Silver: Publications (2000-)

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2007

• Drubin, DA, Way, JC, and Silver, PA. Designing Biological Systems. 2007. Genes and Development, 21:242-54

• Brown, CR and Silver, PA. Transcriptional regulation at the nuclear pore complex. 2007. Curr. Opin Genet Dev.

• 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)

• 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, 109:560-5.

• Silver, PA. Why do so few women speak at scientific meetings. 2007. Nature 446:856.

• McKee, AE and Silver, PA. 2007. Systems perspective on mRNA processing. 2007. Cell Research, in press.

• Way, J. and Silver, PA. Systems engineering without an engineer: Why we need systems biology. 2007, to appear in Complexity.

• Way, J. and Silver, PA. Molecular systems biology in drug development. 2007. Clinical Pharmacology and Therapeutics, in press.

• Ajo-Franklin, CM, Drubin, DA, Eskin, J., Gee, E., Landgraf, D., Philips, I. and Silver, PA. Rational design of memory in eukaryotic cells. 2007. submitted for publication.

• 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. submitted for publication.

• 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 revision.

2006

• 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.

• 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.

• 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.

• 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)

• 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.

• 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.

• 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)

• 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.

• Auld, K. and Silver, PA. Transcriptional regulation by the proteasome as a mechanism for cellular protein homeostasis. 2006. Cell Cycle Abstract.

• McKee, A. and Silver, PA. Systems Biology of Gene Regulation Fulfils its Promise. 2006. Genome Biology 7:316.

• 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.

• 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.

• Brown, CR and Silver, PA. Poreing the right dose. 2006. Nature Cell Biology 8:430-1.

• 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.

• 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

• 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

• 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

2005

• 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
• 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
• 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 Abstract Full data set available here.
• 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 Abstract
• Park, S., Isaacson, R., Kim, H.T., Silver, P.A., and Wagner, G. Ufd1 exhibits the AAA-ATPase fold with two distinct ubiquitin interaction sites. Structure (Camb) 2005. Jul; 13(7):995-1005. Abstract
• 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. 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
• Devroe, E., Silver, P.A., and Engelman, A. HIV-1 incorporates and proteolytically processes human NDR1 and NDR2 serine-threonine kinases. Virology 2005. Jan 5; 331(1):181-9. Abstract

2004

• Hieronymus, H., and Silver, P.A. A systems view of mRNP biology. Genes Dev. 2004. Dec 1,18(23):2845-60.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
• 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
• Silver, P.A. and Way, Jeffrey. The potential for synthetic biology. The Scientist. 2004. Sept. 27; 18(18);30-1. Epub
• Cherepanov, P., Devroe, E., Silver, P.A., and Engelman, A. Identification of an evolutionarily-conserved domain in LEDGF/p75 that binds HIV-1 integrase. J. Biol. Chem. 2004; Sept. 14. Epub
• Turlure, F., Devroe, E., Silver, P.A., and Engelman, A. Human cell proteins and human immunodeficiency virus DNA integration. Front Biosci. 2004; Sept. 1; 9:3187-208. 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
• Casolari, J.M., Brown, C.R., Komili, S., West, J., Hieronymus, H., and Silver, P.A. Genome-wide localization of the nuclear transport machinery reveals coupling of transcriptional status and nuclear organization. Cell. 2004. May 14; 117(4):427-39.Abstract
• Casolari, J.M. and Silver, P.A. Guardian at the gate: preventing unspliced pre-mRNA export. Trends Cell B iol. 2004. May, 14(5):222-5 Abstract
• Devroe, E., Erdjument-Bromage, H., Tempst, P., and Silver, P.A. Human Mob proteins regulate the NDR1 and NDR2 serine-threonine kinases. JBC. April 2, 2004. Abstract
• Devroe, E., and Silver, P.A. Therapeutic potential of retroviral RNAi vectors Expert Opin. Biol. Ther. 2004; 4(3):319-27.
• 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
• Jiang, Y., Minet, E., Zhang, Z., Silver, P.A., and Bai, M. Modulation of interprotomer relationship is important for activation of dimeric calcium-sensing receptor. J. Biol. Chem. 2004. Abstract
• Pierrat, B., Simonen, M., Cueto, M, Mestan, J., Ferrigno, P and Heim, J. SH3GLB, a new endophilin-related protein family featuring an SH3 domain, Genomics 2004 15:222-234. (work done in Silver lab in collaboration with Novartis)

2003

• 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. Abstract
• Hitchcock, A.L., Auld, K., Gygi, S.P., and Silver, P.A. A subset of membrane-associated proteins is ubiquitinated in response to mutations in the endoplasmic reticulum degradation machinery. Proc. Nat. Acad. Sci. 2003, 100(22):12735-40.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
• Brodsky, A.S,, Johnston, A.P,, Trau, M., and Silver, P.A. Analysis of RNA-protein interactions by flow cytometry. Curr. Opin. Mol. Ther 2003; 5(3):235-40. 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
• 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
• 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

2002

• 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
• 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
• 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
• 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
• Devroe, E. and Silver, P.A. Retrovirus-delivered siRNA. BMC Biotechnol. 2002; 2(1): 15. 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
• Damelin, M., Silver, P.A., and Corbett, A.H. Nuclear protein transport. Methods Enzymol. 2002; 351:587-607.
• Brodsky, A..S. and Silver, P.A. Identifying proteins that affect mRNA localization in living cells. Methods 2002; 26(2):151-5.
• Moy, T.I., Boettner, D., Rhodes, J.C., Silver, P.A., and Askew, D.S. Identification of a role for Saccharomyces cerevisiae Cgr1p in pre-rRNA processing and 60S ribosome subunit synthesis. Microbiology 2002; 148 (Pt 4): 1081-1090. 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. 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

2001

• 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. 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
• McBride, A.E. and Silver, P.A. State of the Arg: Protein methylation at arginine comes of age. Cell 2001; 106(1): 5-8.
• Tham, W., Wyithe, J.S., Ferrigno, P.K., Silver, P.A., and Zakian, V.A. Localization of yeast telomeres to the nuclear periphery is separable from transcriptional repression and telomere stability functions. Mol Cell 2001; 8(1): 189-199. 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

2000

• Brodsky, A.S. and Silver, P.A. Pre-mRNA processing factors are required for nuclear export. RNA 2000; 6(12): 1737-1749.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. 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
• 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
• Krebber, H. and Silver, P.A. Directing proteins to nucleus by fusion to nuclear localization signal tags. Methods Enzymol 2000;327:283-96. Abstract
• 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
• Hood, J.K. and Silver, P.A. Diverse nuclear transport pathways regulate cell proliferation and oncogenesis. Biochim Biophys Acta 2000 Jul 31;1471(1):M31-41. 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
• Ferrigno, P. and Silver, P.A. Polyglutamine expansions: proteolysis, chaperones, and the dangers of promiscuity. Neuron 2000 Apr;26(1):9-12. 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
• McBride, A.E., Weiss, V.H., Kim, H.K., Hogle, J.M., and Silver, P.A. Analysis of the yeast arginine methyltransferase Hmt1p/Rmt1p and its in vivo function. Cofactor binding and substrate interactions. J. Biol. Chem. 2000 Feb 4;275(5):3128-36. 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