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:
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 23(1) 110-110 (2022). DOI: 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 17(9): e0274260. (2022). DOI: https://doi.org/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 36(11) 2791-2805 (2022). DOI: https://doi.org/10.1111/1365-2435.14168
Hajibabaei, M. Demystifying eDNA validation. Trends in Ecology & Evolution 37(10) 826-828. (2022). DOI: 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 12(1) 10556-10556 (2022). DOI: https://doi.org/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: https://doi.org/10.1101/2022.03.31.486647
Porter TM, Hajibabaei M. Profile hidden Markov model sequence analysis can help remove putative pseudogenes from DNA barcoding and metabarcoding datasets. BMC Bioinformatics 22, 256 (2021). DOI: 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. 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): 279-285. DOI: /10.1016/j.pecon.2021.03.001
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(1). DOI: /10.1086/712232
Maitland VC, Robinson CV, Porter TM, Hajibabaei M (2020) Freshwater diatom biomonitoring through benthic kick-net metabarcoding. PLOS ONE 15(11): e0242143. DOI: /10.1371/journal.pone.0242143
Bush A, Monk WA Compson ZG, Peters DL, Porter TM, Shokralla S, Wright MTG, Hajibabaei M, Baird DJ. (2020). DNA metabarcoding reveals metacommunity dynamics in a threatened boreal wetland wilderness. Proceedings of the National Academy of Sciences Apr 2020, 117 (15) 8539-8545. DOI: /10.1073/pnas.1918741117
Hajibabaei M, Porter TM, Robinson CV, Baird DJ, Shokralla S, 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(12): e0225409. DOI: /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 7: 337. DOI: /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 14(9): e0220953. DOI: /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 77, 148–167 (2019). DOI: /10.1007/s00248-018-1206-0
Porter TM, Hajibabaei M (2018) Over 2.5 million COI sequences in GenBank and growing. PLOS ONE 13(9): e0200177. DOI: 10.1371/journal.pone.0200177
Majaneva, M., Diserud, O.H., Eagle, S.H.C., Hajibabaei, M., Ekrem, T., (2018) Choice of DNA extraction method affects DNA metabarcoding of unsorted invertebrate bulk samples. Metabarcoding Metagenomics 2. https://doi.org/10.3897/mbmg.2.26664
McGee, K.M., Eaton, W.D., Shokralla, S., Hajibabaei, M., (2018) 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. https://doi.org/10.1007/s00248-018-1206-0
Porter, T.M., Hajibabaei, M., (2018) Automated high throughput animal metabarcode classification. Sci. Rep. 8
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., (2018) Performance of amplicon and shotgun sequencing for accurate biomass estimation in invertebrate community samples. Mol. Ecol. Resour. https://doi.org/10.1111/1755-0998.12888
Majaneva, M., Diserud, O.H., Eagle, S.H.C., Boström, E., Hajibabaei, M., Ekrem, T., (2018) Environmental DNA filtration techniques affect recovered biodiversity. Sci. Rep. 8. https://doi.org/10.1038/s41598-018-23052-8
Porter, T.M., Hajibabaei, M., (2018) Scaling up: A guide to high-throughput genomic approaches for biodiversity analysis. Mol. Ecol. https://doi.org/10.1111/mec.14478
Curry, C.J., Gibson, J.F., Shokralla, S., Hajibabaei, M., Baird, D.J., (2018) Identifying North American freshwater invertebrates using DNA barcodes: are existing COI sequence libraries fit for purpose? Freshw. Sci. 37, 178–189. https://doi.org/10.1086/696613
Eaton, W.D., Shokralla, S., McGee, K.M., Hajibabaei, M., (2017) Using metagenomics to show the efficacy of forest restoration in the New Jersey Pine Barrens. Genome 60, 825–836. https://doi.org/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. (2017) DNA metabarcoding and morphological macroinvertebrate metrics reveal the same changes in boreal watersheds across an environmental gradient. Sci. Rep. 7.
Janzen DH, Burns JM, Cong Q, Hallwachs W, Dapkey T, Manjunath R, Hajibabaei M, et al. (2017) Nuclear genomes distinguish cryptic species suggested by their DNA barcodes and ecology. Proc Natl Acad Sci. 2017 Jul 17;201621504.
Lobo J, Shokralla S, Costa MH, Hajibabaei M, Costa FO. (2017) DNA Metabarcoding For High-Throughput Monitoring Of Estuarine Macrobenthic Communities. Available from: http://biorxiv.org/lookup/doi/10.1101/117168
Bista, I., Carvalho, G.R., Walsh, K., Christmas, M., Hajibabaei, M., Lallias, D., and Creer, S. (2017) Annual time-series analysis of aqueous eDNA reveals ecologically relevant dynamics of lake ecosystem biodiversity. Nat. Commun. DOI: 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. (2017) 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. 266, 169–176.
Mottawea, W., Chiang, C., Mühlbauer, M., Starr, A., Butcher, J., Abujamel, T., Deeke, S., Brandel, A., Zhou, H., Shokralla, S., et al. (2016) Altered Intestinal Microbiota-Host Mitochondria Crosstalk in New Onset Crohn’s Disease. Nat. Commun. 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 (2016) A new way to contemplate Darwin’s tangled bank: how DNA barcodes are reconnecting biodiversity science and biomonitoring. Philos Trans R Soc B Biol Sci. 5;371(1702):20150330.
Hebert PDN, Hollingsworth PM, Hajibabaei M (2016) From writing to reading the encyclopedia of life. Philos Trans R Soc B Biol Sci. 5;371(1702):20150321.
Fahner NA, Shokralla S, Baird DJ, Hajibabaei M (2016) 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 Jun 16;11(6):e0157505.
Porter TM, Shokralla S, Baird D, Golding BG, Hajibabaei M (2016) Ribosomal DNA and Plastid Markers Used to Sample Fungal and Plant Communities from Wetland Soils Reveals Complementary Biotas. PLOS ONE DOI: 10.1371/journal.pone.0142759
Römbke J, Aira M, Backeljau T, Breugelmans K, Domínguez J, Funke E, et al. (2016) DNA barcoding of earthworms (Eisenia fetida/andrei complex) from 28 ecotoxicological test laboratories. Appl Soil Ecol. 104:3–11. http://dx.doi.org/10.1016/j.apsoil.2015.02.010.
Shokralla S, Hellberg RS, Handy SM, King I, Hajibabaei M (2015) A DNA mini-barcoding system for authentication of processed fish products. Scientific Reports 5: 15894. doi: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
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.
Hajibabaei Lab 