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Chris Barnes
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@@ -198,9 +198,6 @@ <h1><b>Current group members</b></h1>
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<div class="col-3"><a href="#Jack_Rutter" class="image fit"><img src="images/people/photo-rutter2.jpg" alt="" /></a>
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Dr Jack Rutter
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</div>
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<div class="col-3"><a href="#Mohamed_Ali_Al_Badri" class="image fit"><img src="images/people/photo-al-badri.jpg" alt="" /></a>
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Dr Mohamed Ali Al-Badri
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</div>
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<div class="col-3"><a href="#Pedro_Fontanarrosa" class="image fit"><img src="images/people/photo-fontanarrosa.jpg" alt="" /></a>
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Dr Pedro Fontanarrosa
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</div>
@@ -256,20 +253,6 @@ <h2>Dr Linda Dekker<br>linda.dekker.09@ucl.ac.uk</h2>
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</p>
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<a class="close" href="#close"></a>
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</div>
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<a href="#x" class="overlay" id="Mohamed_Ali_Al_Badri"></a>
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<h2>Dr Mohamed Ali Al-Badri<br>m.al-badri@ucl.ac.uk</h2>
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<p>I am a Research Fellow in Statistical & Systems Biology in the Division of Biosciences at UCL. My
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work involves using Deep Learning methods to study structural variation in cancer. I completed my
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PhD with the London Interdisciplinary Doctoral Programme (LIDo) at King's College London, where I
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used techniques in computational theoretical physics to simulate biological systems and the
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bio-nano interface. During the PhD, I did an internship at The Alan Turing Institute, where I was
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part of the Uncertainty Quantification of Multi-scale and Multi-physics computer Models (UQMMM)
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project. I have an undergraduate degree in physics with theoretical physics from King's College
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London.
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</p>
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<a class="close" href="#close"></a>
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</div>
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<a href="#x" class="overlay" id="Jack_Rutter"></a>
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<div class="popup">
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<h2>Dr Jack Rutter<br>jack.rutter.16@ucl.ac.uk</h2>
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<div class="content dark style1">
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<div class="container">
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<h1> <b>Past group members</b></h1>
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Dr Bingxin Lu. PDRA 2019-2023. Now a Surrey Future Fellow at <a href="https://www.surrey.ac.uk/people/bingxin-lu"> University of Surrey</a><br>
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Dr Mohamed Ali al-Badri. PDRA 2020-2024. Now a Senior ML Engineer at Nucleome Therapeutics<br>
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Dr Bingxin Lu. PDRA 2019-2023. Now a Surrey Future Fellow at <a href="https://www.surrey.ac.uk/people/bingxin-lu"> University of Surrey</a><br>
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Dr Will Cross. Visiting Fellow 2021-2023. Now a Lecturer (Assistant Prof.) at <a href="https://www.westminster.ac.uk/about-us/our-people/directory/cross-will">University of Westminster </a> <br>
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Dr Alex Fedorec. PhD/PDRA 2014-2022. Now a Lecturer (Assistant Prof.) at <a href=https://iris.ucl.ac.uk/iris/browse/profile?upi=AFEDO75>UCL</a> (<a href=http://ajfedorec.github.io> lab website </a>) <br>
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Dr Neythen Treloar. PhD/PDRA 2018-2023. Now a data scientist at Faculty.ai <br>
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Dr Ke Yan Wen. PDRA 2019-2022. Now at BactoBio <br>
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Dr Behzad Karkaria. PhD/PDRA 2017-2021. Now at BactoBio<br>
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Dr Luca Rosa. PhD student 2017-2021. Now at Micrographia Bio<br>
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Dr Alex Fedorec. PhD/PDRA 2014-2022. Now a Lecturer (Assistant Prof.) at <a href="https://profiles.ucl.ac.uk/41088-alexander-fedorec">UCL</a><br>
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Dr Neythen Treloar. PhD/PDRA 2018-2023. Now a Senior Data Scientist at Bactobio <br>
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Dr Ke Yan Wen. PDRA 2019-2022. Now a Senior Scientist at BactoBio <br>
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Dr Behzad Karkaria. PhD/PDRA 2017-2021. Now a AI/ML Engineer at GSK<br>
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Dr Luca Rosa. PhD student 2017-2021. Now a Synthetic Biology Engineer at Micrographia Bio<br>
