Publications

Updated December 2022.

2022

Bean, B. D. M., Mulvihill, C. J., Garge, R. K., Boutz, D. R., Rousseau, O., Floyd, B. M., Cheney, W., Gardner, E. C., Ellington, A. D., Marcotte, E. M., Gollihar, J. D., Whiteway, M., & Martin, V. J. J. (2022). Functional expression of opioid receptors and other human GPCRs in yeast engineered to produce human sterols. Nature Communications, 13(1), 2882. https://doi.org/10.1038/s41467-022-30570-7

Bhadra, S., Paik, I., Torres, J., Fadanka, S., Gandini, C., Akligoh, H., Molloy, J., & Ellington, A. D. (2022). Preparation and use of cellular reagents: A low‐resource molecular biology reagent platform. Current Protocols, 2(3). https://doi.org/10.1002/cpz1.387

Coronado, J. N., Ngo, P., Anslyn, E. V., & Ellington, A. D. (2022). Chemical insights into flexizyme-mediated tRNA acylation. Cell Chemical Biology. https://doi.org/10.1016/j.chembiol.2022.03.012

d’Oelsnitz, S., Kim, W., Burkholder, N. T., Javanmardi, K., Thyer, R., Zhang, Y., Alper, H. S., & Ellington, A. D. (2022). Using fungible biosensors to evolve improved alkaloid biosyntheses. Nature Chemical Biology, 18(9), 981–989. https://doi.org/10.1038/s41589-022-01072-w

d’Oelsnitz, S., Nguyen, V., Alper, H. S., & Ellington, A. D. (2021). Evolving a generalist biosensor for bicyclic monoterpenes (p. 2021.08.20.457167). bioRxiv. https://www.biorxiv.org/content/10.1101/2021.08.20.457167v1

Dowman, L.J., Kulkarni, S.S., Alegre-Requena, J.V. et al. Site-selective photocatalytic functionalization of peptides and proteins at selenocysteine. Nat Commun 13, 6885 (2022). https://doi.org/10.1038/s41467-022-34530-z

Javanmardi, K., Segall-Shapiro, T. H., Chou, C.-W., Boutz, D. R., Olsen, R. J., Xie, X., Xia, H., Shi, P.-Y., Johnson, C. D., Annapareddy, A., Weaver, S., Musser, J. M., Ellington, A. D., Finkelstein, I. J., & Gollihar, J. D. (2022). Antibody escape and cryptic cross-domain stabilization in the SARS-CoV-2 Omicron spike protein (p. 2022.04.18.488614). bioRxiv. https://www.biorxiv.org/content/10.1101/2022.04.18.488614v1

Kar, S., Bordiya, Y., Rodriguez, N., Kim, J., Gardner, E. C., Gollihar, J. D., Sung, S., & Ellington, A. D. (2022). Orthogonal control of gene expression in plants using synthetic promoters and CRISPR-based transcription factors. Plant Methods, 18(1), 42. https://doi.org/10.1186/s13007-022-00867-1

Kar, S., Bordiya, Y., Rodriguez, N., Kim, J., Gardner, E. C., Gollihar, J., Sung, S., & Ellington, A. D. (2021). Orthogonal control of gene expression in plants using synthetic promoters and CRISPR-based transcription factors (p. 2021.11.16.468903). bioRxiv. https://www.biorxiv.org/content/10.1101/2021.11.16.468903v1

Lee, J., Coronado, J. N., Cho, N., Lim, J., Hosford, B. M., Seo, S., Kim, D. S., Kofman, C., Moore, J. S., Ellington, A. D., Anslyn, E. V., & Jewett, M. C. (2022). Ribosome-mediated biosynthesis of pyridazinone oligomers in vitro. Nature Communications, 13(1), 6322. https://doi.org/10.1038/s41467-022-33701-2

Lu, H., Diaz, D. J., Czarnecki, N. J., Zhu, C., Kim, W., Shroff, R., Acosta, D. J., Alexander, B. R., Cole, H. O., Zhang, Y., Lynd, N. A., Ellington, A. D., & Alper, H. S. (2022). Machine learning-aided engineering of hydrolases for PET depolymerization. Nature, 604(7907), 662–667. https://doi.org/10.1038/s41586-022-04599-z

Mackelprang, R., Adamala, K. P., Aurand, E. R., Diggans, J. C., Ellington, A. D., Evans, S. W., Fortman, J. L. C., Hillson, N. J., Hinman, A. W., Isaacs, F. J., Medford, J. I., Mamaghani, S., Moon, T. S., Palmer, M. J., Peccoud, J., Vitalis, E. A., Hook-Barnard, I., & Friedman, D. C. (2022). Making security viral: Shifting engineering biology culture and publishing. ACS Synthetic Biology, 11(2), 522–527. https://doi.org/10.1021/acssynbio.1c00324

Paik, I., Bhadra, S., & Ellington, A. D. (2022). Charge engineering improves the performance of bst dna polymerase fusions. ACS Synthetic Biology, 11(4), 1488–1496. https://doi.org/10.1021/acssynbio.1c00559

Shroff, R., Ellefson, J. W., Wang, S. S., Boulgakov, A. A., Hughes, R. A., & Ellington, A. D. (2022). Recovery of information stored in modified dna with an evolved polymerase. ACS Synthetic Biology, 11(2), 554–561. https://doi.org/10.1021/acssynbio.1c00575

Simmons, T. R., Ellington, A. D., & Contreras, L. M. (2022). Rnp-based control systems for genetic circuits in synthetic biology beyond crispr. In J. Chappell & M. K. Takahashi (Eds.), Riboregulator Design and Analysis (pp. 1–31). Springer US. https://doi.org/10.1007/978-1-0716-2421-0_1

Wang, S. S., Xiong, E., Bhadra, S., & Ellington, A. D. (2022). Developing predictive hybridization models for phosphorothioate oligonucleotides using high-resolution melting. PLOS ONE, 17(5), e0268575. https://doi.org/10.1371/journal.pone.0268575

Watts, E., Thyer, R., Ellington, A. D., & Brodbelt, J. S. (2022). Integrated top-down and bottom-up mass spectrometry for characterization of diselenide bridging patterns of synthetic selenoproteins. Analytical Chemistry, 94(32), 11175–11184. https://doi.org/10.1021/acs.analchem.2c01433

2021

Austin W Cole, Steven D Tran, Andrew D Ellington, Heat adaptation of phage T7 under an extended genetic code, Virus Evolution, Volume 7, Issue 2, December 2021, veab100, https://doi.org/10.1093/ve/veab100

Bean, B. D. M., Mulvihill, C. J., Garge, R. K., Boutz, D. R., Rousseau, O., Floyd, B. M., Cheney, W., Gardner, E. C., Ellington, A. D., Marcotte, E. M., Gollihar, J. D., Whiteway, M., & Martin, V. J. J. (2021). Functional expression of opioid receptors and other human GPCRs in yeast engineered to produce human sterols. BioRxiv, 2021.05.12.443385. https://doi.org/10.1101/2021.05.12.443385

Bhadra, S., Maranhao, A. C., & Ellington, A. D. (2020). A one-enzyme RT-qPCR assay for SARS-CoV-2, and procedures for reagent production (p. 2020.03.29.013342). bioRxiv. https://www.biorxiv.org/content/10.1101/2020.03.29.013342v5

Bhadra, S., Maranhao, A. C., Paik, I., & Ellington, A. D. (2021). A one-enzyme rt-qpcr assay for sars-cov-2, and procedures for reagent production. Bio-Protocol, 11(2), e3898–e3898.

Bhadra, S., Nguyen, V., Torres, J.-A., Kar, S., Fadanka, S., Gandini, C., Akligoh, H., Paik, I., Maranhao, A. C., Molloy, J., & Ellington, A. D. (2021). Producing molecular biology reagents without purification. PLOS ONE, 16(6), e0252507. https://doi.org/10.1371/journal.pone.0252507

Bhadra, S., Riedel, T. E., Lakhotia, S., Tran, N. D., & Ellington, A. D. (2021). High-surety isothermal amplification and detection of sars-cov-2. MSphere, 6(3), e00911-20. https://doi.org/10.1128/mSphere.00911-20

Bhadra, S., Riedel, T. E., Lakhotia, S., Tran, N. D., & Ellington, A. D. (n.d.). High-surety isothermal amplification and detection of sars-cov-2. MSphere, 6(3), e00911-20. https://doi.org/10.1128/mSphere.00911-20

Carvalho, J., Lopes-Nunes, J., Vialet, B., Rosado, T., Gallardo, E., Vale, J., Eloy, C., Ferreira, S., Palmeira-de-Oliveira, R., Campello, M. P. C., Paulo, A., Barthélémy, P., Mergny, J.-L., Salgado, G. F., Queiroz, J. A., Ellington, A. D., & Cruz, C. (2021). Nanoaggregate-forming lipid-conjugated AS1411 aptamer as a promising tumor-targeted delivery system of anticancer agents in vitro. Nanomedicine: Nanotechnology, Biology and Medicine, 36, 102429. https://doi.org/10.1016/j.nano.2021.102429

Carvalho, J., Lopes-Nunes, J., Vialet, B., Rosado, T., Gallardo, E., Vale, J., Eloy, C., Ferreira, S., Palmeira-de-Oliveira, R., Campello, M. P. C., Paulo, A., Barthélémy, P., Mergny, J.-L., Salgado, G. F., Queiroz, J. A., Ellington, A. D., & Cruz, C. (2021). Nanoaggregate-forming lipid-conjugated AS1411 aptamer as a promising tumor-targeted delivery system of anticancer agents in vitro. Nanomedicine: Nanotechnology, Biology, and Medicine, 102429. https://doi.org/10.1016/j.nano.2021.102429

Chou, L., Grefenstette, N., Johnson, S. S., Graham, H., Mahaffy, P., Kempes, C., Elsila, J. E., Libby, E., Ellington, A., Anslyn, E., Hoehler, T., Girguis, P., Cronin, L., Brinkerhoff, W., & Lollar, B. S. (2021). Towards a more universal life detection strategy. Bulletin of the American Astronomical Society, 53(4). https://doi.org/10.3847/25c2cfeb.53a24171

Chou, L., Grefenstette, N., Johnson, S. S., Graham, H., Mahaffy, P., Kempes, C., Elsila, J. E., Libby, E., Ellington, A., Anslyn, E., Hoehler, T., Girguis, P., Cronin, L., Brinkerhoff, W., & Sherwood Lollar, B. (2021). Towards a more universal life detection strategy. 53, 181. https://doi.org/10.3847/25c2cfeb.53a24171

d’Oelsnitz, S., Kim, W., Burkholder, N. T., Javanmardi, K., Thyer, R., Zhang, Y., Alper, H., & Ellington, A. D. (2021). Using structurally fungible biosensors to evolve improved alkaloid biosyntheses. BioRxiv, 2021.06.07.447399. https://doi.org/10.1101/2021.06.07.447399

d’Oelsnitz, S., Kim, W., Burkholder, N. T., Javanmardi, K., Thyer, R., Zhang, Y., Alper, H., & Ellington, A. D. (2021). Using structurally fungible biosensors to evolve improved alkaloid biosyntheses (p. 2021.06.07.447399). bioRxiv. https://www.biorxiv.org/content/10.1101/2021.06.07.447399v1

