Publications

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2014 ()
  1. Hicks MA, Prather KLJ.  2014.  Bioprospecting in the genomic age. Adv Appl Microbiol. 87:111-46. Google Scholar PubMed

  • Nielsen AAK, Voigt CA.  2014.  Multi-input CRISPR/Cas genetic circuits that interface host regulatory networks. Mol Syst Biol. 10:763. Google Scholar PubMed

  • Zakeri B, Carr PA.  2014.  The limits of synthetic biology. Trends Biotechnol. Google Scholar PubMed

  • Nilgiriwala KSoli, Jiménez J, Rivera PMichael, Del Vecchio D.  2014.  A Synthetic Tunable Amplifying Buffer Circuit in E. coli. ACS Synth Biol. Google Scholar PubMed

  • Shiue E, Brockman IM, Prather KLJ.  2014.  Improving Product Yields on D-Glucose in Escherichia coli via Knockout of pgi and zwf and Feeding of Supplemental Carbon Sources. Biotechnol Bioeng. Google Scholar PubMed

  • Sheppard MJ, Kunjapur AM, Wenck SJ, Prather KLJ.  2014.  Retro-biosynthetic screening of a modular pathway design achieves selective route for microbial synthesis of 4-methyl-pentanol. Nat Commun. 5:5031. Google Scholar PubMed

  • Dhamankar H, Tarasova Y, Martin CH, Prather KLJ.  2014.  Engineering E. coli for the biosynthesis of 3-hydroxy-γ-butyrolactone (3HBL) and 3,4-dihydroxybutyric acid (3,4-DHBA) as value-added chemicals from glucose as a sole carbon source. Metab Eng. 25:72-81. Google Scholar PubMed

  • Rodrigues JL, Sousa M, Prather KLJ, Kluskens LD, Rodrigues LR.  2014.  Selection of Escherichia coli heat shock promoters toward their application as stress probes. J Biotechnol. Google Scholar PubMed

  • Kunjapur AM, Tarasova Y, Prather KLJ.  2014.  Synthesis and Accumulation of Aromatic Aldehydes in an Engineered Strain of Escherichia coli. J Am Chem Soc. Google Scholar PubMed

  • Sanjana NE, Shalem O, Zhang F.  2014.  Improved vectors and genome-wide libraries for CRISPR screening. Nat Methods. 11(8):783-4. Google Scholar PubMed

  • Gonçalves GAL, Oliveira PH, Gomes AG, Prather KLJ, Lewis LA, Prazeres DMF, Monteiro GA.  2014.  Evidence that the insertion events of IS2 transposition are biased towards abrupt compositional shifts in target DNA and modulated by a diverse set of culture parameters. Appl Microbiol Biotechnol. 98(15):6609-19. Google Scholar PubMed

  • Kiani S, Beal J, Ebrahimkhani MR, Huh J, Hall RN, Xie Z, Li Y, Weiss R.  2014.  CRISPR transcriptional repression devices and layered circuits in mammalian cells. Nat Methods. 11(7):723-6. Google Scholar PubMed

  • Wu X, Scott DA, Kriz AJ, Chiu AC, Hsu PD, Dadon DB, Cheng AW, Trevino AE, Konermann S, Chen S et al.  2014.  Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Nat Biotechnol. 32(7):670-6. Google Scholar PubMed

  • Gonçalves GAL, Prather KLJ, Monteiro GA, Carnes AE, Prazeres DMF.  2014.  Plasmid DNA production with Escherichia coli GALG20, a pgi-gene knockout strain: Fermentation strategies and impact on downstream processing. J Biotechnol. 186C:119-127. Google Scholar PubMed

  • Hsu PD, Lander ES, Zhang F.  2014.  Development and applications of CRISPR-Cas9 for genome engineering. Cell. 157(6):1262-78. Google Scholar PubMed

  • Siuti P, Yazbek J, Lu TK.  2014.  Engineering genetic circuits that compute and remember. Nat Protoc. 9(6):1292-300. Google Scholar PubMed

  • Beal J, Wagner TE, Kitada T, Azizgolshani O, Parker JMoberg, Densmore D, Weiss R.  2014.  Model-driven Engineering of Gene Expression from RNA Replicons. ACS Synth Biol. Google Scholar PubMed

  • Nissim L, Perli SD, Fridkin A, Perez-Pinera P, Lu TK.  2014.  Multiplexed and programmable regulation of gene networks with an integrated RNA and CRISPR/Cas toolkit in human cells. Mol Cell. 54(4):698-710. Google Scholar PubMed

  • Gonçalves GAL, Prather KLJ, Monteiro GA, Prazeres DMF.  2014.  Engineering of Escherichia coli strains for plasmid biopharmaceutical production: scale-up challenges. Vaccine. 32(24):2847-50. Google Scholar PubMed

  • Simcikova M, Prather KLJ, Prazeres DMF, Monteiro GA.  2014.  On the dual effect of glucose during production of pBAD/AraC-based minicircles. Vaccine. 32(24):2843-6. Google Scholar PubMed

  • Collins JJ, Maxon M, Ellington A, Fussenegger M, Weiss R, Sauro H.  2014.  Synthetic biology: How best to build a cell. Nature. 509(7499):155-7.  Google Scholar PubMed

  • Chen AY, Deng Z, Billings AN, Seker UOS, Lu MY, Citorik RJ, Zakeri B, Lu TK.  2014.  Synthesis and patterning of tunable multiscale materials with engineered cells. Nat Mater. 13(5):515-23. Google Scholar PubMed

  • Abin-Fuentes A, Leung JC, Mohamed MEl-Said, Wang DIC, Prather KLJ.  2014.  Rate-limiting step analysis of the microbial desulfurization of dibenzothiophene in a model oil system. Biotechnol Bioeng. 111(5):876-84. Google Scholar PubMed

  • Brophy JAN, Voigt CA.  2014.  Principles of genetic circuit design. Nat Methods. 11(5):508-20. Google Scholar PubMed

