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index.html
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<!DOCTYPE HTML>
<!--
Strata by HTML5 UP
html5up.net | @ajlkn
Free for personal and commercial use under the CCA 3.0 license (html5up.net/license)
-->
<html lang="en">
<head>
<!-- Google tag (gtag.js) -->
<script async src="https://www.googletagmanager.com/gtag/js?id=G-FGFTR76WY5"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
gtag('config', 'G-FGFTR76WY5');
</script>
<title>Fabian Spoendlin</title>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1, user-scalable=no" />
<meta name=”keywords” content="machine learning, protein design, antibody, immunoinformatics, biotech, blog posts, academia, research, Oxford" />
<link rel="stylesheet" href="assets/css/main.css" />
<style>
figure {
max-width: 100%;
}
figure img {
max-width: 100%;
}
.col-4 img {
width: 100%;
}
.container {
display: flex;
flex-wrap: wrap;
width: 100%;
padding: 0;
margin: 0;
}
.textbox {
border: 1.5px solid #ccc;
padding: 10px;
max-width: 50%; /* Changed from 100% to 50% */
width: 50%; /* Changed from 100% to 50% */
text-decoration: none;
display: block;
color: gray;
box-sizing: border-box; /* Include padding and border in element's total width and height */
}
.textbox:hover {
background-color: #f1f1f1; /* Add a background color on hover to indicate it's a link */
}
.textbox h2 {
margin-top: 0; /* Remove default margin for the title */
margin-bottom: 0;
font-size: 20px; /* Set the font size for the title */
color: black;
}
.textbox p {
font-size: 16px; /* Set the font size for the text description */
line-height: 1.5;
}
.textbox figure {
text-align: center; /* Center the content inside the figure element */
}
.textbox img {
max-width: 95%; /* Ensure the image scales down to fit the text box */
height: auto; /* Maintain the image's aspect ratio */
}
#three h3 {
margin-top: 30px; /* Adjust the margin-top value as needed to create space before the subtitle */
}
</style>
</head>
<body class="is-preload">
<!-- Header -->
<header id="header">
<div class="inner">
<a href="images/headshot.jpg" class="image avatar"><img src="images/headshot.jpg" alt="" /></a>
<h1><strong>Fabian Spoendlin</strong><br />
DPhil student<br />
Oxford Protein Informatics Group<br />
Department of Statistics<br />
University of Oxford</h1>
</div>
</header>
<!-- Main -->
<div id="main">
<!-- About me -->
<section id="one">
<h2>About Me</h2>
<p>I am a DPhil student in the Oxford Protein Informatics Group at the Department of Statistics at Oxford University and an Industrial Fellow of the Royal Commission 1851. I am interested in developing developing deep learning methods for computational drug development. Currently, the production of new drugs requires tedious wet lab experiments that are associated with high costs. Computational methods have the potential to greatly facilitate the drug discovery process. Specifically, my research focuses on antibodies, a class of proteins of great interest to the pharmaceutical industry, and I am working on improving methods for predicting antibody structures and flexibility from sequence data.</p>
</section>
<!-- Education -->
<section id="two">
<h2>Education</h2>
<div class="row">
<article class="col-4 col-12-xsmall work-item">
<figure>
<img src="images/oxford-logo.jpg" alt="Department of Statistics Logo" />
</figure>
<h3><b>DPhil Statistics</b></h3>
