Publications

Publications

We are committed to open-access research, and make every effort to have our publications available at no cost to the reader. Here is a list of some select publications by members of the Hajibabaei lab and collaborators. Please find a complete list of Dr. Hajibabaei’s publications on his Google Scholar page here.

Selected Publications:

Riley AC, Wright M, Porter TM, Maitland VC, Baird DJ, Hajibabaei M. Biomonitoring 2.0 Refined: observing local change through metaphylogeography using a community-based eDNA metabarcoding monitoring network. BMC Biol. 2025; 23(1). https://doi.org/10.1186/s12915-025-02284-x

Bender CJ, Moir CD, Hajibabaei M, Boulding EG. Morphological and metabarcoding dietary analysis of the cunner wrasse (Tautogolabrus adspersus) revealed significant regional variation, with large overlap between its common prey species and biofouling animals living on salmonid sea cages. J Fish Biol. 2025; 107(1). https://doi.org/10.1111/jfb.70013

Rideout NK, Alavi N, Lapen DR, Hajibabaei M, Mitchell GW, Monk WA, et al. Quality versus quantity: response of riparian bird communities to aquatic insect emergence in agro-ecosystems. Front Sustain Food Syst. 2025; 8:1484377. https://doi.org/10.3389/fsufs.2024.1484377

Hakimzadeh A, Abdala Asbun A, Albanese D, Bernard M, Buchner D, Callahan B, et al. A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses. Mol Ecol Resour. 2024; 24(5):e13847. DOI: 10.1111/1755-0998.13847

Crowley SE, Bentzen P, Kess T, Duffy SJ, Messmer AM, Watson B, et al. eDNA metabarcoding reveals riverine fish community structure and climate associations in northeastern Canada. Environ DNA. 2024; 6(1):e517. https://doi.org/10.1002/edn3.517

Seymour M, Roslin T, Dewaard JR, Perez KH, D’Souza ML, Ratnasingham S, et al. Global arthropod beta-diversity is spatially and temporally structured by latitude. Commun Biol. 2024; 7(1):552. DOI: 10.1038/s42003-024-06199-1

Ilyas U, du Toit LJ, Hajibabaei M, McDonald MR. Influence of plant species, mycorrhizal inoculant, and soil phosphorus level on arbuscular mycorrhizal communities in onion and carrot roots. Front Plant Sci. 2024; 14:1324626. https://doi.org/10.3389/fpls.2023.1324626

Olinger LK, McClenaghan B, Hajibabaei M, Fahner N, Berghuis L, Rajabi H, et al. Looking for the sponge loop: analyses of detritus on a Caribbean forereef using stable isotope and eDNA metabarcoding techniques. PeerJ. 2024; 12:e16970. DOI: 10.7717/peerj.16970

Rudar J, Kruczkiewicz P, Vernygora O, Golding GB, Hajibabaei M, Lung O. Sequence signatures within the genome of SARS-CoV-2 can be used to predict host source. Microbiol Spectr. 2024; 12(4):e03584-23. DOI: 10.1128/spectrum.03584-23

Bush A, Compson Z, Rideout N, Levenstein B, Kattilakoski M, Hajibabaei M, et al. Replicate DNA metabarcoding can discriminate seasonal and spatial abundance shifts in river macroinvertebrate assemblages. Mol Ecol Resour. 2023; 23(6):1275–87. https://doi.org/10.1111/1755-0998.13794

Cote D, McClenaghan B, Desforges J, Fahner N, Hajibabaei M, Chawarski J, et al. Comparing eDNA metabarcoding and conventional pelagic netting to inform biodiversity monitoring in deep ocean environments. ICES J Mar Sci. 2023; 80(10):2545–62. https://doi.org/10.1093/icesjms/fsad169

Hart SC, Porter TM, Basiliko N, Venier L, Hajibabaei M, Morris D. Fungal community dynamics in coarse woody debris across decay stage, tree species, and stand development stage in northern boreal forests. Can J For Res. 2023; 54(1):12–30. DOI: 10.1139/cjfr-2023-0061

McCarthy A, Rajabi H, McClenaghan B, Fahner NA, Porter E, Singer GA, et al. Comparative analysis of fish environmental DNA reveals higher sensitivity achieved through targeted sequence-based metabarcoding. Mol Ecol Resour. 2023; 23(3):581–91. DOI: 10.1111/1755-0998.13732

Rudar J, Golding GB, Kremer SC, Hajibabaei M. Decision tree ensembles utilizing multivariate splits are effective at investigating beta diversity in medically relevant 16S amplicon sequencing data. Microbiol Spectr. 2023; 11(2):e02065-22. DOI: 10.1128/spectrum.02065-22