  • Purcell O, Lu TK.  2014.  Synthetic analog and digital circuits for cellular computation and memory. Curr Opin Biotechnol. 29C:146-155. Google Scholar PubMed

  • Nielsen J, Fussenegger M, Keasling J, Lee SYup, Liao JC, Prather K, Palsson B.  2014. Engineering synergy in biotechnology. Nat Chem Biol. 10(5):319-22. Google Scholar PubMed

  • Roquet N, Lu TK.  2014.  Digital and analog gene circuits for biotechnology. Biotechnol J. 9(5):597-608. Google Scholar PubMed

  • Church GM, Elowitz MB, Smolke CD, Voigt CA, Weiss R.  2014.  Realizing the potential of synthetic biology. Nat Rev Mol Cell Biol. 15(4):289-94. Google Scholar PubMed

  • Sarpeshkar R.  2014.  Analog synthetic biology. Philos Trans A Math Phys Eng Sci. 372(2012):20130110. Google Scholar  PubMed

  • Lee MN, Ye C, Villani A-C, Raj T, Li W, Eisenhaure TM, Imboywa SH, Chipendo PI, F Ran A, Slowikowski K et al..  2014.  Common genetic variants modulate pathogen-sensing responses in human dendritic cells. Science. 343(6175):1246980. Google Scholar  PubMed

  • Gyorgy A, Del Vecchio D.  2014.  Modular composition of gene transcription networks. PLoS Comput Biol. 10(3):e1003486. Google Scholar PubMed

  • Nishimasu H, F Ran A, Hsu PD, Konermann S, Shehata SI, Dohmae N, Ishitani R, Zhang F, Nureki O.  2014.  Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell. 156(5):935-49. Google Scholar PubMed

  • McMahon MD, Prather KLJ.  2014.  Functional screening and in vitro analysis reveal thioesterases with enhanced substrate specificity profiles that improve short-chain fatty acid production in Escherichia coli. Appl Environ Microbiol. 80(3):1042-50. Google Scholar PubMed
  • Shalem O, Sanjana NE, Hartenian E, Shi X, Scott DA, Mikkelsen TS, Heckl D, Ebert BL, Root DE, Doench JG et al.  2014.  Genome-scale CRISPR-Cas9 knockout screening in human cells. Science. 343(6166):84-7. Google Scholar PubMed

  • Pyzocha NK, F Ran A, Hsu PD, Zhang F.  2014.  RNA-guided genome editing of mammalian cells. Methods Mol Biol. 1114:269-77. Google Scholar PubMed

    • 2013 (11)

    1. Aakre CD, Phung TN, Huang D, Laub MT.  2013.  A bacterial toxin inhibits DNA replication elongation through a direct interaction with the β sliding clamp. Mol Cell. 52(5):617-28. Google Scholar PubMed

    2. Le TBK, Imakaev MV, Mirny LA, Laub MT.  2013.  High-resolution mapping of the spatial organization of a bacterial chromosome. Science. 342(6159):731-4. Google Scholar PubMed

    3. F Ran A, Hsu PD, Wright J, Agarwala V, Scott DA, Zhang F.  2013.  Genome engineering using the CRISPR-Cas9 system. Nat Protoc. 8(11):2281-308. Google Scholar PubMed

    4. Wagner JC, Goldfless SJ, Ganesan SM, Lee MCS, Fidock DA, Niles JC.  2013.  An integrated strategy for efficient vector construction and multi-gene expression in Plasmodium falciparum. Malar J. 12:373. Google Scholar PubMed

    5. Farzadfard F, Perli SD, Lu TK.  2013.  Tunable and multifunctional eukaryotic transcription factors based on CRISPR/Cas. ACS Synth Biol. 2(10):604-13. Google Scholar PubMed. Google Scholar PubMed

    6. F Ran A, Hsu PD, Lin C-Y, Gootenberg JS, Konermann S, Trevino AE, Scott DA, Inoue A, Matoba S, Zhang Y et al..  2013.  Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell. 154(6):1380-9. Google Scholar PubMed

    7. Podgornaia AI, Casino P, Marina A, Laub MT.  2013.  Structural basis of a rationally rewired protein-protein interface critical to bacterial signaling. Structure. 21(9):1636-47. Google Scholar PubMed

    8. Hsu PD, Scott DA, Weinstein JA, F Ran A, Konermann S, Agarwala V, Li Y, Fine EJ, Wu X, Shalem O et al..  2013.  DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol. 31(9):827-32. Google Scholar PubMed

    9. Konermann S, Brigham MD, Trevino AE, Hsu PD, Heidenreich M, Cong L, Platt RJ, Scott DA, Church GM, Zhang F.  2013.  Optical control of mammalian endogenous transcription and epigenetic states. Nature. 500(7463):472-6. Google Scholar PubMed. Google Scholar PubMed

    10. Jayanthi S, Nilgiriwala KSoli, Del Vecchio D.  2013.  Retroactivity controls the temporal dynamics of gene transcription. ACS Synth Biol. 2(8):431-41. Google Scholar PubMed

    11. Bikard D, Jiang W, Samai P, Hochschild A, Zhang F, Marraffini LA.  2013.  Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucleic Acids Res. 41(15):7429-37. Google Scholar PubMed

  • Jonas K, Liu J, Chien P, Laub MT.  2013.  Proteotoxic stress induces a cell-cycle arrest by stimulating Lon to degrade the replication initiator DnaA. Cell. 154(3):623-36. Google Scholar PubMedveroxybd.com

  • Zakeri B, Lu TK.  2013.  Synthetic biology of antimicrobial discovery. ACS Synth Biol. 2(7):358-72. Google Scholar PubMed

  • Purcell O, Jain B, Karr JR, Covert MW, Lu TK.  2013.  Towards a whole-cell modeling approach for synthetic biology. Chaos. 23(2):025112. Google Scholar PubMed

  • Daniel R, Rubens JR, Sarpeshkar R, Lu TK.  2013.  Synthetic analog computation in living cells. Nature. 497(7451):619-23. Google Scholar PubMed

