Ellington Lab

About The Ellington Lab

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

• Developing novel genetic codes and synthetic organisms based on engineering the translation apparatus.  

• Developing novel point-of-care diagnostics based on isothermal amplification and DNA computation.  

• Developing new methods for scalable assembly of protein architectures and programmed biomaterials.  
   

2023 Research

• Goike J, Hsieh CL, Horton AP, Gardner EC, Zhou L, Bartzoka F, Wang N, Javanmardi K, Herbert A, Abbassi S, Xie X, Xia H, Shi PY, Renberg R, Segall- Shapiro TH, Terrace CI, Wu W, Shroff R, Byrom M, Ellington AD, Marcotte EM, Musser JM, Kuchipudi SV, Kapur V, Georgiou G, Weaver SC, Dye JM, Boutz DR, McLellan JS, Gollihar JD. SARS-COV-2 Omicron variants conformationally escape a rare quaternary antibody binding mode. Commun Biol. 2023 Dec 11;6(1):1250. PMID: 38082099; PMCID: PMC10713552.

• Ngo PHT, Ishida S, Busogi BB, Do H, Ledesma MA, Kar S, Ellington A. Changes in Coding and Efficiency through Modular Modifications to a One Pot PURE System for In Vitro Transcription and Translation. ACS Synth Biol. 2023 Dec 15;12(12):3771-3777. doi: 10.1021/acssynbio.3c00461. Epub 2023 Dec 5. PMID: 38050859.

• Askari A, Kota S, Ferrell H, Swamy S, Goodman KS, Okoro CC, Spruell Crenshaw IC, Hernandez DK, Oliphant TE, Badrayani AA, Ellington AD, Stovall GM. UTexas Aptamer Database: the collection and long-term preservation of aptamer sequence information. Nucleic Acids Res. 2023 Oct 30:gkad959. Epub ahead of print. PMID: 37904593.

• Kumar N, Towers D, Myers S, Galvin C, Kireev D, Ellington AD, Akinwande D. Graphene Field Effect Biosensor for Concurrent and Specific Detection of SARS- CoV-2 and Influenza. ACS Nano. 2023 Sep 26;17(18):18629-18640. Epub 2023 Sep 13. PMID: 37703454.

• Wang B, Wang SS, Chalk C, Ellington AD, Soloveichik D. Parallel molecular computation on digital data stored in DNA. Proc Natl Acad Sci U S A. 2023 Sep 12;120(37):e2217330120. Epub 2023 Sep 5. PMID: 37669382; PMCID: PMC10500265.

• Kulikova AV, Diaz DJ, Chen T, Cole TJ, Ellington AD, Wilke CO. Two sequence- and two structure-based ML models have learned different aspects of protein biochemistry. Sci Rep. 2023 Aug 16;13(1):13280. PMID: 37587128; PMCID: PMC10432456.

• Maier JM, Valenzuela SA, Stok AV, Menta AK, Shimizu Y, Ngo PH, Ellington AD, Anslyn EV. Peptide Macrocyclization Guided by Reversible Covalent Templating. Chemistry. 2023 Jul 20:e202301949. Epub ahead of print. PMID: 37475574.

• Bhadra S, Esteve-Gasent MD, Ellington AD. Analysis of macerated ticks using Boolean logic gating colorimetric isothermal nucleic acid assays for Lyme Borrelia and Ixodes scapularis ticks. Sci Rep. 2023 Jul 15;13(1):11439. PMID: 37454160; PMCID: PMC10349842.

• Diaz DJ, Kulikova AV, Ellington AD, Wilke CO. Using machine learning to predict the effects and consequences of mutations in proteins. Curr Opin Struct Biol. 2023 Feb;78:102518. Epub 2023 Jan 3. PMID: 36603229; PMCID: PMC9908841.

• Dangerfield TL, Paik I, Bhadra S, Johnson KA, Ellington AD. Kinetics of elementary steps in loop-mediated isothermal amplification (LAMP) show that strand invasion during initiation is rate-limiting. Nucleic Acids Res. 2023 Jan 11;51(1):488-499. PMID: 36583345; PMCID: PMC9841402.

