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2024 journal article
A cell-free transcription-translation pipeline for recreating methylation patterns boosts DNA transformation in bacteria
MOLECULAR CELL, 84(14).
2024 article
Expanding the flexibility of base editing for high-throughput genetic screens in bacteria
Gawlitt, S., Collins, S. P., Yu, Y., Blackman, S. A., Barquist, L., & Beisel, C. L. (2024, March 18). NUCLEIC ACIDS RESEARCH.
2023 article
Interrogating two extensively self-targeting Type I CRISPR-Cas systems in Xanthomonas albilineans reveals distinct anti-CRISPR proteins that block DNA degradation
Wimmer, F., Englert, F., Wandera, K. G., Alkhnbashi, O. S., Collins, S. P., Backofen, R., & Beisel, C. L. (2023, November 28). NUCLEIC ACIDS RESEARCH.
2023 journal article
Systematically attenuating DNA targeting enables CRISPR-driven editing in bacteria
NATURE COMMUNICATIONS, 14(1).
2022 journal article
A target expression threshold dictates invader defense and prevents autoimmunity by CRISPR-Cas13
CELL HOST & MICROBE, 30(8), 1151-+.
2021 review
CRISPR technologies and the search for the PAM-free nuclease
[Review of ]. NATURE COMMUNICATIONS, 12(1).
2021 article
Coupling smartphone and CRISPR-Cas12a for digital and multiplexed nucleic acid detection
Yu, T., Zhang, S., Matei, R., Marx, W., Beisel, C. L., & Wei, Q. (2021, July 23). AICHE JOURNAL, Vol. 7.
2021 journal article
In Situ Biomanufacturing of Small Molecules in the Mammalian Gut by Probiotic Saccharomyces boulardii
ACS SYNTHETIC BIOLOGY, 10(5), 1039–1052.
2021 journal article
Sequence-independent RNA sensing and DNA targeting by a split domain CRISPR-Cas12a gRNA switch
NUCLEIC ACIDS RESEARCH, 49(5), 2985–2999.
2020 journal article
A positive, growth-based PAM screen identifies noncanonical motifs recognized by the S. pyogenes Cas9
SCIENCE ADVANCES, 6(29).
2020 journal article
Characterization of Cas12a nucleases reveals diverse PAM profiles between closely-related orthologs
NUCLEIC ACIDS RESEARCH, 48(10), 5624–5638.
2020 journal article
Competitive Exclusion Is a Major Bioprotective Mechanism of Lactobacilli against Fungal Spoilage in Fermented Milk Products
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 86(7).
2020 article
Methods for characterizing, applying, and teaching CRISPR-Cas systems
Beisel, C. L. (2020, February 1). METHODS, Vol. 172, pp. 1–2.
2020 journal article
Tunable self-cleaving ribozymes for modulating gene expression in eukaryotic systems
PLOS ONE, 15(4).
2020 article
Your Base Editor Might Be Flirting with Single (Stranded) DNA: Faithful On-Target CRISPR Base Editing without Promiscuous Deamination
Collins, S. P., & Beisel, C. L. (2020, September 3). MOLECULAR CELL, Vol. 79, pp. 703–704.
2019 journal article
An educational module to explore CRISPR technologies with a cell-free transcription-translation system
SYNTHETIC BIOLOGY, 4(1).
2019 journal article
An enhanced assay to characterize anti-CRISPR proteins using a cell-free transcription-translation system
METHODS, 172, 42–50.
2019 review
Barriers to genome editing with CRISPR in bacteria
[Review of ]. JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY, 46(9-10), 1327–1341.
2019 article
CRATES: A one-step assembly method for Class 2 CRISPR arrays
TUMOR IMMUNOLOGY AND IMMUNOTHERAPY - MOLECULAR METHODS, Vol. 629, pp. 493–511.
2019 journal article
Distinct timescales of RNA regulators enable the construction of a genetic pulse generator
BIOTECHNOLOGY AND BIOENGINEERING, 116(5), 1139–1151.
2019 journal article
Modular one-pot assembly of CRISPR arrays enables library generation and reveals factors influencing crRNA biogenesis
NATURE COMMUNICATIONS, 10.
2019 journal article
Targeted transcriptional modulation with type I CRISPR-Cas systems in human cells
NATURE BIOTECHNOLOGY, 37(12), 1493-+.
2019 journal article
The Acidaminococcus sp. Cas12a nuclease recognizes GTTV and GCTV as non-canonical PAMs
FEMS MICROBIOLOGY LETTERS, 366(8).
2018 journal article
A detailed cell-free transcription-translation-based assay to decipher CRISPR protospacer-adjacent motifs
Methods, 143, 48–57.
2018 journal article
Advances in CRISPR Technologies for Microbial Strain Engineering
Biotechnology Journal, 13(9), 1800460.
2018 journal article
Bacterial Adaptation to the Host's Diet Is a Key Evolutionary Force Shaping Drosophila-Lactobacillus LESymbiosis
CELL HOST & MICROBE, 24(1), 109-+.
2018 journal article
CRISPR RNA-Dependent Binding and Cleavage of Endogenous RNAs by the Campylobacter jejuni Cas9
MOLECULAR CELL, 69(5), 893-+.
2018 journal article
CRISPR tool puts RNA on the record
Nature, 562(7727), 347–349.