Sharkey MJ, Baker A, McCluskey K, Smith A, Naik S, Ratnasingham S, et al. Minimalist revision of Mesochorus Gravenhorst, 1829 (Hymenoptera: Ichneumonidae: Mesochorinae) from Área de Conservación Guanacaste, Costa Rica, with 158 new species and host records for 129 species. Rev Biol Trop. 2023; 71. DOI: 10.15517/rev.biol.trop..v71iS2.56316

Basset Y, Hajibabaei M, Wright MT, Castillo AM, Donoso DA, Segar ST, et al. Comparison of traditional and DNA metabarcoding samples for monitoring tropical soil arthropods (Formicidae, Collembola and Isoptera). Sci Rep. 2022; 12(1):10762. DOI: 10.1038/s41598-022-14915-2

Farrell MJ, Govender D, Hajibabaei M, van der Bank M, Davies TJ. Environmental DNA as a management tool for tracking artificial waterhole use in savanna ecosystems. Biol Conserv. 2022; 274:109712. DOI: 10.1016/j.biocon.2022.109712

McGee KM, Robinson C, Porter TM, Compson ZG, Hajibabaei M, Baird DJ. eDNA and Bioassessment of Rivers. 2022; https://doi.org/10.1016/B978-0-12-819166-8.00131-6

Robinson CV, Porter TM, Maitland VC, Wright MT, Hajibabaei M. Multi-marker metabarcoding resolves subtle variations in freshwater condition: Bioindicators, ecological traits, and trophic interactions. Ecol Indic. 2022; 145:109603. DOI: 10.1016/j.ecolind.2022.109603

Zaiko A, Greenfield P, Abbott C, von Ammon U, Bilewitch J, Bunce M, et al. Towards reproducible metabarcoding data: Lessons from an international cross-laboratory experiment. Mol Ecol Resour. 2022; 22(2):519–38. DOI: 10.1111/1755-0998.13485

Rudar J, Porter TM, Wright MTG, Golding BG, Hajibabaei M. LANDMark: an ensemble approach to the supervised selection of biomarkers in high-throughput sequencing data. BMC Bioinformatics 2022; 23(1) 110-110. https://doi.org/10.1186/s12859-022-04631-z

Porter, TM, Hajibabaei, M. MetaWorks: A flexible, scalable bioinformatic pipeline for high-throughput multi-marker biodiversity assessments. PLOS ONE. 2022; 17(9): e0274260. DOI: 10.1371/journal.pone.0274260

Rideout NK, Compson ZG, Monk WA, Bruce MR, Hajibabaei M, Porter TM, Wright MTG, Baird DJ. Environmental filtering of macroinvertebrate traits influences ecosystem functioning in a large river floodplain. Functional Ecology. 2022; 36(11) 2791-2805. https://doi.org/10.1111/1365-2435.14168

Hajibabaei, M. Demystifying eDNA validation. Trends in Ecology & Evolution. 2022; 37(10) 826-828. https://doi.org/10.1016/j.tree.2022.06.015

Robinson CV, Porter TM, McGee KM, McCusker M, Wright MTG, Hajibabaei M. Multi-marker DNA metabarcoding detects suites of environmental gradients from an urban harbour. Scientific Reports. 2022; 12(1) 10556-10556. DOI: 10.1038/s41598-022-13262-6

Rudar J, Golding BG, Kremer SC, Hajibabaei M. Decision tree ensembles utilizing multivariate splits are effective at investigating beta-diversity in medically relevant 16s amplicon sequencing data. BioRxiv. 2022. DOI: 10.1128/spectrum.02065-22

Bruno A, Casiraghi M, Bautista M, Hajibabaei M. Stressors acting on aquatic Ecosystems: high-throughput sequencing approaches to shed light on human-nature interactions. Vol. 9, Frontiers in Ecology and Evolution. Frontiers Media SA; 2021. p. 763442. https://doi.org/10.3389/fevo.2021.763442

Eaton WD, McGee KM, Donnelly R, Lemenze A, Larimer M, Hajibabaei M. The impacts of a logging road on the soil microbial communities, and carbon and nitrogen components in a Northern Zone Costa Rican forest. Appl Soil Ecol. 2021; 164:103937. DOI: 10.1016/j.apsoil.2021.103937

