Silver: Publications (By subject)

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(Synthetic Biology and Bioengineering)
(Synthetic Biology and Bioengineering)
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*Haynes K, Ceroni F, Flicker D, Younger A and Silver PA.  A sensitive switch for visualizing natural gene silencing in single cells. 2012.  ACS Synthetic Biology, Mar 16;1(3):99-106.
*Haynes K, Ceroni F, Flicker D, Younger A and Silver PA.  A sensitive switch for visualizing natural gene silencing in single cells. 2012.  ACS Synthetic Biology, Mar 16;1(3):99-106.
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*Lohmueller J, Armel T, and Silver PA. A tunable zinc finger-based framework for Boolean logic computation in mammalian cells.  2012, Nuc Acids Res., Jun;40(11):5180-7. doi: 10.1093/nar/gks142. Epub 2012 Feb 9.
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*Silver PA, Haynes K, Weiss R.  Synthetic meets cell biology. Mol Biol Cell. 2012 Mar;23(6):967.
*Nishida K and Silver PA.  Induction of Biogenic Magnetization and Redox Control by a Component of the Target of Rapamycin Complex 1 Signaling Pathway. PLoS Biology.  2012.  [[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001269].  [http://wyss.harvard.edu/viewpressrelease/78/ Press Release]
*Nishida K and Silver PA.  Induction of Biogenic Magnetization and Redox Control by a Component of the Target of Rapamycin Complex 1 Signaling Pathway. PLoS Biology.  2012.  [[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001269].  [http://wyss.harvard.edu/viewpressrelease/78/ Press Release]

