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publications.html
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---
layout: page
title: Publications
permalink: /publications
top_navbar: false
---
<ul class="publication-legend center-align">
<li><b>Bold</b> = lab members.</li>
<li>* = equal first author contribution.</li>
<li>† = equal senior author contribution.</li>
<li>(A) = alphabetical author order.</li>
<li><i class="fa fa-users circle"></i> = peer-reviewed.</li>
<li><i class="fa fa-user-plus circle"></i> = invited.</li>
<li><i class="fa fa-book circle"></i> = book/chapter.</li>
</ul>
<ul class="collection with-header">
<li class="collection-header">
<h4>In-press and preprints</h4>
</li>
<li class="collection-item avatar">
<i class="fa fa-users circle"></i>
<div>
<div><b>ScalpelSig: Automated Design of Genomic Panels to Expand Clinical Access to Mutational Signature Analysis</b></div>
<div class="light"><b>N Franzese</b>, <b>J Fan</b>, R Sharan, <b>MDM Leiserson</b></div>
<div><i class="source">RECOMB</i> (2021; to appear)</div>
</div>
<div class="publication-links">
</div>
</li>
<li class="collection-item avatar">
<div>
<div><b><a href='https://www.biorxiv.org/content/10.1101/407767v2' target='_new'>Integrated computational and experimental identification of p53, KRAS and VHL mutant selection associated with CRISPR-Cas9 editing</a></b></div>
<div class="light">S Sinha, KB Guerra, K Cheng, <b>MDM Leiserson</b>, DM Wilson, BM Ryan, Z Ronai, JS Lee, AJ Deshpande, E Ruppin.</div>
<div><i class="source">bioRxiv</i> (2018)</div>
</div>
<div class="publication-links">
<a class="red-text" href="https://www.biorxiv.org/content/10.1101/407767v2.full.pdf" target="_new"><i class="fa fa-file-pdf-o" aria-hidden="true"></i> Preprint PDF</a>
<a class="purple-text" href="https://github.com/ruppinlab/crispr_risk" target="_new"><i class="fa fa-github" aria-hidden="true"></i> Repo</a>
</div>
</li>
<li class="collection-header">
<h4>2020</h4>
</li>
<li class="collection-item avatar">
<i class="fa fa-users circle"></i>
<div>
<div><b><a href='http://track.smtpserver.email/9032119/c?p=h5sdR9JYwYCLLUbAGABrxbMOUVUwbu7snQqXf-08pW3eyGBzyZ8_fZOw3jzufvbhaMClugpyxoSwtxkDVQgS7kUYK4WRx1sJzWlYvAje-oBONCYmBe3hU8jf58o7fzjwoFtxSn-j7gVeGPpwDvPsOy59h76mCTDZa17t8YFzbbIUWg54qAHQgUcl1pQVZBRpL0b7tchpaAz38q6w_FsWUDde-uWXqtbAqp54DUfQkOlZabRtdoLtXDf4VCqs9THA3PuG0Tx8MTdvrndZjOJa5w==' target='_new'>Matrix (factorization) reloaded: flexible methods for imputing genetic interactions with cross-species and side information</a></b></div>
<div class="light"><b>J Fan</b>, <b>XC Li</b>, M Crovella, <b>MDM Leiserson</b></div>
<div><i class="source">ECCB/Bioinformatics</i> (2020)</div>
</div>
<div class="publication-links">
<a class="red-text" href="https://watermark.silverchair.com/btaa818.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAtQwggLQBgkqhkiG9w0BBwagggLBMIICvQIBADCCArYGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMy2sy5uG9wbYkdvr-AgEQgIICh9PZOYNxwe3RnJ0_yi2JZv8BFVQXPlr-FEp8h80h3YMYZ5NpGKY0N1aS5g9G3_2bFgCFDu0_x3yNyySuxnl7IW1_wGVlcISHjzovAHFf_zU0SQPkFN-GDARKjcv4Lax2HaF2AsOsYnmXQtxgJQqYRU20Bs2tXLKsF_cqRXo9bveiDkgyt_ZXSYlgTgQIDyF4UjWCYgTFeiBC0wQx1Ua1tHhWQt-wybHLuAEds0opNz_bSHPTz0IBWdcKO5lyxcq29DEr-Xf12Z-XIXT-Ih-tStPJfaAx7izN3t5DkvkDry5t2ffICOLBFYdUEXKupwbjdcoFGSW_ndkRBnYU1V9xOK3NkhYMh9XXL7wZh8JPljIBsDG97qYM_6sV7ueEgjwbfTc1WE3yxiRKjI6vkXVGt8cDf_tfef1UugTt43aOW2vZxVg8StYeqBlG_X7n1r5SLruuRrBtP-tvbV6Ig128KdQwU7vSeA8TXiFeFhIcNzceVzfJznjuCe9I6w2X7qhlkWJSRIbH8NAP78ocAoN8yXbmfOY4nNgkEU9WpI-GCOVKNe6nVd8bdYs6yaEiqRvG6tCe2iopYqzqdS5-3RnUAHr1mnayMfIzi4oLl-BvILH1mIkeR1X2LyAMufa7TFzZ6LOBbkPtO5dhX7ih9AMiwNYLdxvwAJbE8kTAxWo7m8cHp6EjvX4n0tgkthwwOJmexa4f_7RIp8PsyRwJTp93Rffeg_HeXxgEeYVqPWHCVelQ6v9TqjA-73bCVvUjBF4vxSXrVFNN9rVlQtwNM6gp3_hEhRnw2GGH9a8cIZ-miCgCP6b8ipm1plnPwM4JskvBdD2APFk0XiKdRkUI9vZnDAt3oOgXG33c" target="_new"><i class="fa fa-file-pdf-o" aria-hidden="true"></i> PDF</a>