Dinkeloo, K., Cantero, A. M., Paik, I., Vulgamott, A., Ellington, A. D., & Lloyd, A. (2021). Genetic transformation technologies for the common dandelion, Taraxacum officinale. Plant Methods, 17(1), 59. https://doi.org/10.1186/s13007-021-00760-3

Goike, J., Hsieh, C.-L., Horton, A., Gardner, E. C., Bartzoka, F., Wang, N., Javanmardi, K., Herbert, A., Abbassi, S., Renberg, R., Johanson, M. J., Cardona, J. A., Segall-Shapiro, T., Zhou, L., Nissly, R. H., Gontu, A., Byrom, M., Maranhao, A. C., Battenhouse, A. M., … Gollihar, J. D. (2021). Synthetic repertoires derived from convalescent COVID-19 patients enable discovery of SARS-CoV-2 neutralizing antibodies and a novel quaternary binding modality. BioRxiv, 2021.04.07.438849. https://doi.org/10.1101/2021.04.07.438849

Kulikova, A. V., Diaz, D. J., Loy, J. M., Ellington, A. D., & Wilke, C. O. (2021). Learning the local landscape of protein structures with convolutional neural networks. Journal of Biological Physics, 47(4), 435–454. https://doi.org/10.1007/s10867-021-09593-6

Lee, J., Schwarz, K., Yu, H., Krüger, A., Anslyn, E. V., Ellington, A., Moore, J. S., & Jewett, M. (2021). Ribosome-mediated incorporation of fluorescent amino acids into peptides in vitro. Chemical Communications, 10.1039.D0CC07740B. https://doi.org/10.1039/D0CC07740B

Lu, H., Diaz, D. J., Czarnecki, N. J., Zhu, C., Kim, W., Shroff, R., Acosta, D. J., Alexander, B., Cole, H., Zhang, Y. J., Lynd, N., Ellington, A. D., & Alper, H. S. (2021). Deep learning redesign of PETase for practical PET degrading applications (p. 2021.10.10.463845). bioRxiv. https://www.biorxiv.org/content/10.1101/2021.10.10.463845v1

Mackelprang, R., Aurand, E. R., Bovenberg, R. A. L., Brink, K. R., Charo, R. A., Delborne, J. A., Diggans, J., Ellington, A. D., Fortman, J. L. “Clem,” Isaacs, F. J., Medford, J. I., Murray, R. M., Noireaux, V., Palmer, M. J., Zoloth, L., & Friedman, D. C. (2021). Guiding ethical principles in engineering biology research. ACS Synthetic Biology, 10(5), 907–910. https://doi.org/10.1021/acssynbio.1c00129

Miller, A. A., Rao, A. S., Nelakanti, S. R., Kujalowicz, C., Shi, T., Rodriguez, T., Ellington, A. D., & Stovall, G. M. (2021). Systematic review of aptamer sequence reporting in the literature reveals widespread unexplained sequence alterations (p. 2021.11.02.466945). bioRxiv. https://www.biorxiv.org/content/10.1101/2021.11.02.466945v1

Paik, I., Ngo, P. H. T., Shroff, R., Diaz, D. J., Maranhao, A. C., Walker, D. J. F., Bhadra, S., & Ellington, A. D. (2021). Improved bst dna polymerase variants derived via a machine learning approach. Biochemistry, acs.biochem.1c00451. https://doi.org/10.1021/acs.biochem.1c00451

Paik, I., Ngo, P. H. T., Shroff, R., Maranhao, A. C., Walker, D. J. F., Bhadra, S., & Ellington, A. D. (2021). Multi-modal engineering of Bst DNA polymerase for thermostability in ultra-fast LAMP reactions. BioRxiv, 2021.04.15.439918. https://doi.org/10.1101/2021.04.15.439918

Smith, H. H., Hyde, A. S., Simkus, D. N., Libby, E., Maurer, S. E., Graham, H. V., Kempes, C. P., Sherwood Lollar, B., Chou, L., Ellington, A. D., Fricke, G. M., Girguis, P. R., Grefenstette, N. M., Pozarycki, C. I., House, C. H., & Johnson, S. S. (2021). The grayness of the origin of life. Life, 11(6), 498. https://doi.org/10.3390/life11060498

Thyer, R., d’Oelsnitz, S., Blevins, M. S., Klein, D. R., Brodbelt, J. S., & Ellington, A. D. (2021). Directed evolution of an improved aminoacyl-trna synthetase for incorporation of l-3,4-dihydroxyphenylalanine(L-dopa). Angewandte Chemie (International Ed. in English), 60(27), 14811–14816. https://doi.org/10.1002/anie.202100579

Toft, C. J., Moreau, M. J. J., Perutka, J., Mandapati, S., Enyeart, P., Sorenson, A. E., Ellington, A. D., & Schaeffer, P. M. (2021). Delineation of the ancestral tus-dependent replication fork trap. International Journal of Molecular Sciences, 22(24), 13533. https://doi.org/10.3390/ijms222413533

Van Leuven, J. T., Ederer, M. M., Burleigh, K., Scott, L., Hughes, R. A., Codrea, V., Ellington, A. D., Wichman, H. A., & Miller, C. R. (2021). Φx174 attenuation by whole-genome codon deoptimization. Genome Biology and Evolution, 13(2). https://doi.org/10.1093/gbe/evaa214

Wannier, T. M., Ciaccia, P. N., Ellington, A. D., Filsinger, G. T., Isaacs, F. J., Javanmardi, K., Jones, M. A., Kunjapur, A. M., Nyerges, A., Pal, C., Schubert, M. G., & Church, G. M. (2021). Recombineering and mage. Nature Reviews Methods Primers, 1(1), 1–24. https://doi.org/10.1038/s43586-020-00006-x

Xiong, E., Yao, D., Ellington, A. D., & Bhadra, S. (2021). Minimizing leakage in stacked strand exchange amplification circuits. ACS Synthetic Biology, 10(6), 1277–1283. https://doi.org/10.1021/acssynbio.0c00615

2020

Agrawal, N. K., Allen, P., Song, Y. H., Wachs, R. A., Du, Y., Ellington, A. D., & Schmidt, C. E. (2020). Oligonucleotide-functionalized hydrogels for sustained release of small molecule (Aptamer) therapeutics. Acta Biomaterialia, 102, 315–325. https://doi.org/10.1016/j.actbio.2019.11.037

Bhadra, S., Maranhao, A. C., & Ellington, A. D. (2020). A one-enzyme RT-qPCR assay for SARS-CoV-2, and procedures for reagent production. BioRxiv, 2020.03.29.013342. https://doi.org/10.1101/2020.03.29.013342

Bhadra, S., Maranhao, A. C., & Ellington, A. D. (2020). One enzyme reverse transcription qPCR using Taq DNA polymerase. BioRxiv, 2020.05.27.120238. https://doi.org/10.1101/2020.05.27.120238

Boulgakov, A. A., Ellington, A. D., & Marcotte, E. M. (2020). Bringing microscopy-by-sequencing into view. Trends in Biotechnology, 38(2), 154–162. https://doi.org/10.1016/j.tibtech.2019.06.001

Choi, W. S., He, P., Pothukuchy, A., Gollihar, J., Ellington, A. D., & Yang, W. (2020). How a B family DNA polymerase has been evolved to copy RNA. Proceedings of the National Academy of Sciences of the United States of America, 117(35), 21274–21280. https://doi.org/10.1073/pnas.2009415117

Gardner, E. C., Watkins, E. J., Gollihar, J., & Ellington, A. D. (2020). Emulsion-based directed evolution of enzymes and proteins in yeast. In Methods in Enzymology. Academic Press. https://doi.org/10.1016/bs.mie.2020.04.053

Lee, J., Der, B. S., Karamitros, C. S., Li, W., Marshall, N. M., Lungu, O. I., Miklos, A. E., Xu, J., Kang, T. H., Lee, C.-H., Tan, B., Hughes, R. A., Jung, S. T., Ippolito, G. C., Gray, J. J., Zhang, Y., Kuhlman, B., Georgiou, G., & Ellington, A. D. (2020). Computer-based engineering of thermostabilized antibody fragments. AIChE Journal, 66(3), e16864. https://doi.org/10.1002/aic.16864

Leonard, S. P., Powell, J. E., Perutka, J., Geng, P., Heckmann, L. C., Horak, R. D., Davies, B. W., Ellington, A. D., Barrick, J. E., & Moran, N. A. (2020). Engineered symbionts activate honey bee immunity and limit pathogens. Science, 367(6477), 573–576. https://doi.org/10.1126/science.aax9039

Leuven, J. T. V., Ederer, M. M., Burleigh, K., Scott, L., Hughes, R. A., Codrea, V., Ellington, A. D., Wichman, H., & Miller, C. (2020). Φx174 attenuation by whole genome codon deoptimization. BioRxiv, 2020.02.10.942847. https://doi.org/10.1101/2020.02.10.942847

Li, N., Larson, T., Nguyen, H. H., Sokolov, K. V., & Ellington, A. D. (2020). Directed evolution of gold nanoparticle delivery to cells (vol 46, pg 392, 2010). CHEMICAL COMMUNICATIONS, 56(31), 4368-4368.

Shroff, R., Cole, A. W., Diaz, D. J., Morrow, B. R., Donnell, I., Annapareddy, A., Gollihar, J., Ellington, A. D., & Thyer, R. (2020). Discovery of novel gain-of-function mutations guided by structure-based deep learning. ACS Synthetic Biology. https://doi.org/10.1021/acssynbio.0c00345

T. Le, T., Bruckbauer, A., Tahirbegi, B., J. Magness, A., Ying, L., D. Ellington, A., & G. Cass, A. E. (2020). A highly stable RNA aptamer probe for the retinoblastoma protein in live cells. Chemical Science, 11(17), 4467–4474. https://doi.org/10.1039/D0SC01613F

Tanno, H., McDaniel, J. R., Stevens, C. A., Voss, W. N., Li, J., Durrett, R., Lee, J., Gollihar, J., Tanno, Y., Delidakis, G., Pothukuchy, A., Ellefson, J. W., Goronzy, J. J., Maynard, J. A., Ellington, A. D., Ippolito, G. C., & Georgiou, G. (2020). A facile technology for the high-throughput sequencing of the paired VH:VL and TCRβ:TCRα repertoires. Science Advances, 6(17), eaay9093. https://doi.org/10.1126/sciadv.aay9093

Tanno, H., McDaniel, J., Stevens, C., Voss, W., Li, J., Durrett, R., Lee, J., Gollihar, J., Tanno, Y., Delidakis, G., Pothukuchy, A., Ellefson, J., Goronzy, J., Maynard, J., Ellington, A., Ippolito, G., & Georgiou, G. (2020). One step ultra-high-throughput sequencing of the paired antibody VH:VL and TCRβ:α repertoires using cell lysate resistant xenopolymerase in emulsion. The Journal of Immunology, 204(1 Supplement), 86.22-86.22.

