2025
GroovDB in 2025: A community-editable database of small molecule biosensors
Love JD, Rafferty BM, Thomas M, Springer M, Silver PA, d’Oelsnitz S. groovDB in 2025: A community-editable database of small molecule biosensors. bioRxiv. 2025 19 Aug.
The case for Mars terraforming research
DeBenedictis EA, Kite ES, Wordsworth RD, Lanza NL, Cockell CS, Silver PA, Ramirez RM, Cumbers J, Mohseni H, Mason CE, Fischer WW, McKay CP. The case for Mars terraforming research. Nature Astronomy. 2025 13 May; 9, pages 634–639
Microbes can capture carbon and degrade plastic - why aren’t we using them more?
Rappuoli R, Nguyen NK, Bloom DE, Brooke C, Burckhardt RM…Silver PA, Stein LY. Nature. 2025 Mar; 639 (8056):864 - 866. PMID: 40133617.
Comparative evaluation of cell-based assay technologies for scoring drug-induced condensation of SARS-CoV-2 nucleocapsid protein
Quek RT, Shirazinejad CR, Young CL, Hardy KS, Lim S, Elms PJ, McSwiggen DT, Mitchison TJ, Silver PA. Comparative evaluation of cell-based assay technologies for scoring drug-induced condensation of SARS-CoV-2 nucleocapsid protein. SLAS Discov (2025).
Using enantioselective biosensors to evolve asymmetric biocatalysts
d’Oelsnitz Simon, Wantae Kim, Haley Hardtke, Svetlana Ikonomova, Nina Alperovich, Olga Vasilyeva, Michael James, Eric Zigon, Charlie Johnson, Andrew Ellington, Quincey Justman, Michael Springer, Jessie Zhang, Pamela Silver, David Ross. Research Square (2025).
Linker minimization and characterization of Fc-fused interleukin-17A for increased in vivo half-life
Qiu C Wu, Jungmin Lee, Aishwarya Swaminathan, Ashley Winward, Yung Hwang, Merav Socolovsky, Jeffrey C Way, Allon M Klein (2025).
Rational design of selective bispecific EPO-R/CD131 agonists
Kailyn E Doiron, Jeffrey C Way, Pamela A Silver. PEDS (2025).
2024
Synthetic microbiology in sustainability applications
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.
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. (2024)
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. (2024)
Microbial Catalysis for CO2 Sequestration: A Geobiological Approach
Martin Van Den Berghe, Nathan G. Walworth, Neil C. Dalvie, Chris L. Dupont, Michael Springer, M. Grace Andrews, Stephen J. Romaniello, David A. Hutchins, Francesc Montserrat, Pamela A. Silver and Kenneth H. Nealson. (2024)
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)
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).
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 Criddledoi: 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. Mitchisondoi: 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 NoceraProceedings of the National Academy of Sciences 119 (37), e2210538119. LinkBioinspired Design of Artificial Signaling Systems. Jeffrey Way, Devin R Burrill, Pamela A. Silver. August 19.
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.
Making sense of disorder: Investigating intrinsically disordered proteins in the tardigrade proteome via a computational approach.
Lowe NE, Chang RL. bioRxiv. 2022, Jan 31.
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.
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.
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.
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.
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.
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.
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.
Theranostic cells: emerging clinical applications of synthetic biology.
McNerney MP, Doiron KE, Ng TL, Chang TZ, Silver PA. 2021. Nat. Rev. Genet.
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.
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.
Exploring targeting peptide-shell interactions in encapsulin nanocompartments.
Altenburg WJ, Rollins N, Silver PA, Giessen TW. 2021. Sci Rep.
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.
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.
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.
In situ reprogramming of gut bacteria by oral delivery.
Hsu BB, Plant IN, Lyon L, Anastassacos FM, Way JC, Silver PA. 2020. Nat Commun.
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.
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.
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.
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.
Controlling the Implementation of Transgenic Microbes: Are We Ready for What Synthetic Biology Has to Offer?
Stirling F, Silver PA. 2020. Mol. Cell.
Towards a translationally-independent RNA-based synthetic oscillator using deactivated CRISPR-Cas.
Kuo J, Yuan R, Sánchez C, Paulsson J, Silver PA. 2020.
In situ reprogramming of gut bacteria by oral delivery.
Hsu BB, Plant IN, Lyon L, Anastassacos FM, Way JC, Silver PA. 2020.
Genetic tool development in marine protists: emerging model organisms for experimental cell biology.
Faktorová D, et al. 2020. Nat. Methods.
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.
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.
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.
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.
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.
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.
Stable Neutralization of a Virulence Factor in Bacteria Using Temperate Phage in the Mammalian Gut.
Hsu BB, Way JC, Silver PA. 2020. mSystems.
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.
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.
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.
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.
