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<!DOCTYPE HTML>
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<title>Publications - Elias Dohmen</title>
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<h2>Publications</h2>
<p>Peer-reviewed articles, preprints, and book chapters</p>
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<ul class="alt publication-list" id="publication-list">
<li><b>DeNoFo: a file format and toolkit for standardised, comparable de novo gene
annotation</b><br>
Dohmen E, Aubel M, Eicholt LA, Roginski P, Luria V, Karger A, Grandchamp A<br>
<em>preprint on bioRxiv, 2025</em> <a href="https://doi.org/10.1101/2025.03.31.644673"
target="_blank" title="View publication">📄</a>
</li>
<li><b>De Novo Gene Emergence: Summary, Classification, and Challenges of Current Methods</b><br>
Grandchamp A, Aubel M, Eicholt LA, Roginski P, Luria V, Karger A, Dohmen E<br>
<em>preprint on EcoEvoRxiv, 2025</em> <a href="https://doi.org/10.32942/X2DP88" target="_blank"
title="View publication">📄</a>
</li>
<li><b>Reduced regulatory complexity associated with the evolutionary transition to sociality from
cockroaches to termites despite evolutionary parallels with Hymenoptera</b><br>
Jones ARC, Dohmen E, Berger J, Legendre F, Harrison MC, Bornberg-Bauer E<br>
<em>preprint on bioRxiv, 2024</em> <a href="https://doi.org/10.1101/2024.11.25.625201"
target="_blank" title="View publication">📄</a>
</li>
<li><b>Major changes in domain arrangements are associated with the evolution of termites</b><br>
Mikhailova A, Dohmen E, Harrison MC<br>
<em>Journal of Evolutionary Biology, 2024</em> <a href="https://doi.org/10.1093/jeb/voae047"
target="_blank" title="View publication">📄</a>
</li>
<li><b>Comparative Evolutionary Genomics in Insects</b><br>
Feldmeyer B, Bornberg-Bauer E, Dohmen E, Fouks B, Heckenhauer J, Huylmans AK, Jones ARC, Stolle
E, Harrison MC<br>
<em>Comparative Genomics. Methods in Molecular Biology, 2024</em> <a
href="https://doi.org/10.1007/978-1-0716-3838-5_16" target="_blank"
title="View publication">📄</a>
</li>
<li><b>Complex regulatory role of DNA methylation in caste- and age-specific expression of a
termite</b><br>
Harrison MC, Dohmen E, George S, Sillam-Dussès D, Séité S, Vasseur-Cognet M<br>
<em>Open Biology, 2022</em> <a href="https://doi.org/10.1098/rsob.220047" target="_blank"
title="View publication">📄</a>
</li>
<li><b>New Genomic Signals Underlying the Emergence of Human Proto-Genes</b><br>
Grandchamp A, Berk K, Dohmen E, Bornberg-Bauer E<br>
<em>Genes, 2022</em> <a href="https://doi.org/10.3390/genes13020284" target="_blank"
title="View publication">📄</a>
</li>
<li><b>The modular nature of protein evolution: Domain rearrangement rates across eukaryotic
life</b><br>
Dohmen E, Klasberg S, Bornberg-Bauer E, Perrey S, Kemena C<br>
<em>BMC Evolutionary Biology, 2020</em> <a href="https://doi.org/10.1186/s12862-020-1591-0"
target="_blank" title="View publication">📄</a>
</li>
<li><b>Gene content evolution in the arthropods</b><br>
Thomas GWC, Dohmen E, Hughes DST, Murali SC, Poelchau M, Glastad K, Anstead CA, Ayoub NA,
Batterham P, Bellair M, Binford GJ, Chao H, Chen YH, Childers C, Dinh H, Doddapaneni HV, Duan
JJ, Dugan S, Esposito LA, Friedrich M, Garb J, Gasser RB, Goodisman MAD, Gundersen-Rindal DE,
Han Y, Handler AM, Hatakeyama M, Hering L, Hunter WB, Ioannidis P, Jayaseelan JC, Kalra D, Khila
A, Korhonen PK, Lee CE, Lee SL, Li Y, Lindsey ARI, Mayer G, McGregor AP, McKenna DD, Misof B,
Munidasa M, Munoz-Torres M, Muzny DM, Niehuis O, Osuji-Lacy N, Palli SR, Panfilio KA, Pechmann
M, Perry T, Peters RS, Poynton HC, Prpic N-M, Qu J, Rotenberg D, Schal C, Schoville SD, Scully
ED, Skinner E, Sloan DB, Stouthamer R, Strand MR, Szucsich NU, Wijeratne A, Young ND, Zattara
EE, Benoit JB, Zdobnov EM, Pfrender ME, Hackett KJ, Werren JH, Worley KC, Gibbs RA, Chipman AD,
Waterhouse RM, Bornberg-Bauer E, Hahn MW, Richards S<br>
<em>Genome Biology, 2020</em> <a href="https://doi.org/10.1186/s13059-019-1925-7"
