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  <title>Computational Cancer Biology and Epigenomics Lab · KU Leuven</title>
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        <span class="tag tag-outline kicker">KU Leuven · Department of Oncology</span>
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      <h1 class="display">Computational Cancer Biology and Epigenomics</h1>
      <p class="lede">We develop computational methods that read cell identity from the epigenome: which cells make up a tissue or a tumour, where a cancer came from, and how individual cells differ.</p>
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        <a class="btn btn-primary blueprint" href="blog/syto/"><i class="corner tl"></i><i class="corner tr"></i><i class="corner bl"></i><i class="corner br"></i>Read our latest post</a>
        <a class="btn btn-secondary" href="publications/">Publications</a>
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    <section class="section" id="research" aria-labelledby="research-h">
      <div class="section-head"><h2 id="research-h">Research foci</h2></div>
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          <span class="num">01</span>
          <h3>Methylome deconvolution</h3>
          <p>Estimating the cell-type composition of DNA methylation data, from aggregated profiles down to individual sequencing reads, with and without reference panels.</p>
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        <div class="cell">
          <span class="num">02</span>
          <h3>Cancer cell-of-origin inference</h3>
          <p>Using the epigenetic memory carried by tumour cells to trace cancers back to the normal cell types they arose from.</p>
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          <span class="num">03</span>
          <h3>Single-cell and spatial epigenomics</h3>
          <p>Quantifying epigenetic heterogeneity and integrating multiomic measurements in single cells and tissues.</p>
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          <span class="num">04</span>
          <h3>Oncohistone malignancies</h3>
          <p>How mutations in histone genes, such as H3.3-G34W in giant cell tumours of bone, rewire the epigenetic landscape.</p>
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    <section class="section" id="latest" aria-labelledby="latest-h">
      <div class="section-head">
        <h2 id="latest-h">From the blog</h2>
        <a class="more" href="blog/">All posts <svg class="icon" viewBox="0 0 24 24" aria-hidden="true"><path d="M5 12h14"/><path d="m12 5 7 7-7 7"/></svg></a>
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        <figure><a href="blog/syto/"><img src="blog/syto/teaser.webp" width="1600" height="1200" alt="Sequenced DNA reads with methylated and unmethylated CpGs go into cell-type deconvolution, which predicts the cell-type mixture."></a></figure>
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          <div class="card-kicker">Paper explainer · 15 September 2026</div>
          <h3><a href="blog/syto/">Classifying a tissue sample one DNA fragment at a time</a></h3>
          <p>Assigning a DNA fragment to its most likely cell of origin gets harder as the number of possible cell types grows. The solution turned out to be letting the model know when to remain unsure.</p>
          <div class="meta-row"><span>Rizdvanetskyi, Roos, Lutsik</span><span>NeurIPS 2026 · main track</span></div>
          <a class="more" href="blog/syto/">Read the post <svg class="icon" viewBox="0 0 24 24" aria-hidden="true"><path d="M5 12h14"/><path d="m12 5 7 7-7 7"/></svg></a>
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    <section class="section" id="software" aria-labelledby="software-h">
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        <h2 id="software-h">Software</h2>
        <a class="more" href="software/">All software <svg class="icon" viewBox="0 0 24 24" aria-hidden="true"><path d="M5 12h14"/><path d="m12 5 7 7-7 7"/></svg></a>
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            <span class="tool-icon" aria-hidden="true"><svg class="icon" viewBox="0 0 24 24"><path d="M21 12c.552 0 1.005-.449.95-.998a10 10 0 0 0-8.953-8.951c-.55-.055-.998.398-.998.95v8a1 1 0 0 0 1 1z" /><path d="M21.21 15.89A10 10 0 1 1 8 2.83" /></svg></span>
            <div class="card-kicker">Methylome deconvolution</div>
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          <div class="card-title"><a href="https://github.com/CompEpigen/syto">Syto</a></div>
          <p class="card-body">Read-level DNA methylation classification and cell-type deconvolution with deep learning, built on data-driven soft labels.</p>
          <div class="card-links"><a href="https://github.com/CompEpigen/syto">Code</a><a href="https://arxiv.org/abs/2607.04987">Paper</a><a href="blog/syto/">Blog post</a></div>
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          <i class="corner tl"></i><i class="corner tr"></i><i class="corner bl"></i><i class="corner br"></i>
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            <span class="tool-icon" aria-hidden="true"><svg class="icon" viewBox="0 0 24 24"><path d="M12 5a3 3 0 1 0-5.997.125 4 4 0 0 0-2.526 5.77 4 4 0 0 0 .556 6.588A4 4 0 1 0 12 18Z" /><path d="M9 13a4.5 4.5 0 0 0 3-4" /><path d="M6.003 5.125A3 3 0 0 0 6.401 6.5" /><path d="M3.477 10.896a4 4 0 0 1 .585-.396" /><path d="M6 18a4 4 0 0 1-1.967-.516" /><path d="M12 13h4" /><path d="M12 18h6a2 2 0 0 1 2 2v1" /><path d="M12 8h8" /><path d="M16 8V5a2 2 0 0 1 2-2" /><circle cx="16" cy="13" r=".5" /><circle cx="18" cy="3" r=".5" /><circle cx="20" cy="21" r=".5" /><circle cx="20" cy="8" r=".5" /></svg></span>
            <div class="card-kicker">Methylome deconvolution</div>
          </div>
