Center for Quantitative Genome Function: Publications
Burbulis I, Yamaguchi K, Gordon A, Carlson R, Brent R: (2005)
Using protein-DNA chimeras to detect and count small numbers
of molecules. Nat Methods, 2:31-37. [ PubMed | PDF ]
Cao, Y., D. T. Gillespie, and Petzold, L.R. (2005). "Avoiding
negative populations in explicit Poisson tau-leaping." J
Chem Phys 123(5): 054104. [ PubMed | PDF ]
Chan, L. Y., S. Kosuri, 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 CG, Brent R (2005) Regulated cell-to-cell variation
in a cell-fate decision system. Nature, 437:699-706.
[ PubMed |
PDFs: article, supplementary
materials, figures ]
Cook M, Soloveichik D, Winfree E, Bruck J: (2006) Programming
with biochemistry. Submitted.
Fung TH, Ball GI, McQuiade SC, Chao S-H, Colman-Lerner A,
Holl M, Meldrum DR: 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: 2004.
Gordon A, Colman-Lerner A, Chin TE, Benjamin KR, Yu, R.C., 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 BJ, Keating SM, Shapiro BE,
Matthews J, Kovitz BL, Schlistra MJ, Funahashi A, Doyle JC,
et al.: (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.
Levchenko A, Bruck J, Sternberg PW: (2004) Regulatory molecules
that generate biphasic signal response in biological systems.
Systems Biology, 1:139-148.
Lok, L. and R. Brent (2005). "Automatic generation
of cellular reaction networks with Moleculizer 1.0." Nat
Biotechnol 23(1): 131-6. [ PubMed | PDF ]
Lok, L. and R. Brent (2005). "Response to "On-the-fly" or "generate
first" modeling." Nat Biotechnol 23(11): 1345. [
PDF ]
Riedel, M. and J. Bruck (2006). "Exact stochastic simulation
of chemical reactions with event leaping." Submitted.
Shapiro BE, Hucka M, Finney A, Doyle J: (2004) MathSBML:
a package for manipulating SBML-based biological models.
Bioinformatics, 20:2829-2831. [ PubMed | PDF ]
Takahashi, K. (2005). "Protein crowding and localization
in cellular signaling systems (Japanese)." HFSP Newsletter.
[ PubMed ]
Yu R, Gordon A, Colman-Lerner A, Benjamin KR, Pincus D,
Serra E, Holl M, Brent R: (2006) Signal propagation and establishment
in yeast pheromone response system requires fast-acting negative
feedback. Submitted.
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Research publications in preparation
Benjamin KR, Thomson T, Endy D, Brent R: (2006) Careful
measurement reveals qualitative aspects of signaling and
enables construction of principled quantitative models. In
preparation.
Colman-Lerner A, Gordon A, Abola AP, Chin T, Yu R, Brent
R: (2006) Quantification of cis-membrane events in a prototypic
signal transduction pathway. In preparation.
Maxwell R, Resnekov O, Pincus D, Benjamin KR, Smith RD,
Brent R: (2006) Phosphorylation-dependent functional connections
among proteins in an information processing pathway. In preparation.
Pesce CG, Rockwell D, Gordon A, Colman-Lerner A, Brent R:
(2006) Single gene mutants in S.cerevisiae alter fundamental
statistical properties of quantitative system behavior. In
preparation.
Yu R, Gordon A, Colman-Lerner A, Brent R: (2006) Linear
information mapping in pheromone response signal transmission
system requires protein kinase dependent negative feedback.
In preparation.
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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, Weiss R: (2006) Engineering
life: building a fab for biology. Sci Am, 294:44-51. [ PubMed ]
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, Burbulis I: (2005) Reply to "Lamp for tadpoles".
Nature Methods, 2:635-636. [ PubMed | PDF ]
Brent R, Bruck J: (2006) 2020 computing: can computers help
to explain biology? Nature, 440:416-417. [ PubMed | PDF ]
Brent R, Lok L: (2005) Cell biology. A fishing buddy for
hypothesis generators. Science, 308:504-506. [ PubMed | PDF ]
Cook M: Networks of relations. Pasadena: California Institute
of Technology: 2005.
Endy D: (2005) Foundations for engineering biology. Nature,
438:449-453. [ 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: (2004) The need for speed in stochastic simulation.
Nat Biotechnol, 22:964-965. [ PubMed | PDF ]
Shen Y, Smith RD: (2005) Advanced nanoscale separations
and mass spectrometry for sensitive high-throughput proteomics.
Expert Rev Proteomics, 2:431-447. [ PubMed ]
Takahashi K, Nanda S, Arjunan V, Tomita M: (2005) Space
in systems biology of signaling pathways-towards intracellular
molecular crowding in silico. FEBS Letters, 579:1783-1788.
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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 TE, Brent R: (2001) Yeast Cbk1 and
Mob2 activate daughter-specific genetic programs to induce
asymmetric cell fates. Cell, 107:739-750. [ PubMed | PDF ]
Conrads TP, Anderson GA, Veenstra TD, Pasa-Tolic L, Smith
RD (2000) Utility of accurate mass tags for proteome-wide
protein identification. Anal Chem, 72:3349-3354. [ PubMed ]
Endy D, Brent R: (2001) Modelling cellular behaviour. Nature,
409:391-395. [ PubMed | PDF ]
Gibson, M. A. and J. Bruck (2000). "Efficient exact
stochastic simulation of chemical systems with many species
and channels." J. Phys Chem 104: 1876-1889. [ PDF ]
Levchenko A, Bruck J, Sternberg PW: (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
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.
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Publications about Center scientists
"From the cells up".(2005) The Guardian, March
10, 2005.
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
Gehl, J. (2004) Roger
Brent and the Alpha Project. Ubiquity, DOI:
Gibbs, W. W. (2004). Synthetic Life. Scientific American.
May 2004: 75-81.
Johnson, N. (2005). "Steal this genome". East
Bay Express.
Kamenetz (2006). Pop!Stars
2006. Fast Comany: 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.
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