Andrew D Ellington (Andrew Ellington)

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 61

Top Topics

Machine Learning

Gold Nanoparticles

Top Venues

ACS synthetic biology

Nature communications

Communications biology

This page only lists publications with an associated author ORCID identifier.

Publications

Simon D'Oelsnitz, Joshua D Love, Andrew D Ellington, David Ross
Ligify: Automated Genome Mining for Ligand-Inducible Transcription Factors. ACS synthetic biology 13 (8) (2024)
Simon D'Oelsnitz, Sarah K Stofel, Joshua D Love, Andrew D Ellington
Snowprint: a predictive tool for genetic biosensor discovery. Communications biology 7 (1) (2024)
Simon D'Oelsnitz, Joshua D Love, Andrew D Ellington, David Ross
Ligify: Automated Genome Mining for Ligand-Inducible Transcription Factors. ACS synthetic biology 13 (8) (2024)
Daniel J Diaz, Chengyue Gong, Jeffrey Ouyang-Zhang, James M Loy, Jordan Wells, David Yang, Andrew D Ellington, Alexandros G Dimakis, Adam R Klivans
Stability Oracle: a structure-based graph-transformer framework for identifying stabilizing mutations. Nature communications 15 (1) (2024)
Simon D'Oelsnitz, Daniel J Diaz, Wantae Kim, Daniel J Acosta, Tyler L Dangerfield, Mason W Schechter, Matthew B Minus, James R Howard, Hannah Do, James M Loy, Hal S Alper, Yan Jessie Zhang, Andrew D Ellington
Biosensor and machine learning-aided engineering of an amaryllidaceae enzyme. Nature communications 15 (1) (2024)
Daniel J Diaz, Chengyue Gong, Jeffrey Ouyang-Zhang, James M Loy, Jordan Wells, David Yang, Andrew D Ellington, Alexandros G Dimakis, Adam R Klivans
Stability Oracle: a structure-based graph-transformer framework for identifying stabilizing mutations. Nature communications 15 (1) (2024)
Satoshi Ishida, Phuoc H T Ngo, Arno Gundlach, Andrew D Ellington
Engineering Ribosomal Machinery for Noncanonical Amino Acid Incorporation. Chemical reviews 124 (12) (2024)
Simon D'Oelsnitz, Sarah K Stofel, Joshua D Love, Andrew D Ellington
Snowprint: a predictive tool for genetic biosensor discovery. Communications biology 7 (1) (2024)
Simon D'Oelsnitz, Joshua D Love, Andrew D Ellington, David Ross
Ligify: Automated Genome Mining for Ligand-Inducible Transcription Factors. ACS synthetic biology 13 (8) (2024)
Simon D'Oelsnitz, Sarah K Stofel, Joshua D Love, Andrew D Ellington
Snowprint: a predictive tool for genetic biosensor discovery. Communications biology 7 (1) (2024)
Daniel J Diaz, Chengyue Gong, Jeffrey Ouyang-Zhang, James M Loy, Jordan Wells, David Yang, Andrew D Ellington, Alexandros G Dimakis, Adam R Klivans
Stability Oracle: a structure-based graph-transformer framework for identifying stabilizing mutations. Nature communications 15 (1) (2024)
Simon D'Oelsnitz, Daniel J Diaz, Wantae Kim, Daniel J Acosta, Tyler L Dangerfield, Mason W Schechter, Matthew B Minus, James R Howard, Hannah Do, James M Loy, Hal S Alper, Yan Jessie Zhang, Andrew D Ellington
Biosensor and machine learning-aided engineering of an amaryllidaceae enzyme. Nature communications 15 (1) (2024)
Clayton W Kosonocky, Claus O Wilke, Edward M Marcotte, Andrew D Ellington
Mining patents with large language models elucidates the chemical function landscape. Digital discovery 3 (6) (2024)
Clayton W Kosonocky, Claus O Wilke, Edward M Marcotte, Andrew D Ellington
Mining patents with large language models elucidates the chemical function landscape. Digital discovery 3 (6) (2024)
Simon D'Oelsnitz, Sarah K Stofel, Joshua D Love, Andrew D Ellington
Snowprint: a predictive tool for genetic biosensor discovery. Communications biology 7 (1) (2024)
Simon D'Oelsnitz, Sarah K Stofel, Joshua D Love, Andrew D Ellington
Snowprint: a predictive tool for genetic biosensor discovery. Communications biology 7 (1) (2024)
Clayton W Kosonocky, Claus O Wilke, Edward M Marcotte, Andrew D Ellington
