Publications

Peer-reviewed

    2022

  1. Bilal Shaikh, Lucian P Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S Andrews, Azraf Anwar, Moritz E Beber, Frank T Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G Bard Ermentrout, James R Faeder, Andrew P Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H Gennari, Padraig Gleeson, Anne Goelzer, Zachary Haiman, Jan Hasenauer, Joseph L Hellerstein, Henning Hermjakob, Stefan Hoops, Jon C Ison, Diego Jahn, Henry V Jakubowski, Ryann Jordan, Matús̆ Kalas̆, Matthias König, Wolfram Liebermeister, Rahuman S Malik Sheriff, Synchon Mandal, Robert McDougal, J Kyle Medley, Pedro Mendes, Robert Müller, Chris J Myers, Aurelien Naldi, Tung V N Nguyen, David P Nickerson, Brett G Olivier, Drashti Patoliya, Loïc Paulevé, Linda R Petzold, Ankita Priya, Anand K Rampadarath, Johann M Rohwer, Ali S Saglam, Dilawar Singh, Ankur Sinha, Jacky Snoep, Hugh Sorby, Ryan Spangler, Jörn Starruß, Payton J Thomas, David van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P Goldberg, James C Schaff, Michael L Blinov, Herbert M Sauro, Ion I Moraru, and Jonathan R Karr. "BioSimulators: a central registry of simulation engines and services for recommending specific tools". Nucleic Acids Research. 2022. https://doi.org/10.1093/nar/gkac331.

    2. 2021

  2. Freiburger, Andrew Philip and Lucia, Lucian. "Hemp is the 21st century Tobacco: A Review". ACS Journal of Agricultural Science and Technology. 2021. https://doi.org/10.1021/acsagscitech.1c00114 (HTML version).

Pre-print

    2024

  1. Kennedy, Megan S.; Freiburger, Andrew; Cooper, Michael; Beilsmith, Kathleen; St. George, Marissa L.; Kalski, Martin; Cham, Candance; Guzzetta, Alex; Ng, Siew C.; Chan, Francis K.; Rubin, David; Henry, Chris S.; Bergelson, Joy; and Chang, Eugene B. "Diet outperforms microbial transplant to drive microbiome recovery post-antibiotics" bioRxiv. 2024. https://doi.org/10.1101/2024.08.01.606245.

  2. Oliverio, Angela M.; Narrowe, Adrienne B.; Villa, Jorge A.; Rinke, Christian; Hoyt, David W.; Liu, Pengfei; McGivern, Bridget B.; Bechtold, Emily K.; Ellenbogen, Jared B.; Daly, Rebecca A.; Smith, Garrett J.; Angle, Jordan C.; Flynn, Rory M.; Freiburger, Andrew P.; Louie, Katherine B.; Stemple, Brooke; Northern, Trent R.; Henry, Christopher; Miller, Christopher S.; Morin, Timothy H.; Bohrer, Gil; Borton, Mikayla A.; Wrighton, Kelly C. "Mapping the soil microbiome functions shaping wetland methane emissions" bioRxiv. 2024. https://doi.org/10.1101/2024.02.06.579222.

    3. 2023

  3. Faria, José P.; Liu, Filipe; Edirisinghe, Janaka N.; Gupta, Nidhi; Seaver, Samuel M.D.; Freiburger, Andrew P.; Zhang, Qizhi; Weisenhorn, Pamela; Conrad, Neal; Zarecki, Raphy; Song, Hyun-Seob; DeJongh, Matthew; Best, Aaron A.; Cottingham, Robert W.; Arkin, Adam P.; and Henry, Christopher S. "ModelSEED v2: High-throughput genome-scale metabolic model reconstruction with enhanced energy biosynthesis pathway prediction" bioRxiv. 2023. https://doi.org/10.1101/2023.10.04.556561.

  4. Sakkaff, Zahmeeth; Freiburger, Andrew P.; Henry, Christopher; and Nanayakkara, A. "Mental Tasks for Controlling Cursor Movements in a Brain Computer Interface" medRxiv. 2023. https://doi.org/10.1101/2023.08.29.23294785.

  5. Sakkaff, Zahmeeth; Freiburger, Andrew P.; Catlett, Jennie L.; Cashman, Mikaela; Immaneni, Aditya; Buan, Nicole R.; Cohen, Myra B.; Henry, Christopher; and Pierobon, Massimiliano. "A Molecular Communication model for cellular metabolism" bioRxiv. 2023. https://doi.org/10.1101/2023.06.28.546976.

  6. Sakkaff, Zahmeeth; Freiburger, Andrew P.; Gupta, Nidhi; Pierobon, Massimiliano; and Henry, Christopher. "Information- and Communication-Centric Approach in Cell Metabolism for Analyzing Behavior of Microbial Communities" bioRxiv. 2023. https://doi.org/10.1101/2023.08.23.554558.

    7. 2022

  7. Freiburger, Andrew P.; Dewey, Jeffrey A.; Foflonker, Fatima; Babnigg, Gyorgy; Antonopoulos, Dionysios A.; and Henry, Christopher. "A microbial community growth model for dynamic phenotype predictions" bioRxiv. 2022. https://doi.org/10.1101/2022.12.15.520667.

  8. Freiburger, Andrew P.; Molins, Sergi; and Buckley, Heather L. "A One-Dimensional Reactive Transport Model of Geochemical Scaling in Reverse Osmosis Desalination." Pre-print in SSRN. 2022. http://dx.doi.org/10.2139/ssrn.4124149.

    9. 2021

  9. Shaikh, Bilal*; Freiburger, Andrew Philip*; Konig, Matthias; Bergman, Frank T.; Nickerson, David P.; Sauro, Herbert M.; Blinov, Michael L.; Smith, Lucian P.; Moraru, Ion I.; and Karr, Jonathan R. "SED-ML Validator: tool for debugging simulation experiments". Preprint. 2021. https://doi.org/10.48550/arXiv.2106.00844.   * These authors contributed equally to this work.

    2022

  1. Freiburger, Andrew; Shaikh, Bilal; and Karr, Jonathan. "BioSimulations, a platform for sharing and reusing biological simulations: A case study of reproducible and reusable data visualizations with HDF5, HSDS, and Vega". The HDF Group Blog. 2022. https://www.hdfgroup.org/2022/02/biosimulations-a-platform-for-sharing-and-reusing-biological-simulations/.

    2. 2021

  2. Freiburger, Andrew Philip. "Utters versus Oats". Canadian Vegan. Spring 2021. (HTML version).

  3. Freiburger, Andrew Philip. "Sustainable and Nutritious Diet". Canadian Vegan. Winter 2020-2021. (HTML version).