Isaacs, Farren Justin - Yale University - Biological & Biomedical Sciences

个人简介

PhD Boston University, Bioinformatics (2003) BS University of Pennsylvania, Bioengineering MS Boston University, Biomedical Engineering Research Fellow Harvard Medical School

近期论文

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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, Church GM. (2011) Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science, 333(6040):348-53. PMID: 21764749. Wang HH*, Isaacs FJ*, Carr PA, Sun ZZ, Xu G, Forest CR, Church GM (2009) Programming cells by multiplex genome engineering and accelerated evolution. Nature, 460(7257):894-8. Isaacs FJ, Dwyer DJ, Collins JJ (2006) RNA Synthetic Biology. Nature Biotechnology, 24:545-554. Isaacs FJ, Dwyer DJ, Ding C, Pervouchine D, Cantor C and Collins JJ (2004) Engineered Riboregulators Enable Post-Transcriptional Control of Gene Expression. Nature Biotechnology, 22: 841-847. Isaacs FJ*, Hasty J*, Cantor CR, Collins JJ (2003) Prediction and Measurement of an Autoregulatory Genetic Module. Proceedings of the National Academy of Sciences USA, 100:7714-7719. 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. Biotechnol Bioeng. 2017 May; 2017 Feb 2. PMID: 27987323 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. Proc Natl Acad Sci U S A. 2016 Sep 20; 2016 Sep 6. PMID: 27601680 Ma NJ, Isaacs FJ: Genomic Recoding Broadly Obstructs the Propagation of Horizontally Transferred Genetic Elements. Cell Syst. 2016 Aug; 2016 Jul 14. PMID: 27426981 Quintin M, 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 Synth Biol. 2016 Jun 17; 2016 May 11. PMID: 27054880 Muir P, Li S, Lou S, Wang D, Spakowicz DJ, Salichos L, Zhang J, Weinstock GM, Isaacs F, Rozowsky J, Gerstein M: Erratum to: The real cost of sequencing: scaling computation to keep pace with data generation. Genome Biol. 2016 Apr 28; 2016 Apr 28. PMID: 27125642 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 Biol. 2016 Mar 23; 2016 Mar 23. PMID: 27009100 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. Nat Methods. 2016 Feb; 2015 Dec 21. PMID: 26689263 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: Evolution of translation machinery in recoded bacteria enables multi-site incorporation of nonstandard amino acids. Nat Biotechnol. 2015 Dec; 2015 Nov 16. PMID: 26571098 Des Soye BJ, Patel JR, Isaacs FJ, Jewett MC: Repurposing the translation apparatus for synthetic biology. Curr Opin Chem Biol. 2015 Oct; 2015 Jul 15. PMID: 26186264 Oza JP, Aerni HR, Pirman NL, Barber KW, ter Haar CM, Rogulina S, Amrofell MB, Isaacs FJ, Rinehart J, Jewett MC: Robust production of recombinant phosphoproteins using cell-free protein synthesis. Nat Commun. 2015 Sep 9; 2015 Sep 9. PMID: 26350765 Pirman NL, Barber KW, Aerni HR, Ma NJ, Haimovich AD, Rogulina S, Isaacs FJ, Rinehart J: A flexible codon in genomically recoded Escherichia coli permits programmable protein phosphorylation. Nat Commun. 2015 Sep 9; 2015 Sep 9. PMID: 26350500 Haimovich AD, Muir P, Isaacs FJ: Genomes by design. Nat Rev Genet. 2015 Sep; 2015 Aug 11. PMID: 26260262 Gallagher RR, Patel JR, Interiano AL, Rovner AJ, Isaacs FJ: Multilayered genetic safeguards limit growth of microorganisms to defined environments. Nucleic Acids Res. 2015 Feb 18; 2015 Jan 7. PMID: 25567985 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. 2015 Feb 5; 2015 Jan 21. PMID: 25607356 Sawyer N, Gassaway BM, Haimovich AD, Isaacs FJ, Rinehart J, Regan L: Designed phosphoprotein recognition in Escherichia coli. ACS Chem Biol. 2014 Nov 21; 2014 Oct 6. PMID: 25272187 Gallagher RR, Li Z, Lewis AO, Isaacs FJ: Rapid editing and evolution of bacterial genomes using libraries of synthetic DNA. Nat Protoc. 2014 Oct; 2014 Sep 4. PMID: 25188632 Ma NJ, Moonan DW, Isaacs FJ: Precise manipulation of bacterial chromosomes by conjugative assembly genome engineering. Nat Protoc. 2014 Oct; 2014 Sep 4. PMID: 25188631 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 Res. 2014 Apr; 2014 Jan 22. PMID: 24452804 Hakim A, Nguyen JB, Basu K, Zhu DF, Thakral D, Davies PL, Isaacs FJ, Modis Y, Meng W: Crystal structure of an insect antifreeze protein and its implications for ice binding. J Biol Chem. 2013 Apr 26; 2013 Mar 12. PMID: 23486477 Heinemann IU, Rovner AJ, Aerni HR, Rogulina S, Cheng L, Olds W, Fischer JT, Söll D, Isaacs FJ, Rinehart J: Enhanced phosphoserine insertion during Escherichia coli protein synthesis via partial UAG codon reassignment and release factor 1 deletion. FEBS Lett. 2012 Oct 19; 2012 Sep 13. PMID: 22982858