Tran, L., Deckers, T.B., Ho, J. et al. Neonicotinoid-induced signature dysbiosis identified via metagenomic sequencing of the honey bee gut microbiome. Sci Rep 16, 1211 (2026). https://doi.org/10.1038/s41598-025-30907-4
Wizenberg, S. B., M.Pepinelli, B. N.Do, et al. 2025. “Inferring Plant Community Phenology via Bee-Collected Pollen.” Environmental DNA7, no. 4: e70149. https://doi.org/10.1002/edn3.70149.
Tran L, Lansing L, Cunningham M, Ho J, Deckers T, Newman T, Wu L, Gregoris AS, Zorz J, Muntz L, Lee K, Trépanier-Leroux D, Conflitti IM, Pepinelli M, Walsh EM, Morfin N, Powell JE, Moran N, Hoover SE, Pernal SF, Currie RW, Giovenazzo P, Guzman-Novoa E, Jabbari H, Foster LJ, Zayed A, Ortega Polo R, Guarna MM.2025.Gut microbiome metagenomic sequences of honey bees (Apis mellifera) exposed to crops. Microbiol Resour Announc14:e00731-24.https://doi.org/10.1128/mra.00731-24
McAfee, A., Alavi-Shoushtari, N., Labuschagne, R., Tran, L., Higo, H., Pernal, S.F., Giovenazzo, P., Hoover, S.E., Guzman-Novoa, E., Currie, R.W., Wolf Veiga, P., French, S.K., Conflitti, I.M., Pepinelli, M., Borges, D., Walsh, E.M., C.A. Bishop, Zayed, A., Duffe, J., Guarna, M.M.,Foster, L.J. Regional patterns and climatic predictors of viruses in honey bee (Apis mellifera) colonies over time (2025). Scientific Reports 15: 286. {IF=4.6} https://doi.org/10.1038/s41598-024-79675-7
Wizenberg, S.B., French, S.K., Newburn, L.R., Pepinelli, M., Conflitti, I.M., Moubony, M., Ritchie, C., Jamieson, A., Richardson, R.T., Travas, A., Imrit, M.A., Chihata, M., Higo, H., Common, J.,
Walsh, E.M., Bixby, M., Guarna, M.M., Pernal, S.F., Hoover, S.E., Currie, R.W., Giovenazzo, P., Guzman-Novoa, E., Borges, D., Foster, L.J., Zayed, A. Pollen foraging mediates exposure to dichotomous stressor syndromes in honey bees.
(2024). PNAS Nexus (10), pgae440. https://doi.org/10.1093/pnasnexus/pgae440
Bixby, M., French, S.K. Wizenberg, S.B., Jamieson, A., Pepinelli, M.,
Cunningham, M., Conflitti, I., Foster, L.J., Zayed, A., Guarna, M.M. Identifying and modelling the impact of neonicotinoid exposure on honey bee colony profit. (2024). Journal of Economic Entomology 117 (6), 2228- 2241.
https://doi.org/10.1093/jee/toae227
Tran, L., Deckers, T.B., Ho, J. et al. Neonicotinoid-induced signature dysbiosis identified via metagenomic sequencing of the honey bee gut microbiome. Sci Rep 16, 1211 (2026). https://doi.org/10.1038/s41598-025-30907-4
McAfee, A., Alavi-Shoushtari, N., Tran, L. Labuschagne, R., Cunningham, M., Tsvetkov, N., Common, J., Higo, H., Pernal, S.F., Giovenazzo, P., Hoover, S.E., Guzman-Novoa, E., Currie, R.W.,Wolf Veiga, P., French, S.K., Conflitti, I.M., Pepinelli, M., Borges, D., Walsh, E.M., C.A. Bishop, Zayed, A., Duffe, J., Foster, L.J., Guarna, M.M. Climatic predictors of prominent honey bee (Apis mellifera) disease agents: Varroa destructor, Melissococcus plutonius, and Vairimorpha spp. (2024). PLOS Climate. 3(8): e0000485. https://doi.org/10.1371/journal.pclm.0000485.
