For a full list see Google Scholar. 

Plasmid requests: The plasmids we've used for our publications are available from Addgene.

Transcriptional competition biases the effects of second messengers in E. coli

Andrea Ripamonti,  Milan Lacassin,  Rossana Droghetti,  Gregory Bokinsky,  Marco Cosentino Lagomarsino. biorxiv preprint April 2025.

Exogenous fatty acids inhibit fatty acid synthesis through competition between endogenously- and exogenously-generated substrates for phospholipid synthesis in Escherichia coli

Stefan Pieter Hendrik van den Berg, Adja Zoumaro-Djayoon, Flora Yang, Gregory Bokinsky. FEBS Letters. Published online 30 December 2024.

PlsX and PlsY: Additional roles beyond glycerophospholipid synthesis in Gram-negative bacteria

Audrey N Rex, Brent W Simpson, Gregory Bokinsky, M Stephen Trent. mBio (2024). DOI: 10.1128/mbio.02969-24

A temperature-sensitive metabolic valve and a transcriptional feedback loop drive rapid homeoviscous adaptation in Escherichia coli

Loles Hoogerland*, Stefan Pieter Hendrik van den Berg*, Yixing Suo*, Yuta W. Moriuchi*, Adja Zoumaro-Djayoon, Esther Geurken, Flora Yang, Frank Bruggeman, Michael D. Burkart & Gregory Bokinsky. *Contributed equally. Nature Communications volume 15, Article number: 9386 (2024). Open access (biorxiv preprint posted 10 July 2023.)

Harnessing iron‑sulfur enzymes for synthetic biology

Helena Shomar and Gregory Bokinsky. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research. Available online 3 April 2024, 119718. Link

Cellular assays identify barriers impeding iron-sulphur enzyme activity in a non-native prokaryotic host

Francesca D’Angelo*, Elena Fernández-Fueyo*, Pierre Simon Garcia*, Helena Shomar*, Martin Pelosse, Rita Rebelo Manuel, Ferhat Büke, Siyi Liu, Niels van den Broek, Nicolas Duraffourg, Carol de Ram, Martin Pabst, Emmanuelle Bouveret, Simonetta Gribaldo, Béatrice Py, Sandrine Ollagnier de Choudens, Frédéric Barras, Gregory Bokinsky.  *Contributed equally. eLife 11:e70936 (2022). Open access

ppGpp is a bacterial cell size regulator

Ferhat Büke, Jacobi Grilli, Marco Cosentino Lagomarsino, Gregory Bokinsky*, Sander Tans.* Current Biology 32, 1-8 (2022). Publisher website
*Corresponding authors. These authors contributed equally to the manuscript.

Towards a Synthetic Biology Toolset for Metallocluster Enzymes in Biosynthetic Pathways: What We Know and What We Need 

Helena Shomar* & Gregory Bokinsky*. Molecules 26: 6930 (2021). Open access
*Corresponding authors. 

Calibrating the Bacterial Growth Rate Speedometer: A Re-evaluation of the Relationship Between Basal ppGpp, Growth, and RNA Synthesis in Escherichia coli 

N. Imholz*, M. Noga, N. van den Broek, G. Bokinsky*. Frontiers in Microbiology (September 2020). Open access
*Corresponding authors. 

Posttranslational control of PlsB is sufficient to coordinate membrane synthesis with growth in Escherichia coli

M. Noga, F. Büke, N. van den Broek, N. Imholz, N. Scherer, F. Yang, G. Bokinsky. mBio 11:e02703-19 (2020). Open access

Metabolic engineering of a carbapenem antibiotic synthesis pathway in Escherichia coli

H. Shomar, S. Gontier, N. van den Broek, H. Mora, M. Noga, P-L. Hagedoorn, G. Bokinsky. Nature Chemical Biology 14: 794–800 (2018). Publisher's website

Mass spectrometry-based quantification of protein-bound fatty acid synthesis intermediates from Escherichia coli

M. Noga*, M. Cerri, N. Imholz, P. Tulinski, E. Şahin, G. Bokinsky*. Journal of Proteome Research 15: 3617-3623 (2016). Pubmed
*Corresponding authors. 

Before 2014

HipA-triggered growth arrest and β-lactam tolerance in Escherichia coli are mediated by RelA-dependent ppGpp synthesis. G. Bokinsky*, E. Baidoo, S. Akella, H. Burd, D. Weaver, J. Alonso-Gutierrez, H. Garcia-Martin, J. Keasling*. Journal of Bacteriology 195: 3173-3182 (2013). *Corresponding authors. Pubmed

Synthesis of three advanced biofuels from ionic liquid-pretreated switchgrass using engineered Escherichia coli. G. Bokinsky, P. Peralta-Yahya, A. George, B. Holmes, E. Steen, J. Dietrich, T. S. Lee, D. Tullman-Ercek, C. Voigt, B. Simmons, J. Keasling. PNAS 108: 19949-19954 (2011). PNAS link

Microbial production of fatty-acid-derived fuels and chemicals from plant biomass. E. Steen*, Y. Kang*, G. Bokinsky, Z. Hu, A. Schirmer A. McClure, S. Del Cardayre, J. Keasling. Nature 463: 559-562 (2010). *Contributed equally to this work. Nature link

Dynamic binding orientations direct activity of HIV reverse transcriptase. E. Abbondanzieri*, G. Bokinsky*, J. Rausch, J. Zhang, S. Le Grice, X. Zhuang. Nature 453: 184-189 (2008). *Contributed equally to this work. Nature link

Two distinct binding modes of a protein cofactor with its target RNA. G. Bokinsky, L. Nivón, S. Liu, G. Chai, M. Hong, K. M. Weeks, X. Zhuang. Journal of Molecular Biology 361: 771-784 (2006). Pubmed

Single-molecule RNA folding. G. Bokinsky, X. Zhuang. Accounts of Chemical Research 38: 566-573 (2005). Pubmed

Single-molecule enzymology of RNA: Essential functional groups impact catalysis from a distance. D. Rueda*, G. Bokinsky*, M. Rhodes, M. Rust, X. Zhuang, N. Walter. PNAS 101: 10066-10071 (2004). *Contributed equally to this work. Pubmed

Single-molecule transition-state analysis of RNA folding. G. Bokinsky, D. Rueda, V. Misra, A. Gordus, M. Rhodes, H. Babcock, N. Walter, X. Zhuang. PNAS 100: 9302-9307 (2003). Pubmed