THe Ellington lab

What evolves here changes the world


The Ellington lab is an idea factory, where your ideas are welcome.


Throughout its existence, the Ellington Lab has generated impactful new technologies and approaches.  Currently, we are working in several different areas, including: 

  • Developing novel genetic codes and synthetic organisms based on engineering the translation apparatus.  Most recently, post-doctoral fellow Ross Thyer has generated a seleno-Coli capable of making proteins with diselenide bonds (Thyer et al. (2018), Nature Biotechnology, 36:624).

  • Developing novel point-of-care diagnostics based on isothermal amplification and DNA computation.  Most recently, assistant research professor Sanchita Bhadra has developed an assay for typing mosquitoes in the field, with concomitant implications for surveying for Zika and other arthropod-borne diseases (Bhadra et al. (2018), PLoS Neglected and Tropical Diseases, 12:e0006771).

  • Developing new methods for scalable assembly of protein architectures and programmed biomaterials.  Most recently, post-doctoral fellow Anna Simon has generated novel protein architectures based on combining supercharged proteins (Simon et al. (2018), bioRxiv,

To best way to experience the range of innovative projects we carry out is to come by and check us out.  We have an extremely interdisciplinary atmosphere, love to collaborate, and have never met a technology we didn’t like.  We’re in the heart of Texas; are fronted by the Center for Systems and Synthetic Biology, which is filled with like-minded PIs and researchers; maintain our own Gene Synthesis Facility capable of producing 10 kb constructs on demand; and boast a technical staff that keeps everything going supremely well.

Drawing inspiration from the words of our alma mater, Microsoft, and journalist Hunter Thompson, we aim to ride this strange torpedo of science to the end of the known world, and beyond.

Here, there be dragons.


September 7, 2016: Andre's latest paper on evolving orthogonal suppressor tRNAs for modified amino acid incorporation is now available to read.

July 18 - 21, 2016: Several members of the lab attended SEED 2016 in Chicago, where Andy spoke about the functional incorporation of unnatural amino acids into proteomes.

June 24, 2016: Research by Jared, Jimmy, and Raghav on the development of a reverse transcriptase capable of proofreading is featured in this week's issue of Science.

Summer 2016: Eric Verbeke joins the lab as a summer rotation student. Welcome Eric!

May 25, 2016: Bo's paper on anti-ricin antibody discovery through repertoire analysis and yeast surface display is out.

May 23, 2016: The new lab website is under construction.

April 29, 2016: Jared successfully defends his dissertation.

March 31, 2016: A new paper by Cheulhee on expanding oligonucleotide terminal hairpin formation and self-priming (THSP) by incorporating phosphorothioates is now available.

March 23, 2016: Sherry successfully defends her dissertation.


Meet the team. Updated August 2018.

Principal Investigator

Andrew Ellington

Andrew Ellington is the Fraser Professor of Biochemistry at the University of Texas at Austin. He is perhaps best known for the invention of the word "aptamer," but is now most involved in the development and evolution of artificial life, including nucleic acid operating systems that can function both in vitro and in vivo.







Postdoctoral Researchers


Ross Thyer

I completed a B.Sc. and Ph.D. at the University of Western Australia and joined the Ellington lab in 2013. My research interests include the development of biosynthesis pathways and translation machinery for the incorporation of unconventional and unnatural amino acids. I also enjoy beer, rock climbing and frogs!



Technical Staff

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Sanchita Bhadra

"I engineer nucleic acids and proteins into molecular diagnostic devices for detection of infectious and metabolic diseases. My focus is on early and accurate diagnostics not only for presetting therapeutic intervention in clinics but with a broader goal of making diagnostics more affordable and amenable for point-of-care application."

Michelle Byrom

Michelle Byrom received a BS in Microbiology, with Honors, at the University of Texas at Austin. She worked as a research assistant at M.D. Anderson Cancer Center Science Park Research Center for ten years, and joined the Ellington Lab in 2008. Currently, Michelle works on the development of novel biotechnologies for detecting RNA and DNA biomarkers.



Cody McLeland

“I joined the Ellington lab in a collaboration with ARL-S in early 2018. Since then, I’ve been working on biomaterials projects involving microbial electricity production and bioadhesives . When I’m not in the lab, I enjoy getting to know the Austin area, mostly through it’s food and landscape. I also enjoy the occasional video game if time permits!”



Graduate Students


Stella Wang

"I am a graduate student in the lab (joined 2017). My research interests include DNA computing, nucleic acid rational design, and hybridization biophysics. My current projects include characterization of nucleic acid variant thermodynamics using hacked Next-Generation Sequencing chips and distributed in vitro transcriptional circuits for pattern transformation."

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Erhu Xiong

"I graduated with a PhD in Analytical Chemistry from Hunan University and joined the lab in 2016. My research mainly focuses on the development of cheap and easy-to-use electrochemical and fluorescent biosensors based on cascade signal amplification strategy by using nucleic acids circuits for the detection of proteins, nucleic acids, metal ions, and small molecules."


Alex Boulgakov

"I'm a visiting member from the Marcotte lab down the hall. In the Ellington lab. I'm currently developing
novel approaches to single molecule proteomics"



Shaunak Kar

I am a Cell and Molecular Biology graduate student. Apart from being an avid sports fan (especially soccer), I work on developing transcription-based circuits capable of function in a wide variety of organisms.

Austin Cole

Austin Cole graduated from the University of Minnesota Twin Cities in 2015 then joined the lab under co-supervision with James Bull in 2016. He's broadly interested in engineering bacterial communication and understanding genetic constraints of evolution. Outside science Austin enjoys hiking, exercise, jazz, and literature.

Elizabeth (Liz) Gardner


Raghav Shroff



Undergraduate Students


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Ted Rodriguez

"I am an chemistry/philosophy major who joined the lab in spring 2018. My current research is directed towards finding aptamers for diagnostic, therapeutic, and other varying uses. Outside of lab I am a mentor for aptamer research to other undergraduate students and I enjoy reading, beating my roommates at board games, piña coladas, and getting caught in the rain.


Pia Sen

"I am an undergraduate student at UT, and am in the class of 2020. I work on enzyme identification and gene knockouts. Outside of the lab, I’m on the UT debate team and I like adopting cats."

Administrative Assistant

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Jenna Texeira

"I graduated from Baylor University in 2017 and joined the lab in June of 2018. I am an assistant to the Directors of the Center for Systems and Synthetic Biology, within the Department of Molecular Biosciences. Among other things, I provide support for the center's directors with reporting and informational upkeep. Aside from being a member of CSSB, I enjoy swimming, traveling, watching movies, and going to concerts.









Cody McLeland


Recent Alumni


Sandeep Panda

"I am a graduate student in Indian Institute of Technology (IIT) Madras, India. I was selected for the Indo-US Genome Engineering Technology Initiative (GETin) Internship, which enables PhD Scholars from India to gain exposure in the emerging domains of gene editing and synthetic biology. In the Ellington Lab, I worked on engineering and repurposing terpene binding transcriptional repressors as biosensor in Escherichia coli. I also worked on developing a synthetic RNA-based platform, which can facilitate metabolic shunting between pathways in Escherichia coli."



Armin Nourani

Armin was an undergraduate who worked with many lab members on the development of novel nucleic acid biomarker point-of-care diagnostics. He graduated in the Spring of 2016 and will be attending graduate school at Vanderbilt University to pursue a PhD in chemical biology. Armin had a strong love-hate relationship with LAMP but was an overall advocate for regular lamps.


Ella Watkins

Ella worked in the Ellington Lab for 2 years with Jimmy Gollihar. In her time here, she adapted the directed evolution methods of compartmentalized self replication and compartmentalized partnered replication to work with a eukaryotic system. She is now attending the California Institute of Technology for her PhD in Bioengineering.


Yu Sherry Jiang

As an analytical chemistry student working in a biochemistry lab (and occasionally as a TA in biology), I work with DNA a lot: DNA diagnostics, DNA circuits, DNA computers, DNA synthesis, and related point-of-care devices.