He X, Gilmore SR, Sutherland TF, Hajibabaei M, Miller KM, Westfall KM, et al. Biotic signals associated with benthic impacts of salmon farms from eDNA metabarcoding of sediments. Mol Ecol. 2021; 30(13):3158–74. DOI: 10.1111/mec.15814

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

Robinson CV, Baird DJ, Wright MTG, Porter TM, Hartwig K, Hendriks E, Maclean L, Mallinson R, Monk WA, Paquette C, Hajibabaei M. Combining DNA and people power for healthy rivers: Implementing the STREAM community-based approach for global freshwater monitoring. Perspectives in Ecology and Conservation. 2021; 19(3): 279-285. https://doi.org/10.1016/j.pecon.2021.03.001

Rideout NK, Compson ZG, Monk WA, Hajibabaei M, Porter TM, Wright MT, et al. Functional traits link anthropogenic impact and disturbance regimes driving ecosystem function in a floodplain wetland complex. In: ARPHA Conference Abstracts. Pensoft Publishers; 2021. https://doi.org/10.3897/aca.4.e65144

Robinson CV, Porter TM, Wright MTG, Hajibabaei M. Propylene glycol-based antifreeze is an effective preservative for DNA metabarcoding of benthic arthropods. Freshwater Science 2021; 40(1). DOI: 10.1086/712232

Maitland VC, Robinson CV, Porter TM, Hajibabaei M. Freshwater diatom biomonitoring through benthic kick-net metabarcoding. PLOS ONE 2020; 15(11): e0242143.

Basset Y, Donoso DA, Hajibabaei M, Wright MT, Perez KH, Lamarre G, et al. Methodological considerations for monitoring soil/litter arthropods in tropical rainforests using DNA metabarcoding, with a special emphasis on ants, springtails and termites. Metabarcoding Metagenomics. 2020. https://doi.org/10.1371/journal.pone.0242143

Compson ZG, McClenaghan B, Singer GA, Fahner NA, Hajibabaei M. Metabarcoding from microbes to mammals: comprehensive bioassessment on a global scale. Front Ecol Evol. 2020; 8:581835. https://doi.org/10.3389/fevo.2020.581835

Eaton WD, McGee KM, Alderfer K, Jimenez AR, Hajibabaei M. Increase in abundance and decrease in richness of soil microbes following Hurricane Otto in three primary forest types in the Northern Zone of Costa Rica. PloS One. 2020; 15(7):e0231187. https://doi.org/10.1371/journal.pone.0231187

Eaton WD, McGee KM, Hoke E, Lemenze A, Hajibabaei M. Influence of two important leguminous trees on their soil microbiomes and nitrogen cycle activities in a primary and recovering secondary forest in the northern zone of Costa Rica. Soil Syst. 2020; 4(4):65. https://doi.org/10.3390/soilsystems4040065

Fais M, Duarte S, Vieira PE, Sousa R, Hajibabaei M, Canchaya CA, et al. Small-scale spatial variation of meiofaunal communities in Lima estuary (NW Portugal) assessed through metabarcoding. Estuar Coast Shelf Sci. 2020; 238:106683. DOI: 10.1016/j.ecss.2020.106683

Janzen DH, Hallwachs W, Pereira G, Blanco R, Masis A, Chavarria MM, et al. Using DNA-barcoded Malaise trap samples to measure impact of a geothermal energy project on the biodiversity of a Costa Rican old-growth rain forest. Genome. 2020; 63(9):407–36. DOI: 10.1139/gen-2020-0002

Makiola A, Compson ZG, Baird DJ, Barnes MA, Boerlijst SP, Bouchez A, et al. Key questions for next-generation biomonitoring. Front Environ Sci. 2020; 7:197. https://doi.org/10.3389/fenvs.2019.00197

Makiola A, Compson ZG, Baird DJ, Barnes M, Boerlijst SP, Bouchez A, et al. Questions clés pour la prochaine génération de biosurveillance. 2020; 7. https://doi.org/10.3389/fenvs.2019.00197

McClenaghan B, Fahner N, Cote D, Chawarski J, McCarthy A, Rajabi H, et al. Harnessing the power of eDNA metabarcoding for the detection of deep-sea fishes. PloS One. 2020; 15(11):e0236540. https://doi.org/10.1371/journal.pone.0236540

McClenaghan B, Compson ZG, Hajibabaei M. Validating metabarcoding-based biodiversity assessments with multi-species occupancy models: a case study using coastal marine eDNA. PloS One. 2020; 15(3):e0224119. https://doi.org/10.1371/journal.pone.0224119

