Journal Articles

Thomas JA, Frandsen PB, Prendini E, Zhou X, Holzenthal RW. 2020. A multigene phylogeny and timeline for Trichoptera (Insecta). Systematic Entomology.  doi:10.1111/syen.12422

Wipfler B, Koehler W, Frandsen PB, Donath A, Liu S, Machida R, Misof B, Peters RS, Shimizu S, Zhou X, et al. 2020. Phylogenomics changes our understanding about earwig evolution. Systematic Entomology. n/a(n/a).  doi:10.1111/syen.12420

Heckenhauer J, Frandsen PB, Gupta DK, Paule J, Prost S, Schell T, Schneider JV, Stewart RJ, Pauls SU. 2019. Annotated Draft Genomes of Two Caddisfly Species Plectrocnemia conspersa CURTIS and Hydropsyche tenuis NAVAS (Insecta: Trichoptera). Genome Biology and Evolution. 11(12):3445--3451.  doi:10.1093/gbe/evz264

Edelman NB, Frandsen PB, Miyagi M, Clavijo B, Davey J, Dikow RB, García-Accinelli G, Belleghem SM, Patterson N, Neafsey DE, et al. 2019. Genomic architecture and introgression shape a butterfly radiation. 366(6465):594--599.  doi:10.1126/science.aaw2090

Kawahara AY, Plotkin D, Espeland M, Meusemann K, Toussaint EF, Donath A, Gimnich F, Frandsen PB, Zwick A, Reis Md, et al. 2019. Phylogenomics reveals the evolutionary timing and pattern of butterflies and moths.  doi:10.1073/pnas.1907847116

Frandsen PB, Bursell MG, Taylor AM, Wilson SB, Steeneck A, Stewart RJ. 2019. Exploring the underwater silken architectures of caddisworms: comparative silkomics across two caddisfly suborders. Philosophical Transactions of the Royal Society B. 374(1784).  doi:10.1098/rstb.2019.0206

McGlaughlin JE, Frandsen PB, Mey W, Pauls SU. 2019. A Preliminary Phylogeny of Rhyacophilidae with Reference to Fansipangana and the Monophyly of Rhyacophila. Zoosymposia. 14:189-192.  doi:10.11646/zoosymposia.14.1.20

Shevchenko J, Yuni AB, Frandsen PB. 2019. Undergraduate teaching of scientific concepts using DNA barcoding of Trichoptera. Zoosymposia. 14:16-31.  doi:10.11646/zoosymposia.14.1.4

Koepfli K, Tamazian G, Wildt D, Dobrynin P, Kim C, Frandsen PB, Godinho R, Yurchenko AA, Komissarov A, Krasheninnikova K. 2019. Whole Genome Sequencing and Re-sequencing of the Sable Antelope (Hippotragus niger): A Resource for Monitoring Diversity in ex Situ and in Situ Populations. g3--400084.  doi:10.1534/g3.119.400084

Morse JC, Frandsen PB, Graf W, Thomas JA. 2019. Diversity and Ecosystem Services of Trichoptera. Insects. 10(5).  doi:10.3390/insects10050125

Wipfler B, Letsch H, Frandsen PB, Kapli P, Mayer C, Bartel D, Buckley TR, Donath A, Edgerly-Rooks JS, Fujita M, et al. 2019. Evolutionary history of Polyneoptera and its implications for our understanding of early winged insects. Proceedings of the National Academy of Sciences. 201817794.  doi:10.1073/pnas.1817794116

Luo S, Tang M, Frandsen PB, Stewart RJ, Zhou X. 2018. The genome of an underwater architect, the caddisfly Stenopsyche tienmushanensis Hwang (Insecta: Trichoptera). Gigascience. 7(12).  doi:10.1093/gigascience/giy143

Clement RA, Frandsen PB, McKnight T, Nelson CR. 2018. Fly family diversity shows evidence of livestock grazing pressure in Mongolia (Insecta: Diptera). Journal of Insect Conservation. 22(2).  doi:10.1007/s10841-018-0056-x

Schuettpelz E, Frandsen PB, Dikow RB, Brown A, Orli S, Peters M, Metallo A, Funk VA, Dorr LJ. 2017. Applications of deep convolutional neural networks to digitized natural history collections. Biodiversity data journal.