• Szmuc E, Walker DJF, Kireev D, Akinwande D, Lovley DR, Keitz B, Ellington A. Engineering Geobacter pili to produce metal:organic filaments. Biosens Bioelectron. 2023 Feb 15;222:114993. Epub 2022 Dec 6. PMID: 36525710.

2022 Research

• Lee J, Coronado JN, Cho N, Lim J, Hosford BM, Seo S, Kim DS, Kofman C, Moore JS, Ellington AD, Anslyn EV, Jewett MC. Ribosome-mediated biosynthesis of pyridazinone oligomers in vitro. Nat Commun. 2022 Oct 24;13(1):6322. PMID: 36280685; PMCID: PMC9592601.

• d'Oelsnitz S, Love JD, Diaz DJ, Ellington AD. GroovDB: A Database of Ligand- Inducible Transcription Factors. ACS Synth Biol. 2022 Oct 21;11(10):3534-3537. Epub 2022 Sep 30. PMID: 36178800.

• Javanmardi K, Segall-Shapiro TH, Chou CW, Boutz DR, Olsen RJ, Xie X, Xia H, Shi PY, Johnson CD, Annapareddy A, Weaver S, Musser JM, Ellington AD, Finkelstein IJ, Gollihar JD. Antibody escape and cryptic cross-domain stabilization in the SARS-CoV-2 Omicron spike protein. Cell Host Microbe. 2022 Sep 14;30(9):1242-1254.e6. Epub 2022 Aug 4. PMID: 35988543; PMCID: PMC9350683.

• Watts E, Thyer R, Ellington AD, Brodbelt JS. Integrated Top-Down and Bottom- Up Mass Spectrometry for Characterization of Diselenide Bridging Patterns of Synthetic Selenoproteins. Anal Chem. 2022 Aug 16;94(32):11175-11184. Epub 2022 Aug 5. PMID: 35930618.

• Simmons TR, Ellington AD, Contreras LM. RNP-Based Control Systems for Genetic Circuits in Synthetic Biology Beyond CRISPR. Methods Mol Biol. 2022;2518:1-31. PMID: 35666436.

• S d’Oelsnitz, W Kim, NT Burkholder, K Javanmardi, R Thyer, Y Zhang, HS Alper and AD Ellington. Using fungible biosensors to evolve improved alkaloid biosyntheses. Nature Chemical Biology, 1-9. July 7, 2022.

• AD Ellington, D Diaz, I Paik. The Coming Congruence of Synthetic Biology and Machine Learning for Engineering Life. 2022 Astrobiology Science Conference. May 15, 2022.

• H Lu, DJ Diaz, NJ Czarnecki, C Zhu, W Kim, R Shroff, DJ Acosta, ... AD Ellington.... Machine learning-aided engineering of hydrolases for PET depolymerization. Nature 604 (7907), 662-667. April 27, 2022.

• JN Coronado, P Ngo, EV Anslyn, AD Ellington. Chemical insights into flexizyme-mediated tRNA acylation. Cell Chemical Biology. April 11, 2022

• I Paik, S Bhadra, AD Ellington. Charge Engineering Improves the Performance of Bst DNA Polymerase Fusions. ACS Synthetic Biology 11 (4), 1488-1496. March 23, 2022.

• S Bhadra, I Paik, JA Torres, S Fadanka, C Gandini, H Akligoh, J Molloy, ... AD Ellington. Preparation and Use of Cellular Reagents: A Low‐resource Molecular Biology Reagent Platform. Current Protocols 2 (3), e387. March 8, 2022.

• R Mackelprang, KP Adamala, ER Aurand, JC Diggans, AD Ellington, ... Making Security Viral: Shifting Engineering Biology Culture and Publishing. ACS synthetic biology 11 (2), 522-527. February 18, 2022.

