STANFORD UNIVERSITY STANFORD UNIVERSITY SCHOOL OF MEDICINE DEPARTMENT OF BIOCHEMISTRY
         
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Selected Publications

In this Section
Selected Publications
Patents & Inventions
2011

Wallace IM, Urbanus ML, Luciani GM, Burns AR, Han MKL, Wang H, Arora K, Heisler LE, Proctor M, St Onge RP, Roemer T, Roy PJ, Cummins CL, Bader GD, Nislow C, Giaever G. Compound Prioritization Methods Increase Rates of Chemical Probe Discovery in Model Organisms. Chemistry & Biology, Volume 18, Issue 10, 1273-1283, 28 October 2011. [Article]

Smith AM, Durbic T, Oh J, Urbanus M, Proctor M, Heisler LE, Giaever G, Nislow C. Competitive Genomic Screens of Barcoded Yeast Libraries. Vis Exp. 2011 Aug 11;(54). pii: 2864. doi: 10.3791/2864. [PubMed], [Video]

Proctor M, Urbanus ML, Fung EL, Jaramillo DF, Davis RW, Nislow C, Giaever G. The Automated Cell: Compound and Environment Screening System (ACCESS) for Chemogenomic Screening. Methods Mol Biol. 2011;759:239-69. [PubMed]

2010

Fabrizio P, Hoon S, Shamalnasab M, Galbani A, Wei M, Giaever G, Nislow C, Longo VD. Genome-wide screen in Saccharomyces cerevisiae identifies vacuolar protein sorting, autophagy, biosynthetic, and tRNA methylation genes involved in life span regulation. PLoS Genet 6, e1001024 (2010). [PubMed]

Smith AM, Ammar R, Nislow C, Giaever G. A survey of yeast genomic assays for drug and target discovery. Pharmacol Ther 127, 156 (Aug, 2010). [PubMed]

Burns AR, Wallace IM, Wildenhain J, Tyers M, Giaever G, Bader GD, Nislow C, Cutler SR, Roy PJ. A predictive model for drug bioaccumulation and bioactivity in Caenorhabditis elegans. Nature chemical biology 6, 549 (Jul, 2010). [PubMed]

Oh J, Fung E, Price MN, Dehal PS, Davis RW, Giaever G, Nislow C, Arkin AP, Deutschbauer A. A universal TagModule collection for parallel genetic analysis of microorganisms. Nucleic Acids Res 38, e146 (Aug, 2010). [PubMed]

Smith AM, Heisler LE, St Onge RP, Farias-Hesson E, Wallace IM, Bodeau J, Harris AN, Perry KM, Giaever G, Pourmand N, Nislow C. Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples. Nucleic Acids Res 38, e142 (Jul, 2010). [PubMed]

Dowell RD, Ryan O, Jansen A, Cheung D, Agarwala S, Danford T, Bernstein DA, Rolfe PA, Heisler LE, Chin B, Nislow C, Giaever G, Phillips PC, Fink GR, Gifford DK, Boone C. Genotype to phenotype: a complex problem. Science 328, 469 (Apr 23, 2010). [PubMed]

Hillenmeyer ME, Ericson E, Davis RW, Nislow C, Koller D, Giaever G. Systematic analysis of genome-wide fitness data in yeast reveals novel gene function and drug action. Genome Biol 11(3), R30 (2010). Epub 2010/03/17. [PubMed]

Chan JN, Nislow C, Emili A. Recent advances and method development for drug target identification. Trends Pharmacol Sci. 2010 Feb;31(2):82-8. Epub 2009 Dec 7. [PubMed]

Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, Koh JL, Toufighi K, Mostafavi S, Prinz J, St Onge RP, VanderSluis B, Makhnevych T, Vizeacoumar FJ, Alizadeh S, Bahr S, Brost RL, Chen Y, Cokol M, Deshpande R, Li Z, Lin ZY, Liang W, Marback M, Paw J, San Luis BJ, Shuteriqi E, Tong AH, van Dyk N, Wallace IM, Whitney JA, Weirauch MT, Zhong G, Zhu H, Houry WA, Brudno M, Ragibizadeh S, Papp B, Pál C, Roth FP, Giaever G, Nislow C, Troyanskaya OG, Bussey H, Bader GD, Gingras AC, Morris QD, Kim PM, Kaiser CA, Myers CL, Andrews BJ, Boone C. The genetic landscape of a cell. Science. 2010 Jan 22;327(5964):425-31. [PubMed]