Dikow RB, Frandsen PB, Turcatel M, Dikow T. 2017. Genomic and transcriptomic resources for assassin flies including the complete genome sequence of Proctacanthus coquilletti (Insecta: Diptera: Asilidae) and 16 representative transcriptomes. PeerJ. 5:e2951.

Kjer K, Borowiec ML, Frandsen PB, Ware J, Wiegmann BM. 2016. Advances using molecular data in insect systematics. Current opinion in insect science. 18:40--47.

Lanfear R, Frandsen PB, Wright AM, Senfeld T, Calcott B. 2016. PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Molecular biology and evolution. 34(3):772--773.

Zhou X, Frandsen PB, Holzenthal RW, Beet CR, Bennett KR, Blahnik RJ, Cartwright D, Chuluunbat S, Cocks GV. 2016. The Trichoptera barcode initiative: a strategy for generating a species-level Tree of Life. Phil. Trans. R. Soc. B. 371(1702):20160025.

Frandsen PB, Thomson RE. 2016. Collection and preservation of Trichoptera for use in DNA research. Zoosymposia. 10:200--202.

Kjer KM, Thomas JA, Zhou X, Frandsen PB, Prendini E, Holzenthal RW. 2016. Progress on the phylogeny of caddisflies (Trichoptera). Zoosymposia. 10(1):248--256.

Frandsen PB, Zhou X, Flint, Jr O, Kjer KM. 2016. Using DNA barcode data to add leaves to the Trichoptera tree of life. Zoosymposia. 10:193--199.

Kjer KM, Ware JL, Rust J, Wappler T, Lanfear R, Jermiin LS, Zhou X, Aspock H, Aspock U, Beutel RG, et al. 2015. Response to Comment on “Phylogenomics resolves the timing and pattern of insect evolution”. Science. 349(6247):487.

Frandsen PB, Calcott B, Mayer C, Lanfear R. 2015. Automatic selection of partitioning schemes for phylogenetic analyses using iterative k-means clustering of site rates. BMC evolutionary biology. 15(1):13.

Kjer KM, Zhou X, Frandsen PB, Thomas JA, Blahnik RJ. 2014. Moving toward species-level phylogeny using ribosomal DNA and COI barcodes: an example from the diverse caddisfly genus Chimarra (Trichoptera: Philopotamidae). Arthropod Systematics & Phylogeny. 72(3):345--354.

Misof B, Liu S, Meusemann K, Peters RS, Donath A, Mayer C, Frandsen PB, Ware J, Flouri T, Beutel RG, et al. 2014. Phylogenomics resolves the timing and pattern of insect evolution. Science. 346(6210):763--767.

Vshivkova T, Flint O, Holzenthal R, Kjer K, Frandsen PB, Thomson R, Egorov A. 2013. First data on Trichoptera fauna (Insecta) of streams and ponds of Vostok Bay Basin (Peter the Great Bay, Primorye Territory). Freshwater Life.


Nelson CR, Frandsen PB. Geographical history of stoneflies (Insecta: Plecoptera): review and extremes of adaptations in environmentally sensitive species. IBS 2019 Humboldt Meeting & 2nd Latin American Biogeography Meeting. Quito, Ecuador. 2019 .

Nelson CR, McKnight TK, Frandsen PB, Clement RA. Bioassessment of fly family diversity using taxon effort relationships on sites with a continuum of grazing and erosion pressures in Mongolia. Ninth International Congress of Dipterology meeting. Windhoek, Namibia. 2018 .

Frandsen PB. Digging Deep: Applications of Deep Learning to Digitized Museum Collections. Phylopizza. Smithsonian National Museum of Natural History. 2018 .

