Publications

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

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

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

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

 

For older publications, please visit our wiki or search for Silver PA on Pubmed.