  • Wang H, Yang H, Shivalila CS, Dawlaty MM, Cheng AW, Zhang F, Jaenisch R.  2013.  One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell. 153(4):910-8. Google Scholar PubMed

  • Siuti P, Yazbek J, Lu TK.  2013.  Synthetic circuits integrating logic and memory in living cells. Nat Biotechnol. 31(5):448-52. Google Scholar PubMed

  • Pirie CM, De Mey M, Prather KLJones, Ajikumar PKumaran.  2013.  Integrating the protein and metabolic engineering toolkits for next-generation chemical biosynthesis. ACS Chem Biol. 8(4):662-72. Google Scholar PubMed. Google Scholar PubMedir-leasing.ru

  • Ashenberg O, Keating AE, Laub MT.  2013.  Helix bundle loops determine whether histidine kinases autophosphorylate in cis or in trans. J Mol Biol. 425(7):1198-209. Google Scholar PubMed

  • Podgornaia AI, Laub MT.  2013.  Determinants of specificity in two-component signal transduction. Curr Opin Microbiol. 16(2):156-62. Google Scholar PubMedsports74.ru

  • Gora KG, Cantin A, Wohlever M, Joshi KK, Perchuk BS, Chien P, Laub MT.  2013.  Regulated proteolysis of a transcription factor complex is critical to cell cycle progression in Caulobacter crescentus. Mol Microbiol. 87(6):1277-89. Google Scholar PubMed

  • Jiang W, Bikard D, Cox D, Zhang F, Marraffini LA.  2013.  RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat Biotechnol. 31(3):233-9. Google Scholar PubMed

  • Cong L, F Ran A, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA et al..  2013.  Multiplex genome engineering using CRISPR/Cas systems. Science. 339(6121):819-23. Google Scholar PubMed

  • Ashenberg O, Laub MT.  2013.  Using analyses of amino Acid coevolution to understand protein structure and function. Methods Enzymol. 523:191-212. Google Scholar PubMed

    • 2012 (5)

    1. Capra EJ, Perchuk BS, Ashenberg O, Seid CA, Snow HR, Skerker JM, Laub MT.  2012.  Spatial tethering of kinases to their substrates relaxes evolutionary constraints on specificity. Mol Microbiol. 86(6):1393-403. Google Scholar PubMed

    2. Tsokos CG, Laub MT.  2012.  Polarity and cell fate asymmetry in Caulobacter crescentus. Curr Opin Microbiol. 15(6):744-50. Google Scholar PubMed

    3. Belmont BJ, Niles JC.  2012.  Inducible control of subcellular RNA localization using a synthetic protein-RNA aptamer interaction. PLoS One. 7(10):e46868. Google Scholar PubMed

    4. Carr PA, Wang HH, Sterling B, Isaacs FJ, Lajoie MJ, Xu G, Church GM, Jacobson JM.  2012.  Enhanced multiplex genome engineering through co-operative oligonucleotide co-selection. Nucleic Acids Res. 40(17):e132. Google Scholar PubMed

    5. Hsu PD, Zhang F.  2012.  Dissecting neural function using targeted genome engineering technologies. ACS Chem Neurosci. 3(8):603-10. Google Scholar PubMed

  • Del Vecchio D.  2012.  Modularity in signaling systems. Phys Biol. 9(4):045008. Google Scholar PubMed

  • Briggs AW, Rios X, Chari R, Yang L, Zhang F, Mali P, Church GM.  2012.  Iterative capped assembly: rapid and scalable synthesis of repeat-module DNA such as TAL effectors from individual monomers. Nucleic Acids Res. 40(15):e117. Google Scholar PubMed

  • Jayanthi S, Del Vecchio D.  2012.  Tuning genetic clocks employing DNA binding sites. PLoS One. 7(7):e41019. Google Scholar PubMed

  • Cong L, Zhou R, Kuo Y-C, Cunniff M, Zhang F.  2012.  Comprehensive interrogation of natural TALE DNA-binding modules and transcriptional repressor domains. Nat Commun. 3:968. Google Scholar PubMed

  • Zhao W, Dauwels J, Niles JC, Cao J.  2012.  Computational synchronization of microarray data with application to Plasmodium falciparum. Proteome Sci. 10 Suppl 1:S10. Google Scholar PubMed

  • Mei Y, Zhang F.  2012.  Molecular tools and approaches for optogenetics. Biol Psychiatry. 71(12):1033-8. Google Scholar PubMed

  • Capra EJ, Perchuk BS, Skerker JM, Laub MT.  2012.  Adaptive mutations that prevent crosstalk enable the expansion of paralogous signaling protein families. Cell. 150(1):222-32. Google Scholar PubMed

  • Capra EJ, Laub MT.  2012.  Evolution of two-component signal transduction systems. Annu Rev Microbiol. 66:325-47. Google Scholar PubMed

  • Niles JC.  2012.  Malarial parasites accumulate labile zinc pools. Chem Biol. 19(6):660-1. Google Scholar PubMed

  • Cheng AA, Lu TK.  2012.  Synthetic biology: an emerging engineering discipline. Annu Rev Biomed Eng. 14:155-78. Google Scholar PubMed

  • Goldfless SJ, Belmont BJ, de Paz AM, Liu JF, Niles JC.  2012.  Direct and specific chemical control of eukaryotic translation with a synthetic RNA-protein interaction. Nucleic Acids Res. 40(9):e64. Google Scholar PubMed

  • Kato HE, Zhang F, Yizhar O, Ramakrishnan C, Nishizawa T, Hirata K, Ito J, Aita Y, Tsukazaki T, Hayashi S et al.  2012.  Crystal structure of the channelrhodopsin light-gated cation channel. Nature. 482(7385):369-74. Google Scholar PubMed

  • Aakre CD, Laub MT.  2012.  Asymmetric cell division: a persistent issue? Dev Cell. 22(2):235-6. Google Scholar PubMed

