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publications.html
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---
layout: default
---
<section id="banner-publications">
</section>
<section id="main" class="wrapper banner">
<!-- <header class="major">
<h2>Publications</h2>
</header> -->
<div class="container">
<h2>Publications</h2>
<table>
<tr valign="top">
<td align="right" class="bibtexnumber">
[<a name="macklin2017dina">1</a>]
</td>
<td class="bibtexitem">
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.
<em>Biodiversity Information Science and Standards</em>, 2017.
[ <a href="pub_bib#macklin2017dina">bib</a> ]
</td>
</tr>
<tr valign="top">
<td align="right" class="bibtexnumber">
[<a name="hovmoller2017streckkodning">2</a>]
</td>
<td class="bibtexitem">
Rasmus Hovmöller, Mattias Forshage, and Fredrik Ronquist.
Streckkodning av den svenska floran och
faunan--förutsättningar och utmaningar.
<em>PM från Naturhistoriska riksmuseet 2017: 1. Naturhistoriska
riksmuseets småskriftserie</em>, 2017.
[ <a href="pub_bib#hovmoller2017streckkodning">bib</a> ]
</td>
</tr>
<tr valign="top">
<td align="right" class="bibtexnumber">
[<a name="marquina2019new">3</a>]
</td>
<td class="bibtexitem">
Daniel Marquina, Anders F Andersson, and Fredrik Ronquist.
New mitochondrial primers for metabarcoding of insects, designed and
evaluated using in silico methods.
<em>Molecular ecology resources</em>, 19(1):90--104, 2019.
[ <a href="pub_bib#marquina2019new">bib</a> ]
</td>
</tr>
<tr valign="top">
<td align="right" class="bibtexnumber">
[<a name="macklin2018general">4</a>]
</td>
<td class="bibtexitem">
James Macklin, Markus Englund, Falko Glöckler, Mikko Heikkinen, Jana
Hoffmann, Keith Newton, and Fredrick Ronquist.
General introduction to dina.
<em>Biodiversity Information Science and Standards</em>, 2018.
[ <a href="pub_bib#macklin2018general">bib</a> ]
</td>
</tr>
<tr valign="top">
<td align="right" class="bibtexnumber">
[<a name="ronquist2018life">5</a>]
</td>
<td class="bibtexitem">
Fredrik Ronquist, Johan Nylander, Hege Vårdal, and José Luis
Nieves-Aldrey.
Life history of parnips and the evolutionary origin of gall wasps.
<em>Journal of Hymenoptera Research</em>, 65:91--110, 2018.
[ <a href="pub_bib#ronquist2018life">bib</a> ]
</td>
</tr>
<tr valign="top">
<td align="right" class="bibtexnumber">
[<a name="marquina2017insect">6</a>]
</td>
<td class="bibtexitem">
Daniel Marquina, Anders F Andersson, and Fredrik Ronquist.
Insect multilocus metabarcoding: in silico evaluation of old and new
primers.
<em>Genome</em>, 60(11):971--972, 2017.
[ <a href="pub_bib#marquina2017insect">bib</a> ]
</td>
</tr>
<tr valign="top">
<td align="right" class="bibtexnumber">
[<a name="braga2018evolution">7</a>]
</td>
<td class="bibtexitem">
Mariana P Braga, Michael Landis, Sören Nylin, Niklas Janz, and Fredrik
Ronquist.
Evolution of butterfly-plant networks revealed by bayesian inference
of host repertoire.
2018.
[ <a href="pub_bib#braga2018evolution">bib</a> ]
</td>
</tr>
<tr valign="top">
<td align="right" class="bibtexnumber">
[<a name="braga2018bayesian">8</a>]
</td>
<td class="bibtexitem">
Mariana P Braga, Michael Landis, Sören Nylin, Niklas Janz, and Fredrik
Ronquist.
Bayesian analysis of host repertoire evolution.
2018.
[ <a href="pub_bib#braga2018bayesian">bib</a> ]
</td>
</tr>
<tr valign="top">
<td align="right" class="bibtexnumber">
[<a name="lunden2018automatic">9</a>]
</td>
<td class="bibtexitem">
Daniel Lundén, David Broman, Fredrik Ronquist, and Lawrence M Murray.
Automatic alignment of sequential monte carlo inference in
higher-order probabilistic programs.
<em>arXiv preprint arXiv:1812.07439</em>, 2018.
[ <a href="pub_bib#lunden2018automatic">bib</a> ]
</td>
</tr>
<tr valign="top">
<td align="right" class="bibtexnumber">
[<a name="valan2019automated">10</a>]
</td>
<td class="bibtexitem">
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.
<em>Systematic biology</em>, 68(6):876--895, 2019.
