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A. Ellington · SciRah

Researcher profile · Semantic Scholar

A. Ellington

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A. Ellington — researcher profile on SciRah

h-index: 96
Works: 517
Citations: 43K

Most-cited papers

Machine learning-aided engineering of hydrolases for PET depolymerization
Hongyuan Lu, D. Diaz, Natalie J. Czarnecki, Congzhi Zhu +9 more
2022Nature1,000 citations
Semantic Scholar
Hachimoji DNA and RNA. A Genetic System with Eight Building Blocks
Shuichi Hoshika, Nicole A. Leal, M. Kim, Myong-Sang Kim +12 more
2019Science364 citations Open access
Semantic Scholar
Effective design principles for leakless strand displacement systems
Boya Wang, Chris Thachuk, A. Ellington, E. Winfree +1 more
2018Proceedings of the National Academy of Sciences of the United States of America133 citations Open access
Semantic Scholar
Functional Interrogation and Mining of Natively-Paired Human VH:VL Antibody Repertoires
Bo Wang, B. J. Dekosky, Morgan Timm, Jiwon Lee +29 more
2018Nature Biotechnology126 citations Open access
Semantic Scholar
Discovery of Novel Gain-of-Function Mutations Guided by Structure-Based Deep Learning.
Raghav Shroff, Austin W Cole, D. Diaz, Barrett R. Morrow +5 more
2020ACS Synthetic Biology118 citations
Semantic Scholar
Microbiota and Metatranscriptome Changes Accompanying the Onset of Gingivitis
Emily M. Nowicki, Raghav Shroff, J. Singleton, D. Renaud +8 more
2018mBio106 citations Open access
Semantic Scholar
Strand Displacement Probes Combined with Isothermal Nucleic Acid Amplification for Instrument-Free Detection from Complex Samples
Elizabeth A Phillips, Taylor J Moehling, S. Bhadra, A. Ellington +1 more
2018Analytical Chemistry99 citations Open access
Semantic Scholar
Retrons and their applications in genome engineering
Anna J. Simon, A. Ellington, I. Finkelstein
2019Nucleic Acids Research96 citations Open access
Semantic Scholar
Dynamic Programming of a DNA Walker Controlled by Protons.
Dongbao Yao, S. Bhadra, Erhu Xiong, Haojun Liang +2 more
2020ACS Nano95 citations
Semantic Scholar
Recombineering and MAGE
T. Wannier, Peter N. Ciaccia, A. Ellington, Gabriel T. Filsinger +8 more
2021Nature Reviews Methods Primers89 citations Open access
Semantic Scholar
Using fungible biosensors to evolve improved alkaloid biosyntheses
Simon d'Oelsnitz, Wantae Kim, Nathaniel T. Burkholder, Kamyab Javanmardi +4 more
2022Nature Chemical Biology88 citations Open access
Semantic Scholar
Phosphorothioated Primers Lead to Loop-Mediated Isothermal Amplification at Low Temperatures.
Sheng Cai, C. Jung, S. Bhadra, A. Ellington
2018Analytical Chemistry88 citations
Semantic Scholar
Expanding the limits of the second genetic code with ribozymes
Joongoo Lee, Kenneth E. Schwieter, A. Watkins, Do Soon Kim +9 more
2019Nature Communications85 citations Open access
Semantic Scholar
Synthetic evolution
Anna J. Simon, Simon d'Oelsnitz, A. Ellington
2019Nature Biotechnology82 citations
Semantic Scholar
High-Surety Isothermal Amplification and Detection of SARS-CoV-2
S. Bhadra, T. Riedel, S. Lakhotia, N. Tran +1 more
2020bioRxiv81 citations
Semantic Scholar
Supercharging enables organized assembly of synthetic biomolecules
Anna J. Simon, Yi Zhou, Vyas Ramasubramani, Jens Glaser +9 more
2019Nature Chemistry70 citations Open access
Semantic Scholar
Directed evolution of a synthetic phylogeny of programmable Trp repressors
J. Ellefson, Michael P. Ledbetter, A. Ellington
2018Nature Chemical Biology62 citations
