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List of works by Pamela Silver

13C-Labeling the carbon-fixation pathway of a highly efficient artificial photosynthetic system

scientific article published on 15 March 2017

A BioBrick compatible strategy for genetic modification of plants

scientific article published on 20 June 2012

A Catalytic Nanoreactor Based on in Vivo Encapsulation of Multiple Enzymes in an Engineered Protein Nanocompartment

scientific article published on 9 August 2016

A Synthetic System That Senses Candida albicans and Inhibits Virulence Factors

scientific article published on 16 January 2019

A Tunable Protein Piston That Breaks Membranes to Release Encapsulated Cargo

scientific article published on 26 January 2016

A chemical genetic screen identifies inhibitors of regulated nuclear export of a Forkhead transcription factor in PTEN-deficient tumor cells

scientific article

A conserved CCCH-type zinc finger protein regulates mRNA nuclear adenylation and export

scientific article

A distributed cell division counter reveals growth dynamics in the gut microbiota

scientific article

A genome-wide in situ hybridization map of RNA-binding proteins reveals anatomically restricted expression in the developing mouse brain

scientific article

A homologue of the bacterial heat-shock gene DnaJ that alters protein sorting in yeast

scientific article (publication date: 14 February 1991)

A microbead-based system for identifying and characterizing RNA-protein interactions by flow cytometry

scientific article

A sensitive switch for visualizing natural gene silencing in single cells

scientific article published in March 2012

A structurally tunable DNA-based extracellular matrix

scientific article

A subset of membrane-associated proteins is ubiquitinated in response to mutations in the endoplasmic reticulum degradation machinery

scientific article published on 13 October 2003

A synthetic circuit for selectively arresting daughter cells to create aging populations

scientific article

A synthetic system links FeFe-hydrogenases to essential E. coli sulfur metabolism

scientific article

A systems view of mRNP biology

scientific article

A tunable zinc finger-based framework for Boolean logic computation in mammalian cells ⬇️

scientific article published on February 9, 2012

Academic snakes and ladders

scientific article published in Nature

Ambient nitrogen reduction cycle using a hybrid inorganic-biological system

scientific article

An Explanation of Symbols Used for Analysis of FRET Data

scientific article published on 01 October 2006

An alternative splicing network links cell-cycle control to apoptosis

scientific article

An objective function exploiting suboptimal solutions in metabolic networks

scientific article

Analysis of Protein Interactions In Vivo with Fluorescence Resonance Energy Transfer (FRET)

scientific article published on 01 October 2006

Analysis of RNA-protein interactions by flow cytometry

scientific article

Anti-glycophorin single-chain Fv fusion to low-affinity mutant erythropoietin improves red blood cell-lineage specificity

scientific article published on 18 January 2010

Arginine methyltransferase affects interactions and recruitment of mRNA processing and export factors

scientific article published on August 2004

Autoregulation of ribosome biosynthesis by a translational response in fission yeast

scientific article

Bacterial variability in the mammalian gut captured by a single-cell synthetic oscillator

scientific article published on 11 October 2019

Barcoded microbial system for high-resolution object provenance

scientific article published on 01 June 2020

Better together: engineering and application of microbial symbioses

scientific article published on 27 August 2015

Beyond the Four Bases: A Home Run for Synthetic Epigenetic Control?

scientific article published on 01 April 2019

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 preintegration complex function and HIV-1 replication

scientific article

Biological-inorganic hybrid systems as a generalized platform for chemical production

scientific article published on 11 November 2017

Bipartite signals mediate subcellular targeting of tail-anchored membrane proteins in Saccharomyces cerevisiae

scientific article

Building Spatial Synthetic Biology with Compartments, Scaffolds, and Communities

scientific article

Building synthetic cellular organization

scientific article

Building synthetic memory

scientific article published on September 2013

CARM1 regulates estrogen-stimulated breast cancer growth through up-regulation of E2F1.

scientific article published in January 2008

Cell‐to‐cell variability of alternative RNA splicing ⬇️

scientific article published on July 5, 2011

Chimeric Fatty Acyl-Acyl Carrier Protein Thioesterases Provide Mechanistic Insight into Enzyme Specificity and Expression

scientific article published on 01 May 2018

Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1

scientific article

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

scientific article published on December 2004

Communication between levels of transcriptional control improves robustness and adaptivity.

scientific article published on 28 November 2006

Complex cellular logic computation using ribocomputing devices

scientific article published on 26 July 2017

Controlling the Implementation of Transgenic Microbes: Are We Ready for What Synthetic Biology Has to Offer?

