstein, D., Shortle, D. and Rose, M. (1982) Making Mutations in vitro and Putting Them Back Into Yeast. In From Gene to Protein: Translation into Biotechnology (F. Ahmad, J. Schultz, E.E. Smith and W.J. Whelan, eds.), Academic Press, N.Y., pp. 265-274.

Botstein, D. and Maurer, R. (1982) Genetic Approaches to the Analysis of Microbial Development. Ann.Rev.Genetics 16: 61-83.

Botstein, D., Shortle, D. and Rose, M. (1982) Making and Using Mutations in Cloned Genes. In Perspectives on Genes and the Molecular Biology of Cancer (D.L. Robberson and G.F. Saunders, eds.), Raven Press, pp. 81-90.


Winston, F. and Botstein, D. (1981) Control of Lysogenization by Phage P22. I. The P22 cro Gene. J. Mol. Biol. 152: 209-232.

Winston, F. and Botstein, D. (1981) Control of Lysogenization by Phage P22. II. Mutations (clyA) in the c1 Gene that Cause Increased Lysogenization. J. Mol. Biol. 152: 233-245.

Rose, M., Casadaban, M.J. and Botstein, D. (1981) Yeast Genes Fused to b-galactosidase in Escherichia coli can be Expressed Normally in Yeast. Proc. Natl. Acad. Sci. USA 78: 2460-2464.

Carlson, M., Osmond, B.C. and Botstein, D. (1981) Mutants of Yeast Defective in Sucrose Utilization. Genetics 98: 25-40.

Carlson, M., Osmond, B.C. and Botstein, D. (1981) Genetic Evidence for a Silent SUC Gene in Yeast. Genetics 98: 41-54.

Carlson, M., Osmond, B. and Botstein, D. (1981) The SUC Genes of Yeast: A Dispersed Gene Family. Cold Spring Harbor Symp. Quant. Biol. 45: 799-803.

Lacroute, F., Bach, M.L., Chevallier, M.R., Hubert, J.C., Losson, R., Botstein, D. and Loison, D. (1981) Transcriptional Regulation of the Yeast Pyrimidine Genes. In Molecular Genetics of Yeast (D. von Wettstein, J. Friis, M. Kielland-Brandt and A. Stenderup, eds.), Alfred Benzon Symposium 16, Munksgaard, Copenhagen.

Shortle, D. and Botstein, D. (1981) Single-Stranded Gaps as Localized Targets For in vitro Mutagenesis. In Molecular and Cellular Mechanisms of Mutagenesis (J.F. Lemontt and W.M. Generos, eds.), Plenum Press, N.Y., pp. 147-156.

Maurer, R., Osmond, B.C. and Botstein, D. (1981) Genetic Analysis of DNA Replication in Salmonella typhimurium. ICN-UCLA Symp. Mol.Cell.Biol. 21: 375-386.


Botstein, D., White, R.L., Skolnick, M. and Davis, R.W. (1980) Construction of a Genetic Linkage Map in Man Using Restriction Fragment Length Polymorphisms. Am. J. Hum. Genet. 32: 314-331. 

Botstein, D. (1980) A Theory of Modular Evolution for Bacteriophages. Ann. N.Y. Acad. Sci. 354: 484-491. 

Weinstock, G.M., Riggs, P.D. and Botstein, D. (1980) Genetics of Bacteriophage P22. III. The Late Operon. Virology 106: 82-91.

Weinstock, G.M. and Botstein, D. (1980) Genetics of Bacteriophage P22. IV. Correlation of Genetic and Physical Map Using Translocatable Drug-Resistance Elements. Virology 106: 92-99.

Koshland, D. and Botstein, D. (1980) Secretion of Beta-Lactamase Requires the Carboxyl End of the Protein. Cell 20: 749-760.

O'Brien, T.F., Ross, D.G., Guzman, M.A., Medeiros, A.A., Hedges, R.W. and Botstein, D. (1980) Dissemination of an Antibiotic Resistance Plasmid in Hospital Patient Flora. Antimicrob. Agents Chemother. 17: 537-543.

Susskind, M.M. and Botstein, D. (1980) Superinfection Exclusion by lambda Prophage in Lysogens of Salmonella typhimurium. Virology 100: 212-216.

Botstein, D. (1980) A Modular Theory of Virus Evolution. ICN-UCLA Symp. Mol.Cell.Biol. 18: 11-20.


