Publications

CMB Publications (by project leader)

Yaakov Benenson

Rinaudo, K., Bleris, L., Maddamsetti, R., Subramanian, S., Weiss, R. & Benenson, Y. A universal RNAi-based logic evaluator that operates in mammalian cells. Nature Biotechnology, vol.25. 795-801. (2007)

Andrew Murray

Leu, J.-Y. & Murray, A. W. Experimental evolution of mating discrimination in budding yeast. Current Biol. 16, 280-286 (2006).

Thompson, D.A., Desai, M.M., and Murray, A.W. Ploidy Controls the Success of Mutators and Nature of Mutations During Budding Yeast Evolution. Curr. Biol., 16, 1581-1590. (2006)

Segre, A., Murray, A.W., and Leu, J-Y. High-Resolution Mutation Mapping Reveals Parallel Experimental Evolution in Yeast, PLoS Biology, 4, 1372-1385. (2006)

Desai, M.M., Fisher, D.S., and Murray, A.W. The Speed of Evolution and Maintenance of Variation in Asexual Populations. Curr. Biol. 17, 385-94. (2007)

Ingolia, N. and Murray, A.W. Positive Feedback Loops as a Flexible Biological Module. Curr Biol. 17, 668-667. (2007)

Michael Elowitz

Suel GM, Kulkarni RP, Dworkin J, Garcia-Ojalvo J, Elowitz M.B., “Tunability and noise dependence in differentiation dynamics” Science. 23;315(5819):1716-9. (2007)

Kevin Verstrepen

Saerens, S., Verstrepen, K. et al. The Saccharomyces cerevisiae EHT1 and EEB1 genes encode novel enzymes with medium-chain fatty acid ethyl ester synthesis and hydrolysis capacity. J. Biol. Chem. 281, 4446-4456 (2006).

Verstrepen, K. J. & Klis, F. M. Flocculation, adhesion and biofilm formation in yeasts. Molec. Microbiol. 60, 5-15 (2006).

Rando, O.J. and Verstrepen K.J. Timescales of genetic and epigenetic inheritance. Cell, 128: 655-668. (2007)

Legendre, M., Pochet, N., Pak, T. and Verstrepen, K.J. Sequence-based estimation of minisatellite and microsatellite repeat variability. Genome Res. (in press).

Sharad Ramanathan

McClean, M.N., Mody, A., Broach, J.R., Ramanathan, S. March 2007; Cross-talk and decision making in MAP kinase pathways. Nat Genet. 2007 Mar; 39 (3):409-14

Kevin Foster

Xavier, J.B., and Foster, K.R. Cooperation and conflict in microbial biofilms. Proceedings of the National Academy of Sciences, 104: 876-881.(2007)

Foster, K.R., Parkinson, K. and Thompson, C. R. L. What can microbial genetics teach sociobiology? Trends in Genetics, 2007 Feb; 23 (2): 74-80.(2007)

Aviv Regev

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

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]

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]

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., Kaushal, A., Yelensky, R., Pham, T., Regev, A., Koller, D. & Friedman, N. GeneXPress: a visualization and statistical analysis tool for gene expression and sequence data. Proc. 12th Intl Conf. on Intelligent Systems for Molecular Biology (2004). [PDF]

Grad, Y. H., Roth, F. P., Halfon, M. S. & Church, G. M. Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D. pseudoobscura. Bioinformatics 20, 2738-2750 (2004). [PDF]

Lee, S.-I., Pe’er, D., Dudley, A. M., Church, G. M. & Koller, D. Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification.Proc Natl Acad Sci U S A. 2006 Sep 19;103(38):14062-7. Epub 2006.

Wapinski, I. , Pfeffer, A., Friedman,N. and Regev, A. Natural history and evolutionary principles of gene duplication in fungi. Nature. 449: 54-64. doi:10.1038/nature06107 (2007)

Wright, M. A., Kharchenko, P., Church, G. M. & Segrè, D. Chromosomal periodicity of evolutionarily conserved gene pairs. Proc Natl Acad Sci U S A. 2007 Jun 19;104(25):10559-64. (2007)

Daniel Fisher

Ingolia, N.T. Topology and robustness in the Drosophila segment polarity network. PloS Biol. 2, 0805-0815 (2004). [PDF]

Burbank, K. S., Groen, A. C., Perlman, Z. E., Fisher, D. S. & Mitchison, T. J. A new method reveals microtubule minus ends throughout the meiotic spindle. J Cell Biol. 6;175(3):369-75. (2006)

Burbank K.S., Mitchison T.J., Fisher D.S. Slide-and-Cluster models for spindle assembly". Curr Biol. 17, 1373-1383, (2007)

Kurt Thorn

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

Michael Laub

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

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

Biondi, E. G., Reisinger, S. J., Skerker, J. M., Arif, M., Perchuk, B. S., Ryan, K. & Laub, M. T. Regulation of the bacterial cell cycle by an integrated genetic circuit. Nature. 14;444(7121):899-904. (2006)

Oliver Rando

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]

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).

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

Raisner, R. M., Hartley, P. D., Meneghini, M. D., Bao, M. Z., Liu, C. L., Schreiber, S. L., Rando, O. J. & Madhani, H. D. Histone variant H2A.Z marks the 5' ends of both active and inactive genes in euchromatin. Cell 123, 233-248 (2005). [PDF]

Dion M.F., Kaplan T, Kim M, Buratowski S, Friedman N, Rando O.J. Dynamics of replication-independent histone turnover in budding yeast. Science. 315(5817):1405-8. (2007)

Hans Hofmann

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).

Trainor BC, Hofmann HA. Somatostatin and somatostatin receptor gene expression in dominant and subordinate males of an African cichlid fish. Behav Brain Res.179(2):314-20. (2007)

Hofmann, H. A. Gonadotropin-releasing hormone signaling in behavioral plasticity. Curr Opin Neurobiol. 16(3):343-50.(2006)

Aubin-Horth N, Desjardins J.K., Martei Y.M., Balshine S, Hofmann H.A. Masculinized dominant females in a cooperatively breeding species. Mol Ecol. 16(7):1349-58. (2007)

Systems Biology postdoctoral fellows

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). [PubMed]

Savage, V. M., White, E. P., Moses, M. E., Ernest, S. K. M., Enquist, B. J. & Charnov, E. L. Comment on "The illusion of invariant quantities in life histories". Science 312, 198b (2006). [PubMed]

Savage, V. M., Webb, C. T. & Norberg, J. A general multi-trait-based framework for studying the effects of biodiversity on ecosystem functioning. J. Theor. Biol. 247, 213–229 (2007)

Cohen J.E., Jonsson T., Mueller C.B., Godfray, H.C.J. and Savage V.M. Body sizes of hosts and parasitoids in individual relationships. PNAS vol 102, 684-689 (2005)

Allen, A. P., Gillooly, J. F., Savage, V. M. & Brown, J. H. Kinetic effects of temperature on rates of genetic divergence and speciation. PNAS vol. 103 pp. 9130-5 (2006)

Savage V.M. and West G.B. A quantitative, theoretical framework for understanding mammalian sleep. PNAS vol. 104, 1051-1056 (2007)

Savage, V. M., Allen, A. P., Brown, J. H., Gillooly, J. F., Herman, A. B., Woodruff, W. H. & West, G. B. Scaling of number, size, and metabolic rate of cells with body size in mammals. PNAS vol. 104, 4718-4723 (2007).