Center for Quantitative Genome Function: Publications
Research Publications
Burbulis, I., Yamaguchi, K., Yu, R., Resnekov O., and Brent, R. (2007) Quantifying small numbers of molecules with a “near-universal” protein-DNA chimera. Nat Methods. November 4, 2007 (EPub Ahead of Print).[PDF]
Burbulis, I., Yamaguchi, K., Gordon, A., Carlson, R., and Brent, R. (2005)
Using protein-DNA chimeras to detect and count small numbers
of molecules. Nat Methods, 2:31-37. [ PubMed | PDF ]
Cao, Y., Gillespie, D.T. and Petzold, L.R. (2005). Avoiding
negative populations in explicit Poisson tau-leaping. J
Chem Phys 123(5): 054104. [ PubMed | PDF ]
Chan, L. Y., Kosuri, S., and Endy, D. (2005). Refactoring
bacteriophage T7. Mol Syst Biol 1: 2005 0018. [ PubMed | PDF ]
Colman-Lerner, A., Gordon, A., Serra, E., Chin, T., Resnekov, O.,
Endy, D., Pesce, C.G., Brent R. (2005) Regulated cell-to-cell variation
in a cell-fate decision system. Nature, 437:699-706.
[ PubMed |
PDFs: article, supplementary
materials, figures ]
Fett, B., Riedel, M., and Bruck, J. (2007) Synthesizing stochasticity in biochemical systems. Electronic Technical Report.[PDF]
Fung, T.H., Ball, G.I., McQuiade, S.C., Chao, S-H., Colman-Lerner, A.,
Holl, M., and Meldrum, D.R. (2004) Microprinting on On-chip Cultures: Patterning
of Yeast Cell Microarrays using Concalavin-A Adhesion. In
ASME International Mechanical Engineering Congress; Anaheim,
CA: American Society of Mechanical Engineers.
Gordon, A., Colman-Lerner, A., Chin, T.E., Benjamin, K.R., Yu, R.C., and Brent, R.
(2007) Single-cell quantification of molecules and rates using open-source microscope-basd cytometry.
Nat Methods, [PDFs: article, supplement 1, supplement 2, supplement 3, supplement 5].
Hucka, M., Finney, A., Bornstein, B.J., Keating, S.M., Shapiro, B.E.,
Matthews, J., Kovitz, B.L., Schlistra, M.J., Funahashi, A., Doyle, J.C.,
and Kitano, H. (2004) Evolving a Lingua Franca and Associated Software
Infrastructure for Computational Systems Biology: The Systems
Biology Markup Language (SMBL) Project. Systems Biology,
1:41-53. [PubMed]
Lok, L. and Brent, R. (2005). Automatic generation
of cellular reaction networks with Moleculizer 1.0. Nat
Biotechnol 23(1): 131-6. [ PubMed | PDF ]
Maxwell, R., Pincus, D., Tsong, A., Benjamin, K.R., Ryan, C., Smith, R.D., Brent, R. and Resnekov, O., (2007) Functional phosphoproteome analysis of yeast pheromone response system reveals loci of feedforward and feedback control.
Pesce, C. G., Yu, R. C., Rockwell, D. J., Colman-Lerner, A., and Brent, R., (2007). Single gene mutations define axes of quantitative behavior that affect information transmission through a signaling system in yeast.
Pincus, D., Benjamin, K.R., Burbulis, I., Resnekov, O. and Brent, R. (2007) Reagents and resources for the investigation of the pheromone response system.
Shapiro, B.E., Hucka, M., Finney, A., and Doyle, J. (2004) MathSBML:
a package for manipulating SBML-based biological models.
Bioinformatics, 20:2829-2831. [ PubMed | PDF ]
Soloveichik, D., Cook, M. Winfree, E. and Bruck, J. (2007) Computation with Finite Stochastic Chemical Reaction Networks. Electronic Technical Report.[PDF]
Takahashi, K. (2005). Protein crowding and localization
in cellular signaling systems (Japanese). HFSP Newsletter.
[ PubMed ]
Thomson, T.M., Benjamin, K.R., Love, T., Yu, R.C., Gordon, A., Colman-Lerner, A., Endy, D. and Brent, R. (2007) Low abundance of yeast MAPK scaffold suggests tradeoff between system output and dynamic range.
