Publications

grant "Biological Diversity: Generation, Control and Exploitation"

Andrew Murray

Erik F. Y. Hom and Andrew W. Murray. Niche Engineering Demonstrates a Latent Capacity for Fungal-Algal
Mutualism, Science, in press, July 2014,

Huberman, Lori B.; Murray, Andrew W. Genetically Engineered Transvestites Reveal Novel Mating Genes in Budding Yeast GENETICS Volume: 195 Issue: 4 Pages: 1277-+ Published: DEC 2013. PMCID:PMC3832273

Mueller, Melanie J. I.; Neugeboren, Beverly I.; Nelson, David R., Murray, Andrew W. Genetic drift opposes mutualism during spatial population expansion. PNAS Volume: 111 Issue: 3 Pages: 1037-1042 Published: JAN 21 2014; PMCID:PMC3903240

Koschwanez, J., Foster, K., and Murray, A.W. Sucrose utilization in budding yeast as a model for the origin of multicellularity, PLoS Biology, 9 (8), 2011. PMCID: PMC3153487

Gonçalves-Sá, J. and Murray, A.W. Asymmetry in Sexual Pheromones is not Required for ascomycete mating. Curr. Biol. August 23; 21(16), 1337-1346 (2011). PMCID: PMC3159855

Lang GI Murray AW. Mutation Rates across Budding Yeast Chromosome VI Are Correlated with Replication Timing; Genome Biol Evol. Pages: 799-811 2011 DOI: 10.1093/gbe/evr054 PMCID: PMC3170098

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

Lavrentovich, Maxim O.; Koschwanez, John H.; Nelson, David R. Nutrient shielding in clusters of cells. PHYSICAL REVIEW E Volume: 87 Issue: 6 Article Number: 062703 Published: JUN 10 2013, PMCID: PMC4122756

Kirill S. Korolev, Melanie J. I. Mueller, Nilay Karahan, Andrew W. Murray, Oskar Hallatschek and David R. Nelson, Selective sweeps in growing microbial colonies, Phys. Biol. Vol. 9 (2012) 026008. PMCID: PMC3359763.

Kirill S. Korolev, João B. Xavier, David R. Nelson, and Kevin R. Foster, A Quantitative Test of Population Genetics Using Spatiogenetic Patterns in Bacterial Colonies, The American Naturalist, Vol. 178, (2011), pp. 538-552. PMCID: PMC3385003.

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. PMCID: PMC3132887

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

Amir A, Babaeipour F, McIntosh DB, Nelson DR, Jun S. Bending forces plastically deform growing bacterial cell walls. Proc Natl Acad Sci U S A. 2014 Apr 22;111(16):5778-83. doi: 10.1073/pnas.1317497111. PMCID: PMC4000856

Pelletier, J.; Halvorsen, K.; Ha, BY; et al., Woldringh, CL. Wong WP. Jun, S. Physical manipulation of the Escherichia coli chromosome reveals its soft nature. PNAS 109, 40, E2649-E2656 OCT 2 2012; PMCID: PMC3479577

S. Jun and A. Wright, Entropy as the driver of chromosome segregation, Nature Reviews Microbiology 8, 600 (2010). PMCID: PMC3148256

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

Hilfinger, A; Chen, M; Paulsson, J. Using Temporal Correlations and Full Distributions to Separate Intrinsic and Extrinsic Fluctuations in Biological Systems. Phys Review Lett Volume: 109 Issue: 24, DEC 10 (2012) PMCID:PMC3697929

Hilfinger A and Paulsson J (2011) Separating intrinsic from extrinsic fluctuations in dynamic biological systems, Proc. Natl. Acad. Sci. USA, 108:12167-72 (2011). PMCID: PMC3141918.

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

Allan Drummond

Wallace, Edward W. J.; Airoldi, Edoardo M.; Drummond, D. Allan. Estimating Selection on Synonymous Codon Usage from Noisy Experimental Data MOLECULAR BIOLOGY AND EVOLUTION Volume: 30 Issue: 6 Pages: 1438-1453 Published: JUN 2013 PMCID:PMC3649678

Geiler-Samerotte, Kerry A.; Hashimoto, Tatsunori; Dion, Michael F.; Budnik, Bogdan A; Airoldi, Edo M; Drummond, D Allan. Quantifying Condition-Dependent Intracellular Protein Levels Enables High-Precision Fitness Estimates. PLOS ONE Volume: 8 Issue: 9 Article Number: UNSP e75320 Published: SEP 25 2013 PMCID: PMC3783400

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

Naama Barkai

Tamari, Zvi; Rosin, Dalia; Voichek, Yoav; Barkai, Naama. Coordination of Gene Expression and Growth-Rate in Natural Populations of Budding Yeast. PLOS ONE Volume: 9 Issue: FEB 12 2014; PMCID:PMC3923061

Weinberger L, Voichek Y, Tirosh I, Hornung G, Amit I and Barkai N. Expression noise and acetylation profiles distinguishes HDACs functions, Mol Cell 47(2):193-202. July 2012. PMCID: PMC3408861