Yan Du

I graduated from Changchun Institute of Applied Chemistry, Chinese Academy of Sciences (CIAC, CAS), and joined the Ellington Lab in April 2013. My research interests relate to developing DNA circuitry and isothermal nucleic acid amplification technologies, as well as using various signal output methods to realize their bioanalytical applications. For example, I am developing “one-pot” electrochemical platforms that may realize point-of-care diagnostics in the future.


Yousef Okasheh

Yousef was an undergraduate researcher, Beckman Scholar, and hype man for the lab. Apart from research, Yousef is perhaps best known on the Internet through his involvement with multiple Austin-based startups.


Bijoy Desai

Bijoy is now working on "understanding the structural dynamics of translation elongation and its regulation using single molecule total internal reflection fluorescence (TIRF) microscopy" as a postdoctoral researcher at Columbia University.

Peter Allen

Peter is a Chemist from University of Washington in Seattle. He has published papers in journals such as Analytical Chemistry, Electrophoresis, and Biochimica et Biophysica Acta: Molecular Basis of Disease. His research has been at the interface of chemistry and neurobiology he is currently working with robotics, Sequential Injection Analysis and aptamers.


Dilek Cam

Research Interests
Nanoparticle (gold, silver) synthesis and modification, development of rapid test (lateral flow strip) platforms based on antibody and nucleic acid for pathogen detection, nanobiosensors, Surface Enhanced Raman Scattering (SERS).


Alison Moss

Alison was a Biomedical Engineering undergraduate who worked on protein engineering.


Carolyn Hargrave



Bingling Li

Dr. Bingling Li graduated from Changchun Institute of Applied Chemistry and joined the Ellington Lab in February 2010 as a postdoctoral research fellow. Her research interest covers “every aspect” related to DNA based molecular recognition, signal amplification, and signal output. Her dream of doing research is developing a commercialized point-of-care device or analytical device for easy and portable diagnosis.


Nick Marshall

Worked primarily on two disparate projects. One project involved utilizing immuno-therapy to cure cancer. The other project was focused on building electronic communication into microbes to build so called "Cyborgcells." That's right, curing a horrible disease on one hand, creating an apocalyptic scenario on the other. Such is the Ellington Lab…


Beth Marshall

Beth Marshall was a technician that worked on repertoire analysis and antibody engineering.


Shu Jun Zhen

Shu is an Associate Professor from Southwest University, China. She worked on two projects. One was about functional nucleic acid based biosensors. The other one was about super-resolution imaging of the interactions between molecules and plasmonic nanostructures.

Publications (1999–2016)

For publications dating back to 1987, visit Google Scholar.