<a class="purple-text" href="https://github.com/lrgr/emf" target="_new"><i class="fa fa-github" aria-hidden="true"></i> Repo</a>
</div>
</li>
<li class="collection-item avatar">
<i class="fa fa-users circle"></i>
<div>
<div><b><a href='https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-020-00745-2' target='_new'>Network-based approaches elucidate differences within APOBEC and clock-like signatures in breast cancer</a></b></div>
<div class="light">YA Kim, D Wojtowicz, R Sarto Basso, I Sason, <b>W Robinson</b>, DS Hochbaum, <b>MDM Leiserson</b>, R Sharan, F Vandin, TM Pryzytcka</div>
<div><i class="source">Genome Medicine</i> (2020)</div>
</div>
<div class="publication-links">
<a class="red-text" href="https://genomemedicine.biomedcentral.com/track/pdf/10.1186/s13073-020-00745-2" target="_new"><i class="fa fa-file-pdf-o" aria-hidden="true"></i> PDF</a>
</div>
</li>
<li class="collection-item avatar">
<i class="fa fa-users circle"></i>
<div>
<div><b><a href="https://link.springer.com/chapter/10.1007/978-3-030-45257-5_34" target="_new">A mixture model for signature discovery from sparse mutation data</a></b></div>
<div class="light">I Sason, <b>Y Chen</b>, <b>MDM Leiserson</b>, R Sharan.</div>
<div><i class="source">RECOMB</i> (2020)</div>
</div>
<div class="publication-links"></div>
</li>
<li class="collection-item avatar">
<i class="fa fa-user-plus circle"></i>
<div>
<div><b><a href='https://www.worldscientific.com/doi/abs/10.1142/9789811215636_0020' target='_new'>Mutational Signatures: Etiology, Properties, and Role in Cancer</a></b></div>
<div class="light"><b>MDM Leiserson</b>†, T Przytycka†, R Sharan†</div>
<div><i class="source">PSB</i> (2020)</div>
</div>
<div class="publication-links">
<a class="red-text" href="https://psb.stanford.edu/psb-online/proceedings/psb20/Intro_Mutational%20Signatures.pdf" target="_new"><i class="fa fa-file-pdf-o" aria-hidden="true"></i> PDF</a>
</div>
</li>
<li class="collection-item avatar">
<i class="fa fa-users circle"></i>
<div>
<div><b><a href='https://www.worldscientific.com/doi/abs/10.1142/9789811215636_0024' target='_new'>DNA Repair Footprint Uncovers Contribution of DNA Repair Mechanism to Mutational Signatures</a></b></div>
<div class="light">D Wojtowicz, <b>MDM Leiserson</b>, R Sharan, T Przytycka</div>
<div><i class="source">PSB</i> (2020)</div>
</div>
<div class="publication-links">
<a class="red-text" href="https://psb.stanford.edu/psb-online/proceedings/psb20/Wojtowicz.pdf" target="_new"><i class="fa fa-file-pdf-o" aria-hidden="true"></i> PDF</a>
</div>
</li>
<li class="collection-item avatar">
<i class="fa fa-users circle"></i>
<div>
<div><b>PhySigs: Phylogenetic Inference of Mutational Signature Dynamics</b></div>
<div class="light">S Christensen, <b>MDM Leiserson</b>, M El-Kebir</div>
<div><i class="source">PSB</i> (2020)</div>
</div>
<div class="publication-links">
<a class="red-text" href="https://psb.stanford.edu/psb-online/proceedings/psb20/Christensen.pdf" target="_new"><i class="fa fa-file-pdf-o" aria-hidden="true"></i> PDF</a>
<a class="purple-text" href="https://github.com/elkebir-group/PhySigs" target="_new"><i class="fa fa-github" aria-hidden="true"></i> Repo</a>
</div>
</li>
<li class="collection-header">
<h4>2019</h4>
</li>
<li class="collection-item avatar">
<i class="fa fa-users circle"></i>
<div>
<div><b><a href='https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-019-0659-1' target='_new'>Hidden Markov Models Lead to Higher Resolution Maps of Mutation Signature Activity in Cancer</a></b></div>
<div class="light">X Huang*, I Sason*, D Wojtowicz*, Y-A Kim, <b>MDM Leiserson</b>†, Teresa M Przytycka†, Roded Sharan†</div>
<div><i class="source">Genome Medicine</i> (2019)</div>
</div>
<div class="publication-links">
<a class="red-text" href="https://rdcu.be/bLVSv" target="_new"><i class="fa fa-file-pdf-o" aria-hidden="true"></i> PDF</a>
<a class="purple-text" href="https://github.com/lrgr/sigma" target="_new"><i class="fa fa-github" aria-hidden="true"></i> Repo</a>
