Publications

yeast cycle

Selected papers including reviews and commentaries, but excluding current protocols

  1. Burnaevskiy N, Sands B, Yun S, Tedesco PM, Johnson TE, Kaeberlein M, Brent R, Mendenhall A. Chaperone biomarkers of lifespan and penetrance track the dosages of many other proteins. Nat Commun. 2019 Dec 16;10(1):5725
  2. Crane MM, Sands B, Battaglia C, Johnson B, Yun S, Kaeberlein M, Brent R, Mendenhall A. In vivo measurements reveal a single 5'-intron is sufficient to increase protein expression level in Caenorhabditis elegans. Sci Rep. 2019 Jun 24;9(1):9192.
  3. Brent R, Boucheron L. Deep learning to predict microscope images. Nat Methods. 2018 Nov;15(11):868-870
  4. Andrews SS, Brent R, Balázsi G. Transferring information without distortion. Elife. 2018 Oct 25;7. pii: e41894.
  5. Pesce CG, Zdraljevic S, Peria WJ, Bush A, Repetto MV, Rockwell D, Yu RC, Colman-Lerner A, Brent R. Single-cell profiling screen identifies microtubule-dependent reduction of variability in signaling.Mol Syst Biol. 2018 Apr 4;14(4):e7390.
  6. Mendenhall A, Crane MM, Leiser S, Sutphin G, Tedesco PM, Kaeberlein M, Johnson TE, Brent R. Environmental Canalization of Life Span and Gene Expression in Caenorhabditis elegans. J Gerontol A Biol Sci Med Sci. 2017 Aug 1;72(8):1033-1037.
  7. Mendenhall A, Crane MM, Tedesco PM, Johnson TE, Brent R. Caenorhabditis elegans Genes Affecting Interindividual Variation in Life-span Biomarker Gene Expression. J Gerontol A Biol Sci Med Sci. 2017 Oct 1;72(10):1305-1310.
  8. Andrews SS, Peria WJ, Yu RC, Colman-Lerner A, Brent R. Push-Pull and Feedback Mechanisms Can Align Signaling System Outputs with Inputs. Cell Syst. 2016 Nov 23;3(5):444-455.e2.
  9. Cao R, Jenkins P, Peria W, Sands B, Naivar M, Brent R, Houston JP. Phasor plotting with frequency-domain flow cytometry. Opt Express. 2016 Jun 27;24(13):14596-607.
  10. Mendenhall A, Driscoll M, Brent R. Using measures of single-cell physiology and physiological state to understand organismic aging. Aging Cell. 2016 Feb;15(1):4-13.
  11. Sands B, Brent R. Overview of post Cohen-Boyer methods for single segment cloning and for multisegment DNA assembly. Curr Protoc Mol Biol. 2016 Jan;113:3.26.1-3.26.20.
  12. Mendenhall AR, Tedesco PM, Sands B, Johnson TE, Brent R. Single cell quantification of reporter gene expression in live adult caenorhabditis elegans reveals reproducible cell-specific expression patterns and underlying biological variation. PLoS One. 2015 May 6;10(5):e0124289.
  13. Sands, B., Jenkins, P., Peria, W. J., Naivar, M., Houston, J. P., and Brent, R. Measuring and sorting cell populations expressing isospectral fluorescent proteins with different fluorescence lifetimes.PLoS ONE. 2014 9(10):e109940.
  14. Ventura, A. C., Bush, A., Vasen, G., Goldín, M. A., Burkinshaw, B., Bhattacharjee, N., Folch, A., Brent R., Chernomoretz, A., and Colman-Lerner, A. Utilization of extracellular information before ligand-receptor binding reaches equilibrium expands and shifts the input dynamic range. Proc. Natl. Acad. Sci. USA, 2014 111(37):E3860-3869.
  15. Flanigon J, Kamali-Moghaddam M, Burbulis I, Annink C, Steffen M, Oeth P, Brent R, van den Boom D, Landegren U, Cantor C, Multiplex protein detection with DNA readout via mass spectrometry. Nature Biotechnol. 2013 Jan 25;30(2):153-8. doi: 10.1016/j.nbt.2012.11.003. Epub 2012 Nov 28.