2016JournalJung, Allen, Ellington (2016). A stochastic DNA walker that traverses a microparticle surface. Nat Nanotechnol, 11(2), pp. 157–163. (bib)
2016JournalDu, Zhen, Li, Byrom, Jiang, Ellington (2016). Engineering Signaling Aptamers That Rely on Kinetic Rather Than Equilibrium Competition. Anal. Chem., 88(4), pp. 2250–2257. (bib)
2016JournalTack, Ellefson, Thyer, Wang, Gollihar, Forster, Ellington (2016). Addicting diverse bacteria to a noncanonical amino acid. Nat. Chem. Biol., 12(3), pp. 138–140. (bib)
2016JournalMcDaniel, DeKosky, Tanno, Ellington, Georgiou (2016). Ultra-high-throughput sequencing of the immune receptor repertoire from millions of lymphocytes. Nat Protoc, 11(3), pp. 429–442. (bib)
2016JournalMartini, Ellington, Mansy (2016). An in vitro selection for small molecule induced switching RNA molecules. Methods, missing, pp. . (bib)
2016JournalJung, Ellington (2016). A primerless molecular diagnostic: phosphorothioated-terminal hairpin formation and self-priming extension (PS-THSP). Anal Bioanal Chem, missing, pp. . (bib)
2016JournalDeKosky, Lungu, Park, Johnson, Charab, Chrysostomou, Kuroda, Ellington, Ippolito, Gray, Georgiou (2016). Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires. Proc. Natl. Acad. Sci. U.S.A., 113(19), pp. E2636–2645. (bib)
2016JournalHammerling, Gollihar, Mortensen, Alnahhas, Ellington, Barrick (2016). Expanded genetic codes create new mutational routes to rifampicin resistance in Escherichia coli. Mol. Biol. Evol., missing, pp. . (bib)
2015JournalEnyeart, Simpson, Ellington (2015). A microbial model of economic trading and comparative advantage. J. Theor. Biol., 364, pp. 326–343. (bib)
2015JournalMeyer, Ellefson, Ellington (2015). Directed Evolution of a Panel of Orthogonal T7 RNA Polymerase Variants for in Vivo or in Vitro Synthetic Circuitry. ACS Synth Biol, 4(10), pp. 1070–1076. (bib)
2015JournalDeKosky, Kojima, Rodin, Charab, Ippolito, Ellington, Georgiou (2015). In-depth determination and analysis of the human paired heavy- and light-chain antibody repertoire. Nat. Med., 21(1), pp. 86–91. (bib)
2015JournalThyer, Robotham, Brodbelt, Ellington (2015). Evolving tRNA(Sec) for efficient canonical incorporation of selenocysteine. J. Am. Chem. Soc., 137(1), pp. 46–49. (bib)
2015JournalP?osko?, Wagner, Ellington, Jewett, O'Reilly, Booth (2015). Controlled assembly of artificial protein-protein complexes via DNA duplex formation. Bioconjug. Chem., 26(3), pp. 427–434. (bib)
2015JournalBhadra, Ellington (2015). Design, synthesis, and application of Spinach molecular beacons triggered by strand displacement. Meth. Enzymol., 550, pp. 215–249. (bib)
2015JournalJiang, Bhadra, Li, Wu, Milligan, Ellington (2015). Robust strand exchange reactions for the sequence-specific, real-time detection of nucleic acid amplicons. Anal. Chem., 87(6), pp. 3314–3320. (bib)
2015JournalEllington (2015). RNA as a conception. RNA, 21(4), pp. 608. (bib)
2015JournalGoodwin, Gade, Byrom, Herrera, Spears, Anslyn, Ellington (2015). Next-generation sequencing as input for chemometrics in differential sensing routines. Angew. Chem. Int. Ed. Engl., 54(21), pp. 6339–6342. (bib)
2015JournalBhadra, Jiang, Kumar, Johnson, Hensley, Ellington (2015). Real-time sequence-validated loop-mediated isothermal amplification assays for detection of Middle East respiratory syndrome coronavirus (MERS-CoV). PLoS ONE, 10(4), pp. e0123126. (bib)
2015JournalMilligan, Ellington (2015). Using RecA protein to enhance kinetic rates of DNA circuits. Chem. Commun. (Camb.), 51(46), pp. 9503–9506. (bib)
2015JournalMartini, Meyer, Ellefson, Milligan, Forlin, Ellington, Mansy (2015). In Vitro Selection for Small-Molecule-Triggered Strand Displacement and Riboswitch Activity. ACS Synth Biol, 4(10), pp. 1144–1150. (bib)
2015JournalAllen, Khaing, Schmidt, Ellington (2015). 3D Printing with Nucleic Acid Adhesives. ACS Biomater Sci Eng, 1(1), pp. 19–26. (bib)
2015JournalDu, Hughes, Bhadra, Jiang, Ellington, Li (2015). A Sweet Spot for Molecular Diagnostics: Coupling Isothermal Amplification and Strand Exchange Circuits to Glucometers. Sci Rep, 5, pp. 11039. (bib)
2015JournalJung, Ellington (2015). Synthetic biology: Six pack and stack. Nat Chem, 7(8), pp. 617–619. (bib)
2015JournalMeyer, Garry, Hall, Byrom, McDonald, Yang, Yin, Ellington (2015). Transcription yield of fully 2'-modified RNA can be increased by the addition of thermostabilizing mutations to T7 RNA polymerase mutants. Nucleic Acids Res., 43(15), pp. 7480–7488. (bib)
2015JournalCunningham, Scida, Kogan, Wang, Ellington, Crooks (2015). Paper diagnostic device for quantitative electrochemical detection of ricin at picomolar levels. Lab Chip, 15(18), pp. 3707–3715. (bib)
2015JournalMayfield, Fan, Wei, Zhang, Li, Ellington, Etzkorn, Zhang (2015). Chemical Tools To Decipher Regulation of Phosphatases by Proline Isomerization on Eukaryotic RNA Polymerase II. ACS Chem. Biol., 10(10), pp. 2405–2414. (bib)
2015JournalWang, Kluwe, Lungu, DeKosky, Kerr, Johnson, Jung, Rezigh, Carroll, Reyes, Bentz, Villanueva, Altman, Davey, Ellington, Georgiou (2015). Facile Discovery of a Diverse Panel of Anti-Ebola Virus Antibodies by Immune Repertoire Mining. Sci Rep, 5, pp. 13926. (bib)
2015JournalKerr, Jackson, Lungu, Meyer, Demogines, Ellington, Georgiou, Wilke, Sawyer (2015). Computational and Functional Analysis of the Virus-Receptor Interface Reveals Host Range Trade-Offs in New World Arenaviruses. J. Virol., 89(22), pp. 11643–11653. (bib)
2015JournalQuandt, Gollihar, Blount, Ellington, Georgiou, Barrick (2015). Fine-tuning citrate synthase flux potentiates and refines metabolic innovation in the Lenski evolution experiment. Elife, 4, pp. . (bib)
2015JournalFriedman, Ellington (2015). Industrialization of Biology. ACS Synth Biol, 4(10), pp. 1053–1055. (bib)
2015JournalEllington (2015). Landscape-Based Biology. J. Mol. Evol., 81(5-6), pp. 144–145. (bib)
2015JournalMahmood, Hasan, Khan, Allen, Kim, Ellington, Iqbal (2015). One-step tumor detection from dynamic morphology tracking on aptamer-grafted surfaces. Technology (Singap World Sci), 3(4), pp. 194–200. (bib)
2014JournalXu, Tack, Hughes, Ellington, Gray (2014). Structure-based non-canonical amino acid design to covalently crosslink an antibody-antigen complex. J. Struct. Biol., 185(2), pp. 215–222. (bib)
2014JournalBhadra, Codrea, Ellington (2014). G-quadruplex-generating polymerase chain reaction for visual colorimetric detection of amplicons. Anal. Biochem., 445, pp. 38–40. (bib)
2014JournalEllefson, Meyer, Hughes, Cannon, Brodbelt, Ellington (2014). Directed evolution of genetic parts and circuits by compartmentalized partnered replication. Nat. Biotechnol., 32(1), pp. 97–101. (bib)
2014JournalLu, Levy, Kincaid, Ellington (2014). Directed evolution of the substrate specificity of biotin ligase. Biotechnol. Bioeng., 111(6), pp. 1071–1081. (bib)
2014JournalQuandt, Deatherage, Ellington, Georgiou, Barrick (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(6), pp. 2217–2222. (bib)
2014JournalJiang, Bhadra, Li, Ellington (2014). Mismatches improve the performance of strand-displacement nucleic Acid circuits. Angew. Chem. Int. Ed. Engl., 53(7), pp. 1845–1848. (bib)