<a class="red-text" href="https://www.biorxiv.org/content/early/2018/08/16/392639.full.pdf" target="_new"><i class="fa fa-file-pdf-o" aria-hidden="true"></i> Preprint PDF</a>
</div>
</li>
<li class="collection-item avatar">
<i class="fa fa-users circle"></i>
<div>
<div><b><a href='https://academic.oup.com/bioinformatics/article-abstract/35/14/i492/5529117' target='_new'>Modeling Clinical and Molecular Covariates of Mutational Process Activity in Cancer</a></b></div>
<div class="light"><b>W Robinson</b>, R Sharan, <b>MDM Leiserson</b></div>
<div><i class="source">ISMB/Bioinformatics</i> (2019)</div>
</div>
<div class="publication-links">
<a class="red-text" href="https://watermark.silverchair.com/btz340.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAnIwggJuBgkqhkiG9w0BBwagggJfMIICWwIBADCCAlQGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQM7O8vSt54Q793rCImAgEQgIICJfEmCEyGlAC8WIQ8xpFDf2zgnK2uTBpfBV1_q3JnzM7zHtULwS_2dqyjKDT_pRQr4-fqVyqEH3266tHaCNDQ9C0aY9huy_2Mss7udLNBiLTv7VDrvh7NNkNQUuDepf5nsdnb3QjsDH1g8apffyakf6-ParfAPWLrklbsXeAbrK93SuG44YiW44t5olYcGrCCYSJwQirIpwG8e2SoEGRUjs1O94eHuwl-3T803iwN9lMY6r4oY3yRxDW0uHYYuDTpe4EPXNPOj1UdpjINFcwNr0ult39y9tb3za6qiqNJpOZbqZlcC6vSv9OvTqTzxF8IoLSDO-iC0_fXkSGmAnqS-urkfKhyYjrnRrXQdVD5K0I5dBIW91M1Ph8Naca04udT49zf03rCo2zFy5iM55Qj2zi-yBnLG-dZniHpDIaDlY50Kbf4tLR3nb4UL4W3KH8QkNYM1eq1LHfb1vWKYs69bRnTVqGkGb-RoNyAXl71PdofNrta4bBMzwORPblAi4OU9LUxRRLwCa2vh6YZzKBwjR_DX_wXTu3fskF0cI6oKvj21wNXQuZgS-zcd6qtnIFmyRK7mqoH6G40cfUShRHNYpLYr5q8_kLpn91ULDBckzqvbHWbQ77ZV2LEQkoSactzQnbMNpXopiCXINoGLaRaUP-CHE1dVY8iIDWY3Eb91-1j8of36KjzeHnHi_4h6aoPKkeObtrxCi9qqf3QHYtsPtzFAyD8jw" target="_new"><i class="fa fa-file-pdf-o" aria-hidden="true"></i> PDF</a>
<a class="purple-text" href="https://github.com/lrgr/tcsm" target="_new"><i class="fa fa-github" aria-hidden="true"></i> Repo</a>
</div>
</li>
<li class="collection-item avatar">
<i class="fa fa-users circle"></i>
<div>
<div><b><a href='https://link.springer.com/chapter/10.1007/978-3-030-17083-7_15' target='_new'>A sticky multinomial mixture model of strand-coordinated mutational processes in cancer</a></b></div>
<div class="light">I Sason, D Wojtowicz, <b>W Robinson</b>, <b>MDM Leiserson</b>, T Przytycka, R Sharan</div>
<div><i class="source">RECOMB</i> (2019)</div>
</div>
</li>
<li class="collection-item avatar">
<i class="fa fa-users circle"></i>
<div>
<div><b><a href='https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkz132/5371270' target='_new'>Functional protein representations from biological networks enable diverse cross-species inference</a></b></div>
<div class="light"><b>J Fan</b>, A Cannistra, I Fried, T Lim, T Schaffner, M Crovella, B Hescott†, <b>MDM Leiserson</b>†.</div>
<div><i class="source">Nucleic Acids Research</i> (2019). Also oral presentation at <i class="source">RECOMB</i> (2018) </div>
</div>
<div class="publication-links">
<a class="red-text" href="https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkz132/28022332/gkz132.pdf" target="_new"><i class="fa fa-file-pdf-o" aria-hidden="true"></i> PDF</a>
<a class="purple-text" href="https://github.com/lrgr/munk" target="_new"><i class="fa fa-github" aria-hidden="true"></i> Repo</a>
<a class="red-text" href="https://www.biorxiv.org/content/biorxiv/early/2018/03/30/229211.full.pdf" target="_new"><i class="fa fa-file-pdf-o" aria-hidden="true"></i> Preprint PDF</a>
</div>
</li>
<li class="collection-item avatar">
<i class="fa fa-users circle"></i>
<div>
<div><b><a href='https://arxiv.org/abs/1812.08769' target='_new'>What are the biases in my word embedding?</a></b></div>
<div class="light">N Swinger, M De-Arteaga, NT Heffernan IV, <b>MDM Leiserson</b>, AT Kalai.</div>
<div><i class="source">AIES</i> (2019)</div>
</div>
<div class="publication-links">
<a class="red-text" href="http://www.aies-conference.com/wp-content/papers/main/AIES-19_paper_253.pdf" target="_new"><i class="fa fa-file-pdf-o" aria-hidden="true"></i> PDF</a>
