6. Amanda Lanza, John Blazeck, Nathan Crook, and Hal Alper, 2012. Linking yeast Gcn5p catalytic function and gene regulation using a quantitative, graded dominant mutant approach. PLoS ONE 7(4), e36193. Link to paper

5. Amanda Lanza, Nathan Crook, and Hal Alper, 2012. Innovation at the Intersection of Synthetic and Systems Biology. Current Opinion in Biotechnology 23(5), 712-717. Link to paper

16. Aura Ferreiro*, Nathan Crook*, Andrew J. Gasparrini, and Gautam Dantas, 2018.  Multiscale Evolutionary Dynamics of Host-Associated Microbiomes. Cell, 172(6), 1216-1227. Link to paper


15. Nathan Crook*, Jie Sun*, Joe Abatemarco*, James Wagner, Alexander Schmitz, and Hal Alper, 2016. in vivo continuous evolution of genes and pathways in yeast. Nature Communications, 7:13051. Link to paper

14. Amy Langdon*, Nathan Crook*, Gautam Dantas, 2016. The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation. Genome Medicine 8(39). Link to paper

13. Nathan Crook, Jie Sun, Nicholas Morse, Alexander Schmitz, and Hal Alper, 2016. Identification of gene knockdown targets conferring enhanced isobutanol and 1-butanol tolerance to Saccharomyces cerevisiae using a tunable RNAi screening approach. Applied Microbiology and Biotechnology, 100(23), 10005-10018. Link to paper

12. Jinsuk Lee*, Nathan Crook*, Jie Sun, and Hal Alper, 2016. Improvement of lactic acid production by a deletion of ssb1 in Saccharomyces cerevisiae. Journal of Industrial Microbiology & Biotechnology 43(1), 87-96. Link to paper

11. Kate Curran*, Nathan Crook*, Ashty Karim, Akash Gupta, and Hal Alper, 2014. Model-based design of synthetic yeast promoters via tuning of nucleosome architecture. Nature Communications,  5:4002. Link to paper

10. Nathan Crook, Alexander Schmitz, and Hal Alper, 2014. Optimization of a yeast RNA interference system for controlling gene expression and enabling rapid metabolic engineering. ACS Synthetic Biology 3(5), 307–313. Link to paper

9. Nathan Crook and Hal Alper, 2013. Model-Based Design of Synthetic, Biological Systems. Chemical Engineering Science 103, 15 November 2013, 2-11. Link to paper

8. Nathan Crook and Hal Alper, 2013. Classical Strain Improvement. Engineering Complex Phenotypes in Industrial Strains, First Edition 1-33. Edited by Ranjan Patnaik. John Wiley & Sons. Link to paper

7. Eric M. Brustad, Victor S. Lelyveld, Christopher D. Snow, Nathan C. Crook, Sang Taek Jung, Francisco M. Martinez, Timothy J. Scholl,  Alan Jasanoff, Frances H. Arnold, 2012. Structure-Guided Directed Evolution of Highly Selective P450-Based Magnetic Resonance Imaging Sensors for Dopamine and Serotonin. Journal of Molecular Biology 422(2), 245-262. Link to paper


4. Kate Curran, Nathan Crook, and Hal Alper, 2012. Using Flux Balance Analysis to Guide Microbial Metabolic Engineering. Methods in Molecular Biology v. 834: Microbial Metabolic Engineering 197-216. Link to paper

3. Nathan Crook, Elizabeth Freeman, and Hal Alper, 2011. Re-Engineering Multicloning Sites for Function and Convenience. Nucleic Acids Research 39(14), e92. Link to paper

1. Rudi Fasan, Michael M. Chen, Nathan C. Crook and Frances H. Arnold, 2007. Engineered Alkane-Hydroxylating Cytochrome P450BM3 Exhibiting Native-like Catalytic Properties. Angewandte Chemie International Edition 46(44), 8414-8418. Link to paper

2. Rudi Fasan, Nathan C. Crook, Matthew W. Peters, Peter Meinhold, Thomas Buelter, Marco Landwehr, Patrick C. Cirino, and Frances H. Arnold, 2011. Improved Product-Per-Glucose Yields in P450-Dependent Propane Biotransformations Using EngineeredEscherichia coli. Biotechnology and Bioengineering 108(3), 500-510. Link to paper







17. Nathan Crook*, Aura Ferreiro*, Andrew J. Gasparrini, Mitchell W. Pesesky, Molly K. Gibson, Bin Wang, Xiaoqing Sun, Zevin Condiotte, Stephen Dobrowolski, Daniel Peterson, and Gautam Dantas, 2019.  Adaptive Strategies of the Candidate Probiotic E. coli Nissle in the Mammalian Gut.

Cell Host & Microbe


18. Justin M. Vento, Nathan Crook, Chase L. Beisel, 2019.   Barriers to genome editing with CRISPR in bacteria.                      J Ind Microbiol Biotechnol.


19. Nathan Crook, Aura Ferreiro, Zevin Condiotte, Gautam Dantas, 2020. Transcript Barcoding Illuminates the Expression Level of Synthetic Constructs in E. coli Nissle Residing in the Mammalian Gut. ACS SynBio

20. Deniz Durmusoglu*, Ibrahim Al’Abri*, Scott P. Collins, Junrui Cheng, Abdulkerim Eroglu, Chase Beisel, Nathan Crook, 2020.   In Situ Biomanufacturing of Small Molecules in the Mammalian Gut by Probiotic Saccharomyces boulardii.  ACS SynBio

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21. Ibrahim Al’Abri, Deniz Durmusoglu, Nathan Crook, 2021.  What E. coli knows about your 1-year-old infant: Antibiotic use, lifestyle, birth mode, and siblings. Cell Host & Microbe

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22. Deniz Durmusoglu*, Carly M Catella*, Ethan F Purnell*, Stefano Menegatti, Nathan Crook, 2021.  Design and in situ biosynthesis of precision therapies against gastrointestinal pathogens​. Current Opinion in Physiology

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23. Mairead K. Heavey*, Deniz Durmusoglu*, Nathan Crook, Aaron C. Anselmo, 2021.  Discovery and delivery strategies for engineered live biotherapeutic products​. Trends in Biotechnology


24. Ki Yoon KwonSamuel CheesemanAlba Frias-DeDiego,  Haeleen HongJiayi YangWoojin Jung,Hong YinBilly J. MurdochFrank ScholleNathan CrookElisa CrisciMichael D. DickeyVi Khanh TruongTae-il Kim, 2021. 

Liquid Metal Mediated Metallic Coating for Antimicrobial and Antiviral Fabrics​. Advanced Materials

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25. Xingqing Xiao, Sudeep Sarma, Stefano Menegatti, Nathan Crook, Scott T. Magness, and Carol K. Hall 2021. 

In Silico Identification and Experimental Validation of Peptide-Based Inhibitors Targeting Clostridium difficile Toxin A.  ACS Chem. Biol



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27. Ibrahim S Al'Abri, Daniel Haller, Zidan Li, Nathan C Crook, 2022. Inducible Directed Evolution of Complex Phenotypes in Bacteria. Nucleic Acids Research

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