2014JournalEnyeart, Mohr, Ellington, Lambowitz (2014). Biotechnological applications of mobile group II introns and their reverse transcriptases: gene targeting, RNA-seq, and non-coding RNA analysis. Mob DNA, 5(1), pp. 2. (bib)
2014JournalZhao, Tsechansky, Ellington, Marcotte (2014). Revisiting and revising the purinosome. Mol Biosyst, 10(3), pp. 369–374. (bib)
2014JournalGollihar, Levy, Ellington (2014). Biochemistry. Many paths to the origin of life. Science, 343(6168), pp. 259–260. (bib)
2014JournalLavinder, Wine, Giesecke, Ippolito, Horton, Lungu, Hoi, DeKosky, Murrin, Wirth, Ellington, Dorner, Marcotte, Boutz, Georgiou (2014). Identification and characterization of the constituent human serum antibodies elicited by vaccination. Proc. Natl. Acad. Sci. U.S.A., 111(6), pp. 2259–2264. (bib)
2014JournalHammerling, Ellefson, Boutz, Marcotte, Ellington, Barrick (2014). Bacteriophages use an expanded genetic code on evolutionary paths to higher fitness. Nat. Chem. Biol., 10(3), pp. 178–180. (bib)
2014JournalO'Connell, Tsechansky, Royall, Boutz, Ellington, Marcotte (2014). A proteomic survey of widespread protein aggregation in yeast. Mol Biosyst, 10(4), pp. 851–861. (bib)
2014JournalBhadra, Ellington (2014). Design and application of cotranscriptional non-enzymatic RNA circuits and signal transducers. Nucleic Acids Res., 42(7), pp. e58. (bib)
2014JournalMeyer, Ellefson, Ellington (2014). Library generation by gene shuffling. Curr Protoc Mol Biol, 105, pp. Unit 15.12.. (bib)
2014JournalMeyer, Sawyer, Ellington, Wilke (2014). Analyzing machupo virus-receptor binding by molecular dynamics simulations. PeerJ, 2, pp. e266. (bib)
2014JournalLu, Ellington (2014). Design and selection of a synthetic operon. ACS Synth Biol, 3(6), pp. 410–415. (bib)
2014JournalSingh-Blom, Hughes, Ellington (2014). An amino acid depleted cell-free protein synthesis system for the incorporation of non-canonical amino acid analogs into proteins. J. Biotechnol., 178, pp. 12–22. (bib)
2014JournalMelancon, Zhou, Zhang, Xiong, Allen, Wen, Huang, Wallace, Myers, Stafford, Liang, Ellington, Li (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(5), pp. 4530–4538. (bib)
2014JournalJung, Ellington (2014). Diagnostic applications of nucleic acid circuits. Acc. Chem. Res., 47(6), pp. 1825–1835. (bib)
2014JournalBhadra, Ellington (2014). A Spinach molecular beacon triggered by strand displacement. RNA, 20(8), pp. 1183–1194. (bib)
2014JournalByrom, Bhadra, Jiang, Ellington (2014). Exquisite allele discrimination by toehold hairpin primers. Nucleic Acids Res., 42(15), pp. e120. (bib)
2014JournalDu, Lim, Li, Jiang, Sessler, Ellington (2014). Reagentless, ratiometric electrochemical DNA sensors with improved robustness and reproducibility. Anal. Chem., 86(15), pp. 8010–8016. (bib)
2014JournalSegall-Shapiro, Meyer, Ellington, Sontag, Voigt (2014). A 'resource allocator' for transcription based on a highly fragmented T7 RNA polymerase. Mol. Syst. Biol., 10, pp. 742. (bib)
2014JournalAllen, Chen, Simpson, Ellington (2014). Modeling Scalable Pattern Generation in DNA Reaction Networks. Nat Comput, 13(4), pp. 583–595. (bib)
2014JournalStovall, Bedenbaugh, Singh, Meyer, Hatala, Ellington, Hall (2014). In vitro selection using modified or unnatural nucleotides. Curr Protoc Nucleic Acid Chem, 56, pp. 1–33. (bib)
2013JournalLu, Ellington (2013). In vitro selection of proteins via emulsion compartments. Methods, 60(1), pp. 75–80. (bib)
2013JournalWan, Tamuly, Allen, Kim, Bachoo, Ellington, Iqbal (2013). Proliferation and migration of tumor cells in tapered channels. Biomed Microdevices, 15(4), pp. 635–643. (bib)
2013JournalDeKosky, Ippolito, Deschner, Lavinder, Wine, Rawlings, Varadarajan, Giesecke, Dorner, Andrews, Wilson, Hunicke-Smith, Willson, Ellington, Georgiou (2013). High-throughput sequencing of the paired human immunoglobulin heavy and light chain repertoire. Nat. Biotechnol., 31(2), pp. 166–169. (bib)
2013JournalWine, Boutz, Lavinder, Miklos, Hughes, Hoi, Jung, Horton, Murrin, Ellington, Marcotte, Georgiou (2013). Molecular deconvolution of the monoclonal antibodies that comprise the polyclonal serum response. Proc. Natl. Acad. Sci. U.S.A., 110(8), pp. 2993–2998. (bib)
2013JournalZhao, Tsechansky, Swaminathan, Cook, Ellington, Marcotte (2013). Transiently transfected purine biosynthetic enzymes form stress bodies. PLoS ONE, 8(2), pp. e56203. (bib)
2013JournalSingh-Blom, Hughes, Ellington (2013). Residue-specific incorporation of unnatural amino acids into proteins in vitro and in vivo. Methods Mol. Biol., 978, pp. 93–114. (bib)
2013JournalChen, Briggs, McLain, Ellington (2013). Stacking nonenzymatic circuits for high signal gain. Proc. Natl. Acad. Sci. U.S.A., 110(14), pp. 5386–5391. (bib)
2013JournalJiang, Li, Milligan, Bhadra, Ellington (2013). Real-time detection of isothermal amplification reactions with thermostable catalytic hairpin assembly. J. Am. Chem. Soc., 135(20), pp. 7430–7433. (bib)
2013JournalMaranhao, Ellington (2013). Endowing cells with logic and memory. Nat. Biotechnol., 31(5), pp. 413–415. (bib)
2013JournalDer, Kluwe, Miklos, Jacak, Lyskov, Gray, Georgiou, Ellington, Kuhlman (2013). Alternative computational protocols for supercharging protein surfaces for reversible unfolding and retention of stability. PLoS ONE, 8(5), pp. e64363. (bib)
2013JournalWilson, Morton, Deiderick, Gerth, Paul, Gerber, Patel, Ellington, Hunicke-Smith, Patrick (2013). Engineered DNA ligases with improved activities in vitro. Protein Eng. Des. Sel., 26(7), pp. 471–478. (bib)
2013JournalLuo, Yogesha, Cannon, Yan, Ellington, Brodbelt, Zhang (2013). novel modifications on C-terminal domain of RNA polymerase II can fine-tune the phosphatase activity of Ssu72. ACS Chem. Biol., 8(9), pp. 2042–2052. (bib)
2013JournalEnyeart, Chirieleison, Dao, Perutka, Quandt, Yao, Whitt, Keatinge-Clay, Lambowitz, Ellington (2013). Generalized bacterial genome editing using mobile group II introns and Cre-lox. Mol. Syst. Biol., 9, pp. 685. (bib)
2013JournalScida, Li, Ellington, Crooks (2013). DNA detection using origami paper analytical devices. Anal. Chem., 85(20), pp. 9713–9720. (bib)
2013JournalLedbetter, Hwang, Stovall, Ellington (2013). Continuous in vitro evolution of a ribozyme ligase: a model experiment for the evolution of a biomolecule. Biochem Mol Biol Educ, 41(6), pp. 433–442. (bib)
2013JournalChirieleison, Allen, Simpson, Ellington, Chen (2013). Pattern transformation with DNA circuits. Nat Chem, 5(12), pp. 1000–1005. (bib)
2012JournalWan, Mahmood, Li, Allen, Kim, Bachoo, Ellington, Iqbal (2012). Nanotextured substrates with immobilized aptamers for cancer cell isolation and cytology. Cancer, 118(4), pp. 1145–1154. (bib)
2012JournalCho, Xia, Ma, Robertus, Krug, Anslyn, Montelione, Ellington (2012). Identification of influenza virus inhibitors targeting NS1A utilizing fluorescence polarization-based high-throughput assay. J Biomol Screen, 17(4), pp. 448–459. (bib)
2012JournalMagalhaes, Byrom, Yan, Kelly, Li, Furtado, Palliser, Ellington, Levy (2012). A general RNA motif for cellular transfection. Mol. Ther., 20(3), pp. 616–624. (bib)
2012JournalMiklos, Kluwe, Der, Pai, Sircar, Hughes, Berrondo, Xu, Codrea, Buckley, Calm, Welsh, Warner, Zacharko, Carney, Gray, Georgiou, Kuhlman, Ellington (2012). Structure-based design of supercharged, highly thermoresistant antibodies. Chem. Biol., 19(4), pp. 449–455. (bib)
