Publications

Theroux, S., A. Sepulveda, C.L. Abbott, Z. Gold, A.W. Watts, M.E. Hunter, K.E. Klymus, S.L. Hirsch, J.M. Craine, D.N. Jones, R.J. Brown, J.A. Steele, M. Takahashi, R.T. Noble, J.A. Darling. 2025. What is eDNA method standardisation and why do we need it?. Metabarcoding and Metagenomics 9:91-106.

Vasselon, V., S.F. Rivera, E. Acs, S.F.P. Almeida, K.B. Andree, L. Apotheloz-Perret-Gentil, B. Bailet, A. Baricevic, K.K. Beentjes, J. Bettig, A. Bouchez, C. Capelli, C. Chardon, M. Duleba, T. Elersek, C. Genthon, M. Jablonska, L. Jacas, M. Kahlert, M.G. Kelly, J.N. Macher, F. Mauri, M. Moletta-Denat, A. Mortagua, J. Pawlowski, J. Perez-Burillo, M. Pfannkuchen, E. Pilgrim, P. Pissaridou, F. Rimet, K. Stanic, K. Tapolczai, S. Theroux, R. Trobajo, B. Van der Hoorn, M.I. Vasquez, M. Vidal, D. Wanless, J. Warren, J. Zimmermann, B. Paix. 2025. Proficiency testing and cross-laboratory method comparison to support standardisation of diatom DNA metabarcoding for freshwater biomonitoring. Metabarcoding and Metagenomics 9:35-70.

Klymus, K.E., J.D. Baker, C.L. Abbott, R.J. Brown, J.M. Craine, Z. Gold, M.E. Hunter, M.D. Johnson, D.N. Jones, M.J. Jungbluth, S.P. Jungbluth, Y. Lor, A. Maloy, C.M. Merkes, R. Noble, N.V. Patin, A.J. Sepulveda, S.F. Spear, J.A. Steele, M. Takahashi, A.W. Watts, S. Theroux. 2024. The MIEM guidelines: Minimum information for reporting of environmental metabarcoding data. Metabarcoding and Metagenomics 8:489-518.

Kelly, R.P., D.M. Lodge, K.N. Lee, S. Theroux, A.J. Sepulveda, C.A. Scholin, J.M. Craine, E.A. Allan, K.M. Nichols, K.M. Parsons, K.D. Goodwin, Z. Gold, F.P. Chavez, R.T. Noble, C.L. Abbott, M.R. Baerwald, A.M. Naaum, P.M. Thielen, A.L. Simons, C.L. Jerde, J.J. Duda, M.E. Hunter, J.A. Hagan, R.S. Meyer, J.A. Steele, M.Y. Stoeckle, H.M. Bik, C.P. Meyer, E.D. Stein, K.E. James, A.C. Thomas, E. Demir-Hilton, M.A. Timmers, J.F. Griffith, M.J. Weise, S.B. Weisberg. 2024. Toward a national eDNA strategy for the United States. Environmental DNA DOI:10.1002/edn3.432.

Smith, J., D. Shultz, A. Lie, S. Theroux. 2023. Diversity and Prevalence of Cyanobacteria and Cyanotoxins in Los Angeles Region Recreational Lakes and Reservoirs. Technical Report 1309. Southern California Coastal Water Research Project. Costa Mesa, CA.

Simons, A.L., S. Theroux, M. Osborne, S. Nuzhdin, R.D. Mazor, J.A. Steele. 2023. Zeta diversity patterns in metabarcoded lotic algal assemblages as a tool for bioassessment. Ecological Applications DOI:10.1002/eap.2812.

Stepien, C.A., S. Theroux, S.B. Weisberg. 2022. The Second National Workshop on Marine eDNA: A workshop to accelerate the incorporation of eDNA science into environmental management application. Environmental DNA DOI:10.1002/edn3.379.

Mazor, R.D., M. Sutula, S. Theroux, M. Beck, P.R. Ode. 2022. Eutrophication thresholds associated with protection of biological integrity in California wadeable streams. Ecological Indicators 142:109180.

Howard, M.D.A., J. Smith, D.A. Caron, R.M. Kudela, K. Loftin, K. Hayashi, R. Fadness, S. Fricke, J. Kann, M. Roethler, A. Tatters, S. Theroux. 2022. Integrative monitoring strategy for marine and freshwater harmful algal blooms and toxins across the freshwater‐to‐marine continuum. Integrated Environmental Assessment and Management DOI:10.1002/ieam.4651.

