Chase Beisel

Gawlitt, S., Collins, S. P., Yu, Y., Blackman, S. A., Barquist, L., & Beisel, C. L. (2024, March 18). Expanding the flexibility of base editing for high-throughput genetic screens in bacteria. NUCLEIC ACIDS RESEARCH. https://doi.org/10.1093/nar/gkae174

Wimmer, F., Englert, F., Wandera, K. G., Alkhnbashi, O. S., Collins, S. P., Backofen, R., & Beisel, C. L. (2023, November 28). Interrogating two extensively self-targeting Type I CRISPR-Cas systems in Xanthomonas albilineans reveals distinct anti-CRISPR proteins that block DNA degradation. NUCLEIC ACIDS RESEARCH. https://doi.org/10.1093/nar/gkad1097

Collias, D., Vialetto, E., Yu, J., Co, K., Almasi, E. D. H., Ruettiger, A.-S., … Beisel, C. L. (2023). Systematically attenuating DNA targeting enables CRISPR-driven editing in bacteria. NATURE COMMUNICATIONS, 14(1). https://doi.org/10.1038/s41467-023-36283-9

Vialetto, E., Yu, Y., Collins, S. P., Wandera, K. G., Barquist, L., & Beisel, C. L. (2022). A target expression threshold dictates invader defense and prevents autoimmunity by CRISPR-Cas13. CELL HOST & MICROBE, 30(8), 1151-+. https://doi.org/10.1016/j.chom.2022.05.013

Collias, D., & Beisel, C. L. (2021). [Review of CRISPR technologies and the search for the PAM-free nuclease]. NATURE COMMUNICATIONS, 12(1). https://doi.org/10.1038/s41467-020-20633-y

Yu, T., Zhang, S., Matei, R., Marx, W., Beisel, C. L., & Wei, Q. (2021, July 23). Coupling smartphone and CRISPR-Cas12a for digital and multiplexed nucleic acid detection. AICHE JOURNAL, Vol. 7. https://doi.org/10.1002/aic.17365

Durmusoglu, D., Al'Abri, I. S., Collins, S. P., Cheng, J., Eroglu, A., Beisel, C. L., & Crook, N. (2021). In Situ Biomanufacturing of Small Molecules in the Mammalian Gut by Probiotic Saccharomyces boulardii. ACS SYNTHETIC BIOLOGY, 10(5), 1039–1052. https://doi.org/10.1021/acssynbio.0c00562

Collins, S. P., Rostain, W., Liao, C., & Beisel, C. L. (2021). Sequence-independent RNA sensing and DNA targeting by a split domain CRISPR-Cas12a gRNA switch. NUCLEIC ACIDS RESEARCH, 49(5), 2985–2999. https://doi.org/10.1093/nar/gkab100

Collias, D., Leenay, R. T., Slotkowski, R. A., Zuo, Z., Collins, S. P., McGirr, B. A., … Beisel, C. L. (2020). A positive, growth-based PAM screen identifies noncanonical motifs recognized by the S. pyogenes Cas9. SCIENCE ADVANCES, 6(29). https://doi.org/10.1126/sciadv.abb4054

Wandera, K. G., Collins, S. P., Wimmer, F., Marshall, R., Noireaux, V., & Beisel, C. L. (2020). An enhanced assay to characterize anti-CRISPR proteins using a cell-free transcription-translation system. METHODS, 172, 42–50. https://doi.org/10.1016/j.ymeth.2019.05.014

Jacobsen, T., Ttofali, F., Liao, C., Manchalu, S., Gray, B. N., & Beisel, C. L. (2020). Characterization of Cas12a nucleases reveals diverse PAM profiles between closely-related orthologs. NUCLEIC ACIDS RESEARCH, 48(10), 5624–5638. https://doi.org/10.1093/nar/gkaa272

