Pamela A. Silver

Synthetic Biology Platform, Harvard University

Affiliated withHarvard University Harvard Medical School

Research Area

Biography

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JoVE Journal Publications

ArticleTotal : 1	Year
Publication title Cited by 8	2014

Other Publications

Article	Year
Genetic interactions of yeast eukaryotic translation initiation factor 5A (eIF5A) reveal connections to poly(A)-binding protein and protein kinase C signaling. Genetics\| PubMed ID: 11861547	2002
Protein and RNA export from the nucleus. Developmental cell\| PubMed ID: 11879632	2002
The genome-wide localization of Rsc9, a component of the RSC chromatin-remodeling complex, changes in response to stress. Molecular cell\| PubMed ID: 11931764	2002
Identification of a role for Saccharomyces cerevisiae Cgr1p in pre-rRNA processing and 60S ribosome subunit synthesis. Microbiology (Reading, England)\| PubMed ID: 11932453	2002
Identifying proteins that affect mRNA localization in living cells. Methods (San Diego, Calif.)\| PubMed ID: 12054891	2002
Nuclear protein transport. Methods in enzymology\| PubMed ID: 12073370	2002
Requirements for the nuclear export of the small ribosomal subunit. Journal of cell science\| PubMed ID: 12082158	2002
Retrovirus-delivered siRNA. BMC biotechnology\| PubMed ID: 12199908	2002
Nuclear localization of human immunodeficiency virus type 1 preintegration complexes (PICs): V165A and R166A are pleiotropic integrase mutants primarily defective for integration, not PIC nu... Journal of virology\| PubMed ID: 12368302	2002
Intron status and 3'-end formation control cotranscriptional export of mRNA. Genes & development\| PubMed ID: 12414728	2002
In situ analysis of spatial relationships between proteins of the nuclear pore complex. Biophysical journal\| PubMed ID: 12496130	2002
Bipartite signals mediate subcellular targeting of tail-anchored membrane proteins in Saccharomyces cerevisiae. The Journal of biological chemistry\| PubMed ID: 12514182	2003
Genome-wide analysis of RNA-protein interactions illustrates specificity of the mRNA export machinery. Nature genetics\| PubMed ID: 12524544	2003
A microbead-based system for identifying and characterizing RNA-protein interactions by flow cytometry. Molecular & cellular proteomics : MCP\| PubMed ID: 12543929	2002
Nuclear transport as a target for cell growth. Drug discovery today\| PubMed ID: 12565010	2003
Sac3 is an mRNA export factor that localizes to cytoplasmic fibrils of nuclear pore complex. Molecular biology of the cell\| PubMed ID: 12631707	2003
Analysis of RNA-protein interactions by flow cytometry. Current opinion in molecular therapeutics\| PubMed ID: 12870432	2003
Intracellular transport of human immunodeficiency virus type 1 integrase. Journal of cell science\| PubMed ID: 13130095	2003
A subset of membrane-associated proteins is ubiquitinated in response to mutations in the endoplasmic reticulum degradation machinery. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 14557538	2003
Small molecule modulation of the human chromatid decatenation checkpoint. Chemistry & biology\| PubMed ID: 14700634	2003
A chemical genetic screen identifies inhibitors of regulated nuclear export of a Forkhead transcription factor in PTEN-deficient tumor cells. Cancer cell\| PubMed ID: 14706338	2003
Modulation of interprotomer relationships is important for activation of dimeric calcium-sensing receptor. The Journal of biological chemistry\| PubMed ID: 14729680	2004
Nuclear transport and cancer: from mechanism to intervention. Nature reviews. Cancer\| PubMed ID: 14732865	2004
Therapeutic potential of retroviral RNAi vectors. Expert opinion on biological therapy\| PubMed ID: 15006726	2004
Human Mob proteins regulate the NDR1 and NDR2 serine-threonine kinases. The Journal of biological chemistry\| PubMed ID: 15067004	2004
Guardian at the gate: preventing unspliced pre-mRNA export. Trends in cell biology\| PubMed ID: 15130577	2004
