Rational engineering of an erythropoietin fusion protein to treat hypoxia. Lee J, Vernet A, Gruber NG, Kready KM, Burrill DR, Way JC, Silver PA. 2021. Protein Eng Des Sel. Link

Natural and Designed Proteins Inspired by Extremotolerant Organisms Can Form Condensates and Attenuate Apoptosis in Human Cells. Veling MT, Nguyen DT, Thadani NN, Oster ME, Rollins NJ, Brock KP, Bethel NP, Baker D, Way JC, Marks DS, Chang RL, Silver PA. 2021. bioRxiv. Link

Modular and Single-Cell Sensors of Bacterial Ser/Thr Kinase Activity. Zheng CR, Singh A, Libby A, Silver PA, Libby EA. 2021. ACS Synth Biol. Link

Theranostic cells: emerging clinical applications of synthetic biology. McNerney MP, Doiron KE, Ng TL, Chang TZ, Silver PA. 2021. Nat. Rev. Genet. Link

Rational engineering of an erythropoietin fusion protein to treat hypoxia. Lee J, Vernet A, Gruber NG, Kready KM, Burrill DR, Way JC, Silver PA. 2021. bioRxiv. Link

Protein sensors of bacterial kinase activity reveal antibiotic-dependent kinase activation in single cells. Zheng CR, Singh A, Libby A, Silver PA, Libby EA. 2021. bioRxiv. Link

Exploring targeting peptide-shell interactions in encapsulin nanocompartments. Altenburg WJ, Rollins N, Silver PA, Giessen TW. 2021. Sci Rep. Link

High-content screening of coronavirus genes for innate immune suppression reveals enhanced potency of SARS-CoV-2 proteins. Olson EJ, Brown DM, Chang TZ, Ding L, Ng TL, Weiss HS, Koide Y, Koch P, Rollins N, Mach P, Meisinger T, Bricken T, Rollins J, Zhang Y, Molloy C, Zhang Y, Queenan BN, Mitchison T, Marks D, Way JC, Glass JI, Silver PA. 2021. bioRxiv. Link

Engineering Radioprotective Human Cells Using the Tardigrade Damage Suppressor Protein, DSUP. Westover C, Najjar D, Meydan C, Grigorev K, Veling MT, Iosim S, Colon R, Yang S, Restrepo U, Chin C, Butler D, Moszary C, Rahmatulloev S, Afshinnekoo E, Chang RL, Silver PA, Mason CE. 2020. Link

Protein structure, amino acid composition and sequence determine proteome vulnerability to oxidation-induced damage. Chang RL, Stanley JA, Robinson MC, Sher JW, Li Z, Chan YA, Omdahl AR, Wattiez R, Godzik A, Matallana-Surget S. 2020. EMBO J. Link

In situ reprogramming of gut bacteria by oral delivery. Hsu BB, Plant IN, Lyon L, Anastassacos FM, Way JC, Silver PA. 2020. Nat Commun. Link

Valorization of CO2 through lithoautotrophic production of sustainable chemicals in Cupriavidus necator. Nangle SN, Ziesack M, Buckley S, Trivedi D, Loh DM, Nocera DG, Silver PA. 2020. Metab Eng. Link

Toward a Translationally Independent RNA-based Synthetic Oscillator Using Deactivated CRISPR-Cas. Kuo J, Yuan R, Sánchez C, Paulsson J, Silver PA. 2020. Nucleic Acids Res. Link

Synthetic Biology. O’Leary C, Silver P, van Opstal E, Rozo M. Tech Factsheets for Policymakers, Spring 2020 Series. Belfer Center for Science and International Affairs, Harvard Kennedy School. Link

Barcoded Microbial System for High-Resolution Object Provenance. Qian J, Lu Z, Mancuso CP, Jhuang H, Del Carmen Barajas-Ornelas R, Boswell SA, Ramírez-Guadiana FH, Jones V, Sonti A, Sedlack K, Artzi L, Jung G, Arammash M, Pettit ME, Melfi M, Lyon L, Owen SV, Baym M, Khalil AS, Silver PA, Rudner DZ, Springer M. 2020. Science. Link

Controlling the Implementation of Transgenic Microbes: Are We Ready for What Synthetic Biology Has to Offer? Stirling F, Silver PA. 2020. Mol. Cell. Link

Towards a translationally-independent RNA-based synthetic oscillator using deactivated CRISPR-Cas. Kuo J, Yuan R, Sánchez C, Paulsson J, Silver PA. 2020. Link

In situ reprogramming of gut bacteria by oral delivery. Hsu BB, Plant IN, Lyon L, Anastassacos FM, Way JC, Silver PA. 2020. Link