<p><em>Machine Learning for Antibody Flexibility Prediction</em><br />Department of Statistics<br />University of Oxford<br />2021 - 2025</p>
</article>
<article class="col-4 col-12-xsmall work-item">
<img src="images/oxford-logo.jpg" alt="Department of Biochemistry Logo"/>
<h3><b>MSc by Research Biochemistry</b></h3>
<p><em>NMR Study of Transmembrane Receptors</em><br />Department of Biochemisty<br />University of Oxford<br />2020 - 2022</p>
</article>
<article class="col-4 col-12-xsmall work-item">
<img src="images/UCL-logo.png" alt="UCL Logo"/>
<h3><b>BSc Biochemistry</b></h3>
<p>Institute of Structural and Molecular Biology<br />University College London<br />2017 - 2020</p>
</article>
</div>
</section>
<!-- Research -->
<section id="three">
<h2>Research</h2>
<section>
<h3>Papers and Preprints</h3>
<div class="container">
<a href="https://www.frontiersin.org/articles/10.3389/fmolb.2023.1237621/abstract#:~:text=all%206%20Articles-,Improved%20computational%20epitope%20profiling%20using%20structural%20models%20identifies%20a%20broader,that%20bind%20the%20same%20epitope&text=The%20final%2C%20formatted%20version%20of%20the%20article%20will%20be%20published%20soon.&text=The%20function%20of%20an%20antibody,to%20which%20epitope%20it%20engages." class="textbox">
<h2>Improved computational epitope profiling using structural models identifies a broader diversity of antibodies that bind the same epitope.</h2>
<p><strong>Spoendlin FC</strong>, Abanades B, Raybould MIJ, Wong KW, Georges G, and Deane CM. Frontiers in Molecular Biosciences, September 2023.</p>
<figure>
<img src="images/SPACE2_figure.jpg" alt="Figure">
</figure>
</a>
<a href="https://www.cell.com/structure/fulltext/S0969-2126(24)00370-8" class="textbox">
<h2>Assessing AF2's ability to predict structural ensembles of proteins.</h2>
<p>Riccabona JR*, <strong>Spoendlin FC*</strong>, Fischer MA, Loeffler JR, Quoika PK, Jenkins TP, Ferguson JA, et al. Structure, September 2024.</p>
<figure>
<img src="images/AF2_paper_fig_2.jpg" alt="Figure">
</figure>
</a>
<a href="https://aacrjournals.org/cancerres/article/doi/10.1158/0008-5472.CAN-23-2040/742904/Mathematical-Model-Driven-Deep-Learning-Enables" class="textbox">
<h2>Mathematical model-driven deep learning enables personalized adaptive therapy.</h2>
<p>Gallagher K, Strobl MA, Park DS, <strong>Spoendlin FC</strong>, Gatenby RA, Maini PK, and Anderson AR. Cancer Research, April 2024.</p>
<figure>
<img src="images/DRL_image.png" alt="Figure">
</figure>
</a>
</div>
<h3>Conference and Workshop Papers</h3>
<div class="container">
<a href="https://openreview.net/forum?id=or4tArwd5a" class="textbox">
<h2>AbFlex: Predicting the conformational flexibility of antibody CDRs.</h2>
<p><strong>Spoendlin FC</strong>, Wong KW, Georges G, Bujotzek A and Deane CM. ICML 2024 Workshop: Machine Learning for Material and Life Sciences, June 2024.</p>
<figure>
<img src="images/AbFlex_workshop.png" alt="Figure">
</figure>
</a>
</div>
<h3>Master Thesis</h3>
<p><a href="https://ora.ox.ac.uk/objects/uuid:2aed655a-b6b8-4344-874b-4390b8e746b3"><em>Investigating the dynamics of KDEL receptor signalling</em></a>. Jan 2022.<br />Supervisors: Prof Jason Schnell & Prof Simon Newstead.</p>
</section>
</section>
<!-- Blog posts -->
<section id="four">
<h2>Blog Posts</h2>
<a href="https://www.blopig.com/blog/2024/02/making-your-figures-more-accessible/" class="textbox">