scientific article published on 01 May 2020

Converting a Natural Protein Compartment into a Nanofactory for the Size-Constrained Synthesis of Antimicrobial Silver Nanoparticles

scientific article published on 8 June 2016

Coupling and coordination in gene expression processes: a systems biology view

scientific article published on January 2008

Creating Single-Copy Genetic Circuits

scientific article

DNA Ends Alter the Molecular Composition and Localization of Ku Multicomponent Complexes ⬇️

scientific article published on April 24, 2012

De novo-designed translation-repressing riboregulators for multi-input cellular logic

scientific article published on 04 November 2019

Definition of global and transcript-specific mRNA export pathways in metazoans

scientific article

Defossiling fuel: how synthetic biology can transform biofuel production

scientific article

Designing and using RNA scaffolds to assemble proteins in vivo

scientific article published on 06 September 2012

Designing biological compartmentalization

scientific article published on 27 July 2012

Designing biological systems

scientific article published on February 2007

Designing cell-targeted therapeutic proteins reveals the interplay between domain connectivity and cell binding

scientific article

Developmentally induced changes in transcriptional program alter spatial organization across chromosomes

scientific article

Differential recruitment of the splicing machinery during transcription predicts genome-wide patterns of mRNA splicing

scientific article published on 01 December 2006

Dynamic Modulation of the Gut Microbiota and Metabolome by Bacteriophages in a Mouse Model

scientific article published on 04 June 2019

Dynamics in the mixed microbial concourse

scientific article published on December 2010

Dynamics simulations for engineering macromolecular interactions ⬇️

scientific article published on June 1, 2013

Early-Career Scientists Shaping the World

scientific article published on 07 May 2019

Efficient size-independent chromosome delivery from yeast to cultured cell lines

scientific article

Efficient solar-to-fuels production from a hybrid microbial-water-splitting catalyst system

scientific article

Emergent cooperation in microbial metabolism ⬇️

scientific article published on September 7, 2010

Enabling community-based metrology for wood-degrading fungi

scientific article published on 19 March 2020

Encapsulation as a Strategy for the Design of Biological Compartmentalization

scientific article published on 21 September 2015

Engineered Interspecies Amino Acid Cross-Feeding Increases Population Evenness in a Synthetic Bacterial Consortium

scientific article published on 13 August 2019

Engineered bacteria can function in the mammalian gut long-term as live diagnostics of inflammation

scientific article published on 29 May 2017

Engineering Cyanobacteria To Synthesize and Export Hydrophilic Products.

scientific article

Engineering Genetically-Encoded Mineralization and Magnetism via Directed Evolution

scientific article

Engineering a synthetic dual-organism system for hydrogen production

scientific article (publication date: April 2009)

Engineering acyl carrier protein to enhance production of shortened fatty acids

scientific article

Engineering bacteria for diagnostic and therapeutic applications

scientific article published on 5 February 2018

Engineering carbon fixation with artificial protein organelles

scientific article published on 23 January 2017

Engineering cyanobacteria to generate high-value products ⬇️

scientific article published on January 5, 2011

Engineering cyanobacteria to synthesize and export hydrophilic products

scientific article (publication date: June 2010)

Engineering synthetic TAL effectors with orthogonal target sites

scientific article

Enhancement of cell type specificity by quantitative modulation of a chimeric ligand

scientific article

Equipment for In Vivo FRET Analysis

scientific article published on 01 October 2006

Escherichia coli NGF-1, a Genetically Tractable, Efficiently Colonizing Murine Gut Isolate

scholarly article published December 2018

Eukaryotic systems broaden the scope of synthetic biology

scientific article

Exon expression profiling reveals stimulus-mediated exon use in neural cells

scientific article published on January 2007

Experimental Design for In Vivo FRET Analysis

scientific article published on 01 October 2006

Expression of the sub-pathways of the Chloroflexus aurantiacus 3-hydroxypropionate carbon fixation bicycle in E. coli: Toward horizontal transfer of autotrophic growth ⬇️

scientific article published on January 29, 2013

Functional specificity among ribosomal proteins regulates gene expression

scientific article published on November 2007

Genetic interactions of yeast eukaryotic translation initiation factor 5A (eIF5A) reveal connections to poly(A)-binding protein and protein kinase C signaling

scientific article

Genetic tool development in marine protists: emerging model organisms for experimental cell biology

scientific article published on 06 April 2020

Genetically encoded short peptide tags for orthogonal protein labeling by Sfp and AcpS phosphopantetheinyl transferases

scientific article

Genome-wide RNAi screen discovers functional coupling of alternative splicing and cell cycle control to apoptosis regulation

scientific article

Genome-wide analysis of RNA-protein interactions illustrates specificity of the mRNA export machinery

scientific article

Genome-wide analysis of estrogen receptor binding sites

scientific article (publication date: November 2006)