Rappaport, N; Barkai, N. Disentangling signaling gradients generated by equivalent sources
Journal of Biol Physics 38, 2, 267-278, Mar 2012. PMCID: PMC3326141

Hornung, G; Bar-Ziv, R; Rosin, D; et al. Barkai, N. Noise-mean relationship in mutated promoters. Genome Research 22, 12, 2409-2417, Dec 2012. PMCID: PMC3514670

Hornung G, Oren M, Barkai N. Nucleosome organization affects the sensitivity of gene expression to promoter mutations. Mol Cell. 46(3):362-8 (2012) PMCID: PMC3356688

Rosin D, Hornung G, Tirosh I, Gispan A, Barkai N. Promoter nucleosome organization shapes the evolution of gene expression. PLoS Genet (3), (2012) PMCID: PMC3305400

Leehee Weinberger*, Yoav Voichek*, Itay Tirosh, Gil Hornung, Ido Amit and Barkai N. Expression noise and acetylation profiles distinguishes HDACs functions, Mol Cell June 6 (2012) NIHMSID #378435

Michael Elowitz

Levine, Joe H.; Lin, Yihan; Elowitz, Michael B. Functional Roles of Pulsing in Genetic Circuits SCIENCE Volume: 342 Issue: 6163 Pages: 1193-1200 Published: DEC 6 2013 NIHMSID: 596211. PMCID – in process

Young JW, Locke JC, Elowitz MB. Rate of environmental change determines stress response specificity, Proc Natl Acad Sci U S A. (2013) 110(10):4140-5. PMCID: PMC3593889

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) PMCID: PMC3374951

Michael Brenner / Katharina Ribbeck

Fritz, Joerg A.; Seminara, Agnese; Roper, Marcus; Pringle, Anne; Brenner, Michael P. A natural O-ring optimizes the dispersal of fungal spores JOURNAL OF THE ROYAL SOCIETY INTERFACE Volume: 10 Issue: 85 Published: AUG 6 2013 PMCID:PMC3971719

Alim, Karen; Amselem, Gabriel; Peaudecerf, Francois; Brenner, Michael P; Pringle, Anne. Random network peristalsis in Physarum polycephalum organizes fluid flows across an individual. PNAS Volume: 110 Issue: 33 Pages: 13306-13311 Published: AUG 13 2013 PMCID: PMC3746869

Mallarino, R; Campas, O; Fritz, JA.; Brenner MP, Abzhanov A. Closely related bird species demonstrate flexibility between beak morphology and underlying developmental programs. PNAS 109, 40,16222-16227, Oct 2 2012. PMCID: PMC3479598

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

Schmid-Burgk, J. L., Xie, Z., Frank, S., Virreira Winter, S., Mitschka, S., Kolanus, W., Murray, A. & Benenson, Y. Rapid hierarchical assembly of medium-size DNA cassettes. Nucleic Acids Res. 40, e92 (2012). PMCID: PMC3384347

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

Haiser, Henry J.; Gootenberg, David B.; Chatman, Kelly; Sirasani, G.; Baslkus, Emily K, Turnbaugh, Peter J. Predicting and Manipulating Cardiac Drug Inactivation by the Human Gut Bacterium Eggerthella lenta SCIENCE Volume: 341 Issue: 6143 Pages: 295-298 Published: JUL 19 2013 PMCID:PMC3736355

David, Lawrence A.; Maurice, Corinne F.; Carmody, .. Dutton, Rachel; Turnbaugh, Peter. Diet rapidly and reproducibly alters the human gut microbiome. NATURE Volume: 505 Issue: 7484 Pages: 559-+ Published: JAN 23 2014; PMCID:PMC3957428

XMaurice, Corinne F.; Turnbaugh, Peter J. Quantifying the metabolic activities of human-associated microbial communities across multiple ecological scales FEMS MICROBIOLOGY REVIEWS Volume: 37 Issue: 5 Pages: 830-848 Published: SEP 2013 PMCID 3729610

Liou, Alice P.; Paziuk, Melissa; Luevano, Jesus-Mario, Jr.; ..Turnbaugh, Peter J; Kaplan, LM. Conserved Shifts in the Gut Microbiota Due to Gastric Bypass Reduce Host Weight and Adiposity SCIENCE TRANSLATIONAL MEDICINE Volume: 5 Issue: 178 Article Number: 178ra41 Published: MAR 27 2013 PMCID:PMC3652229

Maurice, C. F., Haiser, H. J., Turnbaugh, P.J. Xenobiotics Shape the Physiology and Gene Expression of the Active Human Gut Microbiome. Cell 152,39-50 JAN 17 2013. PMCID: PMC3552296

Greenblum, S., Turnbaugh, P.J., and E. Borenstein. Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease. PNAS, Epub Dec 19 (2011) PMCID: PMC3258644

Reshef, D.N., Reshef, Y.A., Finucane, H.K., Grossman, S.R., McVean, G., Turnbaugh, P.J., Landers, E.S., Mitzenmacher, M., and P.C. Sabeti. Detecting novel associations in large data sets. Science 334, 1518-1524 (2011) PMCID: PMC3325791

Turnbaugh, P.J. and A. Stintzi. Human health and disease in a microbial world. Front. Microbio. 2:190. doi: 10.3389/fmicb.2011.00190 (2011) PMCID: PMC3174398.