Siedler, S., Rau, M. H., Bidstrup, S., Vento, J. M., Aunsbjerg, S. D., Bosma, E. F., … Neves, A. R. (2020). Competitive Exclusion Is a Major Bioprotective Mechanism of Lactobacilli against Fungal Spoilage in Fermented Milk Products. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 86(7). https://doi.org/10.1128/AEM.02312-19

Beisel, C. L. (2020, February 1). Methods for characterizing, applying, and teaching CRISPR-Cas systems. METHODS, Vol. 172, pp. 1–2. https://doi.org/10.1016/j.ymeth.2020.01.004

Jacobsen, T., Yi, G., Al Asafen, H., Jermusyk, A. A., Beisel, C. L., & Reeves, G. T. (2020). Tunable self-cleaving ribozymes for modulating gene expression in eukaryotic systems. PLOS ONE, 15(4). https://doi.org/10.1371/journal.pone.0232046

Collins, S. P., & Beisel, C. L. (2020, September 3). Your Base Editor Might Be Flirting with Single (Stranded) DNA: Faithful On-Target CRISPR Base Editing without Promiscuous Deamination. MOLECULAR CELL, Vol. 79, pp. 703–704. https://doi.org/10.1016/j.molcel.2020.07.030

Collias, D., Marshall, R., Collins, S. P., Beisel, C. L., & Noireaux, V. (2019). An educational module to explore CRISPR technologies with a cell-free transcription-translation system. SYNTHETIC BIOLOGY, 4(1). https://doi.org/10.1093/synbio/ysz005

Vento, J. M., Crook, N., & Beisel, C. L. (2019). [Review of Barriers to genome editing with CRISPR in bacteria]. JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY, 46(9-10), 1327–1341. https://doi.org/10.1007/s10295-019-02195-1

Liao, C., Slotkowski, R. A., & Beisel, C. L. (2019). CRATES: A one-step assembly method for Class 2 CRISPR arrays. TUMOR IMMUNOLOGY AND IMMUNOTHERAPY - MOLECULAR METHODS, Vol. 629, pp. 493–511. https://doi.org/10.1016/bs.mie.2019.04.011

Westbrook, A., Tang, X., Marshall, R., Maxwell, C. S., Chappell, J., Agrawal, D. K., … Franco, E. (2019). Distinct timescales of RNA regulators enable the construction of a genetic pulse generator. BIOTECHNOLOGY AND BIOENGINEERING, 116(5), 1139–1151. https://doi.org/10.1002/bit.26918

Leenay, R. T., Vento, J. M., Shah, M., Martino, M. E., Leulier, F., & Beisel, C. L. (2019). Genome Editing with CRISPR-Cas9 in Lactobacillus plantarum Revealed That Editing Outcomes Can Vary Across Strains and Between Methods. BIOTECHNOLOGY JOURNAL, 14(3). https://doi.org/10.1002/biot.201700583

Liao, C., Ttofali, F., Slotkowski, R. A., Denny, S. R., Cecil, T. D., Leenay, R. T., … Beisel, C. L. (2019). Modular one-pot assembly of CRISPR arrays enables library generation and reveals factors influencing crRNA biogenesis. NATURE COMMUNICATIONS, 10. https://doi.org/10.1038/s41467-019-10747-3

Pickar-Oliver, A., Black, J. B., Lewis, M. M., Mutchnick, K. J., Klann, T. S., Gilcrest, K. A., … Gersbach, C. A. (2019). Targeted transcriptional modulation with type I CRISPR-Cas systems in human cells. NATURE BIOTECHNOLOGY, 37(12), 1493-+. https://doi.org/10.1038/s41587-019-0235-7

Jacobsen, T., Liao, C., & Beisel, C. L. (2019). The Acidaminococcus sp. Cas12a nuclease recognizes GTTV and GCTV as non-canonical PAMs. FEMS MICROBIOLOGY LETTERS, 366(8). https://doi.org/10.1093/femsle/fnz085

Liao, C., Slotkowski, R. A., Achmedov, T., & Beisel, C. L. (2019). The Francisella novicida Cas12a is sensitive to the structure downstream of the terminal repeat in CRISPR arrays. RNA BIOLOGY, 16(4), 404–412. https://doi.org/10.1080/15476286.2018.1526537

