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James M. Carothers - Publications

Affiliations: 
2006-2012 Chemical Biology University of California, Berkeley, Berkeley, CA, United States 
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27/51 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Kiattisewee C, Dong C, Fontana J, Sugianto W, Peralta-Yahya P, Carothers JM, Zalatan JG. Portable bacterial CRISPR transcriptional activation enables metabolic engineering in Pseudomonas putida. Metabolic Engineering. PMID 33930546 DOI: 10.1016/j.ymben.2021.04.002  0.668
2021 Kruyer NS, Sugianto W, Tickman BI, Alba Burbano D, Noireaux V, Carothers JM, Peralta-Yahya P. Membrane Augmented Cell-Free Systems: A New Frontier in Biotechnology. Acs Synthetic Biology. PMID 33749249 DOI: 10.1021/acssynbio.0c00625  0.625
2020 Fontana J, Sparkman-Yager D, Zalatan JG, Carothers JM. Challenges and opportunities with CRISPR activation in bacteria for data-driven metabolic engineering. Current Opinion in Biotechnology. 64: 190-198. PMID 32599515 DOI: 10.1016/J.Copbio.2020.04.005  0.426
2020 Fontana J, Dong C, Kiattisewee C, Chavali VP, Tickman BI, Carothers JM, Zalatan JG. Effective CRISPRa-mediated control of gene expression in bacteria must overcome strict target site requirements. Nature Communications. 11: 1618. PMID 32238808 DOI: 10.1038/S41467-020-15454-Y  0.366
2019 Barajas JF, Wehrs M, To M, Cruickshanks L, Urban R, McKee A, Gladden J, Goh EB, Brown ME, Pierotti D, Carothers JM, Mukhopadhyay A, Keasling JD, Fortman JL, Singer SW, et al. Isolation and Characterization of Bacterial Cellulase Producers for Biomass Deconstruction: A Microbiology Laboratory Course. Journal of Microbiology & Biology Education. 20. PMID 31388393 DOI: 10.1128/Jmbe.V20I2.1723  0.688
2018 Dong C, Fontana J, Patel A, Carothers JM, Zalatan JG. Synthetic CRISPR-Cas gene activators for transcriptional reprogramming in bacteria. Nature Communications. 9: 2489. PMID 29950558 DOI: 10.1038/S41467-018-04901-6  0.362
2018 Fontana J, Voje WE, Zalatan JG, Carothers JM. Prospects for engineering dynamic CRISPR-Cas transcriptional circuits to improve bioproduction. Journal of Industrial Microbiology & Biotechnology. PMID 29740742 DOI: 10.1007/S10295-018-2039-Z  0.362
2018 Fontana J, Dong C, Ham JY, Zalatan JG, Carothers JM. Regulated expression of sgRNAs tunes CRISPRi in E. coli. Biotechnology Journal. e1800069. PMID 29635744 DOI: 10.1002/Biot.201800069  0.359
2016 Hwang C, Carothers JM. Label-free selection of RNA aptamers for metabolic engineering. Methods (San Diego, Calif.). PMID 27339940 DOI: 10.1016/J.Ymeth.2016.06.016  0.48
2016 Burke CR, Carothers JM. RNA-Based Molecular Sensors for Biosynthetic Pathway Design, Evolution, and Optimization Biotechnology For Biofuel Production and Optimization. 117-138. DOI: 10.1016/B978-0-444-63475-7.00005-4  0.356
2016 Beck DAC, Carothers JM, Subramanian V, Pfaendtner J. Data science: Accelerating innovation and discovery in chemical engineering Aiche Journal. DOI: 10.1002/Aic.15192  0.314
2015 Sparkman-Yager D, Correa-Rojas RA, Carothers JM. Kinetic folding design of aptazyme-regulated expression devices as riboswitches for metabolic engineering. Methods in Enzymology. 550: 321-40. PMID 25605393 DOI: 10.1016/Bs.Mie.2014.10.038  0.434