McGee KM, Eaton WD, Porter TM, Hajibabaei M. Differences in the soil microbiomes of Pentaclethra macroloba across tree size and in contrasting land use histories. Plant Soil. 2020; 452:329–45. DOI: 10.1007/s11104-020-04553-w

McGee KM, Porter TM, Wright M, Hajibabaei M. Drivers of tropical soil invertebrate community composition and richness across tropical secondary forests using DNA metasystematics. Sci Rep. 2020; 10(1):18429. https://doi.org/10.1038/s41598-020-75452-4

Porter TM, Hajibabaei M. Putting COI metabarcoding in context: The utility of exact sequence variants (ESVs) in biodiversity analysis. Front Ecol Evol. 2020; 8:248. https://doi.org/10.3389/fevo.2020.00248

Bush A, Monk WA Compson ZG, Peters DL, Porter TM, Shokralla S, Wright MTG, Hajibabaei M, Baird DJ. DNA metabarcoding reveals metacommunity dynamics in a threatened boreal wetland wilderness. Proceedings of the National Academy of Sciences. 2020; 117(15) 8539-8545. DOI: 10.1073/pnas.1918741117

Hajibabaei M, Porter TM, Robinson CV, Baird DJ, Shokralla S, et al. Watered-down biodiversity? A comparison of metabarcoding results from DNA extracted from matched water and bulk tissue biomonitoring samples. PLOS ONE. 2020; 14(12): e0225409. https://doi.org/10.1371/journal.pone.0225409

McGee KM, Robinson CV, Hajibabaei M. 2019.Gaps in DNA-Based Biomonitoring Across the Globe. Frontiers in Ecology and Evolution. 2019; 7(337). https://doi.org/10.3389/fevo.2019.00337

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. 2019; 14(9): e0220953. https://doi.org/10.1371/journal.pone.0220953

McGee, K.M., Eaton, W.D., Shokralla, S. et al. Determinants of Soil Bacterial and Fungal Community Composition Toward Carbon-Use Efficiency Across Primary and Secondary Forests in a Costa Rican Conservation Area. Microb Ecol. 2019; 77, 148–167. DOI: 10.1007/s00248-018-1206-0

Porter TM, Hajibabaei M. Over 2.5 million COI sequences in GenBank and growing. PLOS ONE. 2018; 13(9): e0200177. https://doi.org/10.1371/journal.pone.0200177

Majaneva, M., Diserud, O.H., Eagle, S.H.C., Hajibabaei, M., Ekrem, T. Choice of DNA extraction method affects DNA metabarcoding of unsorted invertebrate bulk samples. Metabarcoding Metagenomics 2. 2018; e26664. https://doi.org/10.3897/mbmg.2.26664

McGee, K.M., Eaton, W.D., Shokralla, S., Hajibabaei, M. Determinants of Soil Bacterial and Fungal Community Composition Toward Carbon-Use Efficiency Across Primary and Secondary Forests in a Costa Rican Conservation Area. Microb. Ecol. 2018; 77(1). DOI: 10.1007/s00248-018-1206-0

Porter, T.M., Hajibabaei, M. Automated high throughput animal metabarcode classification. Sci. Rep 8. 2018; 4226. https://doi.org/10.1038/s41598-018-22505-4

Bista, I., Carvalho, G.R., Tang, M., Walsh, K., Zhou, X., Hajibabaei, M., Shokralla, S., Seymour, M., Bradley, D., Liu, S., Christmas, M., Creer, S.Performance of amplicon and shotgun sequencing for accurate biomass estimation in invertebrate community samples. Mol. Ecol. Resour. 2018. DOI: 10.1111/1755-0998.12888

Majaneva, M., Diserud, O.H., Eagle, S.H.C., Boström, E., Hajibabaei, M., Ekrem, T. Environmental DNA filtration techniques affect recovered biodiversity. Sci. Rep. 8. 2018; 4682. https://doi.org/10.1038/s41598-018-23052-8

Porter, T.M., Hajibabaei, M. Scaling up: A guide to high-throughput genomic approaches for biodiversity analysis. Mol. Ecol. 2018; 27(2). DOI: 10.1111/mec.14478

Curry, C.J., Gibson, J.F., Shokralla, S., Hajibabaei, M., Baird, D.J. Identifying North American freshwater invertebrates using DNA barcodes: are existing COI sequence libraries fit for purpose? Freshw. Sci. 2018; 37, 178–189. DOI: 10.1086/696613

Eaton, W.D., Shokralla, S., McGee, K.M., Hajibabaei, M. Using metagenomics to show the efficacy of forest restoration in the New Jersey Pine Barrens. Genome. 2017; 60(10), 825–836. DOI: 10.1139/gen-2015-0199

