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Pamela A. Silver, PhD


  • Kotula JW, Kerns SJ, Shaket LA, Siraj L, Collins JJ, Way JC, Silver PA.Programmable bacteria detect and record an environmental signal in the mammalian gut.Proc Natl Acad Sci U S A. 2014 Apr 1;111(13):4838-43.
  • Lienert F, Torella JP, Chen JH, Norsworthy M, Richardson RR, Silver PA.Two- and three-input TALE-based AND logic computation in embryonic stem cells.Nucleic Acids Res. 2013 Nov;41(21):9967-75.
  • Wintermute EH, Lieberman TD, Silver PA.An objective function exploiting suboptimal solutions in metabolic networks.BMC Syst Biol. 2013;7:98.
  • Chen AH, Silver PA.Designing biological compartmentalization.Trends Cell Biol. 2012 Dec;22(12):662-70.
  • Delebecque CJ, Silver PA, Lindner AB.Designing and using RNA scaffolds to assemble proteins in vivo.Nat Protoc. 2012 Oct;7(10):1797-807.
  • Adelmant G, Calkins AS, Garg BK, Card JD, Askenazi M, Miron A, Sobhian B, Zhang Y, Nakatani Y, Silver PA, Iglehart JD, Marto JA, Lazaro JB.DNA ends alter the molecular composition and localization of Ku multicomponent complexes.Mol Cell Proteomics. 2012 Aug;11(8):411-21.
  • Chen AJ, Paik JH, Zhang H, Shukla SA, Mortensen R, Hu J, Ying H, Hu B, Hurt J, Farny N, Dong C, Xiao Y, Wang YA, Silver PA, Chin L, Vasudevan S, Depinho RA.STAR RNA-binding protein Quaking suppresses cancer via stabilization of specific miRNA.Genes Dev. 2012 Jul 1;26(13):1459-72.
  • Burrill DR, Inniss MC, Boyle PM, Silver PA.Synthetic memory circuits for tracking human cell fate.Genes Dev. 2012 Jul 1;26(13):1486-97.
  • Agapakis CM, Silver PA.Modular electron transfer circuits for synthetic biology: Insulation of an engineered biohydrogen pathway.Bioengineered Bugs. 2010 11;1(6):413-418.
  • Senapedis WT, Kennedy CJ, Boyle PM, Silver PA.Whole genome siRNA cell-based screen links mitochondria to Akt signaling network through uncoupling of electron transport chain.Mol Biol Cell. 2011 Apr 1.
  • Wang Q, Silver PA.Genome-wide RNAi screen discovers functional coupling of alternative splicing and cell cycle control to apoptosis regulation.Cell Cycle. 2010 Nov 15;9(22):4419-21.
  • Aldaye FA, Senapedis WT, Silver PA, Way JC.A structurally tunable DNA-based extracellular matrix.J Am Chem Soc. 2010 Oct 27;132(42):14727-9.
  • Moore MJ, Wang Q, Kennedy CJ, Silver PA.An alternative splicing network links cell-cycle control to apoptosis.Cell. 2010 Aug 20;142(4):625-36.
  • Silver PA.Knowing when to change: reprogramming (my) life.Nat Cell Biol. 2010 Aug;12(8):730.
  • Afonso B, Silver PA, Ajo-Franklin CM.A synthetic circuit for selectively arresting daughter cells to create aging populations.Nucleic Acids Res. 2010 May;38(8):2727-35.
  • Taylor ND, Way JC, Silver PA, Cironi P.Anti-glycophorin single-chain Fv fusion to low-affinity mutant erythropoietin improves red blood cell-lineage specificity.Protein Eng. Des. Sel. 2010 Apr;23(4):251-60.
  • Savage DF, Afonso B, Chen AH, Silver PA.Spatially ordered dynamics of the bacterial carbon fixation machinery.Science. 2010 Mar 5;327(5970):1258-61.
  • Burrill DR, Silver PA.Making cellular memories.Cell. 2010 Jan 8;140(1):13-8.
  • Haynes KA, Silver PA.Eukaryotic systems broaden the scope of synthetic biology.J Cell Biol. 2009 Nov 30;187(5):589-96. Review.
  • Farny NG, Kedersha NL, Silver PA.Metazoan stress granule assembly is mediated by P-eIF2alpha-dependent and -independent mechanisms.RNA. 2009 Oct;15(10):1814-21.
  • Agapakis CM, Silver PA.Synthetic biology: exploring and exploiting genetic modularity through the design of novel biological networks.Mol Biosyst. 2009 Jul;5(7):704-13. Review.
  • Boyle PM,Silver PA.Harnessing nature's toolbox: regulatory elements for synthetic biology.J R Soc Interface. 2009 Aug 6;6 Suppl 4:S535-46. Review.
  • Hurt JA,Obar RA,Zhai B,Farny NG,Gygi SP,Silver PA.A conserved CCCH-type zinc finger protein regulates mRNA nuclear adenylation and export.J Cell Biol. 2009 Apr 20;185(2):265-77.
  • Lee SI,Dudley AM,Drubin D,Silver PA,Krogan NJ,Pe'er D,Koller D.Learning a prior on regulatory potential from eQTL data.PLoS Genet. 2009 Jan;5(1):e1000358.
  • Hurt JA,Silver PA.mRNA nuclear export and human disease.Dis Model Mech. 2008 Sep-Oct;1(2-3):103-8.
