Silver: Publications (2000-)

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
(2013)
(2014)
(6 intermediate revisions not shown.)
Line 2: Line 2:
__NOTOC__
__NOTOC__
==2014==
==2014==
 +
*Kotula JW*, Kerns SJ*, Shaket LA, Siraj, L, Collins JJ, Way JC, and Silver PA.  Programmable bacteria detect and record an environmental signal in the mammalian gut.  2014. Proc Natl Acad Sci, in press. (*co-first authors)
*Way J, Collins J, Keasling J, and Silver PA.  Integrating Biological Redesign:  Where synthetic biology came from, and where it needs to go.  2014.  Cell, in press.
*Way J, Collins J, Keasling J, and Silver PA.  Integrating Biological Redesign:  Where synthetic biology came from, and where it needs to go.  2014.  Cell, in press.
*Lienert F, Lohmueller J, Garg, A and Silver PA.  Synthetic biology in mammalian cells:Next generation research tools and therapeutics. 2014.  Nature Rev Molecular Cell Biol. Jan 17. doi: 10.1038/nrm3738.
*Lienert F, Lohmueller J, Garg, A and Silver PA.  Synthetic biology in mammalian cells:Next generation research tools and therapeutics. 2014.  Nature Rev Molecular Cell Biol. Jan 17. doi: 10.1038/nrm3738.
 +
*Torella J, Boehm C, Lienert F, Chen J, Way J, and Silver PA. Rapid construction of insulated genetic circuits via synthetic-guided isothermal assembly.  2014.  Nuc Acis Res., Jan 7;42(1):681-9. doi: 10.1093/nar/gkt860
*Weyn-Vanhentenryck S, Sun A, Yan Q, Mele A, Farney N, Zhang Z, Silver PA, Zhang MQ, Krainer AR, Darne;; RB and Zhang C.  HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism. 2014. Cell Reports, in press.
*Weyn-Vanhentenryck S, Sun A, Yan Q, Mele A, Farney N, Zhang Z, Silver PA, Zhang MQ, Krainer AR, Darne;; RB and Zhang C.  HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism. 2014. Cell Reports, in press.
 +
*Mattozzi M, Voges M, Silver P, Way J. Transient gene expression in tobacco using Gibson Assembly and the Gene Gun. 2014. Journal of Visualized Experiments. In press.
 +
*Silver PA and Way JC. Rationalizing Nature. 2014. Nature, in press.
 +
*Torella JP, Lienert F, Bpehm CR, Chen J, Way JC and Silver PA.  Unique nucleotide sequence (UNS)-guided assembly of repetive DNA parts for synthetic biology applications.  2014.  Nature Protocols, in press.
==2013==
==2013==
*Polka J and Silver PA.  Building synthetic cellular organization.  2013. Mol Biol Cell.,  Dec;24(23):3585-7. doi: 10.1091/mbc.E13-03-0155.
*Polka J and Silver PA.  Building synthetic cellular organization.  2013. Mol Biol Cell.,  Dec;24(23):3585-7. doi: 10.1091/mbc.E13-03-0155.
*Chen AH, Robinson-Mosher A, Savage DF, Silver PA, Polka JK (2013) The bacterial carbon-fixing organelle is formed by shell envelopment of preassembled cargo. PLoS ONE 8(9): e76127. doi:10.1371/journal.pone.0076127
*Chen AH, Robinson-Mosher A, Savage DF, Silver PA, Polka JK (2013) The bacterial carbon-fixing organelle is formed by shell envelopment of preassembled cargo. PLoS ONE 8(9): e76127. doi:10.1371/journal.pone.0076127
-
*Myhrvold C, Dai M, Silver PA, and Yin P. Isothermal self-assembly of complex DNA structures under diverse and biocompatible conditions.  2013.  Nano Letters.  Available online at doi:10.1021/nl4019512.
+
*Myhrvold C, Dai M, Silver PA, and Yin P. Isothermal self-assembly of complex DNA structures under diverse and biocompatible conditions.  2013.  Nano Letters.  Sep 11;13(9):4242-8. doi: 10.1021/nl4019512.
*Voges MJ, Way JC, Silver PA and Mattozzi MD.  2013.  Targeting a heterologous protein to multiple plant organelles via rationally designed 5' mRNA tags. J Biol Eng., Sep 8;7(1):20. doi: 10.1186/1754-1611-7-20
*Voges MJ, Way JC, Silver PA and Mattozzi MD.  2013.  Targeting a heterologous protein to multiple plant organelles via rationally designed 5' mRNA tags. J Biol Eng., Sep 8;7(1):20. doi: 10.1186/1754-1611-7-20
*Lienert F, Torella J, Chen J, Norsworthy M, Richardson R, and Silver PA. Two- and three-input TALE-based logic computation in embryonic stem cells.  2013. Nuc Acid Res, Nov;41(21):9967-75. doi: 10.1093/nar/gkt758. Epub 2013 Aug 27.
*Lienert F, Torella J, Chen J, Norsworthy M, Richardson R, and Silver PA. Two- and three-input TALE-based logic computation in embryonic stem cells.  2013. Nuc Acid Res, Nov;41(21):9967-75. doi: 10.1093/nar/gkt758. Epub 2013 Aug 27.
Line 19: Line 24:
*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.,  Mar;16:130-9. doi: 10.1016/j.ymben.2013.01.005. Epub 2013 Jan 29.
*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.,  Mar;16:130-9. doi: 10.1016/j.ymben.2013.01.005. Epub 2013 Jan 29.
*Ford TJ and Silver PA.  Rephrasing the biofuel question.  2013. Microbe, in press.
*Ford TJ and Silver PA.  Rephrasing the biofuel question.  2013. Microbe, in press.
-
*Wintermute EH, Lieberman TD and Silver PA.  An objective function exploiting degeneracy and suboptimality in metabolic networks.  2013.  BMC Systems Biology, accepted for publication
+
*Wintermute EH, Lieberman TD and Silver PA.  An objective function exploiting degeneracy and suboptimality in metabolic networks.  2013.  BMC Systems Biology, Oct 3;7:98. doi: 10.1186/1752-0509-7-98
==2012==
==2012==