Minimizing side effects, maximizing returns: what makes a smart therapeutic design?
Lee J, Redfield K, Way J, Silver P. 2019. Biochem (Lond).
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.
Stable neutralization of virulent bacteria using temperate phage in the mammalian gut.
Hsu B, Way JC, Silver PA. 2019.
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.
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.
Genetic tool development in marine protists: Emerging model organisms for experimental cell biology.
Faktorová D, et al. 2019.
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.
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.
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.
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.
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.
Beyond the Four Bases: A Home Run for Synthetic Epigenetic Control?
Chang TZ, Kuo J, Silver PA. 2019. Mol Cell.
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.
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.
Harnessing undomesticated life.
Libby EA, Silver PA. 2019. Nat Microbiol.
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.
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.
Heterologous Cas9 and non-homologous end joining as a Potentially Organism-Agnostic Knockout (POAK) system in bacteria.
Plant IM. 2019.
Multisite phosphorylation drives phenotypic variation in (p)ppGpp synthetase-dependent antibiotic tolerance.
Libby EA, Reuveni S, Dworkin J. 2019. Nature Communications.
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.
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.
Bacteriophages dynamically modulate the gut microbiota and metabolome.
Hsu BB, Gibson TE, Yeliseyev V, Liu Q, Bry L, Silver PA, Gerber GK. 2018. Biorxiv.
Carbon fixation systems and methods.
Cruz Colón B, Liu C, Ziesack M, Silver PA, Nocera DG. United States Patent US20180265898A1. 2018.
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.
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.
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.
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.
Multisite phosphorylation regulates phenotypic variability in antibiotic tolerance.
Libby E, Reuveni S, Dworkin J. 2018. Biorxiv.
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.
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.
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.
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.
Prokaryotic nanocompartments form synthetic organelles in a eukaryote.
Yu Heng Lau, Tobias Wolfgang Giessen, Wiggert J Altenburg and Pamela A. Silver. 2018. Biorxiv.
Engineering bacteria for diagnostic and therapeutic applications.
Riglar D and Silver PA. 2018, Nature Reviews Microbiology.
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.
Engineered genetic enteric sensor bacteria and uses thereof.
Kotula J, Kerns SJ, Way JC, and Silver PA. United States Patent US10047405B2. 2018.
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.
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.
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.
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.
Rational Design of Evolutionarily Stable Microbial Kill Switches.
Finn Stirling, Lisa Bitzan, John Oliver, Jeffrey Way, Pamela A. Silver. bioRxiv.
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. 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. 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.
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. PMID: 29136557
2016
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.
Microbes use encapsulin protein organelles to sequester toxic reactions.
Tobias Wolfgang Giessen, Pamela Ann Silver. BioRxiv.
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.
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.
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.
A catalytic nanoreactor based on in vivo encapsulation of multiple enzymes in an engineered protein nanocompartment.
Giessen T, Silver PA. ChemBioChem.
Synthetic lipid-containing scaffolds enhance production by co-localizing enzymes.
Myhrvold CA, Polka JK, Silver PA. ACS Synthetic Biology.
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.
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.
Building Spatial Synthetic Biology with Compartments, Scaffolds, and Communities.
Polka JK, Hays SG, Silver PA. Cold Spring Harbor Perspectives in Biology.
Converting a natural protein compartment into a nanofactory for the size-constrained synthesis of antimicrobial silver nanoparticles.
Giessen T, Silver PA. ACS Synthetic Biology.
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.
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.
Pulse Detecting Genetic Circuit – A New Design Approach.
Norman N, Inniss M, Iba H, Way JC. NCBI.
2015
Tools for the Microbiome: Nano and Beyond.
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).ACS Nano. doi: 10.1021/acsnano.5b07826.
A distributed cell division counter reveals growth dynamics in the gut microbiota.
Myhrvold C, Kotula JW, Hicks WM, Conway NJ, Silver PA. (2015). Nature Communications, 6: 10039. PMID: 26615910
Tuning microscale, retractable, membrane-breaking proteins.
Polka JK, Silver PA. (2015). BioRxiv. DOI. Video here.
Encapsulation as a strategy for the design of biological compartmentalization.
Giessen TW, Silver PA. (2015). Journal of Molecular Biology. pii: S0022-2836(15)00520-3. doi: 10.1016/j.jmb.2015.09.009. PMID: 26403362
Better together: engineering and application of microbial symbioses.
Hays SG, Patrick WG, Ziesack M, Oxman N and Silver PA. (2015). Current Opinion in Biotechnology.
Synthetic biology expands control of microorganisms.
Ford TJ and Silver PA. (2015).Current Opinion in Chemical Biology, 28:20-28. PMID: 26056951
Transplantability of a circadian clock to a noncircadian organism.