Emilson, C.E., Thompson, D.G., Venier, L.A., Porter, T.M., Swystun, T., Chartrand, D., Capell, S., and Hajibabaei, M. DNA metabarcoding and morphological macroinvertebrate metrics reveal the same changes in boreal watersheds across an environmental gradient. Sci. Rep. 7. 2017; 12777. https://doi.org/10.1038/s41598-017-13157-x

Janzen DH, Burns JM, Cong Q, Hallwachs W, Dapkey T, Manjunath R, Hajibabaei M, et al. Nuclear genomes distinguish cryptic species suggested by their DNA barcodes and ecology. Proc Natl Acad Sci. 2017; 114(31) 8313-8318. https://doi.org/10.1073/pnas.1621504114

Lobo J, Shokralla S, Costa MH, Hajibabaei M, Costa FO. DNA Metabarcoding For High-Throughput Monitoring Of Estuarine Macrobenthic Communities. 2017. https://doi.org/10.1038/s41598-017-15823-6

Bista, I., Carvalho, G.R., Walsh, K., Christmas, M., Hajibabaei, M., Lallias, D., and Creer, S. Annual time-series analysis of aqueous eDNA reveals ecologically relevant dynamics of lake ecosystem biodiversity. Nat. Commun. 2017; 14087. https://doi.org/10.1038/ncomms14087

Bächtold, A., Kaminski, L.A., Magaldi, L.M., Oliveira, P.S., Del-Claro, K., Janzen, D.H., Burns, J.M., Grishin, N., Hajibabaei, M., Hallwachs, W., et al. Integrative data helps the assessment of a butterfly within the Udranomia kikkawai species complex (Lepidoptera: Hesperiidae): Immature stages, natural history, and molecular evidence. Zool. Anz. – J. Comp. Zool. 2017; 266, 169–176. https://doi.org/10.1016/j.jcz.2016.11.009

Mottawea, W., Chiang, C., Mühlbauer, M., Starr, A., Butcher, J., Abujamel, T., Deeke, S., Brandel, A., Zhou, H., Shokralla, S., et al. Altered Intestinal Microbiota-Host Mitochondria Crosstalk in New Onset Crohn’s Disease. Nat. Commun. 2016; 7(13419). DOI: 10.1038/ncomms13419

Shokralla, S., Gibson, J., King, I., Baird, D., Janzen, D., Hallwachs, W., and Hajibabaei, M. (2016) Environmental DNA Barcode Sequence Capture: Targeted, PCR-free Sequence Capture for Biodiversity Analysis from Bulk Environmental Samples. bioRxiv. DOI: 10.1101/087437

Hajibabaei M, Baird DJ, Fahner NA, Beiko R, Golding GB. A new way to contemplate Darwin’s tangled bank: how DNA barcodes are reconnecting biodiversity science and biomonitoring. Philos Trans R Soc Biol Sci. 2016; 5;371(1702):20150330. doi: 10.1098/rstb.2015.0330

Hebert PDN, Hollingsworth PM, Hajibabaei M. From writing to reading the encyclopedia of life. Philos Trans R Soc Biol Sci. 2016; 5;371(1702):20150321. doi: 10.1098/rstb.2015.0321

Fahner NA, Shokralla S, Baird DJ, Hajibabaei M. Large-Scale Monitoring of Plants through Environmental DNA Metabarcoding of Soil: Recovery, Resolution, and Annotation of Four DNA Markers. Lamb EG, editor. PLOS ONE. 2016; 11(6):e0157505.

Porter TM, Shokralla S, Baird D, Golding BG, Hajibabaei M. Ribosomal DNA and Plastid Markers Used to Sample Fungal and Plant Communities from Wetland Soils Reveals Complementary Biotas. PLOS ONE 2016; 11(1): e0142759.