Revision as of 09:14, 31 May 2014

Back to publications

2014

  • Kotula JW*, Kerns SJ*, Shaket LA, Siraj, L, Collins JJ, Way JC, and Silver PA. Programmable bacteria detect and record an environmental signal in the mammalian gut. 2014. Proc Natl Acad Sci, in press. (*co-first authors)
  • Way J, Collins J, Keasling J, and Silver PA. Integrating Biological Redesign: Where synthetic biology came from, and where it needs to go. 2014. Cell, in press.
  • Lienert F, Lohmueller J, Garg, A and Silver PA. Synthetic biology in mammalian cells:Next generation research tools and therapeutics. 2014. Nature Rev Molecular Cell Biol. Jan 17. doi: 10.1038/nrm3738.
  • Torella J, Boehm C, Lienert F, Chen J, Way J, and Silver PA. Rapid construction of insulated genetic circuits via synthetic-guided isothermal assembly. 2014. Nuc Acis Res., Jan 7;42(1):681-9. doi: 10.1093/nar/gkt860
  • Weyn-Vanhentenryck S, Sun A, Yan Q, Mele A, Farney N, Zhang Z, Silver PA, Zhang MQ, Krainer AR, Darne;; RB and Zhang C. HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism. 2014. Cell Reports, in press.
  • Mattozzi M, Voges M, Silver P, Way J. Transient gene expression in tobacco using Gibson Assembly and the Gene Gun. 2014. Journal of Visualized Experiments. In press.
  • Silver PA and Way JC. Rationalizing Nature. 2014. Nature, in press.
  • Torella JP, Lienert F, Bpehm CR, Chen J, Way JC and Silver PA. Unique nucleotide sequence (UNS)-guided assembly of repetive DNA parts for synthetic biology applications. 2014. Nature Protocols, in press.