  16. Pincus, D., Ryan, C. J., Smith, R. D., Brent, R., and Resnekov, O. Assigning quantitative function to post-translational modifications reveals multiple sites of phosphorylation that tune yeast pheromone signaling output (2013). PLoS One. 8(3):e5654
  17. Thomson, T. M., Benjamin, K. R., Thomson, T. M., Love, T., Yu, R., Gordon, A., Colman-Lerner, A., Endy, D. and Brent, R. Scaffold number in yeast signaling system sets tradeoff between system output and dynamic range (2011). Proc. Natl. Acad. Sci., 108, 20265-20270.
  18. Andrews, S. S., Addy, N. J., Brent, R., and Arkin, A. P. Detailed simulations of cell biology with Smoldyn 2.1. PLoS Comput Biol. 6(3): e1000705 (2011).
  19. Brent, R. (2009) Cell signaling: what is the signal and what information does it carry? FEBS Lett. 583(24):4019-24. Dec 17. Epub. Review. PMID: 19917282
  20. Yu RCResnekov OAbola APAndrews SSBenjamin KRBruck JBurbulis IEColman-Lerner AEndy DGordon AHoll MLok LPesce CGSerra ESmith RDThomson TMTsong AEBrent R. The Alpha project, a model system for systems biology (2008) IET Syst Biol. 2008 Sep;2(5):222-33.
  21. Yu, R., Gordon, A., Colman-Lerner, A., Benjamin, K.R., Pincus, D., Serra, E., Holl, M., Brent, R. (2008) Negative feedback optimizes information transmission in a cell signaling system. Nature, 456, 755-761.
  22. Herrgård M. J., Swainston, N., Dobson, P., Dunn, W. B., Yalçin Arga, K., Arvas, N., Blüthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Li P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, Palson, B.Ø., Sauer. U., Oliver. S. G., Mendes, P. Neilsen, J., and Kell, D. B., A consensus yeast metabolic network obtained from a community approach to systems biology (2008). Nature Biotechnol. 26, 1155-1160.
  23. Soergel, D., Choi, K., Thompson, T., George, B., Morgan-Linial, R., Brent, R., and Endy, D. MONOD: a collaborative tool for manipulating biological knowledge (2008) MIT Synthetic Biology Archive http://dspace.mit.edu/handle/1721.1/41867
  24. Burbulis, I., Yamaguchi, K., Yu, R. C., Resnekov, O., and Brent, R. (2007) Using a "near-universal" protein-DNA chimera to detect and count small numbers of antibodies. Nature Methods 4, 1011-1013
  25. Gordon, A., Colman-Lerner, A., Chin, T.E., Benjamin, K.R., Brent, R. (2007) Single-cell quantification of molecules and rates using open source microscope based cytometry. Nature Methods, 4, 175-181
  26. Brent, R.  Power and responsibility.  (2006)  MIT Synthetic Biology Archive http://hdl.handle.net/1721.1/34913, DOI: 1721.1/34913, https://dspace.mit.edu/bitstream/1721.1/34913/1/PowerandResponsibility.pdf
  27. Brent. R. In the valley of the shadow of death (2003-2006) MIT Synthetic Biology Archive http://hdl.handle.net/1721.1/34914, DOI: 1721.1/34914, https://dspace.mit.edu/bitstream/1721.1/34914/1/Valley2006.pdf
  28. Colman-Lerner, A., Gordon, A., Serra, E., Chin, T., Resnekov, O., Endy, D., Pesce, G. and Brent, R. (2005) Regulated cell-to-cell variation in a cell fate decision systemNature. 437, 699-706
  29. Brent, R., Bruck, J. 2020 computing: can computers help to explain biology? Nature, (2005) 440, 416-417
  30. Brent, R. and Lok, L. A fishing buddy for hypothesis generators. Science 2005, 308, 504-506
  31. Lok, L. and Brent, R. Automatic generation of cellular reaction networks with Moleculizer 1.0. Nature Biotechnology 2005, 23:131-136.
  32. Burbulis, I., Yamaguchi, K., Carlson, R., and Brent, R. Using protein-DNA chimeras to detect and count small numbers of molecules. Nature Methods 2005, 2:31-37.
