Publications | The Su Lab

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src="/images/logo.png" alt="logo"> </span> </a> <input class="nav-toggle" type="checkbox" aria-label="show/hide nav"> <nav> <a href="/projects/" data-tooltip="Projects in the lab"> Projects </a> <a href="/pubs/" data-tooltip="Published works"> Publications </a> <a href="/team/" data-tooltip="Meet the team"> Team </a> <a href="/conduct/" data-tooltip="Code of Conduct"> Code of Conduct </a> <a href="/contact/" data-tooltip="Contact information"> Contact </a> </nav> </header> <main>  <section class="background" data-size="page"> <h1 id="publications"> <i class="icon fa-regular fa-newspaper"></i>Publications</h1> <center>  <img src="../images/wordcloud.png" alt="A word cloud of publication titles" style="width:600px"> </center> <div class="search-box"> <input type="text" class="search-input" oninput="onSearchInput(this)" placeholder="Search items on this page"> <button disabled data-tooltip="Clear search" aria-label="clear search" onclick="onSearchClear()"> <i class="icon fa-solid fa-magnifying-glass"></i> </button> </div> <div class="search-info"></div> <h3 id="2024">2024</h3> <div class="citation-container"> <div class="citation"> <a href="https://doi.org/gtr8pk" class="citation-image" aria-label="Repositioning the Early Pathology of Type 1 Diabetes to the Extraislet Vasculature"> <img src="/images/m_ji2300769f2.png" alt="Repositioning the Early Pathology of Type 1 Diabetes to the Extraislet Vasculature" loading="lazy" onerror="this.src = '/images/fallback.svg'; this.onerror = null;"> </a> <div class="citation-text"> <a href="https://doi.org/gtr8pk" class="citation-title"> Repositioning the Early Pathology of Type 1 Diabetes to the Extraislet Vasculature </a> <div class="citation-authors" data-tooltip="Anne Costanzo, Don Clarke, Marie Holt, Siddhartha Sharma, Kenna Nagy, Xuqian Tan, Lisa Kain, Brian Abe, Sandrine Luce, Christian Boitard, Tine Wyseure, Laurent O Mosnier, Andrew I Su, Catherine Grimes, M G Finn, Paul B Savage, Michael Gottschalk, Jeremy Pettus, Luc Teyton " tabindex="0"> Anne Costanzo, Don Clarke, Marie Holt, Siddhartha Sharma, Kenna Nagy, …, M G Finn, Paul B Savage, Michael Gottschalk, Jeremy Pettus, Luc Teyton </div> <div class="citation-details"> <span class="citation-publisher">The Journal of Immunology</span> · <span class="citation-date">01 Mar 2024</span> · <span class="citation-id">doi:10.4049/jimmunol.2300769</span> · <span class="citation-pmid"> PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/38426888">38426888</a> </span> · <span class="citation-pmcid"> PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10944819">PMC10944819</a> </span> </div> <div class="citation-buttons"> <div class="button-wrapper"> <a class="button" href="/pdf/Costanzo_2024.pdf" data-tooltip="PDF" data-style="bare" aria-label="PDF"> <i class="icon fa-solid fa-newspaper"></i> <span>PDF</span> </a> </div> </div> </div> </div> </div> <div class="citation-container"> <div class="citation"> <a href="https://doi.org/g587fp" class="citation-image" aria-label="Perspectives on tracking data reuse across biodata resources"> <img src="" alt="Perspectives on tracking data reuse across biodata resources" loading="lazy" onerror="this.src = '/images/fallback.svg'; this.onerror = null;"> </a> <div class="citation-text"> <a href="https://doi.org/g587fp" class="citation-title"> Perspectives on tracking data reuse across biodata resources </a> <div class="citation-authors" data-tooltip="Karen E Ross, Frederic B Bastian, Matt Buys, Charles E Cook, Peter D’Eustachio, Melissa Harrison, Henning Hermjakob, Donghui Li, Phillip Lord, Darren A Natale, Bjoern