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. PMCID: PMC3127503

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). PMCID: PMC3139398

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). PMCID: PMC3131843

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

Hill, R. I.; Gilbert, L. E.; Kronforst, M. R.Cryptic genetic and wing pattern diversity in a mimetic Heliconius butterfly MOLECULAR ECOLOGY Volume: 22 Issue: 10 Pages: 2760-2770 Published: MAY 2013 PMCID:PMC3669692

Hines H. M., B. A. Counterman, R. Papa, P. Albuquerque de Moura, M. Z. Cardoso, M. Linares, J. Mallet, R. D. Reed, C. D. Jiggins, M. R. Kronforst and W. O. McMillan. 2011. Wing patterning gene redefines the mimetic history of Heliconius butterflies. Proc. Natl. Acad. Sci. USA 108: 19666-19671. PMCID: PMC3241772

Kunte, K., C. Shea, M. L. Aardema, J. M. Scriber, T. Juenger, L. E. Gilbert and M. R. Kronforst. Sex chromosome mosaicism and hybrid speciation among tiger swallowtail butterflies. PLoS Genetics 7: e1002274. PMCID: PMC3169544

Chamberlain N. L., R. I. Hill, S. W. Baxter, C. D. Jiggins and M. R. Kronforst. 2011. Comparative population genetics of a mimicry locus among hybridizing Heliconius butterfly species. Heredity 107: 200-204. 2011. PMCID: PMC3119732

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

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

Kim, Wook; Racimo, Fernando; Schluter, Jonas; Foster, Kevin R. Importance of positioning for microbial evolution. PNAS Volume: 111 Issue: 16 Pages: E1639-E1647; PMCID: PMC4000849

Caldara M, Friedlander RS, Kavanaugh NL, Aizenberg J, Foster KR, Ribbeck K.
Mucin biopolymers prevent bacterial aggregation by retaining cells in the free-swimming state.
Curr Biol. 22, 2325-30. Dec 18 2012. PMCID:PMC3703787

Vladescu, I.; Lieleg, O.; Jang, S.; Ribbeck, K. An adsorption chromatography assay to probe bulk particle transport through hydrogels. J Pharm Sci. 101, 436-442, Jan 2012. PMCID:PMC3650840

Lieleg, O; Lieleg, C; Bloom, J; et al. Ribbeck K. Mucin Biopolymers As Broad-Spectrum Antiviral Agents. Biomaromolecules 13, 6, 1724-1732, 2012. PMCID: PMC3597216

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) PMCID: PMC3134232

Racherl Dutton

Wolfe BE, Button JE, Santarelli M, Dutton RJ. Cheese rind communities provide tractable systems for in situ and in vitro studies of microbial diversity. Cell. 158, 422-233, 2014

Irene Chen

Jimenez, Jose I.; Xulvi-Brunet, Ramon; Campbell, Gregory W.; Chen, Irene. Comprehensive experimental fitness landscape and evolutionary network for small RNA. PNAS Volume: 110 Issue: 37 Pages: 14984-14989 Published: SEP 10 2013. PMCID:PMC3773786

Freese, Peter D.; Korolev, Kirill S.; Jimenez, Jose I.; Chen, Irene A. Genetic Drift Suppresses Bacterial Conjugation in Spatially Structured Populations BIOPHYSICAL JOURNAL Volume: 106 Issue: 4 Pages: 944-954; PMCID:PMC3944618

Leu, K, Kervio, E ; Obermayer, B ; Turk-MacLeod, RM ; Yuan, C ; Luevano, JM ; Chen, E erland, U ; Richert, C ; Chen, IA.Cascade of Reduced Speed and Accuracy after Errors in Enzyme-Free Copying of Nucleic Acid Sequences. Journal of the American Chemical Society 135, 1, 354-366 Jan 9 2013. PMCID:PMC3557965

Derr J, Manapat ML, Rajamani S, Leu K, Xulvi-Brunet R, Joseph I, Nowak MA, Chen IA. Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences. Nuc. Acids Res. (2012) 40 (10): 4711-4722. PMCID: PMC3378899

X 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. 2011 Oct;39(18):8135-47. Epub 2011 Jun 30. PMCID: PMC3185426

X 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. PMCID: PMC3102678

X Chen IA, Schindlinger M. Quadruplet codons: One small step for a ribosome, one giant leap for proteins. BioEssays, 2010, 32: 650–654. PMCID: PMC3133615

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. Distinct Growth Strategies of Soil Bacteria as Revealed by Large-Scale Colony Tracking. Appl Environ Microbiol. 2012 March; 78(5): 1345–1352. PMCID: PMC3294487

X Vetsigian K, Jajoo R, Kishony R. Structure and Evolution of Streptomyces Interaction Networks in Soil and In Silico. PLoS Biol. 2011 October; 9(10): e1001184. PMCID: PMC3201933

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).