Maxwell, C. S., Jacobsen, T., Marshall, R., Noireaux, V., & Beisel, C. L. (2018). A detailed cell-free transcription-translation-based assay to decipher CRISPR protospacer-adjacent motifs. Methods, 143, 48–57. https://doi.org/10.1016/J.YMETH.2018.02.016

Alper, H. S., & Beisel, C. L. (2018). Advances in CRISPR Technologies for Microbial Strain Engineering. Biotechnology Journal, 13(9), 1800460. https://doi.org/10.1002/BIOT.201800460

Martino, M. E., Joncour, P., Leenay, R., Gervais, H., Shah, M., Hughes, S., … Leulier, F. (2018). Bacterial Adaptation to the Host's Diet Is a Key Evolutionary Force Shaping Drosophila-Lactobacillus LESymbiosis. CELL HOST & MICROBE, 24(1), 109-+. https://doi.org/10.1016/j.chom.2018.06.001

Dugar, G., Leenay, R. T., Eisenbart, S. K., Bischler, T., Aul, B. U., Beisel, C. L., & Sharma, C. M. (2018). CRISPR RNA-Dependent Binding and Cleavage of Endogenous RNAs by the Campylobacter jejuni Cas9. MOLECULAR CELL, 69(5), 893-+. https://doi.org/10.1016/j.molcel.2018.01.032

Beisel, C. L. (2018). CRISPR tool puts RNA on the record. Nature, 562(7727), 347–349. https://doi.org/10.1038/D41586-018-06869-1

Agrawal, D. K., Tang, X., Westbrook, A., Marshall, R., Maxwell, C. S., Lucks, J., … Franco, E. (2018). Mathematical Modeling of RNA-Based Architectures for Closed Loop Control of Gene Expression. ACS SYNTHETIC BIOLOGY, 7(5), 1219–1228. https://doi.org/10.1021/acssynbio.8b00040

Marshall, R., Maxwell, C. S., Collins, S. P., Jacobsen, T., Luo, M. L., Begemann, M. B., … Noireaux, V. (2018). Rapid and Scalable Characterization of CRISPR Technologies Using an E. coli Cell-Free Transcription-Translation System. MOLECULAR CELL, 69(1), 146-+. https://doi.org/10.1016/j.molcel.2017.12.007

Bober, J. R., Beisel, C. L., & Nair, N. U. (2018). Synthetic Biology Approaches to Engineer Probiotics and Members of the Human Microbiota for Biomedical Applications. ANNUAL REVIEW OF BIOMEDICAL ENGINEERING, VOL 20, Vol. 20, pp. 277–300. https://doi.org/10.1146/annurev-bioeng-062117-121019

Fagen, J. R., Collias, D., Singh, A. K., & Beisel, C. L. (2017). Advancing the design and delivery of CRISPR antimicrobials. Current Opinion in Biomedical Engineering, 4, 57–64. https://doi.org/10.1016/J.COBME.2017.10.001

Leenay, R. T., & Beisel, C. L. (2017). [Review of Deciphering, Communicating, and Engineering the CRISPR PAM]. JOURNAL OF MOLECULAR BIOLOGY, 429(2), 177–191. https://doi.org/10.1016/j.jmb.2016.11.024

Marshall, R., Maxwell, C. S., Collins, S. P., Beisel, C. L., & Noireaux, V. (2017). Short DNA Containing chi Sites Enhances DNA Stability and Gene Expression in E-coli Cell-Free Transcription-Translation Systems. BIOTECHNOLOGY AND BIOENGINEERING, 114(9), 2137–2141. https://doi.org/10.1002/bit.26333

Waller, M. C., Bober, J. R., Nair, N. U., & Beisel, C. L. (2017). Toward a genetic tool development pipeline for host-associated bacteria. Current Opinion in Microbiology, 38, 156–164. https://doi.org/10.1016/J.MIB.2017.05.006

Chen, Y. Y., Shapiro, M. G., Ruder, W., Ye, H. F., Kiani, S., Moon, T. S., … Barnes, C. (2017). What is the role of circuit design in the advancement of synthetic biology? Part 1 enabling real-world applications and therapeutics. Cell Systems, 4(4), 370–372.

