List of SD2 Publications
Bartley BA, Choi K, Samineni M, Zundel Z, Nguyen T, Myers CJ, Sauro HM. pySBOL: a python package for genetic design automation and standardization. ACS synthetic biology. 2018 Nov 13;8(7):1515-8.
Bryce D, Goldman RP, DeHaven M, Beal J, Bartley B, Nguyen TT, Walczak N, Weston M, Zheng G, Nowak J, Lee P, Stubbs J, Gaffney N, Vaughn MW, Myers CJ, Moseley RC, Haase S, Deckard A, Cummins B, Leiby N. Round Trip: An Automated Pipeline for Experimental Design, Execution, and Analysis. ACS Synthetic Biology. 2022 Jan 31;11(2):608-22.
Cappello F, Sheng Di ANL PG. Visualization of scientific data lossy reduction error. In Position Papers for the ASCR Workshop on Visualization for Scientific Discovery, Decision-Making, and Communication 2022 Jan.
Carson JP, Fonner J, Vaughn M, Gaffney N, Brown T, Stubbs J, Rosenberg J, Tijerina S, Allen WJ, Ferlanti F, Urrutia J, Ho Ethan, Song J, Gopaulakrishnan S, Prochaska H, Chuah JY, Weston M, Sejnowski T, Harris K, Dahan M. Facilitating collaborative science through portals connected to high-performance computing. In Science Gateways 2023 Annual Conference. 2023.
Cummins B, Moseley RC, Deckard A, Weston M, Zheng G, Bryce D, Nowak J, Gameiro M, Gedeon T, Mischaikow K, Beal J, Johnson T, Vaughn M, Gaffney NI, Gopaulakrishnan S, Urrutia J, Goldman RP, Bartley B, Nguyen TT, Roehner N, Mitchell T, Vrana JD, Clowers KJ, Maheshri N, Becker D, Mikhalev E, Biggers V, Higa T, Mosqueda L, Haase SB. Computational prediction of synthetic circuit function across growth conditions. bioRxiv. 2022 Jan 1.
Cummins B, Vrana J, Moseley RC, Eramian H, Deckard A, Fontanarrosa P, Bryce D, Weston M, Zheng G, Nowak J, Motta FC, Eslami M, Layne K, Goldman RP, Myers CJ, Johnson T, Vaughn MW, Gaffney N, Urrutia J, Gopaulakrishnan S, Biggers V, Higa T, Mosqueda L, Gameiro M, Gedeon T, Mischaikow K, Beal J, Bartley B, Mitchell T, Nguyen TT, Roehner N, Haase SB. Robustness and reproducibility of simple and complex synthetic logic circuit designs using a DBTL loop. bioRxiv. 2022 Jan 1.
Dooley R, Brandt SR, Fonner J. The Agave Platform: An open, science-as-a-service platform for digital science. In Proceedings of the Practice and Experience on Advanced Research Computing 2018 Jul 22 (pp. 1-8).
Eslami M, Borujeni AE, Eramian H, Weston M, Zheng G, Urrutia J, Corbet C, Becker D, Maschhoff P, Clowers K, Cristofaro A Hosseini HD, Gordon DB, Dorfan Y, Singer J, Vaughn M, Gaffney N, Fonner J, Stubbs J, Voight CA, Yeung E. Prediction of whole-cell transcriptional response with machine learning. Bioinformatics. 2022 Jan 15;38(2):404-9.
Garcia BJ, Urrutia J, Zheng G, Becker D, Corbet C, Maschhoff P, Cristofaro A, Gaffney N, Vaughn M, Saxena U, Chen YP Gordon BD, Eslami M. A toolkit for enhanced reproducibility of RNASeq analysis for synthetic biologists. Synthetic Biology. 2022;7(1):ysac012.
