Publications

My Google Scholar page available here. Total Citations: 153

Peer-reviewed

  1. 2026

  2. 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.

  3. 2025

  4. 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.

  5. 2024

  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. 2025

  2. 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.

  3. 2024

  4. 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.

  5. 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.

  6. 2023

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 2022

  12. 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.

  13. 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.

  14. 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.

  15. 2021

  16. 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.

  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).