McAfee, A., French, S.K., Tsvetkov, N., Higo, H., Common, J., Pernal, S.F., Giovenazzo, P., Hoover, S.E., Guzman-Novoa, E., Currie, R.W., Veiga, P.W., Conflitti, I.M., Pepinelli, M., Tran, L., Zayed, A., Guarna, M.M., Foster, L.J. (2024). Higher prevalence of sacbrood virus in highbush blueberry pollination units. Journal of Economic Entomology. 117: 1324–1335, https://doi.org/10.1093/jee/toae119 {IF=2.447}
French, S.K., Pepinelli, M., Conflitti, I.M., Higo, H., Common, J., Bixby, M.E.F., Walsh, E.M., Guarna, M.M., Pernal, S.F., Hoover, S.E., Currie, R.W., Giovenazzo, P., Guzmán-Novoa, E., Foster, L.J., Zayed, A. (2024). Honey bee stressor networks are complex and dependent on crop and region. Current Biology. 34:1893-1903. DOI: https://doi.org/10.1016/j.cub.2024.03.039 {IF=9.2}
Dogantzis, K.A., Raffiudin, R., Putra, R.E., Shaleh, I., Conflitti, I.M., Pepinelli, M., Roberts, J., Holmes, M., Oldroyd, B.P., Zayed, A. and Gloag, R. (2024). Post- invasion selection acts on standing genetic variation despite a severe founding bottleneck. Current Biology. 34:1349-1346. DOI:https://doi.org/10.1016/j.cub.2024.02.010 {IF=9.2}
Wizenberg, S.B., Newburn, L.R., Pepinelli, M., Conflitti, I.M., Richardson, R.T., Hoover, S.E.R., Currie, R.W., Giovenazzo, P., Zayed, A. (2023). Validating a multi-locus metabarcoding approach for characterizing mixed-pollen samples collected by honey bees. Plant Methods, 19:120. https://doi.org/10.1186/s13007-023-01097-9
Wizenberg, S.B., Newburn, L.R., Pepinelli, M., Conflitti, I.M., Moubony, M.,Borges, D., Guarna, M. Guzman-Novoa, E., Foster, L.; Zayed, A. (2023). Environmental metagenetics unveil novel plant-pollinator interactions. Ecology & Evolution, 13:e10645. https://doi.org/10.1002/ece3.10645 {IF=2.91}
Shimabukuro, E. M., Laurindo da Silva, F., Pepinelli, M., Trivinho-Strixino, S., & Lamas, C. J. E. (2023). A new species of Parochlus (Diptera: Chironomidae) reveals intriguing features of larva at the oldest South American highlands. Studies on Neotropical Fauna and Environment, 58(2), 430–438. https://doi.org/10.1080/01650521.2022.2060544
Anderson, K., Pepinelli, M., & Kvist, S. (2020). Natural occurrence of an experimental developmental phenotype in the leech Erpobdella punctata (Leidy 1870) (Annelida: Clitellata: Hirudinea). Invertebrate Reproduction & Development, 64(4), 268–273. https://doi.org/10.1080/07924259.2020.1784298
Jeane Marcelle Cavalcante do Nascimento, Neusa Hamada, Mateus Pepinelli, A new species in Simulium (Trichodagmia) (Diptera: Simuliidae) from Chapada Diamantina region, Brazil: cryptic diversity revealed by morphological and molecular evidence,
Acta Tropica, Volume 206, 2020, 105457, ISSN 0001-706X,
https://doi.org/10.1016/j.actatropica.2020.105457
Lukashevich, E. D., Pepinelli, M., & Currie, D. C. (2020). A new family and genus of Mesozoic Simulioidea (Insecta: Diptera). Journal of Systematic Palaeontology, 18(3), 213–231. https://doi.org/10.1080/14772019.2019.1588796