Yu, R.C., Gordon, A., Colman-Lerner, A., Benjamin, K., Pincus, D., Serra, E., Holl, M. Lok, L., Pesce, G. and Brent, R. (2007). Feedback-mediated dose response alignment reduces loss of information during signal transduction.
Yu, R.C., Resnekov, O., the rest of the Center and Brent, R. (2007) The Center for Quantitative Genome Function: Lessons Learned. IET Systems Biology (solicited).
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Research publications in preparation
Colman-Lerner, A., Gordon, A., Abola, A.P., Chin, T., Yu, R.C. and Brent, R. (2007). Quantification of cis-membrane events in a prototypic signal transduction pathway: how dose response of scaffold recruitment in yeast pheromone response system anticipates receptor occupancy.
Maxwell, R., Pincus, D., Ryan, C. Smith, R.D., Brent, R. and Resnekov, O. (2007) Functional phosphoproteome analysis reveals pheromone-regulated protein-protein interactions between yeast pheromone system proteins and candidate regulators and effectors.
Maxwell, R., Resnekov, O., Ryan, C., Pincus, D., Monroe, M., Brent, R. and Smith, R.D. (2007). A novel phosphoproteomic approach reveals new regulatory loci in the yeast pheromone response system.
Pesce, C. G., Colman-Lerner, A., Rockwell, D. J., and Brent, R. (2007). Motor proteins control subcellular localization of the yeast nucleus to regulate signal amplitude and noise in the yeast pheromone response system.
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Reviews, commentaries and a thesis by Center scientists
Bio FABG, Baker, D., Church, G., Collins, J., Endy, D., Jacobson,
J., Keasling, J., Modrich, P., Smolke, C., and Weiss, R. (2006) Engineering
life: building a fab for biology. Sci Am, 294:44-51. [ PubMed ]
Brent, R. (2006) Power and responsibility. MIT Synthetic Biology Archive.
http://hdl.handle.net/1721.1/34913, DOI: 1721.1/34913 [PDF]
Brent, R. (2003-2006) In the valley of the shadow of death MIT Synthetic Biology Archive.
http://hdl.handle.net/1721.1/34914, DOI: 1721.1/34914 [PDF]
Brent, R.(2004) A partnership between biology and engineering.
Nat Biotechnol, 22:1211-1214. [ PubMed | PDF ]
Brent, R. (2004) Intuition and innumeracy. Cell Biol Educ,
3:88-90. [ PubMed | PDF ]
Brent R: (2004) Building an artificial regulatory system
to understand a natural one. Cell, 116:S73-74, 71 p following
S76. [ PubMed | PDF ]
Brent, R., and Burbulis, I. (2005) Reply to "Lamp for tadpoles".
Nature Methods, 2:635-636. [ PubMed | PDF ]
Brent, R., and Bruck, J. (2006) 2020 computing: can computers help
to explain biology? Nature, 440:416-417. [ PubMed | PDF ]
Brent, R., and Lok, L. (2005) Cell biology. A fishing buddy for
hypothesis generators. Science, 308:504-506. [ PubMed | PDF ]
Bugl, H., Danner, J.P., Molinari, R.J., Mulligan, J.T., Park, H.O., Reichert, B., Roth, D.A., Wagner, R., Budowle, B., Scripp, R.M., Smith, J.A., Steele, S.J., Church, G. and Endy, D. (2007) DNA synthesis and biological security. Nature Biotechnol. 25(6):627-9. [PubMed]
Cook, M. (2005) Networks of relations. Pasadena: California Institute
of Technology: 2005.
Endy, D. (2005) Foundations for engineering biology. Nature,
438:449-453. [ PubMed | PDF ]
Levchenko, A., Bruck, J., and Sternberg, P.W. (2004) Regulatory molecules that generate biphasic signal response in biological systems. Systems Biology, 1:139-148. [PubMed]
Lok, L. (2004) The need for speed in stochastic simulation.