<a class="red-text" href="https://arxiv.org/pdf/1812.08769" target="_new"><i class="fa fa-file-pdf-o" aria-hidden="true"></i> Preprint PDF</a>
</div>
</li>
<li class="collection-header">
<h4>2018</h4>
</li>
<li class="collection-item avatar">
<i class="fa fa-users circle"></i>
<div>
<div><b><a href='https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0208422' target='_new'>A Multifactorial Model of T Cell Expansion and Durable Clinical Benefit in Response to a PD-L1 Inhibitor</a></b></div>
<div class="light"><b>MDM Leiserson</b>, V Syrgkanis, A Gilson, M Dudik, S Gillett, J Chayes, C Borgs, DF Bajorin, J Rosenberg, S Funt, A Snyder, L Mackey.</div>
<div><i class="source">PLoS ONE</i> (2018)</div>
</div>
<div class="publication-links">
<a class="red-text" href="https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0208422&type=printable" target="_new"><i class="fa fa-file-pdf-o">PDF</i></a>
<a class="purple-text" href="https://github.com/lrgr/multifactorial-immune-response" target="_new"><i class="fa fa-github" aria-hidden="true"></i> Repo</a>
<a class="red-text" href="https://www.biorxiv.org/content/biorxiv/early/2017/12/08/231316.full.pdf" target="_new"><i class="fa fa-file-pdf-o" aria-hidden="true"></i> Preprint PDF</a>
</div>
</li>
<li class="collection-item avatar">
<i class="fa fa-users circle"></i>
<div>
<div><b><a href='https://doi.org/10.1073/pnas.1807256115' target='_new'>Criticality in tumor evolution and clinical outcome</a></b></div>
<div class="light">E Persi, YI Wolf, <b>MDM Leiserson</b>, EV Koonin, E Ruppin.</div>
<div><i class="source">Proceedings of the National Academy of Sciences</i> (2018)</div>
</div>
<div class="publication-links">
<a class="red-text" href="https://www.pnas.org/content/pnas/115/47/E11101.full.pdf" target="_new"><i class="fa fa-file-pdf-o">PDF</i></a>
<a class="red-text" href="https://www.biorxiv.org/content/early/2018/05/03/314021" target="_new"><i class="fa fa-file-pdf-o" aria-hidden="true"></i> Preprint PDF</a>
</div>
</li>
<li class="collection-item avatar">
<i class="fa fa-users circle"></i>
<div>
<div><b><a href='https://academic.oup.com/bioinformatics/article/34/17/i972/5093236?' target='_new'>Hierarchical HotNet: identifying hierarchies of altered subnetworks</a></b></div>
<div class="light">M Reyna, <b>MDM Leiserson</b>, BJ Raphael.</div>
<div><i class="source">Bioinformatics/ECCB</i> (2018)</div>
</div>
<div class="publication-links">
<a class="red-text" href="https://watermark.silverchair.com/bty613.pdf" target="_new"><i class="fa fa-file-pdf-o" aria-hidden="true"></i> PDF</a>
<a class="purple-text" href="https://github.com/raphael-group/hierarchical-hotnet" target="_new"><i class="fa fa-github" aria-hidden="true"></i> Repo</a>
</div>
</li>
<li class="collection-item avatar">
<i class="fa fa-users circle"></i>
<div>
<div><b><a href='http://cancerdiscovery.aacrjournals.org/content/early/2018/03/06/2159-8290.CD-17-1327' target='_new'>Genetic mechanisms of immune evasion in colorectal cancer</a></b></div>
<div class="light">C Grasso, M Giannakis, DK Wells, T Hamada, XJ Mu, et al.</div>
<div><i class="source">Cancer Discovery</i> (2018)</div>
</div>
<div class="publication-links">
<a class="red-text" href="http://cancerdiscovery.aacrjournals.org/content/early/2018/03/06/2159-8290.CD-17-1327.full-text.pdf" target="_new"><i class="fa fa-file-pdf-o" aria-hidden="true"></i> PDF</a>
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<div><b><a href='http://www.cell.com/cancer-cell/fulltext/S1535-6108(18)30003-5' target='_new'>The Integrated Genomic Landscape of Thymic Epithelial Tumors</a></b></div>
<div class="light">M Radovich, CR Pickering, I Felau, G Ha, H Zhang, et al.</div>
<div><i class="source">Cancer Cell</i> (2018)</div>
</div>
<div class="publication-links">