<h2>Making your figures more accessible</h2>
</a>
<a href="https://www.blopig.com/blog/2023/12/some-useful-pandas-functions/" class="textbox">
<h2>Some useful pandas functions</h2>
</a>
<a href="https://www.blopig.com/blog/2023/09/current-strategies-to-predict-structures-of-multiple-protein-conformational-states/" class="textbox">
<h2>Current strategies to predict structures of multiple protein conformational states</h2>
</a>
<a href="https://www.blopig.com/blog/2023/04/an-overview-of-clustering-algorithms/" class="textbox">
<h2>An overview of clustering algorithms</h2>
</a>
</section>
<!-- Three -->
<!--
<section id="three">
<h2>Get In Touch</h2>
<p>Accumsan pellentesque commodo blandit enim arcu non at amet id arcu magna. Accumsan orci faucibus id eu lorem semper nunc nisi lorem vulputate lorem neque lorem ipsum dolor.</p>
<div class="row">
<div class="col-8 col-12-small">
<form method="post" action="#">
<div class="row gtr-uniform gtr-50">
<div class="col-6 col-12-xsmall"><input type="text" name="name" id="name" placeholder="Name" /></div>
<div class="col-6 col-12-xsmall"><input type="email" name="email" id="email" placeholder="Email" /></div>
<div class="col-12"><textarea name="message" id="message" placeholder="Message" rows="4"></textarea></div>
</div>
</form>
<ul class="actions">
<li><input type="submit" value="Send Message" /></li>
</ul>
</div>
<div class="col-4 col-12-small">
<ul class="labeled-icons">
<li>
<h3 class="icon solid fa-home"><span class="label">Address</span></h3>
1234 Somewhere Rd.<br />
Nashville, TN 00000<br />
United States
</li>
<li>
<h3 class="icon solid fa-mobile-alt"><span class="label">Phone</span></h3>
000-000-0000
</li>
<li>
<h3 class="icon solid fa-envelope"><span class="label">Email</span></h3>
<a href="#">[email protected]</a>
</li>
</ul>
</div>
</div>
</section>
-->
<!-- Four -->
<!--
<section id="four">
<h2>Elements</h2>
<section>
<h4>Text</h4>
<p>This is <b>bold</b> and this is <strong>strong</strong>. This is <i>italic</i> and this is <em>emphasized</em>.
This is <sup>superscript</sup> text and this is <sub>subscript</sub> text.
This is <u>underlined</u> and this is code: <code>for (;;) { ... }</code>. Finally, <a href="#">this is a link</a>.</p>
<hr />
<header>
<h4>Heading with a Subtitle</h4>
<p>Lorem ipsum dolor sit amet nullam id egestas urna aliquam</p>
</header>
<p>Nunc lacinia ante nunc ac lobortis. Interdum adipiscing gravida odio porttitor sem non mi integer non faucibus ornare mi ut ante amet placerat aliquet. Volutpat eu sed ante lacinia sapien lorem accumsan varius montes viverra nibh in adipiscing blandit tempus accumsan.</p>
<header>
<h5>Heading with a Subtitle</h5>
<p>Lorem ipsum dolor sit amet nullam id egestas urna aliquam</p>
</header>
<p>Nunc lacinia ante nunc ac lobortis. Interdum adipiscing gravida odio porttitor sem non mi integer non faucibus ornare mi ut ante amet placerat aliquet. Volutpat eu sed ante lacinia sapien lorem accumsan varius montes viverra nibh in adipiscing blandit tempus accumsan.</p>
<hr />
<h2>Heading Level 2</h2>
<h3>Heading Level 3</h3>
<h4>Heading Level 4</h4>
<h5>Heading Level 5</h5>
<h6>Heading Level 6</h6>
<hr />
<h5>Blockquote</h5>
<blockquote>Fringilla nisl. Donec accumsan interdum nisi, quis tincidunt felis sagittis eget tempus euismod. Vestibulum ante ipsum primis in faucibus vestibulum. Blandit adipiscing eu felis iaculis volutpat ac adipiscing accumsan faucibus. Vestibulum ante ipsum primis in faucibus lorem ipsum dolor sit amet nullam adipiscing eu felis.</blockquote>