Genome-wide localization of the nuclear transport machinery couples transcriptional status and nuclear organization. Cell\| PubMed ID: 15137937	2004
PRMT3 is a ribosomal protein methyltransferase that affects the cellular levels of ribosomal subunits. The EMBO journal\| PubMed ID: 15175657	2004
REF-ereeing the cytoplasmic fate of mRNA via nuclear export. Developmental cell\| PubMed ID: 15177019	2004
Arginine methyltransferase affects interactions and recruitment of mRNA processing and export factors. Genes & development\| PubMed ID: 15314027	2004
Human cell proteins and human immunodeficiency virus DNA integration. Frontiers in bioscience : a journal and virtual library\| PubMed ID: 15353349	2004
Identification of an evolutionarily conserved domain in human lens epithelium-derived growth factor/transcriptional co-activator p75 (LEDGF/p75) that binds HIV-1 integrase. The Journal of biological chemistry\| PubMed ID: 15371438	2004
Genome-wide mRNA surveillance is coupled to mRNA export. Genes & development\| PubMed ID: 15489286	2004
Class II integrase mutants with changes in putative nuclear localization signals are primarily blocked at a postnuclear entry step of human immunodeficiency virus type 1 replication. Journal of virology\| PubMed ID: 15542626	2004
A systems view of mRNP biology. Genes & development\| PubMed ID: 15574591	2004
HIV-1 incorporates and proteolytically processes human NDR1 and NDR2 serine-threonine kinases. Virology\| PubMed ID: 15582665	2005
The psammaplysenes, specific inhibitors of FOXO1a nuclear export. Journal of natural products\| PubMed ID: 15844952	2005
Developmentally induced changes in transcriptional program alter spatial organization across chromosomes. Genes & development\| PubMed ID: 15905407	2005
Ufd1 exhibits the AAA-ATPase fold with two distinct ubiquitin interaction sites. Structure (London, England : 1993)\| PubMed ID: 16004872	2005
Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell\| PubMed ID: 16009131	2005
A genome-wide in situ hybridization map of RNA-binding proteins reveals anatomically restricted expression in the developing mouse brain. BMC developmental biology\| PubMed ID: 16033648	2005
Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells. Genome biology\| PubMed ID: 16086846	2005
Multiple conformations in the ligand-binding site of the yeast nuclear pore-targeting domain of Nup116p. The Journal of biological chemistry\| PubMed ID: 16105837	2005
The uses of green fluorescent protein in yeasts. Methods of biochemical analysis\| PubMed ID: 16335714	2006
Biochemical and genetic analyses of integrase-interacting proteins lens epithelium-derived growth factor (LEDGF)/p75 and hepatoma-derived growth factor related protein 2 (HRP2) in preintegra... Virology\| PubMed ID: 16337983	2006
Autoregulation of ribosome biosynthesis by a translational response in fission yeast. Molecular and cellular biology\| PubMed ID: 16478994	2006
Genomic association of the proteasome demonstrates overlapping gene regulatory activity with transcription factor substrates. Molecular cell\| PubMed ID: 16543154	2006
Motion as a phenotype: the use of live-cell imaging and machine visual screening to characterize transcription-dependent chromosome dynamics. BMC cell biology\| PubMed ID: 16635267	2006
Pore-ing the right dose. Nature cell biology\| PubMed ID: 16691206	2006
Systems biology of gene regulation fulfills its promise. Genome biology\| PubMed ID: 16719937	2006
Genomic localization of RNA binding proteins reveals links between pre-mRNA processing and transcription. Genome research\| PubMed ID: 16769980	2006
The conserved ATPase Get3/Arr4 modulates the activity of membrane-associated proteins in Saccharomyces cerevisiae. Genetics\| PubMed ID: 16816426	2006
Transcriptional regulation by the proteasome as a mechanism for cellular protein homeostasis. Cell cycle (Georgetown, Tex.)\| PubMed ID: 16861887	2006