  • Arfin SK, Sarpeshkar R.  2012.  An energy-efficient, adiabatic electrode stimulator with inductive energy recycling and feedback current regulation. IEEE Trans Biomed Circuits Syst. 6(1):1-14. Google Scholar PubMed

  • Sanjana NE, Cong L, Zhou Y, Cunniff MM, Feng G, Zhang F.  2012.  A transcription activator-like effector toolbox for genome engineering. Nat Protoc. 7(1):171-92. Google Scholar PubMed

  • Rapoport BI, Turicchia L, Wattanapanitch W, Davidson TJ, Sarpeshkar R.  2012.  Efficient universal computing architectures for decoding neural activity. PLoS One. 7(9):e42492. Google Scholar PubMed

    • 2011 (14)
    1. Zhang F, Vierock J, Yizhar O, Fenno LE, Tsunoda S, Kianianmomeni A, Prigge M, Berndt A, Cushman J, Polle J et al.  2011.  The microbial opsin family of optogenetic tools. Cell. 147(7):1446-57. Google Scholar PubMed

    2. Wattanapanitch W, Sarpeshkar R.  2011.  A low-power 32-channel digitally programmable neural recording integrated circuit. IEEE Trans Biomed Circuits Syst. 5(6):592-602. Google Scholar PubMed

    3. Ashenberg O, Rozen-Gagnon K, Laub MT, Keating AE.  2011.  Determinants of homodimerization specificity in histidine kinases. J Mol Biol. 413(1):222-35. Google Scholar PubMed

    4. Jiang P, Ventura AC, Sontag ED, Merajver SD, Ninfa AJ, Del Vecchio D.  2011.  Load-induced modulation of signal transduction networks. Sci Signal. 4(194):ra67. Google Scholar PubMed

    5. Lu TK, Koeris MS.  2011.  The next generation of bacteriophage therapy. Curr Opin Microbiol. 14(5):524-31. Google Scholar PubMed

    6. Kang JWoong, Lue N, Kong C-R, Barman I, Dingari NC, Goldfless SJ, Niles JC, Dasari RR, Feld MS.  2011.  Combined confocal Raman and quantitative phase microscopy system for biomedical diagnosis. Biomed Opt Express. 2(9):2484-92. Google Scholar PubMed

    7. Abel S, Chien P, Wassmann P, Schirmer T, Kaever V, Laub MT, Baker TA, Jenal U.  2011.  Regulatory cohesion of cell cycle and cell differentiation through interlinked phosphorylation and second messenger networks. Mol Cell. 43(4):550-60. Google Scholar PubMed

    8. Turicchia L, Sarpeshkar R.  2011.  An articulatory silicon vocal tract for speech and hearing prostheses. IEEE Trans Biomed Circuits Syst. 5(4):339-46. Google Scholar PubMed

    9. Isaacs FJ, Carr PA, Wang HH, Lajoie MJ, Sterling B, Kraal L, Tolonen AC, Gianoulis TA, Goodman DB, Reppas NB et al.  2011.  Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science. 333(6040):348-53. Google Scholar PubMed
    10. Jonas K, Y Chen E, Laub MT.  2011.  Modularity of the bacterial cell cycle enables independent spatial and temporal control of DNA replication. Curr Biol. 21(13):1092-101. Google Scholar PubMed

    11. Fleurant M, Kell R, Love J, Jenter C, Volk LA, Zhang F, Bates DW, Simon SR.  2011.  Massachusetts e-Health Project increased physicians’ ability to use registries, and signals progress toward better care. Health Aff (Millwood). 30(7):1256-64. Google Scholar PubMed

    12. Modell JW, Hopkins AC, Laub MT.  2011.  A DNA damage checkpoint in Caulobacter crescentus inhibits cell division through a direct interaction with FtsW. Genes Dev. 25(12):1328-43. Google Scholar PubMed
    13. Ossareh HR, Ventura AC, Merajver SD, Del Vecchio D.  2011.  Long signaling cascades tend to attenuate retroactivity. Biophys J. 100(7):1617-26. Google Scholar PubMed

    14. Valle BDo, Wentz CT, Sarpeshkar R.  2011.  An area and power-efficient analog li-ion battery charger circuit. IEEE Trans Biomed Circuits Syst. 5(2):131-7. Google Scholar PubMed

  • Bow H, Pivkin IV, Diez-Silva M, Goldfless SJ, Dao M, Niles JC, Suresh S, Han J.  2011.  A microfabricated deformability-based flow cytometer with application to malaria. Lab Chip. 11(6):1065-73. Google Scholar PubMed

  • Tsokos CG, Perchuk BS, Laub MT.  2011.  A dynamic complex of signaling proteins uses polar localization to regulate cell-fate asymmetry in Caulobacter crescentus. Dev Cell. 20(3):329-41. Google Scholar PubMed

  • Zhang F, Cong L, Lodato S, Kosuri S, Church GM, Arlotta P.  2011.  Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription. Nat Biotechnol. 29(2):149-53. Google Scholar PubMed

  • Y Chen E, Tropini C, Jonas K, Tsokos CG, Huang KC, Laub MT.  2011.  Spatial gradient of protein phosphorylation underlies replicative asymmetry in a bacterium. Proc Natl Acad Sci U S A. 108(3):1052-7. Google Scholar PubMed
    • 2010 (4)

    1. Siryaporn A, Perchuk BS, Laub MT, Goulian M.  2010.  Evolving a robust signal transduction pathway from weak cross-talk. Mol Syst Biol. 6:452. Google Scholar PubMed

    2. Lu TK.  2010.  Engineering scalable biological systems. Bioeng Bugs. 1(6):378-84. Google Scholar PubMed

    3. Carr PA.  2010.  DNA construction: homemade or ordered out? Nat Methods. 7(11):887-9. Google Scholar PubMed

    4. Oliveira PH, Prather KJones, Prazeres DMF, Monteiro GA.  2010.  Analysis of DNA repeats in bacterial plasmids reveals the potential for recurrent instability events. Appl Microbiol Biotechnol. 87(6):2157-67. Google Scholar PubMed