Bach, M.L., Lacroute, F. and Botstein, D. (1979) Evidence for Transcriptional Regulation of Orotidine-5'-Phospate-Decarboxylase in Yeast by Hybridization mRNA to the Yeast by Structural Gene Cloned in Escherichia coli. Proc. Natl. Acad. Sci. USA 76: 386-390.

Kleckner, R., Reichart, K. and Botstein, D. (1979) Inversions and Deletions of Salmonella Chromosome Generated by the Translocatable Tetracycline-Resistance Element Tn10. J. Mol. Biol. 127: 89-115.

Winston, F., Botstein, D. and Miller, J.H. (1979) Characterization of Amber and Ochre Suppressors in Salmonella typhimurium. J. Bacteriol. 137: 433-439.

Kleckner, N., Steele, D.A., Reichardt, K. and Botstein, D. (1979) Specificity of Insertion by the Translocatable Tetracycline Resistance Element Tn10. Genetics 92: 1023-1040.

Poteete, A.R., Jarvik, V. and Botstein, D. (1979) Encapsulation of Phage P22 DNA in vitro. Virology 95: 550-564.

Poteete, A.R. and Botstein, D. (1979) Purification and Properties of Proteins Essential to DNA Encapsulation by Phage P22. Virology 95: 565-573.

Botstein, D. and Poteete, A.R. (1979) Formation of P22 Generalized Transducing Particles in vitro. Virology 95: 574-576.

Weinstock, G.M., Susskind, M.M. and Botstein, D. (1979) Regional Specificity of Illegitimate Recombination by the Translocatable Ampicillin-Resistance Element Tn1 in the Genome of Phage P22. Genetics 92: 685-710.

Botstein, D., Falco, S.C., Stewart, S., Brennan, M., Scherer, S., Stinchcomb, D.T., Struhl, K. and Davis, R. (1979) Sterile Host Yeasts (SHY): A Eukaryotic System of Biological Containment for Recombinant DNA Experiments. Gene 8: 17-24.

Ross, D.G., Grisafi, P., Kleckner, N. and Botstein, D. (1979) The Ends of Tn10 Are Not IS3. J. Bacteriol. 139: 1097-1101.

Weinstock, G.M. and Botstein, D. (1979) Regional Specificity of Illegitimate Recombination Associated With the Translocatable Ampicillin-Resistance Element Tn1. Cold Spring Harbor Symp. Quant. Biol. 43: 1209-1215.

Moir, D., Stewart, S.E. and Botstein, D. (1979) Analysis of Yeast Cell-Cycle Mutations by Pseudo-Reversion. ICN-UCLA Symp. Mol.Cell.Biol. 14: 85-93.

Campbell, A., Starlinger, P., Berg, D.E., Botstein, D., Lederberg, E.M., Novick, R.P. and Szybalski, W. (1979) Nomenclature of Transposable Elements in Prokaryotes. Plasmid 2: 466-473; Gene 5: 197-206.


Kleckner, N., Barker, D.F., Ross, D.G., Botstein, D., Swan, J.A. and Zabeau, M. (1978) Properties of the Translocatable Tetracycline-Resistance Element Tn10 in Escherichia coli and Bacteriophage Lambda. Genetics 90: 427-467.

Susskind, M.M. and Botstein, D. (1978) Repression and Immunity in Salmonella Phages P22 and L: Phage L Lacks a Functional Secondary Immunity System. Virology 89: 618-622.

Petes, T.D., Broach, J.R., Wensink, P.C., Hereford, L.M., Fink, G.R. and Botstein, D. (1978) Isolation and Analysis of Recombinant DNA Molecules Containing Yeast DNA. Gene 4: 37-49.

Susskind, M.M. and Botstein, D. (1978) The Molecular Genetics of Bacteriophage P22. Microbiol. Rev. 42: 385-413.


Kleckner, N., Roth, J. and Botstein, D. (1977) Genetic Engineering in vivo Using Translocatable Drug-Resistance Elements: New Methods in Bacterial Genetics. J. Mol. Biol. 116: 125-159.

Petes, T.D. and Botstein, D. (1977) Simple Mendelian Inheritance of the Reiterated Ribosomal DNA of Yeast. Proc. Natl. Acad. Sci. USA 74: 5091-5095.

Botstein, D. and Kleckner, N. (1977) Translocation and Illegitimate Recombination by the Tetracycline Resistance Element Tn10. In DNA Insertion Elements, Plasmids and Episomes (S. Adhya, A. Bukhari and J. Shapiro, eds.), Cold Spring Harbor Laboratory Press, N.Y., pp. 185-203.

