Silver: Publications (By subject)

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

Synthetic Biology and Bioengineering

 * 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</B> 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.</B> 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.</B> 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</B> 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</B> 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</B> 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.</B> 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</B> 2002; <I>In Press.</I>
 * Lei, E. P. and Silver, P.A. Intron status and 3'-end formation control cotranscriptional export of mRNA. Genes Dev</B> 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</B> 2002; 115 (Pt  14): 2985-95.Abstract
 * Lei, E.P. and Silver, P.A. Protein and RNA export from the nucleus. Dev Cell.</B> 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</B> 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. </B> 2001; 15(14): 1771-1782. Abstract
 * Brodsky, A.S. and Silver, P.A. Pre-mRNA processing factors are required for nuclear export. RNA</B> 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</B> 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.</B> 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. <B>Cancer Cell.</B> 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. <B>Chem. Biol.</B> 2003; 10(12):1267-79.


 * Kau, T.R., Way, J.C., and Silver, P.A. Nuclear transport and cancer: from mechanism to intervention. <B>Nat. Rev. Cancer. </B> 2004; Feb; 4(2):106-17. Abstract


 * Kau, T.R. and Silver, P.A. Nuclear transport as a target for cell growth. <B>Drug Discov. Today.</B> 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. <B>Genes  Dev</B> 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. <B>Nat. Struct. Biol.</B> 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. <B>RNA</B> 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 <B>J.  Biol. Chem.</B> 2005. Aug 16. Abstract


 * Schroeder, F.C., Kau, T.R., Silver, P.A., and Clardy, J. The psammaplysenes, specific inhibitors of FOXO1a nuclear export.  <B>J Nat Prod</B> 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.  <B>J. Virol.</B> 2004. Dec; 78(23):12735-46.Abstract


 * Devroe, E., Engelman, A., and Silver, P.A. Intracellular transport of human immunodeficiency virus type 1 integrase <B>J. Cell.  Sci.</B> 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. <B>Biophys J.</B> 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. <B>J Virol.</B> 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. <B>J. Cell Sci.</B> 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. <B>J. Cell Sci.</B> 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. <B>Proc. Natl. Acad. Sci. USA</B>  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. <B>Mol. Cell</B> 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. <B>J. Biol. Chem. </B> 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.  <B>Mol Biol Cell</B> 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. <B>J  Cell Biol</B> 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.

In the News

 * NPR Science Friday
 * Bioengineering at Harvard
 * Boston Globe on Synthetic Biology
 * Science Magazine Editor's Choice
 * Silver co-heads Bioengineering Effort at Harvard
 * Ribosomes: More special than you think
 * Synthetic genes give cells something to remember
 * Scientists synthesize memory in yeast cells
 * Profile in Nature Chemical Biology
 * Proteasome recognized as nuclear player on the gene regulation team
 * Undergraduates spend summer creating living machines
 * Systems Biology at Harvard Medical School marks first year
 * Nuclear export inhibitors found in cell-based screen
 * Trends in Cell Biology