2015 Thimmaiah T, Voje WE, Carothers JM. Computational design of RNA parts, devices, and transcripts with kinetic folding algorithms implemented on multiprocessor clusters. Methods in Molecular Biology (Clifton, N.J.). 1244: 45-61. PMID 25487092 DOI: 10.1007/978-1-4939-1878-2_3  0.461
2015 Stevens JT, Carothers JM. Designing RNA-based genetic control systems for efficient production from engineered metabolic pathways. Acs Synthetic Biology. 4: 107-15. PMID 25314371 DOI: 10.1021/Sb400201U  0.411
2014 Goler JA, Carothers JM, Keasling JD. Dual-selection for evolution of in vivo functional aptazymes as riboswitch parts. Methods in Molecular Biology (Clifton, N.J.). 1111: 221-35. PMID 24549623 DOI: 10.1007/978-1-62703-755-6_16  0.722
2013 Carothers JM. Design-driven, multi-use research agendas to enable applied synthetic biology for global health. Systems and Synthetic Biology. 7: 79-86. PMID 24432145 DOI: 10.1007/S11693-013-9118-2  0.383
2013 Cambray G, Guimaraes JC, Mutalik VK, Lam C, Mai QA, Thimmaiah T, Carothers JM, Arkin AP, Endy D. Measurement and modeling of intrinsic transcription terminators. Nucleic Acids Research. 41: 5139-48. PMID 23511967 DOI: 10.1093/Nar/Gkt163  0.325
2012 Zhang F, Carothers JM, Keasling JD. Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids. Nature Biotechnology. 30: 354-9. PMID 22446695 DOI: 10.1038/Nbt.2149  0.666
2011 Carothers JM, Goler JA, Juminaga D, Keasling JD. Model-driven engineering of RNA devices to quantitatively program gene expression. Science (New York, N.Y.). 334: 1716-9. PMID 22194579 DOI: 10.1126/Science.1212209  0.716
2010 Carothers JM, Goler JA, Kapoor Y, Lara L, Keasling JD. Selecting RNA aptamers for synthetic biology: investigating magnesium dependence and predicting binding affinity. Nucleic Acids Research. 38: 2736-47. PMID 20159999 DOI: 10.1093/Nar/Gkq082  0.707
2009 Carothers JM, Goler JA, Keasling JD. Chemical synthesis using synthetic biology. Current Opinion in Biotechnology. 20: 498-503. PMID 19720519 DOI: 10.1016/J.Copbio.2009.08.001  0.715
2007 Hazen RM, Griffin PL, Carothers JM, Szostak JW. Functional information and the emergence of biocomplexity Proceedings of the National Academy of Sciences of the United States of America. 104: 8574-8581. PMID 17494745 DOI: 10.1073/Pnas.0701744104  0.507
2006 Carothers JM, Oestreich SC, Szostak JW. Aptamers selected for higher-affinity binding are not more specific for the target ligand Journal of the American Chemical Society. 128: 7929-7937. PMID 16771507 DOI: 10.1021/Ja060952Q  0.593
2006 Carothers JM, Davis JH, Chou JJ, Szostak JW. Solution structure of an informationally complex high-affinity RNA aptamer to GTP. Rna (New York, N.Y.). 12: 567-79. PMID 16510427 DOI: 10.1261/Rna.2251306  0.56
2006 Carothers JM, Szostak JW. In Vitro Selection of Functional Oligonucleotides and the Origins of Biochemical Activity The Aptamer Handbook: Functional Oligonucleotides and Their Applications. 1-28. DOI: 10.1002/3527608192.ch1  0.465
2005 Plummer KA, Carothers JM, Yoshimura M, Szostak JW, Verdine GL. In vitro selection of RNA aptamers against a composite small molecule-protein surface. Nucleic Acids Research. 33: 5602-10. PMID 16199752 DOI: 10.1093/Nar/Gki867  0.571
2004 Carothers JM, Oestreich SC, Davis JH, Szostak JW. Informational complexity and functional activity of RNA structures. Journal of the American Chemical Society. 126: 5130-7. PMID 15099096 DOI: 10.1021/Ja031504A  0.566
