Publications related to SLAM

2007

Pan X, Yuan DS, Ooi SL, Wang X, Sookhai-Mahadeo S, Meluh P, Boeke JD (2007)
dSLAM analysis of genome-wide genetic interactions in Saccharomyces cerevisiae. Methods 41:206-221

2006

Yuan DS, Irizarry RA (2006)
High-resolution spatial normalization for microarrays containing embedded technical replicates. Bioinformatics 22:3054-3060.

Pan X, Ye P, Yuan DS, Wang X, Bader JS, Boeke JD (2006)
A DNA integrity network in the yeast Saccharomyces cerevisiae. Cell 24:1069-1081.

Ooi SL, Pan X, Peyser BD, Ye P, Meluh PB, Yuan DS, Irizarry RA, Bader JS, Spencer FA, Boeke JD (2006)
Global synthetic-lethality analysis and yeast functional profiling. Trends Genet 22:56-63.

2005

Ye P, Peyser BP, Pan X, Boeke JD, Spencer FA, Bader JS (2005)
Gene function prediction from congruent synthetic lethal interactions in yeast. Molecular Systems Biology 1:E1 - E12.

Qi Y, Ye P, Bader JS (2005)
Genetic Interaction Motif Finding by Expectation Maximization -- a novel statistical framework for inferring gene modules from synthetic lethality. BMC Bioinformatics 6:288.

Ye P, Peyser BD, Spencer FA, Bader JS (2005)
Commensurate distances and similar motifs in genetic congruence and protein interaction networks in yeast. BMC Bioinformatics 6:270.

Peyser BD, Irizarry RA, Tiffany CW, Chen O, Yuan DS, Boeke JD, Spencer FA (2005)
Improved statistical analysis of budding yeast TAG microarrays revealed by defined spike-in pools. Nucleic Acids Res 33:e140.

Yuan DS, Pan X, Ooi SL, Peyser BD, Spencer FA, Irizarry RA, Boeke JD (2005)
Improved microarray methods for profiling the yeast knockout strain collection. Nucleic Acids Res 33:e103.

Irizarry RA, Warren D, Spencer F, Kim IF, Biswal S, et al. (2005)
Multiple-laboratory comparison of microarray platforms.Nat Methods 2:345-350.

2004

Warren CD, Eckley DM, Lee MS, Hanna JS, Hughes A, Peyser B, Jie C, Irizarry R, Spencer FA (2004)
S-phase checkpoint genes safeguard high-fidelity sister chromatid cohesion. Mol Biol Cell 15:1724-1735.

Lee MS, Spencer FA (2004)
Bipolar orientation of chromosomes in Saccharomyces cerevisiae is monitored by Mad1 and Mad2, but not by Mad3. Proc Natl Acad Sci U S A 101:10655-10660.

Arevalo-Rodriguez M, Pan X, Boeke JD, Heitman J (2004)
FKBP12 controls aspartate pathway flux in Saccharomyces cerevisiae to prevent toxic intermediate accumulation. Eukaryot Cell 3:1287-1296.

Pan X, Yuan DS, Xiang D, Wang X, Sookhai-Mahadeo S, Bader JS, Hieter P, Spencer F, Boeke JD (2004)
A robust toolkit for functional profiling of the yeast genome. Mol Cell 16:487-496.

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, et al. (2004)
Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5:R80.

Wu Z, Irizarry RA, Gentleman R, Martinez-Murillo F, Spencer F (2004)
A model based background adjustment for oligonucleotide expression arrays. J Amer Stat Assoc 99:909-917.

Earliest papers

Ooi SL, Shoemaker DD, Boeke JD (2003)
DNA helicase gene interaction network defined using synthetic lethality analyzed by microarray. Nat Genet 35:277-286.

Irizarry R, Ooi SL, Wu Z, Boeke JD (2003)
Use of mixture models in a microarray-based screening procedure for detecting differentially represented yeast mutants. Statist App Genet Mol Biol 2:1-17.

Giaever G et al. (2002)
Functional profiling of the Saccharomyces cerevisiae genome. Nature 418:387-391.

Ooi SL, Shoemaker DD, Boeke JD (2001)
A DNA microarray-based genetic screen for nonhomologous end-joining mutants in Saccharomyces cerevisiae. Science 294:2552-2556.

Submitted manuscripts

Wu Z, Irizarry, RA (2006)
A Statistical Framework for the Analysis of Microarray Probe-Level Data (submitted).