<h5>Preformatted</h5>
<pre><code>i = 0;
while (!deck.isInOrder()) {
print 'Iteration ' + i;
deck.shuffle();
i++;
}
print 'It took ' + i + ' iterations to sort the deck.';</code></pre>
</section>
<section>
<h4>Lists</h4>
<div class="row">
<div class="col-6 col-12-xsmall">
<h5>Unordered</h5>
<ul>
<li>Dolor pulvinar etiam magna etiam.</li>
<li>Sagittis adipiscing lorem eleifend.</li>
<li>Felis enim feugiat dolore viverra.</li>
</ul>
<h5>Alternate</h5>
<ul class="alt">
<li>Dolor pulvinar etiam magna etiam.</li>
<li>Sagittis adipiscing lorem eleifend.</li>
<li>Felis enim feugiat dolore viverra.</li>
</ul>
</div>
<div class="col-6 col-12-xsmall">
<h5>Ordered</h5>
<ol>
<li>Dolor pulvinar etiam magna etiam.</li>
<li>Etiam vel felis at lorem sed viverra.</li>
<li>Felis enim feugiat dolore viverra.</li>
<li>Dolor pulvinar etiam magna etiam.</li>
<li>Etiam vel felis at lorem sed viverra.</li>
<li>Felis enim feugiat dolore viverra.</li>
</ol>
<h5>Icons</h5>
<ul class="icons">
<li><a href="#" class="icon brands fa-twitter"><span class="label">Twitter</span></a></li>
<li><a href="#" class="icon brands fa-facebook-f"><span class="label">Facebook</span></a></li>
<li><a href="#" class="icon brands fa-instagram"><span class="label">Instagram</span></a></li>
<li><a href="#" class="icon brands fa-github"><span class="label">Github</span></a></li>
<li><a href="#" class="icon brands fa-dribbble"><span class="label">Dribbble</span></a></li>
<li><a href="#" class="icon brands fa-tumblr"><span class="label">Tumblr</span></a></li>
</ul>
</div>
</div>
<h5>Actions</h5>
<ul class="actions">
<li><a href="#" class="button primary">Default</a></li>
<li><a href="#" class="button">Default</a></li>
</ul>
<ul class="actions small">
<li><a href="#" class="button primary small">Small</a></li>
<li><a href="#" class="button small">Small</a></li>
</ul>
<div class="row">
<div class="col-6 col-12-small">
<ul class="actions stacked">
<li><a href="#" class="button primary">Default</a></li>
<li><a href="#" class="button">Default</a></li>
</ul>
</div>
<div class="col-6 col-12-small">
<ul class="actions stacked">
<li><a href="#" class="button primary small">Small</a></li>
<li><a href="#" class="button small">Small</a></li>
</ul>
</div>
<div class="col-6 col-12-small">
<ul class="actions stacked">
<li><a href="#" class="button primary fit">Default</a></li>
<li><a href="#" class="button fit">Default</a></li>
</ul>
</div>
<div class="col-6 col-12-small">
<ul class="actions stacked">
<li><a href="#" class="button primary small fit">Small</a></li>
<li><a href="#" class="button small fit">Small</a></li>
</ul>
</div>
</div>
</section>
<section>
<h4>Table</h4>
<h5>Default</h5>
<div class="table-wrapper">
<table>
<thead>
<tr>
<th>Name</th>
<th>Description</th>
<th>Price</th>
</tr>
</thead>
<tbody>
<tr>
<td>Item One</td>
<td>Ante turpis integer aliquet porttitor.</td>
<td>29.99</td>
</tr>
<tr>
<td>Item Two</td>
<td>Vis ac commodo adipiscing arcu aliquet.</td>
<td>19.99</td>
</tr>
<tr>
<td>Item Three</td>
<td> Morbi faucibus arcu accumsan lorem.</td>
<td>29.99</td>
</tr>
<tr>
<td>Item Four</td>
<td>Vitae integer tempus condimentum.</td>
<td>19.99</td>
</tr>
<tr>
<td>Item Five</td>
<td>Ante turpis integer aliquet porttitor.</td>
<td>29.99</td>