          <div class="card-title"><a href="https://github.com/CompEpigen/methylbert">MethylBERT</a></div>
          <p class="card-body">Read-level DNA methylation pattern identification and tumour deconvolution with a Transformer model.</p>
          <div class="card-links"><a href="https://github.com/CompEpigen/methylbert">Code</a><a href="https://doi.org/10.1038/s41467-025-55920-z">Paper</a></div>
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          <i class="corner tl"></i><i class="corner tr"></i><i class="corner bl"></i><i class="corner br"></i>
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            <span class="tool-icon" aria-hidden="true"><svg class="icon" viewBox="0 0 24 24"><rect width="18" height="18" x="3" y="3" rx="2" /><path d="M3 9h18" /><path d="M3 15h18" /><path d="M9 3v18" /><path d="M15 3v18" /></svg></span>
            <div class="card-kicker">Methylation analysis</div>
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          <div class="card-title"><a href="https://github.com/CompEpigen/methrix">methrix</a></div>
          <p class="card-body">R/Bioconductor package for systematic aggregation and analysis of bisulfite sequencing data.</p>
          <div class="card-links"><a href="https://github.com/CompEpigen/methrix">Code</a><a href="methrix/">Docs</a><a href="https://doi.org/10.1093/bioinformatics/btaa1048">Paper</a></div>
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        <div class="card blueprint">
          <i class="corner tl"></i><i class="corner tr"></i><i class="corner bl"></i><i class="corner br"></i>
          <div class="card-head">
            <span class="tool-icon" aria-hidden="true"><svg class="icon" viewBox="0 0 24 24"><path d="M6 9H4.5a2.5 2.5 0 0 1 0-5H6" /><path d="M18 9h1.5a2.5 2.5 0 0 0 0-5H18" /><path d="M4 22h16" /><path d="M10 14.66V17c0 .55-.47.98-.97 1.21C7.85 18.75 7 20.24 7 22" /><path d="M14 14.66V17c0 .55.47.98.97 1.21C16.15 18.75 17 20.24 17 22" /><path d="M18 2H6v7a6 6 0 0 0 12 0V2Z" /></svg></span>
            <div class="card-kicker">Methylation analysis</div>
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          <div class="card-title"><a href="https://compepigen.github.io/PipelineOlympics/">Pipeline Olympics</a></div>
          <p class="card-body">Continuable benchmark of DNA methylation sequencing workflows against an experimental gold standard, with interactive results.</p>
          <div class="card-links"><a href="https://compepigen.github.io/PipelineOlympics/">Website</a><a href="https://github.com/CompEpigen/PipelineOlympics">Code</a><a href="https://doi.org/10.1093/nar/gkaf970">Paper</a></div>
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    </section>

    <section class="section" id="recent" aria-labelledby="recent-h">
      <div class="section-head">
        <h2 id="recent-h">Recent publications</h2>
        <a class="more" href="publications/">All publications <svg class="icon" viewBox="0 0 24 24" aria-hidden="true"><path d="M5 12h14"/><path d="m12 5 7 7-7 7"/></svg></a>
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      <!-- RECENT-PUBLICATIONS:START -->
      <ol class="pubs">
        <li class="pub" data-led>
          <span class="pub-year">2026</span>
          <div>
            <a class="pub-title" href="https://arxiv.org/abs/2607.04987">Data-driven soft labeling scales DNA read classification to whole-body cell-type deconvolution.</a>
            <div class="pub-authors">Rizdvanetskyi D, Roos N, <b>Lutsik P</b></div>
            <div class="pub-venue"><em>NeurIPS 2026 (main track)</em><span class="tag tag-accent">Syto</span><a href="blog/syto/">Blog post</a></div>
          </div>
        </li>
        <li class="pub" data-led>
          <span class="pub-year">2025</span>
          <div>
            <a class="pub-title" href="https://doi.org/10.1093/nar/gkaf970">Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold standard.</a>
            <div class="pub-authors">Lin YY, Breuer K, Weichenhan D … <b>Lutsik P</b></div>
            <div class="pub-venue"><em>Nucleic Acids Res</em><span class="tag tag-accent">Pipeline Olympics</span></div>
          </div>
        </li>
        <li class="pub" data-led>
          <span class="pub-year">2025</span>
          <div>
            <a class="pub-title" href="https://doi.org/10.1038/d41586-025-02256-9">Epigenetic clues from cancer&#x27;s past foretell its future.</a>
            <div class="pub-authors"><b>Lutsik P</b>, Manojlovic V, Vassiliou GS</div>
            <div class="pub-venue"><em>Nature</em><span class="tag tag-outline">Commentary</span></div>
          </div>
        </li>
        <li class="pub" data-led>
          <span class="pub-year">2025</span>
          <div>
            <a class="pub-title" href="https://doi.org/10.1158/2643-3230.BCD-24-0278">Enhancer Hijacking Discovery in Acute Myeloid Leukemia by Pyjacker Identifies MNX1 Activation via Deletion 7q.</a>
            <div class="pub-authors">Sollier E, Riedel A, Toprak UH … <b>Lutsik P</b> … Plass C</div>
            <div class="pub-venue"><em>Blood Cancer Discov</em><span class="tag tag-accent">Pyjacker</span></div>
          </div>
        </li>
        <li class="pub" data-led>
          <span class="pub-year">2025</span>
          <div>
            <a class="pub-title" href="https://doi.org/10.1038/s41467-025-55920-z">MethylBERT enables read-level DNA methylation pattern identification and tumour deconvolution using a Transformer-based model.</a>
            <div class="pub-authors">Jeong Y, Gerhäuser C, Sauter G, Schlomm T, Rohr K, <b>Lutsik P</b></div>
            <div class="pub-venue"><em>Nat Commun</em><span class="tag tag-accent">MethylBERT</span></div>
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        </li>
      </ol>
      <!-- RECENT-PUBLICATIONS:END -->
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