Vizeacoumar FJ, van Dyk NS, Vizeacoumar F, Cheung V, Li J, Sydorskyy Y, Case N, Li Z, Datti A, Nislow C, Raught B, Zhang Z, Frey B, Bloom K, Boone C, Andrews BJ. Integrating high-throughput genetic interaction mapping and high-content screening to explore yeast spindle morphogenesis. J Cell Biol. 2010 Jan 11;188(1):69-81. [PubMed]

2009

Costanzo M, Baryshnikova A, Nislow C, Andrews B, Boone C. You too can play with an edge. Nat Methods. 2009 Nov;6(11):797-8 [PubMed]

Fillingham J, Kainth P, Lambert JP, van Bakel H, Tsui K, Peña-Castillo L, Nislow C, Figeys D, Hughes TR, Greenblatt J, Andrews BJ. Two-color cell array screen reveals interdependent roles for histone chaperones and a chromatin boundary regulator in histone gene repression. Mol Cell. 2009 Aug 14;35(3):340-51. [PubMed]

Yan Z, Berbenetz NM, Giaever G, and Nislow C. Precise gene-dose alleles for chemical genetics. Genetics. (2009) 182 623-6. PMCID:2691769. [PubMed]

Smith AM, Heisler LE, Mellor J, Kaper F, Thompson MJ, Chee M, Roth FP, Giaever G, and Nislow C. Quantitative phenotyping via deep barcode sequencing. Genome Res. (2009) 19 1836-42. PMCID:2765281. [PubMed]

Juneau K, Nislow C, Davis RW. Alternative splicing of PTC7 in Saccharomyces cerevisiae determines protein localization. Genetics. 2009 Sep;183(1):185-94. Epub 2009 Jun 29. [PubMed]

Pierce SE, Davis RW, Nislow C, and Giaever G. Chemogenomic approaches to elucidation of gene function and genetic pathways. Methods Mol Biol. (2009) 548 115-43. [PubMed]

Nislow C. Biotechniques. Self-reporting cells. 2009 Apr;46(5):356-7. Review. [PubMed]

Kemmer D, McHardy LM, Hoon S, Reberioux D, Giaever G, Nislow C, Roskelley CD, and Roberge M. Combining chemical genomics screens in yeast to reveal spectrum of effects of chemical inhibition of sphingolipid biosynthesis. BMC Microbiol. (2009) 9 9. PMCID:2632640. [PubMed]

Jo WJ, Kim JH, Oh E, Jaramillo D, Holman P, Loguinov AV, Arkin AP, Nislow C, Giaever G, and Vulpe CD. Novel insights into iron metabolism by integrating deletome and transcriptome analysis in an iron deficiency model of the yeast Saccharomyces cerevisiae. BMC Genomics. (2009) 10 130. PMCID:2669097. [PubMed]

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, and Boone C. A molecular barcoded yeast ORF library enables mode-of-action analysis of bioactive compounds. Nat Biotechnol. (2009) 27 369-77. [PubMed]

Hess DC, Myers CL, Huttenhower C, Hibbs MA, Hayes AP, Paw J, Clore JJ, Mendoza RM, Luis BS, Nislow C, Giaever G, Costanzo M, Troyanskaya OG, and Caudy AA. Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis. PLoS Genet. (2009) 5 e1000407. PMCID:2648979. [PubMed]

Giaever G, and Nislow C. Knocking sense into regulatory pathways. Nat Biotechnol. (2009) 27 149-50.