[ <a href="pub_bib#valan2019automated">bib</a> ]
</td>
</tr>
<tr valign="top">
<td align="right" class="bibtexnumber">
[<a name="braga2020bayesian">11</a>]
</td>
<td class="bibtexitem">
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.
<em>Systematic Biology</em>, 2020.
[ <a href="pub_bib#braga2020bayesian">bib</a> ]
</td>
</tr>
<tr valign="top">
<td align="right" class="bibtexnumber">
[<a name="ronquist2020completing">12</a>]
</td>
<td class="bibtexitem">
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?
<em>Plos one</em>, 15(3):e0228561, 2020.
[ <a href="pub_bib#ronquist2020completing">bib</a> ]
</td>
</tr>
<tr valign="top">
<td align="right" class="bibtexnumber">
[<a name="glockler2019dina">13</a>]
</td>
<td class="bibtexitem">
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.
<em>Biodiversity Information Science and Standards</em>, 2019.
[ <a href="pub_bib#glockler2019dina">bib</a> ]
</td>
</tr>
<tr valign="top">
<td align="right" class="bibtexnumber">
[<a name="kudlicka2020probabilistic">14</a>]
</td>
<td class="bibtexitem">
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 <em>Uncertainty in Artificial Intelligence</em>, pages 679--689.
PMLR, 2020.
[ <a href="pub_bib#kudlicka2020probabilistic">bib</a> ]
</td>
</tr>
<tr valign="top">
<td align="right" class="bibtexnumber">
[<a name="marquina2019establishing">15</a>]
</td>
<td class="bibtexitem">
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.
<em>Molecular ecology resources</em>, 19(6):1516--1530, 2019.
[ <a href="pub_bib#marquina2019establishing">bib</a> ]
</td>
</tr>
<tr valign="top">
<td align="right" class="bibtexnumber">
[<a name="zhang2020using">16</a>]
</td>
<td class="bibtexitem">
Chi Zhang, John P Huelsenbeck, and Fredrik Ronquist.
Using parsimony-guided tree proposals to accelerate convergence in
bayesian phylogenetic inference.
<em>Systematic Biology</em>, 2020.
[ <a href="pub_bib#zhang2020using">bib</a> ]
</td>
</tr>
<tr valign="top">
<td align="right" class="bibtexnumber">
[<a name="karlsson2020swedish">17</a>]
</td>
<td class="bibtexitem">
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.
<em>Biodiversity Data Journal</em>, 8, 2020.
[ <a href="pub_bib#karlsson2020swedish">bib</a> ]
</td>
</tr>
<tr valign="top">
<td align="right" class="bibtexnumber">
[<a name="marquina2020effect">18</a>]
</td>
<td class="bibtexitem">
Daniel Marquina, Fredrik Ronquist, and Piotr Lukasik.
The effect of ethanol concentration on the preservation of insects
for biodiversity studies.
<em>bioRxiv</em>, 2020.
[ <a href="pub_bib#marquina2020effect">bib</a> ]
</td>
</tr>
<tr valign="top">
<td align="right" class="bibtexnumber">
[<a name="marquina2020evaluation">19</a>]
</td>
<td class="bibtexitem">
Daniel Marquina, Tomas Roslin, Piotr Lukasik, and Fredrik Ronquist.
Evaluation of non-destructive extraction protocols for metabarcoding
of insects.
2020.
[ <a href="pub_bib#marquina2020evaluation">bib</a> ]
</td>
</tr>
<tr valign="top">
<td align="right" class="bibtexnumber">
[<a name="ronquist2020probabilistic">20</a>]
</td>
<td class="bibtexitem">
Fredrik Ronquist, Jan Kudlicka, Viktor Senderov, Johannes Borgström,
Nicolas Lartillot, Daniel Lundén, Lawrence Murray, Thomas B Schön,
and David Broman.
Probabilistic programming: a powerful new approach to statistical
phylogenetics.
<em>BioRxiv</em>, 2020.
[ <a href="pub_bib#ronquist2020probabilistic">bib</a> ]
</td>
</tr>
<tr valign="top">
<td align="right" class="bibtexnumber">
[<a name="hartop2020scuttling">21</a>]
</td>
<td class="bibtexitem">
Emily Hartop, Sibylle Häggqvist, Sven Olof Ulefors, and Fredrik Ronquist.
Scuttling towards monophyly: phylogeny of the mega-diverse genus
megaselia (diptera: Phoridae).
<em>Systematic Entomology</em>, 2020.
[ <a href="pub_bib#hartop2020scuttling">bib</a> ]
</td>
</tr>
<tr valign="top">
<td align="right" class="bibtexnumber">
[<a name="gobbo2020inquilines">22</a>]
</td>
<td class="bibtexitem">
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.
<em>Genome biology and evolution</em>, 2020.
[ <a href="pub_bib#gobbo2020inquilines">bib</a> ]
</td>
</tr>
</table>
</section>