Mining patents with large language models elucidates the chemical function landscape. Digital discovery 3 (6) (2024)
Simon D'Oelsnitz, Joshua D Love, Andrew D Ellington, David Ross
Ligify: Automated Genome Mining for Ligand-Inducible Transcription Factors. ACS synthetic biology (2024)
Simon D'Oelsnitz, Daniel J Diaz, Wantae Kim, Daniel J Acosta, Tyler L Dangerfield, Mason W Schechter, Matthew B Minus, James R Howard, Hannah Do, James M Loy, Hal S Alper, Yan Jessie Zhang, Andrew D Ellington
Biosensor and machine learning-aided engineering of an amaryllidaceae enzyme. Nature communications 15 (1) (2024)
Satoshi Ishida, Phuoc H T Ngo, Arno Gundlach, Andrew D Ellington
Engineering Ribosomal Machinery for Noncanonical Amino Acid Incorporation. Chemical reviews (2024)
Clayton W Kosonocky, Claus O Wilke, Edward M Marcotte, Andrew D Ellington
Mining patents with large language models elucidates the chemical function landscape. Digital discovery 3 (6) (2024)
Simon D'Oelsnitz, Daniel J Diaz, Wantae Kim, Daniel J Acosta, Tyler L Dangerfield, Mason W Schechter, Matthew B Minus, James R Howard, Hannah Do, James M Loy, Hal S Alper, Yan Jessie Zhang, Andrew D Ellington
Biosensor and machine learning-aided engineering of an amaryllidaceae enzyme. Nature communications 15 (1) (2024)
Ali Askari, Sumedha Kota, Hailey Ferrell, Shriya Swamy, Kayla S Goodman, Christine C Okoro, Isaiah C Spruell Crenshaw, Daniela K Hernandez, Taylor E Oliphant, Akshata A Badrayani, Andrew D Ellington, Gwendolyn M Stovall
UTexas Aptamer Database: the collection and long-term preservation of aptamer sequence information. Nucleic acids research (2023)
Anastasiya V Kulikova, Daniel J Diaz, Tianlong Chen, T Jeffrey Cole, Andrew D Ellington, Claus O Wilke
Two sequence- and two structure-based ML models have learned different aspects of protein biochemistry. Scientific reports 13 (1) (2023)
Clayton W Kosonocky, Andrew D Ellington
Evolving to Evolve, Dan Tawfik's Insights into Protein Engineering. Biochemistry 62 (2) (2023)
Anastasiya V Kulikova, Daniel J Diaz, Tianlong Chen, T Jeffrey Cole, Andrew D Ellington, Claus O Wilke
Sequence and structure based deep learning models represent different aspects of protein biochemistry. bioRxiv : the preprint server for biology (2023)
Clayton W Kosonocky, Andrew D Ellington
Evolving to Evolve, Dan Tawfik's Insights into Protein Engineering. Biochemistry 62 (2) (2023)
Jule Goike, Ching-Lin Hsieh, Andrew P Horton, Elizabeth C Gardner, Ling Zhou, Foteini Bartzoka, Nianshuang Wang, Kamyab Javanmardi, Andrew Herbert, Shawn Abbassi, Xuping Xie, Hongjie Xia, Pei-Yong Shi, Rebecca L Renberg, Thomas H Segall-Shapiro, Cynthia I Terrace, Wesley Wu, Raghav Shroff, Michelle Byrom, Andrew D Ellington, Edward M Marcotte, James M Musser, Suresh V Kuchipudi, Vivek Kapur, George Georgiou, Scott C Weaver, John M Dye, Daniel R Boutz, Jason S Mclellan, Jimmy D Gollihar
SARS-COV-2 Omicron variants conformationally escape a rare quaternary antibody binding mode. Communications biology 6 (1) (2023)
Neelotpala Kumar, Dalton Towers, Samantha Myers, Cooper Galvin, Dmitry Kireev, Andrew D Ellington, Deji Akinwande
Graphene Field Effect Biosensor for Concurrent and Specific Detection of SARS-CoV-2 and Influenza. ACS nano (2023)
Phuoc H T Ngo, Satoshi Ishida, Bianca B Busogi, Hannah Do, Maximiliano A Ledesma, Shaunak Kar, Andrew D Ellington
Changes in Coding and Efficiency through Modular Modifications to a One Pot PURE System for In Vitro Transcription and Translation. ACS synthetic biology (2023)
Simon D'Oelsnitz, Wantae Kim, Nathaniel T Burkholder, Kamyab Javanmardi, Ross Thyer, Yan Jessie Zhang, Hal S Alper, Andrew D Ellington
Using fungible biosensors to evolve improved alkaloid biosyntheses. Nature chemical biology 18 (9) (2022)
