Publications

CMB Publications (by project leader)

grant "Biological Diversity: Generation, Control and Exploitation"

Andrew Murray

Brown CA, Murray AW, Verstrepen KJ. Rapid expansion and functional divergence of subtelomeric gene families in yeasts. Curr Biol. 2010 May 25;20(10):895-903. Epub 2010 May 13. PMCID: PMC2877759

Lang GI, Murray AW, Botstein D. The cost of gene expression underlies a fitness trade-off in yeast. Proc Natl Acad Sci U S A. 2009 Apr 7;106(14):5755-60. Epub 2009 Mar 19. PMCID: PMC2658138

David Nelson

K. S. Korolev, M. Avlund, O. Hallatschek and D. R. Nelson, Genetic demixing and evolutionary forces in the one-dimensional stepping stone model, Review of Modern Physics 82, 1691 (2010). PMCID: PMC2975585

Kevin Verstrepen

Vinces M, Legendre M, Caldara M, Hagihara M and Verstrepen KJ. Unstable tandem repeats in promoters confer transcriptional evolvability. Science. 2009 May 29;324(5931):1213-6. NIHMS305995

Scott Smukalla, Marina Caldara, Nathalie Pochet, Anne Beauvais, Stephanie Guadagnini, Chen Yan, Marcelo D Vinces, An Jansen, Marie Christine Prevost, Jean-Paul Latgé, Gerald R Fink, Kevin R Foster, Kevin J Verstrepen; FLO1 is a variable green beard gene that drives biofilm-like cooperation in budding yeast; Cell, vol. 135 (4) pp. 726-37 (2008) PMCID: PMC2703716

Suckjoon Jun

S. Jun and A. Wright, Entropy as the driver of chromosome segregation, Nature Reviews Microbiology 8, 600 (2010). NIHMSID 301289

P. Wang*, L. Robert*, J. Pelletier, W. Dang, F. Taddei, A. Wright, S. Jun. Robust growth of Escherichia coli. Current Biology, 2010 Jun 22;20(12):1099-103. PMCID: PMC2902570

Johan Paulsson

Lestas I, Vinnicombe G, and Paulsson J. (2010). Fundamental limits on the suppression of molecular fluctuations, Nature. 467(73120:174-8. PMCID: PMC2996232

Hilfinger A and Paulsson J (2011) Separating intrinsic from extrinsic fluctuations in dynamic biological systems, Proc. Natl. Acad. Sci. USA, In Press

Allan Drummond

Kerry A. Geiler-Samerotte, Michael F. Dion, Bogdan A. Budnik, Stephanie M. Wang, Daniel L. Hartl, and D. Allan Drummond, Misfolded proteins impose a dosage-dependent fitness cost and trigger a cytosolic unfolded protein response in yeast, Proc Natl Acad Sci USA 2011 January 11; 108(2): 680–685. PMCID: PMC3021021

Wilke CO, Drummond DA. Signatures of protein biophysics in coding sequence evolution. Curr Opin Struct Biol. 2010 Jun;20(3):385-9. Epub 2010 Apr 13. Review. PMCID: PMC2764353

Drummond DA, Wilke CO, The evolutionary consequences of erroneous protein synthesis. Nat Rev Genet. 2009 Oct;10(10):715-24. PMCID: PMC2764353

Drummond DA, Wilke CO. Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell. 2008 Jul 25;134(2):341-52. PMCID: PMC2696314

Michael Elowitz

Locke JC, Elowitz MB. Using movies to analyse gene circuit dynamics in single cells. Nat Rev Microbiol. 2009 May;7(5):383-92. PMCID: PMC2853934

Eldar A, Chary VK, Xenopoulos P, Fontes ME, Losón OC, Dworkin J, Piggot PJ, Elowitz MB. Partial penetrance facilitates developmental evolution in bacteria. Nature. 2009 Jul 23;460(7254):510-4. Epub 2009 Jul 5. PMCID: PMC2716064

Cai L, Dalal CK, Elowitz MB. Frequency-modulated nuclear localization bursts coordinate gene regulation, Nature. 2008 Sep 25;455(7212):485-490, PMCID: PMC2695983

Dunlop MJ, Cox RS 3rd, Levine JH, Murray RM, Elowitz MB. Nat Genet. 2008 Dec;40(12):1493-8.Regulatory activity revealed by dynamic correlations in gene expression noise. PMCID: PMC2829635