<a class="red-text" href="http://www.cell.com/cancer-cell/pdf/S1535-6108(18)30003-5.pdf" target="_new"><i class="fa fa-file-pdf-o" aria-hidden="true"></i> PDF</a>
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<div>
<div><b><a href='http://proceedings.mlr.press/v81/dwork18a.html' target='_new'>Decoupled Classifiers for Group-Fair and Efficient Machine Learning</a></b></div>
<div class="light">C Dwork, N Immorlica, A Kalai, <b>MDM Leiserson</b> (A).</div>
<div><i class="source">Proceedings of the 1st Conference on Fairness, Accountability and Transparency</i> (2018)</div>
</div>
<div class="publication-links">
<a class="red-text" href="http://proceedings.mlr.press/v81/dwork18a/dwork18a.pdf" target="_new"><i class="fa fa-file-pdf-o" aria-hidden="true"></i> PDF</a>
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<a class="red-text" href="https://arxiv.org/abs/1707.06613" target="_new"><i class="fa fa-file-pdf-o" aria-hidden="true"></i> Preprint PDF</a>
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<h4>2017</h4>
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<div><b><a href='http://www.cell.com/cancer-cell/abstract/S1535-6108%2817%2930299-4' target='_new'>Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma</a></b></div>
<div class="light">The Cancer Genome Atlas Research Network</div>
<div><i class="source">Cancer Cell</i> (2017)</div>
</div>
<div class="publication-links">
<a class="red-text" href="http://www.cell.com/cancer-cell/pdfExtended/S1535-6108(17)30299-4" target="_new"><i class="fa fa-file-pdf-o" aria-hidden="true"></i> PDF</a>
<a class="blue-text" href="{{ site.base_url }}/assets/files/bibtek/wext.bib" target="_new"><i class="fa fa-file-text" aria-hidden="true"></i> BibTek</a>
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<div><b><a href='http://www.cell.com/trends/molecular-medicine/fulltext/S1471-4914(17)30143-0' target='_new'>Precision oncology: the road ahead</a></b></div>
<div class="light">D Senft, <b>MDM Leiserson</b>, E Ruppin, ZA Ronai</div>
<div><i class="source">Trends in Molecular Medicine</i> (2017)</div>
</div>
<div class="publication-links">
<a class="red-text" href="http://www.cell.com/trends/molecular-medicine/pdf/S1471-4914(17)30143-0.pdf" target="_new"><i class="fa fa-file-pdf-o" aria-hidden="true"></i> PDF</a>
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<h4>2016</h4>
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<div><b><a href='https://academic.oup.com/bioinformatics/article/32/17/i736/2450792' target='_new'>A weighted exact test for mutually exclusive mutations in cancer</a></b></div>
<div class="light"><b>MDM Leiserson</b>, MA Reyna, BJ Raphael.</div>
<div><i class="source">Bioinformatics/ISMB</i> (2016)</div>
</div>
<div class="publication-links">
<a class="red-text" href="https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/bioinformatics/32/17/10.1093_bioinformatics_btw462/2/btw462.pdf?Expires=1495041968&Signature=cCHUHP98zMloh82sXvKBw42gUIR76c~erDIjAqk-kiYQ0r6MRsGLPtnQNrn8sEURHqv0fT1T7SIewrIOvXQCSsMrMXTgerljHu~pLMh0XqXeKnunSRR-f4x30Jo0ylojR-VgMSjCtCGrheaV~SrACx9Pb6UGk4X17z0sffREH6LF4EL4gTrqY0NNhNQrWqHbuHyq3d-MLCU~BqgjYEWErWvs4Jeyqq3S-LYWMyLjyZld2atuyGsX443380FPqgLr4Pzz3lqTYCU866ysZmxapsSO9me3xBpSeqy5HabWvUTrRvOav491hs7d9HHdmPiR10F4pDeAq21TiZ8KrEcGwA__&Key-Pair-Id=APKAIUCZBIA4LVPAVW3Q" target="_new"><i class="fa fa-file-pdf-o" aria-hidden="true"></i> PDF</a>
<a class="orange-text" href="http://compbio.cs.brown.edu/projects/wext/" target="_new"><i class="fa fa-window-maximize"></i> Website</a>
<a class="purple-text" href="https://github.com/raphael-group/wext" target="_new"><i class="fa fa-github" aria-hidden="true"></i> Repo</a>
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<h4>2015</h4>
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<div><b><a href='http://www.nature.com/ncomms/2015/151209/ncomms10086/full/ncomms10086.html' target='_new'>Patterns and functional implications of rare germline variants across 12 cancer types</a></b></div>