Chen AH, Lubkowicz D, Yeong V, Chang RL and Silver PA. (2015). Science Advances, 1(5):e1500358. PMID: 26229984
Using synthetic RNAs as scaffolds and regulators.
Myhrvold C, Silver PA. (2015). Nat Struct Mol Biol. 22(1), 8-10. PMID: 25565027
Efficient solar-to-fuels production from a hybrid microbial-water-splitting catalyst system.
Torella JP, Gagliardi CJ, Chen JS, Bediako DK, Colón B, Way JC, Silver PA, Nocera DG. (2015). Proc Natl Acad Sci U S A. 112(8), 2337-42. PMID: 25675518
Identification and selective expansion of functionally superior T cells expressing chimeric antigen receptors.
Chang ZL, Silver PA, Chen YY. (2015). J Transl Med. 13, 161. PMID: 25990251
Enhancement of E. coli acyl-CoA synthetase FadD activity on medium chain fatty acids.
Ford TJ and Way JC. (2015). PeerJ, 3:e1040. PMID: 26157619
Production of fatty acids in Ralstonia eutropha H16 by engineering B-oxidation and carbon storage.
Chen JS, Colón B, Dusel B, Ziesack M, Way JC, Torella JP. (2015). PeerJ, 3:e1468.
MICROBIOME: A unified initiative to harness Earth’s microbiomes.
Alicisatos AP, Blaser MJ, Brodie EL, Chun M, Dangl JL et al. Unified Microbiome Initiative Consortium. (2015). Science, 350:507-8. PMID: 26511287.
2014
Designing cell-targeted therapeutic proteins reveals the interplay between domain connectivity and cell binding.
Robinson-Mosher A, Chen JH, Way J, Silver PA. (2014). Biophys J. 107(10), 2456-66. PMID: 25418314
Toehold switches: de-novo-designed regulators of gene expression.
Green AA, Silver PA, Collins JJ, Yin P. (2014). Cell. 159(4), 925-39. PMCID: PMC4265554
Induced sensitivity of Bacillus subtilis colony morphology to mechanical media compression.
Polka JK, Silver PA. (2014). PeerJ. 2, e597. PMID:25289183
Unique nucleotide sequence-guided assembly of repetitive DNA parts for synthetic biology applications.
Torella JP, Lienert F, Boehm CR, Chen JH, Way JC, Silver PA. (2014). Nat Protoc. 9(9), 2075-89. PMID: 25101822
In vivo co-localization of enzymes on RNA scaffolds increases metabolic production in a geometrically dependent manner.
Sachdeva G, Garg A, Godding D, Way JC, Silver PA. (2014). Nucleic Acids Res. 42(14), 9493-503. PMID: 25034694
Synthetic biology: Engineering explored.
Silver PA, Way JC, Arnold FH, Meyerowitz JT. (2014). Nature. 509(7499), 166-7. PMID: 24805338
Transient gene expression in tobacco using Gibson assembly and the Gene Gun.
Mattozzi MD, Voges MJ, Silver PA, Way JC. (2014). J Vis Exp. 86. PMID: 24796418
Integrating biological redesign: where synthetic biology came from and where it needs to go.
Way JC, Collins JJ, Keasling JD, Silver PA. (2014). Cell. 157(1), 151-61. PMID: 24679533.
Programmable bacteria detect and record an environmental signal in the mammalian gut.
Kotula JW, Kerns SJ, Shaket LA, Siraj L, Collins JJ, Way JC, Silver PA. (2014). Proc Natl Acad Sci U S A. 111(13), 4838-43. PMID: 24639514
HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism.
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). Cell Rep. 6(6), 1139-52. PMID: 24613350
Synthetic biology in mammalian cells: next generation research tools and therapeutics.
Lienert F, Lohmueller JJ, Garg A, Silver PA. (2014). Nat Rev Mol Cell Biol. 15(2), 95-107. PMID: 24434884
Making science a desirable career.
Polka JK, Krukenberg KA. (2014). Science. 346(6215), 1422. PMID: 25504725.
2013
Building synthetic cellular organization.
Polka JK, Silver PA. (2013). Mol Biol Cell. 24(23): 3585-7 PMID: 24288075
Tailored fatty acid synthesis via dynamic control of fatty acid elongation.
Torella JP, Ford TJ, Kim SN, Chen AM, Way JC, Silver PA. (2013). Proc Natl Acad Sci U S A. 110(28), 11290-5. PMID: 23798438
An objective function exploiting suboptimal solutions in metabolic networks.
Wintermute EH, Lieberman TD, Silver PA. (2013). BMC Syst Biol. 7, 98. PMID: 24088221
Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly.
Torella JP, Boehm CR, Lienert F, Chen JH, Way JC, Silver PA. (2013). Nucleic Acids Res. 42(1), 681-9. PMID: 24078086
Building synthetic memory.