Yao, D., Bhadra, S., Xiong, E., Liang, H., Ellington, A. D., & Jung, C. (2020). Dynamic programming of a dna walker controlled by protons. ACS Nano, 14(4), 4007–4013. https://doi.org/10.1021/acsnano.9b08166

Zamanian-Daryoush, M., Gogonea, V., DiDonato, A. J., Buffa, J. A., Choucair, I., Levison, B. S., Hughes, R. A., Ellington, A. D., Huang, Y., Li, X. S., DiDonato, J. A., & Hazen, S. L. (2020). Site-specific 5-hydroxy-tryptophan incorporation into apolipoprotein A-I impairs cholesterol efflux activity and high density lipoprotein biogenesis. Journal of Biological Chemistry, jbc.RA119.012092. https://doi.org/10.1074/jbc.RA119.012092

Zhang, F., & Ellington, A. D. (2020). Hurdling and hurtling toward new genetic codes. ACS Central Science. https://doi.org/10.1021/acscentsci.0c01549

2019

Boulgakov AA, Ellington AD, Marcotte EM. Bringing Microscopy-By-Sequencing into View. Trends Biotechnol. 2019 Jul 6. pii: S0167-7799(19)30134-9. doi: 10.1016/j.tibtech.2019.06.001

Colleen Mulvihill, Andrew Ellington; Synthetic GPCRs and signal transduction cascades. Emerg Top Life Sci 11 November 2019; 3 (5): 609–614. doi: https://doi.org/10.1042/ETLS20190035

DiEuliis D, Ellington AD, Gronvall GK, Imperiale MJ. (2019) Does Biotechnology Pose New Catastrophic Risks?. In: . Current Topics in Microbiology and Immunology. Springer, Berlin, Heidelberg

Gardner E, Ellington A. Reprogramming the brain with synthetic neurobiology. Curr Opin Biotechnol. 2018;58:37-44. Epub 2018/11/21. doi: 10.1016/j.copbio.2018.10.013. PubMed PMID: 30458406.

Hoshika S, Leal N, Kim MJ, Kim MS, Karalkar NB, Kim HJ, Bates AM, Watkins NE, SantaLucia HA, Meyer AJ, DasGupta S, Piccirilli JA, Ellington AD, SantaLucia J, Gerogiadis MM, Benner S. Hachimoji DNA and RNA: A genetic system with eight building blocks. Science. 22 February 2019. pg. 884-887. doi 10.1126/science.aat0971. vol. 363. issue 6429

Jiang Y, Li X, Morrow BR, Pothukuchy A, Gollihar J, Novak R, Reilly CB, Ellington AD, Walt DR. Single-Molecule Mechanistic Study of Enzyme Hysteresis. ACS Cent. Sci. 2019, 5, 10, 1691-1698. Publication Date:September 24, 2019. doi.org/10.1021/acscentsci.9b00718

Johnson, S.S., Graham, H., Anslyn, E., Brinckerhoff, W., Conrad, P., Cronin, L., Ellington, A., Elsila, J., Girguis, P., Grubisic, A., House, C., Kempes, C., Li, X.. E. Libby, P. Mahaffy, J. Nadeau, A. Roussel, B. Sherwood Lollar, A. Steele. Future Approaches to Life Detection on Mars. 2019, LPI Contributions, 2089, 6374.

Lee J, Schwieter KE, Watkins AM, Kim DS, Yu H, Schwarz KJ, Lim J, Coronado J, Byrom M, Anslyn EV, Ellington AD, Moore JS, Jewett MC. Expanding the limits of the second genetic code with ribozymes. Nat Commun 10, 5097 (2019) doi:10.1038/s41467-019-12916-w.

Lim, BJ, Hwang, I, Ellington, A & Sessler, JL 2019, 'Synthesis of Ferrocene Derivatives Allowing Linear Free Energy Studies of Redox Potentials' Helvetica Chimica Acta, vol. 102, no. 2, e1800186. https://doi.org/10.1002/hlca.201800186

Meinke JL, Simon AJ, Wagner DT, Morrow BR, You S, Ellington AD, Keatinge-Clay AT. Employing 25-Residue Docking Motifs from Modular Polyketide Synthases as Orthogonal Protein Connectors. ACS Synth. Biol. 2019, 8, 9, 2017-2024. Publication Date:August 30, 2019. doi.org/10.1021/acssynbio.9b00047

Park D, Ellington AD, Jung C. Selection of self-priming molecular replicators. Nucleic Acids Res. 2019;47(5):2169-76. Epub 2019/01/31. doi: 10.1093/nar/gkz044. PubMed PMID: 30698805; PMCID: PMC6412129.

Shroff R, Cole A, Morrow B, Diaz D, Donnell I, Gollihar J, Ellington AD, Thyer R. A structure-based deep learning framework for protein engineering. bioRxiv 833905; doi: https://doi.org/10.1101/833905

Simon AJ, Ellington AD, Finkelstein IJ. Retrons and their applications in genome engineering, Nucleic Acids Research, gkz865, https://doi.org/10.1093/nar/gkz865

Simon AJ, d’Oelsnitz S, Ellington AD. Synthetic evolution. Nature Biotechnology. 2019;37(7):730-43. doi: 10.1038/s41587-019-0157-4.

Simon AJ, Zhou Y, Ramasubramani V, Glaser J, Pothukuchy A, Gollihar J, Gerberich JC, Leggere JC, Morrow BR, Jung C, Glotzer SC, Taylor DW, Ellington AD. Supercharging enables organized assembly of synthetic biomolecules. Nat Chem. 2019;11(3):204-12. Epub 2019/01/16. doi: 10.1038/s41557-018-0196-3. PubMed PMID: 30643229.

Stovall GM, Huynh V, Engelman S, Ellington AD. Aptamers in Education: Undergraduates Make Aptamers and Acquire 21st Century Skills Along the Way. Sensors (Basel). 2019;19(15):3270. Published 2019 Jul 25. doi:10.3390/s19153270

Tanno H, Gould TM, Durrett RE, McDaniel JR, Cao W, Gollihar J, Steven C, Tanno Y, Ellington AD, Ippolito GC, Hildebrand W, Georgiou G, Goronzy JJ. The Journal of Immunology May 1, 2019, 202 (1 Supplement) 71.15;

Wang SS, Ellington AD. Pattern Generation with Nucleic Acid Chemical Reaction Networks. Chem Rev. 2019;119(10):6370-83. Epub 2019/03/14. doi: 10.1021/acs.chemrev.8b00625. PubMed PMID: 30865429.

2018

Garry DJ, Meyer AJ, Ellefson JW, Bull JJ, Ellington AD. Predicting evolution of the transcription regulatory network in a bacteriophage. Genome Biol Evol. 2018 Sep 1. doi: 10.1093/gbe/evy191. [Epub ahead of print] PubMed PMID: 30184065.

Bhadra S, Riedel TE, Saldaña MA, Hegde S, Pederson N, Hughes GL, Ellington AD. Direct nucleic acid analysis of mosquitoes for high fidelity species identification and detection of Wolbachia using a cellphone. PLoS Negl Trop Dis. 2018 Aug 30;12(8):e0006671. doi: 10.1371/journal.pntd.0006671. eCollection 2018 Aug. PubMed PMID: 30161131.

Bhadra S, Pothukuchy A, Shroff R, Cole AW, Byrom M, Ellefson JW, Gollihar JD, Ellington AD. Cellular reagents for diagnostics and synthetic biology. PLoS One. 2018 Aug 15;13(8):e0201681. doi: 10.1371/journal.pone.0201681. eCollection 2018. PubMed PMID: 30110361; PubMed Central PMCID: PMC6093680.

Abil Z, Ellington AD. Compartmentalized Self-Replication for Evolution of a DNA Polymerase. Curr Protoc Chem Biol. 2018 Mar;10(1):1-17. doi: 10.1002/cpch.34. PubMed PMID: 30040233.

Kar S, Ellington AD. In Vitro Transcription Networks Based on Hairpin Promoter Switches. ACS Synth Biol. 2018 Aug 17;7(8):1937-1945. doi: 10.1021/acssynbio.8b00172. Epub 2018 Aug 1. PubMed PMID: 30021064.

Cai S, Jung C, Bhadra S, Ellington AD. Phosphorothioated Primers Lead to Loop-Mediated Isothermal Amplification at Low Temperatures. Anal Chem. 2018 Jul 17;90(14):8290-8294. doi: 10.1021/acs.analchem.8b02062. Epub 2018 Jul 5. PubMed PMID: 29968462.

Garry DJ, Ellington AD, Molineux IJ, Bull JJ. Viral attenuation by engineered protein fragmentation. Virus Evol. 2018 Jun 19;4(1):vey017. doi: 10.1093/ve/vey017. eCollection 2018 Jan. PubMed PMID: 29942657; PubMed Central PMCID: PMC6009699.

Thyer R, Shroff R, Klein DR, d'Oelsnitz S, Cotham VC, Byrom M, Brodbelt JS, Ellington AD. Custom selenoprotein production enabled by laboratory evolution of recoded bacterial strains. Nat Biotechnol. 2018 Aug;36(7):624-631. doi: 10.1038/nbt.4154. Epub 2018 Jun 4. PubMed PMID: 29863724; PubMed Central PMCID: PMC6035053.

Akhmetov A, Laurent JM, Gollihar J, Gardner EC, Garge RK, Ellington AD, Kachroo AH, Marcotte EM. Single-step Precision Genome Editing in Yeast Using CRISPR-Cas9. Bio Protoc. 2018 Mar 20;8(6). pii: e2765. doi: 10.21769/BioProtoc.2765. PubMed PMID: 29770349; PubMed Central PMCID: PMC5951413.

Baldridge KC, Jora M, Maranhao AC, Quick MM, Addepalli B, Brodbelt JS, Ellington AD, Limbach PA, Contreras LM. Directed Evolution of Heterologous tRNAs Leads to Reduced Dependence on Post-transcriptional Modifications. ACS Synth Biol. 2018 May 18;7(5):1315-1327. doi: 10.1021/acssynbio.7b00421. Epub 2018 Apr 25. PubMed PMID: 29694026.

Phillips EA, Moehling TJ, Bhadra S, Ellington AD, Linnes JC. Strand Displacement Probes Combined with Isothermal Nucleic Acid Amplification for Instrument-Free Detection from Complex Samples. Anal Chem. 2018 Jun 5;90(11):6580-6586. doi: 10.1021/acs.analchem.8b00269. Epub 2018 May 8. PubMed PMID: 29667809; PubMed Central PMCID: PMC5990927.