<div class="light">C Lu*, M Xie*, MC Wendl*, J Wang*, MD McLellan*, <b>MDM Leiserson</b>*, K Huang, MA Wyczalkowski, R Jayasinghe, T Banerjee, J Ning, P Tripathi, Q Zhang, B Niu, K Ye, HK Schmidt, RS Fulton, JF McMichael, P Batra, C Kandoth, M Bharadwaj, DC Koboldt, CA Miller, KL Kanchi, JM Eldred, DE Larson, JS Welch, M You, BA Ozenberger, R Govindan, MJ Walter, MJ Ellis, ER Mardis, TA Graubert, JF Dipersio, TJ Ley, RK Wilson, PJ Goodfellow, BJ Raphael, F Chen, KJ Johnson, JD Parvin, L Ding</div>
<div><i class="source">Nature Communications</i> (2015)</div>
</div>
<div class="publication-links">
<a class="red-text" href="http://rdcu.be/fKv6" target="_new"><i class="fa fa-file-pdf-o" aria-hidden="true"></i> PDF</a>
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<div><b><a href='http://www.nejm.org/doi/full/10.1056/NEJMoa1505917#t=article' target='_new'>Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma</a></b></div>
<div class="light">The Cancer Genome Atlas Research Network</div>
<div><i class="source">New England Journal of Medicine</i> (2015)</div>
</div>
<div class="publication-links">
<a class="red-text" href="http://www.nejm.org/doi/pdf/10.1056/NEJMoa1505917" target="_new"><i class="fa fa-file-pdf-o" aria-hidden="true"></i> PDF</a>
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<div><b><a href='http://www.cambridge.org/us/academic/subjects/statistics-probability/statistics-life-sciences-medicine-and-health/integrating-omics-data' target='_new'>Integrating Omics Data: Analyzing combinations of somatic mutations in cancer genomes</a></b></div>
<div class="light"><b>MDM Leiserson</b>, BJ Raphael</div>
<div><i class="source">Cambridge University Press (eds: G.C. Teng, D. Ghosh, X.J. Zhou)</i> (2015) [Book chapter]</div>
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<div><b><a href='http://www.genomebiology.com/2015/16/1/160' target='_new'>CoMEt: A Statistical Approach to Identify Combinations of Mutually Exclusive Alterations in Cancer</a></b></div>
<div class="light"><b>MDM. Leiserson</b>*, HT Wu*, F Vandin, BJ Raphael</div>
<div><i class="source">Genome Biology</i> (2015)</div>
</div>
<div class="publication-links">
<a class="red-text" href="http://www.genomebiology.com/content/pdf/s13059-015-0700-7.pdf" target="_new"><i class="fa fa-file-pdf-o" aria-hidden="true"></i> PDF</a>
<a class="orange-text" href="http://compbio-research.cs.brown.edu/comet" target="_new"><i class="fa fa-window-maximize"></i> Website</a>
<a class="purple-text" href="https://github.com/raphael-group/comet" target="_new"><i class="fa fa-github" aria-hidden="true"></i> Repo</a>
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<a class="green-text" href="http://arxiv.org/abs/1503.08224" target="_new"><i class="fa fa-external-link" aria-hidden="true"></i> Preprint</a>
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<div><b><a href='http://www.nature.com/nmeth/journal/v12/n6/full/nmeth.3412.html' target='_new'>MAGI: visualization and collaborative annotation of genomic aberrations</a></b></div>
<div class="light"><b>MDM Leiserson</b>, CC Gramazio, J Hu, HT Wu, DH Laidlaw, BJ Raphael</div>
<div><i class="source">Nature Methods</i> (2015)</div>
</div>
<div class="publication-links">
<a class="red-text" href="http://rdcu.be/cYaG" target="_new"><i class="fa fa-file-pdf-o" aria-hidden="true"></i> PDF</a>
<a class="orange-text" href="http://magi.brown.edu" target="_new"><i class="fa fa-window-maximize"></i> Website</a>
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<div><b><a href='http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3168.html' target='_new'>Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes</a></b></div>
<div class="light"><b>MDM Leiserson</b>*, F Vandin*, HT Wu, JR Dobson, JV Eldridge, JL Thomas, A Papoutsaki, Y Kim, B Niu, M McLellan, MS Lawrence, A Gonzalez-Perez, D Tamborero, Y Cheng, GA Ryslik, N Lopez-Bigas, G Getz, L Ding, BJ Raphael</div>