Genetic tool development in marine protists: emerging model organisms for experimental cell biology. Faktorová D, et al. 2020. Nat. Methods. Link

The case for biotech on Mars. Nangle SN, Wolfson MY, Hartsough L, Ma NJ, Mason CE, Merighi M, Nathan V, Silver PA, Simon M, Swett J, Thompson DB, Ziesack M. 2020. Nat. Biotechnol. Link

Enabling community-based metrology for wood-degrading fungi. Perez R, Luccioni M, Kamakaka R, Clamons S, Gaut N, Stirling F, Adamala KP, Silver PA, Endy D. 2020. Fungal Biol Biotechnol. Link

Forensic microbial system for high-resolution object provenance. Qian J, Lu Z, Mancuso CP, Jhuang H, del Carmen Barajas-Ornelas R, Boswell S, Ramírez-Guadiana FH, Jones V, Sonti A, Sedlack K, Artzi L, Jung G, Arammash M, Melfi M, Lyon L, Owen SV, Baym M, Khalil AS, Silver P, Rudner D, Springer M. 2020. Link

Unraveling Oxidative Stress Resistance: Molecular Properties Govern Proteome Vulnerability. Chang RL, Stanley JA, Robinson MC, Sher JW, Li Z, Chan YA, Omdahl AR, Wattiez R, Godzik A, Matallana-Surget S. 2020. Link

Synthetic Cassettes for pH-Mediated Sensing, Counting, and Containment. Stirling F, Naydich A, Bramante J, Barocio R, Certo M, Wellington H, Redfield E, O’Keefe S, Gao S, Cusolito A, Way J, Silver P. 2020. Cell Rep. Link

Valorization of CO2 through lithoautotrophic production of sustainable chemicals in Cupriavidus necator. Nangle SN, Ziesack M, Buckley S, Trivedi D, Loh D, Nocera DG, Silver PA. 2020. Link

Stable Neutralization of a Virulence Factor in Bacteria Using Temperate Phage in the Mammalian Gut. Hsu BB, Way JC, Silver PA. 2020. mSystems. Link


The Discovery of Twenty-Eight New Encapsulin Sequences, Including Three in Anammox Bacteria. Tracey JC, Coronado M Giessen TW, Lau MCY, Silver PA, Ward BB. 2019. Sci Rep. Link

Rational Design of a Bifunctional AND-Gate Ligand To Modulate Cell–Cell Interactions. Lee J, Andyna Vernet A, Redfield K, Lu S, Ghiran IC, Way JC, Silver PA. 2019. ACS Synth. Biol. Link

De novo-designed translation-repressing riboregulators for multi-input cellular logic. Kim J, Zhou Y, Carlson PD, Teichmann M, Chaudhary S, Simmel FC, Silver PA, Collins JJ, Lucks JB, Yin P, Green AA. 2019. Nature Chemical Biology. Link

Enabling community-based metrology for wood-degrading fungi. Perez R, Luccioni M, Gaut N, Stirling F, Kamakaka R, Adamala KP, Silver PA, Endy D. 2019. Link

Minimizing side effects, maximizing returns: what makes a smart therapeutic design? Lee J, Redfield K, Way J, Silver P. 2019. Biochem (Lond). Link

Bacterial variability in the mammalian gut captured by a single-cell synthetic oscillator. Riglar DT, Richmond DL, Potvin-Trottier L, Verdegaal AA, Naydich AD, Bakshi S, Leoncini E, Lyon LG, Paulsson J, Silver PA. 2019. Nat. Commun. Link

Stable neutralization of virulent bacteria using temperate phage in the mammalian gut. Hsu B, Way JC, Silver PA. 2019. Link

Synthetic cassettes for pH-mediated sensing, counting and containment. Stirling F, Naydich A, Bramante J, Barocio R, Certo M, Wellington H, Redfield E, O’Keefe S, Gao S, Cusolito A, Way J, Silver PA. 2019. Link

Engineered Interspecies Amino Acid Cross-Feeding Increases Population Evenness in a Synthetic Bacterial Consortium. Ziesack M, Gibson T, Oliver JKW, Shumaker AM, Hsu BB, Riglar DT, Giessen TW, DiBenedetto NV, Bry L, Way JC, Silver PA, Gerber GK. 2019. mSystems. Link

Genetic tool development in marine protists: Emerging model organisms for experimental cell biology. Faktorová D, et al. 2019. Link

Rational Design of a Bifunctional AND-Gate Ligand to Modulate Cell-Cell Interactions. Lee J, Vernet A, Redfield K, Lu S, Ghiran IC, Way JC, Silver PA. 2019. Link