Solenopsin, the alkaloidal component of the fire ant (Solenopsis invicta), is a naturally occurring inhibitor of phosphatidylinositol-3-kinase signaling and angiogenesis. Blood\| PubMed ID: 16990598	2007
Genome-wide analysis of estrogen receptor binding sites. Nature genetics\| PubMed ID: 17013392	2006
The unfolded protein response transducer Ire1p contains a nuclear localization sequence recognized by multiple beta importins. Molecular biology of the cell\| PubMed ID: 17035634	2006
Communication between levels of transcriptional control improves robustness and adaptivity. Molecular systems biology\| PubMed ID: 17130867	2006
Genome-wide identification of functionally distinct subsets of cellular mRNAs associated with two nucleocytoplasmic-shuttling mammalian splicing factors. Genome biology\| PubMed ID: 17137510	2006
The role of protein arginine methylation in the formation of silent chromatin. Genes & development\| PubMed ID: 17158743	2006
Differential recruitment of the splicing machinery during transcription predicts genome-wide patterns of mRNA splicing. Molecular cell\| PubMed ID: 17189192	2006
Designing biological systems. Genes & development\| PubMed ID: 17289915	2007
Transcriptional regulation at the nuclear pore complex. Current opinion in genetics & development\| PubMed ID: 17317147	2007
Why do so few women speak at science meetings? Nature\| PubMed ID: 17443161	2007
Genetically encoded short peptide tags for orthogonal protein labeling by Sfp and AcpS phosphopantetheinyl transferases. ACS chemical biology\| PubMed ID: 17465518	2007
Systems perspectives on mRNA processing. Cell research\| PubMed ID: 17621309	2007
Exon expression profiling reveals stimulus-mediated exon use in neural cells. Genome biology\| PubMed ID: 17683528	2007
Rational design of memory in eukaryotic cells. Genes & development\| PubMed ID: 17875664	2007
Functional specificity among ribosomal proteins regulates gene expression. Cell\| PubMed ID: 17981122	2007
Coupling and coordination in gene expression processes: a systems biology view. Nature reviews. Genetics\| PubMed ID: 18071322	2008
Global analysis of mRNA splicing. RNA (New York, N.Y.)\| PubMed ID: 18083834	2008
Definition of global and transcript-specific mRNA export pathways in metazoans. Genes & development\| PubMed ID: 18086857	2008
CARM1 regulates estrogen-stimulated breast cancer growth through up-regulation of E2F1. Cancer research\| PubMed ID: 18172323	2008
Defossiling fuel: how synthetic biology can transform biofuel production. ACS chemical biology\| PubMed ID: 18205286	2008
Enhancement of cell type specificity by quantitative modulation of a chimeric ligand. The Journal of biological chemistry\| PubMed ID: 18230610	2008
Global histone acetylation induces functional genomic reorganization at mammalian nuclear pore complexes. Genes & development\| PubMed ID: 18316479	2008
Intron delays and transcriptional timing during development. Developmental cell\| PubMed ID: 18331713	2008
Intron length increases oscillatory periods of gene expression in animal cells. Genes & development\| PubMed ID: 18703678	2008
mRNA nuclear export and human disease. Disease models & mechanisms\| PubMed ID: 19048072	2008
Learning a prior on regulatory potential from eQTL data. PLoS genetics\| PubMed ID: 19180192	2009
Engineering a synthetic dual-organism system for hydrogen production. Applied and environmental microbiology\| PubMed ID: 19201964	2009
Harnessing nature's toolbox: regulatory elements for synthetic biology. Journal of the Royal Society, Interface / the Royal Society\| PubMed ID: 19324675	2009
A conserved CCCH-type zinc finger protein regulates mRNA nuclear adenylation and export. The Journal of cell biology\| PubMed ID: 19364924	2009
Synthetic biology: exploring and exploiting genetic modularity through the design of novel biological networks. Molecular bioSystems\| PubMed ID: 19562109	2009