Genome-wide identification of functionally distinct subsets of cellular mRNAs associated with two nucleocytoplasmic-shuttling mammalian splicing factors

scientific article published on January 2006

Genome-wide localization of the nuclear transport machinery couples transcriptional status and nuclear organization

scientific article

Genome-wide mRNA surveillance is coupled to mRNA export

scientific article published on 15 October 2004

Genomic association of the proteasome demonstrates overlapping gene regulatory activity with transcription factor substrates

scientific article

Genomic localization of RNA binding proteins reveals links between pre-mRNA processing and transcription

scientific article

Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells

scientific article

Global analysis of mRNA splicing

scientific article

Global histone acetylation induces functional genomic reorganization at mammalian nuclear pore complexes

scientific article

Guardian at the gate: preventing unspliced pre-mRNA export

scientific article published in May 2004

HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism

scientific article published on 06 March 2014

HIV-1 incorporates and proteolytically processes human NDR1 and NDR2 serine-threonine kinases

scientific article

Harnessing nature's toolbox: regulatory elements for synthetic biology

scientific article

Harnessing undomesticated life

scientific article published on 01 February 2019

Human Mob proteins regulate the NDR1 and NDR2 serine-threonine kinases

scientific article

Human cell proteins and human immunodeficiency virus DNA integration

scientific article published in September 2004

Identification and selective expansion of functionally superior T cells expressing chimeric antigen receptors

scientific article published on 20 May 2015

Identification of a Fifth Antibacterial Toxin Produced by a Single Bacteroides fragilis Strain

scientific article published on 26 March 2019

Identification of a role for Saccharomyces cerevisiae Cgr1p in pre-rRNA processing and 60S ribosome subunit synthesis

scientific article

Identification of an evolutionarily conserved domain in human lens epithelium-derived growth factor/transcriptional co-activator p75 (LEDGF/p75) that binds HIV-1 integrase

scientific article

Identifying proteins that affect mRNA localization in living cells

scientific article published on 01 February 2002

Improving carbon fixation pathways ⬇️

scientific article published on May 29, 2012

In situ analysis of spatial relationships between proteins of the nuclear pore complex

scientific article

In situ reprogramming of gut bacteria by oral delivery

scientific article published on 06 October 2020

In vivo co-localization of enzymes on RNA scaffolds increases metabolic production in a geometrically dependent manner

scientific article

Indirect immunofluorescence labeling in the yeast Saccharomyces cerevisiae

scientific article published in November 2009

Induced sensitivity of Bacillus subtilis colony morphology to mechanical media compression

scientific article published on 30 September 2014

Induced sensitivity of Bacillus subtilis colony morphology to mechanical media compression

Induction of Biogenic Magnetization and Redox Control by a Component of the Target of Rapamycin Complex 1 Signaling Pathway ⬇️

scientific article published on February 28, 2012

Insulation of a synthetic hydrogen metabolism circuit in bacteria

scientific article

Integrating biological redesign: where synthetic biology came from and where it needs to go

scientific article

Intracellular transport of human immunodeficiency virus type 1 integrase

scientific article published on 16 September 2003

Intron delays and transcriptional timing during development

scientific article

Intron length increases oscillatory periods of gene expression in animal cells

scientific article published on 14 August 2008

Intron status and 3'-end formation control cotranscriptional export of mRNA.

scientific article published on November 2002

Isothermal self-assembly of complex DNA structures under diverse and biocompatible conditions

scientific article published on 26 August 2013

Joint DAC/IWBDA special session engineering biology

Knowing when to change: reprogramming (my) life ⬇️

scientific article published on 01 August 2010

Large protein organelles form a new iron sequestration system with high storage capacity

scientific article published on 08 July 2019

Large-scale recoding of a bacterial genome by iterative recombineering of synthetic DNA.

scientific article published on 12 May 2017

Learning a prior on regulatory potential from eQTL data

scientific article

Making cellular memories

scientific article

Mammalian Cells Engineered To Produce New Steroids.