• R Shroff, JW Ellefson, SS Wang, AA Boulgakov, RA Hughes, AD Ellington. Recovery of Information Stored in Modified DNA with an Evolved Polymerase. ACS Synthetic Biology 11 (2), 554-561. February 3, 2022.

• S d’Oelsnitz, V Nguyen, HS Alper, AD Ellington. Evolving a Generalist Biosensor for Bicyclic Monoterpenes. ACS Synthetic Biology 11 (1), 265-272. January 5, 2022.

• S Kar, Y Bordiya, N Rodriguez, J Kim, EC Gardner, JD Gollihar, S Sung, ... AD Ellington. Orthogonal control of gene expression in plants using synthetic promoters and CRISPR-based transcription factors. Research Square (preprint). January 3, 2022.

• K Javanmardi, TH Segall-Shapiro, CW Chou, DR Boutz, RJ Olsen, X Xie, ... AD Ellington. Antibody escape and cryptic cross-domain stabilization in the SARS-CoV-2 Omicron spike protein. bioRxiv. January 1, 2022.

   

2021 Research

• CJ Toft, MJJ Moreau, J Perutka, S Mandapati, P Enyeart, AE Sorenson, ... Delineation of the Ancestral Tus-Dependent Replication Fork Trap.  International Journal of Molecular Sciences 22 (24), 135332021. December 16, 2021.

• AW Cole, SD Tran, AD Ellington. Heat adaptation of phage T7 under an extended genetic code. Virus Evolution 7 (2), veab1002021. December 1, 2021.

• I Paik, PHT Ngo, R Shroff, DJ Diaz, AC Maranhao, DJF Walker, S Bhadra, ... Improved Bst DNA Polymerase Variants Derived via a Machine Learning Approach. Biochemistry. November 11, 2021.

• AV Kulikova, DJ Diaz, JM Loy, AD Ellington, CO Wilke. Learning the local landscape of protein structures with convolutional neural networks. Journal of Biological Physics 47 (4), 435-4542021. November 9, 2021

• KK Miller, SK Springthorpe, J Imbrogno, DJF Walker, S Gadiyar, BK Keitz, ... Biocompatible Materials Enabled by Biobased Production of Pyomelanin Isoforms Using an Engineered Yarrowia lipolytica. Advanced Functional Materials, 21093662021. November 5, 2021.

• J Carvalho, J Lopes-Nunes, B Vialet, T Rosado, E Gallardo, J Vale, ... Nanoaggregate-forming lipid-conjugated AS1411 aptamer as a promising tumor-targeted delivery system of anticancer agents in vitro. Nanomedicine: Nanotechnology, Biology and Medicine 36, 1024292021. August 2021.

• K Dinkeloo, AM Cantero, I Paik, A Vulgamott, AD Ellington, A Lloyd. Genetic transformation technologies for the common dandelion, Taraxacum officinale. Plant Methods 17 (1), 1-812021. June 9, 2021.

• S Bhadra, V Nguyen, JA Torres, S Kar, S Fadanka, C Gandini, H Akligoh, ... Producing molecular biology reagents without purification. PloS one 16 (6), e025250722021. June 1, 2021.

• HH Smith, AS Hyde, DN Simkus, E Libby, SE Maurer, HV Graham, ... The Grayness of the Origin of Life. Life 11 (6), 4982021. May 29, 2021.

• S Bhadra, TE Riedel, S Lakhotia, ND Tran, AD Ellington. High-surety isothermal amplification and detection of SARS-CoV-2. Msphere 6 (3), e00911-2072021. May 19, 2021.

• E Xiong, D Yao, AD Ellington, S Bhadra. Minimizing Leakage in Stacked Strand Exchange Amplification Circuits. ACS Synthetic Biology May 18, 2021.

• R Mackelprang, ER Aurand, RAL Bovenberg, KR Brink, RA Charo, ...Guiding Ethical Principles in Engineering Biology Research. ACS synthetic biology12021. May 12, 2021.

