Access peer-reviewed, scientific papers published by STREAM members below. All listed papers concern applications of DNA metabarcoding and DNA-based biomonitoring.


Rudar, J., Porter, T.M.,  Wright, M., Golding, B. & Hajibabaei, M. (2022). LANDMark: an ensemble approach to the supervised selection of biomarkers in high-throughput sequencing data. BMC Bioinformatics 23 (1). Access here.

Robinson, C.V.Porter, T.M.Maitland, V.C., Wright, M.T.G. & Hajibabaei, M. (2022). Multi-marker metabarcoding resolves subtle variations in freshwater condition: Bioindicators, ecological traits, and trophic interactions. Ecological Indicators 145. Access here.

Rideout, N.K., Compson, Z.G., Monk, W.A., Bruce, M.R., Hajibabaei, M., Porter, T.M., Wright, M.T.G. & Baird, D.J. (2022). Environmental filtering of macroinvertebrate traits influences ecosystem functioning in a large river floodplain. Functional Ecology 36 (11). Access here. 

Farrell, M.J., Govender, D., Hajibabaei, M., van der Bank, M. & Davies, T.J. (2022). Environmental DNA as a management tool for tracking artificial waterhole use in savanna ecosystems. Biological Conservation 274. Access here.

Porter, T.M. & Hajibabaei, M. (2022). MetaWorks: A flexible, scalable bioinformatic pipeline for high-throughput multi-marker biodiversity assessments. PLoS ONE 17 (9): e0274260. Access here.

Hajibabaei, M. (2022). Demystifying eDNA validation. Trends in Ecology & Evolution 37 (10). Access here.

Robinson, C.V.Porter, T.M.McGee K.M., McCusker, M., Wright, M.T.G. & Hajibabaei, M. (2022). Multi-marker DNA metabarcoding detects suites of environmental gradients from an urban harbour. Scientific Reports 12. Access here.

McGee K.M., Robinson C.V., Porter T.M., Compson Z.G., Hajibabaei, M., Baird, D.J. (2022). eDNA and bioassessment of rivers. Encyclopedia of Inland Waters (2). Access here.


Robinson, C.V., Baird, D.J., Wright, M.T.G., Porter, T.M., Hartwig, K., Hendriks, E., Maclean, L., Mallinson, R., Monk, W.A., Paquette, C., & Hajibabaei, M. (2021). Combining DNA and people power for healthy rivers: Implementing the STREAM community-based approach for global freshwater monitoring. Perspectives in Ecology and Conservation 19 (3). Access here.

Robinson, C.V., Wright, M.T.G., Porter, T.M., & Hajibabaei, M. (2021). Propylene glycol-based antifreeze as an effective preservative for bulk-benthos DNA metabarcoding of macroinvertebrates. Freshwater Science 40 (1). Access here.

Porter T.M., & Hajibabaei, M. (2021). Profile hidden Markov model sequence analysis can help remove putative pseudogenes from DNA barcoding and metabarcoding datasets. BMC Bioinformatics 22 (1). Access here.


Maitland, V.C., Robinson C.V., Porter, T.M., & Hajibabaei, M. (2020). Freshwater diatom biomonitoring through benthic kick-net metabarcoding. PLoS ONE 15 (11): e0242143. Access here.

Compson, Z.G., McClenaghan, B., Singer, G.A., Fahner, N.A., & Hajibabaei, M. (2020). Metabarcoding from microbes to mammals: Comprehensive bioassessment on a global scale. Frontiers in Ecology & Evolution 8:581835. Access here.

Bush, A., Monk, W.A., Compson, Z.G., Peters, D.L., Porter, T.M., Shokralla, S., Wright, M.T.G., Hajibabaei, M., & Baird, D.J. (2020). DNA metabarcoding reveals metacommunity dynamics in a threatened boreal wetland wilderness. PNAS 117 (15) 8539-8545. Access here


Hajibabaei, M., Porter, T.M., Robinson, C.V., Baird, D.J., Shokralla, S., & Wright, M.T.G. (2019). Watered-down biodiversity? A comparison of metabarcoding results from DNA extracted from matched water and bulk tissue biomonitoring samples. PLoS ONE 14 (12): e0225409. Access here.

McGee, K.M., Robinson, C.V., & Hajibabaei, M. (2019). Gaps in DNA-based biomonitoring across the globe. Frontiers in Ecology and Evolution, 7, 337. Access here.

Compson, Z.G., Monk, W.A., Hayden, B., Bush, A., O’Malley, Z., Hajibabaei, M., Porter, T.M., Wright, M.T.G., Baker, C.J.O., Al Manir, M.S., Curry, R.A., & Baird, D.J. (2019). Network-based biomonitoring: Exploring freshwater food webs with stable isotope analysis and DNA metabarcoding. Frontiers in Ecology & Evolution 7:395. Access here.


Emilson, C.E., Thompson, D.G., Venier, L.A., Porter, T.M., Swystun, T., Chartrand, D., Capell, S., & Hajibabaei, M. (2017). DNA metabarcoding and morphological macroinvertebrate metrics reveal the same changes in boreal watersheds across an environmental gradient. Scientific Reports 7, 12777. Access here.


Hajibabaei, M., Baird, D.J., Fahner, N.A., Beiko, R., & Golding, G.B. (2016). A new way to contemplate Darwin’s tangled bank: how DNA barcodes are reconnecting biodiversity science and biomonitoring. Philosophical Transactions of the Royal Society B, 371, 20150330. Access here.


Gibson, J.F., Shokralla, S., Curry, C., Baird, D.J., Monk, W.A., King, I., & Hajibabaei, M. (2015). Large-scale biomonitoring of remote and threatened ecosystems via high-throughput sequencing. PLoS ONE 10(10): e0138432. Access here.


Hajibabaei, M., Spall, J.L., Shokralla, S., & van Konynenburg, S. (2012). Assessing biodiversity of a freshwater benthic macroinvertebrate community through non-destructive environmental barcoding of DNA from preservative ethanol. BMC Ecology, 12 (28). Access here.

Shokralla, S., Spall, J.L., Gibson, J.F., & Hajibabaei, M. (2012). Next-generation sequencing technologies for environmental DNA research. Molecular Ecology, 21 (8), 1794-1805. Access here

Baird, D.J., & Hajibabaei, M. (2012). Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next‐generation DNA sequencing. Molecular Ecology, 21 (8), 2039-2044. Access here.


Hajibabaei, M., Shokralla, S., Zhou, X., Singer, G.A.C., & Baird, D.J. (2011). Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos. PLoS ONE, 6(4): e17497. Access here.