Semantic Scholar
Improved Bst DNA Polymerase Variants Derived via a Machine Learning Approach
I. Paik, Phuoc H. T. Ngo, Raghav Shroff, D. Diaz +4 more
2021Biochemistry57 citations Open access
Semantic Scholar
Using machine learning to predict the effects and consequences of mutations in proteins
D. Diaz, Anastasiya V. Kulikova, A. Ellington, C. Wilke
2023Current Opinion in Structural Biology54 citations Open access
Semantic Scholar
Kinetics of elementary steps in loop-mediated isothermal amplification (LAMP) show that strand invasion during initiation is rate-limiting
Tyler L. Dangerfield, I. Paik, S. Bhadra, K. Johnson +1 more
2022Nucleic Acids Research52 citations Open access
Semantic Scholar
Evolving a generalist biosensor for bicyclic monoterpenes
Simon d'Oelsnitz, V. Nguyen, H. Alper, A. Ellington
2021bioRxiv51 citations Open access
Semantic Scholar
Custom selenoprotein production enabled by laboratory evolution of recoded bacterial strains
Ross Thyer, Raghav Shroff, Dustin R. Klein, Simon d'Oelsnitz +4 more
2018Nature Biotechnology43 citations Open access
Semantic Scholar
Pattern Generation with Nucleic Acid Chemical Reaction Networks.
Siyuan S Wang, A. Ellington
2019Chemical Reviews38 citations
Semantic Scholar
Evolution of a Thermophilic Strand-Displacing Polymerase Using High-Temperature Isothermal Compartmentalized Self-Replication.
John N. Milligan, Raghav Shroff, D. Garry, A. Ellington
2018Biochemistry38 citations Open access
Semantic Scholar
Parallel molecular computation on digital data stored in DNA
Boya Wang, Siyuan S Wang, Cameron T. Chalk, A. Ellington +1 more
2022bioRxiv35 citations Open access
Semantic Scholar
One enzyme reverse transcription qPCR using Taq DNA polymerase
S. Bhadra, A. C. Maranhao, I. Paik, A. Ellington
2020bioRxiv34 citations Open access
Semantic Scholar
Single-Molecule Mechanistic Study of Enzyme Hysteresis
Yu Jiang, Xiang Li, Barrett R. Morrow, A. Pothukuchy +5 more
2019ACS Central Science34 citations Open access
Semantic Scholar
HotProtein: A Novel Framework for Protein Thermostability Prediction and Editing
Tian-Long Chen, Chengyue Gong, D. Diaz, Xuxi Chen +6 more
2023International Conference on Learning Representations33 citations
Semantic Scholar
Antibody escape and cryptic cross-domain stabilization in the SARS-CoV-2 Omicron spike protein
Kamyab Javanmardi, Thomas H. Segall-Shapiro, Chia-Wei Chou, D. Boutz +11 more
2022Cell Host and Microbe33 citations Open access
Semantic Scholar
Charge Engineering Improves the Performance of Bst DNA Polymerase Fusions
I. Paik, S. Bhadra, A. Ellington
2022ACS Synthetic Biology33 citations Open access
Semantic Scholar
Orthogonal control of gene expression in plants using synthetic promoters and CRISPR-based transcription factors
Shaunak Kar, Yogendra Bordiya, Nestor Rodriguez, Junghyun Kim +4 more
2021Plant Methods29 citations Open access
Semantic Scholar
Directed evolution of an improved aminoacyl-tRNA synthetase for incorporation of L-3,4-dihydroxyphenylalanine (L-DOPA)
Ross Thyer, Simon d'Oelsnitz, Molly S. Blevins, Dustin R. Klein +2 more
2021Angewandte Chemie29 citations Open access
Semantic Scholar
Construction of synthetic T7 RNA polymerase expression systems.
Shaunak Kar, A. Ellington
2018Methods28 citations
Semantic Scholar
Functional expression of opioid receptors and other human GPCRs in yeast engineered to produce human sterols
Björn D. M. Bean, Colleen J. Mulvihill, Riddhiman K. Garge, D. Boutz +9 more
2021Nature Communications26 citations Open access