target="_blank" title="View publication">📄</a>
</li>
<li><b>Higher-order epistasis shapes the fitness landscape of a xenobiotic-degrading enzyme</b><br>
Yang G, Anderson DW, Baier F, Dohmen E, Hong N, Carr PD, Kamerlin SCL, Jackson C, Bornberg-Bauer
E, Tokuriki N<br>
<em>Nature Chemical Biology, 2019</em> <a href="https://doi.org/10.1038/s41589-019-0386-3"
target="_blank" title="View publication">📄</a>
</li>
<li><b>DOGMA: a web server for proteome and transcriptome quality assessment</b><br>
Kemena C, Dohmen E, Bornberg-Bauer E<br>
<em>Nucleic Acids Research, 2019</em> <a href="https://doi.org/10.1093/nar/gkz366"
target="_blank" title="View publication">📄</a>
</li>
<li><b>Reactive oxygen species (ROS) and the heat stress response of Daphnia pulex: ROS-mediated
activation of hypoxia-inducible factor 1 (HIF-1) and heat shock factor 1 (HSF-1) and the
clustered expression of stress genes</b><br>
Klumpen E, Hoffschröer N, Zeis B, Gigengack U, Dohmen E, Paul RJ<br>
<em>Biol. Cell, 2017</em> <a href="https://doi.org/10.1111/boc.201600017" target="_blank"
title="View publication">📄</a>
</li>
<li><b>DOGMA: domain-based transcriptome and proteome quality assessment</b><br>
Dohmen E, Kremer LPM, Bornberg-Bauer E, Kemena C<br>
<em>Bioinformatics, 2016</em> <a href="https://doi.org/10.1093/bioinformatics/btw231"
target="_blank" title="View publication">📄</a>
</li>
<li><b>Protein Domains as Molecular Markers for Large Scale Sequence Analysis</b><br>
Elias Dohmen<br>
<em>PhD Thesis , 2020</em> <a href="http://dx.doi.org/10.13140/RG.2.2.14518.20807"
target="_blank" title="View publication">📄</a>
</li>
<li><b>Detect de novo expressed ORFs in transcriptomes with DESwoMAN</b><br>
Grandchamp A, Lebherz MK, Dohmen E<br>
<em>preprint on bioRxiv, 2025</em> <a href="https://doi.org/10.1101/2025.06.10.658796"
target="_blank" title="View publication">📄</a>
</li>
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title: "Detect de novo expressed ORFs in transcriptomes with DESwoMAN",
authors: "Grandchamp A, Lebherz MK, Dohmen E",
journal: "preprint on bioRxiv",
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link: "https://doi.org/10.1101/2025.06.10.658796",
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{
title: "DeNoFo: a file format and toolkit for standardised, comparable de novo gene annotation",
authors: "Dohmen E, Aubel M, Eicholt LA, Roginski P, Luria V, Karger A, Grandchamp A",
journal: "preprint on bioRxiv",
year: 2025,
link: "https://doi.org/10.1101/2025.03.31.644673",
type: "preprint"
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{
title: "De Novo Gene Emergence: Summary, Classification, and Challenges of Current Methods",
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journal: "preprint on EcoEvoRxiv",
year: 2025,
link: "https://doi.org/10.32942/X2DP88",
type: "preprint"
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title: "Reduced regulatory complexity associated with the evolutionary transition to sociality from cockroaches to termites despite evolutionary parallels with Hymenoptera",
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journal: "preprint on bioRxiv",
year: 2024,
link: "https://doi.org/10.1101/2024.11.25.625201",
type: "preprint"
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{
title: "Major changes in domain arrangements are associated with the evolution of termites",
authors: "Mikhailova A, Dohmen E, Harrison MC",
journal: "Journal of Evolutionary Biology",
year: 2024,
link: "https://doi.org/10.1093/jeb/voae047",
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{
title: "Comparative Evolutionary Genomics in Insects",
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{
title: "Complex regulatory role of DNA methylation in caste- and age-specific expression of a termite",
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journal: "Open Biology",
year: 2022,
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{
title: "New Genomic Signals Underlying the Emergence of Human Proto-Genes",