Sharad Ramanathan

Mody A, Weiner J, Ramanathan S. Modularity of MAP kinases allows deformation of their signalling pathways. Nat Cell Biol. Apr;11(4):484-91.(2009) Paper

Michael Brenner / Katharina Ribbeck

Lucy Colwell, M. P. Brenner and K. Ribbeck, “Charge as a selection criterion for translocation through the nuclear pore complex”, Plos Comp. Biol. 6 (4): e1000747 (2010). PMCID: PMC2858669

O. Campas, R. Mallarnio, A. Herrel, A. Abzhanov and M.P. Brenner, Scaling and Shear Tranformations capture beak shape variation in Darwin’s finches, Proc. Natl. Acad. Sci. (2010), 107: 3356-3360. PMCID: PMC2840476

Tim Mitchison

Huang HC, Mitchison TJ, Shi J. (2010) Stochastic competition between mechanistically independent slippage and death pathways determines cell fate during mitotic arrest. PLoS One. 2010 Dec 21;5(12):e15724. PMID: 21203573 PMCID: PMC3006339

Hsiao-Chun Huang, Jue Shi, James D. Orth and T. J. Mitchison (2009) Evidence that mitotic exit is a better cancer therapeutic target than spindle assembly. Cancer Cell. 16:347-58. PMCID: PMC2758291

Dumont S, Mitchison TJ. Compression regulates mitotic spindle length by a mechanochemical switch at the poles. Curr Biol. 2009 Jul 14;19(13):1086-95. Epub 2009 Jun 18. PMCID: PMC2722833

Dumont S, Mitchison TJ. Force and length in the mitotic spindle. Curr Biol. 2009 Sep 15;19(17):R749-61. Review. PMCID: PMC2791830

Wühr M, Chen Y, Dumont S, Groen AC, Needleman DJ, Salic A, Mitchison TJ. Evidence for an upper limit to mitotic spindle length. Curr Biol. 2008 Aug 26;18(16):1256-61. PMCID: PMC2561182

Yaakov Benenson

Leisner, M., Bleris, L., Lohmueller, J., Xie, Z., Benenson, Y. Rationally-designed logic integration of regulatory signals in mammalian cells. 2010. Nature Nanotechnology, 5 (9): 666 – 670 PMCID: PMC2934882

Xie, Z., Liu, S. J., Bleris, L., Benenson, Y. Logic integration of mRNA signals by an RNAi-based molecular computer. 2010. Nucleic Acids Research 38: 2692-2701. PMCID: PMC2860122

Benenson Y. RNA-based computation in live cells. 2009. Current Opinion in Biotechnology 20:471-8 (Invited review) PMCID: PMC2764246

Benenson, Y. Small hairpin RNA as a small molecule sensor. Molecular Systems Biology 2008 4:227 (Invited review) PMCID: PMC2583088

Benenson Y. Biocomputers: from test tubes to live cells. 2009. Molecular Biosystems 5:675 – 685. Review PMCID: PMC2714485

Benenson Y. RNA-based computation in live cells. Curr Opin Biotechnol. 2009 Aug;20(4):471-8. Epub 2009 Aug 31. PMCID: PMC2764246

Peter Turnbaugh

Jumpertz, R., Le, D.S., Turnbaugh, P.J., Trinidad, C., Bogardus, C., Gordon, J.I., and J. Krakoff. Energy-balance studies reveal associations between gut microbes, caloric load, and nutrient absorption in humans. AJCN, Epub 2011 May 4.

Gonzalez, A., Stombaugh, J., Lozupone, C., Turnbaugh, P.J., Gordon, J.I., and R. Knight. The mind-body microbial continuum. Diag. Clin. Neuro. 13, 55-62 (2011).

Patil, K.R., Haider, P., Pope, P.B., Turnbaugh, P.J., Morrison, M., Scheffer, T., and A.C. McHardy. Taxonomic metagenome sequence assignment with structured output models. Nat. Methods 8, 191-192 (2011).