  33. Brent, R. A partnership between biology and engineering. Nature Biotechnology 2004, 22, 1211-1214.
  34. Brent, R. Building an artificial regulatory system to understand a natural one. Cell 2004, 116 (2 Suppl) S73-S76
  35. Brent, R. Intuition and innumeracy. Cell Biol. Educ. 2004, 3, 88-90
  36. Mendelsohn, A. Hamer, J. Zhaoyuan, B.W. Brent, R. Cyclin D3 activates Caspase 2, connecting cell proliferation with cell death. Proc. Natl. Acad. Sci. USA, 2002 99, 6871-6876
  37. Endy, D. and Brent, R. Modeling cellular behavior. Nature 2001, 409, 391-395
  38. Colman-Lerner, A. Chin, T. and Brent, R. Yeast Cbk1 and Mob2 proteins kinase activate distinct daughter-specific genetic programs that induce asymmetric cell fates. Cell 2001, 107, 739-750
  39. Colman-Lerner, A. and Brent, R. Using peptide aptamers to analyse the proteome. Trends in Cell Biology, New Technologies in the life sciences, a Trends Guide, Supplement, 2000,12, 56-60
  40. Geyer, R., and Brent, R. Selection of genetic agents from random peptide aptamer expression libraries. Methods Enzymol. 2000, 328, 171-208
  41. Brent, R. and Kodadek, T. Interaction, assembly and processing: Life on an interface. Current Opinion in Chemical Biology, 2000, 4, 3-15.
  42. Brent, R. Genomic Biology, Cell, 2000, 100, 169-183.
  43. Colas, P., Cohen, B., Ferrigno, P., Silver, P. A., and Brent, R. Targeted modification and transportation of cellular proteins. Proc. Natl. Acad. Sci. USA, 2000, 97, 13720-13725
  44. Meroni, G., Cairo, S., Merla, G., Messali, S., Brent, R., Ballabio A, Reymond A. Mlx, a new Max-like bHLHZip family member: the center stage of a novel transcription factor regulatory pathway?Oncogene, 2000, 19, 3266-3277.
  45. Raj, L., Hanes, S. D., Appel, L. F., Badam, E. Fernandez, M., Finley, R. L. Jr., Brent, R., and Weir, M. Targeted localized degradation of Paired protein in Drosophila development. Current Biology, 2000, 10, 1265-1272.
  46. Fabbrizio, E., Le Cam, L., Polanowska, J., Kaczorek, M., Lamb, N., Brent, R., and Sardet, C. Inhibition of mammalian cell proliferation by genetically selected peptide aptamers that functionally antagonize E2F activity, Oncogene, 1999, 18, 4357-4363.
  47. Mendelsohn, A. R., and Brent, R. Protein interaction methods: toward an endgame. Science 1999, 284, 1948-1950.
  48. Brent. R., and Carlson, R. Double stranded DNA arrays: next steps in the surface campaign, Nature Biotechnology, 1999, 17, 536-537.
  49. Brent, R. Functional genomics: learning to think about gene expression data. Current Biology, 1999, 9, 338-341.
  50. Geyer, R., Colman-Lerner, A., Chin, T. and Brent, R. "Mutagenesis" by peptide aptamers identifies genetic network members and pathway connections. Proc. Natl. Acad. Sci. USA, 1999, 96, 8567-8572
  51. Mendelsohn, A. R., and Brent, R. Postgenomic protein analysis: the next bend in the river. Nature Biotechnology, 1998, 16, 520-521
  52. Colas, P., and Brent, R. The impact of two-hybrid and related methods on biotechnology. Trends in Biotechnology, 1998, 16, 355-363.
  53. Cohen, B., Colas, P, and Brent, R. A novel cell cycle inhibitor isolated from a combinatorial library, Proc. Natl. Acad. Sci. USA, 1998, 95, 14272-14277
  54. Marti, F., Xu, C. W., Selvakuman, A., Brent, R., Dupont, B., and King, P. D. LCK phosphorylated human killer cell inhibitory receptors recruit and activate phosphatidylinositol 3-kinase, Proc. Natl. Acad. Sci. USA, 1998, 95, 11810-11815
  55. Current Protocols in Molecular Biology, chapter 22, Nucleic acid arrays  (editor).  1987-2008. Current Protocols in Molecular Biology (ed F. M. Ausubel, R. Brent, D. D. Moore, J. Seidman, J. A. Smith, and K. Struhl) John Wiley and Sons, New York. I did limited writing for this chapter.
  56. Brent, R., and Finley, R. L., Jr. Understanding gene and allele function with two-hybrid methods. Ann. Rev. Genetics, 1997. 31, 663-704.