Nowicki EM, Shroff R, Singleton JA, Renaud DE, Wallace D, Drury J, Zirnheld J, Colleti B, Ellington AD, Lamont RJ, Scott DA, Whiteley M. Microbiota and Metatranscriptome Changes Accompanying the Onset of Gingivitis. MBio. 2018 Apr 17;9(2). pii: e00575-18. doi: 10.1128/mBio.00575-18. PubMed PMID: 29666288; PubMed Central PMCID: PMC5904416.

Johnson SS, Anslyn EV, Graham HV, Mahaffy PR, Ellington AD. Fingerprinting Non-Terran Biosignatures. Astrobiology. 2018 Jul;18(7):915-922. doi: 10.1089/ast.2017.1712. Epub 2018 Mar 8. PubMed PMID: 29634318; PubMed Central PMCID: PMC6067094.

Milligan JN, Shroff R, Garry DJ, Ellington AD. Evolution of a Thermophilic Strand-Displacing Polymerase Using High-Temperature Isothermal Compartmentalized Self-Replication. Biochemistry. 2018 Aug 7;57(31):4607-4619. doi: 10.1021/acs.biochem.8b00200. Epub 2018 Apr 18. PubMed PMID: 29629759.

Leonard SP, Perutka J, Powell JE, Geng P, Richhart DD, Byrom M, Kar S, Davies BW, Ellington AD, Moran NA, Barrick JE. Genetic Engineering of Bee Gut Microbiome Bacteria with a Toolkit for Modular Assembly of Broad-Host-Range Plasmids. ACS Synth Biol. 2018 May 18;7(5):1279-1290. doi: 10.1021/acssynbio.7b00399. Epub 2018 Apr 13. PubMed PMID: 29608282; PubMed Central PMCID: PMC5963681.

Kar S, Ellington AD. Construction of synthetic T7 RNA polymerase expression systems. Methods. 2018 Jul 1;143:110-120. doi: 10.1016/j.ymeth.2018.02.022. Epub 2018 Mar 5. PubMed PMID: 29518499.

Ellefson JW, Ledbetter MP, Ellington AD. Directed evolution of a synthetic phylogeny of programmable Trp repressors. Nat Chem Biol. 2018 Apr;14(4):361-367. doi: 10.1038/s41589-018-0006-7. Epub 2018 Feb 26. PubMed PMID: 29483643.

Tack DS, Cole AC, Shroff R, Morrow BR, Ellington AD. Evolving Bacterial Fitness with an Expanded Genetic Code. Sci Rep. 2018 Feb 19;8(1):3288. doi: 10.1038/s41598-018-21549-w. PubMed PMID: 29459649; PubMed Central PMCID: PMC5818497.

2017

Abil Z, Ellefson JW, Gollihar JD, Watkins E, Ellington AD. Compartmentalized partnered replication for the directed evolution of genetic parts and circuits. Nat Protoc. 2017;12(12):2493-512. Epub 2017/11/10. doi: 10.1038/nprot.2017.119. PubMed PMID: 29120463; PMCID: PMC6053311.

Cammarata M, Thyer R, Lombardo M, Anderson A, Wright D, Ellington A, Brodbelt JS. Characterization of trimethoprim resistant E. coli dihydrofolate reductase mutants by mass spectrometry and inhibition by propargyl-linked antifolates. Chem Sci. 2017;8(5):4062-72. Epub 2017/05/01. doi: 10.1039/c6sc05235e. PubMed PMID: 29967675; PMCID: PMC6020862.

Damase TR, Ellington AD, Allen PB. Purification of single-stranded DNA by co-polymerization with acrylamide and electrophoresis. Biotechniques. 2017;62(6):275-82. Epub 2017/06/20. doi: 10.2144/000114557. PubMed PMID: 28625157.

Du, Y., Pothukuchy, A., Gollihar, J.D., Nourani, A., Li, B., Ellington, A.D. (2017 Jan 19). Coupling Sensitive Nucleic Acid Amplification with Commercial Pregnancy Test Strips. Angew. Chem. Int. Ed. Engl. 56(4):992-996. PMID: 27990727. PMCID: PMC5240841. doi:10.1002/anie.201609108

Entzminger KC, Hyun JM, Pantazes RJ, Patterson-Orazem AC, Qerqez AN, Frye ZP, Hughes RA, Ellington AD, Lieberman RL, Maranas CD, Maynard JA. De novo design of antibody complementarity determining regions binding a FLAG tetra-peptide. Sci Rep. 2017;7(1):10295. Epub 2017/09/02. doi: 10.1038/s41598-017-10737-9. PubMed PMID: 28860479; PMCID: PMC5579192.

Gade AM, Meadows MK, Ellington AD, Anslyn EV. Differential array sensing for cancer cell classification and novelty detection. Org Biomol Chem. 2017;15(46):9866-74. Epub 2017/11/16. doi: 10.1039/c7ob02174g. PubMed PMID: 29139514.

Hughes RA, Ellington AD. Synthetic DNA Synthesis and Assembly: Putting the Synthetic in Synthetic Biology. Cold Spring Harb Perspect Biol. 2017;9(1). Epub 2017/01/05. doi: 10.1101/cshperspect.a023812. PubMed PMID: 28049645; PMCID: PMC5204324.

Jiang YS, Riedel TE, Popoola JA, Morrow BR, Cai S, Ellington AD, Bhadra S. Portable platform for rapid in-field identification of human fecal pollution in water. Water Res. 2018;131:186-95. Epub 2017/12/27. doi: 10.1016/j.watres.2017.12.023. PubMed PMID: 29278789; PMCID: PMC5999531.

Jiang YS, Stacy A, Whiteley M, Ellington AD, Bhadra S. Amplicon Competition Enables End-Point Quantitation of Nucleic Acids Following Isothermal Amplification. Chembiochem. 2017;18(17):1692-5. Epub 2017/06/20. doi: 10.1002/cbic.201700317. PubMed PMID: 28628741; PMCID: PMC5890436.

Jung C, Allen PB, Ellington AD. A Simple, Cleated DNA Walker That Hangs on to Surfaces. ACS Nano. 2017;11(8):8047-54. Epub 2017/07/19. doi: 10.1021/acsnano.7b02693. PubMed PMID: 28719175.

Jung C, Hawkins JA, Jones SK, Jr., Xiao Y, Rybarski JR, Dillard KE, Hussmann J, Saifuddin FA, Savran CA, Ellington AD, Ke A, Press WH, Finkelstein IJ. Massively Parallel Biophysical Analysis of CRISPR-Cas Complexes on Next Generation Sequencing Chips. Cell. 2017;170(1):35-47.e13. Epub 2017/07/01. doi: 10.1016/j.cell.2017.05.044. PubMed PMID: 28666121; PMCID: PMC5552236.

Kimoto M, Meyer AJ, Hirao I, Ellington AD. Genetic alphabet expansion transcription generating functional RNA molecules containing a five-letter alphabet including modified unnatural and natural base nucleotides by thermostable T7 RNA polymerase variants. Chem Commun (Camb). 2017;53(91):12309-12. Epub 2017/11/03. doi: 10.1039/c7cc06661a. PubMed PMID: 29094732.

Laber JR, Dear BJ, Martins ML, Jackson DE, DiVenere A, Gollihar JD, Ellington AD, Truskett TM, Johnston KP, Maynard JA. Charge Shielding Prevents Aggregation of Supercharged GFP Variants at High Protein Concentration. Mol Pharm. 2017;14(10):3269-80. Epub 2017/09/06. doi: 10.1021/acs.molpharmaceut.7b00322. PubMed PMID: 28870080; PMCID: PMC5624851.

Maranhao, A.C., Ellington, A.D. (2017 Jan 20). Evolving Orthogonal Suppressor tRNAs To Incorporate Modified Amino Acids. ACS Synth Biol. 6(1):108-119. PMID: 27600875. doi:10.1021/acssynbio.6b00145

Wang, B., Thachuk, C., Ellington, A.D., Soloveichik, D. (2017 Sep). The Design Space of Strand Displacement Cascades with Toehold-Size Clamps, in: Brijder, R., Qian, L. (Eds.), DNA Computing and Molecular Programming. Springer International Publishing, Cham, pp. 64–81.

2016

Azat Akhmetov, Andrew D. Ellington, Edward M. Marcotte. A highly parallel strategy for storage of digital information in living cells. bioRxiv 096792; doi: 10.1101/096792.

Cammarata MB, Thyer R, Rosenberg J, Ellington A, Brodbelt JS. Correction to "Structural Characterization of Dihydrofolate Reductase Complexes by Top-Down Ultraviolet Photodissociation Mass Spectrometry". J Am Chem Soc. 2016;138(9):3252. Epub 2016/02/27. doi: 10.1021/jacs.6b01611. PubMed PMID: 26919090.

DeKosky BJ, Lungu OI, Park D, Johnson EL, Charab W, Chrysostomou C, Kuroda D, Ellington AD, Ippolito GC, Gray JJ, Georgiou G. Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires. Proc Natl Acad Sci U S A. 2016;113(19):E2636-45. Epub 2016/04/27. doi: 10.1073/pnas.1525510113. PubMed PMID: 27114511; PMCID: PMC4868480.

Du Y, Pothukuchy A, Gollihar JD, Nourani A, Li B, Ellington AD. Coupling Sensitive Nucleic Acid Amplification with Commercial Pregnancy Test Strips. Angew Chem Int Ed Engl. 2017;56(4):992-6. Epub 2016/12/19. doi: 10.1002/anie.201609108. PubMed PMID: 27990727; PMCID: PMC5240841.

Du Y, Zhen SJ, Li B, Byrom M, Jiang YS, Ellington AD. Engineering Signaling Aptamers That Rely on Kinetic Rather Than Equilibrium Competition. Anal Chem. 2016;88(4):2250-7. Epub 2016/01/12. doi: 10.1021/acs.analchem.5b03930. PubMed PMID: 26750592.

Ellefson, J.W., Gollihar, J., Shroff, R., Shivram, H., Iyer, V.R., Ellington, A.D. (2016 Jun 27). Synthetic evolutionary origin of a proofreading reverse transcriptase. Science 352(6293):1590–1593. PMID: 27339990. doi:10.1126/science.aaf5409

Hammerling MJ, Gollihar J, Mortensen C, Alnahhas RN, Ellington AD, Barrick JE. Expanded Genetic Codes Create New Mutational Routes to Rifampicin Resistance in Escherichia coli. Mol Biol Evol. 2016;33(8):2054-63. Epub 2016/05/18. doi: 10.1093/molbev/msw094. PubMed PMID: 27189550.

Jung C, Ellington AD. A primerless molecular diagnostic: phosphorothioated-terminal hairpin formation and self-priming extension (PS-THSP). Anal Bioanal Chem. 2016;408(30):8583-91. Epub 2016/04/02. doi: 10.1007/s00216-016-9479-y. PubMed PMID: 27032410; PMCID: PMC5045755.