2012JournalIppolito, Hoi, Reddy, Carroll, Ge, Rogosch, Zemlin, Shultz, Ellington, Vandenberg, Georgiou (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(4), pp. e35497. (bib)
2012JournalZhang, Wang, Chen, Bowman, Luo, Noel, Ellington, Etzkorn, Zhang (2012). Structural and kinetic analysis of prolyl-isomerization/phosphorylation cross-talk in the CTD code. ACS Chem. Biol., 7(8), pp. 1462–1470. (bib)
2012JournalIlyas, Asghar, Allen, Duhon, Ellington, Iqbal (2012). Electrical detection of cancer biomarker using aptamers with nanogap break-junctions. Nanotechnology, 23(27), pp. 275502. (bib)
2012JournalAllen, Arshad, Li, Chen, Ellington (2012). DNA circuits as amplifiers for the detection of nucleic acids on a paperfluidic platform. Lab Chip, 12(16), pp. 2951–2958. (bib)
2012JournalRomero, Stone, Lamb, Chantranupong, Krause, Miklos, Hughes, Fechtel, Ellington, Arnold, Georgiou (2012). SCHEMA-designed variants of human Arginase I and II reveal sequence elements important to stability and catalysis. ACS Synth Biol, 1(6), pp. 221–228. (bib)
2012JournalMiklos, Hughes, Ellington (2012). Design and assembly of large synthetic DNA constructs. Curr Protoc Mol Biol, Chapter 3, pp. Unit3.23. (bib)
2012JournalHughes, Miklos, Ellington (2012). Enrichment of error-free synthetic DNA sequences by CEL I nuclease. Curr Protoc Mol Biol, Chapter 3, pp. Unit3.24. (bib)
2012JournalMeyer, Ellefson, Ellington (2012). Abiotic self-replication. Acc. Chem. Res., 45(12), pp. 2097–2105. (bib)
2012JournalLi, Jiang, Chen, Ellington (2012). Probing spatial organization of DNA strands using enzyme-free hairpin assembly circuits. J. Am. Chem. Soc., 134(34), pp. 13918–13921. (bib)
2012JournalCha, Byrom, Mead, Ellington, Wallingford, Marcotte (2012). Evolutionarily repurposed networks reveal the well-known antifungal drug thiabendazole to be a novel vascular disrupting agent. PLoS Biol., 10(8), pp. e1001379. (bib)
2012JournalTang, Deschner, Allen, Cho, Sermas, Maurer, Ellington, Willson (2012). Analysis of DNA-guided self-assembly of microspheres using imaging flow cytometry. J. Am. Chem. Soc., 134(37), pp. 15245–15248. (bib)
2012JournalLi, Chen, Ellington (2012). Adapting enzyme-free DNA circuits to the detection of loop-mediated isothermal amplification reactions. Anal. Chem., 84(19), pp. 8371–8377. (bib)
2012JournalWan, Liu, Allen, Asghar, Mahmood, Tan, Duhon, Kim, Ellington, Iqbal (2012). Capture, isolation and release of cancer cells with aptamer-functionalized glass bead array. Lab Chip, 12(22), pp. 4693–4701. (bib)
2012JournalOpazo, Levy, Byrom, Schafer, Geisler, Groemer, Ellington, Rizzoli (2012). Aptamers as potential tools for super-resolution microscopy. Nat. Methods, 9(10), pp. 938–939. (bib)
2012JournalRay, Cheek, Sharaf, Li, Ellington, Sullenger, Shaw, White (2012). Aptamer-mediated delivery of chemotherapy to pancreatic cancer cells. Nucleic Acid Ther, 22(5), pp. 295–305. (bib)
2012JournalO'Connell, Zhao, Ellington, Marcotte (2012). Dynamic reorganization of metabolic enzymes into intracellular bodies. Annu. Rev. Cell Dev. Biol., 28, pp. 89–111. (bib)
2012JournalJiang, Li, Chen, Ellington (2012). Coupling two different nucleic acid circuits in an enzyme-free amplifier. Molecules, 17(11), pp. 13211–13220. (bib)
2012JournalAllen, Chen, Ellington (2012). Spatial control of DNA reaction networks by DNA sequence. Molecules, 17(11), pp. 13390–13402. (bib)
2012JournalDavidson, Meyer, Ellefson, Levy, Ellington (2012). An in vitro autogene. ACS Synth Biol, 1(5), pp. 190–196. (bib)
2011JournalHargrove, Ellington, Anslyn, Sessler (2011). Chemical functionalization of oligodeoxynucleotides with multiple boronic acids for the polyvalent binding of saccharides. Bioconjug. Chem., 22(3), pp. 388–396. (bib)
2011JournalAllen, Ellington (2011). Sequential injection analysis for optimization of molecular biology reactions. Anal. Chem., 83(6), pp. 2194–2200. (bib)
2011JournalHughes, Miklos, Ellington (2011). Gene synthesis: methods and applications. Meth. Enzymol., 498, pp. 277–309. (bib)
2011JournalMeyer, Ellington (2011). Molecular evolution picks up the PACE. Nat. Biotechnol., 29(6), pp. 502–503. (bib)
2011JournalLi, Nguyen, Byrom, Ellington (2011). Inhibition of cell proliferation by an anti-EGFR aptamer. PLoS ONE, 6(6), pp. e20299. (bib)
2011JournalLi, Ellington, Chen (2011). Rational, modular adaptation of enzyme-free DNA circuits to multiple detection methods. Nucleic Acids Res., 39(16), pp. e110. (bib)
2011JournalEnyeart, Ellington (2011). Synthetic biology: a yeast for all reasons. Nature, 477(7365), pp. 413–414. (bib)
2011JournalAlicea, Marvin, Miklos, Ellington, Looger, Schreiter (2011). Structure of the Escherichia coli phosphonate binding protein PhnD and rationally optimized phosphonate biosensors. J. Mol. Biol., 414(3), pp. 356–369. (bib)
2010JournalDavidson, VAN Blarcom, Levy, Ellington (2010). Emulsion based selection of T7 promoters of varying activity. Pac Symp Biocomput, missing, pp. 433–443. (bib)
2010JournalLee, Icoz, Roberts, Ellington, Savran (2010). Diffractometric detection of proteins using microbead-based rolling circle amplification. Anal. Chem., 82(1), pp. 197–202. (bib)
2010JournalLi, Larson, Nguyen, Sokolov, Ellington (2010). Directed evolution of gold nanoparticle delivery to cells. Chem. Commun. (Camb.), 46(3), pp. 392–394. (bib)
2010JournalGardner, Li, Ellington, Brodbelt (2010). Infrared multiphoton dissociation of small-interfering RNA anions and cations. J. Am. Soc. Mass Spectrom., 21(4), pp. 580–591. (bib)
2010JournalGe, Mazor, Hunicke-Smith, Ellington, Georgiou (2010). Rapid construction and characterization of synthetic antibody libraries without DNA amplification. Biotechnol. Bioeng., 106(3), pp. 347–357. (bib)
2010JournalHall, Arshad, Seo, Bowman, Corley, Jhaveri, Ellington (2010). In vitro selection of RNA aptamers to a protein target by filter immobilization. Curr Protoc Nucleic Acid Chem, Chapter 9, pp. 1–27. (bib)
2010JournalWang, Khaing, Li, Hall, Schmidt, Ellington (2010). Aptamer antagonists of myelin-derived inhibitors promote axon growth. PLoS ONE, 5(3), pp. e9726. (bib)
2010JournalTipps, Lawshe, Ellington, Mihic (2010). Identification of novel specific allosteric modulators of the glycine receptor using phage display. J. Biol. Chem., 285(30), pp. 22840–22845. (bib)
2010JournalChen, Ellington (2010). Shaping up nucleic acid computation. Curr. Opin. Biotechnol., 21(4), pp. 392–400. (bib)
2010JournalHughes, Ellington (2010). Rational design of an orthogonal tryptophanyl nonsense suppressor tRNA. Nucleic Acids Res., 38(19), pp. 6813–6830. (bib)
2010JournalReddy, Ge, Miklos, Hughes, Kang, Hoi, Chrysostomou, Hunicke-Smith, Iverson, Tucker, Ellington, Georgiou (2010). Monoclonal antibodies isolated without screening by analyzing the variable-gene repertoire of plasma cells. Nat. Biotechnol., 28(9), pp. 965–969. (bib)
2010JournalKluwe, Ellington (2010). Evolution. RNA GPS. Science, 330(6002), pp. 330–331. (bib)
2010JournalConnell, Wessel, Parsek, Ellington, Whiteley, Shear (2010). Probing prokaryotic social behaviors with bacterial "lobster traps". MBio, 1(4), pp. . (bib)
