50) Nilsson, R.H., Jansson, A.T., Wurzbacher, C., Anslan, S., Belford, P., Corcoll, N., Dombrowski, A., Ghobad-Nejhad, M., Gustavsson, M., Gómez-Martinez, D., Khan, F.K., Khomich, M., Lennartsdotter, C., Lund, D., Van Der Merwe, B., Mikryukov, V., Peterson, M., Porter, T.M., Põlme, S., Retter, A., Sanchez-Garcia, M., Svantesson, S., Svedberg, P., Vu, D., Ryberg, M., Abarenkov, K., Kristiansson, E. (2024) 20 years of bibliometric data illustrates a lack of concordance between journal impact factor and fungal species discovery in systematic mycology.  MycoKeys, 110: 273-285.  https://mycokeys.pensoft.net/article/136048/   

49) Hakimzadeh, A., Abdala, A., Albanese, D., Bernard, M., Buchner, D., Callahan, B., Caporaso, J.G., Curd, E., Djemiel, C., Brandström Durling, M.,  Elbrecht, V., Gold, Z., Gweon, H., Hajibabaei, M., Hildebrand, F., Mikryukov, V., Normandeau, E., Özkurt, E., Palmer, J.M., Pascal, G., Porter, T.M., Straub, D., Vasar, M., Vetrovsky, T., Zafeiropoulos, H., Anslan, S. (2023) A pile of pipelines: an overview of the bioinformatics software for metabarcoding data analyses.  Molecular Ecology Resources, 24 (5): e13847.   https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13847 

48) Hart, S., Porter, T.M., Basiliko, N., Venier, L., Hajibabaei, M., Morris, D. (2023) Fungal community dynamics in coarse woody debris across decay stage, tree species, and stand development stage in northern boreal forests.  Canadian Journal of Forest Research, 54 (1): 12-30.  https://cdnsciencepub.com/doi/full/10.1139/cjfr-2023-0061 

47) Porter, T.M., Smenderovac, E., Morris, D., Venier, L. (2023) All boreal forest successional stages needed to maintain the full suite of soil biodiversity, community composition, and function following wildfire.  Scientific Reports, 13: 7978.  https://doi.org/10.1038/s41598-023-30732-7

46) Smenderovac E, Hoage J, Porter TM, et al (2023) Boreal forest soil biotic communities are affected by harvesting, site preparation with no additional effects of higher biomass removal 5 years post-harvest. Forest Ecology and Management 528:120636. https://doi.org/10.1016/j.foreco.2022.120636

45) Robinson CV, Porter TM, Maitland VC, et al (2022) Multi-marker metabarcoding resolves subtle variations in freshwater condition: Bioindicators, ecological traits, and trophic interactions. Ecological Indicators 145:109603. https://doi.org/10.1016/j.ecolind.2022.109603

44) Porter TM, Hajibabaei M (2022) MetaWorks: A flexible, scalable bioinformatic pipeline for high-throughput multi-marker biodiversity assessments. PLoS ONE 17:e0274260. https://doi.org/10.1371/journal.pone.0274260

43) Rideout NK, Compson ZG, Monk WA, et al (2022) Environmental filtering of macroinvertebrate traits influences ecosystem functioning in a large river floodplain. Functional Ecology 36:2791–2805. https://doi.org/10.1111/1365-2435.14168

42) Robinson CV, Porter TM, McGee KM, et al (2022) Multi-marker DNA metabarcoding detects suites of environmental gradients from an urban harbour. Sci Rep 12:10556. https://doi.org/10.1038/s41598-022-13262-6

41) Rudar J, Porter TM, Wright M, et al (2022) LANDMark: an ensemble approach to the supervised selection of biomarkers in high-throughput sequencing data. BMC Bioinformatics 23:110. https://doi.org/10.1186/s12859-022-04631-z

40) Smenderovac E, Emilson C, Porter TM, et al (2022) Forest soil biotic communities show few responses to wood ash applications at multiple sites across Canada. Sci Rep 12:4171. https://doi.org/10.1038/s41598-022-07670-x

39) Porter TM, Hajibabaei M (2021) Profile hidden Markov model sequence analysis can help remove putative pseudogenes from DNA barcoding and metabarcoding datasets. BMC Bioinformatics 22:256. https://doi.org/10.1186/s12859-021-04180-x

38) Robinson CV, Baird DJ, Wright MTG, et al (2021) Combining DNA and people power for healthy rivers: Implementing the STREAM community-based approach for global freshwater monitoring. Perspectives in Ecology and Conservation 19:279–285. https://doi.org/10.1016/j.pecon.2021.03.001

37) Robinson CV, Porter TM, Wright MTG, Hajibabaei M (2021) Propylene glycol-based antifreeze is an effective preservative for DNA metabarcoding of benthic arthropods. Freshwater Science 40:77–87. https://doi.org/10.1086/712232