King, J., Botstein, D., Casjens, S., Earnshaw, W., Harrison, S. and Lenk, E. (1977) Structure and Assembly of the Capsid of Bacteriophage P22. Phil. Trans. R. Soc. Lond. B. 276: 37-49.
Petes, T.D., Hereford, L.M. and Botstein, D. (1977) Simple Mendelian Inheritance of the Repeating Yeast Ribosomal RNA Genes. Cold Spring Harbor Symp. Quant. Biol. 42: 1201-1207.

Campbell, A., Berg, D., Botstein, D., Lederberg, E., Novick, R., Starlinger, P. and Szybalski, W. (1977) Nomenclature of Transposable Elements in Prokaryotes. In DNA Insertion Elements, Plasmids and Episomes (S. Adhya, A. Bukhari and J. Shapiro, eds.), Cold Spring Harbor Laboratory Press, N.Y., pp. 15-22.

Petes, D., Hereford, L.M. and Botstein, D. (1977) Organization of Yeast Ribosomal DNA. ICN-UCLA Symp. Mol. Cell Biol. 8: 239-246.


Brandriss, M.C., Stewart, J.W., Sherman, F. and Botstein, D. (1976) Substitution of Serine Caused by a Recessive Lethal Suppressor in Yeast. J. Mol. Biol. 102: 467-476.

Gesteland, R.F., Wolfner, M., Grisafi, P., Fink, G., Botstein, D. and Roth, J.R. (1976) Yeast Suppressors of UAA and UAG Nonsense Codons Work Efficiently in vitro Via tRNA. Cell 7: 381-390.

Hilliker, S. and Botstein, D. (1976) Specificity of Genetic Elements Controlling Regulation of Early Functions in Temperate Bacteriophages. J. Mol. Biol 106: 537-566.

Chan, R.K. and Botstein, D. (1976) Specialized Transduction by Bacteriophage P22 in Salmonella typhimurium: Genetic and Physical Structure of the Transducing Genomes and the Prophage Attachment Site. Genetics 83: 433-458.


Botstein, D., Lew, K.K., Jarvik, V.M. and Swanson, C.A., Jr. (1975) Role of Antirepressor in the Bipartite Control of Repression and Immunity by Bacteriophage P22. J. Mol. Biol. 91: 439-462.

Jarvik, J. and Botstein, D. (1975) Conditional-Lethal Mutations That Suppress Genetic Defects in Morphogenesis by Altering Structural Proteins. Proc. Natl. Acad. Sci. USA 72: 2738-2742.

Kleckner, N., Chan, R.K., Tye, B.K. and Botstein, D. (1975) Mutagenesis by Insertion of a Drug-Resistance Element Carrying an Inverted Repetition. J. Mol. Biol. 97: 561-575.

Susskind, M.M. and Botstein, D. (1975) Mechanism of Action of Salmonella Phage P22 Antirepressor. J. Mol. Biol. 98: 413-424.

Hilliker, S. and Botstein, D. (1975) An Early Regulatory Gene of Salmonella Phage P22 Analogous to Gene N of Coliphage Lambda. Virology 68: 510-524.

Brandriss, M.C., Soll, L. and Botstein, D. (1975) Recessive Lethal Amber Suppressor in Yeast. Genetics 79: 551-560.

Roberts, J.W., Roberts, C.W., Hilliker, S. and Botstein, D. (1975) Transcription Termination and Regulation in Bacteriophage P22 and Lambda. In RNA Polymerase (M. Chamberline and R. Losick, eds.), Cold Spring Harbor Laboratory Press, N.Y., pp. 707-718.


Tye, B.K., Chan, R.K. and Botstein, D. (1974) Packaging of an Oversize Transducing Genome by Salmonella Phage P22. J. Mol. Biol. 85: 485-500.

Tye, B.K., Huberman, J.A. and Botstein, D. (1974) Non-random Circular Permutation of Phage P22 DNA. J. Mol. Biol. 85: 501-527.

Young, I.T., Levinstone, D., Eden, M., Tye, B.K. and Botstein, D. (1974) Appendix: Alignment of Partial Denaturation Maps of Circularly Permuted DNA by Computer. J. Mol. Biol. 85: 528-532.

Botstein, D. and Herskowitz, I. (1974) Properties of Hybrids Between the Salmonella Phage P22 and Coliphage Lambda. Nature 251: 584-589.

Susskind, M.M., Botstein, D. and Wright, A. (1974) Superinfection Exclusion by P22 Prophage in Lysogens of Salmonella typhimurium. III. Failure of Superinfecting Phage DNA to Enter sieA+ Lysogens. Virology 62: 350-366.

