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<!DOCTYPE HTML>
<html>
<head>
<title>Research - Elias Dohmen</title>
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<h1><a href="index.html">Elias Dohmen</a></h1>
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<li><a href="index.html">Home</a></li>
<li><a href="aboutme.html">About Me</a></li>
<li><a href="research.html">My Research</a></li>
<li><a href="tools.html">Tools</a></li>
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<li><a href="teaching.html">Teaching</a></li>
<li><a href="publications.html">Publications</a></li>
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<section id="research-intro" class="wrapper style2 special"
style="background: rgba(0,0,0,0.65); border-radius: 18px; box-shadow: 0 2px 16px 0 rgba(0,0,0,0.18); margin-top: 32px; margin-bottom: 32px;">
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<div style="flex: 2 1 350px; min-width: 260px;">
<header>
<h2>My Research</h2>
</header>
<p style="color:#eee; max-width: 800px; margin: 0 auto; text-align: left;">
Scientific research, to me, is about more than solving puzzles — it's about curiosity and
building the tools to explore the bigger picture with creativity and openness.
In a time of unprecedented data availability, we face not a shortage of information, but a need
for innovative, reproducible methods that help us interpret it meaningfully and responsibly.
</p>
<p style="color:#eee; max-width: 800px; margin: 0 auto; text-align: left;">
My work bridges evolutionary biology and computational science, with a focus on comparative
OMICS, phylogenomics, and the development of open-source tools for biological data analysis.
I aim to transform complex data into clear biological insight.
</p>
<p style="color:#eee; max-width: 800px; margin: 0 auto; text-align: left;">
I'm committed to transparent, scalable, and collaborative research. Reproducibility and
accessibility are central to how I design and share methods - ensuring science remains a
collective, cumulative effort.
</p>
<p style="color:#eee; max-width: 800px; margin: 0 auto; text-align: left;">
Below you'll find an overview of my research interests and selected projects I am currently
leading or contributing to. These span basic evolutionary questions to applied method
development — all
united by the idea that science must be open, curious, and useful to make a real difference.
</p>
</div>
<div style="flex: 1 1 220px; min-width: 180px; max-width: 320px; align-self: flex-start;">
<img src="images/press/methylation_DNA.jpg" alt="Epigenetics DNA methylation"
style="width:100%; border-radius: 12px; box-shadow: 0 2px 12px 0 rgba(0,0,0,0.18); margin-top: 8px;" />
</div>
</div>
</section>
<section id="tools" class="wrapper style2 special"
style="background: rgba(0,0,0,0.60); border-radius: 18px; box-shadow: 0 2px 16px 0 rgba(0,0,0,0.18); backdrop-filter: blur(1.5px);">
<div class="inner">
<header class="major">
<h2>Research Interests</h2>
<p>Driven by curiosity and collaboration, my research integrates insights from multiple disciplines
across the following focus areas:</p>
</header>
<ul class="features" style="display: flex; flex-wrap: wrap; gap: 40px 4%; justify-content: center;">
<li class="icon" style="flex: 1 1 48%; max-width: 48%; min-width: 380px;">
<!-- Protein Domains -->
<img class="image center" style="width:100%;padding-bottom:10px;padding-top:6px;"
src="images/logos/domainworld.png" alt="DomainWorld" />
<p style="font-size:smaller;">
<strong>Protein domains</strong>
are the structural and functional building blocks of proteins, enabling modular
rearrangements that drive protein innovation.
Due to their high conservation across vast evolutionary timescales, protein domains are
ideal molecular markers for evolutionary analyses and large-scale comparative proteomics.
