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Farren Isaacs - Publications

Affiliations: 
Yale University, New Haven, CT 
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41 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
2023 Asin-Garcia E, Garcia-Morales L, Bartholet T, Liang Z, Isaacs FJ, Martins Dos Santos VAP. Metagenomics harvested genus-specific single-stranded DNA-annealing proteins improve and expand recombineering in Pseudomonas species. Nucleic Acids Research. PMID 37941137 DOI: 10.1093/nar/gkad1024  0.314
2022 Zomorrodi AR, Hemez C, Arranz-Gibert P, Wu T, Isaacs FJ, Segrè D. Computational design and engineering of an strain producing the nonstandard amino acid -aminophenylalanine. Iscience. 25: 104562. PMID 35789833 DOI: 10.1016/j.isci.2022.104562  0.621
2022 Shapiro DM, Mandava G, Yalcin SE, Arranz-Gibert P, Dahl PJ, Shipps C, Gu Y, Srikanth V, Salazar-Morales AI, O'Brien JP, Vanderschuren K, Vu D, Batista VS, Malvankar NS, Isaacs FJ. Protein nanowires with tunable functionality and programmable self-assembly using sequence-controlled synthesis. Nature Communications. 13: 829. PMID 35149672 DOI: 10.1038/s41467-022-28206-x  0.319
2022 Radford F, Elliott SD, Schepartz A, Isaacs FJ. Targeted editing and evolution of engineered ribosomes in vivo by filtered editing. Nature Communications. 13: 180. PMID 35013328 DOI: 10.1038/s41467-021-27836-x  0.418
2021 Wannier TM, Ciaccia PN, Ellington AD, Filsinger GT, Isaacs FJ, Javanmardi K, Jones MA, Kunjapur AM, Nyerges A, Pal C, Schubert MG, Church GM. Recombineering and MAGE. Nature Reviews. Methods Primers. 1. PMID 35540496 DOI: 10.1038/s43586-020-00006-x  0.566
2021 Tang TC, Tham E, Liu X, Yehl K, Rovner AJ, Yuk H, de la Fuente-Nunez C, Isaacs FJ, Zhao X, Lu TK. Hydrogel-based biocontainment of bacteria for continuous sensing and computation. Nature Chemical Biology. PMID 33820990 DOI: 10.1038/s41589-021-00779-6  0.573
2019 Arranz-Gibert P, Patel JR, Isaacs FJ. The Role of Orthogonality in Genetic Code Expansion. Life (Basel, Switzerland). 9. PMID 31284384 DOI: 10.3390/Life9030058  0.338
2018 Ma NJ, Hemez CF, Barber KW, Rinehart J, Isaacs FJ. Organisms with alternative genetic codes resolve unassigned codons via mistranslation and ribosomal rescue. Elife. 7. PMID 30375330 DOI: 10.7554/Elife.34878  0.361
2018 Arranz-Gibert P, Vanderschuren K, Isaacs FJ. Next-generation genetic code expansion. Current Opinion in Chemical Biology. 46: 203-211. PMID 30072242 DOI: 10.1016/j.cbpa.2018.07.020  0.398
2018 Martin RW, Des Soye BJ, Kwon YC, Kay J, Davis RG, Thomas PM, Majewska NI, Chen CX, Marcum RD, Weiss MG, Stoddart AE, Amiram M, Ranji Charna AK, Patel JR, Isaacs FJ, et al. Cell-free protein synthesis from genomically recoded bacteria enables multisite incorporation of noncanonical amino acids. Nature Communications. 9: 1203. PMID 29572528 DOI: 10.1038/S41467-018-03469-5  0.325
2017 Barbieri EM, Muir P, Akhuetie-Oni BO, Yellman CM, Isaacs FJ. Precise Editing at DNA Replication Forks Enables Multiplex Genome Engineering in Eukaryotes. Cell. PMID 29153834 DOI: 10.1016/j.cell.2017.10.034  0.67
2016 Gan R, Perez JG, Carlson ED, Ntai I, Isaacs FJ, Kelleher NL, Jewett MC. Translation system engineering in Escherichia coli enhances non-canonical amino acid incorporation into proteins. Biotechnology and Bioengineering. PMID 27987323 DOI: 10.1002/Bit.26239  0.324