Large protein organelles form a new iron sequestration system with high storage capacity. Giessen TW, Orlando BJ, Verdegaal AA, Chambers MG, Gardener J, Bell DC, Birrane G, Liao M, Silver PA. 2019. eLife. Link

Synthetic Gene Circuits Enable Systems-Level Biosensor Trigger Discovery at the Host-Microbe Interface. Naydich AD, Nangle SN, Bues JJ, Trivedi D, Nissar N, Inniss MC, Niederhuber MJ, Way JC, Silver PA, Riglar DT. 2019. mSystems. Link

Dynamic Modulation of the Gut Microbiota and Metabolome by Bacteriophages in a Mouse Model. Hsu BB, Gibson TE, Yeliseyev V, Liu Q, Lyon L, Bry L, Silver PA, Gerber GK. 2019. Cell Host Microbe. Link

Early-Career Scientists Shaping the World. Cristea IM, Dorrestein PC, Eisen JA, Gilbert JA, Huber JA, Jansson JK, Knight R, Pollard KS, Raes J, Silver PA, Webster NS, Xu J. 2019. mSystems. Link

Beyond the Four Bases: A Home Run for Synthetic Epigenetic Control? Chang TZ, Kuo J, Silver PA. 2019. Mol Cell. Link

Synthetic gene circuits enable systems-level biosensor discovery at the host-microbe interface. Naydich AD, Nangle SN, Bues JJ, Trivedi D, Nissar N, Inniss MC, Niederhuber MJ, Way JC, Silver PA, Riglar DT. 2019. Link

Identification of a fifth antibacterial toxin produced by a single Bacteroides fragilis strain. Shumaker AM, McEneany VL, Coyne MJ, Silver PA, Comstock LE. 2019. J Bacteriol. Link

Harnessing undomesticated life. Libby EA, Silver PA. 2019. Nat Microbiol. Link

A synthetic system that senses Candida albicans and inhibits virulence factors. Tscherner M, Giessen TW, Markey L, Kumamoto C, Silver PA. 2019. ACS Synth Biol. Link

Structure and function of a 9.6 megadalton bacterial iron storage compartment. Giessen TW, Orlando BJ, Verdegaal AA, Chambers MG, Gardener J, Bell DC, Birrane G, Liao M, Silver PA. Link

Heterologous Cas9 and non-homologous end joining as a Potentially Organism-Agnostic Knockout (POAK) system in bacteria. Plant IM. 2019. Link

Multisite phosphorylation drives phenotypic variation in (p)ppGpp synthetase-dependent antibiotic tolerance. Libby EA, Reuveni S, Dworkin J. 2019. Nature Communications. Link


De-Novo-Designed Translational Repressors for Multi-Input Cellular Logic. Kim J, Zhou Y, Carlson P, Teichmann M, Simmel FC, Silver PA, Collins JJ, Lucks JB, Yin P, Green AA. Link

Variability of bacterial behavior in the mammalian gut captured using a growth-linked single-cell synthetic gene oscillator. Riglar DT, Richmond DT, Potvin-Trottier L, Verdegaal AA, Naydich AD, Bakshi S, Leoncini E, Paulsson J, Silver PA. 2018. Biorxiv. Link

Escherichia coli NGF-1 – a genetically tractable, efficiently colonizing murine gut isolate. Ziesack M, Karrenbelt MAP, Bues J, Schaefer E, Silver PA, Way, J. 2018. Microbial Resource Announcement. (in press)

Bacteriophages dynamically modulate the gut microbiota and metabolome. Hsu BB, Gibson TE, Yeliseyev V, Liu Q, Bry L, Silver PA, Gerber GK. 2018. Biorxiv. Link

Carbon fixation systems and methods.  Cruz Colón B, Liu C, Ziesack M, Silver PA, Nocera DG.  United States Patent US20180265898A1. 2018. Link

Inducible Cooperation in a Synthetic Gut Bacterial Consortium Introduces Population Balance and Stability. Ziesack M, Gibson T, Shumaker AM, Oliver JKW, Riglar DT, Giessen TW, DiBenedetto NV, Lall K, Hsu BB, Bry L, Way JC, Silver PA, Gerber GK.  2018. Biorxiv. Link

Quorum sensing can be repurposed to promote information transfer between bacteria in the mammalian gut. Kim, Suhyun; Kerns, S. Jordan; Ziesack, Marika; Bry, Lynn; Gerber, Georg; Way, Jeffrey; Silver, Pamela 2018. ACS Synthetic Biology. Link