</tr>
</tbody>
<tfoot>
<tr>
<td colspan="2"></td>
<td>100.00</td>
</tr>
</tfoot>
</table>
</div>
<h5>Alternate</h5>
<div class="table-wrapper">
<table class="alt">
<thead>
<tr>
<th>Name</th>
<th>Description</th>
<th>Price</th>
</tr>
</thead>
<tbody>
<tr>
<td>Item One</td>
<td>Ante turpis integer aliquet porttitor.</td>
<td>29.99</td>
</tr>
<tr>
<td>Item Two</td>
<td>Vis ac commodo adipiscing arcu aliquet.</td>
<td>19.99</td>
</tr>
<tr>
<td>Item Three</td>
<td> Morbi faucibus arcu accumsan lorem.</td>
<td>29.99</td>
</tr>
<tr>
<td>Item Four</td>
<td>Vitae integer tempus condimentum.</td>
<td>19.99</td>
</tr>
<tr>
<td>Item Five</td>
<td>Ante turpis integer aliquet porttitor.</td>
<td>29.99</td>
</tr>
</tbody>
<tfoot>
<tr>
<td colspan="2"></td>
<td>100.00</td>
</tr>
</tfoot>
</table>
</div>
</section>
<section>
<h4>Buttons</h4>
<ul class="actions">
<li><a href="#" class="button primary">Primary</a></li>
<li><a href="#" class="button">Default</a></li>
</ul>
<ul class="actions">
<li><a href="#" class="button large">Large</a></li>
<li><a href="#" class="button">Default</a></li>
<li><a href="#" class="button small">Small</a></li>
</ul>
<ul class="actions fit">
<li><a href="#" class="button primary fit">Fit</a></li>
<li><a href="#" class="button fit">Fit</a></li>
</ul>
<ul class="actions fit small">
<li><a href="#" class="button primary fit small">Fit + Small</a></li>
<li><a href="#" class="button fit small">Fit + Small</a></li>
</ul>
<ul class="actions">
<li><a href="#" class="button primary icon solid fa-download">Icon</a></li>
<li><a href="#" class="button icon solid fa-download">Icon</a></li>
</ul>
<ul class="actions">
<li><span class="button primary disabled">Primary</span></li>
<li><span class="button disabled">Default</span></li>
</ul>
</section>
<section>
<h4>Form</h4>
<form method="post" action="#">
<div class="row gtr-uniform gtr-50">
<div class="col-6 col-12-xsmall">
<input type="text" name="demo-name" id="demo-name" value="" placeholder="Name" />
</div>
<div class="col-6 col-12-xsmall">
<input type="email" name="demo-email" id="demo-email" value="" placeholder="Email" />
</div>
<div class="col-12">
<select name="demo-category" id="demo-category">
<option value="">- Category -</option>
<option value="1">Manufacturing</option>
<option value="1">Shipping</option>
<option value="1">Administration</option>
<option value="1">Human Resources</option>
</select>
</div>
<div class="col-4 col-12-small">
<input type="radio" id="demo-priority-low" name="demo-priority" checked>
<label for="demo-priority-low">Low Priority</label>
</div>
<div class="col-4 col-12-small">
<input type="radio" id="demo-priority-normal" name="demo-priority">
<label for="demo-priority-normal">Normal Priority</label>
</div>
<div class="col-4 col-12-small">
<input type="radio" id="demo-priority-high" name="demo-priority">
<label for="demo-priority-high">High Priority</label>
</div>
<div class="col-6 col-12-small">
<input type="checkbox" id="demo-copy" name="demo-copy">
<label for="demo-copy">Email me a copy of this message</label>
</div>
<div class="col-6 col-12-small">
<input type="checkbox" id="demo-human" name="demo-human" checked>
<label for="demo-human">I am a human and not a robot</label>
</div>
<div class="col-12">
<textarea name="demo-message" id="demo-message" placeholder="Enter your message" rows="6"></textarea>
</div>
<div class="col-12">
<ul class="actions">
