Publications

My Google Scholar page available here. Total Citations: 248 · h-index: 6 · i10-index: 6

Peer-reviewed

  1. 2026

  2. Borton, Mikayla A.; 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; Northen, Trent R.; Henry, Christopher; Miller, Christopher S.; Morin, Timothy H.; Bohrer, Gil; and Wrighton, Kelly C. "Mapping the soil microbiome functions shaping wetland methane emissions" mSystems. 2026. https://doi.org/10.1128/msystems.00680-25.

  3. Wood-Charlson, Elisha M.; Henry, Christopher S.; Dehal, Paramvir S.; Mahmud, Gazi; Allen, Benjamin H.; Beilsmith, Kathleen; Blair, D. Dakota; Canon, Shane; Cashman, Mikaela; Chivian, Dylan; Cottingham, Robert; Crockett, Zachary; Dow, Ellen G.; Drake, Meghan; Edirisinghe, Janaka N.; Faria, José P.; Freiburger, Andrew; Gu, Tianhao; Gupta, Prachi; Ireland, A. J.; Jungbluth, Sean; Kamimura, Roy; Keller, Keith; Khan, Ahmed; Kishore, Dileep; Klos, Dan; Liu, Filipe; Lyon, David; Neely, Christopher; O'Grady, Katherine L.; Price, Gavin; Ranjan, Priya; Riehl, William J.; Sadkhin, Boris; Seaver, Sam; Terry, Gwyneth A.; Wang, Yue; Weisenhorn, Pamela; Yang, Ziming; Yoo, Shinjae; and Arkin, Adam P. "KBase: Open-source platform for collaborative biological data analysis and publication" Journal of Molecular Biology. 2026. https://doi.org/10.1016/j.jmb.2026.169676.

  4. 2025

  5. 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 in mice" Nature. 2025. https://doi.org/10.1038/s41586-025-08937-9.

  6. Borton, Mikayla A; McGivern, Bridget B; Willi, Kathryn R; Woodcroft, Ben J; Mosier, Annika C; Singleton, Derick M; Bambakidis, Ted; Pelly, Aaron; Daly, Rebecca A; Liu, Filipe; Freiburger, Andrew; Edirisinghe, Janaka N; Faria, José P; Danczak, Robert; Leleiwi, Ikaia; Goldman, Amy E; Wilkins, Michael J; Hall, Ed K; Pennacchio, Christa; Roux, Simon; Eloe-Fadrosh, Emiley A; Good, Stephen P; Sullivan, Matthew B; Wood-Charlson, Elisha M; Miller, Christopher S; Ross, Matthew R V; Henry, Christopher S; Crump, Byron C; Stegen, James C; Wrighton, Kelly C. "A functional microbiome catalogue crowdsourced from North American rivers" Nature. 2025. https://doi.org/10.1038/s41586-024-08240-z

  7. 2022

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

  9. 2021

  10. 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

  1. 2026

  2. Freiburger, Andrew; Faria, Jose P.; Zhu, Ray; Edirisinghe, Janaka N.; Liu, Filipe; Taylor, Cooper; Setlur, Vibhav; Giessmann, Robert T.; Beber, Moritz E.; Noor, Elad; Upadhyay, Vikas; Anand, Mohit; Maranas, Costas D.; Huss, Sebastian; Nikoloski, Zoran; Arkin, Adam P.; Cottingham, Robert W.; Wood-Charlson, Elisha M.; Ramanathan, Arvind; Henry, Christopher S.; and Seaver, Samuel M.D. "The ModelSEED Biochemistry Database, 2026 update: grading multi-source thermodynamics" bioRxiv. 2026. https://doi.org/10.64898/2026.09.15.751859.

  3. 2025

  4. Freiburger, Andrew; Krikke, James; Dietlin, Nathanial; Lucia, Lucian; and Kovacs, Dalila. "Chemical Characterization of Commercial Willow Hybrids—a Potentially Superior Renewable Feedstock" Preprints. 2025. https://doi.org/10.20944/preprints202510.1671.v1.

  5. 2024

  6. 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.

  7. 2023

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 2022

  13. 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.

  14. 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.

  15. Freiburger, Andrew P.; Krikke, Jim K.; Lucia, Lucian A.; Kovacs, Dalila. "Chemical Characterizations of Commercial Willow Biomass." Zenodo. 2022. https://doi.org/10.5281/zenodo.6374777.

  16. 2021

  17. 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". arXiv. 2021. https://doi.org/10.48550/arXiv.2106.00844.   * These authors contributed equally to this work.

Thesis

  1. 2022

  2. Freiburger, Andrew Philip. "Computational models for research in medicine and desalination". Master of Applied Science thesis, Department of Civil Engineering, University of Victoria. 2022. https://hdl.handle.net/1828/13880.

  1. 2022

  2. 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/.

  3. 2021

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

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