<div><i class="source">Nature Genetics</i> (2015)</div>
</div>
<div class="publication-links">
<a class="red-text" href="http://rdcu.be/bOYh" target="_new"><i class="fa fa-file-pdf-o" aria-hidden="true"></i> PDF</a>
<a class="orange-text" href="http://compbio.cs.brown.edu/projects/hotnet/" target="_new"><i class="fa fa-window-maximize"></i> Website</a>
<a class="purple-text" href="https://github.com/raphael-group/hotnet2" target="_new"><i class="fa fa-github" aria-hidden="true"></i> Repo</a>
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<h4>2014</h4>
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<div><b><a href='http://www.cell.com/cell/abstract/S0092-8674(14)00876-9' target='_new'>Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin</a></b></div>
<div class="light">KA Hoadley, C Yau, DM Wolf, AD Cherniack, D Tamborero, S Ng, <b>MDM Leiserson</b>, B Niu, MD McLellan, V Uzunangelov, J Zhang, C Kandoth, R Akbani, H Shen, L Omberg, A Chu, AA Margolin, LJ van’t Veer, N Lopez-Bigas, PW Laird, BJ Raphael, L Ding, AG Robertson, LA Byers, GB Mills, JN Weinstein, C Van Waes, Z Chen, EA Collisson, TCGA Research Network, CC Benze, CM Peroue, JM Stuart</div>
<div><i class="source">Cell</i> (2014)</div>
</div>
<div class="publication-links">
<a class="red-text" href="http://www.cell.com/cell/pdf/S0092-8674(14)00876-9.pdf" target="_new"><i class="fa fa-file-pdf-o" aria-hidden="true"></i> PDF</a>
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<div><b><a href='http://www.nature.com/nature/journal/v513/n7517/full/nature13480.html' target='_new'>Comprehensive molecular characterization of gastric adenocarcinoma</a></b></div>
<div class="light">The Cancer Genome Atlas Research Network</div>
<div><i class="source">Nature</i> (2014)</div>
</div>
<div class="publication-links">
<a class="red-text" href="http://rdcu.be/r2pA" target="_new"><i class="fa fa-file-pdf-o" aria-hidden="true"></i> PDF</a>
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<div><b><a href='http://www.nature.com/ncomms/2014/140122/ncomms4156/full/ncomms4156.html' target='_new'>Integrated analysis of germline and somatic variants in ovarian cancer</a></b></div>
<div class="light">KL Kanchi, KJ Johnson, C Lu, MD McLellan, <b>MDM Leiserson</b>, MC Wendl, Q Zhang, DC Koboldt, M Xie, C Kandoth, JF McMichael, MA Wyczalkowski, DE Larson, HK Schmidt, CA Miller, RS Fulton, PT Spellman, ER Mardis, TE Druley, TA Graubert, PJ Goodfellow, BJ Raphael, R K Wilson, L Ding</div>
<div><i class="source">Nature Communications</i> (2014)</div>
</div>
<div class="publication-links">
<a class="red-text" href="http://rdcu.be/r2pG" target="_new"><i class="fa fa-file-pdf-o" aria-hidden="true"></i> PDF</a>
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<h4>2013</h4>
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<div>
<div><b><a href='http://www.sciencedirect.com/science/article/pii/S0959437X13001354' target='_new'>Network analysis of GWAS data</a></b></div>
<div class="light"><b>MDM Leiserson</b>, JV Eldridge, S Ramachandran, BJ Raphael</div>
<div><i class="source">Current Opinion in Genetics & Development</i> (2013)</div>
</div>
<div class="publication-links">
<a class="red-text" href="http://ac.els-cdn.com/S0959437X13001354/1-s2.0-S0959437X13001354-main.pdf?_tid=d320da4e-5b66-11e3-9f0a-00000aacb361&acdnat=1385998473_4bc4eccdd09fdf8108bc2e3004c36b9d" target="_new"><i class="fa fa-file-pdf-o" aria-hidden="true"></i> PDF</a>
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<div><b><a href='http://www.nature.com/nature/journal/v502/n7471/full/nature12634.html' target='_new'>Mutational landscape and significance across 12 major cancer types</a></b></div>
<div class="light">C Kandoth, MD McLellan, F Vandin, K Ye, B Niu, C Lu, M Xie, Q Zhang, JF McMichael, MA Wyczalkowski, <b>MDM Leiserson</b>, CA Miller, JS Welch, MJ Walter, MC Wendl, TJ Ley, RK Wilson, BJ Raphael, L Ding</div>