Mammalian Cells Engineered to Produce Novel Steroids. Spady ES, Wyche TP, Rollins NJ, Clardy J, Way JC, Silver PA. Chembiochem. 2018 Jun 21. doi: 10.1002/cbic.201800214. Link

A synthetic system that combats fungal infections. Michael Tscherner, Tobias W Giessen, Laura Markey, Carol A Kumamoto, Pamela A Silver. 2018. doi: Link

Multisite phosphorylation regulates phenotypic variability in antibiotic tolerance. Libby E, Reuveni S, Dworkin J.  2018. Biorxiv. Link

A synthetic bacterial information transfer system functions in the mammalian gut. Suhyun Kim, S. Jordan Kerns, Marika Ziesack, Lynn Bry, Georg K Gerber, Jeffrey C Way, Pamela A Silver. 2018 Apr. doi: Link.

Prokaryotic nanocompartments form synthetic organelles in a eukaryote. Lau YH, Giessen TW, Altenburg WJ, Silver PA. Nat Commun. 2018 Apr 3;9(1):1311. doi: 10.1038/s41467-018-03768-x. PMID: 29615617. Link

Chimeric Fatty Acyl-ACP Thioesterases Provide Mechanistic Insight into Enzyme Specificity and Expression. Ziesack M, Rollins N, Shah A, Dusel B, Webster G, Silver PA, Way JC. Mar 16, 2018. Appl Environ Microbiol.

Mammalian Cells Engineered to Produce Novel Steroids. Emma Sarah Spady, Thomas P Wyche, Nathanael J Rollins, Jon Clardy, Jeffrey C Way, Pamela A. Silver.  2018. Biorxiv. Link

Prokaryotic nanocompartments form synthetic organelles in a eukaryote. Yu Heng Lau, Tobias Wolfgang Giessen, Wiggert J Altenburg and Pamela A. Silver. 2018. Biorxiv. Link

Engineering bacteria for diagnostic and therapeutic applications. Riglar D and Silver PA. 2018,  Nature Reviews Microbiology. Link 

Synthetic RNA Scaffolds for Spatial Engineering in Cells. Sachdeva G*, Myhrvold C*, Yin P, and Silver PA. 2018.  Synthetic Biology, ed by S Smolke. Wiley. Link

Engineered genetic enteric sensor bacteria and uses thereof.  Kotula J, Kerns SJ, Way JC, and Silver PA.  United States Patent US10047405B2. 2018. Link

Efficient size-independent chromosome delivery from yeast to cultured cell lines. Brown DM, Chan YA, Desai PJ, Grzesik P, Oldfield LM, Vashee S, Way JC, Silver PA, Glass JI. 2017. Nucleic Acids Res.

Rational Design of Evolutionarily Stable Microbial Kill Switches. Stirling F, Bitzan L, O’Keefe S, Redfield E, Oliver JWK, Way J, Silver PA. Mol Cell. 2017 Nov 16;68(4):686-697.e3. doi: 10.1016/j.molcel.2017.10.033. PMID: 29149596 Erratum: 30340025

Complex cellular logic computation using ribocomputing devices.  Alexander A. Green, Jongmin Kim, Duo Ma, Pamela A. Silver, James J. Collins, and Peng Yin. Nature. Link

Ambient nitrogen reduction cycle using a hybrid inorganic–biological system. Chong Liu, Kelsey K. Sakimoto, Brendan C. Colón, Pamela A. Silver, and Daniel G. Nocera. PNAS. Link

Engineered bacteria can function in the mammalian gut long-term as live diagnostics of inflammation. Riglar DT, Giessen TW, Baym M, Kerns SJ, Niederhuber MJ, Bronson RT, Kotula JW, Gerber GK, Way JC, Silver PA. Nat Biotechnol. Link

Rapid genome recoding by iterative recombineering of synthetic DNA. Yu Heng Lau, Finn Stirling, James Kuo, Michiel AP Karrenbelt, Yujia A Chan, Adam Riesselman, Connor A Horton, Elena Schaefer, David Lips, Matthew T Weinstock, Daniel G Gibson, Jeffrey C Way, Pamela A. Silver. Nucleic Acids Research Link and bioRxiv Link

Rational Design of Evolutionarily Stable Microbial Kill Switches. Finn Stirling, Lisa Bitzan, John Oliver, Jeffrey Way, Pamela A. Silver. bioRxiv. Link

13C-Labeling the carbon-fixation pathway of a highly efficient artificial photosynthetic system. Liu C, Nangle SN, Colón BC, Silver PA, Nocera DG. Faraday Discuss. PMID: 28294218