Systems-level engineering of nonfermentative metabolism in yeast. Genetics\| PubMed ID: 19564482	2009
Metazoan stress granule assembly is mediated by P-eIF2alpha-dependent and -independent mechanisms. RNA (New York, N.Y.)\| PubMed ID: 19661161	2009
Eukaryotic systems broaden the scope of synthetic biology. The Journal of cell biology\| PubMed ID: 19948487	2009
Anti-glycophorin single-chain Fv fusion to low-affinity mutant erythropoietin improves red blood cell-lineage specificity. Protein engineering, design & selection : PEDS\| PubMed ID: 20083493	2010
Making cellular memories. Cell\| PubMed ID: 20085698	2010
A synthetic circuit for selectively arresting daughter cells to create aging populations. Nucleic acids research\| PubMed ID: 20150416	2010
Insulation of a synthetic hydrogen metabolism circuit in bacteria. Journal of biological engineering\| PubMed ID: 20184755	2010
Spatially ordered dynamics of the bacterial carbon fixation machinery. Science (New York, N.Y.)\| PubMed ID: 20203050	2010
Engineering cyanobacteria to synthesize and export hydrophilic products. Applied and environmental microbiology\| PubMed ID: 20363793	2010
Knowing when to change: reprogramming (my) life. Nature cell biology\| PubMed ID: 20680000	2010
An alternative splicing network links cell-cycle control to apoptosis. Cell\| PubMed ID: 20705336	2010
Emergent cooperation in microbial metabolism. Molecular systems biology\| PubMed ID: 20823845	2010
A structurally tunable DNA-based extracellular matrix. Journal of the American Chemical Society\| PubMed ID: 20925350	2010
Genome-wide RNAi screen discovers functional coupling of alternative splicing and cell cycle control to apoptosis regulation. Cell cycle (Georgetown, Tex.)\| PubMed ID: 21088477	2010
Dynamics in the mixed microbial concourse. Genes & development\| PubMed ID: 21123647	2010
Engineering cyanobacteria to generate high-value products. Trends in biotechnology\| PubMed ID: 21211860	2011
Synthetic circuit identifies subpopulations with sustained memory of DNA damage. Genes & development\| PubMed ID: 21363961	2011
Rewiring hydrogenase-dependent redox circuits in cyanobacteria. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 21368150	2011
Informing biological design by integration of systems and synthetic biology. Cell\| PubMed ID: 21414477	2011
Whole genome siRNA cell-based screen links mitochondria to Akt signaling network through uncoupling of electron transport chain. Molecular biology of the cell\| PubMed ID: 21460183	2011
Modular electron transfer circuits for synthetic biology: insulation of an engineered biohydrogen pathway. Bioengineered bugs\| PubMed ID: 21468209	2010
Towards a synthetic chloroplast. PloS one\| PubMed ID: 21533097	2011
A synthetic system links FeFe-hydrogenases to essential E. coli sulfur metabolism. Journal of biological engineering\| PubMed ID: 21615937	2011
Visualization of single mRNAs reveals temporal association of proteins with microRNA-regulated mRNA. Nucleic acids research\| PubMed ID: 21653551	2011
Synthetic reversal of epigenetic silencing. The Journal of biological chemistry\| PubMed ID: 21669865	2011
Recording cellular experiences of DNA damage. Cell cycle (Georgetown, Tex.)\| PubMed ID: 21670599	2011
Organization of intracellular reactions with rationally designed RNA assemblies. Science (New York, N.Y.)\| PubMed ID: 21700839	2011
Cell-to-cell variability of alternative RNA splicing. Molecular systems biology\| PubMed ID: 21734645	2011
Parts plus pipes: synthetic biology approaches to metabolic engineering. Metabolic engineering\| PubMed ID: 22037345	2012
Modularity of a carbon-fixing protein organelle. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 22184212	2012
Rerouting carbon flux to enhance photosynthetic productivity. Applied and environmental microbiology\| PubMed ID: 22307292	2012
A tunable zinc finger-based framework for Boolean logic computation in mammalian cells. Nucleic acids research\| PubMed ID: 22323524	2012