Since my PhD, I've been fascinated by these building blocks, developing several tools based
on them — earning me the nickname <strong>Dr. Domain</strong>.<br />
Visit the <a href="tools.html" style="color:lightcyan">tools</a> page to explore programs
I've developed in this
field, check out related <a href="teaching.html" style="color:lightcyan">teaching</a>
projects, or browse relevant
<a href="publications.html" style="color:lightcyan">publications</a>:<br />
<span style="display:inline-block; margin-left:0.5em;">
<a href="https://doi.org/10.1186/s12862-020-1591-0" target="_blank"
title="The modular nature of protein evolution: Domain rearrangement rates across eukaryotic life"
style="margin-right:6px;">📄</a>
<a href="https://doi.org/10.1093/bioinformatics/btw231" target="_blank"
title="DOGMA: domain-based transcriptome and proteome quality assessment"
style="margin-right:6px;">📄</a>
<a href="https://doi.org/10.1186/s13059-019-1925-7" target="_blank"
title="Gene content evolution in the arthropods" style="margin-right:6px;">📄</a>
<a href="http://dx.doi.org/10.13140/RG.2.2.14518.20807" target="_blank"
title="Protein Domains as Molecular Markers for Large Scale Sequence Analysis">📄</a>
<a href="https://doi.org/10.1093/jeb/voae047" target="_blank"
title="Major changes in domain arrangements are associated with the evolution of termites"
style="margin-right:6px;">📄</a>
<a href="https://doi.org/10.1007/978-1-0716-3838-5_16" target="_blank"
title="Comparative Evolutionary Genomics in Insects"
style="margin-right:6px;">📄</a>
<a href="https://doi.org/10.1093/nar/gkz366" target="_blank"
title="DOGMA: a web server for proteome and transcriptome quality assessment"
style="margin-right:6px;">📄</a>
</span>
</p>
</li>
<!-- De novo genes -->
<li class="icon" style="flex: 1 1 48%; max-width: 48%; min-width: 380px;">
<img class="image center" style="width:97%;padding-bottom:10px;padding-top:6px;"
src="images/tools/denofo-logo.jpg" alt="" />
<p style="font-size:smaller;">
<strong>De novo genes</strong>
arise from previously non-coding genomic regions, challenging the traditional view that new
genes primarily emerge through duplication of existing ones.
These genes, often rapidly evolving and functionally novel, represent a dynamic and emerging
field of study.
In collaboration with researchers like <a href="https://orcid.org/0000-0003-3018-3138"
style="color:lightcyan">Anna Grandchamp</a>,
I focus on standardising methods for detecting and annotating de novo genes, aiming to
improve reproducibility and comparability across studies.<br />
For related tools, see the <a href="tools.html" style="color:lightcyan">tools</a> page,
explore associated <a href="teaching.html" style="color:lightcyan">teaching</a> projects, or
browse relevant <a href="publications.html" style="color:lightcyan">publications</a>:<br />
<span style="display:inline-block; margin-left:0.5em;">
<a href="https://doi.org/10.1101/2025.03.31.644673" target="_blank"
title="DeNoFo: a file format and toolkit for standardised, comparable de novo gene annotation"
style="margin-right:6px;">📄</a>
<a href="https://doi.org/10.32942/X2DP88" target="_blank"
title="De Novo Gene Emergence: Summary, Classification, and Challenges of Current Methods"
style="margin-right:6px;">📄</a>
<a href="https://doi.org/10.3390/genes13020284" target="_blank"
title="New Genomic Signals Underlying the Emergence of Human Proto-Genes"
style="margin-right:6px;">📄</a>
<a href="https://doi.org/10.1101/2025.06.10.658796" target="_blank"
title="Detect de novo expressed ORFs in transcriptomes with DESwoMAN"
style="margin-right:6px;">📄</a>
</span>
</p>
</li>
<!-- Epigenetics and Gene Regulation -->
<li class="icon" style="flex: 1 1 48%; max-width: 48%; min-width: 380px;">
<img class="image center" style="width:100%;padding-bottom:10px;"
src="images/press/comp_omics_integration.jpg" alt="epigenetics" />
<p style="font-size:smaller;">
<strong>Epigenetics and Gene Regulation</strong>
are intricate fields that pose significant challenges when integrating diverse OMICS data
types - such as transcriptomics and methylomics - to understand how factors like methylation
or transcription factor binding influence gene expression.