• R Thyer, S d'Oelsnitz, MS Blevins, DR Klein, JS Brodbelt, AD Ellington. Directed evolution of an improved aminoacyl‐tRNA synthetase for incorporation of L‐3, 4‐dihydroxyphenylalanine (L‐DOPA). Angewandte Chemie 42021. April 19, 2021.

• LL Chou, N Grefenstette, SS Johnson, H Graham, P Mahaffy, C Kempes, ...Towards a more universal life detection strategy Bulletin of the American Astronomical Society 53 (4), 18112021. March 18, 2021.

• JT Van Leuven, MM Ederer, K Burleigh, LA Scott, RA Hughes, V Codrea, ... ΦX174 Attenuation by Whole-Genome Codon Deoptimization. Genome biology and evolution 13 (2), evaa21432021. February, 2021.

• S Bhadra, AC Maranhao, I Paik, AD Ellington. A one-enzyme RT-qPCR assay for SARS-CoV-2, and procedures for reagent production. Bio-protocol 11 (2), e3898-e3898202021. January 20, 2021.

• TM Wannier, PN Ciaccia, AD Ellington, GT Filsinger, FJ Isaacs, ... Recombineering and MAGE. Nature Reviews Methods Primers 1 (1), 1-2482021. January 14, 2021.

• S Kar, Y Bordiya, N Rodriguez, J Kim, EC Gardner, J Gollihar, S Sung, ... Orthogonal control of gene expression in plants using synthetic promoters and CRISPR-based transcription factors. bioRxiv 2021.

• AA Miller, AS Rao, SR Nelakanti, C Kujalowicz, T Shi, T Rodriguez, ... Systematic Review of Aptamer Sequence Reporting in the Literature Reveals Widespread Unexplained Sequence Alterations. bioRxiv 2021.

• H Lu, DJ Diaz, NJ Czarnecki, CJ Zhu, W Kim, DJ Acosta, B Alexander, ... Deep learning redesign of PETase for practical PET degrading applications. bioRxiv 2021.

• S d’Oelsnitz, V Nguyen, HS Alper, AD Ellington. Evolving a generalist biosensor for bicyclic monoterpenes. bioRxiv 12021.

• C Toft, M Moreau, J Perutka, S Mandapati, P Enyeart, A Sorenson, ...Defining the prototypical DNA replication fork trap in bacteria. bioRxiv 2021.

• S d'Oelsnitz, W Kim, NT Burkholder, R Thyer, Y Zhang, HS Alper, ... Using structurally fungible biosensors to evolve improved alkaloid biosyntheses. bioRxiv 2021.

• BDM Bean, CJ Mulvihill, RK Garge, DR Boutz, O Rousseau, BM Floyd, ... Functional expression of opioid receptors and other human GPCRs in yeast engineered to produce human sterols. bioRxiv 2021.

• I Paik, PHT Ngo, R Shroff, AC Maranhao, DJF Walker, S Bhadra, ... Multi-modal engineering of Bst DNA polymerase for thermostability in ultra-fast LAMP reactions. bioRxiv 2021.

• JD Gollihar, JS McLellan, DR Boutz, J Goike, A Horton, EC Gardner, ...Synthetic repertoires derived from convalescent COVID-19 patients enable discovery of SARS-CoV-2 neutralizing antibodies and a novel quaternary binding modality. bioRxiv 2021.

• J Lee, KJ Schwarz, H Yu, A Krüger, EV Anslyn, AD Ellington, JS Moore, ... Ribosome-mediated incorporation of fluorescent amino acids into peptides in vitro. Chemical Communications 57 (21), 2661-2664. 2021.

2020 Research

• F Zhang, & AD Ellington. Hurdling and hurtling toward new genetic codes. ACS Central Science. December 10, 2020.

• R Shroff, AW Cole, DJ Diaz, BR Morrow, I Donnell, A Annapareddy, J Gollihar, AD Ellington, & R Thyer. Discovery of novel gain-of-function mutations guided by structure-based deep learning. ACS Synthetic Biology. October 16, 2020.

