pub

[1]	Elzbieta Iwaszkiewicz-Eggebrecht, Piotr Lukasik, Mateusz Buczek, Junchen Deng, Emily A. Hartop, Harald Havnås, Monika Prus-Frankowska, Carina R. Ugarph, Paulina Viteri, Anders F. Andersson, Tomas Roslin, Ayco J. M. Tack, Fredrik Ronquist, and Andreia Miraldo. Favis: Fast and versatile protocol for non-destructive metabarcoding of bulk insect samples. PLOS ONE, 18(7):1--13, 07 2023. [ bib \| DOI \| Url ]
[2]	Emily Hartop, Amrita Srivathsan, Fredrik Ronquist, and Rudolf Meier. Towards Large-Scale Integrative Taxonomy (LIT): Resolving the Data Conundrum for Dark Taxa. Systematic Biology, 71(6):1404--1422, 05 2022. [ bib \| DOI \| arXiv \| Url ]
[3]	Jakub Truszkowski, Allison Perrigo, David Broman, Fredrik Ronquist, and Alexandre Antonelli. Online tree expansion could help solve the problem of scalability in Bayesian phylogenetics. Systematic Biology, page syad045, 07 2023. [ bib \| DOI \| arXiv \| Url ]
[4]	Daniel Lundén, Gizem Çaylak, Fredrik Ronquist, and David Broman. Automatic alignment in higher-order probabilistic programming languages. In Thomas Wies, editor, Programming Languages and Systems, pages 535--563, Cham, 2023. Springer Nature Switzerland. [ bib ]
[5]	Elzbieta Iwaszkiewicz-Eggebrecht, Emma Granqvist, Mateusz Buczek, Monika Prus, Jan Kudlicka, Tomas Roslin, Ayco J. M. Tack, Anders F. Andersson, Andreia Miraldo, Fredrik Ronquist, and Piotr Lukasik. Optimizing insect metabarcoding using replicated mock communities. Methods in Ecology and Evolution, 14(4):1130--1146, 2023. [ bib \| DOI \| arXiv \| Url ]
[6]	Daniel Lundén, Joey Öhman, Jan Kudlicka, Viktor Senderov, Fredrik Ronquist, and David Broman. Compiling universal probabilistic programming languages with efficient parallel sequential monte carlo inference. In Programming Languages and Systems, pages 29--56, Cham, 2022. Springer International Publishing. [ bib \| DOI \| Url \| Pdf ]
[7]	Mariana P. Braga, Niklas Janz, Sören Nylin, Fredrik Ronquist, and Michael J. Landis. Phylogenetic reconstruction of ancestral ecological networks through time for pierid butterflies and their host plants. Ecology Letters, 24:2134 --2145, 2021. [ bib \| DOI \| Url \| Pdf ]
[8]	Miroslav Valan, Dominik Vondráček, and Fredrik Ronquist. Awakening a taxonomist's third eye: exploring the utility of computer vision and deep learning in insect systematics. Systematic Entomology, 46:757--766, 2021. [ bib \| DOI \| Url \| Pdf ]
[9]	Emily Hartop. A multi-faceted approach to a "dark taxon" : The hyperdiverse and poorly known scuttle flies (Diptera: Phoridae). PhD thesis, Station Linné, 2021. [ bib \| Url \| Pdf ]
[10]	Emily Hartop, Amrita Srivathsan, Fredrik Ronquist, and Rudolf Meier. Large-scale Integrative Taxonomy (LIT): resolving the data conundrum for dark taxa. bioRxiv, 2021. [ bib \| DOI \| Url \| Pdf ]
[11]	Miroslav Valan. Automated image-based taxon identification using deep learning and citizen-science contributions. PhD thesis, Stockholm University, Department of Zoology, 2021. [ bib \| Url \| Pdf ]
[12]	Fredrik Ronquist, Jan Kudlicka, Viktor Senderov, Johannes Borgström, Nicolas Lartillot, Daniel Lundén, Lawrence D. Murray, Thomas B. Schön, and David Broman. Universal probabilistic programming offers a powerful approach to statistical phylogenetics. Communications Biology, 4:244, 2021. [ bib \| DOI \| Url \| Pdf ]
[13]	Paula Arribas, Carmelo Andújar, Martin I. Bidartondo, Kristine Bohmann, Éric Coissac, Simon Creer, Jeremy R. deWaard, Vasco Elbrecht, Gentile F. Ficetola, Marta Goberna, Susan Kennedy, Henrik Krehenwinkel, Florian Leese, Vojtech Novotny, Fredrik Ronquist, Douglas W. Yu, Lucie Zinger, Thomas J. Creedy, Emmanouil Meramveliotakis, Víctor Noguerales, Isaac Overcast, Hélène Morlon, Alfried P. Vogler, Anna Papadopoulou, and Brent C. Emerson. Connecting high-throughput biodiversity inventories: Opportunities for a site-based genomic framework for global integration and synthesis. Molecular Ecology, 30:1120--1135, 2021. [ bib \| DOI \| Url ]
[14]	Emily Hartop, Sibylle Häggqvist, Sven Olof Ulefors, and Fredrik Ronquist. Scuttling towards monophyly: phylogeny of the mega-diverse genus Megaselia (Diptera: Phoridae). Systematic Entomology, 46:71--82, 2021. [ bib \| DOI \| Url ]
[15]	Daniel Marquina, Mateusz Buczek, Fredrik Ronquist, and Piotr Lukasik. The effect of ethanol concentration on the morphological and molecular preservation of insects for biodiversity studies. PeerJ, 9:e10799, 2021. [ bib \| DOI \| Url ]
[16]	Mariana P Braga, Michael J Landis, Sören Nylin, Niklas Janz, and Fredrik Ronquist. Bayesian inference of ancestral host-parasite interactions under a phylogenetic model of host repertoire evolution. Systematic Biology, 69:1149--1162, 2020. [ bib \| DOI \| Url ]