Do Nascimento, J. M. C., Hamada, N., Pepinelli, M., & Mardini, L. B. L. F. (2019). Redescription of adults of Simulium jeteri (Py-Daniel, Darwich, Mardini, Strieder & Coscarón, 2005) (Diptera: Simuliidae). Zootaxa, 4563(2), 249 266. https://doi.org/10.11646/zootaxa.4563.2.2
Koroiva, R., Souza, M.S., Roque, F. O. Pepinelli, M. DNA Barcodes for Forensically Important Fly Species in Brazil. Journal of Medical Entomology tjy045. doi: https://doi.org/10.1093/jme/tjy045 . 2018
Mateus Pepinelli, Douglas C Currie, The identity of giant black flies (Diptera: Simuliidae) in Baltic amber: insights from large-scale photomicroscopy, micro-CT scanning and geometric morphometrics, Zoological Journal of the Linnean Society, Volume 181, Issue 4, December 2017, Pages 846 866, https://doi.org/10.1093/zoolinnean/zlx021
Koroiva R, Pepinelli M, Rodrigues ME, Roque FdO, Lorenz-Lemke AP, Kvist S (2017) DNA barcoding of odonates from the Upper Plata basin: Database creation and genetic diversity estimation. PLoS ONE 12(8): e0182283. https://doi.org/10.1371/journal.pone.0182283
Sebastian Vernal, Mateus Pepinelli, Claudio Casanova, Thais M. Goulart, Olivia Kim, Natalia A. De Paula, Mara C. Pinto, Anderson Sá-Nunes, Ana Maria Roselino, Insights into the epidemiological link between biting flies and pemphigus foliaceus in southeastern Brazil, Acta Tropica, Volume 176, 2017,
Pages 455-462, ISSN 0001-706X,
https://doi.org/10.1016/j.actatropica.2017.09.015
Shimabukuro, E.M., Pepinelli, M. & Trivinho-Strixino, S. (2017)Brazilian Pseudochironomini (Diptera: Chironomidae) Part 1. New Pseudochironomus Malloch from highlands. Zootaxa, 4317 (1), 134–154. https://doi.org/10.11646/zootaxa.4317.1.6
Shimabukuro, E.M., Pepinelli, M. & Trivinho-Strixino, S. (2017) Two new species of Podonomus Philippi (Diptera: Chironomidae: Podonominae) from mountains of Southeastern Brazil. Zootaxa, 4290 (1), 155–166. https://doi.org/10.11646/zootaxa.4290.1.9
Roque, F.d.O., Zampiva, N.K., Valente-Neto, F., Menezes, J.F.S., Hamada, N., Pepinelli, M., Siqueira, T. and Swan, C. (2016), Deconstructing richness patterns by commonness and rarity reveals bioclimatic and spatial effects in black fly metacommunities. Freshw Biol, 61: 923-932. https://doi.org/10.1111/fwb.12757
Souza, M.S., Pepinelli, M., de Almeida, E.C., Ochoa-Quintero, J.M. and Roque, F.O. (2016), Blow Flies from Forest Fragments Embedded in Different Land Uses: Implications for Selecting Indicators in Forensic Entomology. J Forensic Sci, 61: 93-98. https://doi.org/10.1111/1556-4029.12869
Shimabukuro, E.M., Pepinelli, M., Perbiche-Neves, G. and Trivinho-Strixino, S. (2015), A new trap for collecting aquatic and semi-aquatic insects from madicolous habitats. Insect Conserv Divers, 8: 578-583. https://doi.org/10.1111/icad.12135
Trivinho-Strixino, S. & Pepinelli, M. (2015) A systematic study on Endotribelos Grodhaus (Diptera: Chironomidae) from Brazil including DNA barcoding to link males and females. Zootaxa, 3936 (1), 1–41. https://doi.org/10.11646/zootaxa.3936.1.1
Sheyla Regina Marques Couceiro, Neusa Hamada, Lúcia Beatriz Sagot, Mateus Pepinelli, Black-fly assemblage distribution patterns in streams in disturbed areas in southern Brazil, Acta Tropica, Volume 140, 2014, Pages 26-33, ISSN 0001-706X,