Induction of biogenic magnetization and redox control by a component of the target of rapamycin complex 1 signaling pathway. PLoS biology\| PubMed ID: 22389629	2012
A sensitive switch for visualizing natural gene silencing in single cells. ACS synthetic biology\| PubMed ID: 22530199	2012
DNA ends alter the molecular composition and localization of Ku multicomponent complexes. Molecular & cellular proteomics : MCP\| PubMed ID: 22535209	2012
Engineering synthetic TAL effectors with orthogonal target sites. Nucleic acids research\| PubMed ID: 22581776	2012
Natural strategies for the spatial optimization of metabolism in synthetic biology. Nature chemical biology\| PubMed ID: 22596204	2012
Improving carbon fixation pathways. Current opinion in chemical biology\| PubMed ID: 22647231	2012
A BioBrick compatible strategy for genetic modification of plants. Journal of biological engineering\| PubMed ID: 22716313	2012
STAR RNA-binding protein Quaking suppresses cancer via stabilization of specific miRNA. Genes & development\| PubMed ID: 22751500	2012
Synthetic memory circuits for tracking human cell fate. Genes & development\| PubMed ID: 22751502	2012
Designing biological compartmentalization. Trends in cell biology\| PubMed ID: 22841504	2012
Designing and using RNA scaffolds to assemble proteins in vivo. Nature protocols\| PubMed ID: 22955695	2012
Spatial and temporal organization of chromosome duplication and segregation in the cyanobacterium Synechococcus elongatus PCC 7942. PloS one\| PubMed ID: 23112856	2012
Expression of the sub-pathways of the Chloroflexus aurantiacus 3-hydroxypropionate carbon fixation bicycle in E. coli: Toward horizontal transfer of autotrophic growth. Metabolic engineering\| PubMed ID: 23376595	2013
PQBP1, a factor linked to intellectual disability, affects alternative splicing associated with neurite outgrowth. Genes & development\| PubMed ID: 23512658	2013
Protein scaffold-activated protein trans-splicing in mammalian cells. Journal of the American Chemical Society\| PubMed ID: 23621664	2013
Tailored fatty acid synthesis via dynamic control of fatty acid elongation. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 23798438	2013
Dynamics simulations for engineering macromolecular interactions. Chaos (Woodbury, N.Y.)\| PubMed ID: 23822508	2013
Isothermal self-assembly of complex DNA structures under diverse and biocompatible conditions. Nano letters\| PubMed ID: 23978049	2013
Two- and three-input TALE-based AND logic computation in embryonic stem cells. Nucleic acids research\| PubMed ID: 23982518	2013
Targeting a heterologous protein to multiple plant organelles via rationally designed 5' mRNA tags. Journal of biological engineering\| PubMed ID: 24011257	2013
The bacterial carbon-fixing organelle is formed by shell envelopment of preassembled cargo. PloS one\| PubMed ID: 24023971	2013
Building synthetic memory. Current biology : CB\| PubMed ID: 24028965	2013
Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly. Nucleic acids research\| PubMed ID: 24078086	2014
An objective function exploiting suboptimal solutions in metabolic networks. BMC systems biology\| PubMed ID: 24088221	2013
Building synthetic cellular organization. Molecular biology of the cell\| PubMed ID: 24288075	2013
Synthetic biology in mammalian cells: next generation research tools and therapeutics. Nature reviews. Molecular cell biology\| PubMed ID: 24434884	2014
HITS-CLIP and Integrative Modeling Define the Rbfox Splicing-Regulatory Network Linked to Brain Development and Autism. Cell reports\| PubMed ID: 24613350	2014
Programmable bacteria detect and record an environmental signal in the mammalian gut. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 24639514	2014
Integrating Biological Redesign: Where Synthetic Biology Came From and Where It Needs to Go. Cell\| PubMed ID: 24679533	2014