  • Ventura AC, Jiang P, Van Wassenhove L, Del Vecchio D, Merajver SD, Ninfa AJ.  2010.  Signaling properties of a covalent modification cycle are altered by a downstream target. Proc Natl Acad Sci U S A. 107(22):10032-7. Google Scholar PubMed

  • Moon TSeok, Dueber JE, Shiue E, Prather KLJones.  2010.  Use of modular, synthetic scaffolds for improved production of glucaric acid in engineered E. coli. Metab Eng. 12(3):298-305. Google Scholar PubMed

  • Tavakoli M, Turicchia L, Sarpeshkar R.  2010.  An ultra-low-power pulse oximeter implemented with an energy-efficient transimpedance amplifier. IEEE Trans Biomed Circuits Syst. 4(1):27-38. Google Scholar PubMed

  • Belmont BJ, Niles JC.  2010.  Engineering a direct and inducible protein-RNA interaction to regulate RNA biology. ACS Chem Biol. 5(9):851-61. Google Scholar PubMed

  • Martin CH, Wu D, Prather KLJones.  2010.  Integrated bioprocessing for the pH-dependent production of 4-valerolactone from levulinate in Pseudomonas putida KT2440. Appl Environ Microbiol. 76(2):417-24. Google Scholar PubMed

    • 2009 (2)

    1. Carr PA, Church GM.  2009.  Genome engineering.  Nat Biotechnol. 27(12):1151-62. Google Scholar PubMed

    2. Lu TK, Khalil AS, Collins JJ.  2009.  Next-generation synthetic gene networks. Nat Biotechnol. 27(12):1139-50. Google Scholar PubMed

  • Fay L, Misra V, Sarpeshkar R.  2009.  A micropower electrocardiogram amplifier. IEEE Trans Biomed Circuits Syst. 3(5):312-20. Google Scholar PubMed

  • Prather KLJones, Jaramillo A.  2009.  Editorial: Focus on synthetic biology. Biotechnol J. 4(10):1367. Google Scholar PubMed

  • Ghaemi R, Sun J, Iglesias PA, Del Vecchio D.  2009.  A method for determining the robustness of bio-molecular oscillator models. BMC Syst Biol. 3:95. Google Scholar PubMed

  • Moon TSeok, Yoon S-H, Ching M-JTsang Mui, Lanza AM, Prather KLJones.  2009.  Enzymatic assay of D-glucuronate using uronate dehydrogenase. Anal Biochem. 392(2):183-5. Google Scholar PubMed

  • Oliveira PH, Prather KJones, Prazeres DMF, Monteiro GA.  2009.  Structural instability of plasmid biopharmaceuticals: challenges and implications. Trends Biotechnol. 27(9):503-11. Google Scholar PubMed

  • Nielsen DR, Leonard E, Yoon S-H, Tseng H-C, Yuan C, Prather KLJones.  2009.  Engineering alternative butanol production platforms in heterologous bacteria. Metab Eng. 11(4-5):262-73. Google Scholar PubMed

  • Mukunda G, Oye KA, Mohr SC.  2009.  What rough beast? Politics Life Sci. 28(2):2-26. Google Scholar PubMed

  • Varadarajan PAmur, Del Vecchio D.  2009.  Design and characterization of a three-terminal transcriptional device through polymerase per second. IEEE Trans Nanobioscience. 8(3):281-9. Google Scholar PubMed

  • 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. Google Scholar PubMed

  • Niles JC, Derisi JL, Marletta MA.  2009.  Inhibiting Plasmodium falciparum growth and heme detoxification pathway using heme-binding DNA aptamers. Proc Natl Acad Sci U S A. 106(32):13266-71. Google Scholar PubMed

  • Arfin SK, Long MA, Fee MS, Sarpeshkar R.  2009.  Wireless neural stimulation in freely behaving small animals. J Neurophysiol. 102(1):598-605. Google Scholar PubMed

  • Leonard E, Runguphan W, O’Connor S, Prather KJones.  2009.  Opportunities in metabolic engineering to facilitate scalable alkaloid production. Nat Chem Biol. 5(5):292-300. Google Scholar PubMed

  • Tseng H-C, Martin CH, Nielsen DR, Prather KLJones.  2009.  Metabolic engineering of Escherichia coli for enhanced production of (R)- and (S)-3-hydroxybutyrate. Appl Environ Microbiol. 75(10):3137-45. Google Scholar PubMed

  • Martin CH, Nielsen DR, Solomon KV, Prather KLJones.  2009.  Synthetic metabolism: engineering biology at the protein and pathway scales. Chem Biol. 16(3):277-86. Google Scholar PubMed

  • Lu TK, Collins JJ.  2009.  Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy. Proc Natl Acad Sci U S A. 106(12):4629-34. Google Scholar PubMed

  • Yoon S-H, Moon TSeok, Iranpour P, Lanza AM, Prather KJones.  2009.  Cloning and characterization of uronate dehydrogenases from two pseudomonads and Agrobacterium tumefaciens strain C58. J Bacteriol. 191(5):1565-73. Google Scholar PubMed

  • Nielsen DR, Prather KJones.  2009.  In situ product recovery of n-butanol using polymeric resins. Biotechnol Bioeng. 102(3):811-21. Google Scholar PubMed

  • Moon TSeok, Yoon S-H, Lanza AM, Roy-Mayhew JD, Prather KLJones.  2009.  Production of glucaric acid from a synthetic pathway in recombinant Escherichia coli. Appl Environ Microbiol. 75(3):589-95. Google Scholar PubMed

  • Martin CH, Prather KLJones.  2009.  High-titer production of monomeric hydroxyvalerates from levulinic acid in Pseudomonas putida. J Biotechnol. 139(1):61-7. Google Scholar PubMed

    • 2008 (2)
    1. Mandal S, Sarpeshkar R.  2008.  Power-efficient impedance-modulation wireless data links for biomedical implants. IEEE Trans Biomed Circuits Syst. 2(4):301-15. Google Scholar PubMed