Nat Biotechnol, 22:964-965. [ PubMed | PDF ]
Lok, L. (2002) Pathfinder and other tools for analyzing signal transduction networks. Ann N Y Acad Sci, 971:589-594. [ PubMed | PDF ]
Lok, L. (2002) Software for signaling networks, electronic and cellular. Science STKE. 2002(122):PE11
Lok, L. and Brent, R. (2005). "Response to "On-the-fly" or "generate first" modeling." Nat Biotechnol 23(11): 1345. [ PDF ]
Shen, Y., and Smith, R.D. (2005) Advanced nanoscale separations
and mass spectrometry for sensitive high-throughput proteomics.
Expert Rev Proteomics, 2:431-447. [ PubMed ]
Takahashi, K. (2007) The E-Cell project and challenges in computational systems biology. Proceedings from computational biophysics to systems biology (CBSB07) Julich, Germany
Takahashi, K., Nanda, S., Arjunan, V., and Tomita, M. (2005) Space
in systems biology of signaling pathways-towards intracellular
molecular crowding in silico. FEBS Letters, 579:1783-1788.
Takahashi, K. (2005) Protein crowding and localization in cellular signaling systems, HFSP Newsletter. 19: (in Japanese).
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Important papers that lay the framework for the Center
Brent, R. (2000) Genomic biology. Cell, 100:169-183. [ PubMed | PDF ]
Colman-Lerner, A., Chin, T.E., and Brent, R. (2001) Yeast Cbk1 and
Mob2 activate daughter-specific genetic programs to induce
asymmetric cell fates. Cell, 107:739-750. [ PubMed | PDF ]
Conrads, T.P., Anderson, G.A., Veenstra, T.D., Pasa-Tolic, L., and Smith,
R.D. (2000) Utility of accurate mass tags for proteome-wide
protein identification. Anal Chem, 72:3349-3354. [ PubMed ]
Endy, D., and Brent, R. (2001) Modelling cellular behaviour. Nature,
409:391-395. [ PubMed | PDF ]
Gibson, M. A. and Bruck, J. (2000). "Efficient exact
stochastic simulation of chemical systems with many species
and channels." J. Phys Chem 104: 1876-1889. [ PDF ]
Levchenko, A., Bruck, J., and Sternberg, P.W. (2000) Scaffold proteins may biphasically affect the levels of mitogen-activated protein kinase signaling and reduce its threshold properties. Proc Natl Acad Sci U S A, 97:5818-5823. [ PubMed ]
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Publications about Center science
Hybrid Open-Source Imaging Software Helps Team Measure Individual Fluorophore Dynamics. (2007) Cell-Based Assay News.Vol. 4(6).
Molecular tadpoles for quantitation of biomolecules (2005).
American Chemical Society. 87A.
Nolan, G. (2005). "Tadpoles by the tail." Nat
Methods 2(1): 11-12.
Owens, J. (2005). "Fishing for proteins." Nature
Reviews Drug Discovery S3.
Salisbury, M.W. (2007) Under One Roof. Genome Technology
Zelinska, E. (2007) A Little Lab Tackles a Big Question.The Scientist. July.pp 37-42
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Publications about Center scientists
Boutin, P. (2005) Swimming For Cancer. Slate Magazine
Editors (2004). Ten Emerging Technologies That Will Change Your World. MIT Technology Review. February: 32-51.
Ferber, D. (2005). "Microbes Made to Order." Science
303: 158-161
From the cells up.(2005) The Guardian, March 10, 2005.
Gehl, J. (2004) Roger
Brent and the Alpha Project. Ubiquity.
Gibbs, W. W. (2004). Synthetic Life. Scientific American.
May 2004: 75-81.
Johnson, N. (2005). "Steal this genome". East
Bay Express.
Kamenetz, D. (2006). Pop!Stars
2006. Fast Company: 107.
Lowe, D. (2005). "Tadpoles
to the rescue?"
Morton, O. (2005). Life,
Reinvented. Wired Magazine. 13.
Rhoten, D. (2005) Mind
the Gap. Inside Higher Education.
Russel, J. (2004) Synthetic Biology: The Real Thing. Bio-IT
World.
Young Investigator Wednesday Profile. (2007) Ian Burbulis, Senior Research Fellow, Molecular Sciences Institute. Genome Technology Online. October 3, 2007.
Young Investigator Wednesday Profile. (2007) Alejandro Colman-Lerner, Co-investigator at the Center for Quantitative Genome Function and Investigator at IFIBYNE, Buenos Aires, Argentina. Genome Technology Online. October 31, 2007.
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