Visualising and interpreting such large, noisy datasets requires robust, scalable
approaches.
In various collaborations, I develop methods ranging from methylation databases to
gene co-expression networks, always striving to find intuitive ways to analyse and present
complex data.<br />
Explore related tools on the <a href="tools.html" style="color:lightcyan">tools</a> page,
browse relevant <a href="teaching.html" style="color:lightcyan">teaching</a> projects, or
view my <a href="publications.html" style="color:lightcyan">publications</a>:<br />
<span style="display:inline-block; margin-left:0.5em;">
<a href="https://doi.org/10.1098/rsob.220047" target="_blank"
title="Complex regulatory role of DNA methylation in caste- and age-specific expression of a termite"
style="margin-right:6px;">📄</a>
<a href="https://doi.org/10.1101/2024.11.25.625201" target="_blank"
title="Reduced regulatory complexity associated with the evolutionary transition to sociality from cockroaches to termites despite evolutionary parallels with Hymenoptera"
style="margin-right:6px;">📄</a>
<a href="https://doi.org/10.1007/978-1-0716-3838-5_16" target="_blank"
title="Comparative Evolutionary Genomics in Insects"
style="margin-right:6px;">📄</a>
<a href="https://doi.org/10.1186/s13059-019-1925-7" target="_blank"
title="Gene content evolution in the arthropods" style="margin-right:6px;">📄</a>
<a href="https://doi.org/10.1111/boc.201600017" target="_blank"
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"
style="margin-right:6px;">📄</a>
</span>
</p>
</li>
<!-- Insects -->
<li class="icon" style="flex: 1 1 48%; max-width: 48%; min-width: 380px;">
<img class="image center" style="width:100%;padding-bottom:10px;" src="images/press/insects.jpg"
alt="insects" />
<p style="font-size:smaller;">
<strong>Insects</strong>
are the most diverse and species-rich group of animals on Earth, having adapted over 500
million years to thrive in nearly every ecosystem.
Their relevance spans from public health (e.g. disease-vectoring mosquitoes) to agriculture
(pollinators) and ageing/longevity (e.g. the extraordinary lifespan of termite queens).
While I work across all domains of life - from bacteria and fungi to plants and
mammals - insects consistently capture my attention.
They frequently display some of the most fascinating evolutionary innovations, particularly
in the context of adaptation and complex traits.<br />
Visit the <a href="tools.html">tools</a> page for programs I've developed, explore related
<a href="teaching.html">teaching</a> projects, or view relevant <a
href="publications.html">publications</a>:<br />
<span style="display:inline-block; margin-left:0.5em;">
<a href="https://doi.org/10.1186/s13059-019-1925-7" target="_blank"
title="Gene content evolution in the arthropods" style="margin-right:6px;">📄</a>
<a href="https://doi.org/10.1007/978-1-0716-3838-5_16" target="_blank"
title="Comparative Evolutionary Genomics in Insects"
style="margin-right:6px;">📄</a>
<a href="https://doi.org/10.1093/jeb/voae047" target="_blank"
title="Major changes in domain arrangements are associated with the evolution of termites"
style="margin-right:6px;">📄</a>
<a href="https://doi.org/10.1098/rsob.220047" target="_blank"
title="Complex regulatory role of DNA methylation in caste- and age-specific expression of a termite"
style="margin-right:6px;">📄</a>
<a href="https://doi.org/10.1101/2024.11.25.625201" target="_blank"
title="Reduced regulatory complexity associated with the evolutionary transition to sociality from cockroaches to termites despite evolutionary parallels with Hymenoptera"
style="margin-right:6px;">📄</a>
<a href="https://doi.org/10.1186/s12862-020-1591-0" target="_blank"
title="The modular nature of protein evolution: Domain rearrangement rates across eukaryotic life"
style="margin-right:6px;">📄</a>
</span>
</p>
</li>
</ul>
</div>
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