Irving, K., K.T. Taniguchi-Quan, A. Aprahamian, C. Rivers, G. Sharp, R.D. Mazor, S. Theroux, A. Holt, R. Peek, E.D. Stein. 2022. Application of Flow-Ecology Analysis to Inform Prioritization for Stream Restoration and Management Actions. Frontiers in Environmental Science 9:787462.

Bueno de Mesquita, C.P., J. Zhou, S. Theroux, S.G. Tringe. 2021. Methanogenesis and Salt Tolerance Genes of a Novel Halophilic Methanosarcinaceae Metagenome-Assembled Genome from a Former Solar Saltern. Genes 12:1609.

Zhou, J., S. Theroux, C.P. Bueno de Mesquita, W.H. Hartman, Y. Tian, S.G. Tringe. 2021. Microbial drivers of methane emissions from unrestored industrial salt ponds. The ISME Journal DOI:10.1038/s41396-021-01067-w.

Charles, D.F., M.G. Kelly, R.J. Stevenson, S. Poikane, S. Theroux, A. Zgrundo, M. Cantonati. 2021. Benthic algae assessments in the EU and the US: Striving for consistency in the face of great ecological diversity . Ecological Indicators DOI:10.1016/j.ecolind.2020.107082.

Howard, M.D.A., R.M. Kudela, K. Hayashi, A.O. Tatters, D.A. Caron, S. Theroux, S. Oehrle, M. Roethler, A. Donovan, K. Loftin, Z. Laughrey. 2021. Multiple co-occurring and persistently detected cyanotoxins and associated cyanobacteria in adjacent California lakes. Toxicon 192:1-14.

Theroux, S., R.D. Mazor, M.W. Beck, P.R. Ode, E.D. Stein, M. Sutula. 2020. Predictive biological indices for algae populations in diverse stream environments. Ecological Indicators DOI:10.1016/j.ecolind.2020.106421.

Paul, M.J., B. Jessup, L.R. Brown, J.L. Carter, M. Cantonati, D.F. Charles, J. Gerritsen, D.B. Herbst, R. Stancheva, J. Howard, B. Isham, R. Lowe, R.D. Mazor, P.K. Mendex, P.R. Ode, A. O'Dowd, J. Olson, Y. Pan, A.C. Rehn, S. Spaulding, M. Sutula, S. Theroux. 2020. Characterizing benthic macroinvertebrate and algal biological condition gradient models for California wadeable Streams, USA. Ecological Indicators DOI:10.1016/j.ecolind.2020.106618.

Aylagas, E., A. Borja, X. Pochon, A. Zaiko, N. Keeley, K. Bruce, P. Hong, G.M. Ruiz, E.D. Stein, S. Theroux, N. Geraldi, A. Ortega, L. Gajdzik, D.J. Coker, Y. Katan, T. Hikmawan, A. Saleem, S. Alamer, B.H. Jones, C.M. Duarte, J. Pearman, S. Carvalho. 2020. Translational Molecular Ecology in practice: Linking DNA-based methods to actionable marine environmental management. Science of the Total Environment DOI:10.1016/j.scitotenv.2020.140780.

Beck, M.W., C. O'Hara, J.S. Stewart-Lowndes, R.D. Mazor, S. Theroux, D.J. Gillett, B. Lane, G. Gearheart. 2020. The importance of open science for biological assessment of aquatic environments. PeerJ DOI:10.7717/peerj.9539.

Simons, A.L., R.D. Mazor, S. Theroux. 2019. Using Co‐occurrence Network Topology in Assessing Ecological Stress in Benthic Macroinvertebrate Communities. Ecology and Evolution DOI:10.1002/ece3.5751.

Beck, M., R.D. Mazor, S. Theroux, K.C. Schiff. 2019. The Stream Quality Index: A multi-indicator tool for enhancing environmental management. Environmental and Sustainability Indicators DOI:10.1016/j.indic.2019.100004.

Beck, M., R.D. Mazor, S. Theroux, K.C. Schiff. 2019. The Stream Quality Index: A Multi-Indicator Tool for Enhancing Environmental Management Communication. Technical Report 1080. Southern California Coastal Water Research Project. Costa Mesa, CA.