Ammar R, Smith AM, Heisler LE, Giaever G, and Nislow C. A comparative analysis of DNA barcode microarray feature size. BMC Genomics. (2009) 10 471. PMCID:2765990. [PubMed]

2008

Badis G, Chan ET, van Bakel H, Pena-Castillo L, Tillo D, Tsui K, Carlson CD, Gossett AJ, Hasinoff MJ, Warren CL, Gebbia M, Talukder S, Yang A, Mnaimneh S, Terterov D, Coburn D, Li Yeo A, Yeo ZX, Clarke ND, Lieb JD, Ansari AZ, Nislow C, Hughes TR.. A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol Cell. 2008 Dec 26;32(6):878-87. [PubMed]

Yu L, Lopez A, Anaflous A, El Bali B, Hamal A, Ericson E, Heisler LE, McQuibban A, Giaever G, Nislow C, Boone C, Brown GW, Bellaoui M. Chemical-genetic profiling of imidazo[1,2-a]pyridines and -pyrimidines reveals target pathways conserved between yeast and human cells. PLoS Genet. 2008 Nov;4(11):e1000284. Epub 2008 Nov 28. PMID: 19043571 [PubMed]

Yan Z, Costanzo M, Heisler LE, Paw J, Kaper F, Andrews BJ, Boone C, Giaever G. and Nislow C. Yeast Barcoders: a chemogenomic application of a universal donor-strain collection carrying bar-code identifiers. Nat Methods. (2008) 5 719-25. [PubMed]

Musso G, Costanzo M, Huangfu M, Smith AM, Paw J, San Luis BJ, Boone C, Giaever G, Nislow C, Emili A, and Zhang Z. The extensive and condition-dependent nature of epistasis among whole-genome duplicates in yeast. Genome Res. (2008) 18 1092-9. PMCID:2493398. [PubMed]

Mani R, St Onge RP, Hartman JL, Giaever G, and Roth FP. Defining genetic interaction. Proc Natl Acad Sci U S A. (2008) 105 3461-6. PMCID:2265146. [PubMed]

Lopez A, Parsons AB, Nislow C, Giaever G, and Boone C. Chemical-genetic approaches for exploring the mode of action of natural products. Prog Drug Res. (2008) 66 237, 239-71. [PubMed]

Lehar J, Stockwell BR, Giaever G, and Nislow C. Combination chemical genetics. Nat Chem Biol. (2008) 4 674-81. [PubMed]

Jo WJ, Loguinov A, Chang M, Wintz H, Nislow C, Arkin AP, Giaever G, and Vulpe CD. Identification of genes involved in the toxic response of Saccharomyces cerevisiae against iron and copper overload by parallel analysis of deletion mutants. Toxicol Sci. (2008) 101 140-51. [PubMed]

Hoon S, St Onge RP, Giaever G, Nislow C. Yeast chemical genomics and drug discovery: an update. Trends Pharmacol Sci. 2008 Aug 26. [Epub ahead of print]. [PubMed]

Hoon S, Smith AM, Wallace IM, Suresh S, Miranda M, Fung E, Proctor M, Shokat KM, Zhang C, Davis RW, Giaever G, St Onge RP, Nislow C. An integrated platform of genomic assays reveals small-molecule bioactivities. Nat Chem Biol. 2008 Aug;4(8):498-506. Epub 2008 Jul 11. PMID: 18622389 [PubMed]

Ericson E, Gebbia M, Heisler LE, Wildenhain J, Tyers M, Giaever G, Nislow C. Off-target effects of psychoactive drugs revealed by genome-wide assays in yeast. PLoS Genet. 2008 Aug 8;4(8):e1000151. PMID: 18688276 [PubMed]

Hillenmeyer ME, Fung E, Wildenhain J, Pierce SE, Hoon S, Lee W, Proctor M, St Onge RP, Tyers M, Koller D, Altman RB, Davis RW, Nislow C, Giaever G. The Chemical Genomic Portrait of Yeast: Uncovering a Phenotype for All Genes. Science 18 April 2008: Vol. 320. no. 5874, pp. 362 - 365 [Web supplement]

Arnoldo A, Curak J, Kittanakom S, Chevelev I, Lee VT, Sahebol-Amri M, Koscik B, Ljuma L, Roy PJ, Bedalov A, Giaever G, Nislow C, Merrill AR, Lory S, Stagljar I. Identification of small molecule inhibitors of Pseudomonas aeruginosa exoenzyme S using a yeast phenotypic screen. PLoS Genet. 2008 Feb 29;4(2):e1000005. Erratum in: PLoS Genet. 2008 Apr;4(4). PMID: 18454192 [PubMed]

Nislow C, and Giaever G. Chemical Genomic Tools for Understanding Gene Function and Drug Action. Methods in Microbiology (in press).

