Publications

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

 

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

 

2008

 

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

 

2007

Bacher JM, Ellington AD, 2007. Global incorporation of unnatural amino acids in Escherichia coli. Methods Mol Biol 352, 23–34. doi:10.1385/1-59745-187-8:23

Chen X, Li N, Ellington AD, 2007. Ribozyme catalysis of metabolism in the RNA world. Chem Biodivers 4, 633–655. doi:10.1002/cbdv.200790055

Cho EJ, Ellington AD, 2007. Optimization of the biological component of a bioelectrochemical cell. Bioelectrochemistry 70, 165–172. doi:10.1016/j.bioelechem.2006.03.031

Chu T, Ebright J, Ellington AD, 2007. Using aptamers to identify and enter cells. Curr Opin Mol Ther 9, 137–144.

Davidson EA, Ellington AD, 2007. Synthetic RNA circuits. Nat Chem Biol 3, 23–28. doi:10.1038/nchembio846

Ellington AD, 2007. Whats so great about RNA. ACS Chem Biol 2, 445–448. doi:10.1021/cb700139t

Ellington AD, Ebright J, Chu T, Levy M, 2007. Using aptamers for cell-specific labeling and delivery. Am Assoc Cancer Res Educ Book 51–55.

Hall B, Hesselberth JR, Ellington AD, 2007. Computational selection of nucleic acid biosensors via a slip structure model. Biosens Bioelectron 22, 1939–1947. doi:10.1016/j.bios.2006.08.019

Sokolov K, Nida D, Descour M, Lacy A, Levy M, Hall B, Dharmawardhane S, Ellington AD, Korgel B, Richards-Kortum R, 2007. Molecular optical imaging of the therapeutic targets of cancer. Adv Cancer Res 96, 299–344.

Sooter LJ, Gates-Shannon P, Ellington AD, 2007. Automated assessment of the DNA-binding capacity of a proteome by in vitro selection. JALA 12, 135–142. doi:10.1016/j.jala.2007.02.003

Yang L, Fung CW, Cho EJ, Ellington AD, 2007. Real-time rolling circle amplification for protein detection. Anal Chem 79, 3320–3329. doi:10.1021/ac062186b

 

2006

Bacher JM, Ellington AD, 2007. Global incorporation of unnatural amino acids in Escherichia coli. Methods Mol Biol 352, 23–34. doi:10.1385/1-59745-187-8:23

Chen X, Li N, Ellington AD, 2007. Ribozyme catalysis of metabolism in the RNA world. Chem Biodivers 4, 633–655. doi:10.1002/cbdv.200790055

Cho EJ, Ellington AD, 2007. Optimization of the biological component of a bioelectrochemical cell. Bioelectrochemistry 70, 165–172. doi:10.1016/j.bioelechem.2006.03.031

Chu T, Ebright J, Ellington AD, 2007. Using aptamers to identify and enter cells. Curr Opin Mol Ther 9, 137–144.

Davidson EA, Ellington AD, 2007. Synthetic RNA circuits. Nat Chem Biol 3, 23–28. doi:10.1038/nchembio846

Ellington AD, 2007. Whats so great about RNA. ACS Chem Biol 2, 445–448. doi:10.1021/cb700139t

Ellington AD, Ebright J, Chu T, Levy M, 2007. Using aptamers for cell-specific labeling and delivery. Am Assoc Cancer Res Educ Book 51–55.

Hall B, Hesselberth JR, Ellington AD, 2007. Computational selection of nucleic acid biosensors via a slip structure model. Biosens Bioelectron 22, 1939–1947. doi:10.1016/j.bios.2006.08.019

Sokolov K, Nida D, Descour M, Lacy A, Levy M, Hall B, Dharmawardhane S, Ellington AD, Korgel B, Richards-Kortum R, 2007. Molecular optical imaging of the therapeutic targets of cancer. Adv Cancer Res 96, 299–344.

Sooter LJ, Gates-Shannon P, Ellington AD, 2007. Automated assessment of the DNA-binding capacity of a proteome by in vitro selection. JALA 12, 135–142. doi:10.1016/j.jala.2007.02.003

Yang L, Fung CW, Cho EJ, Ellington AD, 2007. Real-time rolling circle amplification for protein detection. Anal Chem 79, 3320–3329. doi:10.1021/ac062186b

 

2005

Bacher JM, Ellington AD, 2007. Global incorporation of unnatural amino acids in Escherichia coli. Methods Mol Biol 352, 23–34. doi:10.1385/1-59745-187-8:23

Chen X, Li N, Ellington AD, 2007. Ribozyme catalysis of metabolism in the RNA world. Chem Biodivers 4, 633–655. doi:10.1002/cbdv.200790055

Cho EJ, Ellington AD, 2007. Optimization of the biological component of a bioelectrochemical cell. Bioelectrochemistry 70, 165–172. doi:10.1016/j.bioelechem.2006.03.031

Chu T, Ebright J, Ellington AD, 2007. Using aptamers to identify and enter cells. Curr Opin Mol Ther 9, 137–144.

Davidson EA, Ellington AD, 2007. Synthetic RNA circuits. Nat Chem Biol 3, 23–28. doi:10.1038/nchembio846

Ellington AD, 2007. Whats so great about RNA. ACS Chem Biol 2, 445–448. doi:10.1021/cb700139t

Ellington AD, Ebright J, Chu T, Levy M, 2007. Using aptamers for cell-specific labeling and delivery. Am Assoc Cancer Res Educ Book 51–55.

Hall B, Hesselberth JR, Ellington AD, 2007. Computational selection of nucleic acid biosensors via a slip structure model. Biosens Bioelectron 22, 1939–1947. doi:10.1016/j.bios.2006.08.019

Sokolov K, Nida D, Descour M, Lacy A, Levy M, Hall B, Dharmawardhane S, Ellington AD, Korgel B, Richards-Kortum R, 2007. Molecular optical imaging of the therapeutic targets of cancer. Adv Cancer Res 96, 299–344.

Sooter LJ, Gates-Shannon P, Ellington AD, 2007. Automated assessment of the DNA-binding capacity of a proteome by in vitro selection. JALA 12, 135–142. doi:10.1016/j.jala.2007.02.003

Yang L, Fung CW, Cho EJ, Ellington AD, 2007. Real-time rolling circle amplification for protein detection. Anal Chem 79, 3320–3329. doi:10.1021/ac062186b