<div><i class="source">Nature</i> (2013)</div>
</div>
<div class="publication-links">
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<div><b><a href='http://www.nature.com/ng/journal/v45/n10/full/ng.2764.html' target='_new'>The Cancer Genome Atlas Pan-Cancer analysis project</a></b></div>
<div class="light">The Cancer Genome Atlas Research Network, JN Weinstein, EA Collisson, GB Mills, KR Mills Shaw, BA Ozenberger, K Ellrott, I Shmulevich, C Sander, JM Stuart</div>
<div><i class="source">Nature Genetics</i> (2013)</div>
</div>
<div class="publication-links">
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<div><b><a href='http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003054' target='_new'>Simultaneous Identification of Multiple Driver Pathways in Cancer</a></b></div>
<div class="light"><b>MDM Leiserson</b>, D Blokh, R Sharan†, BJ Raphael†</div>
<div><i class="source">PLoS Computational Biology</i> (2013)</div>
</div>
<div class="publication-links">
<a class="red-text" href="http://www.ploscompbiol.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pcbi.1003054&representation=PDF" target="_new"><i class="fa fa-file-pdf-o" aria-hidden="true"></i> PDF</a>
<a class="orange-text" href="http://compbio.cs.brown.edu/projects/multi-dendrix" target="_new"><i class="fa fa-window-maximize"></i> Website</a>
<a class="purple-text" href="http://mdml.github.io/multi-dendrix" target="_new"><i class="fa fa-github" aria-hidden="true"></i> Repo</a>
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<div><b><a href='http://www.nejm.org/doi/full/10.1056/NEJMoa1301689#t=articleTop' target='_new'>Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia</a></b></div>
<div class="light">The Cancer Genome Atlas Research Network</div>
<div><i class="source">New England Journal of Medicine</i> (2013)</div>
</div>
<div class="publication-links">
<a class="red-text" href="http://www.nejm.org/doi/pdf/10.1056/NEJMoa1301689" target="_new"><i class="fa fa-file-pdf-o" aria-hidden="true"></i> PDF</a>
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<div><b><a href='http://www.biomedcentral.com/1471-2105/14/23' target='_new'>Genecentric: a package to uncover graph-theoretic structure in high-throughput epistasis data</a></b></div>
<div class="light">A Gallant, <b>MDM Leiserson</b>, M Kachalov, L Cowen, B Hescott</div>
<div><i class="source">BMC Bioinformatics</i> (2013)</div>
</div>
<div class="publication-links">
<a class="red-text" href="http://www.biomedcentral.com/content/pdf/1471-2105-14-23.pdf" target="_new"><i class="fa fa-file-pdf-o" aria-hidden="true"></i> PDF</a>
<a class="purple-text" href="http://bcb.cs.tufts.edu/genecentric/" target="_new"><i class="fa fa-github" aria-hidden="true"></i> Repo</a>
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<h4>2011</h4>
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<div><b><a href='http://online.liebertpub.com/doi/abs/10.1089/cmb.2011.0191' target='_new'>Inferring Mechanisms of Compensation from E-MAP and SGA Data Using Local Search Algorithms for Max Cut</a></b></div>
<div class="light"><b>MDM Leiserson</b>, D Tatar, L Cowen, B Hescott</div>
<div><i class="source">Journal of Computational Biology/RECOMB</i> (2011)</div>
</div>
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<a class="red-text" href="http://online.liebertpub.com/doi/pdfplus/10.1089/cmb.2011.0191" target="_new"><i class="fa fa-file-pdf-o" aria-hidden="true"></i> PDF</a>
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<h4>2009</h4>
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<div><b><a href='http://online.liebertpub.com/doi/abs/10.1089/cmb.2009.0178' target='_new'>Evaluating Between-Pathway Models with Expression Data</a></b></div>
<div class="light">B Hescott, <b>MDM Leiserson</b>, D Slonim, L Cowen</div>
<div><i class="source">Journal of Computational Biology/RECOMB</i> (2009)</div>
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