• WS Choi, P He, A Pothukuchy, J Gollihar, AD Ellington, & W Yang. 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. June 15, 2020.

• JTV Leuven, MM Ederer, K Burleigh, L Scott, RA Hughes, V Codrea, AD Ellington, H Wichman, & C Miller. Φx174 attenuation by whole genome codon deoptimization. BioRxiv, 2020.02.10.942847.  2020.

• N Li, T Larson, HH Nguyen, KV Sokolov, & AD Ellington. Directed evolution of gold nanoparticle delivery to cells (vol 46, pg 392, 2010). CHEMICAL COMMUNICATIONS, 56(31), 4368-4368.  2020.

• TT Le, A Bruckbauer, B Tahirbegi, AJ Magness, L Ying, AD Ellington, & AEG Cass. A highly stable RNA aptamer probe for the retinoblastoma protein in live cells. Chemical Science, 11(17), 4467–4474.  2020.

• H Tanno, JR McDaniel, CA Stevens, WN Voss, J Li, R Durrett, J Lee, J Gollihar, Y Tanno, G Delidakis, A Pothukuchy, JW Ellefson, JJ Goronzy, JA Maynard, AD Ellington, GC Ippolito, & G Georgiou. A facile technology for the high-throughput sequencing of the paired VH:VL and TCRβ:TCRα repertoires. Science Advances, 6(17), eaay9093. April 22, 2020.

• M Zamanian-Daryoush, V Gogonea, AJ DiDonato, JA Buffa, I Choucair, BS Levison, RA Hughes, AD Ellington, Y Huang, XS Li, JA DiDonato, & SL Hazen. 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. April 2020.

• D Yao, S Bhadra, E Xiong, H Liang, AD Ellington, & C Jung. Dynamic programming of a dna walker controlled by protons. ACS Nano, 14(4), 4007–4013. March 13, 2020.

• AA Boulgakov, AD Ellington, & EM Marcotte. (2020). Bringing microscopy-by-sequencing into view. Trends in Biotechnology, 38(2), 154–162. February 1, 2020.

• H Tanno, J McDaniel, C Stevens, W Voss, J Li, R Durrett, J Lee, J Gollihar, Y Tanno, G Delidakis, A Pothukuchy, J Ellefson, J Goronzy, J Maynard, A Ellington, G Ippolito, & G Georgiou. 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.  2020.

• SP Leonard, JE Powell, J Perutka, P Geng, LC Heckmann, RD Horak, BW Davies, AD Ellington, JE Barrick, & NA Moran.  Engineered symbionts activate honey bee immunity and limit pathogens. Science, 367(6477), 573–576. January 30, 2020.

• NK Agrawal, P Allen, YH Song, RA Wachs, Y Du, AD Ellington, & CE Schmidt. (2020). Oligonucleotide-functionalized hydrogels for sustained release of small molecule (Aptamer) therapeutics. Acta Biomaterialia, 102, 315–325. January 15, 2020.

• S Bhadra, AC Maranhao, & AD Ellington. A one-enzyme RT-qPCR assay for SARS-CoV-2, and procedures for reagent production. BioRxiv, 2020.03.29.013342. 2020.

• S Bhadra, AC Maranhao, & AD Ellington . One enzyme reverse transcription qPCR using Taq DNA polymerase. BioRxiv, 2020.05.27.120238.  2020.

• EC Gardner, EJ Watkins, J Gollihar, & AD Ellington. Emulsion-based directed evolution of enzymes and proteins in yeast. In Methods in Enzymology. Academic Press.  2020.

• J Lee, BS Der, CS Karamitros, W Li, NM Marshall, OI Lungu, AE Miklos, J Xu, TH Kang, C-H Lee, B Tan, RA Hughes, ST Jung, GC Ippolito, JJ Gray, Y Zhang, B Kuhlman, G Georgiou, & AD Ellington. Computer-based engineering of thermostabilized antibody fragments. AIChE Journal, 66(3), e16864.  2020.