scientific article published on 26 July 2018

Metazoan stress granule assembly is mediated by P-eIF2alpha-dependent and -independent mechanisms

scientific article

Modular electron transfer circuits for synthetic biology: insulation of an engineered biohydrogen pathway

scientific article published on November 2010

Modularity of a carbon-fixing protein organelle

scientific article

Modulation of interprotomer relationships is important for activation of dimeric calcium-sensing receptor

scientific article

Motion as a phenotype: the use of live-cell imaging and machine visual screening to characterize transcription-dependent chromosome dynamics

scientific article published on 24 April 2006

Multiple conformations in the ligand-binding site of the yeast nuclear pore-targeting domain of Nup116p

scientific article published on 16 August 2005

Natural strategies for the spatial optimization of metabolism in synthetic biology ⬇️

scientific article published on May 17, 2012

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

scientific article

Nuclear protein transport

scientific article

Nuclear transport and cancer: from mechanism to intervention

scientific article published on February 2004

Nuclear transport as a target for cell growth

scientific article

Organization of intracellular reactions with rationally designed RNA assemblies

scientific article (publication date: 22 July 2011)

PQBP1, a factor linked to intellectual disability, affects alternative splicing associated with neurite outgrowth

scientific article

PRMT3 is a ribosomal protein methyltransferase that affects the cellular levels of ribosomal subunits

scientific article

Pamela Silver: synthesizing a new biology. Interview by Caitlin Sedwick

scientific article published on February 2012

Parts plus pipes: synthetic biology approaches to metabolic engineering

scientific article

Pore-ing the right dose

scientific article published in May 2006

Programmable bacteria detect and record an environmental signal in the mammalian gut

scientific article (publication date: April 2014)

Prokaryotic nanocompartments form synthetic organelles in a eukaryote

scientific article published on 3 April 2018

Protein Scaffold-Activated Protein Trans-Splicing in Mammalian Cells ⬇️

scientific article published on May 8, 2013

Protein and RNA export from the nucleus

scientific article

Publisher Correction: Genetic tool development in marine protists: emerging model organisms for experimental cell biology

scientific article published on 15 April 2020

Quorum Sensing Can Be Repurposed To Promote Information Transfer between Bacteria in the Mammalian Gut

scientific article published on 31 August 2018

REF-ereeing the cytoplasmic fate of mRNA via nuclear export

scientific article published on June 2004

Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly

scientific article published on 26 September 2013

Rational Design of Evolutionarily Stable Microbial Kill Switches

scientific article

Rational Design of Evolutionarily Stable Microbial Kill Switches

scientific article published on 01 October 2018

Rational Design of a Bifunctional AND-Gate Ligand To Modulate Cell-Cell Interactions

scientific article published on 19 December 2019

Rational design of memory in eukaryotic cells

scientific article

Recording cellular experiences of DNA damage ⬇️

scientific article published on August 1, 2011

Requirements for the nuclear export of the small ribosomal subunit.

scientific article

Rerouting Carbon Flux To Enhance Photosynthetic Productivity ⬇️

scientific article published on February 3, 2012

Retrovirus-delivered siRNA

scientific article

Rewiring hydrogenase-dependent redox circuits in cyanobacteria ⬇️

scientific article published on February 22, 2011

STAR RNA-binding protein Quaking suppresses cancer via stabilization of specific miRNA

scientific article

Sac3 is an mRNA export factor that localizes to cytoplasmic fibrils of nuclear pore complex

scientific article

Small molecule modulation of the human chromatid decatenation checkpoint

scientific article published on December 2003

Solenopsin, the alkaloidal component of the fire ant (Solenopsis invicta), is a naturally occurring inhibitor of phosphatidylinositol-3-kinase signaling and angiogenesis

scientific article

Spatial and Temporal Organization of Chromosome Duplication and Segregation in the Cyanobacterium Synechococcus elongatus PCC 7942 ⬇️

scientific article published on October 24, 2012

Spatially ordered dynamics of the bacterial carbon fixation machinery

scientific article

Stable Neutralization of a Virulence Factor in Bacteria Using Temperate Phage in the Mammalian Gut

scientific article published on 28 January 2020

Streptomyces thermoautotrophicus does not fix nitrogen

scientific article

Structure and function of a 9.6 megadalton bacterial iron storage compartment: Supplementary Material

Super-resolution microscopy of the ß-carboxysome reveals a homogenous matrix.

scientific article published on 09 August 2017

Synthetic Cassettes for pH-Mediated Sensing, Counting, and Containment

scientific article published on 01 March 2020

Synthetic Gene Circuits Enable Systems-Level Biosensor Trigger Discovery at the Host-Microbe Interface.