[17]	Fredrik Ronquist, Mattias Forshage, Sibylle Häggqvist, Dave Karlsson, Rasmus Hovmöller, Johannes Bergsten, Kevin Holston, Tom Britton, Johan Abenius, Bengt Andersson, et al. Completing Linnaeus's inventory of the Swedish insect fauna: only 5,000 species left? PLOS ONE, 15(3):e0228561, 2020. [ bib \| DOI \| Url ]
[18]	Jan Kudlicka, Lawrence M Murray, Fredrik Ronquist, and Thomas B Schön. Probabilistic programming for birth-death models of evolution using an alive particle filter with delayed sampling. In Uncertainty in Artificial Intelligence, pages 679--689. PMLR, 2020. [ bib \| Url ]
[19]	Chi Zhang, John P Huelsenbeck, and Fredrik Ronquist. Using parsimony-guided tree proposals to accelerate convergence in Bayesian phylogenetic inference. Systematic Biology, 69:1016--1032, 2020. [ bib \| DOI \| Url ]
[20]	Dave Karlsson, Mattias Forshage, Kevin Holston, and Fredrik Ronquist. The data of the Swedish Malaise Trap Project, a countrywide inventory of Sweden's insect fauna. Biodiversity Data Journal, 8:e56286, 2020. [ bib \| DOI \| Url ]
[21]	Dave Karlsson, Emily Hartop, Mattias Forshage, Mathias Jaschhof, and Fredrik Ronquist. The Swedish Malaise trap project: a 15 year retrospective on a countrywide insect inventory. Biodiversity Data Journal, 8:e47255, 2020. [ bib \| DOI \| Url ]
[22]	Daniel Marquina Hernández. Debugging metabarcoding for insect biodiversity studies. PhD thesis, Stockholm University, Department of Zoology, 2020. [ bib \| Url \| Pdf ]
[23]	Fredrik Ronquist, Jan Kudlicka, Viktor Senderov, Johannes Borgström, Nicolas Lartillot, Daniel Lundén, Lawrence Murray, Thomas B. Schön, and David Broman. Universal probabilistic programming offers a powerful approach to statistical phylogenetics. bioRxiv, 2020. [ bib \| DOI \| Url \| Pdf ]
[24]	Erik Gobbo, Nicolas Lartillot, Jack Hearn, Graham N Stone, Yoshihisa Abe, Christopher W Wheat, Tatsuya Ide, and Fredirik Ronquist. From inquilines to gall inducers: Genomic signature of a life-style transition in Synergus gall wasps. Genome biology and evolution, 12:2060--2073, 2020. [ bib \| DOI \| Url ]
[25]	Falko Glöckler, James Macklin, Fredrik Ronquist, and Jana Hoffmann. DINA: Open Source and Open Services-A modern approach for natural history collection management systems and research. Biodiversity Information Science and Standards, 2019. [ bib \| DOI \| Url ]
[26]	Daniel Marquina, Anders F Andersson, and Fredrik Ronquist. New mitochondrial primers for metabarcoding of insects, designed and evaluated using in silico methods. Molecular Ecology Resources, 19(1):90--104, 2019. [ bib \| DOI \| Url ]
[27]	Daniel Marquina, Rodrigo Esparza-Salas, Tomas Roslin, and Fredrik Ronquist. Establishing arthropod community composition using metabarcoding: Surprising inconsistencies between soil samples and preservative ethanol and homogenate from Malaise trap catches. Molecular ecology resources, 19(6):1516--1530, 2019. [ bib \| DOI \| Url ]
[28]	Miroslav Valan, Karoly Makonyi, Atsuto Maki, Dominik Vondráček, and Fredrik Ronquist. Automated taxonomic identification of insects with expert-level accuracy using effective feature transfer from convolutional networks. Systematic Biology, 68(6):876--895, 2019. [ bib \| DOI \| Url ]
[29]	Mariana Pires Braga. Evolution of host repertoires and the diversification of butterflies. PhD thesis, Stockholm University, Department of Zoology, 2019. [ bib \| Url \| Pdf ]
[30]	Daniel Lundén, David Broman, Fredrik Ronquist, and Lawrence M Murray. Automatic alignment of sequential Monte Carlo inference in higher-order probabilistic programs. arXiv preprint arXiv:1812.07439, 2018. [ bib \| Url ]
[31]	James Macklin, Markus Englund, Falko Glöckler, Mikko Heikkinen, Jana Hoffmann, Keith Newton, and Fredrick Ronquist. General introduction to DINA. Biodiversity Information Science and Standards, 2018. [ bib \| DOI \| Url ]
[32]	Fredrik Ronquist, Johan Nylander, Hege Vårdal, and José Luis Nieves-Aldrey. Life history of Parnips and the evolutionary origin of gall wasps. Journal of Hymenoptera Research, 65:91--110, 2018. [ bib \| DOI \| Url ]
[33]	Rasmus Hovmöller, Mattias Forshage, and Fredrik Ronquist. Streckkodning av den svenska floran och faunan--förutsättningar och utmaningar. PM från Naturhistoriska riksmuseet 2017: 1. Naturhistoriska riksmuseets småskriftserie, 2017. [ bib \| Url ]
[34]	James Macklin, Falko Glöckler, Jana Hoffmann, Fredrik Ronquist, Stefan Daume, and Elspeth Haston. DINA: Open Source and Open Services-A Modern Approach for Sustainable Natural History Collection Management Systems. Biodiversity Information Science and Standards, 2017. [ bib \| DOI \| Url \| Pdf ]

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