Former Fellows’ Publications

Dion MF; Kaplan T, Kim M, Buratowski S, Friedman N, Rando OJ. Dynamics of replication-independent histone turnover in budding yeast. Science. 2007 Mar 9;315(5817):1405-8.

Hegreness, M., Shoresh, N., Hartl, D. & Kishony, R. An equivalence principle for the incorporation of favorable mutations in asexual populations. Science 311, 1615-1617 (2006). (PDF)

Yeh, P., Tschumi, A. & Kishony, R. Functional classification of drugs by properties of their pairwise interactions. Nature Genetics 38, 489-494 (2006). (PDF)

Biondi, E., Skerker, J. M., Ariv, M., Prasol, M., Perchuk, B. & Laub, M. A phosphorelay system controls stalk biogenesis during cell cycle progression in Caulobacter crescentus. Molec. Microbiol. 59, 386-401 (2006). (PDF)

Liu, C., Kaplan, T., Kim, M., Buratowski, S., Schreiber, S. L., Friedman, N. & Rando, O. J. Single-nucleosome mapping of histone modifications in S. cerevisiae. PLOS Biol. 3, e328 (2005). (PDF)

Skerker, J., Prasol, M., Perchuk, B., Biondi, E. & Laub, M. Two-component signal transduction pathways regulating growth and cell cycle progression in a bacterium: a system-level analysis. PLOS Biol. 3, e334 (2005). (PDF)

Aubin-Horth, N., Landry, C., Letcher, B. & Hofmann, H. Alternative life histories shape brain gene expression profiles in males of the same population. Proc. R. Soc. B. 272, 1655-1662 (2005). (PDF)

Segrè, D., DeLuna, A., Church, G. M. & Kishony, R. Modular epistasis in yeast metabolism. Nature Genetics 37, 77-83 (2005). (PDF)

Casolari, J., Brown, C., Drubin, D., Rando, O. & Silver, P. Developmentally induced changes in transcriptional program alter spatial organization across chromosomes. Genes & Development 19, 1188-1198 (2005). (PDF)

Segal, E., Friedman, N., Kaminski, N., Regev, A. & Koller, D. From signatures to models: understanding cancer using microarrays. Nature Genetics 37, S38-S45 (2005). (PDF)

Yuan, G. C., Liu, Y.-J., Dion, M. F., Slack, M. D., Wu, L. F., Altschuler, S. J. & Rando, O. J. Genome-scale identification of nucleosome positions in S. cerevisiae. Science 309, 626-630 (2005). (PDF)

Tanay, A., Regev, A. & Shamir, R. Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast. PNAS 102, 7203-7208 (2005). (PDF)

Dion, M., Altschuler, S., Wu, L. & Rando, O. J. Genomic characterization reveals a simple histone H4 acetylation code. PNAS 102, 5501-5506 (2005). (PDF)

Segal, E., Pe'er, D., Regev, A., Koller, D. & Friedman, N. Learning module networks. J. Machine Learning Res. 6, 557-588 (2005). (PDF)

Aubin-Horth, N., Letcher, B. H. & Hofmann, H. A. Interaction of rearing environment and reproductive tactic on gene expression profiles in Atlantic salmon. J. Hered. 96, 261-278 (2005). (PDF)

Renn, S. C. P., Aubin-Horth, N. & Hofmann, H. A. Biologically meaningful expression profiling across species using heterologous hybridization to a cDNA microarray. BMC Genomics 5,
10.1186/1471-2164-5-42 (2004). (PDF)

Perlman, Z. E., Slack, M. D., Feng, Y., Mitchison, T. J., Wu, L. F. & Altschuler, S. J. Multidimensional drug profiling by automated microscopy. Science 306, 1194-1198 (2004). (PDF)

Sheff, M. A. & Thorn, K. S. Optimized cassettes for fluorescent protein tagging in Saccharomyces cerevisiae. Yeast 21, 661-670 (2004). (PDF)

Wedlich-Soldner, R., Altschuler, S., Wu, L. & Li, R. Spontaneous cell polarization through actomyosin-based delivery of the Cdc42 GTPase. Science 299, 1231-1235 (2003).

Townsend, J., Cavalieri, D. & Hartl, D. Population genetic variation in genome-wide gene expression Mol. Biol. Evol. 20, 955-963 (2003).

Hofmann, H. A. Functional genomics of neural and behavioral plasticity. J Neurobiol 54, 272-282 (2003). (PDF)

Segal, E., Friedman, N., Koller, D. & Regev, A. A module map showing conditional activity of expression modules in cancer. Nature Genetics 36, 1090-1098 (2004). (PDF)

Marion, R. M., Regev, A., Segal, E., Barash, Y., Koller, D., Friedman, N. & O'Shea, E. K. Sfp1 is a stress- and nutrient-sensitive regulator of ribosomal protein gene expression. PNAS 101, 14315-14322 (2004). (PDF)

Nachman, I., Regev, A. & Friedman, N. Inferring quantitative models of regulatory networks from expression data. Bioinformatics 20 (Suppl. 1), i248-i256 (2004). (PDF)

Segal, E., Shapira, M., Regev, A., Pe'er, D., Botstein, D., Koller, D. & Friedman, N. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nature Genetics 10.1038/ng1165 (2003). (PDF)

Jacobs, C., Ausmees, N., Cordwell, S. J., Shapiro, L. & Laub, M. T. Functions of the CckA histidine kinase in Caulobacter cell cycle control. Molec. Microbiol. 47, 1279-1290 (2003).

Rando, O. J., Chi, T. H. & Crabtree, G. R. Second messenger control of chromatin remodeling. Nature Struct. Biol. 10, 81-83 (2003).

Laub, M. T., Chen, S. L., Shapiro, L. & McAdams, H. H. Genes directly controlled by CtrA, a master regulator of the Caulobacter cell cycle. PNAS 99, 4632-4637 (2002).

Pe'er, D., Regev, A. & Tanay, A. Minreg: inferring an active regulator set. Bioinformatics 18, S258-S267 (2002)

Wu, L. F. et al. Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters. Nature Genetics 31, 255-265 (2002).

Grosu, P., Townsend, J. P., Hartl, D. L. & Cavalieri, D. Pathway Processor: a tool for integrating whole-genome expression results into metabolic networks. Genome Research 12, 1121-1126 (2002).

Ball, C. A. et al. (including Cavalieri, D.) Standards for microarray data. Science 18, 298 (2002). See also http://www.mged.org/Workgroups/MIAME/miame_checklist.html.

MacBeath, G. Protein microarrays and proteomics. Nature Genetics 32, 526-532 (2002).

MacBeath, G. Proteomics comes to the surface. Nature Biotechnol. 19, 828-829 (2001).

MacBeath, G. & Schreiber, S. L. Printing proteins as microarrays for high-throughput function determination. Science 289, 1760-1763 (2000).