    2. Turicchia L, Sarpeshkar R.  2008.  An analog integrated-circuit vocal tract. IEEE Trans Biomed Circuits Syst. 2(4):316-27. Google Scholar PubMed

  • Leonard E, Nielsen D, Solomon K, Prather KJones.  2008.  Engineering microbes with synthetic biology frameworks. Trends Biotechnol. 26(12):674-81. Google Scholar PubMed

  • Rodrigo G, Carrera J, Prather KJones, Jaramillo A.  2008.  DESHARKY: automatic design of metabolic pathways for optimal cell growth. Bioinformatics. 24(21):2554-6. Google Scholar PubMed

  • Prather KLJones, Martin CH.  2008.  De novo biosynthetic pathways: rational design of microbial chemical factories. Curr Opin Biotechnol. 19(5):468-74. Google Scholar PubMed

  • Sarpeshkar R, Wattanapanitch W, Arfin SK, Rapoport BI, Mandal S, Baker MW, Fee MS, Musallam S, Andersen RA.  2008.  Low-power circuits for brain-machine interfaces. IEEE Trans Biomed Circuits Syst. 2(3):173-83. Google Scholar PubMed

  • Irmen CP, Siegel SM, Carr PA.  2008.  Localization of SSeCKS in unmyelinated primary sensory neurons. J Brachial Plex Peripher Nerve Inj. 3:8. Google Scholar PubMed

  • Del Vecchio D, Ninfa AJ, Sontag ED.  2008.  Modular cell biology: retroactivity and insulation. Mol Syst Biol. 4:161. Google Scholar PubMed
    • 2007 (7)
    1. Sarpeshkar R.  2007.  A Low-Power Blocking-Capacitor-Free Charge-Balanced Electrode-Stimulator Chip With Less Than 6 nA DC Error for 1-mA Full-Scale Stimulation. IEEE Trans Biomed Circuits Syst. 1(3):172-83. Google Scholar PubMed

    2. Wattanapanitch W, Fee M, Sarpeshkar R.  2007.  An energy-efficient micropower neural recording amplifier. IEEE Trans Biomed Circuits Syst. 1(2):136-47. Google Scholar PubMed

    3. Chien P, Perchuk BS, Laub MT, Sauer RT, Baker TA.  2007.  Direct and adaptor-mediated substrate recognition by an essential AAA+ protease. Proc Natl Acad Sci U S A. 104(16):6590-5. Google Scholar PubMed

    4. Kong DS, Carr PA, Chen L, Zhang S, Jacobson JM.  2007.  Parallel gene synthesis in a microfluidic device. Nucleic Acids Res. 35(8):e61. Google Scholar PubMed

    5. Baker MW, Sarpeshkar R.  2007.  Feedback analysis and design of RF power links for low-power bionic systems. IEEE Trans Biomed Circuits Syst. 1(1):28-38. Google Scholar PubMed

    6. Oxenham AJ, Simonson AM, Turicchia L, Sarpeshkar R.  2007.  Evaluation of companding-based spectral enhancement using simulated cochlear-implant processing. J Acoust Soc Am. 121(3):1709-16. Google Scholar PubMed

    7. Sit J-J, Simonson AM, Oxenham AJ, Faltys MA, Sarpeshkar R.  2007.  A low-power asynchronous interleaved sampling algorithm for cochlear implants that encodes envelope and phase information. IEEE Trans Biomed Eng. 54(1):138-49. Google Scholar PubMed

    2006 (5)
    1. Biondi EG, Reisinger SJ, Skerker JM, Arif M, Perchuk BS, Ryan KR, Laub MT.  2006.  Regulation of the bacterial cell cycle by an integrated genetic circuit. Nature. 444(7121):899-904. Google Scholar PubMed

    2. Prather KLJones, M Edmonds C, Herod JW.  2006.  Identification and characterization of IS1 transposition in plasmid amplification mutants of E. coli clones producing DNA vaccines. Appl Microbiol Biotechnol. 73(4):815-26. Google Scholar PubMed

    3. Niles JC, Marletta MA.  2006.  Utilizing RNA aptamers to probe a physiologically important heme-regulated cellular network. ACS Chem Biol. 1(8):515-24. Google Scholar PubMed

    4. Cheng JY, Zhang F, Chuang VP, Mayes AM, Ross CA.  2006.  Self-assembled one-dimensional nanostructure arrays. Nano Lett. 6(9):2099-103. Google Scholar PubMed

    5. Lu TK, Zhak, ii S, Dallos P, Sarpeshkar R.  2006.  Fast cochlear amplification with slow outer hair cells. Hear Res. 214(1-2):45-67. Google Scholar PubMed

  • Niles JC, Wishnok JS, Tannenbaum SR.  2006.  Peroxynitrite-induced oxidation and nitration products of guanine and 8-oxoguanine: structures and mechanisms of product formation. Nitric Oxide. 14(2):109-21. Google Scholar PubMed

  • Montgomery DL, Prather KJones.  2006.  Design of plasmid DNA constructs for vaccines. Methods Mol Med. 127:11-22. Google Scholar PubMed

    • 2005 (1)
    1. Sarpeshkar R, Salthouse C, Sit J-J, Baker MW, Zhak SM, Lu TKT, Turicchia L, Balster S.  2005.  An ultra-low-power programmable analog bionic ear processor. IEEE Trans Biomed Eng. 52(4):711-27. Google Scholar PubMed
  • Henderson PT, Neeley WL, Delaney JC, Gu F, Niles JC, Hah SSoo, Tannenbaum SR, Essigmann JM.  2005.  Urea lesion formation in DNA as a consequence of 7,8-dihydro-8-oxoguanine oxidation and hydrolysis provides a potent source of point mutations. Chem Res Toxicol. 18(1):12-8. Google Scholar PubMed
    • 2004 (1)

    1. Carr PA, Park JS, Lee Y-J, Yu T, Zhang S, Jacobson JM.  2004.  Protein-mediated error correction for de novo DNA synthesis. Nucleic Acids Res. 32(20):e162. Google Scholar PubMed