Goldman RP, Moseley R, Roehner N, Cummins B, Vrana JD, Clowers KJ, Bryce D, Beal J, DeHaven M, Nowak J, Higa T, Biggers V, Lee P, Hunt JP, Mosqueda L, Haase SB, Weston M, Zheng G, Deckard A, Gopaulakrishnan S, Stubbs JF, Gaffney NI, Vaughn MW, Maheshri N, Mikhalev E, Bartley B, Markeloff R, Mitchell T, Nguyen T, Sumorok D, Walczak N, Myers C, Zungel Z, Hatch B, Scholz J, Colonna-Romano J. Highly-automated, high-throughput replication of yeast-based logic circuit design assessments. Synthetic Biology. 2022;7(1):ysac018.
Hancock DY, Fischer J, Lowe JM, Snapp-Childs W, Pierce M, Marru S, Coulter JE, Vaughn M, Beck B, Merchant N, Skidmore E, Jacobs G. Jetstream2: Accelerating cloud computing via Jetstream. In Practice and Experience in Advanced Research Computing 2021 Jul 17 (pp. 1-8).
Mante JV. Promotion of Data Reuse in Synthetic Biology (Doctoral dissertation, University of Colorado at Boulder).
Mante J, Abam J, Potzsch IM, Singh P, Beal J, Myers CJ. Excel-SBOL converter: Creating SBOL from excel templates and vice versa. bioRxiv. 2022 Jan 1.
Motta F, Tralie C, Bedini R, Bini F, Bini G, Eramian H, Gameiro M, Haase S, Haddox H, Harer J, Leiby N, Marinozzi F, Novotney S, Rocklin G, Singer J, Strickland D, Vaughn M. Hyperparameter optimization of topological features for machine learning applications. In2019 18th IEEE International Conference On Machine Learning And Applications (ICMLA) 2019 Dec 16 (pp. 1107-1114). IEEE.
Nicholas G. Active Meta-Learning (Doctoral dissertation).
Singer JM, Novotney S, Strickland D, Haddox HK, Leiby N, Rocklin GJ, Chow CM, Roy A, Bera AK, Motta FC, Cao L, Strauch EM, Chidyausiku TM, Ford A, Ho E, Zaitzeff A, Mackenzie CO, Eramian H, DiMaio F, Grigoryan G, Vaughn M, Stewaft LJ, Baker D, Klavins E. Large-scale design and refinement of stable proteins using sequence-only models. PloS one. 2022 Mar 14;17(3):e0265020.
Stubbs J, Cardone R, Packard M, Jamthe A, Padhy S, Terry S, Looney J, Meiring J, Black S, Dahan M, Cleveland S, Jacobs G. Tapis: An api platform for reproducible, distributed computational research. In Future of Information and Communication Conference 2021 Apr 29 (pp. 878-900). Springer, Cham.
Stubbs J, Garcia C, Looney J, Jamthe A, Packard M, Vaughn M. Enabling Science with Functions-as-a-Service: New Features and Usage of the Abaco Platform. Gateways 20. 2020 Oct.
Stubbs J, Looney J, Poindexter M, Chalhoub E, Zynda GJ, Ferlanti ES, Vaughn M, Fonner JM, Dahan M. Integrating jupyter into research computing ecosystems: Challenges and successes in architecting jupyterhub for collaborative research computing ecosystems. In Practice and Experience in Advanced Research Computing 2020 Jul 26 (pp. 91-98).
Stubbs J, Vaughn M, Looney J. Rapid Development of Scalable, Distributed Computation with Abaco. In IWSG 2018 Jun.
Tang Y, Li Z, Nellikkal MA, Eramian H, Chan EM, Norquist AJ, Hsu DF, Schrier J. Improving data and prediction quality of high-throughput perovskite synthesis with model fusion. Journal of chemical information and modeling. 2021 Apr 2;61(4):1593-602.
Tynes M. Tensor Factorizations for Recommending Perovskite Crystallization Trials (Doctoral dissertation, Fordham University).