2007

Suter B, Fetchko MJ, Imhof R, Graham CI, Stoffel-Studer I, Zbinden C, Raghavan M, Lopez L, Beneti L, Hort J, Fillingham J, Greenblatt JF, Giaever G, Nislow C, and Stagljar I. Examining protein–protein interactions using endogenously tagged yeast arrays: The Cross-and-Capture system. Genome Res. 2007 December; 17(12): 1774–1782. doi: 10.1101/gr.6667007. PMCID: PMC2099586 [PubMed]

Gassner NC, Tamble CM, Bock JE, Cotton N, White KN, Tenney K, St Onge RP, Proctor MJ, Giaever G, Nislow C, Davis RW, Crews P, Holman TR, Lokey RS. Accelerating the discovery of biologically active small molecules using a high-throughput yeast halo assay. J Nat Prod 70(3):383-90 (2007). [PubMed]

Lee W, Tillo D, Bray N, Morse RH, Davis RW, Hughes TR, Nislow C. A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet. 2007 Oct;39(10):1235-44. Epub 2007 Sep 16. [PubMed]

St Onge RP, Mani R, Oh J, Proctor M, Fung E, Davis RW, Nislow C, Roth FP, Giaever G. Systematic pathway analysis using high-resolution fitness profiling of combinatorial gene deletions. Nat Genet 39(2): 199-206 (2007) (Subject of Highlight in Nat Rev Genet 8: 87 (2007). [Publisher Full Text]

2006

Juneau K, Miranda M, Hillenmeyer ME, Nislow C, Davis RW. Introns regulate RNA and protein abundance in yeast. Genetics. 2006 Sep;174(1):511-8. Epub 2006 Jul 2. [PubMed]

Pierce SE, Fung EL, Jaramillo DF, Chu AM, Davis RW, Nislow C, Giaever, G. A unique and universal molecular barcode array. Nat Methods, 2006 Aug;3(8):601-3. [PubMed]

2005

Lee W, St Onge RP, Proctor M, Flaherty P, Jordan MI, Arkin AP, Davis RW, Nislow C, Giaever G. Genome-Wide Requirements for Resistance to Functionally Distinct DNA-Damaging Agents. PLoS Genet. 2005 Aug 19;1(2):e24 [Epub][PubMed], [Web supplement]

Flaherty P, Giaever G, Kumm J, Jordan MI, Arkin AP. A latent variable model for chemogenomic profiling. Bioinformatics. 2005 Aug 1;21(15):3286-93. Epub 2005 May 26. [PubMed], [Publisher Full Text]

Wall DP, Hirsh AE, Fraser HB, Kumm J, Giaever G, Eisen MB, Feldman MV. Functional genomic analysis of the rates of protein evolution. Proc Natl Acad Sci U S A. 2005 Apr 12;102(15):5483-8. Epub 2005 Mar 30. [PubMed], [Publisher Full Text]

Deutschbauer AM, Jaramillo DF, Proctor M, Kumm J, Hillenmeyer ME, Davis RW, Giaever G. Mechanisms of haploinsufficiency revealed by genome-wide profiling in yeast. Genetics. 2005 Apr;169(4):1915-25. Epub 2005 Feb 16. [Web supplement], [Epub]

2004

Fraser HB, Hirsh AE, Giaever G, Kumm J, and Eisen M. Noise Minimization in Eukaryotic Gene Expression. PLOS Biology 2(6):E137. Epub Apr 27 (2004). [Publisher Full Text]

Giaever G, Flaherty P, Kumm J, Proctor M, Nislow C, Jaramillo DF, Chu AM, Jordan MI, Arkin AP, Davis RW. Chemogenomic profiling: identifying the functional interactions of small molecules in yeast. Proc Natl Acad Sci 101(22):793-8 (2004). Subject of review: Hughes T., Andrews B., Boone C.  Old drugs, new tricks: using genetically sensitized yeast to reveal drug targets.  Cell 116(1):5-7 (2004). [Publisher Full Text]