  • Niles JC, Wishnok JS, Tannenbaum SR.  2004.  Spiroiminodihydantoin and guanidinohydantoin are the dominant products of 8-oxoguanosine oxidation at low fluxes of peroxynitrite: mechanistic studies with 18O. Chem Res Toxicol. 17(11):1510-9. Google Scholar PubMed

  • Niles JC, Wishnok JS, Tannenbaum SR.  2004.  Mass spectrometric identification of 4-hydroxy-2,5-dioxo-imidazolidine-4-carboxylic acid during oxidation of 8-oxoguanosine by peroxynitrite and KHSO5/CoCl2. Chem Res Toxicol. 17(11):1501-9. Google Scholar PubMed

  • Yu H, Niles JC, Wishnok JS, Tannenbaum SR.  2004.  Spirodihydantoin is a minor product of 5-hydroxyisourate in urate oxidation. Org Lett. 6(19):3417-20. Google Scholar PubMed

    • 2003 (1)

    1. O’Connor KOSteel, Mowat DL, Scott HM, Carr PA, Dorland JL, Tai KFan WYoun.  2003.  A randomized trial of two public health nurse follow-up programs after early obstetrical discharge: an examination of breastfeeding rates, maternal confidence and utilization and costs of health services. Can J Public Health. 94(2):98-103. Google Scholar PubMed

    2002 (4)
    1. Sia SK, Carr PA, Cochran AG, Malashkevich VN, Kim PS.  2002.  Short constrained peptides that inhibit HIV-1 entry. Proc Natl Acad Sci U S A. 99(23):14664-9. Google Scholar PubMed

    2. Sarpeshkar R, O’Halloran M.  2002.  Scalable hybrid computation with spikes. Neural Comput. 14(9):2003-38. Google Scholar PubMed

    3. Aldor IS, Kim S-W, Prather KLJones, Keasling JD.  2002.  Metabolic engineering of a novel propionate-independent pathway for the production of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) in recombinant Salmonella enterica serovar typhimurium. Appl Environ Microbiol. 68(8):3848-54. Google Scholar PubMed
    4. Siegel SM, Grove BD, Carr PA.  2002.  SSeCKS immunolabeling in rat primary sensory neurons. Brain Res. 926(1-2):126-36. Google Scholar PubMed

  • Lee JM, Niles JC, Wishnok JS, Tannenbaum SR.  2002.  Peroxynitrite reacts with 8-nitropurines to yield 8-oxopurines. Chem Res Toxicol. 15(1):7-14. Google Scholar PubMed

    • 2001 ()

    1. Niles JC, Wishnok JS, Tannenbaum SR.  2001.  A novel nitroimidazole compound formed during the reaction of peroxynitrite with 2′,3′,5′-tri-O-acetyl-guanosine. J Am Chem Soc. 123(49):12147-51. Google Scholar PubMed

  • Niles JC, Wishnok JS, Tannenbaum SR.  2001.  Spiroiminodihydantoin is the major product of the 8-oxo-7,8-dihydroguanosine reaction with peroxynitrite in the presence of thiols and guanosine photooxidation by methylene blue. Org Lett. 3(7):963-6. Google Scholar PubMed

    • 2000 ()
    1. Carr PA, Roller MJ, Zaruba RA.  2000.  Peptidergic input to immunohistochemically-identified Renshaw cells. Brain Res. 887(1):194-8. Google Scholar PubMed
  • Alvarez FJ, Villalba RM, Carr PA, Grandes P, Somohano PM.  2000.  Differential distribution of metabotropic glutamate receptors 1a, 1b, and 5 in the rat spinal cord. J Comp Neurol. 422(3):464-87. Google Scholar PubMed
  • Hahnloser RH, Sarpeshkar R, Mahowald MA, Douglas RJ, Seung HS.  2000.  Digital selection and analogue amplification coexist in a cortex-inspired silicon circuit. Nature. 405(6789):947-51. Google Scholar PubMed

  • Huang A, Noga BR, Carr PA, Fedirchuk B, Jordan LM.  2000.  Spinal cholinergic neurons activated during locomotion: localization and electrophysiological characterization. J Neurophysiol. 83(6):3537-47. Google Scholar PubMed

  • Niles JC, Wishnok JS, Tannenbaum SR.  2000.  A novel nitration product formed during the reaction of peroxynitrite with 2′,3′,5′-tri-O-acetyl-7,8-dihydro-8-oxoguanosine: N-nitro-N’-[1-(2,3,5-tri-O-acetyl-beta-D-erythro-pentofuranosyl)- 2, 4-dioxoimidazolidin-5-ylidene]guanidine. Chem Res Toxicol. 13(5):390-6. Google Scholar PubMed

  • Crone B, Dodabalapur A, Lin YY, Filas RW, Bao Z, LaDuca A, Sarpeshkar R, Katz HE, Li W.  2000.  Large-scale complementary integrated circuits based on organic transistors. Nature. 403(6769):521-3. Google Scholar PubMedberryjam.ru

    • 1999 ()

    1. Niles JC, Burney S, Singh SP, Wishnok JS, Tannenbaum SR.  1999.  Peroxynitrite reaction products of 3′,5′-di-O-acetyl-8-oxo-7, 8-dihydro-2′-deoxyguanosine. Proc Natl Acad Sci U S A. 96(21):11729-34. Google Scholar PubMedtrevordiy.wordpress.com

  • Eckert DM, Malashkevich VN, Hong LH, Carr PA, Kim PS.  1999.  Inhibiting HIV-1 entry: discovery of D-peptide inhibitors that target the gp41 coiled-coil pocket. Cell. 99(1):103-15. Google Scholar PubMed
  • Burney S, Niles JC, Dedon PC, Tannenbaum SR.  1999.  DNA damage in deoxynucleosides and oligonucleotides treated with peroxynitrite. Chem Res Toxicol. 12(6):513-20. Google Scholar PubMed