Widespread distribution of encapsulin nanocompartments reveals functional diversity. Tobias Giessen, Pamela Silver. Nature Microbiology. PMID: 28263314

Engineering carbon fixation with artificial protein organelles. Tobias Giessen, Pamela Silver. Current Opinion in Biotechnology. PMID: 28126670

Synthetic Photosynthetic Consortia Define Interactions Leading to Robustness and Photoproduction. Stephanie G. Hays, Leo L.W. Yan, Pamela A. Silver, Daniel C. Ducat. Journal of Biological Engineering. PMID: 28127397

Mimicking lichens: incorporation of yeast strains together with sucrose-secreting cyanobacteria improves survival, growth, ROS removal, and lipid production in a stable mutualistic co-culture production platform.  Li T, Li CT, Butler K, Hays SG, Guarnieri MT, Oyler GA, Betenbaugh MJ. Biotechnol Biofuels. 2017 Mar 21;10:55. doi: 10.1186/s13068-017-0736-x. eCollection 2017. PMID: 28344645

Using Engineered Bacteria to Characterize Infection Dynamics and Antibiotic Effects In Vivo. Certain LK, Way JC, Pezone MJ, Collins JJ. Cell Host Microbe. 2017 Aug 30. pii: S1931-3128(17)30305-0. doi: 10.1016/j.chom.2017.08.001. [Epub ahead of print] PMID: 28867388

Super-resolution microscopy of the ß-carboxysome reveals a homogenous matrix. Kuo J, Stirling F, Niederhuber MJ, Lambert TJ, Yapp C, Silver PA, Polka JK. Mol Biol Cell. 2017 Oct 1;28(20):2734-2745. doi: 10.1091/mbc.E17-01-0069. Epub 2017 Aug 9. PMID: 28963440

Synthetic genome recoding: new genetic codes for new features. Kuo J, Stirling F, Lau YH, Shulgina Y, Way JC, Silver PA. Curr Genet. 2017 Oct 5. doi: 10.1007/s00294-017-0754-z. [Epub ahead of print] Review. PMID: 28983660

Solar-powered CO2 reduction by a hybrid biological | inorganic system. Liu C, Colon BE, Silver PA and Nocera DG J of Photochemistry and Photobiology, 2017. Link

Biological-inorganic hybrid systems as a generalized platform for chemical production. Nangle SN, Sakimoto KK, Silver PA, Nocera DG Curr Opin Chem Biol. 2017 Nov 11;41:107-113. doi: 10.1016/j.cbpa.2017.10.023. [Epub ahead of print] PMID: 29136557

Efficient size-independent chromosome delivery from yeast to cultured cell lines. Brown DM, Chan YA, Desai PJ, Grzesik P, Oldfield LM, Vashee S, Way JC, Silver PA, Glass JI. Nucleic Acids Research. Link

Super-resolution microscopy of the β-carboxysome reveals a homogenous matrix. Matthew J Niederhuber, Talley J Lambert, Clarence Yapp, Pamela A. Silver, Jessica K Polka. BioRxiv. Link

Microbes use encapsulin protein organelles to sequester toxic reactions. Tobias Wolfgang Giessen, Pamela Ann Silver. BioRxiv. Link

Engineering Genetically-Encoded Mineralization and Magnetism via Directed Evolution. Xueliang Liu, Paola A Lopez, Tobias W Giessen, Michael Giles, Jeffrey C Way, and Pamela A Silver. Scientific Reports. Link

Long-term monitoring of inflammation in the mammalian gut using programmable commensal bacteria. David T Riglar, Michael Baym, S Jordan Kerns, Matthew J Niederhuber, Roderick T Bronson, Jonathan W Kotula, Georg K Gerber, Jeffrey C Way, Pamela A. Silver. BioRxiv. Link

Ribocomputing devices for sophisticated in vivo logic computation. Alexander A Green, Jongmin Kim, Duo Ma, Pamela A Silver, James J Collins, Peng Yin. NANOCOM’16 Proceedings of the 3rd ACM International Conference on Nanoscale Computing and Communication. Article No. 11. Link

A catalytic nanoreactor based on in vivo encapsulation of multiple enzymes in an engineered protein nanocompartment. Giessen T, Silver PA. ChemBioChem. Link

Synthetic lipid-containing scaffolds enhance production by co-localizing enzymes. Myhrvold CA, Polka JK, Silver PA. ACS Synthetic Biology. Link

Creating Single-Copy Genetic Circuits. Lee JW, Gyorgy A, Cameron DE, Pysenson N, Choi KR, Way JC, Silver PA, Del Vecchio D, Collins JJ. Molecular Cell. Link