  • Swinburne IA,Miguez DG,Landgraf D,Silver PA.Intron length increases oscillatory periods of gene expression in animal cells.Genes Dev. 2008 Sep 1;22(17):2342-6.
  • Swinburne IA, Silver PA.Intron delays and transcriptional timing during development.Dev Cell. 2008 Mar;14(3):324-30. Review.
  • Brown CR, Kennedy CJ, Delmar VA, Forbes DJ, Silver PA.Global histone acetylation induces functional genomic reorganization at mammalian nuclear pore complexes.Genes Dev. 2008 Mar 1;22(5):627-39.
  • Cironi P, Swinburne IA, Silver PA.Enhancement of cell type specificity by quantitative modulation of a chimeric ligand.J Biol Chem. 2008 Mar 28;283(13):8469-76.
  • Frietze S, Lupien M, Silver PA, Brown M.CARM1 regulates estrogen-stimulated breast cancer growth through up-regulation of E2F1.Cancer Res. 2008 Jan 1;68(1):301-6.
  • Farny NG, Hurt JA, Silver PA.Definition of global and transcript-specific mRNA export pathways in metazoans.Genes Dev. 2008 Jan 1;22(1):66-78.
  • Moore MJ, Silver PA.Global analysis of mRNA splicing.RNA. 2008 Feb;14(2):197-203. Review.
  • Komili S, Silver PA.Coupling and coordination in gene expression processes: a systems biology view.Nat Rev Genet. 2008 Jan;9(1):38-48. Review.
  • Komili S, Farny NG, Roth FP, Silver PA.Functional specificity among ribosomal proteins regulates gene expression.Cell. 2007 Nov 2;131(3):557-71.
  • Ajo-Franklin CM, Drubin DA, Eskin JA, Gee EP, Landgraf D, Phillips I, Silver PA.Rational design of memory in eukaryotic cells.Genes Dev. 2007 Sep 15;21(18):2271-6.
  • McKee AE, Silver PA.Systems perspectives on mRNA processing.Cell Res. 2007 Jul;17(7):581-90. Review.
  • Drubin DA, Way JC, Silver PA.Designing biological systems.Genes Dev. 2007 Feb 1;21(3):242-54. Review.
  • Moore MJ, Schwartzfarb EM, Silver PA, Yu MC.Differential recruitment of the splicing machinery during transcription predicts genome-wide patterns of mRNA splicing.Mol Cell. 2006 Dec 28;24(6):903-15.
  • Yu MC, Lamming DW, Eskin JA, Sinclair DA, Silver PA.The role of protein arginine methylation in the formation of silent chromatin.Genes Dev. 2006 Dec 1;20(23):3249-54.
  • Tsankov AM, Brown CR, Yu MC, Win MZ, Silver PA, Casolari JM.Communication between levels of transcriptional control improves robustness and adaptivity.Mol Syst Biol. 2006;2:65.
  • Carroll JS, Meyer CA, Song J, Li W, Geistlinger TR, Eeckhoute J, Brodsky AS, Keeton EK, Fertuck KC, Hall GF, Wang Q, Bekiranov S, Sementchenko V, Fox EA, Silver PA, Gingeras TR, Liu XS, Brown M.Genome-wide analysis of estrogen receptor binding sites.Nat Genet. 2006 Nov;38(11):1289-97.
  • Auld KL, Brown CR, Casolari JM, Komili S, Silver PA.Genomic association of the proteasome demonstrates overlapping gene regulatory activity with transcription factor substrates.Mol Cell. 2006 Mar 17;21(6):861-71.
  • Carroll JS, Liu XS, Brodsky AS, Li W, Meyer CA, Szary AJ, Eeckhoute J, Shao W, Hestermann EV, Geistlinger TR, Fox EA, Silver PA, Brown M.Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1.Cell. 2005 Jul 15;122(1):33-43.
  • Casolari JM, Brown CR, Komili S, West J, Hieronymus H, Silver PA.Genome-wide localization of the nuclear transport machinery couples transcriptional status and nuclear organization.Cell. 2004 May 14;117(4):427-39.
  • Kau TR, Way JC, Silver PA.Nuclear transport and cancer: from mechanism to intervention.Nat Rev Cancer. 2004 Feb;4(2):106-17.
  • Kau TR, Schroeder F, Ramaswamy S, Wojciechowski CL, Zhao JJ, Roberts TM, Clardy J, Sellers WR, Silver PA.A chemical genetic screen identifies inhibitors of regulated nuclear export of a Forkhead transcription factor in PTEN-deficient tumor cells.Cancer Cell. 2003 Dec;4(6):463-76.
  • Hitchcock A, Auld K, Gygi SP, Silver PA.A subset of membrane-associated proteins are ubiquitinated and targeted for ER-associated degradation.Proc Natl Acad Sci U S A. 2003;100:12735-40.
  • Haggarty SJ, Koeller KM, Kau T, Silver PA, Roberge M, Schreiber SL.Chemical genetic modifiers screens: Small molecule suppressors of the ATR-dependent chromatid catenation checkpoint.Chem Biol. 2003;10:1267-1279.
  • Kau T, Silver PA.Nuclear transport as a target of growth control.Eval & Prog Plan. 2003;8:78-85.
  • Hieronymus H, Silver PA.Genome-wide analysis of RNA-protein interactions illustrates specificity of the mRNA export machinery.Nat Genet. 2003 Feb;33(2):155-61.