36) Maitland VC, Robinson CV, Porter TM, Hajibabaei M (2020) Freshwater diatom biomonitoring through benthic kick-net metabarcoding. PLoS ONE 15:e0242143. https://doi.org/10.1371/journal.pone.0242143

35) McGee KM, Porter TM, Wright M, Hajibabaei M (2020) Drivers of tropical soil invertebrate community composition and richness across tropical secondary forests using DNA metasystematics. Sci Rep 10:18429. https://doi.org/10.1038/s41598-020-75452-4

34) Porter TM, Hajibabaei M (2020) Putting COI Metabarcoding in Context: The Utility of Exact Sequence Variants (ESVs) in Biodiversity Analysis. Front Ecol Evol 8:248. https://doi.org/10.3389/fevo.2020.00248

33) McGee KM, Eaton WD, Porter TM, Hajibabaei M (2020) Differences in the soil microbiomes of Pentaclethra macroloba across tree size and in contrasting land use histories. Plant Soil 452:329–345. https://doi.org/10.1007/s11104-020-04553-w

32) Bush A, Monk WA, Compson ZG, et al (2020) DNA metabarcoding reveals metacommunity dynamics in a threatened boreal wetland wilderness. Proc Natl Acad Sci USA 117:8539–8545. https://doi.org/10.1073/pnas.1918741117

31) Makiola A, Compson ZG, Baird DJ, et al (2020) Key Questions for Next-Generation Biomonitoring. Front Environ Sci 7:197. https://doi.org/10.3389/fenvs.2019.00197

30) Edge TA, Baird DJ, Bilodeau G, et al (2020) The Ecobiomics project: Advancing metagenomics assessment of soil health and freshwater quality in Canada. Science of The Total Environment 710:135906. https://doi.org/10.1016/j.scitotenv.2019.135906

29) Porter TM, Morris DM, Basiliko N, et al (2019) Variations in terrestrial arthropod DNA metabarcoding methods recovers robust beta diversity but variable richness and site indicators. Sci Rep 9:18218. https://doi.org/10.1038/s41598-019-54532-0

28) Compson ZG, Monk WA, Hayden B, et al (2019) Network-Based Biomonitoring: Exploring Freshwater Food Webs With Stable Isotope Analysis and DNA Metabarcoding. Front Ecol Evol 7:395. https://doi.org/10.3389/fevo.2019.00395

27) Hajibabaei M, Porter TM, Robinson CV, et al (2019) Watered-down biodiversity? A comparison of metabarcoding results from DNA extracted from matched water and bulk tissue biomonitoring samples. PLoS ONE 14:e0225409. https://doi.org/10.1371/journal.pone.0225409

26) Bush A, Compson ZG, Monk WA, et al (2019) Studying Ecosystems With DNA Metabarcoding: Lessons From Biomonitoring of Aquatic Macroinvertebrates. Front Ecol Evol 7:434. https://doi.org/10.3389/fevo.2019.00434

25) Hajibabaei M, Porter TM, Wright M, Rudar J (2019) COI metabarcoding primer choice affects richness and recovery of indicator taxa in freshwater systems. PLoS ONE 14:e0220953. https://doi.org/10.1371/journal.pone.0220953

24) McGee KM, Eaton WD, Porter TM, et al (2019) Soil microbiomes associated with two dominant Costa Rican tree species, and implications for remediation: A case study from a Costa Rican conservation area. Applied Soil Ecology 137:139–153. https://doi.org/10.1016/j.apsoil.2019.02.007

23) Erdozain M, Thompson DG, Porter TM, et al (2019) Metabarcoding of storage ethanol vs. conventional morphometric identification in relation to the use of stream macroinvertebrates as ecological indicators in forest management. Ecological Indicators 101:173–184. https://doi.org/10.1016/j.ecolind.2019.01.014

22) Porter TM, Hajibabaei M (2018) Over 2.5 million COI sequences in GenBank and growing. PLoS ONE 13:e0200177. https://doi.org/10.1371/journal.pone.0200177

21) Porter TM, Hajibabaei M (2018) Scaling up: A guide to high-throughput genomic approaches for biodiversity analysis. Molecular Ecology 27:313–338. https://doi.org/10.1111/mec.14478

20) Porter TM, Hajibabaei M (2018) Automated high throughput animal CO1 metabarcode classification. Scientific Reports 8:4226. https://doi.org/10.1038/s41598-018-22505-4

19) Emilson CE, Thompson DG, Venier LA, et al (2017) DNA metabarcoding and morphological macroinvertebrate metrics reveal the same changes in boreal watersheds across an environmental gradient. Scientific Reports 7:. https://doi.org/10.1038/s41598-017-13157-x