Grown, Printed, and Biologically Augmented: An Additively Manufactured Microfluidic Wearable, Functionally Templated for Synthetic Microbes. Christoph Bader,* William G. Patrick,* Dominik Kolb, Stephanie G. Hays, Steven Keating, Sunanda Sharma, Daniel Dikovsky, Boris Belocon, James C. Weaver, Pamela A. Silver, and Neri Oxman. 3D printing and additive manufacturing. Link

Building Spatial Synthetic Biology with Compartments, Scaffolds, and Communities. Polka JK, Hays SG, Silver PA. Cold Spring Harbor Perspectives in Biology. Link

Converting a natural protein compartment into a nanofactory for the size-constrained synthesis of antimicrobial silver nanoparticles. Giessen T, Silver PA. ACS Synthetic Biology. Link

Water splitting-biosynthetic system with CO₂ reduction efficiencies exceeding photosynthesis. Liu C, Colón BC, Ziesack M, Silver PA, Nocera DG. Science. PMID: 27257255

A targeted erythropoietin that selectively stimulates red blood cell expansion in vivo. Burrill DR, Vernet A, Collins JJ, Silver PA, Way JC. Proceedings of the National Academy of Sciences USA. PMID: 27114509

A tunable protein piston that breaks membranes to release encapsulated cargo. Polka J, Silver PA. ACS Synthetic Biology. PMID: 26814170.

Streptomyces thermoautotrophicus does not fix nitrogen. MacKellar D, Lieber L, Norman JS, Bolger A, Tobin C, Murray JW, Oksaksin M, Chang RL, Ford TJ, Nguyen PQ, Woodward J, Permingeat H, Joshi N, Silver PA, Usadel B, Rutherford A, Friesen ML, and Prell J. Science Reports, 6:20086. Link

Engineering Acyl Carrier Protein to Enhance Production of Shortened Fatty Acids. Xueliang Liu, Wade M. Hicks, Pamela A. Silver, Jeffrey C. Way. Biotechnology for Biofuels, 9:24. Link

Pulse Detecting Genetic Circuit – A New Design Approach. Norman N, Inniss M, Iba H, Way JC. NCBI. Link

Biteen JS, Blainey PC, Cardon ZG, Chun M, Church GM, Dorrestein PC, Fraser SE, Gilbert JA, Jansson JK, Knight R, Miller JF, Ozcan A, Prather KA, Quake SR, Ruby EG, Silver PA, Taha S, van den Engh G, Weiss PS, Wong GCL, Wright AT, Young TD. (2015). Tools for the Microbiome: Nano and Beyond. ACS Nano. doi: 10.1021/acsnano.5b07826. Link. (Review)

Myhrvold C, Kotula JW, Hicks WM, Conway NJ, Silver PA. (2015). A distributed cell division counter reveals growth dynamics in the gut microbiota. Nature Communications, 6: 10039. PMID: 26615910

Polka JK, Silver PA. (2015). Tuning microscale, retractable, membrane-breaking proteins. On bioRxiv. DOI. Video here.

Giessen TW, Silver PA.  (2015). Encapsulation as a strategy for the design of biological compartmentalization. Journal of Molecular Biology. pii: S0022-2836(15)00520-3. doi: 10.1016/j.jmb.2015.09.009. PMID: 26403362 (Review)

Hays SG, Patrick WG, Ziesack M, Oxman N and Silver PA. (2015). Better together: engineering and application of microbial symbioses. Current Opinion in Biotechnology. Link. (Review)

Ford TJ and Silver PA. (2015). Synthetic biology expands control of microorganisms. Current Opinion in Chemical Biology, 28:20-28. PMID: 26056951 (Review)

Chen AH, Lubkowicz D, Yeong V, Chang RL and Silver PA. (2015). Transplantability of a circadian clock to a noncircadian organism. Science Advances, 1(5):e1500358. PMID: 26229984

Myhrvold C, Silver PA. (2015). Using synthetic RNAs as scaffolds and regulators. Nat Struct Mol Biol. 22(1), 8-10. PMID: 25565027 (Review)

Torella JP, Gagliardi CJ, Chen JS, Bediako DK, Colón B, Way JC, Silver PA, Nocera DG. (2015). Efficient solar-to-fuels production from a hybrid microbial-water-splitting catalyst system. Proc Natl Acad Sci U S A. 112(8), 2337-42. PMID: 25675518

Chang ZL, Silver PA, Chen YY. (2015). Identification and selective expansion of functionally superior T cells expressing chimeric antigen receptors. J Transl Med. 13, 161. PMID: 25990251

Ford TJ and Way JC. (2015). Enhancement of E. coli acyl-CoA synthetase FadD activity on medium chain fatty acids.  PeerJ, 3:e1040. PMID: 26157619

Chen JS, Colón B, Dusel B, Ziesack M, Way JC, Torella JP. (2015). Production of fatty acids in Ralstonia eutropha H16 by engineering B-oxidation and carbon storage. PeerJ, 3:e1468. Link.