Inyup Paik, Sanchita Bhadra, Andrew D Ellington
Charge Engineering Improves the Performance of Bst DNA Polymerase Fusions. ACS synthetic biology 11 (4) (2022)
Joongoo Lee, Jaime N Coronado, Namjin Cho, Jongdoo Lim, Brandon M Hosford, Sangwon Seo, Do Soon Kim, Camila Kofman, Jeffrey S Moore, Andrew D Ellington, Eric V Anslyn, Michael C Jewett
Ribosome-mediated biosynthesis of pyridazinone oligomers in vitro. Nature communications 13 (1) (2022)
Björn D M Bean, Colleen J Mulvihill, Riddhiman K Garge, Daniel R Boutz, Olivier Rousseau, Brendan M Floyd, William Cheney, Elizabeth C Gardner, Andrew D Ellington, Edward M Marcotte, Jimmy D Gollihar, Malcolm Whiteway, Vincent J J Martin
Functional expression of opioid receptors and other human GPCRs in yeast engineered to produce human sterols. Nature communications 13 (1) (2022)
Raghav Shroff, Jared W Ellefson, Siyuan Stella Wang, Alexander A Boulgakov, Randall A Hughes, Andrew D Ellington
Recovery of Information Stored in Modified DNA with an Evolved Polymerase. ACS synthetic biology 11 (2) (2022)
Rebecca Mackelprang, Katarzyna P Adamala, Emily R Aurand, James C Diggans, Andrew D Ellington, Samuel Weiss Evans, J L Clem Fortman, Nathan J Hillson, Albert W Hinman, Farren J Isaacs, June I Medford, Shadi Mamaghani, Tae Seok Moon, Megan J Palmer, Jean Peccoud, Elizabeth A Vitalis, India Hook-Barnard, Douglas C Friedman
Making Security Viral: Shifting Engineering Biology Culture and Publishing. ACS synthetic biology 11 (2) (2022)
Eleanor Watts, Ross Thyer, Andrew D Ellington, Jennifer S Brodbelt
Integrated Top-Down and Bottom-Up Mass Spectrometry for Characterization of Diselenide Bridging Patterns of Synthetic Selenoproteins. Analytical chemistry 94 (32) (2022)
Simon D'Oelsnitz, Vylan Nguyen, Hal S Alper, Andrew D Ellington
Evolving a Generalist Biosensor for Bicyclic Monoterpenes. ACS synthetic biology 11 (1) (2022)
Simon D'Oelsnitz, Joshua D Love, Daniel J Diaz, Andrew D Ellington
GroovDB: A Database of Ligand-Inducible Transcription Factors. ACS synthetic biology 11 (10) (2022)
Alexandra A Miller, Abhijit S Rao, Sujana R Nelakanti, Christopher Kujalowicz, Ted Shi, Ted Rodriguez, Andrew D Ellington, Gwendolyn M Stovall
Systematic Review of Aptamer Sequence Reporting in the Literature Reveals Widespread Unexplained Sequence Alterations. Analytical chemistry 94 (22) (2022)
Sanchita Bhadra, Timothy E Riedel, Simren Lakhotia, Nicholas D Tran, Andrew D Ellington
High-Surety Isothermal Amplification and Detection of SARS-CoV-2. mSphere 6 (3) (2021)
Erhu Xiong, Dongbao Yao, Andrew D Ellington, Sanchita Bhadra
Minimizing Leakage in Stacked Strand Exchange Amplification Circuits. ACS synthetic biology 10 (6) (2021)
Rebecca Mackelprang, Emily R Aurand, Roel A L Bovenberg, Kathryn R Brink, R Alta Charo, Jason A Delborne, James Diggans, Andrew D Ellington, Jeffrey L Clem Fortman, Farren J Isaacs, June I Medford, Richard M Murray, Vincent Noireaux, Megan J Palmer, Laurie Zoloth, Douglas C Friedman
Guiding Ethical Principles in Engineering Biology Research. ACS synthetic biology 10 (5) (2021)
Anastasiya V Kulikova, Daniel J Diaz, James M Loy, Andrew D Ellington, Claus O Wilke
Learning the local landscape of protein structures with convolutional neural networks. Journal of biological physics 47 (4) (2021)
Timothy M Wannier, Peter N Ciaccia, Andrew D Ellington, Gabriel T Filsinger, Farren J Isaacs, Kamyab Javanmardi, Michaela A Jones, Aditya M Kunjapur, Akos Nyerges, Csaba Pal, Max G Schubert, George M Church
Recombineering and MAGE. Nature reviews. Methods primers 1 (2021)
Ross Thyer, Simon d'Oelsnitz, Molly S Blevins, Dustin R Klein, Jennifer S Brodbelt, Andrew D Ellington