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Ms Clare Robinson. Research Assistant 2019-2020. Now doing a PhD with David Riglar, Imperial College <br>
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Dr Josh Russell-Buckland. PhD student 2016-2020. Now a software engineer at Guardian News and Media <br>
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Dr Marc Williams. PhD student 2014-2018. Now a Research Fellow with Sohrab Shah, Memorial Sloan Kettering <br>
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Dr Tanel Ozdemir. PhD student 2013-2017. Now an Investment Associate at AlbionVC <br>
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Dr Lourdes Sriraja. PhD student 2013-2017. Now a PDRA with Tariq Enver, UCL Cancer Institute <br>
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Dr Mae Woods. PDRA 2013-2018. Now at Baylor College of Medicine <br>
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Dr Miriam Leon. PhD student 2012-2016. Now a data scientist at Stitch Fix <br>
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Dr Miriam Leon. PhD student 2012-2016. Now a Senior Data Scientist at Lyft <br>
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<br>
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</div>
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</div>
@@ -395,10 +379,13 @@ <h2>Mutational processes</h2>
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<img width="50%" src="images/science/PDTO-model.jpg" alt="" />
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<figcaption>Fig: Modelling chromosomal gain and loss within a stochastic branching process </figcaption>
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</figure>
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<p> MA al-Badri, WCH Cross, CP Barnes (2024).
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Explainable deep learning on 7500 whole genomes elucidates cancer-specific patterns of chromosomal instability.
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bioRxiv, <a href=https://doi.org/10.1101/2024.03.08.584160> 2024.03.08.584160 </a></p>
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<p> B Lu, S Winnall, W Cross, CP Barnes (2024).
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Cell-cycle dependent DNA repair and replication unifies patterns of chromosome instability
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bioRxiv, 2024.01. 03.574048</p>
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Cell-cycle dependent DNA repair and replication unifies patterns of chromosome instability.
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bioRxiv, <a href=https://doi.org/10.1101/2024.01.03.574048> 2024.01.03.574048</a></p>
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<p> Lu, B., Curtius, K., Graham, T.A., Yang, Z., Barnes, C.P. (2023).
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CNETML: maximum likelihood inference of phylogeny from copy number profiles of multiple samples.
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</figcaption>
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</figure>
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<p> JW Rutter, L Dekker, C Clare, AJH Fedorec, CP Barnes (2023)
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An antimicrobial peptide expression platform for targeting pathogenic bacterial species
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bioRxiv, 2023.10. 09.561505
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</p>
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<p> C Clare, JW Rutter, AJH Fedorec, S Frank, CP Barnes (2024).
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Bacterial microcompartment utilisation in the human commensal Escherichia coli Nissle 1917.
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bioRxiv, 2024.05. 13.593892</p>
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<p> JW Rutter, L Dekker, C Clare, ZF Slendebroek, KA Owen, JAK McDonald, AJH Fedorec, CP Barnes (2024).
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A bacteriocin expression platform for targeting pathogenic bacterial species.
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Nature Communications 15 (1), 6332, doi:<a href=https://doi.org/10.1038/s41467-024-50591-8> 10.1038/s41467-024-50591-8</a></p>
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<p> Karkaria, B.D., Manhart, A., Fedorec, A.J.H., Barnes, C.P. (2022).
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Chaos in synthetic microbial communities.
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of a morphogen gradient produced from two sources A and B</figcaption>
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</figure>
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<p> AJH Fedorec, NJ Treloar, KY Wen, L Dekker, QH Ong, G Jurkeviciute, ... (2023)
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<p> AJH Fedorec, NJ Treloar, KY Wen, L Dekker, QH Ong, G Jurkeviciute, E Lyu, JW Rutter, KJY Zhang, L Rosa, A Zaikin, CP Barnes (2024).
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Emergent digital bio-computation through spatial diffusion and engineered bacteria
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bioRxiv, 2023.07. 07.548081 </p>
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Nature Communications 15 (1), 4896, doi:<a href="https://doi.org/10.1038/s41467-024-49264-3"> 10.1038/s41467-024-49264-3</a><p></p>
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</p>
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<p> Otero-Muras, I., Perez-Carrasco, R., Banga, J.R., Barnes, C.P. (2023).
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Automated design of gene circuits with optimal mushroom-bifurcation behavior.

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