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RESEARCH PAPER · ACS Synthetic Biology · 2022

Round Trip: An Automated Pipeline for Experimental Design, Execution, and Analysis

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9 direct citing papers in this saved network. Explore the next layer with second-order citations.

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42 direct citing works

Round Trip: An Automated Pipeline for Experimental Design, Execution, and AnalysisOriginalA toolkit for enhanced reproducibility of RNASeq analysis for synthetic biologists5Computational Prediction of Synthetic Circuit Function Across Growth Conditions2Collaborative methods to enhance reproducibility and accelerate discovery20Advancing reproducibility can ease the ‘hard truths’ of synthetic biology11Robustness and reproducibility of simple and complex synthetic logic circuit designs using a DBTL loop18Characterization of Integrase and Excisionase Activity in a Cell-Free Protein Expression System Using a Modeling and Analysis Pipeline17From bench to biofactory: high-throughput technologies and automated workflows to accelerate biomanufacturing17Prediction of enzyme inhibition (IC50) using a combination of protein–ligand docking and semiempirical quantum mechanics7Simulation-Based Diagnostic Learning with Diagnostic Trouble Box (DTB): Enhancing Analytical Thinking Skills in Vocational Automotive Education1

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  1. A toolkit for enhanced reproducibility of RNASeq analysis for synthetic biologists

    Synthetic Biology · 2022-02-01

    Benjamin J. Garcia, Joshua A. Urrutia, George Zheng, Diveena Becker, Carolyn Corbet, Paul Maschhoff, Alexander W. Cristofaro, Niall I. Gaffney, Matthew W. Vaughn, Uma Saxena, Yi-Pei Chen, D. Benjamin Gordon, Mohammed Eslami

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  2. Computational Prediction of Synthetic Circuit Function Across Growth Conditions

    bioRxiv (Cold Spring Harbor Laboratory) · 2022-06-13

    Bree Cummins, Robert C. Moseley, Anastasia Deckard, Mark Weston, George Zheng, Daniel Bryce, Joshua Nowak, Marcio Gameiro, Tomáš Gedeon, Konstantin Mischaikow, Jacob Beal, Tessa Johnson, Matthew W. Vaughn, Niall I. Gaffney, Shweta Gopaulakrishnan, Joshua A. Urrutia, Robert P. Goldman, Bryan Bartley, Tramy Nguyen, Nicholas Roehner, Tom Mitchell, Justin D. Vrana, Katie J. Clowers, Narendra Maheshri, Diveena Becker, Ekaterina Mikhalev, Vanessa Biggers, Trissha Higa, Lorraine Mosqueda, Steven B. Haase

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  3. Collaborative methods to enhance reproducibility and accelerate discovery

    Digital Discovery · 2022-11-29

    Drew A. Leins, Steven B. Haase, Mohammed Eslami, Joshua Schrier, Jared Freeman

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  4. Advancing reproducibility can ease the ‘hard truths’ of synthetic biology

    Synthetic Biology · 2023-01-01

    Matthew W. Lux, Elizabeth A. Strychalski, Gary J. Vora

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  5. Robustness and reproducibility of simple and complex synthetic logic circuit designs using a DBTL loop

    Synthetic Biology · 2023-01-01

    Bree Cummins, Justin D. Vrana, Robert C. Moseley, Hamed Eramian, Anastasia Deckard, Pedro Fontanarrosa, Daniel Bryce, Mark Weston, George Zheng, Joshua Nowak, Francis C. Motta, Mohammed Eslami, Kara Layne Johnson, Robert P. Goldman, Chris J. Myers, Tessa Johnson, Matthew W. Vaughn, Niall I. Gaffney, Joshua A. Urrutia, Shweta Gopaulakrishnan, Vanessa Biggers, Trissha Higa, Lorraine Mosqueda, Marcio Gameiro, Tomáš Gedeon, Konstantin Mischaikow, Jacob Beal, Bryan Bartley, Tom Mitchell, Tramy Nguyen, Nicholas Roehner, Steven B. Haase

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  6. Characterization of Integrase and Excisionase Activity in a Cell-Free Protein Expression System Using a Modeling and Analysis Pipeline

    ACS Synthetic Biology · 2023-01-30

    Ayush Pandey, Makena L. Rodriguez, William Poole, Richard M. Murray

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  7. From bench to biofactory: high-throughput technologies and automated workflows to accelerate biomanufacturing

    Current Opinion in Biotechnology · 2025-06-10

    Christopher J. Petzold, Aindrila Mukhopadhyay

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  8. Prediction of enzyme inhibition (IC50) using a combination of protein–ligand docking and semiempirical quantum mechanics

    Journal of Molecular Modeling · 2025-07-12

    Robert Charles Glen, Jason C. Cole, James J. P. Stewart

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  9. Simulation-Based Diagnostic Learning with Diagnostic Trouble Box (DTB): Enhancing Analytical Thinking Skills in Vocational Automotive Education

    Salud Ciencia y Tecnología · 2025-07-29

    Valiant Lukad Perdana Sutrisno, Pardjono Pardjono, Wagiran Wagiran, Muhammad Nurtanto, Dianna Ratnawati, Anna Marganingsih, Farid Mutohhari

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