Lee J, Boutz DR, Chromikova V, Joyce MG, Vollmers C, Leung K, Horton AP, DeKosky BJ, Lee CH, Lavinder JJ, Murrin EM, Chrysostomou C, Hoi KH, Tsybovsky Y, Thomas PV, Druz A, Zhang B, Zhang Y, Wang L, Kong WP, Park D, Popova LI, Dekker CL, Davis MM, Carter CE, Ross TM, Ellington AD, Wilson PC, Marcotte EM, Mascola JR, Ippolito GC, Krammer F, Quake SR, Kwong PD, Georgiou G. Molecular-level analysis of the serum antibody repertoire in young adults before and after seasonal influenza vaccination. Nat Med. 2016;22(12):1456-64. Epub 2016/11/08. doi: 10.1038/nm.4224. PubMed PMID: 27820605; PMCID: PMC5301914.

Lim J, Lynch VM, Edupuganti R, Ellington A, Anslyn EV. Synthesis and structural analyses of phenylethynyl-substituted tris(2-pyridylmethyl)amines and their copper(ii) complexes. Dalton Trans. 2016;45(26):10585-98. Epub 2016/06/07. doi: 10.1039/c6dt00473c. PubMed PMID: 27264275.

Mahmood MA, Hasan MR, Khan UJ, Allen PB, Kim YT, Ellington AD, Iqbal SM. One-step tumor detection from dynamic morphology tracking on aptamer-grafted surfaces. Technology (Singap World Sci). 2015;3(4):194-200. Epub 2016/01/12. doi: 10.1142/s2339547815500089. PubMed PMID: 26753172; PMCID: PMC4703374.

Martini L, Ellington AD, Mansy SS. An in vitro selection for small molecule induced switching RNA molecules. Methods. 2016;106:51-7. Epub 2016/02/24. doi: 10.1016/j.ymeth.2016.02.010. PubMed PMID: 26899430.

McDaniel JR, DeKosky BJ, Tanno H, Ellington AD, Georgiou G. Ultra-high-throughput sequencing of the immune receptor repertoire from millions of lymphocytes. Nat Protoc. 2016;11(3):429-42. Epub 2016/02/06. doi: 10.1038/nprot.2016.024. PubMed PMID: 26844430.

Paff ML, Nuismer SL, Ellington A, Molineux IJ, Bull JJ. Virus wars: using one virus to block the spread of another. PeerJ. 2016;4:e2166. Epub 2016/07/15. doi: 10.7717/peerj.2166. PubMed PMID: 27413636; PMCID: PMC4933091.

Paff ML, Nuismer SL, Ellington AD, Molineux IJ, May RH, Bull JJ. Design and engineering of a transmissible antiviral defense. J Biol Eng. 2016;10:12. Epub 2016/10/19. doi: 10.1186/s13036-016-0033-4. PubMed PMID: 27752283; PMCID: PMC5062863.

Simon AJ, Ellington AD. Recent advances in synthetic biosafety. F1000Res. 2016;5. Epub 2016/09/17. doi: 10.12688/f1000research.8365.1. PubMed PMID: 27635235; PMCID: PMC5007755.

Singh-Blom A, Hughes RA, Ellington AD. Corrigendum to "An amino acid depleted cell-free protein synthesis system for the incorporation of non-canonical amino acid analogs into proteins" [J. Biotechnol. 178 (2014) 12-22]. J Biotechnol. 2016;231:296. Epub 2016/07/30. doi: 10.1016/j.jbiotec.2016.06.031. PubMed PMID: 27470576.

Tack DS, Ellefson JW, Thyer R, Wang B, Gollihar J, Forster MT, Ellington AD. Addicting diverse bacteria to a noncanonical amino acid. Nat Chem Biol. 2016;12(3):138-40. Epub 2016/01/19. doi: 10.1038/nchembio.2002. PubMed PMID: 26780407.

Talukder P, Dedkova LM, Ellington AD, Yakovchuk P, Lim J, Anslyn EV, Hecht SM. Synthesis of alanyl nucleobase amino acids and their incorporation into proteins. Bioorg Med Chem. 2016;24(18):4177-87. Epub 2016/07/28. doi: 10.1016/j.bmc.2016.07.008. PubMed PMID: 27452282; PMCID: PMC4992614.

Wang B, Kluwe CA, Lungu OI, DeKosky BJ, Kerr SA, Johnson EL, Tanno H, Lee CH, Jung J, Rezigh AB, Carroll SM, Reyes AN, Bentz JR, Villanueva I, Altman AL, Davey RA, Ellington AD, Georgiou G. Corrigendum: Facile Discovery of a Diverse Panel of Anti-Ebola Virus Antibodies by Immune Repertoire Mining. Sci Rep. 2016;6:27229. Epub 2016/06/11. doi: 10.1038/srep27229. PubMed PMID: 27282782; PMCID: PMC4901487.

Wang B, Lee CH, Johnson EL, Kluwe CA, Cunningham JC, Tanno H, Crooks RM, Georgiou G, Ellington AD. Discovery of high affinity anti-ricin antibodies by B cell receptor sequencing and by yeast display of combinatorial VH:VL libraries from immunized animals. MAbs. 2016;8(6):1035-44. Epub 2016/05/26. doi: 10.1080/19420862.2016.1190059. PubMed PMID: 27224530; PMCID: PMC4968101.

Zhu Z, Tang Y, Jiang YS, Bhadra S, Du Y, Ellington AD, Li B. Strand-Exchange Nucleic Acid Circuitry with Enhanced Thermo-and Structure- Buffering Abilities Turns Gene Diagnostics Ultra-Reliable and Environmental Compatible. Sci Rep. 2016;6:36605. Epub 2016/11/05. doi: 10.1038/srep36605. PubMed PMID: 27812041; PMCID: PMC5095676.

2015

Allen PB, Khaing Z, Schmidt CE, Ellington AD. 3D Printing with Nucleic Acid Adhesives. ACS Biomater Sci Eng. 2015;1(1):19-26. Epub 2015/05/20. doi: 10.1021/ab500026f. PubMed PMID: 25984570; PMCID: PMC4426351.

Bhadra S, Ellington AD. Design, synthesis, and application of Spinach molecular beacons triggered by strand displacement. Methods Enzymol. 2015;550:215-49. Epub 2015/01/22. doi: 10.1016/bs.mie.2014.10.049. PubMed PMID: 25605388; PMCID: PMC4429879.

Bhadra S, Jiang YS, Kumar MR, Johnson RF, Hensley LE, Ellington AD. Real-time sequence-validated loop-mediated isothermal amplification assays for detection of Middle East respiratory syndrome coronavirus (MERS-CoV). PLoS One. 2015;10(4):e0123126. Epub 2015/04/10. doi: 10.1371/journal.pone.0123126. PubMed PMID: 25856093; PMCID: PMC4391951.

Cammarata MB, Thyer R, Rosenberg J, Ellington A, Brodbelt JS. Structural Characterization of Dihydrofolate Reductase Complexes by Top-Down Ultraviolet Photodissociation Mass Spectrometry. J Am Chem Soc. 2015;137(28):9128-35. Epub 2015/07/01. doi: 10.1021/jacs.5b04628. PubMed PMID: 26125523.

Cunningham JC, Scida K, Kogan MR, Wang B, Ellington AD, Crooks RM. Paper diagnostic device for quantitative electrochemical detection of ricin at picomolar levels. Lab Chip. 2015;15(18):3707-15. Epub 2015/08/01. doi: 10.1039/c5lc00731c. PubMed PMID: 26224395.

DeKosky, BJ, Kojima, T, Rodin, A, Charab, W, Ippolito, GC, Ellington, AD, and Georgiou, G. (2015 Jan). In-depth determination and analysis of the human paired heavy- and light-chain antibody repertoire. Nat Med 21(1):86–91. PMID: 25501908. doi:10.1038/nm.3743

Du Y, Hughes RA, Bhadra S, Jiang YS, Ellington AD, Li B. A Sweet Spot for Molecular Diagnostics: Coupling Isothermal Amplification and Strand Exchange Circuits to Glucometers. Sci Rep. 2015;5:11039. Epub 2015/06/09. doi: 10.1038/srep11039. PubMed PMID: 26050646; PMCID: PMC4458886.

Duclair S, Gautam A, Ellington A, Prasad VR. High-affinity RNA Aptamers Against the HIV-1 Protease Inhibit Both In Vitro Protease Activity and Late Events of Viral Replication. Mol Ther Nucleic Acids. 2015;4:e228. Epub 2015/02/18. doi: 10.1038/mtna.2015.1. PubMed PMID: 25689224; PMCID: PMC4345311.

Ellington AD. Landscape-Based Biology. J Mol Evol. 2015;81(5-6):144-5. Epub 2015/10/21. doi: 10.1007/s00239-015-9706-8. PubMed PMID: 26480829.

Ellington AD. RNA as a conception. Rna. 2015;21(4):608. Epub 2015/03/18. doi: 10.1261/rna.050443.115. PubMed PMID: 25780159; PMCID: PMC4371301.

Enyeart, PJ, Simpson, ZB, Ellington, AD. (2015 Jan 7). A microbial model of economic trading and comparative advantage. J Theor Biol 364:326–343. PMID: 25265557. doi:10.1016/j.jtbi.2014.09.030

Friedman DC, Ellington AD. Industrialization of Biology. ACS Synth Biol. 2015;4(10):1053-5. Epub 2015/10/17. doi: 10.1021/acssynbio.5b00190. PubMed PMID: 26471233.

Goodwin S, Gade AM, Byrom M, Herrera B, Spears C, Anslyn EV, Ellington AD. Next-generation sequencing as input for chemometrics in differential sensing routines. Angew Chem Int Ed Engl. 2015;54(21):6339-42. Epub 2015/04/01. doi: 10.1002/anie.201501822. PubMed PMID: 25826754; PMCID: PMC4426058.

Jiang YS, Bhadra S, Li B, Wu YR, Milligan JN, Ellington AD. Robust strand exchange reactions for the sequence-specific, real-time detection of nucleic acid amplicons. Anal Chem. 2015;87(6):3314-20. Epub 2015/02/25. doi: 10.1021/ac504387c. PubMed PMID: 25708458.

Jung C, Allen PB, Ellington AD. A stochastic DNA walker that traverses a microparticle surface. Nat Nanotechnol. 2016;11(2):157-63. Epub 2015/11/03. doi: 10.1038/nnano.2015.246. PubMed PMID: 26524397; PMCID: PMC4740228.

Jung C, Ellington AD. Synthetic biology: Six pack and stack. Nat Chem. 2015;7(8):617-9. Epub 2015/07/24. doi: 10.1038/nchem.2313. PubMed PMID: 26201734.

Kerr SA, Jackson EL, Lungu OI, Meyer AG, Demogines A, Ellington AD, Georgiou G, Wilke CO, Sawyer SL. Computational and Functional Analysis of the Virus-Receptor Interface Reveals Host Range Trade-Offs in New World Arenaviruses. J Virol. 2015;89(22):11643-53. Epub 2015/09/12. doi: 10.1128/jvi.01408-15. PubMed PMID: 26355089; PMCID: PMC4645654.