Luo, M. L., Leenay, R. T., & Beisel, C. L. (2016). [Review of Current and future prospects for CRISPR-based tools in bacteria]. BIOTECHNOLOGY AND BIOENGINEERING, 113(5), 930–943. https://doi.org/10.1002/bit.25851

Luo, M. L., & Beisel, C. L. (2016). Engineering genes with CRISPR-Cas9. Chemical Engineering Progress , 112(9), 36–41.

Leenay, R. T., Maksimchuk, K. R., Slotkowski, R. A., Agrawal, R. N., Gomaa, A. A., Briner, A. E., … Beisel, C. L. (2016). Identifying and Visualizing Functional PAM Diversity across CRISPR-Cas Systems. MOLECULAR CELL, 62(1), 137–147. https://doi.org/10.1016/j.molcel.2016.02.031

Beisel, C. L., & Afroz, T. (2016, February). Rethinking the Hierarchy of Sugar Utilization in Bacteria. JOURNAL OF BACTERIOLOGY, Vol. 198, pp. 374–376. https://doi.org/10.1128/jb.00890-15

Luo, M. L., Jackson, R. N., Denny, S. R., Tokmina-Lukaszewska, M., Maksimchuk, K. R., Lin, W., … Beisel, C. L. (2016). The CRISPR RNA-guided surveillance complex in Escherichia coli accommodates extended RNA spacers. NUCLEIC ACIDS RESEARCH, 44(15), 7385–7394. https://doi.org/10.1093/nar/gkw421

Sun, W., Ji, W., Hall, J. M., Hu, Q., Wang, C., Beisel, C. L., & Gu, Z. (2015). Cover Picture: Self-Assembled DNA Nanoclews for the Efficient Delivery of CRISPR-Cas9 for Genome Editing (Angew. Chem. Int. Ed. 41/2015). Angewandte Chemie International Edition, 54(41), 11877–11877. https://doi.org/10.1002/ANIE.201508399

Afroz, T., Luo, M. L., & Beisel, C. L. (2015). Impact of Residual Inducer on Titratable Expression Systems. PLOS ONE, 10(9). https://doi.org/10.1371/journal.pone.0137421

Luo, M. L., Mullis, A. S., Leenay, R. T., & Beisel, C. L. (2015). Repurposing endogenous type I CRISPR-Cas systems for programmable gene repression. NUCLEIC ACIDS RESEARCH, 43(1), 674–681. https://doi.org/10.1093/nar/gku971

Sun, W., Ji, W., Hall, J. M., Hu, Q., Wang, C., Beisel, C. L., & Gu, Z. (2015). Self-Assembled DNA Nanoclews for the Efficient Delivery of CRISPR-Cas9 for Genome Editing. Angewandte Chemie International Edition, 54(41), 12029–12033. https://doi.org/10.1002/ANIE.201506030

Afroz, T., Biliouris, K., Boykin, K. E., Kaznessis, Y., & Beisel, C. L. (2015). Trade-offs in Engineering Sugar Utilization Pathways for Titratable Control. ACS SYNTHETIC BIOLOGY, 4(2), 141–149. https://doi.org/10.1021/sb400162z

Beisel, C. L., Gomaa, A. A., & Barrangou, R. (2014). A CRISPR design for next-generation antimicrobials. GENOME BIOLOGY, Vol. 15. https://doi.org/10.1186/s13059-014-0516-x

Afroz, T., Biliouris, K., Kaznessis, Y., & Beisel, C. L. (2014). Bacterial sugar utilization gives rise to distinct single-cell behaviours. MOLECULAR MICROBIOLOGY, 93(6), 1093–1103. https://doi.org/10.1111/mmi.12695

Beisel, C. L., Bloom, R. J., & Smolke, C. D. (2014). Construction of ligand-responsive microRNAs that operate through inhibition of Drosha processing. Artificial Riboswitches: Methods and Protocols, 1111, 259–267.