2018 journal article
Genome Editing with CRISPR-Cas9 in Lactobacillus plantarum Revealed That Editing Outcomes Can Vary Across Strains and Between Methods
BIOTECHNOLOGY JOURNAL, 14(3).
2018 journal article
Mathematical Modeling of RNA-Based Architectures for Closed Loop Control of Gene Expression
ACS SYNTHETIC BIOLOGY, 7(5), 1219–1228.
2018 journal article
Rapid and Scalable Characterization of CRISPR Technologies Using an E. coli Cell-Free Transcription-Translation System
MOLECULAR CELL, 69(1), 146-+.
2018 article
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.
2018 journal article
The Francisella novicida Cas12a is sensitive to the structure downstream of the terminal repeat in CRISPR arrays
RNA BIOLOGY, 16(4), 404–412.
2017 journal article
Advancing the design and delivery of CRISPR antimicrobials
Current Opinion in Biomedical Engineering, 4, 57–64.
2017 review
Deciphering, Communicating, and Engineering the CRISPR PAM
[Review of ]. JOURNAL OF MOLECULAR BIOLOGY, 429(2), 177–191.
2017 journal article
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.
2017 journal article
Toward a genetic tool development pipeline for host-associated bacteria
Current Opinion in Microbiology, 38, 156–164.
2017 journal article
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.
2016 journal article
Engineering genes with CRISPR-Cas9
Chemical Engineering Progress , 112(9), 36–41.
2016 journal article
Identifying and Visualizing Functional PAM Diversity across CRISPR-Cas Systems
MOLECULAR CELL, 62(1), 137–147.
2016 journal article
The CRISPR RNA-guided surveillance complex in Escherichia coli accommodates extended RNA spacers
NUCLEIC ACIDS RESEARCH, 44(15), 7385–7394.
2015 journal article
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.
2015 review
Current and future prospects for CRISPR-based tools in bacteria
[Review of ]. BIOTECHNOLOGY AND BIOENGINEERING, 113(5), 930–943.
2015 journal article
Impact of Residual Inducer on Titratable Expression Systems
PLOS ONE, 10(9).
2015 article
Rethinking the Hierarchy of Sugar Utilization in Bacteria
Beisel, C. L., & Afroz, T. (2016, February). JOURNAL OF BACTERIOLOGY, Vol. 198, pp. 374–376.
2015 journal article
Self-Assembled DNA Nanoclews for the Efficient Delivery of CRISPR-Cas9 for Genome Editing
Angewandte Chemie International Edition, 54(41), 12029–12033.
2014 article
A CRISPR design for next-generation antimicrobials
GENOME BIOLOGY, Vol. 15.
2014 journal article
Bacterial sugar utilization gives rise to distinct single-cell behaviours
MOLECULAR MICROBIOLOGY, 93(6), 1093–1103.
2014 journal article
Construction of ligand-responsive microRNAs that operate through inhibition of Drosha processing
Artificial Riboswitches: Methods and Protocols, 1111, 259–267.
2014 journal article
Guide RNA Functional Modules Direct Cas9 Activity and Orthogonality
MOLECULAR CELL, 56(2), 333–339.
2014 journal article
Programmable Removal of Bacterial Strains by Use of Genome-Targeting CRISPR-Cas Systems
MBIO, 5(1).
2014 journal article
Repurposing endogenous type I CRISPR-Cas systems for programmable gene repression
NUCLEIC ACIDS RESEARCH, 43(1), 674–681.
2014 journal article
Trade-offs in Engineering Sugar Utilization Pathways for Titratable Control
ACS SYNTHETIC BIOLOGY, 4(2), 141–149.
2013 journal article
Understanding and exploiting feedback in synthetic biology
CHEMICAL ENGINEERING SCIENCE, 103, 79–90.
2012 journal article
Multiple factors dictate target selection by Hfq-binding small RNAs
The EMBO Journal, 31(8), 1961–1974.
2011 journal article
Design of small molecule-responsive microRNAs based on structural requirements for Drosha processing
Nucleic Acids Research, 39(7), 2981–2994.
2011 article
Discriminating tastes: physiological contributions of the Hfq-binding small RNA Spot 42 to catabolite repression
RNA Biology, Vol. 8, pp. 1–5.
2011 journal article
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.
2011 journal article
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.
2010 review
Base pairing small RNAs and their roles in global regulatory networks
[Review of ]. FEMS MICROBIOLOGY REVIEWS, 34(5), 866–882.
2009 journal article
Conformational analysis of gossypol and its derivatives by molecular mechanics
Journal of Molecular Structure [Including Theochem], 3(1).
2009 journal article
Design Principles for Riboswitch Function
PLOS COMPUTATIONAL BIOLOGY, 5(4).
2008 journal article
Model-guided design of ligand-regulated RNAi for programmable control of gene expression
Molecular Systems Biology, 4, 224.
2008 journal article
Model‐guided design of ligand‐regulated RNAi for programmable control of gene expression
Molecular Systems Biology, 4(1), 224.
2005 journal article
Conformational analysis of gossypol and its derivatives by molecular mechanics
Journal of Molecular Structure: THEOCHEM, 730(1-3), 51–58.
2005 journal article
Conformational analysis of gossypol and its derivatives by molecular mechanics
Journal of Molecular Structure, 730, 51–58.
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