Directed Evolution of an Improved Aminoacyl-tRNA Synthetase for Incorporation of L-3,4-Dihydroxyphenylalanine (L-DOPA). Angewandte Chemie (International ed. in English) 60 (27) (2021)
Inyup Paik, Phuoc H T Ngo, Raghav Shroff, Daniel J Diaz, Andre C Maranhao, David J F Walker, Sanchita Bhadra, Andrew D Ellington
Improved Bst DNA Polymerase Variants Derived via a Machine Learning Approach. Biochemistry (2021)
Hidetaka Tanno, Jonathan R McDaniel, Christopher A Stevens, William N Voss, Jie Li, Russell Durrett, Jiwon Lee, Jimmy Gollihar, Yuri Tanno, George Delidakis, Arti Pothukuchy, Jared W Ellefson, Jorg J Goronzy, Jennifer A Maynard, Andrew D Ellington, Gregory C Ippolito, George Georgiou
A facile technology for the high-throughput sequencing of the paired VH:VL and TCRβ:TCRα repertoires. Science advances 6 (17) (2020)
Dongbao Yao, Sanchita Bhadra, Erhu Xiong, Haojun Liang, Andrew D Ellington, Cheulhee Jung
Dynamic Programming of a DNA Walker Controlled by Protons. ACS nano 14 (4) (2020)
Sean P Leonard, J Elijah Powell, Jiri Perutka, Peng Geng, Luke C Heckmann, Richard D Horak, Bryan W Davies, Andrew D Ellington, Jeffrey E Barrick, Nancy A Moran
Engineered symbionts activate honey bee immunity and limit pathogens. Science (New York, N.Y.) 367 (6477) (2020)
Sanchita Bhadra, Andre C Maranhao, Inyup Paik, Andrew D Ellington
One-Enzyme Reverse Transcription qPCR Using Taq DNA Polymerase. Biochemistry 59 (49) (2020)
Raghav Shroff, Austin W Cole, Daniel J Diaz, Barrett R Morrow, Isaac Donnell, Ankur Annapareddy, Jimmy Gollihar, Andrew D Ellington, Ross Thyer
Discovery of Novel Gain-of-Function Mutations Guided by Structure-Based Deep Learning. ACS synthetic biology 9 (11) (2020)
Joongoo Lee, Kenneth E Schwieter, Andrew M Watkins, Do Soon Kim, Hao Yu, Kevin J Schwarz, Jongdoo Lim, Jaime N Coronado, Michelle Byrom, Eric V Anslyn, Andrew D Ellington, Jeffrey S Moore, Michael C Jewett
Expanding the limits of the second genetic code with ribozymes. Nature communications 10 (1) (2019)
Anna J Simon, Simon d'Oelsnitz, Andrew D Ellington
Synthetic evolution. Nature biotechnology 37 (7) (2019)
Anna J Simon, Yi Zhou, Vyas Ramasubramani, Jens Glaser, Arti Pothukuchy, Jimmy Gollihar, Jillian C Gerberich, Janelle C Leggere, Barrett R Morrow, Cheulhee Jung, Sharon C Glotzer, David W Taylor, Andrew D Ellington
Supercharging enables organized assembly of synthetic biomolecules. Nature chemistry 11 (3) (2019)
Gwendolyn M Stovall, Vincent Huynh, Shelly Engelman, Andrew D Ellington
Aptamers in Education: Undergraduates Make Aptamers and Acquire 21st Century Skills Along the Way. Sensors (Basel, Switzerland) 19 (15) (2019)
Shuichi Hoshika, Nicole A Leal, Myong-Jung Kim, Myong-Sang Kim, Nilesh B Karalkar, Hyo-Joong Kim, Alison M Bates, Norman E Watkins, Holly A SantaLucia, Adam J Meyer, Saurja DasGupta, Joseph A Piccirilli, Andrew D Ellington, John SantaLucia, Millie M Georgiadis, Steven A Benner
Hachimoji DNA and RNA: A genetic system with eight building blocks. Science (New York, N.Y.) 363 (6429) (2019)
Siyuan Stella Wang, Andrew D Ellington
Pattern Generation with Nucleic Acid Chemical Reaction Networks. Chemical reviews 119 (10) (2019)
Jessica L Meinke, Anna J Simon, Drew T Wagner, Barrett R Morrow, Shaochen You, Andrew D Ellington, Adrian T Keatinge-Clay
Employing 25-Residue Docking Motifs from Modular Polyketide Synthases as Orthogonal Protein Connectors. ACS synthetic biology 8 (9) (2019)
Cheulhee Jung, Peter B Allen, Andrew D Ellington
A Simple, Cleated DNA Walker That Hangs on to Surfaces. ACS nano 11 (8) (2017)
Joshua R Laber, Barton J Dear, Matheus L Martins, Devin E Jackson, Andrea DiVenere, Jimmy D Gollihar, Andrew D Ellington, Thomas M Truskett, Keith P Johnston, Jennifer A Maynard
Charge Shielding Prevents Aggregation of Supercharged GFP Variants at High Protein Concentration. Molecular pharmaceutics 14 (10) (2017)