2013

  • Polka J and Silver PA. Building synthetic cellular organization. 2013. Mol Biol Cell., Dec;24(23):3585-7. doi: 10.1091/mbc.E13-03-0155.
  • Chen AH, Robinson-Mosher A, Savage DF, Silver PA, Polka JK (2013) The bacterial carbon-fixing organelle is formed by shell envelopment of preassembled cargo. PLoS ONE 8(9): e76127. doi:10.1371/journal.pone.0076127
  • Myhrvold C, Dai M, Silver PA, and Yin P. Isothermal self-assembly of complex DNA structures under diverse and biocompatible conditions. 2013. Nano Letters. Sep 11;13(9):4242-8. doi: 10.1021/nl4019512.
  • Voges MJ, Way JC, Silver PA and Mattozzi MD. 2013. Targeting a heterologous protein to multiple plant organelles via rationally designed 5' mRNA tags. J Biol Eng., Sep 8;7(1):20. doi: 10.1186/1754-1611-7-20
  • Lienert F, Torella J, Chen J, Norsworthy M, Richardson R, and Silver PA. Two- and three-input TALE-based logic computation in embryonic stem cells. 2013. Nuc Acid Res, Nov;41(21):9967-75. doi: 10.1093/nar/gkt758. Epub 2013 Aug 27.
  • Innis M and Silver PA. Building synthetic memory. 2013. Current Biology, Sep 9;23(17):R812-6. doi: 10.1016/j.cub.2013.06.047
  • Torella J*, Ford T*, Chen A, Kim S, Way JC and Silver PA. Tailored fatty acid synthesis via dynamic control of fatty acid elongation. 2013. Proc Natl Acad Sci, Jul 9;110(28):11290-5. doi: 10.1073/pnas.1307129110
  • Robinson-Mosher A, Shinar T, Silver PA and Way J. Dynamics simulations for engineering macromolecular interactions. 2013. Chaos, Jun;23(2):025110. doi: 10.1063/1.4810915.
  • Selgrade D, Lohmueller J, Lienert F and Silver PA. Protein scaffold-activated protein trans-splicing in mammalian cells. 2013. J American Chem Soc. May 22;135(20):7713-9. doi: 10.1021/ja401689b
  • Wang QQ, Moore MJ, Adelmant G, Marto JA and Silver PA. PQBP1, a factor linked to intellectual disability, affects alternative splicing associated with neurite outgrowth. 2013. Genes and Dev., Mar 15;27(6):615-26. doi: 10.1101/gad.212308.112.
  • 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., Mar;16:130-9. doi: 10.1016/j.ymben.2013.01.005. Epub 2013 Jan 29.
  • Ford TJ and Silver PA. Rephrasing the biofuel question. 2013. Microbe, in press.
  • Wintermute EH, Lieberman TD and Silver PA. An objective function exploiting degeneracy and suboptimality in metabolic networks. 2013. BMC Systems Biology, Oct 3;7:98. doi: 10.1186/1752-0509-7-98