Römbke J, Aira M, Backeljau T, Breugelmans K, Domínguez J, Funke E, et al. DNA barcoding of earthworms (Eisenia fetida/andrei complex) from 28 ecotoxicological test laboratories. Appl Soil Ecol. 2016; 104() :3–11. http://dx.doi.org/10.1016/j.apsoil.2015.02.010

Shokralla S, Hellberg RS, Handy SM, King I, Hajibabaei M. A DNA mini-barcoding system for authentication of processed fish products. Scientific Reports 7. 2015; 15894. https://doi.org/10.1038/srep15894

Gibson JF, Shokralla S, Curry C, Baird DJ, Monk WA, King I, Hajibabaei M (2015) Large-scale biomonitoring of remote and threatened ecosystems via high-throughput sequencing. PLOS ONE 10(10): e0138432. doi:10.1371/journal.pone.0138432

McClenaghan B, Gibson JF, Shokralla, S, & Hajibabaei M (2015) Discrimination of grasshopper (Orthoptera: Acrididae) diet and niche overlap using next-generation sequencing of gut contents. Ecology and Evolution DOI: 10.1002/ece3.1585

Gibson JF, Stein ED, Baird DJ, Finlayson CM, Zhang X, Hajibabaei M (2015) Wetland Ecogenomics – The Next Generation of Wetland Biodiversity and Functional Assessment. Wetland Science and Practice 32: 27-32 DOI: 10.1672/UCRT083-282

Shokralla, S., Porter T. M., Gibson, J. F., Dobosz, R., Janzen, D. H., Hallwachs, W., Golding, G. B., & Hajibabaei, M. (2015) Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform. Scientific Reports 5: 9687 DOI: 10.1038/srep0968

Shafer ABA, Wolf JBW, Alves PC, Bergström L, Bruford MW, Brännström I, et al. (2015) Genomics and the challenging translation into conservation practice. Trends Ecol Evol. 30(2):78–87.

Bertrand, C., Janzen, D. H., Hallwachs, W., Burns, J. M., Gibson, J. F., Shokralla, S., & Hajibabaei, M. (2014). Mitochondrial and nuclear phylogenetic analysis with Sanger and next-generation sequencing shows that, in Área de Conservación Guanacaste, NW Costa Rica, the skipper butterfly Urbanus belli (Hesperiidae) comprises three morphologically cryptic species. BMC Evolutionary Biology.

Gibson, J. F., Shokralla, S., Porter, T. M., King, I., van Konynenburg, S., Janzen, D.H, Hallwachs, W., & Hajibabaei, M. (2014). Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics. Proceedings of the National Academy of Sciences of the United States of America.

Shokralla S, Gibson JF, Nikbakht H, Janzen DH, Hallwachs W, Hajibabaei M (2014) Next-generation DNA barcoding: using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimens. Molecular Ecology Resources. DOI: 10.1111/1755-0998.12236

Porter TM, Gibson JM, Shokralla S, Baird DJ, Golding GB, Hajibabaei M (2014) Rapid and accurate taxonomic classification of insect (Class Insecta) cytochrome c oxidase subunit 1 (COI) DNA barcode sequences using a naïve Bayesian classifier. Molecular Ecology Resources. DOI: 10.1111/1755-0998.12240

Brown, J.W., Janzen, D.H., Hallwachs, W., Zahiri, R., Hajibabaei, M., and Hebert, P.D.N. (2014). Cracking Complex Taxonomy of Costa Rican Moths: Anacrusis Zeller (Lepidoptera: Tortricidae: Tortricinae). J. Lepidopterists’ Soc. 68, 248–263. DOI: 10.18473/lepi.v68i4.a3

Vincent B, Hajibabaei M, Rougerie R (2014) A striking new genus and species of tiger-moth (Lepidoptera: Erebidae, Arctiinae, Arctiini) from the Caribbean, with molecular and morphological analysis of its systematic placement. Zootaxa 3760 (2): 289–300.

Chacon IA, Janzen DH, Hallwachs W, Sullivan JB, Hajibabaei M. (2013) Cryptic species within cryptic moths: new species of Dunama Schaus (Notodontidae, Nystaleinae) in Costa Rica. Zookeys 264:11-45.

Burns JM, Janzen DH, Hallwachs W, Hajibabaei M. (2013) DNA Barcodes Reveal yet Another New Species of Venada (Lepidoptera: Hesperiidae) in Northwestern Costa Rica. P Entomol Soc Wash 115:37-47.

Grishin N, Burns JM, Janzen DH, Hallwachs W, Hajibabaei M. (2013) Oxynetra:facies and DNA barcodes point to a new species from Costa Rica (Hesperiidae: Pyrginae: Pyrrhopygini). Journal of Lepidopterists’ Society 67:1-14.

Janzen DH, Hallwachs W, Harvey DJ, Darrow K, Rougerie R, et al. (2012) What happens to the traditional taxonomy when a well-known tropical saturniid moth fauna is DNA barcoded? Invertebrate Systematics 26: 478-505.