2016 Napolitano MG, Landon M, Gregg CJ, Lajoie MJ, Govindarajan L, Mosberg JA, Kuznetsov G, Goodman DB, Vargas-Rodriguez O, Isaacs FJ, Söll D, Church GM. Emergent rules for codon choice elucidated by editing rare arginine codons in Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America. 113: E5588-97. PMID 27601680 DOI: 10.1073/Pnas.1605856113  0.755
2016 Ma NJ, Isaacs FJ. Genomic Recoding Broadly Obstructs the Propagation of Horizontally Transferred Genetic Elements. Cell Systems. PMID 27426981 DOI: 10.1016/j.cels.2016.06.009  0.331
2016 Boeke JD, Church G, Hessel A, Kelley NJ, Arkin A, Cai Y, Carlson R, Chakravarti A, Cornish VW, Holt L, Isaacs FJ, Kuiken T, Lajoie M, Lessor T, Lunshof J, et al. The Genome Project-Write. Science (New York, N.Y.). PMID 27256881 DOI: 10.1126/Science.Aaf6850  0.785
2016 Quintin MJ, Ma NJ, Ahmed S, Bhatia S, Lewis A, Isaacs FJ, Densmore D. Merlin: Computer-Aided Oligonucleotide Design for Large Scale Genome Engineering with MAGE. Acs Synthetic Biology. PMID 27054880 DOI: 10.1021/Acssynbio.5B00219  0.358
2016 Muir P, Li S, Lou S, Wang D, Spakowicz DJ, Salichos L, Zhang J, Weinstock GM, Isaacs F, Rozowsky J, Gerstein M. The real cost of sequencing: scaling computation to keep pace with data generation. Genome Biology. 17: 53. PMID 27009100 DOI: 10.1186/S13059-016-0917-0  0.331
2016 Taylor ND, Garruss AS, Moretti R, Chan S, Arbing MA, Cascio D, Rogers JK, Isaacs FJ, Kosuri S, Baker D, Fields S, Church GM, Raman S. Engineering an allosteric transcription factor to respond to new ligands. Nature Methods. 13: 177-83. PMID 26689263 DOI: 10.1038/Nmeth.3696  0.767
2015 Amiram M, Haimovich AD, Fan C, Wang YS, Aerni HR, Ntai I, Moonan DW, Ma NJ, Rovner AJ, Hong SH, Kelleher NL, Goodman AL, Jewett MC, Söll D, Rinehart J, ... Isaacs FJ, et al. Evolution of translation machinery in recoded bacteria enables multi-site incorporation of nonstandard amino acids. Nature Biotechnology. PMID 26571098 DOI: 10.1038/Nbt.3372  0.336
2015 Rovner AJ, Haimovich AD, Katz SR, Li Z, Grome MW, Gassaway BM, Amiram M, Patel JR, Gallagher RR, Rinehart J, Isaacs FJ. Corrigendum: Recoded organisms engineered to depend on synthetic amino acids. Nature. PMID 26416756 DOI: 10.1038/Nature15537  0.744
2015 Haimovich AD, Muir P, Isaacs FJ. Genomes by design. Nature Reviews. Genetics. 16: 501-16. PMID 26260262 DOI: 10.1038/nrg3956  0.443
2015 Des Soye BJ, Patel JR, Isaacs FJ, Jewett MC. Repurposing the translation apparatus for synthetic biology. Current Opinion in Chemical Biology. 28: 83-90. PMID 26186264 DOI: 10.1016/J.Cbpa.2015.06.008  0.312
2015 Rovner AJ, Haimovich AD, Katz SR, Li Z, Grome MW, Gassaway BM, Amiram M, Patel JR, Gallagher RR, Rinehart J, Isaacs FJ. Recoded organisms engineered to depend on synthetic amino acids. Nature. 518: 89-93. PMID 25607356 DOI: 10.1038/Nature14095  0.811
2015 Gallagher RR, Patel JR, Interiano AL, Rovner AJ, Isaacs FJ. Multilayered genetic safeguards limit growth of microorganisms to defined environments. Nucleic Acids Research. 43: 1945-54. PMID 25567985 DOI: 10.1093/Nar/Gku1378  0.36
2014 Gallagher RR, Li Z, Lewis AO, Isaacs FJ. Rapid editing and evolution of bacterial genomes using libraries of synthetic DNA. Nature Protocols. 9: 2301-16. PMID 25188632 DOI: 10.1038/Nprot.2014.082  0.342
2014 Ma NJ, Moonan DW, Isaacs FJ. Precise manipulation of bacterial chromosomes by conjugative assembly genome engineering. Nature Protocols. 9: 2285-300. PMID 25188631 DOI: 10.1038/nprot.2014.081  0.35