  57. Brent, R. Raising the next generation of scientific pioneers. Journal of NIH Research, 1997.  9, 37-38.
  58. Brent, R. Looms to weave genomic nets. Nature Genetics, 1997. 16, 216-217. 
  59. Finley, R, and Brent R., 1997.  Two-hybrid analysis of genetic networks. In "The Two Hybrid System", P. Bartel and S. Fields, editors, Oxford University Press, London.
  60. Golemis, E. and Brent R., 1997. The interaction trap. In "The Two Hybrid System", P. Bartel and S. Fields, editors, Oxford University Press, London.
  61. Xu, C. W., Mendelsohn, A., and Brent, R. Cells that register logical relationships among proteins. Proc. Natl. Acad. Sci. USA, 1997, 94, 12473-12478
  62. Meroni, G., Reymond, A., Borsani, G. Tanigami, A., Tonlorenzi, R., Lo Nigro, C., Messali, S., Zollo, M., Ledbetter, D. H., Brent, R., Ballabio, A., and Carrozzo, R. Rox, a novel bHLH-Zip expressed in quiescent cells that heterodimerizes with Max, binds a non-canonical E box, and acts as a transcriptional repressor. EMBO Journal, 1997, 16, 2892-2906
  63. Thomas, B. J., Zavitz, K. H., Dong, X., Lane, M. E., Weigman, K., Finley, R., Brent, R., Lehner, C. F., and Zipursky, S. L. roughex downregulates G2 cyclins in G1. Genes and Development, 1997, 10, 1289-1298
  64. Finley, R., Thomas, B.J., Zipursky, L., and Brent, R. Isolation of Drosophila cyclin D, whose expression in the morphogenetic furrow precedes entry into S phase. Proc. Natl. Acad. Sci. USA, 1996, 93, 3011-3015
  65. Colas, P., Cohen, B., Jessen, T., Grishina, I., McCoy, J., and Brent, R. Genetic selection of peptide aptamers that recognize and inhibit Cyclin-dependent kinase 2. Nature 1996, 380, 548-550
  66. Finley, R., and Brent, R. The interaction trap. In DNA cloning - expression systems: a practical approach. (ed D. Glover and B. D. Hanes) Oxford University Press, Oxford, England. 1996.
  67. Clemens, Karen E., Brent, R., Gyuris, J., and Munger, K. Characterization of protein/protein interaction domains of the human papillomavirus E7 oncoprotein. Virology 1995, 214, 289-293
  68. Zervos A, Faccio, L, Gatto, J., and Kyriakis, J., and Brent, R. Mxi2, a mitogen-activated protein kinase that recognizes and phosphorylates Max protein. Proc. Natl. Acad. Sci. USA. 1995, 92, 10531-10534
  69. Steingrimsson, E., Sawadogo, M., Gilbert, D., Zervos, A.S., Brent, R., Blanar, M.A., Fisher, D.E., Copeland, N.G., and Jenkins, N.A. Murine chromosomal location of five bHLH-zip transcription factor genes. Genomics 1995; 28, 179- 183.
  70. Reymond, A. and Brent, R. p16 from human tumors shows diminished interaction with Cdk4. Oncogene 1995, 11: 1173-1178.
  71. Estojak, J., Brent, R., and Golemis, E. Correlation of two hybrid affinity data with in vitro measurements. Mol. Cell. Biol. 1995. 15, 5820-5829
  72. Su, L-K., Burrell, M., Hill, D.E., Gyuris, J., Brent, R., Wiltshire, R., Trent, J., Vogelstein, B., and Kinzler, K.W. APC binds to the novel protein, EB1. Cancer Research 1995, 55, 2972-2977
  73. Mendelsohn, A, and Brent, R.  Biotechnology applications of interaction trap/ two-hybrid systems. Current opinion in Biotechnology, 1994, 5, 482-486.
  74. Khazak, V., Sadhale, P., Woychik, N. A., Brent, R., and Golemis, E. A. Human RNA polymerase II subunit hsRPB7 functions in yeast and influences stress survival and cell morphology. Mol Biol Cell 1995, 6, 759-775.
  75. Lee, J. W., Choi, H., S., Gyuris, J., Brent, R., and Moore, D. D. Two classes of proteins dependent on either the presence or absence of thyroid hormone for interaction with the thyroid hormone receptor. Molecular Endocrinology 1995, 9: 243-254.