Frandsen PB. Digging Deep: Applications of Deep Learning to Digitized Museum Collections. Department of Biology Seminar. University of Florida Department of Biology, Gainesville, FL. 2017 .

Frandsen PB. Reconstructing the caddisfly (Insecta: Trichoptera) tree of life using transcriptomes and targeted exon capture. Department Seminar. University of Florida Genetics Institute, Gainesville, FL. 2017 .

Yeole G, Sahdev S, Collins M, Thompson A, Dikow RB, Frandsen PB, Orli S, Figueiredo J. A Pipeline for Processing Specimen Images in iDigBio - Applying and Generalizing an Examination of Mercury Use in Preparing Herbarium Specimens. TDWIG. 2017 .

Frandsen PB. A whirlwind tour of using transcriptomes in phylogenetics: lessons learned from the 1KITE project. 1st Workshop on Phylogenetics and Evolutionary Biology. Institute of Zoology, Chinese Academy of Sciences, Beijing, China. 2017 .

Frandsen PB. "Big Data" Insect Phylogenetics. IGERT Tropical Biology Course. Smithsonian Tropical Research Institute, Gamboa, Panama. 2017 .

Frandsen PB. Using DNA barcode data to fill out the leaves of the Trichoptera tree of life. Frontiers in Phylogenetics Symposium. Smithsonian National Museum of Natural History, Washington, D.C. 2016 .

Frandsen PB, Lanfear R, Calcott B, Mayer C, Misof B, Zhou X, Kjer K. Model selection for phylogenomics. International Congress of Entomology, Symposum: Progress in Insect Phylogenomics: The Scale and Complexity of Next-Gen Datasets and Analysis. Orlando, FL, USA. 2016 .

Frandsen PB. A tale of two data sets: unraveling deep evolutionary splits within Trichoptera using transcriptomes and targeted exon capture. ANIC, CSIRO seminar. Australian National Insect Collection, Commonwealth Scientific and Industrial Research Organisation, Canberra, New South Wales, Australia. 2016 .

Frandsen PB. Uraveling the caddisfly (Trichoptera) tree of life using targeted bait capture. Department of Entomology Seminar. Smithsonian National Museum of Natural History, Washington, D.C. 2015 .

Frandsen PB. Phylogenetic model selection and data filtering on large data sets: a case study with the caddisflies (Insecta: Trichoptera). Department of Entomology Seminar, University of Maryland. University of Maryland, College Park, MD. 2015 .

Frandsen PB. Using PartitionFinder to Select Optimal Partitioning Schemes for Phylogenomics. 1KITE annual meeting. Vienna, Austria. 2015 .

Frandsen PB. 1KITE: Model selection in phylogenomics. 7th Dresden Meeting on Insect Phylogeny. Dresden, Germany. 2015 .

Frandsen PB. Automatic selection of partitioned phylogenetic models on large datasets: a case study with caddisflies (Insecta: Trichoptera). Phylopizza. Smithsonian National Museum of Natural History, Washington, D.C. 2015 .

Frandsen PB. Phylogenetic models and caddisfly evolution. 23andme seminar. Mountain View, CA. 2015 .

Frandsen PB. Automatic selection of optimal partitioning schemes in phylogenetics. University of Connecticut Seminar. Storrs, Connecticut. 2014 .

Frandsen PB, Thomas J, Zhou X, Kjer K. New instights on the phylogeny of Trichoptera: transcriptomes and new techniques. 6th Dresden Meeting on Insect Phylogeny. Dresden, Germany. 2013 .

Frandsen PB, Thomson R. Collecting Trichoptera for Molecular Research. XIVth International Symposium on Trichoptera. Vladivostok, Russia. 2012 .

Frandsen PB, Nelson CR, Hapairai L. The Ants (Hymenoptera: Formicidae) of Maupiti, French Polynesia. Utah Academy of Sciences, Arts, and Letters. Provo, UT. 2009 .

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