2012

  • 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.
  • 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
  • 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-.
  • 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.
  • Garg A, Lohmueller J, Silver PA and Armel T. Engineering synthetic TAL effectors with orthogonal target sites. 2012. Nuc Acids Res, Aug;40(15):7584-95. doi: 10.1093/nar/gks404. Epub 2012 May 11.
  • Adelmant G, Calkins AS, Garg B, Card JD, Askenaz M, Miron A, Sobhian B, Zhang Y, Nakatani Y, Silver PA, Iglehart JD, Marto JA and Lazaro J. DNA ends alter the molecular composition and localization of Ku multi-component complexes. 2012. Mol & Cell Prot., Aug;11(8):411-21. doi: 10.1074/mcp.M111.013581. Epub 2012 Apr 24.
  • Agapakis CM, Boyle PM and Silver PA. Natural strategies for the spatial optimization of metabolism in synthetic biology. 2012. Nature Chem Biol., May 17;8(6):527-35.
  • Ducat D and Silver PA. Improving carbon fixation pathways. 2012. Curr Op in Chem Biol., Aug;16(3-4):337-44. doi: 10.1016/j.cbpa.2012.05.002. Epub 2012 May 29.
  • Boyle PM, Burrill DR, Inniss MC, Agapakis CM, Deardon A, Dewerd J, Gedeon MA, Quinn J, Paull ML, Raman AM, Theilman MR, Wang L, Winn JG, Medvedik O, Schellenberg, K,Haynes KA, Viel A, Brenner TJ, Church GM, Shah JV and Silver PA. A Biobrick compatible Strategy for genetic modification of plants. 2012. J Biol Eng., Jun 20;6(1):8. doi: 10.1186/1754-1611-6-8.
  • Chen A-J, PalK J, Zhang H, Shukla SA, Mortensen R, Hu J, Ying H, Hu B, Hurt J, Farny N, Don C, Xiao Y, Wang A, Silver PA, Chin L, Vasudevan S, and DePinho R. STAR RNA-binding protein quaking suppresses cancer via stabilization of specific miRNA. 2012. Genes and Dev. 26:1459-1472.
  • Chen A and Silver PA. Designing biological compartmentalization. 2012. Trends in Cell Biol., Dec;22(12):662-70. doi: 10.1016/j.tcb.2012.07.002. Epub 2012 Jul 27.
  • Delebeque C, Silver PA, and Lindner A. Assembling proteins in vivo on designed RNA scaffolds. 2012. Nature Protocols, Oct;7(10):1797-807. doi: 10.1038/nprot.2012.102. Epub 2012 Sep 6.
  • Chen AH, Afonso D, Savage D and Silver PA. Spatial and Temporal Organization of Chromosome Duplication and Segregation in the Cyanobacterium Synechococcus elongatus PCC 7942. PLoS One. 2012;7(10):e47837. doi: 10.1371/journal.pone.0047837. Epub 2012 Oct 242012.
  • PLoS Collection in Synthetic Biology [2]
  • Silver PA. Designing biological systems to report on disease. 2012. Cancer Research. December 13, 2012 72:IA4; doi:10.1158/1538-7445.CSB12-IA4

