Modelling the propagation of turbid density inflows into a stratified lake: Daecheong Reservoir, Korea. - S. W. Chung; Matthew R. Hipsey; Jörg Imberger (Environ. Model. Softw., 2009)

Sensitivity analysis for complex ecological models - A new approach. - Vardit Makler-Pick; Gideon Gal; Malka Gorfine; Matthew R. Hipsey; Yohay Carmel (Environ. Model. Softw., 2011)

Time-scale dependence in numerical simulations: Assessment of physical, chemical, and biological predictions in a stratified lake at temporal scales of hours to months. - Emily L. Kara; Paul C. Hanson; David P. Hamilton; Matthew R. Hipsey; Katherine D. McMahon; Jordan S. Read; Luke A. Winslow; John Dedrick; Kevin Rose; Cayelan C. Carey; Stefan Bertilsson; David da Motta Marques; et al. (Environ. Model. Softw., 2012)

Novel approaches to address challenges in modelling aquatic ecosystems. - Gideon Gal; Matthew R. Hipsey; Karsten Rinke; Barbara J. Robson (Environ. Model. Softw., 2014)

A three-dimensional hydro-geochemical model to assess lake acidification risk. - Matthew R. Hipsey; S. Ursula Salmon; Luke M. Mosley (Environ. Model. Softw., 2014)

Serving many at once: How a database approach can create unity in dynamical ecosystem modelling. - Wolf M. Mooij; Robert J. Brederveld; Jeroen J. M. de Klein; Don L. DeAngelis; Andrea S. Downing; Michiel Faber; Daan J. Gerla; Matthew R. Hipsey; Jochem 't Hoen; Jan H. Janse; Annette B. G. Janssen; Michel Jeuken; et al. (Environ. Model. Softw., 2014)

Sediment diagenesis models: Review of approaches, challenges and opportunities. - Daniel W. Paraska; Matthew R. Hipsey; S. Ursula Salmon (Environ. Model. Softw., 2014)

Stable isotopes reduce parameter uncertainty of an estuarine carbon cycling model. - Sri Adiyanti; Bradley D. Eyre; Damien T. Maher; Isaac Santos; Lindsay Golsby-Smith; Perrine Mangion; Matthew R. Hipsey (Environ. Model. Softw., 2016)

The role of bioirrigation in sediment phosphorus dynamics and blooms of toxic cyanobacteria in a temperate lagoon. - Yafei Zhu; Matthew R. Hipsey; Andrew McCowan; John Beardall; Perran L. M. Cook (Environ. Model. Softw., 2016)

A multi-lake comparative analysis of the General Lake Model (GLM): Stress-testing across a global observatory network. - Louise C. Bruce; Marieke A. Frassl; George B. Arhonditsis; Gideon Gal; David P. Hamilton; Paul C. Hanson; Amy L. Hetherington; John M. Melack; Jordan S. Read; Karsten Rinke; Anna Rigosi; Dennis Trolle; et al. (Environ. Model. Softw., 2018)

A system of metrics for the assessment and improvement of aquatic ecosystem models. - Matthew R. Hipsey; Gideon Gal; George B. Arhonditsis; Cayelan C. Carey; J. Alex Elliott; Marieke A. Frassl; Jan H. Janse; Lee de Mora; Barbara J. Robson (Environ. Model. Softw., 2020)

dycdtools: an R Package for Assisting Calibration and Visualising Outputs of an Aquatic Ecosystem Model. - Songyan Yu; Christopher McBride; Marieke A. Frassl; Matthew R. Hipsey; David P. Hamilton (R J., 2023)

Phytoplankton group classification by integrating trait information and observed environmental thresholds. - Hoang Vuong Dang; Kermode Stephanie; Peisheng Huang; Cayelan C. Carey; Matthew R. Hipsey (Ecol. Informatics, 2025)