Kerr, SA, Jackson, EL, Lungu, OI, Meyer, AG, Demogines, A, Ellington, AD, Georgiou, G, Wilke, CO, Sawyer, SL. (2015 Nov 15). Computational and Functional Analysis of the Virus-Receptor Interface Reveals Host Range Trade-Offs in New World Arenaviruses. J Virol 89:11643–11653. PMID: 26355089. PMCID: PMC4645654. doi:10.1128/JVI.01408-15

Mahmood, MAI, Hasan, MR, Khan, UJM, Allen, PB, Kim, Y-T, Ellington, AD, Iqbal, SM. (2015 Dec). One-step tumor detection from dynamic morphology tracking on aptamer-grafted surfaces. Technology (Singap World Sci) 3(4):194–200. PMID: 26753172. PMCID: PMC4703374. doi:10.1142/S2339547815500089

Martini L, Meyer AJ, Ellefson JW, Milligan JN, Forlin M, Ellington AD, Mansy SS. In Vitro Selection for Small-Molecule-Triggered Strand Displacement and Riboswitch Activity. ACS Synth Biol. 2015;4(10):1144-50. Epub 2015/05/16. doi: 10.1021/acssynbio.5b00054. PubMed PMID: 25978303.

Mayfield JE, Fan S, Wei S, Zhang M, Li B, Ellington AD, Etzkorn FA, Zhang YJ. Chemical Tools To Decipher Regulation of Phosphatases by Proline Isomerization on Eukaryotic RNA Polymerase II. ACS Chem Biol. 2015;10(10):2405-14. Epub 2015/09/04. doi: 10.1021/acschembio.5b00296. PubMed PMID: 26332362; PMCID: PMC4788383.

Meyer AJ, Garry DJ, Hall B, Byrom MM, McDonald HG, Yang X, Yin YW, Ellington AD. Transcription yield of fully 2'-modified RNA can be increased by the addition of thermostabilizing mutations to T7 RNA polymerase mutants. Nucleic Acids Res. 2015;43(15):7480-8. Epub 2015/07/26. doi: 10.1093/nar/gkv734. PubMed PMID: 26209133; PMCID: PMC4551944.

Meyer, AJ, Ellefson, JW, and Ellington, AD. (2015 Oct 16). Directed Evolution of a Panel of Orthogonal T7 RNA Polymerase Variants for in Vivo or in Vitro Synthetic Circuitry. ACS Synth Biol 4(10):1070-6. PMID: 25279711. doi:10.1021/sb500299c

Milligan JN, Ellington AD. Using RecA protein to enhance kinetic rates of DNA circuits. Chem Commun (Camb). 2015;51(46):9503-6. Epub 2015/05/15. doi: 10.1039/c5cc02261d. PubMed PMID: 25967118; PMCID: PMC4446201.

Ploskon E, Wagner SC, Ellington AD, Jewett MC, O'Reilly R, Booth PJ. Controlled assembly of artificial protein-protein complexes via DNA duplex formation. Bioconjug Chem. 2015;26(3):427-34. Epub 2015/01/21. doi: 10.1021/bc500473s. PubMed PMID: 25603321.

Quandt EM, Gollihar J, Blount ZD, Ellington AD, Georgiou G, Barrick JE. Fine-tuning citrate synthase flux potentiates and refines metabolic innovation in the Lenski evolution experiment. Elife. 2015;4. Epub 2015/10/16. doi: 10.7554/eLife.09696. PubMed PMID: 26465114; PMCID: PMC4718724.

Stovall GM, Bedenbaugh RS, Singh S, Meyer AJ, Hatala PJ, Ellington AD, Hall B. In vitro selection using modified or unnatural nucleotides. Curr Protoc Nucleic Acid Chem. 2014;56:9.6.1-33. Epub 2015/01/22. doi: 10.1002/0471142700.nc0906s56. PubMed PMID: 25606981; PMCID: PMC4068349.

Thyer, R, Robotham, SA, Brodbelt, JS, and Ellington, AD. (2015 Jan 14). Evolving tRNA(Sec) for efficient canonical incorporation of selenocysteine. J Am Chem Soc 137(1):46–49. PMID: 25521771. PMCID: PMC4432777. doi:10.1021/ja510695g

Wang B, Kluwe CA, Lungu OI, DeKosky BJ, Kerr SA, Johnson EL, Tanno H, Lee CH, Jung J, Rezigh AB, Carroll SM, Reyes AN, Bentz JR, Villanueva I, Altman AL, Davey RA, Ellington AD, Georgiou G. Facile Discovery of a Diverse Panel of Anti-Ebola Virus Antibodies by Immune Repertoire Mining. Sci Rep. 2015;5:13926. Epub 2015/09/12. doi: 10.1038/srep13926. PubMed PMID: 26355042; PMCID: PMC4564727.

2014

Bhadra S, Codrea V, Ellington AD, 2014. G-quadruplex-generating polymerase chain reaction for visual colorimetric detection of amplicons. Anal Biochem 445, 38–40. doi:10.1016/j.ab.2013.10.010

Bhadra S, Ellington AD, 2014a. A Spinach molecular beacon triggered by strand displacement. RNA (epub ahead of print). doi:10.1261/rna.045047.114

Bhadra S, Ellington AD, 2014b. Design and application of cotranscriptional non-enzymatic RNA circuits and signal transducers. Nucleic Acids Res 42, e58. doi:10.1093/nar/gku074

Byrom M, Bhadra S, Jiang YS, Ellington AD, 2014. Exquisite allele discrimination by toehold hairpin primers. Nucleic Acids Res (epub ahead of print). doi:10.1093/nar/gku558

Cannon JR, Kluwe C, Ellington A, Brodbelt JS, 2014. Characterization of green fluorescent proteins by 193 nm ultraviolet photodissociation mass spectrometry. Proteomics 14, 1165–1173. doi:10.1002/pmic.201300364

Collins JJ, Maxon M, Ellington A, Fussenegger M, Weiss R, Sauro H, 2014. Synthetic biology How best to build a cell. Nature 509, 155–157.

Deschner R, Tang H, Allen P, Hall C, Hlis R, Ellington A, Willson CG, 2014. Progress Report on the Generation of Polyfunctional Microscale Particles for Programmed Self-Assembly. Chem Mater 26, 1457–1462. doi:10.1021/cm403637v

Du Y, Lim BJ, Li B, Jiang YS, Sessler JL, Ellington AD, 2014. Reagentless, Ratiometric Electrochemical DNA Sensors with Improved Robustness and Reproducibility. Anal Chem (epub ahead of print). doi:10.1021/ac5025254

Ellefson JW, Meyer AJ, Hughes RA, Cannon JR, Brodbelt JS, Ellington AD, 2014. Directed evolution of genetic parts and circuits by compartmentalized partnered replication. Nat Biotechnol 32, 97–101. doi:10.1038/nbt.2714

Enyeart PJ, Mohr G, Ellington AD, Lambowitz AM, 2014. Biotechnological applications of mobile group II introns and their reverse transcriptases gene targeting, RNA-seq, and non-coding RNA analysis. Mob DNA 5, 2. doi:10.1186/1759-8753-5-2

Gao L, He J, Xu W, Zhang J, Hui J, Guo Y, Li W, Yu C, 2014. Ultrasensitive electrochemical biosensor based on graphite oxide, Prussian blue, and PTC-NH2 for the detection of α2,6-sialylated glycans in human serum. Biosens Bioelectron (epub ahead of print). doi:10.1016/j.bios.2014.06.031

Gollihar J, Levy M, Ellington AD, 2014. Many paths to the origin of life. Science 343, 259–260. doi:10.1126/science.1246704

Hammerling MJ, Ellefson JW, Boutz DR, Marcotte EM, Ellington AD, Barrick JE, 2014. Bacteriophages use an expanded genetic code on evolutionary paths to higher fitness. Nat Chem Biol 10, 178–180. doi:10.1038/nchembio.1450

Jiang YS, Bhadra S, Li B, Ellington AD, 2014. Mismatches improve the performance of strand-displacement nucleic Acid circuits. Angew Chem Int Ed Engl 53, 1845–1848. doi:10.1002/anie.201307418

Jung C, Ellington AD, 2014. Diagnostic Applications of Nucleic Acid Circuits. Acc Chem Res (epub ahead of print). doi:10.1021/ar500059c

Lavinder JJ, Wine Y, Giesecke C, Ippolito GC, Horton AP, Lungu OI, Hoi KH, DeKosky BJ, Murrin EM, Wirth MM, Ellington AD, Dorner T, Marcotte EM, Boutz DR, Georgiou G, 2014. Identification and characterization of the constituent human serum antibodies elicited by vaccination. Proc Natl Acad Sci U S A 111, 2259–2264. doi:10.1073/pnas.1317793111

Lu WC, Ellington AD, 2014. Design and Selection of a Synthetic Operon. ACS Synth Biol (epub ahead of print). doi:10.1021/sb400160m

Lu WC, Levy M, Kincaid R, Ellington AD, 2014. Directed evolution of the substrate specificity of biotin ligase. Biotechnol Bioeng 111, 1071–1081. doi:10.1002/bit.25176

Melancon MP, Zhou M, Zhang R, Xiong C, Allen P, Wen X, Huang Q, Wallace M, Myers JN, Stafford RJ, Liang D, Ellington AD, Li C, 2014. Selective uptake and imaging of aptamer- and antibody-conjugated hollow nanospheres targeted to epidermal growth factor receptors overexpressed in head and neck cancer. ACS Nano 8, 4530–4538. doi:10.1021/nn406632u

Meyer AG, Sawyer SL, Ellington AD, Wilke CO, 2014. Analyzing machupo virus-receptor binding by molecular dynamics simulations. PeerJ 2, e266. doi:10.7717/peerj.266

Meyer AJ, Ellefson JW, Ellington AD, 2014. Library generation by gene shuffling. Curr Protoc Mol Biol 105, Unit 15.12. doi:10.1002/0471142727.mb1512s105

O’Connell JD, Tsechansky M, Royall A, Boutz DR, Ellington AD, Marcotte EM, 2014. A proteomic survey of widespread protein aggregation in yeast. Mol Biosyst 10, 851–861. doi:10.1039/c3mb70508k

Quandt EM, Deatherage DE, Ellington AD, Georgiou G, Barrick JE, 2014. Recursive genomewide recombination and sequencing reveals a key refinement step in the evolution of a metabolic innovation in Escherichia coli. Proc Natl Acad Sci U S A 111, 2217–2222. doi:10.1073/pnas.1314561111

Singh-Blom A, Hughes RA, Ellington AD, 2014. An amino acid depleted cell-free protein synthesis system for the incorporation of non-canonical amino acid analogs into proteins. J Biotechnol 178, 12–22. doi:10.1016/j.jbiotec.2014.02.009

Stovall GM, Bedenbaugh RS, Singh S, Meyer AJ, Hatala PJ, Ellington AD, Hall B, 2014. In Vitro Selection Using Modified or Unnatural Nucleotides, in: Curr Protoc Nucleic Acid Chem. p. Unit 9.6.1–Unit9.6.33.