Revision as of 13:58, 20 January 2013

THIS PAGE IS A WORK IN PROGRESS - NOT A COMPLETE LIST YET

Contents

Synthetic Biology and Bioengineering

  • Mattozzi M, Ziesack M, Voges MJ, Silver PA, Way JC. Expression of the sub-pathways of the Chloroflexus aurantiacus 3-hydroxypropionate carbon fixation bicycle in E. coli: Toward horizontal transfer of autotrophic growth. 2013. Metabolic Eng., accepted for publication.
  • Ford TJ and Silver PA. Rephrasing the biofuel question. 2013. Microbe, in press.
  • Ducat DC, Avelar-Rivas JA, Way JC and Silver PA. Re-routing carbon-flux to enhance photosynthetic productivity. 2012. App & Env Eng., 2012 Apr;78(8):2660-.
  • Burrill DR, Inniss MC, Boyle PM and Silver PA. Synthetic memory circuits for tracking human cell fate. 2012. Genes & Dev., 26:1486-1497.
  • Haynes K, Ceroni F, Flicker D, Younger A and Silver PA. A sensitive switch for visualizing natural gene silencing in single cells. 2012. ACS Synthetic Biology, Mar 16;1(3):99-106.
  • Lohmueller J, Armel T, and Silver PA. A tunable zinc finger-based framework for Boolean logic computation in mammalian cells. 2012, Nuc Acids Res., Jun;40(11):5180-7. doi: 10.1093/nar/gks142. Epub 2012 Feb 9.
  • Silver PA, Haynes K, Weiss R. Synthetic meets cell biology. Mol Biol Cell. 2012 Mar;23(6):967.
  • Nishida K and Silver PA. Induction of Biogenic Magnetization and Redox Control by a Component of the Target of Rapamycin Complex 1 Signaling Pathway. PLoS Biology. 2012. [[1]. Press Release
  • Kennedy, CJ, Boyle, PM, Waks, Z, and Silver, PA Systems-level engineering of non-fermentation metabolism in yeast. 2009. Genetics, in press.
  • Waks, Z. and Silver, PA. Engineering a synthetic dual organism system for hydrogen production. 2009. Applied and Environmental Microbiology. 75:1867-75.
  • Savage, DF, Way, J and Silver, PA. Defossilling fuel: how synthetic biology can transform biofuel production. 2008. ACS Chem. Biol. 3:13-6.
  • Cironi, P, Swinburne, IA, and Silver, PA. Enhancement of cell-type specificity by quantitative modulation of a chimeric ligand. 2008. J. Biol Chem.
  • Drubin, DA, Way, JC, and Silver, PA. Designing Biological Systems. 2007. Genes and Development, 21:242-54
  • Ajo-Franklin, CM, Drubin, DA, Eskin, J., Gee, E., Landgraf, D., Philips, I. and Silver, PA. Rational design of memory in eukaryotic cells. 2007. Genes and Development, 2271-6.
  • Zhou, Z.*, Cironi, P.*, Lin, AJ.*, Xu, Y., Hrvatin, S., Golan, DE., Silver, PA., Walsh, CT., Yin, J. Genetically encoded short peptide tags for orthogonal protein labeling by Sfp and AcpS phosphopantetheinyl transferases. 2007. ACS Chemical Biology, 2:337-346. (* These authors contribute equally)
  • Phillips I, Silver P, A New Biobrick Assembly Strategy Designed for Facile Protein Engineering, MIT Synthetic Biology Working Group Reports, published online 20 April 2006 at MIT dspace (doi: 1721.1/32535)
  • Drubin, DA., Garakani, AM., and Silver, PA. Motion as phenotype. The use of live-cell imaging and machine visual screening to characterize transcription-dependent chromosome dynamics. 2006. BMC Cell Biology, 7:19. Abstract.
  • Hitchcock, A.L., Kahana, J.A., and Silver, P.A. The uses of green fluorescent protein in yeasts. 2006. Methods Biochem Anal. 47:179-201
  • Brodsky, A.S. and Silver, P.A. A microbead-based system for identifying and characterizing RNA-protein interactions by flow cytometry. Mol Cell Proteomics 2002; 1(12): 922-9. Abstract
  • Devroe, E. and Silver, P.A. Retrovirus-delivered siRNA. BMC Biotechnol. 2002; 2(1): 15. Abstract
  • Krebber, H. and Silver, P.A. Directing proteins to nucleus by fusion to nuclear localization signal tags. Methods Enzymol 2000;327:283-96. Abstract
  • Colas, P., Cohen, B., Ferrigno, P.K., Silver, P.A., and Brent, R. Targeted modification and transportation of cellular proteins. Proc.Natl.Acad.Sci. USA 2000 Dec 5; 97(25): 13720-13725.

Systems Biology

  • Lee, S., Dudley, AM, Drubin, D., Silver, PA, Krogan, N., Pe'er, D., and Koller, D. Learning a Prior on Regulatory Potential from eQTL data. 2009, PLos Genetics, in press.
  • Way, J. and Silver, PA. Molecular systems biology in drug development. 2007. Clinical Pharmacology and Therapeutics, in press.
  • Komili, S., Farny, NG, Roth, FP and Silver, PA. Functional specificity among ribosomal proteins regulates gene expression. 2007. Cell 131:557-71.
  • McKee, AE and Silver, PA. 2007. Systems perspective on mRNA processing. 2007. Cell Research, 7:581-90.
  • Way, J. and Silver, PA. Systems engineering without an engineer: Why we need systems biology. 2007, Complexity, 13:22-29.
  • Komili, S. and Silver, PA. Coupling of gene expression mechanisms - insights from global studiess. 2007. Nature Reviews in Genetics. In press.
  • Moore, M. and Silver, PA. Global analysis of mRNA splicing. 2007. RNA, in press.
  • Moore, M., Schwartzfarb, EM, Silver, PA and Yu, MC. Differential recruitment of the splicing machinery during transcription predicts genome-wide patterns of mRNA splicing. 2006. Molecular Cell, 24:903-915.
  • Tsankov, A., Brown, C., Yu, M., Win, M., Silver, PA. and Casolari, J. Communication between levels of transcriptional organization improve robustness and adaptivity. 2006, Molecular Systems Biology, 2:65 (featured article)