https://doi.org/10.1016/j.actatropica.2014.07.018
Mateus Pepinelli, Mike Spironello, Douglas C. Currie, Geometric morphometrics as a tool for interpreting evolutionary transitions in the black fly wing (Diptera: Simuliidae), Zoological Journal of the Linnean Society, Volume 169, Issue 2, 1 October 2013, Pages 377–388, https://doi.org/10.1111/zoj.12065
Trivinho-Strixino S, Pepinelli M, Siqueira T, de Oliveira Roque F. DNA barcoding of Podonomus (Chironomidae, Podonominae) enables stage association of a named species and reveals hidden diversity in Brazilian inselbergs. Annales de Limnologie – International Journal of Limnology. 2012;48(4):411-423. https://doi.org/10.1051/limn/2012032
de Souza, L.O.I., Pepinelli, M. & Neiss, U.G. (2012) The larva of Neoneura ethela Williamson, 1917 (Odonata: Protoneuridae). Zootaxa, 3318 (1), 63–67. https://doi.org/10.11646/zootaxa.3318.1.5
da Silva, F. L., Wiedenbrug, S., Trivinho-Strixino, S., de Oliveira, C. S. N., & Pepinelli, M. (2012). Two new species of Hudsonimyia Roback, 1979 (Diptera: Chironomidae: Tanypodinae) from Neotropical Region unveiled by morphology and DNA barcoding. Journal of Natural History, 46(25–26), 1615–1638. https://doi.org/10.1080/00222933.2012.681315
Pepinelli, M. (2011). Checklist of Simuliidae (Insecta, Diptera) from São Paulo State, Brazil. Biota Neotropica, 11(4). Retrieved from https://www.biotaneotropica.org.br/BN/article/view/980
Hamada, N., Pepinelli, M., Mattos-Glória, A. & Luz, S.L.B. (2010) A new black fly species from Brazil, closely related to Simulium guianense Wise (Diptera, Simuliidae), revealed by morphology and DNA barcoding. Zootaxa, 2428 (1), 22–36. https://doi.org/10.11646/zootaxa.2428.1.2
Karina Bertazo, Claudiney Biral dos Santos and Israel de Souza Pinto et al. Distribuição de espécies de borrachudos (Diptera: Simuliidae) do Espírito Santo, Brasil. Biota Neotrop.. 2010. Vol. 10(3):129-132. https://doi.org/10.1590/S1676-06032010000300013
Pepinelli, Mateus & Siqueira, Tadeu & Salles, Frederico & Shimbori, Eduardo. (2009). First report of Simuliidae and Chironomidae (Diptera) living on nymphs of Lachlania Hagen (Ephemeroptera: Oligoneuriidae) in South America. Biota Neotropica. 9. 245-247. https://doi.org/10.1590/S1676-06032009000100023
Wiedenbrug, S., Mendes, H.F., Pepinelli, M. & Trivinho-Strixino, S. (2009) Review of the genus Onconeura Andersen et Sæther (Diptera: Chironomidae), with the description of four new species from Brazil. Zootaxa, 2265 (1), 1–26. https://doi.org/10.11646/zootaxa.2265.1.1
Pepinelli M, Hamada N, Currie DC. Simulium (Inaequalium) marins, a new species of black fly (Diptera: Simuliidae) from inselbergs in Brazil. Mem Inst Oswaldo Cruz. 2009 Aug;104(5):728-35. https://doi.org/10.1590/S0074-02762009000500012
Landeiro, Victor & Pepinelli, Mateus & Hamada, Neusa. (2009). Species Richness and Distribution of Blackflies (Diptera: Simuliidae) in the Chapada Diamantina Region, Bahia, Brazil. Neotropical entomology. 38. 332-9. https://doi.org/10.1590/S1519-566X2009000300006