  76. Finley, R. L., and Brent, R. Binary and ternary interactions between Drosophila cell cycle regulators. Proc. Natl. Acad. Sci. USA, 1994, 91, 12980-12984
  77. Paroush, Z., Finley, R., Brent, R., and Ish-Horowicz, D. Interactions between Groucho and bHLH proteins mediate transcription repression during Drosophila neurogenesis, segmentation, and sex-determination. Cell 1994, 79, 805-816
  78. Hanes, S. D and Brent, R. Backwards Bicoid? Structure, 1994, 2, 894.
  79. Cuomo, C., Kirch, S., Gyuris, J, Brent, R., and Oettinger, M. A. Rch1, a protein that specifically interacts with RAG-1 and affects V(D)J recombination. Proc. Natl. Acad. Sci. USA. 1994, 91, 6156-6160
  80. Hanes S, Riddehough G, Ish-Horowicz D, and Brent R. Specific DNA recognition and intersite spacing are critical for action of the Bicoid.
  81. Edelhoff, S., Ayer, D.E., Zervos, A.S., Steingrimsson, E., Jenkins, N.A., Copeland, N.G., Eisenman, R.N., Brent, R., and Disteche, C. Mapping of two genes encoding members of a distinct subfamily of Max interacting proteins: Mad to human chromosome 2 and mouse chromosome 6, and Mxi1 to human chromosome 10 and mouse chromosome 19. Oncogene 1994, 9, 665-668
  82. Gyuris J, Golemis E, Chertkov H, and Brent R. Cdi1, a human tyrosine phosphatase that associates with Cdk2 during G1. Cell. 1993, 75, 791-803.
  83. Zervos A, Gyuris J, and Brent R. Mxi1, a protein that specifically interacts with Max to bind Myc/Max recognition sites. Cell. 1993, 72, 223-232
  84. Golemis E, and Brent R. Fused protein domains inhibit DNA binding by LexA. Mol Cell Biol 1992; 12:3006-3014.
  85. Kamens J, Brent R. Native Rel and Dorsal proteins recognize distinct DNA sequences. New Biologist 1991, 10, 1005-1013
  86. Hanes SD and Brent R. A genetic model for the interaction of the homeodomain recognition helix with DNA. Science 1991, 251, 426-430.
  87. Kamens J, Richardson P, Mosialos G, Brent R, Gilmore T. Oncogenic transformation by vRel requires an amino-terminal activation domain. Mol Cell Biol 1990, 6, 2840-2847.
  88. Hanes SD, Brent R. DNA specificity of the Bicoid activator protein is determined by the homeodomain recognition helix residue 9. Cell 1989, 57, 1275-1283.
  89. Samson M-L, Jackson-Grusby L, Brent R. Gene activation and DNA binding by Drosophila Ubx and abd-A proteins. Cell 1989, 57, 1045-1052.
  90. Lech K, Anderson K, Brent R. DNA-bound Fos proteins activate transcription in yeast. Cell 1988, 53, 179-184.
  91. Brent R. How to run a very small factory. Cell 1986; 47; 329-330.
  92. Silver PA, Brent R, Ptashne M. DNA binding is not sufficient for nuclear localization of regulatory proteins in Saccharomyces cerevisiae. Mol Cell Biol 1986, 6, 4763-4766.
  93. Brent R, Ptashne M. A eukaryotic transcriptional activator bearing the DNA specificity of a prokaryotic repressor. Cell 1985, 43, 729-736.
  94. Brent R. Repression of transcription in yeast. Cell 1985; 42:3-4.
  95. Brent R, Ptashne M. A bacterial repressor protein or a yeast transcriptional terminator can block upstream activation of a yeast gene. Nature 1984, 312, 612-615.
  96. Ebina Y, Takahara Y, Kishi F, Nakazawa A, Brent R. LexA protein is a repressor of the Colecin E1 gene. J Biol Chem 1983, 248, 13258-13261.
  97. Kenyon C, Brent R, Ptashne M, Walker G. Regulation of damage inducible genes in Escherichia coli. J Mol Biol 1982, 610, 445-457.
  98. Brent R. Regulation and autoregulation by lexA protein. Biochimie 1982; 64, 565-569.
  99. Brent R, Ptashne M. Mechanism of action of the lexA gene product. Proc Natl Acad Sci 1981, 78, 4204-4208.
  100. Brent R, Ptashne M. The wild-type lexA gene product represses its own promoter. Proc. Natl. Acad. Sci. 1980, 77, 1932-1938.