Low-probability matches (unlikely to be authored by this person)
2017 Gander MW, Vrana JD, Voje WE, Carothers JM, Klavins E. Digital logic circuits in yeast with CRISPR-dCas9 NOR gates. Nature Communications. 8: 15459. PMID 28541304 DOI: 10.1038/Ncomms15459  0.285
2021 Khakimzhan A, Garenne D, Tickman B, Fontana J, Carothers J, Noireaux V. Complex dependence of CRISPR-Cas9 binding strength on guide RNA spacer lengths. Physical Biology. PMID 34102625 DOI: 10.1088/1478-3975/ac091e  0.278
2021 Tickman BI, Burbano DA, Chavali VP, Kiattisewee C, Fontana J, Khakimzhan A, Noireaux V, Zalatan JG, Carothers JM. Multi-layer CRISPRa/i circuits for dynamic genetic programs in cell-free and bacterial systems. Cell Systems. PMID 34800362 DOI: 10.1016/j.cels.2021.10.008  0.263
2023 Alba Burbano D, Cardiff RAL, Tickman BI, Kiattisewee C, Maranas CJ, Zalatan JG, Carothers JM. Engineering activatable promoters for scalable and multi-input CRISPRa/i circuits. Proceedings of the National Academy of Sciences of the United States of America. 120: e2220358120. PMID 37463216 DOI: 10.1073/pnas.2220358120  0.255
2018 Dong C, Fontana J, Patel A, Carothers JM, Zalatan JG. Author Correction: Synthetic CRISPR-Cas gene activators for transcriptional reprogramming in bacteria. Nature Communications. 9: 4318. PMID 30323295 DOI: 10.1038/S41467-018-06909-4  0.236
2023 Sugianto W, Altin-Yavuzarslan G, Tickman BI, Kiattisewee C, Yuan SF, Brooks SM, Wong J, Alper HS, Nelson A, Carothers JM. Gene expression dynamics in input-responsive engineered living materials programmed for bioproduction. Materials Today. Bio. 20: 100677. PMID 37273790 DOI: 10.1016/j.mtbio.2023.100677  0.231
1999 Kopp E, Medzhitov R, Carothers J, Xiao C, Douglas I, Janeway CA, Ghosh S. ECSIT is an evolutionarily conserved intermediate in the Toll/IL-1 signal transduction pathway. Genes & Development. 13: 2059-71. PMID 10465784 DOI: 10.1101/Gad.13.16.2059  0.226
2022 Kiattisewee C, Karanjia AV, Legut M, Daniloski Z, Koplik SE, Nelson J, Kleinstiver BP, Sanjana NE, Carothers JM, Zalatan JG. Expanding the Scope of Bacterial CRISPR Activation with PAM-Flexible dCas9 Variants. Acs Synthetic Biology. PMID 36378874 DOI: 10.1021/acssynbio.2c00405  0.21
2023 Martin HG, Radivojevic T, Zucker J, Bouchard K, Sustarich J, Peisert S, Arnold D, Hillson N, Babnigg G, Marti JM, Mungall CJ, Beckham GT, Waldburger L, Carothers J, Sundaram S, et al. Perspectives for self-driving labs in synthetic biology. Current Opinion in Biotechnology. 79: 102881. PMID 36603501 DOI: 10.1016/j.copbio.2022.102881  0.192
2023 Shin J, Porubsky V, Carothers J, Sauro HM. Standards, dissemination, and best practices in systems biology. Current Opinion in Biotechnology. 81: 102922. PMID 37004298 DOI: 10.1016/j.copbio.2023.102922  0.144
2016 Cambray G, Guimaraes JC, Mutalik VK, Lam C, Mai QA, Thimmaiah T, Carothers JM, Arkin AP, Endy D. Measurement and modeling of intrinsic transcription terminators. Nucleic Acids Research. PMID 27131373 DOI: 10.1093/nar/gkw379  0.087
2011 Archibeck MJ, Cummins T, Carothers J, Junick DW, White RE. A comparison of two implant systems in restoration of hip geometry in arthroplasty. Clinical Orthopaedics and Related Research. 469: 443-6. PMID 21082363 DOI: 10.1007/s11999-010-1678-9  0.069