Hernandez, L.M., Hamada, N., Pepinelli, M., Kikuchi, R.M. Description of the larva of Simulium lobatoi Luna Dias, Hernández, Maia-Herzog & Shelley (Diptera: Simuliidae) from Brazil. Zootaxa 1732: 65-68, 2008 https://doi.org/10.11646/zootaxa.1732.1.6
Pepinelli, M., Hamada, N., Trivinho-Strixino, S. Larval description of Simulium (Notolepria) cuasiexiguum and Simulium (Chirostilbia) obesum and new records of black fly species (Diptera: Simuliidae) in the States of São Paulo and Minas Gerais, Brazil. Neotropical Entomology 35: 698- 704, 2006 https://doi.org/10.1590/S1519-566X2006000500019
Hamada, N., Hernandez, L.M., Luz, S.L.B., Pepinelli, M. Simulium (Chirostilbia) jefersoni, a new species of black fly (Diptera: Simuliidae) from the state of Bahia, Brazil. Zootaxa 1123: 21-37, 2006 https://doi.org/10.11646/zootaxa.1123.1.2
Pepinelli, M., Hamada, N., Luz, S.L.B. Simulium (Inaequalium) margaritatum, a new species of black fly (Diptera: Simuliidae) from the central region of Bahia State, Brazil. Zootaxa 1167: 47-60, 2006 https://doi.org/10.11646/zootaxa.1167.1.4
Hamada, N., Pepinelli, M., Hernandez, L.M. Simulium nunesdemelloi (Diptera: Simuliidae), a new species of black fly from the northwestern region of Amazonas State, Brazil. Zootaxa 1371: 23-35, 2006 https://doi.org/10.11646/zootaxa.1371.1.2
Pepinelli, M., Trivinho-Strixino, S., Hamada, N. Imaturos de Simuliidae (Diptera, Nematocera) e caracterização de seus criadouros no Parque Estadual Intervales, SP, Brasil. Revista Brasileira de Entomologia 49: 527-530, 2005 https://doi.org/10.1590/S0085-56262005000400012
Pepinelli, M., Hamada, N., Trivinho-Strixino, S. Simulium (Thyrsopelma) duodenicornium, a new black fly species (Diptera: Simuliidae) from the Southeast Region of Brazil. Zootaxa 1040: 17 – 29, 2005 https://doi.org/10.1590/S0085-56262005000400012
Hamada, N., Pepinelli, M. Simulium (Chirostilbia) bifenestratum (Diptera, Simuliidae), a new black-fly species from the Atlantic forest, State of São Paulo, Brazil. Memórias do Instituto Oswaldo Cruz 99: 45-52, 2004 https://doi.org/10.1590/S0074-02762004000100008
Pepinelli, M., Trivinho-Strixino, S., Hamada, N. Description of Simulium (Chirostilbia) friedlanderi Py-Daniel, 1987 (Insecta: Diptera: Simuliidae) female. Biota Neotropica 3: 1-3, 2003 https://doi.org/10.1590/S1676-06032003000200008
Salles, F.F., Francischetti, C.N., Roque, F.O., Pepinelli, M., Trivinho-Strixino, S. Levantamento preliminar dos gêneros e espécies de Baetidae (Insecta: Ephemeroptera) do Estado de São Paulo, com ênfase em coletas realizadas em córregos florestados de baixa ordem. Biota Neotropica 3, 2003 https://doi.org/10.1590/S1676-06032003000200011
Pepinelli, M., Trivinho-Strixino, S., Hamada, N. New records of Simuliidae (Diptera, Nematocera) in the State of São Paulo, Brazil. Revista Brasileira de Entomologia 47: 653-655, 2003 https://doi.org/10.1590/S0085-56262003000400020
Pepinelli, M., Trivinho-Strixino, S. O comprimento da antena na determinação dos estádios larvais de Simulium nigrimanum Macquart, 1838. Entomologia y Vectores 10: 307-317, 2003 https://www.cabidigitallibrary.org/doi/full/10.5555/20033174189
Pepinelli Lab 