18) Porter TM, Shokralla S, Baird D, et al (2016) Ribosomal DNA and Plastid Markers Used to Sample Fungal and Plant Communities from Wetland Soils Reveals Complementary Biotas. PLOS ONE 11:e0142759. https://doi.org/10.1371/journal.pone.0142759

17) Shokralla S, Porter TM, Gibson JF, et al (2015) Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform. Scientific Reports 5:9687. https://doi.org/10.1038/srep09687

16) Nilsson RH, Tedersoo L, Ryberg M, et al (2015) A Comprehensive, Automatically Updated Fungal ITS Sequence Dataset for Reference-Based Chimera Control in Environmental Sequencing Efforts. Microbes and Environments 30:145–150. https://doi.org/10.1264/jsme2.ME14121

15) Gibson J, Shokralla S, Porter TM, et al (2014) Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics. PNAS 111:8007–8012. https://doi.org/10.1073/pnas.1406468111

14) Nilsson R, Hyde K, Pawłowska J, et al (2014) Improving ITS sequence data for identification of plant pathogenic fungi. Fungal Diversity 67:11–19. https://doi.org/10.1007/s13225-014-0291-8 *Special issue on plant pathogens

13) Devault AM, McLoughlin K, Jaing C, et al (2014) Ancient pathogen DNA in archaeological samples detected with a Microbial Detection Array. Scientific Reports 4:. https://doi.org/10.1038/srep04245

12) Porter TM, Gibson JF, Shokralla S, et al (2014) Rapid and accurate taxonomic classification of insect (class Insecta) cytochrome c oxidase subunit 1 (COI) DNA barcode sequences using a naïve Bayesian classifier. Mol Ecol Resour 14:929–942. https://doi.org/10.1111/1755-0998.12240

11) Mahmoudi N, Porter TM, Zimmerman AR, et al (2013) Rapid Degradation of Deepwater Horizon Spilled Oil by Indigenous Microbial Communities in Louisiana Saltmarsh Sediments. Environmental Science & Technology 47:13303–13312. https://doi.org/10.1021/es4036072

10) Porter TM, Golding GB, King C, et al (2013) Amplicon pyrosequencing late Pleistocene permafrost: the removal of putative contaminant sequences and small-scale reproducibility. Molecular Ecology Resources 13:798–810. https://doi.org/10.1111/1755-0998.12124

9) Nilsson RH, Tedersoo L, Abarenkov K, et al (2012) Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences. MycoKeys 4, 4:37–63. https://doi.org/10.3897/mycokeys.4.3606

8) Porter TM, Golding GB (2012) Factors That Affect Large Subunit Ribosomal DNA Amplicon Sequencing Studies of Fungal Communities: Classification Method, Primer Choice, and Error. PLoS ONE 7:e35749. https://doi.org/10.1371/journal.pone.0035749

7) Porter TM, Golding GB (2011) Are similarity- or phylogeny-based methods more appropriate for classifying internal transcribed spacer (ITS) metagenomic amplicons? New Phytologist 192:775–782. https://doi.org/10.1111/j.1469-8137.2011.03838.x

6) Porter TM, Martin W, James TY, et al (2011) Molecular phylogeny of the Blastocladiomycota (Fungi) based on nuclear ribosomal DNA. Fungal Biology 115:381–392. https://doi.org/10.1016/j.funbio.2011.02.004

5) Gryganskyi AP, Lee SC, Litvintseva AP, et al (2010) Structure, Function, and Phylogeny of the Mating Locus in the Rhizopus oryzae Complex. PLOS ONE 5:e15273. https://doi.org/10.1371/journal.pone.0015273

4) Porter TM, Skillman JE, Moncalvo J-M (2008) Fruiting body and soil rDNA sampling detects complementary assemblage of Agaricomycotina (Basidiomycota, Fungi) in a hemlock-dominated forest plot in southern Ontario. Molecular Ecology 17:3037–3050. https://doi.org/10.1111/j.1365-294X.2008.03813.x

3) Bidartondo MI (2008) Preserving Accuracy in GenBank. Science 319:1616–1616. https://doi.org/10.1126/science.319.5870.1616a

2) Porter TM, Schadt CW, Rizvi L, et al (2008) Widespread occurrence and phylogenetic placement of a soil clone group adds a prominent new branch to the fungal tree of life. Molecular Phylogenetics and Evolution 46:635–644. https://doi.org/10.1016/j.ympev.2007.10.002

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McGee KM, Robinson C, Porter TM, et al (2022) eDNA and Bioassessment of Rivers. In: Encyclopedia of Inland Waters. Elsevier, pp 537–548

James TY, Porter TM, Martin WW (2014) Blastocladiomycota. In: Systematics and Evolution. Springer, Berlin, Heidelberg

Schmidt SK, Wilson KL, Meyer AF, et al (2008) The missing fungi: new insights from culture-independent molecular studies of soil. https://www.cabdirect.org/cabdirect/abstract/20083157158. Accessed 6 Jul 2016