Semantic Scholar
A one-enzyme RT-qPCR assay for SARS-CoV-2, and procedures for reagent production
S. Bhadra, A. C. Maranhao, I. Paik, A. Ellington
2020bioRxiv25 citations Open access
Semantic Scholar
Ribosomal incorporation of cyclic β-amino acids into peptides using in vitro translation.
Joongoo Lee, Rafael Torres, Do Soon Kim, M. Byrom +2 more
2020Chemical Communications25 citations
Semantic Scholar
A facile technology for the high-throughput sequencing of the paired VH:VL and TCRβ:TCRα repertoires
Hidetaka Tanno, Jonathan R. McDaniel, Christopher A. Stevens, William N. Voss +13 more
2020Science Advances25 citations Open access
Semantic Scholar
The Grayness of the Origin of Life
Hillary H. Smith, A. Hyde, D. Simkus, E. Libby +12 more
2021Life24 citations Open access
Semantic Scholar
Systematic Review of Aptamer Sequence Reporting in the Literature Reveals Widespread Unexplained Sequence Alterations
Alexandra A. Miller, Abhijith Rao, Sujana R. Nelakanti, Christopher Kujalowicz +4 more
2021bioRxiv24 citations Open access
Semantic Scholar
Cellular reagents for diagnostics and synthetic biology
S. Bhadra, A. Pothukuchy, Raghav Shroff, Austin W Cole +4 more
2018PLoS ONE24 citations Open access
Semantic Scholar
Direct nucleic acid analysis of mosquitoes for high fidelity species identification and detection of Wolbachia using a cellphone
S. Bhadra, T. Riedel, Miguel A. Saldaña, Shivanand Hegde +3 more
2018bioRxiv24 citations Open access
Semantic Scholar
GroovDB: A Database of Ligand-Inducible Transcription Factors
Simon d'Oelsnitz, Joshua D. Love, D. Diaz, A. Ellington
2022bioRxiv23 citations Open access
Semantic Scholar
Chemical insights into flexizyme-mediated tRNA acylation.
Jaime N. Coronado, Phuoc H. T. Ngo, E. Anslyn, A. Ellington
2022Cell Chemical Biology21 citations Open access
Semantic Scholar
Producing molecular biology reagents without purification
S. Bhadra, Vylan Nguyen, Jose-Angel Torres, Shaunak Kar +7 more
2021PLoS ONE21 citations Open access
Semantic Scholar
Learning the local landscape of protein structures with convolutional neural networks
Anastasiya V. Kulikova, D. Diaz, James M. Loy, A. Ellington +1 more
2021Journal of biological physics (Print)21 citations Open access
Semantic Scholar
Snowprint: a predictive tool for genetic biosensor discovery
Simon d'Oelsnitz, Sarah K. Stofel, Joshua D. Love, A. Ellington
2023bioRxiv20 citations Open access
Semantic Scholar
Ribosome-mediated biosynthesis of pyridazinone oligomers in vitro
Joongoo Lee, Jaime N. Coronado, Namjin Cho, Jongdoo Lim +8 more
2022Nature Communications20 citations Open access
Semantic Scholar
Nanoaggregate-forming lipid-conjugated AS1411 aptamer AS a promising tumor-targeted delivery system of anticancer agents in vitro.
Josué Carvalho, Jéssica Lopes-Nunes, Brune Vialet, T. Rosado +13 more
2021Nanomedicine: Nanotechnology, Biology and Medicine19 citations
Semantic Scholar
ΦX174 Attenuation by Whole-Genome Codon Deoptimization
J. T. Van Leuven, M. Ederer, Katelyn Burleigh, L. Scott +5 more
2020bioRxiv18 citations Open access
Semantic Scholar
Site-specific 5-hydroxytryptophan incorporation into apolipoprotein A-I impairs cholesterol efflux activity and high-density lipoprotein biogenesis
M. Zamanian-Daryoush, V. Gogonea, Anthony j. DiDonato, J. Buffa +8 more
2020Journal of Biological Chemistry17 citations Open access
Semantic Scholar

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Simon d'Oelsnitz

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