<li><input type="submit" value="Send Message" class="primary" /></li>
<li><input type="reset" value="Reset" /></li>
</ul>
</div>
</div>
</form>
</section>
<section>
<h4>Image</h4>
<h5>Fit</h5>
<div class="box alt">
<div class="row gtr-50 gtr-uniform">
<div class="col-12"><span class="image fit"><img src="images/fulls/05.jpg" alt="" /></span></div>
<div class="col-4"><span class="image fit"><img src="images/thumbs/01.jpg" alt="" /></span></div>
<div class="col-4"><span class="image fit"><img src="images/thumbs/02.jpg" alt="" /></span></div>
<div class="col-4"><span class="image fit"><img src="images/thumbs/03.jpg" alt="" /></span></div>
<div class="col-4"><span class="image fit"><img src="images/thumbs/04.jpg" alt="" /></span></div>
<div class="col-4"><span class="image fit"><img src="images/thumbs/05.jpg" alt="" /></span></div>
<div class="col-4"><span class="image fit"><img src="images/thumbs/06.jpg" alt="" /></span></div>
<div class="col-4"><span class="image fit"><img src="images/thumbs/03.jpg" alt="" /></span></div>
<div class="col-4"><span class="image fit"><img src="images/thumbs/02.jpg" alt="" /></span></div>
<div class="col-4"><span class="image fit"><img src="images/thumbs/01.jpg" alt="" /></span></div>
</div>
</div>
<h5>Left & Right</h5>
<p><span class="image left"><img src="images/avatar.jpg" alt="" /></span>Fringilla nisl. Donec accumsan interdum nisi, quis tincidunt felis sagittis eget. tempus euismod. Vestibulum ante ipsum primis in faucibus vestibulum. Blandit adipiscing eu felis iaculis volutpat ac adipiscing accumsan eu faucibus. Integer ac pellentesque praesent tincidunt felis sagittis eget. tempus euismod. Vestibulum ante ipsum primis in faucibus vestibulum. Blandit adipiscing eu felis iaculis volutpat ac adipiscing accumsan eu faucibus. Integer ac pellentesque praesent. Donec accumsan interdum nisi, quis tincidunt felis sagittis eget. tempus euismod. Vestibulum ante ipsum primis in faucibus vestibulum. Blandit adipiscing eu felis iaculis volutpat ac adipiscing accumsan eu faucibus. Integer ac pellentesque praesent tincidunt felis sagittis eget. tempus euismod. Vestibulum ante ipsum primis in faucibus vestibulum. Blandit adipiscing eu felis iaculis volutpat ac adipiscing accumsan eu faucibus. Integer ac pellentesque praesent.</p>
<p><span class="image right"><img src="images/avatar.jpg" alt="" /></span>Fringilla nisl. Donec accumsan interdum nisi, quis tincidunt felis sagittis eget. tempus euismod. Vestibulum ante ipsum primis in faucibus vestibulum. Blandit adipiscing eu felis iaculis volutpat ac adipiscing accumsan eu faucibus. Integer ac pellentesque praesent tincidunt felis sagittis eget. tempus euismod. Vestibulum ante ipsum primis in faucibus vestibulum. Blandit adipiscing eu felis iaculis volutpat ac adipiscing accumsan eu faucibus. Integer ac pellentesque praesent. Donec accumsan interdum nisi, quis tincidunt felis sagittis eget. tempus euismod. Vestibulum ante ipsum primis in faucibus vestibulum. Blandit adipiscing eu felis iaculis volutpat ac adipiscing accumsan eu faucibus. Integer ac pellentesque praesent tincidunt felis sagittis eget. tempus euismod. Vestibulum ante ipsum primis in faucibus vestibulum. Blandit adipiscing eu felis iaculis volutpat ac adipiscing accumsan eu faucibus. Integer ac pellentesque praesent.</p>
</section>
</section>
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