Xu J, Tack D, Hughes RA, Ellington AD, Gray JJ, 2014. Structure-based non-canonical amino acid design to covalently crosslink an antibody-antigen complex. J Struct Biol 185, 215–222. doi:10.1016/j.jsb.2013.05.003

Zhao A, Tsechansky M, Ellington AD, Marcotte EM, 2014. Revisiting and revising the purinosome. Mol Biosyst 10, 369–374. doi:10.1039/c3mb70397e

2013

Allen PB, Chen X, Simpson ZB, Ellington AD, 2013. Modeling scalable pattern generation in DNA reaction networks. Nat Computing (epub ahead of print). doi:10.1007/s11047-013-9392-7

Chen X, Briggs N, McLain JR, Ellington AD, 2013. Stacking nonenzymatic circuits for high signal gain. Proc Natl Acad Sci U S A 110, 5386–5391. doi:10.1073/pnas.1222807110

Chirieleison SM, Allen PB, Simpson ZB, Ellington AD, Chen X, 2013. Pattern transformation with DNA circuits. Nat Chem 5, 1000–1005. doi:10.1038/nchem.1764

DeKosky BJ, Ippolito GC, Deschner RP, Lavinder JJ, Wine Y, Rawlings BM, Varadarajan N, Giesecke C, Dörner T, Andrews SF, Wilson PC, Hunicke-Smith SP, Willson CG, Ellington AD, Georgiou G, 2013. High-throughput sequencing of the paired human immunoglobulin heavy and light chain repertoire. Nat Biotechnol 31, 166–169. doi:10.1038/nbt.2492

Der BS, Kluwe C, Miklos AE, Jacak R, Lyskov S, Gray JJ, Georgiou G, Ellington AD, Kuhlman B, 2013. Alternative computational protocols for supercharging protein surfaces for reversible unfolding and retention of stability. PLoS One 8, e64363. doi:10.1371/journal.pone.0064363

Ellington AD, Ellefson J, 2013. The genome as the unit of engineering. The science and applications of synthetic and systems biology 150–159.

Enyeart PJ, Chirieleison SM, Dao MN, Perutka J, Quandt EM, Yao J, Whitt JT, Keatinge-Clay AT, Lambowitz AM, Ellington AD, 2013a. Generalized bacterial genome editing using mobile group II introns and Cre-lox. Mol Syst Biol 9, 685. doi:10.1038/msb.2013.41

Jiang YS, Li B, Milligan JN, Bhadra S, Ellington AD, 2013. Real-time detection of isothermal amplification reactions with thermostable catalytic hairpin assembly. J Am Chem Soc 135, 7430–7433. doi:10.1021/ja4023978

Kang Y, Lu A, Ellington AD, Jewett MC, O’Reilly RK, 2013. Effect of Complementary Nucleobase Interactions on the Copolymer Composition of RAFT Copolymerizations. ACS Macro Lett 2, 581–586. doi:10.1021/mz4001833

Ledbetter MP, Hwang TW, Stovall GM, Ellington AD, 2013. Continuous in vitro evolution of a ribozyme ligase - a model experiment for the evolution of a biomolecule. Biochem Mol Biol Educ 41, 433–442. doi:10.1002/bmb.20742

Lu WC, Ellington AD, 2013. In vitro selection of proteins via emulsion compartments. Methods 60, 75–80. doi:10.1016/j.ymeth.2012.03.008

Luo Y, Yogesha SD, Cannon JR, Yan W, Ellington AD, Brodbelt JS, Zhang Y, 2013. novel modifications on C-terminal domain of RNA polymerase II can fine-tune the phosphatase activity of Ssu72. ACS Chem Biol 8, 2042–2052. doi:10.1021/cb400229c

Maranhao AC, Ellington AD, 2013. Endowing cells with logic and memory. Nat Biotechnol 31, 413–415. doi:10.1038/nbt.2573

Quandt EM, Ellington AD, 2013. Directed evolution, in: The Princeton Guide to Evolution. pp. Unit 7, p774–Unit 7, p779.

Robotham SA, Kluwe C, Cannon JR, Ellington A, Brodbelt JS, 2013. De novo sequencing of peptides using selective 351 nm ultraviolet photodissociation mass spectrometry. Anal Chem 85, 9832–9838. doi:10.1021/ac402309h

Saldanha RJ, Pemberton A, Shiflett P, Perutka J, Whitt JT, Ellington AD, Lambowitz AM, Kramer R, Taylor D, Lamkin TJ, 2013. Rapid targeted gene disruption in Bacillus anthracis. BMC Biotechnol 13, 72. doi:10.1186/1472-6750-13-72

Scida K, Li B, Ellington AD, Crooks RM, 2013. DNA detection using origami paper analytical devices. Anal Chem 85, 9713–9720. doi:10.1021/ac402118a

Singh-Blom A, Hughes RA, Ellington AD, 2013. Residue-specific incorporation of unnatural amino acids into proteins in vitro and in vivo. Methods Mol Biol 978, 93–114. doi:10.1007/978-1-62703-293-3_7

Villanueva I, Pappas T, Kluwe C, Kerr S, Allen R, Georgiou G, Ellington AD, Bentz J, Davey R, Altman A, 2013. A multiplexed approach for rapid filovirus detection.

Wan Y, Tamuly D, Allen PB, Kim YT, Bachoo R, Ellington AD, Iqbal SM, 2013. Proliferation and migration of tumor cells in tapered channels. Biomed Microdevices 15, 635–643. doi:10.1007/s10544-012-9721-0

Wilson RH, Morton SK, Deiderick H, Gerth ML, Paul HA, Gerber I, Patel A, Ellington AD, Hunicke-Smith SP, Patrick WM, 2013. Engineered DNA ligases with improved activities in vitro. Protein Eng Des Sel 26, 471–478. doi:10.1093/protein/gzt024

Wine Y, Boutz DR, Lavinder JJ, Miklos AE, Hughes RA, Hoi KH, Jung ST, Horton AP, Murrin EM, Ellington AD, Marcotte EM, Georgiou G, 2013. Molecular deconvolution of the monoclonal antibodies that comprise the polyclonal serum response. Proc Natl Acad Sci U S A 110, 2993–2998. doi:10.1073/pnas.1213737110

Zhao A, Tsechansky M, Swaminathan J, Cook L, Ellington AD, Marcotte EM, 2013. Transiently transfected purine biosynthetic enzymes form stress bodies. PLoS One 8, e56203. doi:10.1371/journal.pone.0056203

2012

Allen PB, Arshad SA, Li B, Chen X, Ellington AD, 2012a. DNA circuits as amplifiers for the detection of nucleic acids on a paperfluidic platform. Lab Chip 12, 2951–2958. doi:10.1039/c2lc40373k

Allen PB, Chen X, Ellington AD, 2012b. Spatial control of DNA reaction networks by DNA sequence. Molecules 17, 13390–13402. doi:10.3390/molecules171113390

Allen PB, Chen X, Simpson ZB, Ellington AD, 2012c. Modeling scalable pattern generation in DNA reaction networks. Artif Life 13, 441–448. doi:10.7551/978-0-262-31050-5-ch058

Cha HJ, Byrom M, Mead PE, Ellington AD, Wallingford JB, Marcotte EM, 2012. Evolutionarily repurposed networks reveal the well-known antifungal drug thiabendazole to be a novel vascular disrupting agent. PLoS Biol 10, e1001379. doi:10.1371/journal.pbio.1001379

Chen X, 2012. Expanding the rule set of DNA circuitry with associative toehold activation. J Am Chem Soc 134, 263–271. doi:10.1021/ja206690a

Cho EJ, Xia S, Ma LC, Robertus J, Krug RM, Anslyn EV, Montelione GT, Ellington AD, 2012. Identification of influenza virus inhibitors targeting NS1A utilizing fluorescence polarization-based high-throughput assay. J Biomol Screen 17, 448–459. doi:10.1177/1087057111431488

Davidson EA, Meyer AJ, Ellefson JW, Levy M, Ellington AD, 2012. An in vitro autogene. ACS Synth Biol 1, 190–196. doi:10.1021/sb3000113

Ellington AD, 2012. Origins for everyone. Evolution (N Y) 5, 361–366. doi:10.1007/s12052-012-0440-z

Hughes RA, Miklos AE, Ellington AD, 2012. Enrichment of error-free synthetic DNA sequences by CEL I nuclease, in: Curr Protoc Mol Biol. p. Unit3.24.

Ilyas A, Asghar W, Allen PB, Duhon H, Ellington AD, Iqbal SM, 2012. Electrical detection of cancer biomarker using aptamers with nanogap break-junctions. Nanotechnology 23, 275502. doi:10.1088/0957-4484/23/27/275502

Ippolito GC, Hoi KH, Reddy ST, Carroll SM, Ge X, Rogosch T, Zemlin M, Shultz LD, Ellington AD, Vandenberg CL, Georgiou G, 2012. Antibody repertoires in humanized NOD-scid-IL2Rγ(null) mice and human B cells reveals human-like diversification and tolerance checkpoints in the mouse. PLoS One 7, e35497. doi:10.1371/journal.pone.0035497

Jiang Y, Li B, Chen X, Ellington AD, 2012. Coupling two different nucleic acid circuits in an enzyme-free amplifier. Molecules 17, 13211–13220. doi:10.3390/molecules171113211

Li B, Chen X, Ellington AD, 2012a. Adapting enzyme-free DNA circuits to the detection of loop-mediated isothermal amplification reactions. Anal Chem 84, 8371–8377. doi:10.1021/ac301944v

Li B, Ellington AD, 2012. Electrochemical techniques as a powerful readout methods for aptamer-based biosensors. Conjugates and Sensors, RSC Biomolecular Sciences Series 211–241. doi:10.1039/9781849734936-00211

Li B, Jiang Y, Chen X, Ellington AD, 2012b. Probing spatial organization of DNA strands using enzyme-free hairpin assembly circuits. J Am Chem Soc 134, 13918–13921. doi:10.1021/ja300984b

Liu C, Ellington AD, 2012. DNA nanotechnology From biology and beyond, in: Nucleic Acids Nanotechnology, Nucleic Acids and Molecular Biology Series. p. (book chapter).

Magalhães ML, Byrom M, Yan A, Kelly L, Li N, Furtado R, Palliser D, Ellington AD, Levy M, 2012. A general RNA motif for cellular transfection. Mol Ther 20, 616–624. doi:10.1038/mt.2011.277

Mascini, M., Palchetti, I., Tombelli, S., 2012. Nucleic Acid and Peptide Aptamers: Fundamentals and Bioanalytical Aspects. Angew. Chem. Int. Ed. 51, 1316–1332. doi:10.1002/anie.201006630

Meyer AJ, Ellefson JW, Ellington AD, 2012. Abiotic self-replication. Acc Chem Res 45, 2097–2105. doi:10.1021/ar200325v

Miklos AE, Hughes RA, Ellington AD, 2012a. Design and assembly of large synthetic DNA constructs, in: Curr Protoc Mol Biol. p. Unit3.23.