2010JournalWan, Kim, Li, Cho, Bachoo, Ellington, Iqbal (2010). Surface-immobilized aptamers for cancer cell isolation and microscopic cytology. Cancer Res., 70(22), pp. 9371–9380. (bib)
2010JournalManickam, Chevalier, McDermott, Ellington, Hassibi (2010). A CMOS Electrochemical Impedance Spectroscopy (EIS) Biosensor Array. IEEE Trans Biomed Circuits Syst, 4(6), pp. 379–390. (bib)
2009JournalEllington, Chen, Robertson, Syrett (2009). Evolutionary origins and directed evolution of RNA. Int. J. Biochem. Cell Biol., 41(2), pp. 254–265. (bib)
2009JournalNarayanaswamy, Moradi, Niu, Hart, Davis, McGary, Ellington, Marcotte (2009). Systematic definition of protein constituents along the major polarization axis reveals an adaptive reuse of the polarization machinery in pheromone-treated budding yeast. J. Proteome Res., 8(1), pp. 6–19. (bib)
2009JournalPai, Ellington (2009). Using RNA aptamers and the proximity ligation assay for the detection of cell surface antigens. Methods Mol. Biol., 504, pp. 385–398. (bib)
2009JournalSeo, Jeong, Leysath, Ellington, Iverson, Georgiou (2009). Engineering antibody fragments to fold in the absence of disulfide bonds. Protein Sci., 18(2), pp. 259–267. (bib)
2009JournalLi, Ebright, Stovall, Chen, Nguyen, Singh, Syrett, Ellington (2009). Technical and biological issues relevant to cell typing with aptamers. J. Proteome Res., 8(5), pp. 2438–2448. (bib)
2009JournalEllington (2009). Back to the future of nucleic acid self-amplification. Nat. Chem. Biol., 5(4), pp. 200–201. (bib)
2009JournalPiasecki, Hall, Ellington (2009). Nucleic acid pool preparation and characterization. Methods Mol. Biol., 535, pp. 3–18. (bib)
2009JournalHall, Cater, Levy, Ellington (2009). Kinetic optimization of a protein-responsive aptamer beacon. Biotechnol. Bioeng., 103(6), pp. 1049–1059. (bib)
2009JournalSimpson, Tsai, Nguyen, Chen, Ellington (2009). Modelling amorphous computations with transcription networks. J R Soc Interface, 6 Suppl 4, pp. S523–533. (bib)
2009JournalNarayanaswamy, Levy, Tsechansky, Stovall, O'Connell, Mirrielees, Ellington, Marcotte (2009). Widespread reorganization of metabolic enzymes into reversible assemblies upon nutrient starvation. Proc. Natl. Acad. Sci. U.S.A., 106(25), pp. 10147–10152. (bib)
2009JournalTabor, Salis, Simpson, Chevalier, Levskaya, Marcotte, Voigt, Ellington (2009). A synthetic genetic edge detection program. Cell, 137(7), pp. 1272–1281. (bib)
2009JournalDavidson, Dlugosz, Levy, Ellington (2009). Directed evolution of proteins in vitro using compartmentalization in emulsions. Curr Protoc Mol Biol, Chapter 24, pp. Unit 24.6. (bib)
2009JournalHwang, Codrea, Ellington (2009). Motifs from the deep. J. Biol., 8(8), pp. 72. (bib)
2009JournalChen, Denison, Levy, Ellington (2009). Direct selection for ribozyme cleavage activity in cells. RNA, 15(11), pp. 2035–2045. (bib)
2009JournalHall, Micheletti, Satya, Ogle, Pollard, Ellington (2009). Design, synthesis, and amplification of DNA pools for in vitro selection. Curr Protoc Mol Biol, Chapter 24, pp. Unit 24.2. (bib)
2009JournalHall, Arshad, Seo, Bowman, Corley, Jhaveri, Ellington (2009). In vitro selection of RNA aptamers to a protein target by filter immobilization. Curr Protoc Mol Biol, Chapter 24, pp. Unit 24.3. (bib)
2009JournalHall, Micheletti, Satya, Ogle, Pollard, Ellington (2009). Design, synthesis, and amplification of DNA pools for in vitro selection. Curr Protoc Nucleic Acid Chem, Chapter 9, pp. Unit 9.2. (bib)
2009JournalChen, Ellington (2009). Design principles for ligand-sensing, conformation-switching ribozymes. PLoS Comput. Biol., 5(12), pp. e1000620. (bib)
2009JournalCho, Lee, Ellington (2009). Applications of aptamers as sensors. Annu Rev Anal Chem (Palo Alto Calif), 2, pp. 241–264. (bib)
2008JournalRajendran, Ellington (2008). Selection of fluorescent aptamer beacons that light up in the presence of zinc. Anal Bioanal Chem, 390(4), pp. 1067–1075. (bib)
2008JournalEllington (2008). Q &A. Andrew D. Ellington. Curr. Biol., 18(5), pp. R184–185. (bib)
2008JournalEllington (2008). Man versus machine versus ribozyme. PLoS Biol., 6(5), pp. e132. (bib)
2008JournalYang, Ellington (2008). Real-time PCR detection of protein analytes with conformation-switching aptamers. Anal. Biochem., 380(2), pp. 164–173. (bib)
2008JournalTabor, Bayer, Simpson, Levy, Ellington (2008). Engineering stochasticity in gene expression. Mol Biosyst, 4(7), pp. 754–761. (bib)
2008JournalCowperthwaite, Ellington (2008). Bioinformatic analysis of the contribution of primer sequences to aptamer structures. J. Mol. Evol., 67(1), pp. 95–102. (bib)
2008JournalLevy, Ellington (2008). Directed evolution of streptavidin variants using in vitro compartmentalization. Chem. Biol., 15(9), pp. 979–989. (bib)
2008JournalLi, Wang, Pothukuchy, Syrett, Husain, Gopalakrisha, Kosaraju, Ellington (2008). Aptamers that recognize drug-resistant HIV-1 reverse transcriptase. Nucleic Acids Res., 36(21), pp. 6739–6751. (bib)
2008JournalPaukstelis, Ellington (2008). Rolling out DNA nanostructures in vivo. Proc. Natl. Acad. Sci. U.S.A., 105(46), pp. 17593–17594. (bib)
2008JournalFan, Wu, Martiniuk, Hale, Ellington, Tchou-Wong (2008). Protective effects of anti-ricin A-chain RNA aptamer against ricin toxicity. World J. Gastroenterol., 14(41), pp. 6360–6365. (bib)
2008JournalPai, Roberts, Ellington (2008). Aptamer amplification: divide and signal. Expert Opin Med Diagn, 2(12), pp. 1333–1346. (bib)
2008JournalGnanam, Hall, Shen, Piasecki, Vernados, Galyov, Smither, Kitto, Titball, Ellington, Brown (2008). Development of aptamers specific for potential diagnostic targets in Burkholderia pseudomallei. Trans. R. Soc. Trop. Med. Hyg., 102 Suppl 1, pp. S55–57. (bib)
2007JournalCho, Ellington (2007). Optimization of the biological component of a bioelectrochemical cell. Bioelectrochemistry, 70(1), pp. 165–172. (bib)
2007JournalHall, Hesselberth, Ellington (2007). Computational selection of nucleic acid biosensors via a slip structure model. Biosens Bioelectron, 22(9-10), pp. 1939–1947. (bib)
2007JournalBacher, Ellington (2007). Global incorporation of unnatural amino acids in Escherichia coli. Methods Mol. Biol., 352, pp. 23–34. (bib)
2007JournalDavidson, Ellington (2007). Synthetic RNA circuits. Nat. Chem. Biol., 3(1), pp. 23–28. (bib)
2007JournalYang, Fung, Cho, Ellington (2007). Real-time rolling circle amplification for protein detection. Anal. Chem., 79(9), pp. 3320–3329. (bib)
2007JournalChen, Li, Ellington (2007). Ribozyme catalysis of metabolism in the RNA world. Chem. Biodivers., 4(4), pp. 633–655. (bib)
2007JournalChu, Ebright, Ellington (2007). Using aptamers to identify and enter cells. Curr. Opin. Mol. Ther., 9(2), pp. 137–144. (bib)
2007JournalEllington (2007). What's so great about RNA?. ACS Chem. Biol., 2(7), pp. 445–448. (bib)
2006JournalChu, Shieh, Lavery, Levy, Richards-Kortum, Korgel, Ellington (2006). Labeling tumor cells with fluorescent nanocrystal-aptamer bioconjugates. Biosens Bioelectron, 21(10), pp. 1859–1866. (bib)
2006JournalNarayanaswamy, Niu, Scouras, Hart, Davies, Ellington, Iyer, Marcotte (2006). Systematic profiling of cellular phenotypes with spotted cell microarrays reveals mating-pheromone response genes. Genome Biol., 7(1), pp. R6. (bib)
