J. Carothers

发表

Functional information and the emergence of biocomplexity

Patrick L. Griffin, J. Szostak, R. Hazen, 2007, Proceedings of the National Academy of Sciences.

Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids

J. Keasling, J. Carothers, Fuzhong Zhang, 2012, Nature Biotechnology.

Measurement and modeling of intrinsic transcription terminators

Vivek K. Mutalik, Joao C. Guimaraes, A. Arkin, 2013, Nucleic acids research.

Synthetic CRISPR-Cas gene activators for transcriptional reprogramming in bacteria

J. Carothers, J. G. Zalatan, Chen Dong, 2018, Nature Communications.

Selecting RNA aptamers for synthetic biology: investigating magnesium dependence and predicting binding affinity

Jonathan A. Goler, J. Keasling, J. Carothers, 2010, Nucleic acids research.

Chemical synthesis using synthetic biology.

Jonathan A. Goler, J. Keasling, J. Carothers, 2009, Current opinion in biotechnology.

Model-Driven Engineering of RNA Devices to Quantitatively Program Gene Expression

Jay D Keasling, James M Carothers, Jonathan A Goler, 2011, Science.

Regulated Expression of sgRNAs Tunes CRISPRi in E. coli.

James M Carothers, Jason Fontana, J. Carothers, 2018, Biotechnology journal.

In Vitro Selection of Functional Oligonucleotides and the Origins of Biochemical Activity

J. Szostak, J. Carothers, 2006 .

Solution structure of an informationally complex high-affinity RNA aptamer to GTP.

James M Carothers, J. Szostak, J. Chou, 2006, RNA.

aptamer to GTP Solution structure of an informationally complex high-affinity RNA

J. Szostak, J. Chou, J. Carothers, 2006 .

Aptamers selected for higher-affinity binding are not more specific for the target ligand.

J. Szostak, J. Carothers, S. Oestreich, 2006, Journal of the American Chemical Society.

Multi-state design of kinetically-controlled RNA aptamer ribosensors

J. Carothers, Crista Burke, D. Sparkman-Yager, 2017, bioRxiv.

RNA-Based Molecular Sensors for Biosynthetic Pathway Design, Evolution, and Optimization

J. Carothers, Cassandra R Burke, Cassandra R. Burke, 2016 .

Dual-selection for evolution of in vivo functional aptazymes as riboswitch parts.

Jay D Keasling, James M Carothers, Jonathan A Goler, 2014, Methods in molecular biology.

Kinetic folding design of aptazyme-regulated expression devices as riboswitches for metabolic engineering.

J. Carothers, D. Sparkman-Yager, Rodrigo A Correa-Rojas, 2015, Methods in enzymology.

Informational Complexity and Functional Activity of RNA Structures

James M. Carothers, Jack W. Szostak, J. Szostak, 2004, Journal of the American Chemical Society.

Challenges and opportunities with CRISPR activation in bacteria for data-driven metabolic engineering.

J. Carothers, J. G. Zalatan, Jason Fontana, 2020, Current opinion in biotechnology.

Digital logic circuits in yeast with CRISPR-dCas 9 NOR

Gates, William E. Voje, Justin D. Vrana, 2017 .

Expanding the scope of bacterial CRISPR activation with PAM-flexible dCas9 variants

Neville E. Sanjana, N. Sanjana, J. Carothers, 2022, bioRxiv.

Perspectives for self-driving labs in synthetic biology.

Tyler W. H. Backman, Jose Manuel Martí, Daniel B. Arnold, 2022, Current opinion in biotechnology.

Data science: Accelerating innovation and discovery in chemical engineering

James M. Carothers, Jim Pfaendtner, Venkat R. Subramanian, 2016 .

Digital logic circuits in yeast with CRISPR-dCas9 NOR gates

James M. Carothers, Eric Klavins, William E. Voje, 2017, Nature Communications.

Membrane Augmented Cell-Free Systems: A New Frontier in Biotechnology.

Benjamin I. Tickman, V. Noireaux, J. Carothers, 2021, ACS synthetic biology.

Complex dependence of CRISPR-Cas9 binding strength on guide RNA spacer lengths

Benjamin I. Tickman, V. Noireaux, J. Carothers, 2021, Physical biology.

Programming Gene Expression by Engineering Transcript Stability Control and Processing in Bacteria

Jason T. Stevens, J. Carothers, 2018 .

Designing RNA-based genetic control systems for efficient production from engineered metabolic pathways.

Jason T Stevens, James M Carothers, Jason T. Stevens, 2015, ACS synthetic biology.

Prospects for engineering dynamic CRISPR–Cas transcriptional circuits to improve bioproduction

James M. Carothers, Jason Fontana, William E. Voje, 2018, Journal of Industrial Microbiology & Biotechnology.

Robust digital logic circuits in eukaryotic cells with CRISPR/dCas9 NOR gates

James M. Carothers, William E. Voje, Miles Winston Gander, 2016, bioRxiv.

In vitro selection of RNA aptamers against a composite small molecule-protein surface

James M. Carothers, Gregory L. Verdine, Masahiro Yoshimura, 2005, Nucleic acids research.

Standards, dissemination, and best practices in systems biology.

H. Sauro, J. Carothers, Janis Shin, 2023, Current opinion in biotechnology.

Synthetic CRISPR-Cas gene activators for transcriptional reprogramming in bacteria

J. Carothers, Chen Dong, Jason Fontana, 2018, Nature Communications.

Isolation and Characterization of Bacterial Cellulase Producers for Biomass Deconstruction: A Microbiology Laboratory Course†

James M. Carothers, Jay D. Keasling, Jesus F. Barajas, 2019, Journal of microbiology & biology education.

Multi-layer CRISPRa/i circuits for dynamic genetic programs in cell-free and bacterial systems.

Benjamin I. Tickman, V. Noireaux, J. Carothers, 2021, Cell systems.

Design-driven, multi-use research agendas to enable applied synthetic biology for global health

James M. Carothers, J. Carothers, 2013, Systems and Synthetic Biology.

Gene expression dynamics in input-responsive engineered living materials programmed for bioproduction

Benjamin I. Tickman, H. Alper, J. Carothers, 2023, Materials today. Bio.

Portable bacterial CRISPR transcriptional activation enables metabolic engineering in Pseudomonas putida.

J. Carothers, Chen Dong, Jason Fontana, 2021, Metabolic engineering.

Effective CRISPRa-mediated control of gene expression in bacteria must overcome strict target site requirements

James M. Carothers, Benjamin I. Tickman, Jesse G. Zalatan, 2019, Nature Communications.

Label-free selection of RNA aptamers for metabolic engineering.

J. Carothers, Chuhern Hwang, 2016, Methods.

Engineering activatable promoters for scalable and multi-input CRISPRa/i circuits

Benjamin I. Tickman, J. Carothers, Cholpisit Kiattisewee, 2023, Proceedings of the National Academy of Sciences of the United States of America.

ECSIT is an evolutionarily conserved intermediate in the Toll/IL-1 signal transduction pathway.

C. Janeway, C. Xiao, S. Ghosh, 1999, Genes & development.

Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids

J. Keasling, J. Carothers, Fuzhong Zhang, 2012, Nature Biotechnology.

Data science: Accelerating innovation and discovery in chemical engineering

J. Carothers, J. Pfaendtner, V. Subramanian, 2016 .

Computational design of RNA parts, devices, and transcripts with kinetic folding algorithms implemented on multiprocessor clusters.

Tim Thimmaiah, William E Voje, James M Carothers, 2015, Methods in molecular biology.