Inniss MC, Silver PA. (2013). Curr Biol. 23(17), R812-6. PMID: 24028965
The bacterial carbon-fixing organelle is formed by shell envelopment of preassembled cargo.
Chen AH, Robinson-Mosher A, Savage DF, Silver PA, Polka JK. (2013). PLoS One. 8(9), e76127. PMID: 24023971
Targeting a heterologous protein to multiple plant organelles via rationally designed 5′ RNA tags.
Voges MJ, Silver PA, Way JC, Mattozzi MD. (2013). J Bio Eng. 7(1), 20. PMID: 24011257
Two- and three-input TALE-based AND logic computation in embryonic stem cells.
Lienert F, Torella JP, Chen JH, Norsworthy M, Richardson RR, Silver PA. (2013). Nucleic Acids Res. 41(21), 9967-75. PMID: 23982518
Isothermal self-assembly of complex DNA structures under diverse and biocompatible conditions.
Myhrvold C, Dai M, Silver PA, Yin P. (2013). Nano Lett. 13(9), 4242-8. PMID: 23978049
Dynamics simulations for engineering macromolecular interactions.
Robinson-Mosher A, Shinar T, Silver PA, Way J. (2013). Chaos. 23(2), 025110. PMID:23822508
Protein scaffold-activated protein trans-splicing in mammalian cells.
Selgrade DF, Lohmueller JJ, Lienert F, Silver PA. (2013). J Am Chem Soc. 135(20), 7713-9. PMID: 23621664
PQBP1, a factor linked to intellectual disability, affects alternative splicing associated with neurite outgrowth.
Wang Q, Moore MJ, Adelmant G, Marto JA, Silver PA. (2013). Genes Dev. 27(6), 615-26. PMID: 23512658
Expression of the sub-pathways of the Chloroflexus aurantiacus 3-hydroxypropionate carbon fixation bicycle in E. coli: Toward horizontal transfer of autotrophic growth.
Mattozzi Md, Ziesack M, Voges MJ, Silver PA, Way JC. (2013). Metab Eng. 16, 130-9. PMID: 23376595
2012
Spatial and temporal organization of chromosome duplication and segregation in the cyanobacterium Synechococcus elongatus PCC 7942.
Chen AH, Afonso B, Silver PA, Savage DF. (2012). PLoS One. 7(10), e47837. PMID: 23112856
Designing biological compartmentalization.
Chen AH, Silver PA. (2012). Trends Cell Biol. 22(12), 662-70. PMID: 22841504
Synthetic memory circuits for tracking human cell fate.
Burrill DR, Inniss MC, Boyle PC, Silver PA. (2012). Genes & Development. 26(13), 1486-97. PMID: 22751502
STAR RNA-binding protein Quaking suppresses cancer via stabilization of specific miRNA.
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). Genes Dev. 26(13), 1459-72. PMID:22751500
A BioBrick compatible strategy for genetic modification of plants.
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). J Biol Eng. 6(1), 8. PMID: 22716313
Improving carbon fixation pathways.
Ducat DC, Silver PA. (2012). Curr Opin Chem Biol. 16(3-4), 337-44. PMID: 22647231
Natural strategies for the spatial optimization of metabolism in synthetic biology.
Agapakis CM, Boyle PM, Silver PA. (2012). Nat Chem Biol 8(6), 527-35. PMID:22596204
Engineering synthetic TAL effectors with orthogonal target sites.
Garg A, Lohmueller JJ, Silver PA, Armel TZ. (2012). Nucleic Acids Res. 40(15), 7584-95. PMID:22581776
DNA ends alter the molecular composition and localization of Ku multicomponent complexes.
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). Mol Cell Proteomics. 11(8), 411-21. PMID: 22535209
A sensitive switch for visualizing natural gene silencing in single cells.
Haynes KA, Ceroni F, Flicker D, Younger A, Silver PA. (2012). ACS Synth Biol. 1(3), 99-106. PMID: 22530199
Induction of biogenic magnetization and redox control by a component of the target of rapamycin complex 1 signaling pathway.
Nishida K, Silver PA. (2012). PLoS Biol. 10(2), e1001269. PMID: 22389629
A tunable zinc finger-based framework for Boolean logic computation in mammalian cells.
Lohmueller JJ, Armel TZ, Silver PA. (2012). Nucleic Acids Res. 40(11), 5180-7. PMID: 22323524
Rerouting carbon flux to enhance photosynthetic productivity.
Ducat DC, Avelar-Rivas JA, Way JC, Silver PA. (2012). Appl Environ Microbiol. 78(8), 2660-8. PMID:22307292
Modularity of a carbon-fixing protein organelle.
Bonacci W, Teng PK, Afonso B, Niederholtmeyer H, Grob P, Silver PA, Savage DF. (2012). Proc Natl Acad Sci U S A. 109(2), 478-83. PMID: 22184212