2006JournalNarayanaswamy, Ellington (2006). Engineering RNA-based circuits. Handb Exp Pharmacol, missing(173), pp. 423–445. (bib)
2006JournalSchmid, Manthiram, Grayson, Willson, Meiring, Bell, Ellington, Willson (2006). Feature multiplexing–improving the efficiency of microarray devices. Angew. Chem. Int. Ed. Engl., 45(20), pp. 3338–3341. (bib)
2006JournalLee, Stovall, Ellington (2006). Aptamer therapeutics advance. Curr Opin Chem Biol, 10(3), pp. 282–289. (bib)
2006JournalTabor, Levy, Ellington (2006). Deoxyribozymes that recode sequence information. Nucleic Acids Res., 34(8), pp. 2166–2172. (bib)
2006JournalChu, Twu, Ellington, Levy (2006). Aptamer mediated siRNA delivery. Nucleic Acids Res., 34(10), pp. e73. (bib)
2006JournalChu, Marks, Lavery, Faulkner, Rosenblum, Ellington, Levy (2006). Aptamer:toxin conjugates that specifically target prostate tumor cells. Cancer Res., 66(12), pp. 5989–5992. (bib)
2006JournalGaribotti, Knudsen, Ellington, Seeman (2006). Functional DNAzymes organized into two-dimensional arrays. Nano Lett., 6(7), pp. 1505–1507. (bib)
2006JournalKnudsen, Lee, Ellington, Savran (2006). Ribozyme-mediated signal augmentation on a mass-sensitive biosensor. J. Am. Chem. Soc., 128(50), pp. 15936–15937. (bib)
2006JournalCho, Collett, Szafranska, Ellington (2006). Optimization of aptamer microarray technology for multiple protein targets. Anal. Chim. Acta, 564(1), pp. 82–90. (bib)
2006JournalTabor, Davidson, Ellington (2006). Developing RNA tools for engineered regulatory systems. Biotechnol. Genet. Eng. Rev., 22, pp. 21–44. (bib)
2005JournalHughes, Ellington (2005). Mistakes in translation don't translate into termination. Proc. Natl. Acad. Sci. U.S.A., 102(5), pp. 1273–1274. (bib)
2005JournalCollett, Cho, Lee, Levy, Hood, Wan, Ellington (2005). Functional RNA microarrays for high-throughput screening of antiprotein aptamers. Anal. Biochem., 338(1), pp. 113–123. (bib)
2005JournalCho, Yang, Levy, Ellington (2005). Using a deoxyribozyme ligase and rolling circle amplification to detect a non-nucleic acid analyte, ATP. J. Am. Chem. Soc., 127(7), pp. 2022–2023. (bib)
2005JournalDavidson, Ellington (2005). Engineering regulatory RNAs. Trends Biotechnol., 23(3), pp. 109–112. (bib)
2005JournalYan, Bell, Breeden, Ellington (2005). Aptamers: prospects in therapeutics and biomedicine. Front. Biosci., 10, pp. 1802–1827. (bib)
2005JournalFlores, Ellington (2005). A modified consensus approach to mutagenesis inverts the cofactor specificity of Bacillus stearothermophilus lactate dehydrogenase. Protein Eng. Des. Sel., 18(8), pp. 369–377. (bib)
2005JournalLevy, Griswold, Ellington (2005). Direct selection of trans-acting ligase ribozymes by in vitro compartmentalization. RNA, 11(10), pp. 1555–1562. (bib)
2005JournalCollett, Cho, Ellington (2005). Production and processing of aptamer microarrays. Methods, 37(1), pp. 4–15. (bib)
2005JournalKeller, Breeden, Zhang, Ellington, Brodbelt (2005). Electrospray ionization of nucleic acid aptamer/small molecule complexes for screening aptamer selectivity. J Mass Spectrom, 40(10), pp. 1327–1337. (bib)
2005JournalPai, Ellington, Levy (2005). Proximity ligation assays with peptide conjugate 'burrs' for the sensitive detection of spores. Nucleic Acids Res., 33(18), pp. e162. (bib)
2005JournalEllington, Bull (2005). Evolution. Changing the cofactor diet of an enzyme. Science, 310(5747), pp. 454–455. (bib)
2005JournalBryant, Cox, Wang, Hogle, Ellington, Coen (2005). Binding of herpes simplex virus-1 US11 to specific RNA sequences. Nucleic Acids Res., 33(19), pp. 6090–6100. (bib)
2005JournalLevy, Cater, Ellington (2005). Quantum-dot aptamer beacons for the detection of proteins. Chembiochem, 6(12), pp. 2163–2166. (bib)
2005JournalLevskaya, Chevalier, Tabor, Simpson, Lavery, Levy, Davidson, Scouras, Ellington, Marcotte, Voigt (2005). Synthetic biology: engineering Escherichia coli to see light. Nature, 438(7067), pp. 441–442. (bib)
2005JournalBayer, Booth, Knudsen, Ellington (2005). Arginine-rich motifs present multiple interfaces for specific binding by RNA. RNA, 11(12), pp. 1848–1857. (bib)
2004JournalLee, Hesselberth, Meyers, Ellington (2004). Aptamer database. Nucleic Acids Res., 32(Database issue), pp. 95–100. (bib)
2004JournalHoffman, Khrapov, Cox, Yao, Tong, Ellington (2004). AANT: the Amino Acid-Nucleotide Interaction Database. Nucleic Acids Res., 32(Database issue), pp. D174–181. (bib)
2004JournalRobertson, Knudsen, Ellington (2004). In vitro selection of ribozymes dependent on peptides for activity. RNA, 10(1), pp. 114–127. (bib)
2004JournalKnudsen, Ellington (2004). Ribozyme déjà vu. Nat. Struct. Mol. Biol., 11(4), pp. 301–303. (bib)
2004JournalSavran, Knudsen, Ellington, Manalis (2004). Micromechanical detection of proteins using aptamer-based receptor molecules. Anal. Chem., 76(11), pp. 3194–3198. (bib)
2004JournalKirby, Cho, Gehrke, Bayer, Park, Neikirk, McDevitt, Ellington (2004). Aptamer-based sensor arrays for the detection and quantitation of proteins. Anal. Chem., 76(14), pp. 4066–4075. (bib)
2004JournalChelliserrykattil, Ellington (2004). Evolution of a T7 RNA polymerase variant that transcribes 2'-O-methyl RNA. Nat. Biotechnol., 22(9), pp. 1155–1160. (bib)
2004JournalMeyers, Lee, Cowperthwaite, Ellington (2004). The robustness of naturally and artificially selected nucleic acid secondary structures. J. Mol. Evol., 58(6), pp. 681–691. (bib)
2004JournalHughes, Robertson, Ellington, Levy (2004). The importance of prebiotic chemistry in the RNA world. Curr Opin Chem Biol, 8(6), pp. 629–633. (bib)
2004JournalManimala, Wiskur, Ellington, Anslyn (2004). Tuning the specificity of a synthetic receptor using a selected nucleic acid receptor. J. Am. Chem. Soc., 126(50), pp. 16515–16519. (bib)
2004JournalBacher, Hughes, Tze-Fei Wong, Ellington (2004). Evolving new genetic codes. Trends Ecol. Evol. (Amst.), 19(2), pp. 69–75. (bib)
2003JournalHesselberth, Robertson, Knudsen, Ellington (2003). Simultaneous detection of diverse analytes with an aptazyme ligase array. Anal. Biochem., 312(2), pp. 106–112. (bib)
2003JournalLevy, Ellington (2003). Peptide-templated nucleic acid ligation. J. Mol. Evol., 56(5), pp. 607–615. (bib)
2003JournalLevy, Ellington (2003). Exponential growth by cross-catalytic cleavage of deoxyribozymogens. Proc. Natl. Acad. Sci. U.S.A., 100(11), pp. 6416–6421. (bib)
2003JournalChelliserrykattil, Ellington (2003). Autogene selections. Methods Mol. Biol., 230, pp. 27–43. (bib)
2003JournalTabor, Ellington (2003). Playing to win at DNA computation. Nat. Biotechnol., 21(9), pp. 1013–1015. (bib)
2003JournalRajendran, Ellington (2003). In vitro selection of molecular beacons. Nucleic Acids Res., 31(19), pp. 5700–5713. (bib)
2003JournalBacher, Bull, Ellington (2003). Evolution of phage with chemically ambiguous proteomes. BMC Evol. Biol., 3, pp. 24. (bib)
2003JournalAli, Kirby, Goodey, Rodriguez, Ellington, Neikirk, McDevitt (2003). DNA hybridization and discrimination of single-nucleotide mismatches using chip-based microbead arrays. Anal. Chem., 75(18), pp. 4732–4739. (bib)
2002JournalMatsumura, Ellington (2002). Mutagenic polymerase chain reaction of protein-coding genes for in vitro evolution. Methods Mol. Biol., 182, pp. 259–267. (bib)