Genome Organization and Dynamics

  • Brown, CR, Kennedy, CJ, Delmar, VA, Forbes, DJ, and Silver, PA. Global histone acetylation induces functional genomic reorganization at mammalian nuclear pore complexes. 2008. Genes and Dev., in press.
  • Brown, CR and Silver, PA. Transcriptional regulation at the nuclear pore complex. 2007. Curr. Opin Genet Dev. 2:100-6.
  • Yu, MC, Lamming, DW, Eskin, JA, Sinclair, DA, and Silver, PA. The role of protein arginine methylation in formation of silent chromatin. 2006, Genes and Development, 20:3249-5
  • Auld, KL., Brown, CR., Casolari, JM., Komili, S. and Silver, PA. Genomic Association of the Proteasome Demonstrates Overlapping Gene Regulatory Activity with Transcription Factor Substrates. 2006. Molecular Cell, 21:861-871. Absract.
  • Carroll, JS, Meyer, CA, Song, J., Li, W., Geistlinger, TR, Eeckhoute, J., Brodsky, A., Krasnickas, K., Fertuck, KC, Hall, G., Wang, Q., Bekiranov, S., Sementchenko, V., Fox, EF., Silver, PA, Gingeras, T., Liu, XS, and Brown, M. Genome-wide analysis of estrogen receptor binding sites. 2006. Nature Genetics, 38:1289-97.
  • Casolari, J.M., Brown, C.R., Drubin, D.A., Rando, O.J., and Silver, P.A. Developmentally induced changes in transcriptional program alter spatial organization across chromosomes. Genes Dev. 2005. May 15;19(10):1188-98.
  • Carrol, J.S., Liu, X.S., C.R., Brodsky, A.S., Meyer, C.A., Li, W., Szary, A., Shao, W., Hesterman, E., Geistlinger, T.R., Fox, E.A., Silver, P.A., and Brown, M. Chromosome-wide mapping of estrogen receptor binding reveals long-range combinatorial regulation requiring forkhead proteins. Cell. 2005. July 15;122(1):33-43
  • Casolari, J.M., Brown, C.R., Drubin, D.A., Rando, O.J., and Silver, P.A. Developmentally induced changes in transcriptional program alter spatial organization across chromosomes. Genes Dev. 2005. May 15;19(10):1188-98.
  • Brodsky, A.S., Meyer, C.A., Hall, G., Swinburne, I.A., Keenan, B.J., Liu, X.S., Fox, E.A., and., Silver, P.A. Genomic mapping of RNA Polymerase II reveals sites of co-transcriptional regulation in human cells. Genome Biology. 2005. Jul 15:6(8): R64 Abstract
  • Damelin, M., Simon, I., Moy, T.I., Wilson, B., Komili, S., Tempst, P., Roth, F.P., Young, R.A., Carins, B.R., and Silver, P.A. The genome-wide localization of Rsc9, a component of the RSC chromatin-remodeling complex, changes in response to stress. Mol Cell 2002; 9 (3): 563-73.