2009 Archibeck MJ, Junick DW, Cummins T, Carothers J, White RE. Polyethylene exchange in a second-generation cementless acetabular component. The Journal of Arthroplasty. 24: 69-72. PMID 19577889 DOI: 10.1016/j.arth.2009.05.004  0.049
2015 Cady RK, McAllister PJ, Spierings EL, Messina J, Carothers J, Djupesland PG, Mahmoud RA. A randomized, double-blind, placebo-controlled study of breath powered nasal delivery of sumatriptan powder (AVP-825) in the treatment of acute migraine (The TARGET Study). Headache. 55: 88-100. PMID 25355310 DOI: 10.1111/head.12472  0.048
2004 Hess DC, Abe T, Hill WD, Studdard AM, Carothers J, Masuya M, Fleming PA, Drake CJ, Ogawa M. Hematopoietic origin of microglial and perivascular cells in brain. Experimental Neurology. 186: 134-44. PMID 15026252 DOI: 10.1016/j.expneurol.2003.11.005  0.042
2010 Canuso CM, Lindenmayer JP, Kosik-Gonzalez C, Turkoz I, Carothers J, Bossie CA, Schooler NR. A randomized, double-blind, placebo-controlled study of 2 dose ranges of paliperidone extended-release in the treatment of subjects with schizoaffective disorder. The Journal of Clinical Psychiatry. 71: 587-98. PMID 20492853 DOI: 10.4088/Jcp.09M05564Yel  0.04
1918 Carothers JM. Correction - Electric Furnace Smelting of Phosphate Rock, Etc. Journal of Industrial & Engineering Chemistry. 10: 239-239. DOI: 10.1021/IE50099A609  0.04
2009 Canuso CM, Dirks B, Carothers J, Kosik-Gonzalez C, Bossie CA, Zhu Y, Damaraju CV, Kalali AH, Mahmoud R. Randomized, double-blind, placebo-controlled study of paliperidone extended-release and quetiapine in inpatients with recently exacerbated schizophrenia. The American Journal of Psychiatry. 166: 691-701. PMID 19411369 DOI: 10.1176/appi.ajp.2009.08040613  0.036
2002 Hess DC, Hill WD, Martin-Studdard A, Carroll J, Brailer J, Carothers J. Bone marrow as a source of endothelial cells and NeuN-expressing cells After stroke. Stroke; a Journal of Cerebral Circulation. 33: 1362-8. PMID 11988616 DOI: 10.1161/01.STR.0000014925.09415.C3  0.034
2009 Mahoney OM, Clarke HD, Mont MA, McGrath MS, Zywiel MG, Dennis DA, Kim RH, Carothers J. Primary total knee arthroplasty: the impact of technique. The Journal of Bone and Joint Surgery. American Volume. 91: 59-61. PMID 19648628 DOI: 10.2106/JBJS.I.00413  0.033
2013 Obaidi M, Offman E, Messina J, Carothers J, Djupesland PG, Mahmoud RA. Improved pharmacokinetics of sumatriptan with Breath Powered™ nasal delivery of sumatriptan powder. Headache. 53: 1323-33. PMID 23992438 DOI: 10.1111/head.12167  0.029
2002 Hess DC, Hill WD, Martin-Studdard A, Carothers J, Brailer J, Carroll J. Blood into brain after stroke. Trends in Molecular Medicine. 8: 452-3. PMID 12223318 DOI: 10.1016/S1471-4914(02)02404-8  0.028
2010 Canuso CM, Schooler N, Carothers J, Turkoz I, Kosik-Gonzalez C, Bossie CA, Walling D, Lindenmayer JP. Paliperidone extended-release in schizoaffective disorder: a randomized, controlled study comparing a flexible dose with placebo in patients treated with and without antidepressants and/or mood stabilizers. Journal of Clinical Psychopharmacology. 30: 487-95. PMID 20814330 DOI: 10.1097/Jcp.0B013E3181Eeb600  0.025
2000 Amond J, Carothers J. The anatomy of a firing. When you finally act, it's often later than you think. Dental Assistant (Chicago, Ill. : 1994). 69: 24-6. PMID 11218289  0.023
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