Publications
For a complete listing of publications on PubMed, click here
2024
Synthetic microbiology in sustainability applications
(Link to article in Nature HERE!) Jones, E.M., Marken, J.P. & Silver, P.A. Synthetic microbiology in sustainability applications. Nat Rev Microbiol (2024). https://doi.org/10.1038/s41579-023-01007-9
Sustainable B12-Dependent Dehalogenation of Organohalides in E. coli
Ng TL, Silver PA. Sustainable B12-Dependent Dehalogenation of Organohalides in E. coli. ACS Chem Biol. 2024 Jan 22. doi: 10.1021/acschembio.3c00585. Epub ahead of print. PMID: 38254247.
Tardigrade secretory proteins protect biological structures from desiccation
S Lim, CB Reilly, Z Barghouti, B Marelli, JC Way, PA Silver
Communications Biology 7 (1), 633. Link to article here
LanTERN: A Fluorescent Sensor That Specifically Responds to Lanthanides
Ethan M. Jones Yang Su Chris Sander Quincey A. Justman Michael Springer*
and Pamela A. Silver*
ACS Synth. Biol. 2024, 13, 3, 958–962. Link to article here
Microbial Catalysis for CO2 Sequestration: A Geobiological Approach
https://cshperspectives.cshlp.org/content/16/5/a041673.short
Simultaneous enhancement of multiple functional properties using evolution-informed protein design
Benjamin Fram, Yang Su, Ian Truebridge, Adam J Riesselman, John B Ingraham, Allesandro Passera, Eve Napier, Nicole N Thadani, Samuel Lim, Kristen Roberts, Gurleen Kaur, Michael A Stiffler, Debora S Marks, Christopher D Bahl, Amir R Khan, Chris Sander, Nicholas P Gauthier
Nature Communications 15, Article 5141 (2024) Link to article
2023
High spontaneous integration rates of end-modified linear DNAs upon mammalian cell transfection
Lim, S., Yocum, R.R., Silver, P.A. et al. High spontaneous integration rates of end-modified linear DNAs upon mammalian cell transfection. Sci Rep 13, 6835 (2023). https://doi-org.ezp-prod1.hul.harvard.edu/10.1038/s41598-023-33862-0
Screen for Modulation of Nucleocapsid Protein Condensation Identifies Small Molecules with Anti-Coronavirus Activity.
Quek RT, Hardy KS, Walker SG, Nguyen DT, de Almeida Magalhães T, Salic A, Gopalakrishnan SM, Silver PA, Mitchison TJ.
ACS Chem Biol. 2023 Feb 16:acschembio.2c00908. doi: 10.1021/acschembio.2c00908.
PMID: 36795767 Free PMC article.
Bioinspired Design of Artificial Signaling Systems.
Way JC, Burrill DR, Silver PA.
Biochemistry. 2023 Jan 17;62(2):178-186. doi: 10.1021/acs.biochem.2c00368. Epub 2022 Aug 19.
PMID: 35984429 Review.
2022
Biocatalytic Formation of Novel Polyesters with para-Hydroxyphenyl groups in the Backbone – Engineering Cupriavidus necator for production of high-performance materials from CO2 and electricity. Nils JH Averesch, Vince E Pane, Frauke Kracke, Marika Ziesack, Shannon N Nangle, Pamela A Silver, Robert W Waymouth, Craig S Criddle
doi: https://doi.org/10.1101/2021.12.12.472320
A screen for modulation of nucleocapsid protein condensation identifies small molecules with anti-coronavirus activity. Rui Tong Quek, Kierra S. Hardy, Stephen G. Walker, Dan T. Nguyen, Taciani de Almeida Magalhães, Adrian Salic, Sujatha M. Gopalakrishnan, Pamela A. Silver, Timothy J. Mitchison
doi: https://doi.org/10.1101/2022.12.05.519191
Riboflavin synthesis from gaseous nitrogen and carbon dioxide by a hybrid inorganic-biological system. RS Sherbo, PA Silver, DG Nocera
Proceedings of the National Academy of Sciences 119 (37), e2210538119. Link
Bioinspired Design of Artificial Signaling Systems. Jeffrey Way, Devin R Burrill, Pamela A. Silver. August 19; Link
Multi-omics analysis of Dsup expressing human cells reveals open chromatin architectural dynamics underlying radioprotection.Westover C, Najjar D, Meydan C, Grigorev K, Veling MT, Chang RL, Chin C, Butler D, Afshin EE, Silver P, Mason C. bioRxiv. 2022, Mar 27; Link
Making sense of disorder: Investigating intrinsically disordered proteins in the tardigrade proteome via a computational approach. Lowe NE, Chang RL. bioRxiv. 2022, Jan 31; Link
High content screening and computational prediction reveal viral genes that suppress innate immune response. Ng TL, Olson EJ, Yoo TY, Weiss HS, Koide Y, Koch PD, Rollins NJ, Mach P, Meisinger T, Bricken T, Chang TZ, Molloy CW, Zurcher J, Mitchison T, Glass JI, Marks DS, Way JC, Silver PA. 2022. mSystems. 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, Lim S, Baker D, Way JC, Marks DS, Chang RL, Silver PA. 2022. ACS Synth Biol. Link
2021
High content screening and computational prediction reveal viral genes that suppress innate immune response. Ng TL, Olson EJ, Yoo TY, Weiss HS, Koide Y, Koch PD, Rollins NJ, Mach P, Meisinger T, Bricken T, Chang TZ, Molloy CW, Zurcher J, Mitchison T, Glass JI, Marks DS, Way JC, Silver PA. 2021. bioRxiv. Link
Biocatalytic formation of novel polyesters with para-hydroxyphenyl groups in the backbone – engineering cupriavidus necator for production of high-performance materials from CO2 and electricity. Averesch NJH, Pane VE, Kracke F, Ziesack M, Nangle SN, Silver PA, Waymouth RM, Criddle CS. 2021. bioRxiv. 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. 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
2020
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
2019
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
2018
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. Microbiol Resour Announce. Link
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: https://doi.org/10.1101/342287. 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: https://doi.org/10.1101/308734. 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
Solar-powered CO2 reduction by a hybrid biological/inorganic system. Liu C, Colon BE, Silver PA, Nocera DG. Photochem Photobiol A 2018 358, 411-415.
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. 2018. Appl Environ Microbiol. Link
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
2017
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
2016
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
2015
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.
2014
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.
2013
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
2012
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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