RNA and Ribosome Dynamics

  • Hurt, J., Farny, N. and Silver, PA. A conserved CCCH-zinc finger type protein regulates mRNA nuclear adenylation and export. 2009. J. Cell Biol., 185:279-290.
  • Farny, NG, Hurt, JA and Silver, PA. Definition of global and transcript-specific mRNA export pathways in metazoans. 2008. Genes & Dev., in press.
  • Moore, M. and Silver, PA. Global analysis of mRNA splicing. 2007. RNA, in press.
  • McKee, AE and Silver, PA. 2007. Systems perspective on mRNA processing. 2007. Cell Research, 7:581-90.
  • McKee, A., Neretti, N., Carvalho, LE, Meyer, CA, Fox, EA, Brodsky, AS, and Silver, PA, Exon expression profiling reveals stimulus-mediated exon use in neural cells. 2007. Genome Biology, in R15.
  • Moore, M., Schwartzfarb, EM, Silver, PA and Yu, MC. Differential recruitment of the splicing machinery during transcription predicts genome-wide patterns of mRNA splicing. 2006. Molecular Cell, 24:903-915.
  • Swinburne, IA., Meyer, CA., Liu, S., Silver, PA, and Brodsky, AS. Genomic localization of RNA binding proteins reveals links between pre-mRNA processing and transcription, 2006. Genome Research, Abstract.
  • Gama-Carva;ho, M., Barbosa-Morais, N., Brodsky, A., Silver, PA and Carmo-Fonesca, M. Genome wide identification of functionally distinct subsets of cellular mRNAs associated with two nucleocytoplasmic-shuttling mammalian splicing factors. 2006. Genome Biology, in press
  • Bachand, F., Lackner, D., Bahler, J., and Silver, PA. Autoregulation of ribosome bio-synthesis by a translational response in fission yeast. 2006. Mol Cell Biol., 26:1731-42. Absract
  • McKee, A.E., Minet, E., Stern, C., Riahi, S., Stiles, C.D., and., Silver, P.A. A genome-wide in situ hybridization map of RNA-binding proteins reveals anatomically restricted expression in the developing mouse brain. BMC Dev Biol. 2005. July 20;5(1):14
  • Hieronymus, H., Yu, M.C., and Silver, P.A. Genome-wide mRNA surveillance is coupled to the mRNA export. Genes Dev. 2004. Nov 1; 18(21):2652-62.Abstract
  • Yu, M.C., Bachand F., McBride, A.E., Komili, S., Casolari, J.M., and Silver, P.A. Arginine methyltransferase affects interactions and recruitment of mRNA processing and export factors. Genes Dev 2004, Aug. 15. 18(16):2024-35. Abstract
  • McKee A.E.. and Silver, P.A. REF-ereeing the cytoplasmic fate of mRNA via nuclear export. Dev Cell 2004. July 7; 23(13):2641-50.Abstract
  • Bachand, F. and Silver, P.A. PRMT3 is a ribosomal protein methyltransferase that affects the cellular levels of ribosomal subunits. EMBO J 2004. July 7; 23(13):2641-50.Abstract
  • Hieronymus, H. and Silver, P.A. Genome-wide analysis of RNA-protein interactions illustrates specificity of the mRNA export machinery. Nat. Genet. 2003; 33(2):155-61. Abstract
  • Lei, E.P., Stern, C.A., Fahrenkrog, B., Krebber, H., Moy, T.I., Aebi, U. and Silver, P.A., Sac3 is an mRNA export factor that localizes to the cytoplasmic fibrils of the nuclear pore complex. Mol Biol Cell 2002; In Press.
  • Lei, E. P. and Silver, P.A. Intron status and 3'-end formation control cotranscriptional export of mRNA. Genes Dev 2002; 16: 2761-2766. Abstract
  • Moy, T.I., and Silver, P.A. Requirements for the nuclear export of the small ribosomal subunit. J Cell Sci 2002; 115 (Pt 14): 2985-95.Abstract
  • Lei, E.P. and Silver, P.A. Protein and RNA export from the nucleus. Dev Cell. 2002; 2 (3): 261-72. Abstract
  • Valentini, S.R., Casolari, J.M., Oliveira, C.C., Silver, P.A. and McBride, A.E. Genetic interactions of yeast eukaryotic translation initiation factor 5A (eIF5A) reveal connections to poly(A)-binding protein and protein kinase C signaling. Genetics 2002; 160 (2): 393-405. Abstract
  • Lei, E.P., Krebber, H., and Silver, P.A. Messenger RNAs are recruited for nuclear export during transcription. Genes Dev. 2001; 15(14): 1771-1782. Abstract
  • Brodsky, A.S. and Silver, P.A. Pre-mRNA processing factors are required for nuclear export. RNA 2000; 6(12): 1737-1749.Abstract
  • Stage-Zimmermann, T., Schmidt, U. and Silver, P.A. Factors Affecting Nuclear Export of the 60S Ribosomal Subunit In Vivo. Mol Biol Cell 2000 Nov;11(11):3777-3789. Abstract
  • Shen, E.C., Stage-Zimmermann, T., Chui, P., and Silver, P.A. The yeast mRNA binding protein Npl3p interacts with the Cap Binding Complex. J. Biol. Chem. 2000 May 22. Abstract