Miklos AE, Kluwe C, Der BS, Pai S, Sircar A, Hughes RA, Berrondo M, Xu J, Codrea V, Buckley PE, Calm AM, Welsh HS, Warner CR, Zacharko MA, Carney JP, Gray JJ, Georgiou G, Kuhlman B, Ellington AD, 2012b. Structure-based design of supercharged, highly thermoresistant antibodies. Chem Biol 19, 449–455. doi:10.1016/j.chembiol.2012.01.018

O’Connell JD, Zhao A, Ellington AD, Marcotte EM, 2012. Dynamic reorganization of metabolic enzymes into intracellular bodies. Annu Rev Cell Dev Biol 28, 89–111. doi:10.1146/annurev-cellbio-101011-155841

Opazo F, Levy M, Byrom M, Schäfer C, Geisler C, Groemer TW, Ellington AD, Rizzoli SO, 2012. Aptamers as potential tools for super-resolution microscopy. Nat Methods 9, 938–939. doi:10.1038/nmeth.2179

Ray P, Cheek MA, Sharaf ML, Li N, Ellington AD, Sullenger BA, Shaw BR, White RR, 2012. Aptamer-mediated delivery of chemotherapy to pancreatic cancer cells. Nucleic Acid Ther 22, 295–305. doi:10.1089/nat.2012.0353

Romero PA, Stone E, Lamb C, Chantranupong L, Krause A, Miklos AE, Hughes RA, Fechtel B, Ellington AD, Arnold FH, Georgiou G, 2012. SCHEMA-designed variants of human Arginase I and II reveal sequence elements important to stability and catalysis. ACS Synth Biol 1, 221–228. doi:10.1021/sb300014t

Tang H, Deschner R, Allen P, Cho Y, Sermas P, Maurer A, Ellington AD, Willson CG, 2012a. Analysis of DNA-guided self-assembly of microspheres using imaging flow cytometry. J Am Chem Soc 134, 15245–15248. doi:10.1021/ja3066896

Tang H, Deschner R, Cho Y, Sermas P, Maurer A, Allen P, Ellington AD, Willson CG, 2012b. Investigation of Poly(methyl methacrylate) Copolymers for DNA Conjugation. PMSE Preprints Vol. 106.

Wan Y, Liu Y, Allen PB, Asghar W, Mahmood MA, Tan J, Duhon H, Kim YT, Ellington AD, Iqbal SM, 2012a. Capture, isolation and release of cancer cells with aptamer-functionalized glass bead array. Lab Chip 12, 4693–4701. doi:10.1039/c2lc21251j

Wan Y, Mahmood MA, Li N, Allen PB, Kim YT, Bachoo R, Ellington AD, Iqbal SM, 2012b. Nanotextured substrates with immobilized aptamers for cancer cell isolation and cytology. Cancer 118, 1145–1154. doi:10.1002/cncr.26349

Zhang M, Wang XJ, Chen X, Bowman ME, Luo Y, Noel JP, Ellington AD, Etzkorn FA, Zhang Y, 2012. Structural and kinetic analysis of prolyl-isomerization-phosphorylation cross-talk in the CTD code. ACS Chem Biol 7, 1462–1470. doi:10.1021/cb3000887

2011

Alicea I, Marvin JS, Miklos AE, Ellington AD, Looger LL, Schreiter ER, 2011. Structure of the Escherichia coli phosphonate binding protein PhnD and rationally optimized phosphonate biosensors. J Mol Biol 414, 356–369. doi:10.1016/j.jmb.2011.09.047

Allen PB, Ellington AD, 2011. Sequential injection analysis for optimization of molecular biology reactions. Anal Chem 83, 2194–2200. doi:10.1021/ac103098u

Bhadra S, Pothukuchy A, Ellington AD, 2011. Ribozymes as molecular biology reagents. From nucleic acids sequences to molecular medicine: RNA technologies 293–312. doi:10.1007/978-3-642-27426-8_12

Ellington AD, 2011. Amorphous Computation with a DNA-based Edge Detector.

Enyeart PJ, Ellington AD, 2011. Synthetic biology a yeast for all reasons. Nature 477, 413–414. doi:10.1038/477413a

Hargrove AE, Ellington AD, Anslyn EV, Sessler JL, 2011. Chemical functionalization of oligodeoxynucleotides with multiple boronic acids for the polyvalent binding of saccharides. Bioconjug Chem 22, 388–396. doi:10.1021/bc100376x

Hughes RA, Miklos AE, Ellington AD, 2011. Gene synthesis methods and applications. Methods Enzymol 498, 277–309. doi:10.1016/B978-0-12-385120-8.00012-7

Li B, Ellington AD, Chen X, 2011. Rational, modular adaptation of enzyme-free DNA circuits to multiple detection methods. Nucleic Acids Res 39, e110. doi:10.1093/nar/gkr504

Li N, Nguyen HH, Byrom M, Ellington AD, 2011. Inhibition of cell proliferation by an anti-EGFR aptamer. PLoS One 6, e20299. doi:10.1371/journal.pone.0020299

Meyer AJ, Ellington AD, 2011. Molecular evolution picks up the PACE. Nat Biotechnol 29, 502–503. doi:10.1038/nbt.1884

Ramalingam D, Duclair S, Datta SA, Ellington AD, Rein A, Prasad VR, 2011. RNA aptamers directed to human immunodeficiency virus type 1 Gag polyprotein bind to the matrix and nucleocapsid domains and inhibit virus production. J Virol 85, 305–314. doi:10.1128/JVI.02626-09

Reveal B, Garcia C, Ellington A, Macdonald PM, 2011. Multiple RNA binding domains of Bruno confer recognition of diverse binding sites for translational repression. RNA Biol 8, 1047–1060. doi:10.4161/rna.8.6.17542

Singh RR, Bingling L, Ellington AD, Hassibi A, 2011. A CMOS Σ-Δ photodetector array for bioluminescence-based DNA sequencing, in: VLSI Circuits (VLSIC), 2011 Symposium. pp. 96–97.

Stewart S, Syrett A, Pothukuchy A, Bhadra S, Ellington AD, Anslyn E, 2011. Identifying protein variants with cross-reactive aptamer arrays. ChemBioChem 12, 2021–2024. doi:10.1002/cbic.201100046

You L, Cho EJ, Leavitt J, Ma LC, Montelione GT, Anslyn EV, Krug RM, Ellington AD, Robertus JD, 2011. Synthesis and evaluation of quinoxaline derivatives as potential influenza NS1A protein inhibitors. Bioorg Med Chem Lett 21, 3007–3011. doi:10.1016/j.bmcl.2011.03.042

2010

Chen X, Ellington AD, 2010. Shaping up nucleic acid computation. Curr Opin Biotechnol 21, 392–400. doi:10.1016/j.copbio.2010.05.003

Codrea V, Hayner M, Hall B, Jhaveri S, Ellington AD, 2010. In vitro selection of RNA aptamers to a small molecule target, in: Curr Protoc Nucleic Acid Chem. p. Unit 9.5.1–Unit 9.523.

Connell JL, Wessel AK, Parsek MR, Ellington AD, Whiteley M, Shear JB, 2010. Probing prokaryotic social behaviors with bacterial lobster traps. MBio 1(4). doi:10.1128/mBio.00202-10

Davidson EA, VAN Blarcom T, Levy M, Ellington AD, 2010. Emulsion based selection of t7 promoters of varying activity. Pac Symp Biocomput 433–443.

Eckhoff G, Codrea V, Ellington AD, Chen X, 2010. Beyond allostry Catalytic regulation of a deoxyribozyme through an entropy-driven DNA amplifier. Journal of Systems Chemistry 1, 13. doi:10.1186/1759-2208-1-13

Gardner MW, Li N, Ellington AD, Brodbelt JS, 2010. Infrared multiphoton dissociation of small-interfering RNA anions and cations. J Am Soc Mass Spectrom 21, 580–591. doi:10.1016/j.jasms.2009.12.011

Ge X, Mazor Y, Hunicke-Smith SP, Ellington AD, Georgiou G, 2010. Rapid construction and characterization of synthetic antibody libraries without DNA amplification. Biotechnol Bioeng 106, 347–357. doi:10.1002/bit.22712

Hall B, Arshad S, Seo K, Bowman C, Corley M, Jhaveri SD, Ellington AD, 2010. In vitro selection of RNA aptamers to a protein target by filter immobilization, in: Curr Protoc Nucleic Acid Chem. p. Unit 9.3.1–Unit 9.327.

Hughes RA, Ellington AD, 2010. Rational design of an orthogonal tryptophanyl nonsense suppressor tRNA. Nucleic Acids Res 38, 6813–6830. doi:10.1093/nar/gkq521

Keefe AD, Pai S, Ellington AD, 2010. Aptamers as therapeutics. Nat Rev Drug Discov 9, 537–550. doi:10.1038/nrd3141

Kluwe C, Ellington AD, 2010. Evolution. RNA GPS. Science 330, 330–331. doi:10.1126/science.1197667

Larson T, Li N, Ellington AD, Sokilov K, 2010. Rapid conjugation of nucleic acids to gold nanoparticles for cancer cell targeting.

Lee J, Icoz K, Roberts A, Ellington AD, Savran CA, 2010. Diffractometric detection of proteins using microbead-based rolling circle amplification. Anal Chem 82, 197–202. doi:10.1021/ac901716d

Li N, Larson T, Nguyen HH, Sokolov KV, Ellington AD, 2010. Directed evolution of gold nanoparticle delivery to cells. Chem Commun (Camb) 46, 392–394. doi:10.1039/b920865h

Manickam A, Chevalier A, McDermott M, Ellington AD, Hassibi A, 2010. A CMOS Electrochemical Impedance Spectroscopy (EIS) Biosensor Array. IEEE Trans Biomed Circuits Syst 4, 379–390. doi:10.1109/TBCAS.2010.2081669

Reddy ST, Ge X, Miklos AE, Hughes RA, Kang SH, Hoi KH, Chrysostomou C, Hunicke-Smith SP, Iverson BL, Tucker PW, Ellington AD, Georgiou G, 2010. Monoclonal antibodies isolated without screening by analyzing the variable-gene repertoire of plasma cells. Nat Biotechnol 28, 965–969. doi:10.1038/nbt.1673

Tipps ME, Lawshe JE, Ellington AD, Mihic SJ, 2010. Identification of novel specific allosteric modulators of the glycine receptor using phage display. J Biol Chem 285, 22840–22845. doi:10.1074/jbc.M110.130815

Wan Y, Kim YT, Li N, Cho SK, Bachoo R, Ellington AD, Iqbal SM, 2010. Surface-immobilized aptamers for cancer cell isolation and microscopic cytology. Cancer Res 70, 9371–9380. doi:10.1158/0008-5472.CAN-10-0568

Wang Y, Khaing ZZ, Li N, Hall B, Schmidt CE, Ellington AD, 2010. Aptamer antagonists of myelin-derived inhibitors promote axon growth. PLoS One 5, e9726. doi:10.1371/journal.pone.0009726

2009