2002JournalFlores, Ellington (2002). Increasing the thermal stability of an oligomeric protein, beta-glucuronidase. J. Mol. Biol., 315(3), pp. 325–337. (bib)
2002JournalLevy, Ellington (2002). In vitro selection of a deoxyribozyme that can utilize multiple substrates. J. Mol. Evol., 54(2), pp. 180–190. (bib)
2002JournalLevy, Ellington (2002). ATP-dependent allosteric DNA enzymes. Chem. Biol., 9(4), pp. 417–426. (bib)
2002JournalRajendran, Ellington (2002). Selecting nucleic acids for biosensor applications. Comb. Chem. High Throughput Screen., 5(4), pp. 263–270. (bib)
2002JournalCox, Rajendran, Riedel, Davidson, Sooter, Bayer, Schmitz-Brown, Ellington (2002). Automated acquisition of aptamer sequences. Comb. Chem. High Throughput Screen., 5(4), pp. 289–299. (bib)
2002JournalHartig, Najafi-Shoushtari, Grune, Yan, Ellington, Famulok (2002). Protein-dependent ribozymes report molecular interactions in real time. Nat. Biotechnol., 20(7), pp. 717–722. (bib)
2002JournalYan, Ellington (2002). Aptamers as potential diagnostic reagents for diabetes. Diabetes Technol. Ther., 4(3), pp. 339–346. (bib)
2002JournalBacher, Reiss, Ellington (2002). Anticipatory evolution and DNA shuffling. Genome Biol., 3(8), pp. REVIEWS1021. (bib)
2002JournalSooter, Ellington (2002). Reflections on a novel therapeutic candidate. Chem. Biol., 9(8), pp. 857–858. (bib)
2002JournalCox, Hayhurst, Hesselberth, Bayer, Georgiou, Ellington (2002). Automated selection of aptamers against protein targets translated in vitro: from gene to aptamer. Nucleic Acids Res., 30(20), pp. e108. (bib)
2002JournalHesselberth, Ellington (2002). A (ribo) switch in the paradigms of genetic regulation. Nat. Struct. Biol., 9(12), pp. 891–893. (bib)
2002JournalThompson, Syrett, Knudsen, Ellington (2002). Group I aptazymes as genetic regulatory switches. BMC Biotechnol., 2, pp. 21. (bib)
2002JournalYang, Bassett, Li, Luxon, Herzog, Shope, Aronson, Prow, Leary, Kirby, Ellington, Gorenstein (2002). Construction and selection of bead-bound combinatorial oligonucleoside phosphorothioate and phosphorodithioate aptamer libraries designed for rapid PCR-based sequencing. Nucleic Acids Res., 30(23), pp. e132. (bib)
2002JournalKnudsen, Robertson, Ellington (2002). In vitro selection using modified or unnatural nucleotides. Curr Protoc Nucleic Acid Chem, Chapter 9, pp. Unit 9.6. (bib)
2001JournalMatsumura, Ellington (2001). In vitro evolution of beta-glucuronidase into a beta-galactosidase proceeds through non-specific intermediates. J. Mol. Biol., 305(2), pp. 331–339. (bib)
2001JournalMatsumura, Olsen, Ellington (2001). Optimization of heterologous gene expression for in vitro evolution. BioTechniques, 30(3), pp. 474–476. (bib)
2001JournalHoffman, Hesselberth, Ellington (2001). Switching nucleic acids for antibodies. Nat. Biotechnol., 19(4), pp. 313–314. (bib)
2001JournalRobertson, Hesselberth, Ellington (2001). Optimization and optimality of a short ribozyme ligase that joins non-Watson-Crick base pairings. RNA, 7(4), pp. 513–523. (bib)
2001JournalCox, Ellington (2001). DNA computation function. Curr. Biol., 11(9), pp. R336. (bib)
2001JournalChristian, Reilly, Mokler, Wincott, Ellington (2001). Elucidation of the initial step of oligonucleotide fragmentation in matrix-assisted laser desorption/ionization using modified nucleic acids. J. Am. Soc. Mass Spectrom., 12(6), pp. 744–753. (bib)
2001JournalLevy, Ellington (2001). The descent of polymerization. Nat. Struct. Biol., 8(7), pp. 580–582. (bib)
2001JournalRobertson, Ellington (2001). In vitro selection of nucleoprotein enzymes. Nat. Biotechnol., 19(7), pp. 650–655. (bib)
2001JournalBacher, Ellington (2001). Selection and characterization of Escherichia coli variants capable of growth on an otherwise toxic tryptophan analogue. J. Bacteriol., 183(18), pp. 5414–5425. (bib)
2001JournalLevy, Ellington (2001). RNA world: catalysis abets binding, but not vice versa. Curr. Biol., 11(16), pp. R665–667. (bib)
2001JournalCox, Ellington (2001). Automated selection of anti-protein aptamers. Bioorg. Med. Chem., 9(10), pp. 2525–2531. (bib)
2001JournalLevy, Ellington (2001). Selection of deoxyribozyme ligases that catalyze the formation of an unnatural internucleotide linkage. Bioorg. Med. Chem., 9(10), pp. 2581–2587. (bib)
2001JournalSooter, Riedel, Davidson, Levy, Cox, Ellington (2001). Toward automated nucleic acid enzyme selection. Biol. Chem., 382(9), pp. 1327–1334. (bib)
2001JournalChelliserrykattil, Cai, Ellington (2001). A combined in vitro/in vivo selection for polymerases with novel promoter specificities. BMC Biotechnol., 1, pp. 13. (bib)
2001JournalPollard, Bell, Ellington (2001). Design, synthesis, and amplification of DNA pools for construction of combinatorial pools and libraries. Curr Protoc Mol Biol, Chapter 24, pp. Unit 24.2. (bib)
2001JournalJhaveri, Ellington (2001). In vitro selection of RNA aptamers to a protein target by filter immobilization. Curr Protoc Mol Biol, Chapter 24, pp. Unit 24.3. (bib)
2001JournalPollard, Bell, Ellington (2001). Design, synthesis, and amplification of DNA pools for in vitro selection. Curr Protoc Nucleic Acid Chem, Chapter 9, pp. Unit 9.2. (bib)
2001JournalJhaveri, Ellington (2001). In vitro selection of RNA aptamers to a protein target by filter immobilization. Curr Protoc Nucleic Acid Chem, Chapter 9, pp. Unit 9.3. (bib)
2000JournalHesselberth, Miller, Robertus, Ellington (2000). In vitro selection of RNA molecules that inhibit the activity of ricin A-chain. J. Biol. Chem., 275(7), pp. 4937–4942. (bib)
2000JournalHirao, Madin, Endo, Yokoyama, Ellington (2000). RNA aptamers that bind to and inhibit the ribosome-inactivating protein, pepocin. J. Biol. Chem., 275(7), pp. 4943–4948. (bib)
2000JournalRobertson, Ellington (2000). Design and optimization of effector-activated ribozyme ligases. Nucleic Acids Res., 28(8), pp. 1751–1759. (bib)
2000JournalEllington, Khrapov, Shaw (2000). The scene of a frozen accident. RNA, 6(4), pp. 485–498. (bib)
2000JournalMarshall, Ellington (2000). In vitro selection of RNA aptamers. Meth. Enzymol., 318, pp. 193–214. (bib)
2000JournalHesselberth, Robertson, Jhaveri, Ellington (2000). In vitro selection of nucleic acids for diagnostic applications. J. Biotechnol., 74(1), pp. 15–25. (bib)
2000JournalJhaveri, Rajendran, Ellington (2000). In vitro selection of signaling aptamers. Nat. Biotechnol., 18(12), pp. 1293–1297. (bib)
1999JournalMatsumura, Wallingford, Surana, Vize, Ellington (1999). Directed evolution of the surface chemistry of the reporter enzyme beta-glucuronidase. Nat. Biotechnol., 17(7), pp. 696–701. (bib)
1999JournalZidek, Stone, Lato, Pagel, Miao, Ellington, Novotny (1999). NMR mapping of the recombinant mouse major urinary protein I binding site occupied by the pheromone 2-sec-butyl-4,5-dihydrothiazole. Biochemistry, 38(31), pp. 9850–9861. (bib)
1999JournalJames, Ellington (1999). The fidelity of template-directed oligonucleotide ligation and the inevitability of polymerase function. Orig Life Evol Biosph, 29(4), pp. 375–390. (bib)
1999JournalMarshall, Ellington (1999). Molecular parasites that evolve longer genomes. J. Mol. Evol., 49(5), pp. 656–663. (bib)
1999JournalMarshall, Ellington (1999). Training ribozymes to switch. Nat. Struct. Biol., 6(11), pp. 992–994. (bib)
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