Disease Pathways

  • Arbiser, JL, Kau, T., Silver, PA, Bain, J., Bai, X., and Bowen, P. Solenopsin, the alkaloidal component of the fire ant (Solenopsis invicta), is a naturally occurring inhibitor of phosphatidylinositol-3-kinase signaling and angiogenesis. 2007. Blood, 109:560
  • Frietze, S., Lupien, M., Silver, PA and Brown, N. Coactivator associated arginine methyltransferase CARM1 is required for estrogen stimulated breast cancer growth through regulation of E2F1. 2007. Cancer Research, in press
  • Vandegraaff, N., Devroe, E., Turlure, F., Silver, P.A., and Engelman, A. Genetic and biochemical analyses of integrase-interaction proteins lens epithelium-derived growth factor (LEDGF/p75) and hepatoma-derived growth factor 2 (HRP2) in preintegration complex formation and HIV replication. 2006, Virology, in press. Abstract
  • Kau, T.R., Schroeder, F., Ramazwamy, S., Wojciechowski, C.L., Zhao, J.J., Roberts, T.M., Clardy, J., Sellers, W.R., and Silver, P.A. A Chemical genetic screen identifies inhibitors of regulated nuclear export of a Forkhead transcription factor in PTEN deficient tumor cells. Cancer Cell. 2003; 4(6):463-76. Abstract
  • Haggarty, S.J., Koeller, K.M., Kau, T.R., Silver, P.A., Roberge, M., and Schreiber, S.L. Small molecule modulation of the human chromatid decatenation checkpoint. Chem. Biol. 2003; 10(12):1267-79.
  • Kau, T.R., Way, J.C., and Silver, P.A. Nuclear transport and cancer: from mechanism to intervention. Nat. Rev. Cancer. 2004; Feb; 4(2):106-17. Abstract
  • Kau, T.R. and Silver, P.A. Nuclear transport as a target for cell growth. Drug Discov. Today. 2003; 8(2):78-85. Abstract

Protein Methylation

  • Frietze, S., Lupien, M., Silver, PA and Brown, N. Coactivator associated arginine methyltransferase CARM1 is required for estrogen stimulated breast cancer growth through regulation of E2F1. 2008. Cancer Research, in press.
  • Yu, MC, Lamming, DW, Eskin, JA, Sinclair, DA, and Silver, PA. The role of protein arginine methylation in formation of silent chromatin. 2006, Genes and Development, 20:3249-54
  • Yu, M.C., Bachand F., McBride, A.E., Komili, S., Casolari, J.M., and Silver, P.A. Arginine methyltransferase affects interactions and recruitment of mRNA processing and export factors. Genes Dev 2004, Aug. 15. 18(16):2024-35. Abstract
  • Weiss, V. H., McBride, A. E., Kim, H. K., Hogle, J. M., and Silver, P. A. The structure and oligomerization of the yeast arginine methyltransferase, Hmt1. Nat. Struct. Biol. 2000; 7: 1165-1171. Abstract
  • Valentini, S.R., Weiss, V.H., and Silver, P.A. Arginine methylation and binding of Hrp1p to the efficiency element for mRNA 3'-end formation. RNA 1999; 5(2):272-80.