authors: "Grandchamp A, Berk K, Dohmen E, Bornberg-Bauer E",
journal: "Genes",
year: 2022,
link: "https://doi.org/10.3390/genes13020284",
type: "peer-reviewed journal paper"
},
{
title: "The modular nature of protein evolution: Domain rearrangement rates across eukaryotic life",
authors: "Dohmen E, Klasberg S, Bornberg-Bauer E, Perrey S, Kemena C",
journal: "BMC Evolutionary Biology",
year: 2020,
link: "https://doi.org/10.1186/s12862-020-1591-0",
type: "peer-reviewed journal paper"
},
{
title: "Gene content evolution in the arthropods",
authors: "Thomas GWC, Dohmen E, Hughes DST, Murali SC, Poelchau M, Glastad K, Anstead CA, Ayoub NA, Batterham P, Bellair M, Binford GJ, Chao H, Chen YH, Childers C, Dinh H, Doddapaneni HV, Duan JJ, Dugan S, Esposito LA, Friedrich M, Garb J, Gasser RB, Goodisman MAD, Gundersen-Rindal DE, Han Y, Handler AM, Hatakeyama M, Hering L, Hunter WB, Ioannidis P, Jayaseelan JC, Kalra D, Khila A, Korhonen PK, Lee CE, Lee SL, Li Y, Lindsey ARI, Mayer G, McGregor AP, McKenna DD, Misof B, Munidasa M, Munoz-Torres M, Muzny DM, Niehuis O, Osuji-Lacy N, Palli SR, Panfilio KA, Pechmann M, Perry T, Peters RS, Poynton HC, Prpic N-M, Qu J, Rotenberg D, Schal C, Schoville SD, Scully ED, Skinner E, Sloan DB, Stouthamer R, Strand MR, Szucsich NU, Wijeratne A, Young ND, Zattara EE, Benoit JB, Zdobnov EM, Pfrender ME, Hackett KJ, Werren JH, Worley KC, Gibbs RA, Chipman AD, Waterhouse RM, Bornberg-Bauer E, Hahn MW, Richards S",
journal: "Genome Biology",
year: 2020,
link: "https://doi.org/10.1186/s13059-019-1925-7",
type: "peer-reviewed journal paper"
},
{
title: "Protein Domains as Molecular Markers for Large Scale Sequence Analysis",
authors: "Dohmen E",
journal: "PhD Thesis",
year: 2020,
link: "http://dx.doi.org/10.13140/RG.2.2.14518.20807",
type: "Thesis"
},
{
title: "Higher-order epistasis shapes the fitness landscape of a xenobiotic-degrading enzyme",
authors: "Yang G, Anderson DW, Baier F, Dohmen E, Hong N, Carr PD, Kamerlin SCL, Jackson C, Bornberg-Bauer E, Tokuriki N",
journal: "Nature Chemical Biology",
year: 2019,
link: "https://doi.org/10.1038/s41589-019-0386-3",
type: "peer-reviewed journal paper"
},
{
title: "DOGMA: a web server for proteome and transcriptome quality assessment",
authors: "Kemena C, Dohmen E, Bornberg-Bauer E",
journal: "Nucleic Acids Research",
year: 2019,
link: "https://doi.org/10.1093/nar/gkz366",
type: "peer-reviewed journal paper"
},
{
title: "Reactive oxygen species (ROS) and the heat stress response of Daphnia pulex: ROS-mediated activation of hypoxia-inducible factor 1 (HIF-1) and heat shock factor 1 (HSF-1) and the clustered expression of stress genes",
authors: "Klumpen E, Hoffschröer N, Zeis B, Gigengack U, Dohmen E, Paul RJ",
journal: "Biol. Cell",
year: 2017,
link: "https://doi.org/10.1111/boc.201600017",
type: "peer-reviewed journal paper"
},
{
title: "DOGMA: domain-based transcriptome and proteome quality assessment",
authors: "Dohmen E, Kremer LPM, Bornberg-Bauer E, Kemena C",
journal: "Bioinformatics",
year: 2016,
link: "https://doi.org/10.1093/bioinformatics/btw231",
type: "peer-reviewed journal paper"
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if (sortType === 'year-desc') return b.year - a.year;
if (sortType === 'year-asc') return a.year - b.year;
if (sortType === 'journal') return a.journal.localeCompare(b.journal);
if (sortType === 'title') return a.title.localeCompare(b.title);
if (sortType === 'authors') return a.authors.localeCompare(b.authors);
return 0;
});
renderPublications(filtered);
}
document.addEventListener('DOMContentLoaded', function () {
renderPublications(publications);
document.getElementById('pub-filter').addEventListener('input', filterAndSortPublications);
document.getElementById('pub-filter-type').addEventListener('change', filterAndSortPublications);
document.getElementById('pub-sort').addEventListener('change', filterAndSortPublications);
document.getElementById('pub-type').addEventListener('change', filterAndSortPublications);
});
</script>
</body>
</html>