Quince, C., Lanzen, A., Davenport, R.J., and P.J. Turnbaugh. Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12, 38 (2011). PMCID: PMC3045300

Marcus Kronforst

de Moura PA, Quek SP, Cardoso MZ, Kronforst MR. Comparative population genetics of mimetic Heliconius butterflies in an endangered habitat; Brazil's Atlantic Forest. BMC Genet. 2011 Jan 20;12:9. PMCID: PMC3035028

Albuquerque de Moura, P., S. P. Quek, M. Z. Cardoso and M. R. Kronforst. 2011. Comparative population genetics of mimetic Heliconius butterflies in an endangered habitat; Brazil’s Atlantic forest. BMC Genetics 12: 9. PMCID: PMC3035028

Quek, S. P., B. A. Counterman, P. Albuquerque de Moura, M. Z. Cardoso, C. R. Marshall, W. O. McMillan and M. R. Kronforst. 2010. Dissecting comimetic radiations in Heliconius reveals divergent histories of convergent butterflies. Proc. Natl. Acad. Sci. USA 107: 7365-7370. PMCID: PMC2867687

Baxter, S. W., N. Nadeau, L. Maroja, P. Wilkinson, B. Counterman, A. Dawson, M. Beltran, S. Perez-Espona, N. Chamberlain, L. Ferguson, R. Clark, C. Davidson, R. Glithero, J. Mallet, W. O. McMillan, M. R. Kronforst, M. Joron, R. H. ffrench-Constant and C. D. Jiggins. 2010. Genomic hotspots for adaptation: the population genetics of Müllerian mimicry in the Heliconius melpomene clade. PLoS Genetics 6(2): e1000794. PMCID: PMC2816687

Chamberlain, N. L., R. I. Hill, D. D. Kapan, L. E. Gilbert and M. R. Kronforst. 2009. Polymorphic butterfly reveals the missing link in ecological speciation. Science 326: 847-850. PMCID: PMC2875868

Katharina Ribbeck

Lieleg O and Ribbeck K. Biological hydrogels as selective diffusion barriers. 2011. Trends in Cell Biology, in press

Lieleg O, Vladescu I, Ribbeck K. Characterization of particle translocation through mucin hydrogels. Biophys J. 2010 May 19;98(9):1782-9.PMCID: PMC2862156

Lieleg O, Caldara M, Baumgärtel R and Ribbeck K, Mechanical robustness of Pseudomonas aeruginosa biofilms, Soft Matter, Soft Matter, 7(7), 3307-3314 (2011)

Irene Chen

Leu K, Obermayer B, Rajamani S, Gerland U, Chen IA. The prebiotic evolutionary advantage of transferring genetic information from RNA to DNA. Nuc. Acids Res. In press.

Lin A, Jimenez J, Derr J, Vera P, Manapat ML, Esvelt KM, Villanueva L, Liu DR, Chen IA. Inhibition of bacterial conjugation by phage M13 and its protein g3p: quantitative analysis and model. PLoS One 2011, 6(5): e19991.

Chen IA, Schindlinger M. Quadruplet codons: One small step for a ribosome, one giant leap for proteins. BioEssays, 2010, 32: 650–654. NIHMSID: 302527

Rajamani S, Ichida JK, Antal T, Treco DA, Leu K, Nowak MA, Szostak JW, Chen IA. Effect of stalling after mismatches on the error catastrophe in non-enzymatic nucleic acid replication. J. Am. Chem. Soc. 2010, 132, 5880–5885. PMCID: PMC2857888

Manapat ML, Chen IA, Nowak MA. The basic reproductive ratio of life. J. Theor. Biol. 2010, 263(3): 317-327. PMCID: PMC2827768

Roy Kishony

Ernebjerg M, Kishony R. Dynamic phenotypic clustering in noisy ecosystems. PLoS Comput Biol. 2011 Mar;7(3):e1002017. Epub 2011 Mar 17. PubMed PMID: 21445229; PMCID: PMC3060162

Chait R, Shrestha S, Shah AK, Michel JB, Kishony R. A differential drug screen for compounds that select against antibiotic resistance. PLoS One. 2010 Dec 8;5(12):e15179. PubMed PMID: 21209699; PMCID: PMC2999542

grant "Modular Biology: Experiment, Theory and Computation"

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)

Lang G. I. and Andrew Murray, A.W. Estimating the per-base-pair mutation rate in the yeast Saccharomyces cerevisiae. Genetics. vol. 178 (1) pp. 67-82 (2008)

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).