scientific article

Synthetic Lipid-Containing Scaffolds Enhance Production by Colocalizing Enzymes

scientific article published on 3 August 2016

Synthetic biology expands chemical control of microorganisms

scientific article

Synthetic biology in mammalian cells: next generation research tools and therapeutics

scientific article

Synthetic biology: Engineering explored

scientific article published in May 2014

Synthetic biology: exploring and exploiting genetic modularity through the design of novel biological networks

scientific article published on 14 May 2009

Synthetic circuit identifies subpopulations with sustained memory of DNA damage

scientific article

Synthetic genome recoding: new genetic codes for new features

scientific article published on 5 October 2017

Synthetic lipid-containing scaffolds enhance production by co-localizing enzymes

article

Synthetic meets cell biology

scientific article published in March 2012

Synthetic memory circuits for tracking human cell fate

scientific article

Synthetic photosynthetic consortia define interactions leading to robustness and photoproduction

scientific article published on 23 January 2017

Synthetic reversal of epigenetic silencing

scientific article (publication date: 5 August 2011)

Systems biology of gene regulation fulfills its promise

scientific article published on 22 May 2006

Systems perspectives on mRNA processing

scientific article published on July 2007

Targeted erythropoietin selectively stimulates red blood cell expansion in vivo

scientific article published on 25 April 2016

Targeting a heterologous protein to multiple plant organelles via rationally designed 5' mRNA tags

scientific article published on 8 September 2013

The Discovery of Twenty-Eight New Encapsulin Sequences, Including Three in Anammox Bacteria

scientific article published on 27 December 2019

The J-NABS 25th anniversary issue: reflecting on the past, synthesizing the present, and projecting into the future

article published in 2010

The bacterial carbon-fixing organelle is formed by shell envelopment of preassembled cargo

scientific article (publication date: 2013)

The case for biotech on Mars

scientific article published on 01 April 2020

The conserved ATPase Get3/Arr4 modulates the activity of membrane-associated proteins in Saccharomyces cerevisiae

scientific article

The genome-wide localization of Rsc9, a component of the RSC chromatin-remodeling complex, changes in response to stress

scientific article

The psammaplysenes, specific inhibitors of FOXO1a nuclear export

scientific article published in April 2005

The role of protein arginine methylation in the formation of silent chromatin

scientific article

The unfolded protein response transducer Ire1p contains a nuclear localization sequence recognized by multiple beta importins

scientific article

The uses of green fluorescent protein in yeasts.

scientific article

Therapeutic potential of retroviral RNAi vectors

scientific article published on March 2004

Toehold switches: de-novo-designed regulators of gene expression

scientific article

Tools for the Microbiome: Nano and Beyond

scientific article published on 22 December 2015

Toward a translationally independent RNA-based synthetic oscillator using deactivated CRISPR-Cas

scientific article published on 01 July 2020

Towards a Synthetic Chloroplast ⬇️

scientific article published on April 20, 2011

Transcriptional regulation at the nuclear pore complex

scientific article published on 20 February 2007

Transcriptional regulation by the proteasome as a mechanism for cellular protein homeostasis

scientific article published on 17 July 2006

Transient gene expression in tobacco using Gibson assembly and the Gene Gun.

scientific article published on 18 April 2014

Transplantability of a circadian clock to a noncircadian organism

scientific article published on January 2015

Two- and three-input TALE-based AND logic computation in embryonic stem cells

scientific article published on 27 August 2013

Ufd1 exhibits the AAA-ATPase fold with two distinct ubiquitin interaction sites

scientific article

Unique nucleotide sequence-guided assembly of repetitive DNA parts for synthetic biology applications

scientific article

Using synthetic RNAs as scaffolds and regulators

scientific article published on 01 January 2015

Valorization of CO2 through lithoautotrophic production of sustainable chemicals in Cupriavidus necator

scientific article published on 19 September 2020

Visualization of single mRNAs reveals temporal association of proteins with microRNA-regulated mRNA.

scientific article

Water splitting-biosynthetic system with CO₂ reduction efficiencies exceeding photosynthesis

scientific article

Whole genome siRNA cell-based screen links mitochondria to Akt signaling network through uncoupling of electron transport chain ⬇️

scientific article published on May 15, 2011

Why do so few women speak at science meetings?

scientific article published in Nature

Widespread distribution of encapsulin nanocompartments reveals functional diversity

scientific article

mRNA nuclear export and human disease

scientific article published on September 2008

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