Alicisatos AP, Blaser MJ, Brodie EL, Chun M, Dangl JL et al. Unified Microbiome Initiative Consortium. (2015). MICROBIOME: A unified initiative to harness Earth’s microbiomes. Science, 350:507-8. PMID: 26511287.

Robinson-Mosher A, Chen JH, Way J, Silver PA. (2014). Designing cell-targeted therapeutic proteins reveals the interplay between domain connectivity and cell binding. Biophys J. 107(10), 2456-66. PMID: 25418314

Green AA, Silver PA, Collins JJ, Yin P. (2014). Toehold switches: de-novo-designed regulators of gene expression. Cell. 159(4), 925-39. PMCID: PMC4265554

Polka JK, Silver PA. (2014). Induced sensitivity of Bacillus subtilis colony morphology to mechanical media compression. PeerJ. 2, e597. PMID:25289183

Torella JP, Lienert F, Boehm CR, Chen JH, Way JC, Silver PA. (2014). Unique nucleotide sequence-guided assembly of repetitive DNA parts for synthetic biology applications. Nat Protoc. 9(9), 2075-89. PMID: 25101822

Sachdeva G, Garg A, Godding D, Way JC, Silver PA. (2014). In vivo co-localization of enzymes on RNA scaffolds increases metabolic production in a geometrically dependent manner. Nucleic Acids Res. 42(14), 9493-503. PMID: 25034694

Silver PA, Way JC, Arnold FH, Meyerowitz JT. (2014). Synthetic biology: Engineering explored. Nature. 509(7499), 166-7. PMID: 24805338 (Review).

Mattozzi MD, Voges MJ, Silver PA, Way JC. (2014). Transient gene expression in tobacco using Gibson assembly and the Gene Gun. J Vis Exp. 86. PMID: 24796418

Way JC, Collins JJ, Keasling JD, Silver PA. (2014). Integrating biological redesign: where synthetic biology came from and where it needs to go. Cell. 157(1), 151-61. PMID: 24679533. (Review).

Kotula JW, Kerns SJ, Shaket LA, Siraj L, Collins JJ, Way JC, Silver PA. (2014). Programmable bacteria detect and record an environmental signal in the mammalian gut. Proc Natl Acad Sci U S A. 111(13), 4838-43. PMID: 24639514

Weyn-Vanhentenryck SM, Mele A, Yan Q, Sun S, Farny N, Zhang Z, Xue C, Herre M, Silver PA, Zhang MQ, Krainer AR, Darnell RB, Zhang C. (2014). HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism. Cell Rep. 6(6), 1139-52. PMID: 24613350

Lienert F, Lohmueller JJ, Garg A, Silver PA. (2014). Synthetic biology in mammalian cells: next generation research tools and therapeutics. Nat Rev Mol Cell Biol. 15(2), 95-107. PMID: 24434884 (Review).

Polka JK, Krukenberg KA. (2014). Making science a desirable career. Science. 346(6215), 1422. PMID: 25504725.

Polka JK, Silver PA. (2013). Building synthetic cellular organization. Mol Biol Cell. 24(23): 3585-7. PMID: 24288075 (Review).

Torella JP, Ford TJ, Kim SN, Chen AM, Way JC, Silver PA. (2013). Tailored fatty acid synthesis via dynamic control of fatty acid elongation. Proc Natl Acad Sci U S A. 110(28), 11290-5. PMID: 23798438

Wintermute EH, Lieberman TD, Silver PA. (2013). An objective function exploiting suboptimal solutions in metabolic networks. BMC Syst Biol. 7, 98. PMID:24088221

Torella JP, Boehm CR, Lienert F, Chen JH, Way JC, Silver PA. (2013). Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly. Nucleic Acids Res. 42(1), 681-9. PMID: 24078086

Inniss MC, Silver PA. (2013). Building synthetic memory. Curr Biol. 23(17), R812-6. PMID: 24028965 (Review).