Susskind, M.M., Wright A. and Botstein, D. (1974) Superinfection Exclusion by P22 Prophage in Lysogens of Salmonella typhimurium. IV. Genetics and Physiology of sieB Exclusion. Virology 62: 367-384.
Tye, B.K. and Botstein, D. (1974) P22 Morphogenesis II. Mechanisms of DNA Encapsulation. J. Supramolecular Structure 2: 225-238.9.

Botstein, D. and Susskind, M.M. (1974) Regulation of Lysogeny and the Evolution of Temperate Bacterial Viruses. From Mechanisms of Virus Disease (W.S. Robinson & C.F. Fox, eds.) W.A. Benjamin, Inc. pp. 363-384


Davies, R., Sinskey, A.J. and Botstein, D. (1973) Deoxyribonucleic Acid Repair in a Highly Radiation-Resistant Strain of Salmonella typhimurium. J. Bacteriol. 114: 357-366.

Jarvik, J. and Botstein, D. (1973) A Genetic Method for Determining the Order of Events in a Biological Pathway. Proc. Natl. Acad. Sci. USA 70: 2046-2050.

Botstein, D., Waddell, C.H. and King, J.A. (1973) Mechanism of Head Assembly and DNA Encapsulation in Salmonella Phage P22. I. Genes, Proteins, Structures, and DNA Maturation. J. Mol. Biol. 80: 669-695.

King, J.A., Lenk, E.H. and Botstein, D. (1973) Mechanism of Head Assembly and DNA Encapsulation in Salmonella Phage P22. II. Morphogenetic Pathway. J. Mol. Biol. 80: 697-731.


Chan, R.K. and Botstein, D. (1972) Genetics of Bacteriophage P22. I. Isolation of Prophage Deletions Which Affect Immunity to Superinfection. Virology 49: 257-267.

Botstein, D., Chan, R.K. and Waddell, C.H. (1972) Genetics of Bacteriophage P22. II. Gene Order and Gene Function. Virology 49: 268-282.

Ebel-Tsipis, J., Botstein, D. and Fox, M.S. (1972) Generalized Transduction by Phage P22 in Salmonella typhimurium. I. The Molecular Origin of Transducing DNA. J. Mol. Biol. 71: 433-448.

Ebel-Tsipis, J., Fox, M.S. and Botstein, D. (1972) Generalized Transduction by Phage P22 in Salmonella typhimurium. II. Mechanisms of Integration of Transducing DNA. J. Mol. Biol. 71: 449-469.

Watanabe, T., Ogata, Y., Chan, R.K. and Botstein, D. (1972) Specialized Transduction of Tetracycline Resistance by Phage P22 in Salmonella typhimurium. I. Transduction of R Factor 222 by P22. Virology 50: 874-882.

Chan, R.K., Botstein, D., Watanabe, T. and Ogata, Y. (1972) Specialized Transduction of Tetracycline Resistance by Phage P22 in Salmonella typhimurium. II. Properties of a High-Frequency Transducing Lysate. Virology 50: 883-898.


Ebel-Tsipis, J. and Botstein, D. (1971) Superinfection Exclusion by P22 Prophage in Lysogens of Salmonella typhimurium I. Exclusion of Generalized Transducing Particles. Virology 45: 629-652.

Susskind, M., Wright, A. and Botstein, D. (1971) Superinfection Exclusion by P22 Prophage in Lysogens of Salmonella typhimurium. II. Genetic Evidence for Two Exclusion Systems. Virology 45: 629-637.


Botstein, D. and Matz, M.J. (1970) A Recombination Function Essential to the Growth of Bacteriophage P22. J. Mol. Biol. 54: 417-440


Botstein, D. and Jones, E.W.(1969) Nonrandom Mutagenesis of the E. coli Genome by Nitrosoguanidine. J. Bacteriol. 98: 847-848.


Botstein, D. (1968) Synthesis and Maturation of Phage P22 DNA. I. Identification of Intermediates. J. Mol. Biol. 34: 621-643.

Botstein, D. and Levine, M. (1968) Synthesis and Maturation of Phage P22 DNA. II. Properties of Temperature-Sensitive Phage Mutants Defective in DNA Metabolism. J. Mol. Biol. 34: 643-654.

Botstein, D. and Levine, M. (1968) Intermediates in the Synthesis of Phage P22 DNA. Cold Spring Harbor Symp. Quant. Biol. 33: 659-667.


Botstein, D. (1967) Sedimentation Analysis of Replicating Phage P22 DNA. Bacteriol.Proc. 161.