2014 Gregg CJ, Lajoie MJ, Napolitano MG, Mosberg JA, Goodman DB, Aach J, Isaacs FJ, Church GM. Rational optimization of tolC as a powerful dual selectable marker for genome engineering. Nucleic Acids Research. 42: 4779-90. PMID 24452804 DOI: 10.1093/Nar/Gkt1374  0.734
2014 Bazak L, Haviv A, Barak M, Jacob-Hirsch J, Deng P, Zhang R, Isaacs FJ, Rechavi G, Li JB, Eisenberg E, Levanon EY. A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes. Genome Research. 24: 365-76. PMID 24347612 DOI: 10.1101/Gr.164749.113  0.387
2013 Lajoie MJ, Rovner AJ, Goodman DB, Aerni HR, Haimovich AD, Kuznetsov G, Mercer JA, Wang HH, Carr PA, Mosberg JA, Rohland N, Schultz PG, Jacobson JM, Rinehart J, Church GM, ... Isaacs FJ, et al. Genomically recoded organisms expand biological functions. Science (New York, N.Y.). 342: 357-60. PMID 24136966 DOI: 10.1126/Science.1241459  0.741
2012 Carr PA, Wang HH, Sterling B, Isaacs FJ, Lajoie MJ, Xu G, Church GM, Jacobson JM. Enhanced multiplex genome engineering through co-operative oligonucleotide co-selection. Nucleic Acids Research. 40: e132. PMID 22638574 DOI: 10.1093/Nar/Gks455  0.806
2011 Isaacs FJ, Carr PA, Wang HH, Lajoie MJ, Sterling B, Kraal L, Tolonen AC, Gianoulis TA, Goodman DB, Reppas NB, Emig CJ, Bang D, Hwang SJ, Jewett MC, Jacobson JM, et al. Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science (New York, N.Y.). 333: 348-53. PMID 21764749 DOI: 10.1126/Science.1205822  0.734
2010 Callura JM, Dwyer DJ, Isaacs FJ, Cantor CR, Collins JJ. Tracking, tuning, and terminating microbial physiology using synthetic riboregulators. Proceedings of the National Academy of Sciences of the United States of America. 107: 15898-903. PMID 20713708 DOI: 10.1073/Pnas.1009747107  0.748
2009 Wang HH, Isaacs FJ, Carr PA, Sun ZZ, Xu G, Forest CR, Church GM. Programming cells by multiplex genome engineering and accelerated evolution. Nature. 460: 894-8. PMID 19633652 DOI: 10.1038/Nature08187  0.722
2006 Blake WJ, Balázsi G, Kohanski MA, Isaacs FJ, Murphy KF, Kuang Y, Cantor CR, Walt DR, Collins JJ. Phenotypic consequences of promoter-mediated transcriptional noise. Molecular Cell. 24: 853-65. PMID 17189188 DOI: 10.1016/J.Molcel.2006.11.003  0.761
2006 Isaacs FJ, Dwyer DJ, Collins JJ. RNA synthetic biology. Nature Biotechnology. 24: 545-54. PMID 16680139 DOI: 10.1038/Nbt1208  0.641
2005 Isaacs FJ, Blake WJ, Collins JJ. Molecular biology. Signal processing in single cells. Science (New York, N.Y.). 307: 1886-8. PMID 15790834 DOI: 10.1126/Science.1110797  0.688
2004 Blake WJ, Isaacs FJ. Synthetic biology evolves. Trends in Biotechnology. 22: 321-4. PMID 15245901 DOI: 10.1016/J.Tibtech.2004.04.008  0.706
2004 Isaacs FJ, Dwyer DJ, Ding C, Pervouchine DD, Cantor CR, Collins JJ. Engineered riboregulators enable post-transcriptional control of gene expression. Nature Biotechnology. 22: 841-7. PMID 15208640 DOI: 10.1038/Nbt986  0.638
2003 Isaacs FJ, Hasty J, Cantor CR, Collins JJ. Prediction and measurement of an autoregulatory genetic module. Proceedings of the National Academy of Sciences of the United States of America. 100: 7714-9. PMID 12808135 DOI: 10.1073/Pnas.1332628100  0.44
2001 Hasty J, Isaacs F, Dolnik M, McMillen D, Collins JJ. Designer gene networks: Towards fundamental cellular control. Chaos (Woodbury, N.Y.). 11: 207-220. PMID 12779454 DOI: 10.1063/1.1345702  0.46
2001 Hasty J, McMillen D, Isaacs F, Collins JJ. Computational studies of gene regulatory networks: in numero molecular biology. Nature Reviews. Genetics. 2: 268-79. PMID 11283699 DOI: 10.1038/35066056  0.516
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