Briner, A. E., Donohoue, P. D., Gomaa, A. A., Selle, K., Slorach, E. M., Nye, C. H., … Barrangou, R. (2014). Guide RNA Functional Modules Direct Cas9 Activity and Orthogonality. MOLECULAR CELL, 56(2), 333–339. https://doi.org/10.1016/j.molcel.2014.09.019

Gomaa, A. A., Klumpe, H. E., Luo, M. L., Selle, K., Barrangou, R., & Beisel, C. L. (2014). Programmable Removal of Bacterial Strains by Use of Genome-Targeting CRISPR-Cas Systems. MBIO, 5(1). https://doi.org/10.1128/mbio.00928-13

Afroz, T., & Beisel, C. L. (2013). Understanding and exploiting feedback in synthetic biology. CHEMICAL ENGINEERING SCIENCE, 103, 79–90. https://doi.org/10.1016/j.ces.2013.02.017

Beisel, C. L., Updegrove, T. B., Janson, B. J., & Storz, G. (2012). Multiple factors dictate target selection by Hfq-binding small RNAs. The EMBO Journal, 31(8), 1961–1974. https://doi.org/10.1038/emboj.2012.52

Beisel CL, C., YY, C. S. J., Hoff KG, & CD, S. (2011). Design of small molecule-responsive microRNAs based on structural requirements for Drosha processing. Nucleic Acids Research, 39(7), 2981–2994.

Beisel, C. L., & Storz, G. (2011). Discriminating tastes: physiological contributions of the Hfq-binding small RNA Spot 42 to catabolite repression. RNA Biology, Vol. 8, pp. 1–5.

Beisel, C. L., & Storz, G. (2011). The Base-Pairing RNA Spot 42 Participates in a Multioutput Feedforward Loop to Help Enact Catabolite Repression in Escherichia coli. Molecular Cell, 41(3), 286–297. https://doi.org/10.1016/j.molcel.2010.12.027

CL, B., & G, S. (2011). The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli. Molecular Cell, 41, 1–12.

Beisel, C. L., & Storz, G. (2010). [Review of Base pairing small RNAs and their roles in global regulatory networks]. FEMS MICROBIOLOGY REVIEWS, 34(5), 866–882. https://doi.org/10.1111/j.1574-6976.2010.00241.x

Bayer TS, H. K. G., Beisel CL, L. J. J., & CD, S. (2009). Conformational analysis of gossypol and its derivatives by molecular mechanics. Journal of Molecular Structure [Including Theochem], 3(1).

Beisel, C. L., & Smolke, C. D. (2009). Design Principles for Riboswitch Function. PLOS COMPUTATIONAL BIOLOGY, 5(4). https://doi.org/10.1371/journal.pcbi.1000363

Beisel CL, B. T. S., Hoff KG, & CD, S. (2008). Model-guided design of ligand-regulated RNAi for programmable control of gene expression. Molecular Systems Biology, 4, 224.

Beisel, C. L., Bayer, T. S., Hoff, K. G., & Smolke, C. D. (2008). Model‐guided design of ligand‐regulated RNAi for programmable control of gene expression. Molecular Systems Biology, 4(1), 224. https://doi.org/10.1038/msb.2008.62

Beisel, C. L., Dowd, M. K., & Reilly, P. J. (2005). Conformational analysis of gossypol and its derivatives by molecular mechanics. Journal of Molecular Structure: THEOCHEM, 730(1-3), 51–58. https://doi.org/10.1016/j.theochem.2005.05.010

Beisel CL, D. M. K., & PJ, R. (2005). Conformational analysis of gossypol and its derivatives by molecular mechanics. Journal of Molecular Structure, 730, 51–58.