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. PMID: 24023971

Voges MJ, Silver PA, Way JC, Mattozzi MD. (2013). Targeting a heterologous protein to multiple plant organelles via rationally designed 5′ RNA tags. J Bio Eng. 7(1), 20. PMID: 24011257

Lienert F, Torella JP, Chen JH, Norsworthy M, Richardson RR, Silver PA. (2013). Two- and three-input TALE-based AND logic computation in embryonic stem cells. Nucleic Acids Res. 41(21), 9967-75. PMID: 23982518

Myhrvold C, Dai M, Silver PA, Yin P. (2013). Isothermal self-assembly of complex DNA structures under diverse and biocompatible conditions. Nano Lett. 13(9), 4242-8. PMID: 23978049

Robinson-Mosher A, Shinar T, Silver PA, Way J. (2013). Dynamics simulations for engineering macromolecular interactions. Chaos. 23(2), 025110. PMID:23822508

Selgrade DF, Lohmueller JJ, Lienert F, Silver PA. (2013). Protein scaffold-activated protein trans-splicing in mammalian cells. J Am Chem Soc. 135(20), 7713-9. PMID: 23621664

Wang Q, Moore MJ, Adelmant G, Marto JA, Silver PA. (2013). PQBP1, a factor linked to intellectual disability, affects alternative splicing associated with neurite outgrowth. Genes Dev. 27(6), 615-26. PMID: 23512658

Mattozzi Md, Ziesack M, Voges MJ, Silver PA, Way JC. (2013). Expression of the sub-pathways of the Chloroflexus aurantiacus 3-hydroxypropionate carbon fixation bicycle in E. coli: Toward horizontal transfer of autotrophic growth. Metab Eng. 16, 130-9. PMID: 23376595

Chen AH, Afonso B, Silver PA, Savage DF. (2012). Spatial and temporal organization of chromosome duplication and segregation in the cyanobacterium Synechococcus elongatus PCC 7942. PLoS One. 7(10), e47837. PMID: 23112856

Chen AH, Silver PA. (2012). Designing biological compartmentalization. Trends Cell Biol. 22(12), 662-70. PMID: 22841504 (Review).

Burrill DR, Inniss MC, Boyle PC, Silver PA. (2012). Synthetic memory circuits for tracking human cell fate. Genes & Development. 26(13), 1486-97. PMID: 22751502

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. (2012). STAR RNA-binding protein Quaking suppresses cancer via stabilization of specific miRNA. Genes Dev. 26(13), 1459-72. PMID:22751500

Boyle PM, Burrill DR, Inniss MC, Agapakis CM, Deardon A, Dewerd JG, Gedeon MA, Quinn JY, Paull ML, Raman AM, Theilmann MR, Wang L, Winn JC, Medvedik O, Schellenberg K, Haynes KA, Viel A, Brenner TJ, Church GM, Shah JV, Silver PA. (2012). A BioBrick compatible strategy for genetic modification of plants. J Biol Eng. 6(1), 8. PMID: 22716313

Ducat DC, Silver PA. (2012). Improving carbon fixation pathways. Curr Opin Chem Biol. 16(3-4), 337-44. PMID: 22647231 (Review).

Agapakis CM, Boyle PM, Silver PA. (2012). Natural strategies for the spatial optimization of metabolism in synthetic biology. Nat Chem Biol 8(6), 527-35. PMID:22596204 (Review).

Garg A, Lohmueller JJ, Silver PA, Armel TZ. (2012). Engineering synthetic TAL effectors with orthogonal target sites. Nucleic Acids Res. 40(15), 7584-95. PMID:22581776

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. (2012). DNA ends alter the molecular composition and localization of Ku multicomponent complexes. Mol Cell Proteomics. 11(8), 411-21. PMID: 22535209

Haynes KA, Ceroni F, Flicker D, Younger A, Silver PA. (2012). A sensitive switch for visualizing natural gene silencing in single cells. ACS Synth Biol. 1(3), 99-106. PMID: 22530199

Nishida K, Silver PA. (2012). Induction of biogenic magnetization and redox control by a component of the target of rapamycin complex 1 signaling pathway. PLoS Biol. 10(2), e1001269. PMID: 22389629

Lohmueller JJ, Armel TZ, Silver PA. (2012). A tunable zinc finger-based framework for Boolean logic computation in mammalian cells. Nucleic Acids Res. 40(11), 5180-7. PMID: 22323524

Ducat DC, Avelar-Rivas JA, Way JC, Silver PA. (2012). Rerouting carbon flux to enhance photosynthetic productivity. Appl Environ Microbiol. 78(8), 2660-8. PMID:22307292

Bonacci W, Teng PK, Afonso B, Niederholtmeyer H, Grob P, Silver PA, Savage DF. (2012). Modularity of a carbon-fixing protein organelle. Proc Natl Acad Sci U S A. 109(2), 478-83. PMID: 22184212


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