Nuclear Transport

  • Goffin, L., Vodala, S., Fraser, C., Ryan, J., Timms, M., Meusburger, S., Catimel, B., Nice, EC, Silver, PA., Xiao, CY, Jans, DA., and Gething, MJ. The unfolded protein response transducer Ire1p contains a nuclear localization sequence recognized by multiple beta importins. 2006. Mol Bio Cell, 17:5309-5322.
  • Robinson, M.A., Park, S., Sun, Z.Y., Silver, P.A., Wagner, G., and Hogle, J.M. Multiple conformations in the ligand-binding site of the yeast nuclear pore targeting domain of Nup116p J. Biol. Chem. 2005. Aug 16. Abstract
  • Schroeder, F.C., Kau, T.R., Silver, P.A., and Clardy, J. The psammaplysenes, specific inhibitors of FOXO1a nuclear export. J Nat Prod 2005. Apr; 68(4):574-6. Abstract
  • Lu, R., Limon, A., Devroe, E., Cherepanov, P., Silver, P.A., and Engelman, Class II integrase mutants with changes in putative nuclear localization signals are primarily blocked at a post-nuclear entry step of human immunodeficiency virus type 1 replication. J. Virol. 2004. Dec; 78(23):12735-46.Abstract
  • Devroe, E., Engelman, A., and Silver, P.A. Intracellular transport of human immunodeficiency virus type 1 integrase J. Cell. Sci. 2003; 116(Pt21):4401-8. Abstract
  • Damelin, M. and Silver, P.A. In situ analysis of spatial relationships between proteins of the nuclear pore complex. Biophys J. 2002; 83(6): 3626-36.Abstract
  • Limon A., Devroe, E., Lu, R., Ghory, H.Z., Silver, P.A., and Engelman, A. Nuclear localization of human immunodeficiency virus type 1 preintegration complexes (PICs): V165A and R166A are pleiotropic integrase mutants primarily defective for integration, not PIC nuclear import. J Virol. 2002; 76(21): 10598-607.Abstract
  • Hood, J.K., Hwang, W.W., and Silver, P.A. The Saccharomyces cerevisiae cyclin Clb2p is targeted to multiple subcellular locations by cis- and trans-acting determinants. J. Cell Sci. 2001; 114 (3): 589-597. Abstract
  • Hood, J.K., Casolari, J.M., and Silver, P.A. Nup2p is located on the nuclear side of the nuclear pore complex and coordinates Srp1p/importin-alpha export. J. Cell Sci. 2000 Apr;113 (Pt 8):1471-80. Abstract
  • Jones, A.L., Quimby, B.B., Hood, J.K., Ferrigno, P., Keshava, P.H., Silver, P.A., and Corbett, A.H. SAC3 may link nuclear protein export to cell cycle progression. Proc. Natl. Acad. Sci. USA 2000 Mar 28;97(7):3224-9. Abstract
  • Damelin, M. and Silver, P.A. Mapping interactions between nuclear transport factors in living cells reveals pathways through the nuclear pore complex. Mol. Cell 2000; 5: 133-140. Abstract

Membranes and Proteins

  • Auld, K., Hitchcock, AL, Doherty, HK, Frietze, S., Huang, LS and Silver PA . A conserved ATPase Get3/Arr4 modulates the activity of membrane-associated proteins in Saccharomyces cerevisiae. 2006. Genetics, 174:215-27.
  • Beilharz T., Egan, B., Silver, P.A. Hofmann, K., and Lithgow, T. Bipartite signals mediate subcellular targeting of tail-anchored membrane protein in saccharomyces cerevisiae. J. Biol. Chem. 2003; [epub ahead of print].Abstract
  • Hitchcock, A.L., Krebber, H., Frietze, S., Lin, A., Latterich, M., and Silver, P.A. The conserved Npl4 protein complex mediates proteasome-dependent membrane-bound transcription factor activation. Mol Biol Cell 2001; 12 (10): 3226-3241.
  • Prinz, W.A., Grzyb, L., Veenhuis, M., Kahana, J.A., Silver, P.A. and Rapoport, T.A. Mutants affecting the structure of the cortical endoplasmic reticulum in Saccharomyces cerevisiae. J Cell Biol 2000 Aug 7;150(3):461-74. Abstract

Social Commentaries

  • Silver, PA. Why do so few women speak at scientific meetings. 2007. Nature 446:85
  • Silver. PA. Academic snakes and ladders. 2007. Nature 11:449.
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