2011

  • Bonacci W, Teng PK, Afonso B, Niederholtmeyer H, Grob P, Silver PA and Savage DF. Modularity of a carbon-fixing organelle. 2011. Proc Natl Acad Sci., in press.
  • Burrill DR, Boyle PM, and Silver p1. 2011. A new approach to an old problem: Synthetic biology tools for human disease & metabolism. Cold Spring Harbor 76th Symposium on Quantitative Biology.
  • Silver P. Biology in this Century. 2011. Harvard Magazine. Sept/Oct issue.
  • Delebecque CJ, Lindner AB, Silver PA, and Aldaye FA. Organization of intracellular reactions with rationally designed RNA assemblies. Science, 2011. 333:470-4. (published online in ScienceExpress June 23, 2011.
  • Haynes KA, Silver P. Synthetic reversal of epigenetic silencing. J Biol Chem. 2011 Jun 12. [Epub ahead of print]
  • Ducat D, Sachdeva G and Silver PA. Rewiring Hydrogenase-dependent Redox Circuits in Cyanobacteria. 2011. Proc Natl Acad Sci, 108:3941-6.
  • Ducat D, Way J, and Silver PA. Engineering Cyanobacteria to Generate High-Value Products. 2011. Trends in Biotechnology, Feb;29(2):95-103. Epub 2011 Jan 5.
  • Burrill D and Silver PA. Synthetic circuit identifies sub-populations with sustained memory of DNA damage. 2011. Genes & Dev., 25:434-9.
  • Smolke CD and Silver PA. Informing biological design by integration of systems and synthetic biology. 2011. Cell, 144:855-9.
  • Agapakis CM, Niederholtmeyer H, Noche RR, Lieberman TD, Megason SG, Way JC and Silver PA. 2011. Towards a synthetic chloroplast. PLoS One, Apr 20;6(4):e18877.
  • Senapedis WT, Kennedy CJ, Boyle PM and Silver PA. Whole genome siRNA cell-based screen links mitochondria to Akt signaling network through uncoupling of electron transport chain. 2011. Mol Biol Cell., May;22(10):1791-805. Epub 2011 Apr 1.
  • Waks Z, Klein AM and Silver PA. Cell-to-cell variability of alternative RNA splicing. 2011. Nature Mol Systems Biol. accepted for publication.
  • Boyle PM and Silver PA. Parts plus pipes: synthetic biology approaches to metabolic engineering. 2011. Metabolic Engineering May;14(3):223-32. Epub 2011 Oct 25.
  • Shih J, Waks Z, Kedersha N, Silver PA. Visualization of single mRNAs reveals temporal association of proteins with microRNA-regulated mRNA. 2011. Nuc Acids Res. Jun 7. [Epub ahead of print].
  • Barstow B, Agapakis CM, Boyle PM, Grandl G, Silver PA and Wintermute EH. A synthetic system links FeFe-hydrogenases to essential E. coli sulfur metabolism. 2011. J Biol Eng. May 26;5(1):7. [Epub ahead of print].
  • Burrill D and Silver PA. Recording cellular experience of DNA damage. 2011. Cell Cycle, Aug 1;10(15).[Epub ahead of print]in press.
  • Way JC, Silver PA and Howard RJ. Sun-driven microbial synthesis of chemicals in space. 2011. International Journal of Astrobiology. In press.

2010

  • Aldaye FA, Senapedis WT, Silver PA, and Way JC. A structurally tunable DNA-based extracellular matrix. 2010. JACS, 132:14727-9.
  • Wintermute EH and Silver PA. Dynamics in the mixed microbial concourse. 2010 Genes and Development, 24:2603-14.
  • Wintermute EH and Silver PA. Emergent cooperation in microbial metabolism. 2010. Nature Mol Sys Biol., 6:407.
  • Moore MJ, Wang Q, Kennedy CJ and Silver PA. An alternative splicing network links cell cycle control to apoptosis. 2010. Cell, 142:625-36.
  • Waks Z and Silver PA. Nuclear origins of cell-to-cell variability. 2010. Cold Spring Harbor 75th Symposium in Quantitative Biology.
  • Niederholtmeyer, H, Wolfstadter, BT, Savage, DF, Silver PA, and Way JC. Engineering synthesis and export of hydrophilic products from cyanobacteria. 2010. App. & Env. Engineering, 76(11)3462-6.
  • Savage DF*, Afonso B*, Chen A and Silver PA. Spatially ordered dynamics of the bacterial carbon fixation machinery. 2010. Science, 327:1258-61
  • Agapakis C, Ducat D, Boyle PM, Wintermute EH, Way JC and Silver PA. Insulation of a synthetic hydrogen metabolism circuit in bacteria. 2010. J. of Biol. Eng., Feb 25 [3].
  • Afonso B, Silver PA, and Ajo-Franklin C. A synthetic circuit for selectively arresting daughter cell to create aging populations. 2010. Nucleic Acids Res., Jan 26 [4].
  • Taylor N, Way J, Silver PA, and Cironi P. An erythropoietin-derived chimeric protein with improved red-cell line lineage. 2010. Protein Engineering and Design, Jan 18 [5].
  • Agapakis C and Silver PA. Modular electron transfer circuits for synthetic biology: insulation of an engineered biohydrogen pathway. 2010. Bioengineered Bugs, in press
  • Wang QQ and Silver PA. Genome-wide RNAi Screen Discovers Functional Coupling of Alternative Splicing and Cell Cycle Control to Apoptosis Regulation. 2010. Cell Cycle.
  • Silver PA. Knowing when to change: Reprogramming (my) life. 2010. Nature Cell Biology, 8:730.