Hajibabaei, M, Spall, JL, Shokralla, S and 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 DOI: 10.1186/1472-6785-12-28

Wallace LJ, Boilard SMAL, Eagle SHC, Spall JL, Shokralla S, Hajibabaei M. (2012) DNA barcodes for everyday life: Routine authentication of Natural Health Products. Food Research International 49: 446-452. DOI: 10.1016/j.foodres.2012.07.048

Hajibabaei M (2012) The golden age of DNA metasystematics. Trends in Genetics. 28: 535-537. DOI: 10.1016/j.tig.2012.08.001

Shokralla S, Spall JL, Gibson JF, Hajibabaei M (2012) Next-generation DNA sequencing technologies for environmental DNA research. Molecular Ecology 21: 1794-1805. DOI: 10.1111/j.1365-294X.2012.05538.x

Baird DJ, Hajibabaei M (2012) Biomonitoring 2.0: A new paradigm in ecosystem assessment made possible by next generation sequencing. Molecular Ecology 21: 2039-2044. DOI: 10.1111/j.1365-294X.2012.05519.x

Janzen DH, Hallwachs W, Burns JM, Hajibabaei M, Bertrand C, et al. (2011) Reading the complex skipper butterfly fauna of one tropical place. PLoS One 6: e19874.

Shokralla S, Zhou X, Janzen DH, Hallwachs W, Landry JF, Hajibabaei M (2011) Pyrosequencing for mini-barcoding of fresh and old museum specimens. PLoS One 6: e21252. doi:10.1371/journal.pone.0021252

Wilson J, Rougerie R, Schonfeld J, Janzen D, Hallwachs W, et al. (2011) When species matches are unavailable are DNA barcodes correctly assigned to higher taxa? An assessment using sphingid moths. BMC Ecology doi:10.1186/1472-6785-11-18.

Hajibabaei M, McKenna C (2011) DNA Mini-barcodes. In: Kress WJ, Erickson DL, editors. Methods in Molecular Biology, DNA BARCODES: METHODS AND PROTOCOLS. Berlin: Humana Press, Springer Science+Publishing Media, LLC. pp. in press.

Hajibabaei M, Shokralla S, Zhou X, Singer GAC, Baird DJ (2011) Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos. PLoS ONE 6: e17497.

Kesanakurti PR, Fazekas AJ, Burgess KS, Percy DM, Newmaster SG, Graham SW, Barrett SCH, Hajibabaei M and Husband BC (2011) Spatial patterns of plant diversity below-ground as revealed by DNA barcoding. Molecular Ecology, no. doi: 10.1111/j.1365-294X.2010.04989.x

Baird DJ, Pascoe TJ, Zhou X, Hajibabaei M (2011) Building freshwater macroinvertebrate DNA-barcode libraries from reference collection material: formalin preservation vs specimen age.. Journal of the North American Benthological Society 30: 125-130.

Burgess KS, Fazekas AJ, Kesanakurti PR, Graham SW, Husband BC, et al. (2011) Discriminating plant species in a local temperate flora using the rbcL+matK DNA barcode. Methods in Ecology and Evolution DOI: 10.1111/j.2041-210X.2011.00092.x.

Baird DJ, Baker CJO, Brua R, Hajibabaei M, McNicol K, Pascoe T, de Zwart D (2011) Towards a knowledge infrastructure for traits-based ecological risk assessment. Integrated Environmental Assessment and Management 7:209-215.

Shokralla S, Singer GAC, Hajibabaei M (2010) Direct PCR amplification and sequencing of specimens’ DNA from preservative ethanol. BioTechniques 48:233-234. Listed among high ranking papers and a commentary was published about this work.

Albu M, Nikbakht H, Hajibabaei M, Hickey DA (2010) The DNA Barcode Linker. Molecular Ecology Resources, doi: 10.1111/j.1755-0998.2010.02901.x

Wilson JJ, Landry JF, Janzen DH, Hallwachs W, Nazari V, Hajibabaei M, Hebert PDN (2010) Identity of the ailanthus webworm moth (Lepidoptera: Yponomeutidae), a complex of two species: evidence from DNA barcoding, morphology and ecology. ZooKeys 46: 41–60.

Burns JM, Janzen DH, Hallwachs W, Hajibabaei M, et al. (2010) Genitalia, DNA barcodes, larval facies, and foodplants place the mimetic species Neoxeniades molion in Rhinthon (Hesperiidae: Hesperiinae). Journal of the Lepidopterists’ Society, 2010, 64: 69-78.

Hollingsworth PM, and 51 others (2009). A DNA barcode for land plants. Proceedings of the National Academy of Sciences U.S.A., 106:12794-12797.