  • Tretyakova NY, Niles JC, Burney S, Wishnok JS, Tannenbaum SR.  1999.  Peroxynitrite-induced reactions of synthetic oligonucleotides containing 8-oxoguanine. Chem Res Toxicol. 12(5):459-66. Google Scholar PubMed

  • Carr PA, Pearson JC, Fyffe RE.  1999.  Distribution of 5-hydroxytryptamine-immunoreactive boutons on immunohistochemically-identified Renshaw cells in cat and rat lumbar spinal cord. Brain Res. 823(1-2):198-201. Google Scholar PubMed

  • Burney S, Caulfield JL, Niles JC, Wishnok JS, Tannenbaum SR.  1999.  The chemistry of DNA damage from nitric oxide and peroxynitrite. Mutat Res. 424(1-2):37-49. Google Scholar PubMed

  • Bracken C, Carr PA, Cavanagh J, Palmer AG.  1999.  Temperature dependence of intramolecular dynamics of the basic leucine zipper of GCN4: implications for the entropy of association with DNA. J Mol Biol. 285(5):2133-46. Google Scholar PubMed

    • 1998 ()

    1. Sarpeshkar R.  1998.  Analog versus digital: extrapolating from electronics to neurobiology. Neural Comput. 10(7):1601-38. Google Scholar PubMed

  • Carr PA, Alvarez FJ, Leman EA, Fyffe RE.  1998.  Calbindin D28k expression in immunohistochemically identified Renshaw cells. Neuroreport. 9(11):2657-61. Google Scholar PubMed

  • Carr PA, Fearing DA, Palmer AG.  1998.  3D accordion spectroscopy for measuring 15N and 13CO relaxation rates in poorly resolved NMR spectra. J Magn Reson. 132(1):25-33. Google Scholar PubMed

  • Carr PA, Wenner P.  1998.  Calcitonin gene-related peptide: distribution and effects on spontaneous rhythmic activity in embryonic chick spinal cord. Brain Res Dev Brain Res. 106(1-2):47-55. Google Scholar PubMed

  • Carr PA, Haftel V, Alvarez FJ, Cope TC, Fyffe RE.  1998.  Effect of sciatic nerve transection or TTX application on enzyme activity in rat spinal cord. Neuroreport. 9(2):357-61. Google Scholar PubMed

    • 1997 ()

    1. Carr PA, Erickson HP, Palmer AG.  1997.  Backbone dynamics of homologous fibronectin type III cell adhesion domains from fibronectin and tenascin. Structure. 5(7):949-59. Google Scholar PubMed

  • Alvarez FJ, Dewey DE, Carr PA, Cope TC, Fyffe RE.  1997.  Downregulation of metabotropic glutamate receptor 1a in motoneurons after axotomy. Neuroreport. 8(7):1711-6. Google Scholar PubMed

    • 1995 ()

    1. Carr PA, Huang A, Noga BR, Jordan LM.  1995.  Cytochemical characteristics of cat spinal neurons activated during fictive locomotion. Brain Res Bull. 37(2):213-8. Google Scholar PubMed

    1994 ()
    1. Akke M, Carr PA, Palmer AG.  1994.  Heteronuclear-correlation NMR spectroscopy with simultaneous isotope filtration, quadrature detection, and sensitivity enhancement using z rotations. J Magn Reson B. 104(3):298-302. Google Scholar PubMed

  • Carr PA, Noga BR, Nance DM, Jordan LM.  1994.  Intracellular labeling of cat spinal neurons using a tetramethylrhodamine-dextran amine conjugate. Brain Res Bull. 34(5):447-51. Google Scholar PubMed

    • 1993 ()

    1. Carr PA, Nagy JI.  1993.  Emerging relationships between cytochemical properties and sensory modality transmission in primary sensory neurons. Brain Res Bull. 30(3-4):209-19. Google Scholar PubMed

    1991 ()

    1. Carr PA, Yamamoto T, Karmy G, Nagy JI.  1991.  Cytochemical relationships and central terminations of a unique population of primary afferent neurons in rat. Brain Res Bull. 26(6):825-43. Google Scholar PubMed

  • Karmy G, Carr PA, Yamamoto T, Chan SH, Nagy JI.  1991.  Cytochrome oxidase immunohistochemistry in rat brain and dorsal root ganglia: visualization of enzyme in neuronal perikarya and in parvalbumin-positive neurons. Neuroscience. 40(3):825-39. Google Scholar PubMed
    • 1990 ()

    1. Carr PA, Yamamoto T, Nagy JI.  1990.  Calcitonin gene-related peptide in primary afferent neurons of rat: co-existence with fluoride-resistant acid phosphatase and depletion by neonatal capsaicin. Neuroscience. 36(3):751-60. Google Scholar PubMed

    1989 ()

    1. Yamamoto T, Carr PA, Baimbridge KG, Nagy JI.  1989.  Parvalbumin- and calbindin D28k-immunoreactive neurons in the superficial layers of the spinal cord dorsal horn of rat. Brain Res Bull. 23(6):493-508. Google Scholar PubMed

  • Carr PA, Yamamoto T, Karmy G, Baimbridge KG, Nagy JI.  1989.  Parvalbumin is highly colocalized with calbindin D28k and rarely with calcitonin gene-related peptide in dorsal root ganglia neurons of rat. Brain Res. 497(1):163-70. Google Scholar PubMed

  • Carr PA, Yamamoto T, Staines WA, Whittaker ME, Nagy JI.  1989.  Quantitative histochemical analysis of cytochrome oxidase in rat dorsal root ganglia and its co-localization with carbonic anhydrase. Neuroscience. 33(2):351-62. Google Scholar PubMed

  • Carr PA, Yamamoto T, Karmy G, Baimbridge KG, Nagy JI.  1989.  Analysis of parvalbumin and calbindin D28k-immunoreactive neurons in dorsal root ganglia of rat in relation to their cytochrome oxidase and carbonic anhydrase content. Neuroscience. 33(2):363-71. Google Scholar PubMed