2009

  • Haynes, K and Silver, PA Eukaryotic systems broaden the scope of synthetic biology. 2009. J Cell Biol. 187:589-96.
  • Kennedy, CJ*, Boyle, PM*, Waks, Z, and Silver, PA Systems-level engineering of non-fermentative metabolism in yeast. 2009. Genetics, 183:385-97.
  • 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 Jan5(1):e1000358.
  • Waks, Z. and Silver, PA. Engineering a synthetic dual organism system for hydrogen production. 2009. Applied and Environmental Microbiology. 75:1867-75.
  • Boyle, PM and Silver, PA. Harnessing nature's toolbox: regulatory elements for synthetic biology. 2009. Journal of the Royal Society. 4:535-46.
  • 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.
  • Agapakis, CM. and Silver, PA. Synthetic Biology: Exploring and exploiting genetic modularity through the design of novel biological networks. 2009. Molecular BioSystems, 5:704-713. (special issue)
  • Farny, N., Kadersha, NL, and Silver, PA. Metazoan stress granule assembly is mediated by eIF2a-dependent and independent mechanisms. 2009. RNA, 15:1814-21.
  • Birmingham, A., Selfors, LM, Wrobel, D, Kennedy, CJ, Shanks, E, Santoyo-Lopez, J, Dumican, DJ, Long, A, Kelleher, D, Smith, Q, Beijersbergen, RL, Ghazi, P and Shamu, C. Statistical methods for analysis of high-throughput RNA interference screens. 2009. Nature Methods, 8:569-75.

2008

  • Farny, NG, Hurt, JA and Silver, PA. Definition of global and transcript-specific mRNA export pathways in metazoans. 2008. Genes & Dev., 22:66-78.
  • 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. 283:8469-76.
  • Frietze, S., Lupien, M., Silver, PA and Brown, M. CARM1 regulates estrogen-stimulated breast cancer growth through up-regulation of E2F1. 2008. Cancer Research. 68:301-306.
  • Moore, M. and Silver, PA. Global analysis of mRNA splicing. 2008. RNA, 14:66-78.
  • Komili, S. and Silver, PA. Coupling of gene expression mechanisms - insights from global studiess. 2007. Nature Reviews in Genetics. 9:38-48.
  • 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., 22:627-39.
  • Swinburne IA, and Silver PA. Intron delays and transcriptional timing during development. Dev Cell. 2008 Mar;14(3):324-30.
  • Swinburne IA, Miguez, D, Landgraf, D and Silver, PA. Intron length increases oscillatory periods of gene expression in animal cells. 2008. Genes & Dev., 22:2342-6.
  • Hurt, JA and Silver, PA. mRNA export and human disease. 2008. Disease Models and Mechanisms, 1:103-108.

2007

  • 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.
  • Komili, S., Farny, NG, Roth, FP and Silver, PA. Functional specificity among ribosomal proteins regulates gene expression. 2007. Cell 131:557-71.
  • Way, J. and Silver, PA. Molecular systems biology in drug development. 2007. Clinical Pharmacology and Therapeutics, 82:586-90.
  • Brown, CR and Silver, PA. Transcriptional regulation at the nuclear pore complex. 2007. Curr. Opin Genet Dev. 2:100-6.
  • 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)
  • 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, 7:581-90.
  • Way, J. and Silver, PA. Systems engineering without an engineer: Why we need systems biology. 2007, Complexity, 13:22-29.
  • 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.
  • Silver. PA. Academic snakes and ladders. 2007. Nature 11:449.

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
Personal tools