Giaever G. A chemical genomics approach to understanding drug action. Trends Pharmacol Sci. 24(9):444-6 (2003). [PubMed]

2003

Nislow C, and Giaever G. "Chemogenomics: tools for protein families" and "Chemical genomics: chemical and biological integration" Pharmacogenomics. Jan;4(1):15-8 (2003). [PubMed]

2002

Giaever G, Chu AM, Ni L, Connelly C, Riles L, Véronneau S, Dow S, Lucau-Danila A, Anderson K, André B, Arkin AP, Astromoff A, El-Bakkoury M, Bangham R, Benito R, Brachat S, Campanaro S, Curtiss M, Davis K, Deutschbauer A, Entian KD, Flaherty P, Foury F, Garfinkel DJ, Gerstein M, Gotte D, Güldener U, Hegemann JH, Hempel S, Herman Z, Jaramillo DF, Kelly DE, Kelly SL, Kötter P, LaBonte D, Lamb DC, Lan N, Liang H, Liao H, Liu L, Luo C, Lussier M, Mao R, Menard P, Ooi SL, Revuelta JL, Roberts CJ, Rose M, Ross-Macdonald P, Scherens B, Schimmack G, Shafer B, Shoemaker DD, Sookhai-Mahadeo S, Storms RK, Strathern JN, Valle G, Voet M, Volckaert G, Wang CY, Ward TR, Wilhelmy J, Winzeler EA, Yang Y, Yen G, Youngman E, Yu K, Bussey H, Boeke JD, Snyder M, Philippsen P, Davis RW, Johnston M. Functional profiling of the Saccharomyces cerevisiae genomeNature 418(6896):387-91 (2002). [Web supplement]

Steinmetz LM, Scharfe C, Deutschbauer AM, Mokranjac D, Herman ZS, Jones T, Chu AM, Giaever G, Prokisch H, Oefner PJ, Davis RW. Systematic screen for human disease genes in yeast. Nat Genet. 31(4):400-4 (2002). [PubMed]

Birrell GW, Brown JA, Wu HI, Giaever G, Chu AM, Davis RW, Brown JM. Transcriptional response of Saccharomyces cerevisiae to DNA-damaging agents does not identify the genes that protect against these agents. Proc Natl Acad Sci 99(13):8778-83 (2002). [Publisher Full Text]

2001

Birell GW, Giaever G, Chu A, Davis RW, and Brown JM. A genome-wide screen in Sacharromyces cerevisiae for genes affecting UV radiation sensitivity. Proc. Natl. Acad. Sci. 98 (22): 12608-12613 (2001). [Publisher Full Text]

1999

Giaever G, Shoemaker DD, Jones TW, Liang H, Winzeler E, Astromoff A, and Davis RW. Genomic profiling of drug sensitivities via induced haploinsufficiencyNature Genetics 21: 278-283 (1999) (Subject of News & Views by Stephen Oliver, same issue). [PubMed]

Winzeler E. et al. Functional characterization of the Saccharomyces cerevisiae genome by comprehensive and precise gene deletion and massively parallel analysis. Science 285: 901-906 (1999).

Patents

Giaever G. and Davis RW. (2004) Identification of drugs and drug targets by detection of the stress response. US Patent # 6,743,583.

Giaever G, Shoemaker DD, and Davis RW. (2000) Highly parallel and sensitive method for identifying drugs and drug targets. US Patent #6,046,002

Nislow C, and Wong K. (2004) Aspergillus Fumigatus Profilin. Patent US Patent #6,743,897.

Finney M, et al. (2004) Electrophoresis Assembly and Method of Casting Electrophoresis Gels. US Patent #6, 682,641.

Nislow C, Sakowicz R, and Beraud C. (2003) Antifungal Assay. US Patent #6,627,408.

Nislow C, Sakowicz R, and Beraud C. (2002) Antifungal Assay. US Patent #6,468,760.

Nislow C, and Wong K. (2002) Aspergillus Fumigatus Cofilin. US Patent #6,458,930.

Nislow C, and Wong K. (2002) Aspergillus Fumigatus Profilin. US Patent #6,403,372.

Nislow C, Sakowicz R, and Beraud C. (2001) Antifungal Assay. US Patent #6,284,480.

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