Janzen DH, and 45 others (2009) Integration of DNA barcoding into an ongoing inventory of complex tropical biodiversity. Molecular Ecology Resources, 9s1:1-26.

Fazekas AJ, Kesanakurti PR, Burgess KS, Percy DM, Graham SW, Barrett SC, Newmaster SG, Hajibabaei M, Husband BC (2009) Are plant species inherently harder to discriminate than animal species using DNA barcoding markers? Molecular Ecology Resources, 9s1:130-139.

Hajibabaei M, Singer GAC (2009) Googling DNA Sequences on the World Wide Web. BMC Bioinformatics Suppl 14:4 pp.

Singer GAC, Hajibabaei M (2009) iBarcode.org: web-based molecular biodiversity analysis. BMC Bioinfomatics 2009, 10 Suppl 6:S14.

Burns JM, Janzen DH, Hallwachs W, Hajibabaei M, and Hebert PDN (2009) Genitalia, DNA barcodes, and life histories synonymize Telles with Thracides–a genus in which Telles arcalaus looks out of place (Hesperiidae: Hesperiinae). Journal of the Lepidopterists’ Society, 63(3): 141-153.

Zimmermann J, Hajibabaei M, Blackburn DC, Hanken J, Cantin E, Posfai J, Evans TC, Jr. (2008) DNA damage in preserved specimens and tissue samples: a molecular assessment. Frontiers in Zoology, 5:18.

Meusnier I, Singer GAC, Landry JF, Hickey DA, Hebert PDN, Hajibabaei M (2008) A universal DNA mini-barcode for biodiversity analysis. BMC Genomics 2008, 9:214. (Ranked as highly accessed article)

Fazekas AJ, Burgess KS, Kesanakurti PR, Graham SW, Newmaster SG, Husband BC, Percy DM, Hajibabaei M, Barrett SC (2008). Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well. PLoS One, 3:e2802.

Burns JM, Janzen DH, Hajibabaei M, Hallwachs W, Hebert PDN (2008) DNA barcodes and cryptic species of skipper butterflies in the genus Perichares in Area de Conservación Guanacaste, Costa Rica. Proceedings of the National Academy of Sciences U.S.A., 105:6350-6355.

Hajibabaei M, Singer GAC, Hebert PDN, Hickey DA (2007) DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. Trends in Genetics, 23:167-172. (Published as cover story and ranked 5th in the Top 25 Hottest Articles in April-June 2007)

Hajibabaei M, Singer GAC, Clare EL, Hebert PDN (2007) Design and applicability of DNA arrays and DNA barcodes in biodiversity monitoring. BMC Biology, 5:24. (Ranked as highly accessed article)

Burns JM, Janzen DH, Hajibabaei M, Hallwachs W, Hebert PDN (2007) DNA barcodes of closely related (but morphologically and ecologically distinct) species of skipper butterflies (Hesperiidae) differ by only one to three nucleotides. Journal of the Lepidopterists’ Society, 61:138-153.

Hajibabaei M, Xia J, Drouin G (2006) Seed plant phylogeny: gnetophytes are derived conifers and a sister group to Pinaceae. Molecular Phylogenetics and Evolution, 40:208-217.

Hajibabaei M, Smith MA, Janzen DH, Rodriguez JJ, Whitfield JB, Hebert PDN (2006) A minimalist barcode can identify a specimen whose DNA is degraded.. Molecular Ecology Notes, 6:959-964. (Ranked among top 20 accessed papers on journal’s website)

Hajibabaei M, Singer GAC, Hickey DA (2006) Benchmarking DNA barcodes: An assessment using available primate sequences. Genome, 49:851-854.

Hajibabaei M, Janzen DH, Burns JM, Hallwachs W, Hebert PD (2006) DNA barcodes distinguish species of tropical Lepidoptera. Proceedings of the National Academy of Sciences U.S.A., 103:968-971. (Presented as cover image and ranked 4th among 50th Most-Read Articles in January 2006)

Janzen DH, Hajibabaei M, Burns JM, Hallwachs W, Remigio E, Hebert PD (2005) Wedding biodiversity inventory of a large and complex Lepidoptera fauna with DNA barcoding. Philosophical Transactions of the Royal Society B: Biological Sciences, 360:1835-1845.

Hajibabaei M, deWaard JR, Ivanova NV, Ratnasingham S, Dooh RT, Kirk SL, Mackie PM, Hebert PDN (2005) Critical factors for assembling a high volume of DNA barcodes. Philosophical Transactions of the Royal Society B: Biological Sciences, 360:1959-1967.