Peters, Paul W Sternberg, Andrew I Su, Matthew Thakur, Paul D Thomas, Alex Bateman, Alex Bateman, Maria-Jesus Martin, Sandra Orchard, Michele Magrane, Shadab Ahmad, Emily H Bowler-Barnett, Hema Bye-A-Jee, Paul Denny, Tunca Dogan, ThankGod Ebenezer, Jun Fan, Leonardo Jose da Costa Gonzales, Abdulrahman Hussein, Alexandr Ignatchenko, Giuseppe Insana, Rizwan Ishtiaq, Vishal Joshi, Dushyanth Jyothi, Swaathi Kandasaamy, Antonia Lock, Aurelien Luciani, Jie Luo, Yvonne Lussi, Pedro Raposo, Daniel L Rice, Rabie Saidi, Rafael Santos, Elena Speretta, James Stephenson, Prabhat Totoo, Nidhi Tyagi, Preethi Vasudev, Kate Warner, Rossana Zaru, Supun Wijerathne, Khawaja Talal Ibrahim, Minjoon Kim, Juan Marin, Alan J Bridge, Lucila Aimo, Ghislaine Argoud-Puy, Andrea H Auchincloss, Kristian B Axelsen, Parit Bansal, Delphine Baratin, Teresa M Batista Neto, Jerven T Bolleman, Emmanuel Boutet, Lionel Breuza, Blanca Cabrera Gil, Cristina Casals-Casas, Elisabeth Coudert, Beatrice Cuche, Edouard de Castro, Anne Estreicher, Maria L Famiglietti, Marc Feuermann, Elisabeth Gasteiger, Sebastien Gehant, Arnaud Gos, Nadine Gruaz, Chantal Hulo, Nevila Hyka-Nouspikel, Florence Jungo, Arnaud Kerhornou, Philippe Le Mercier, Damien Lieberherr, Patrick Masson, Anne Morgat, Ivo Pedruzzi, Sandrine Pilbout, Lucille Pourcel, Sylvain Poux, Monica Pozzato, Manuela Pruess, Nicole Redaschi, Catherine Rivoire, Christian J A Sigrist, Shyamala Sundaram, Anastasia Sveshnikova, Cathy H Wu, Cecilia N Arighi, Chuming Chen, Yongxing Chen, Hongzhan Huang, Kati Laiho, Minna Lehvaslaiho, Peter McGarvey, Darren A Natale, Karen Ross, C R Vinayaka, Yuqi Wang, Jian Zhang " tabindex="0"> Karen E Ross, Frederic B Bastian, Matt Buys, Charles E Cook, Peter D’Eustachio, …, Darren A Natale, Karen Ross, C R Vinayaka, Yuqi Wang, Jian Zhang </div> <div class="citation-details"> <span class="citation-publisher">Bioinformatics Advances</span> · <span class="citation-date">01 Jan 2024</span> · <span class="citation-id">doi:10.1093/bioadv/vbae057</span> · <span class="citation-pmid"> PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/38721398">38721398</a> </span> · <span class="citation-pmcid"> PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11076920">PMC11076920</a> </span> </div> </div> </div> </div> <h3 id="2023">2023</h3> <div class="citation-container"> <div class="citation"> <a href="https://doi.org/gtrg2b" class="citation-image" aria-label="DrugMechDB: A Curated Database of Drug Mechanisms"> <img src="https://media.springernature.com/full/springer-static/image/art%3A10.1038%2Fs41597-023-02534-z/MediaObjects/41597_2023_2534_Fig1_HTML.png" alt="DrugMechDB: A Curated Database of Drug Mechanisms" loading="lazy" onerror="this.src = '/images/fallback.svg'; this.onerror = null;"> </a> <div class="citation-text"> <a href="https://doi.org/gtrg2b" class="citation-title"> DrugMechDB: A Curated Database of Drug Mechanisms </a> <div class="citation-authors" tabindex="0"> Adriana Carolina Gonzalez-Cavazos, Anna Tanska, Michael Mayers, Denise Carvalho-Silva, Brindha Sridharan, Patrick A. Rewers, Umasri Sankarlal, Lakshmanan Jagannathan, Andrew I. Su </div> <div class="citation-details"> <span class="citation-publisher">Scientific Data</span> · <span class="citation-date">16 Sep 2023</span> · <span class="citation-id">doi:10.1038/s41597-023-02534-z</span> · <span class="citation-pmid"> PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/37717042">37717042</a> </span> · <span class="citation-pmcid"> PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10505144">PMC10505144</a> </span> </div> <div class="citation-buttons"> <div class="button-wrapper"> <a class="button" href="/pdf/Gonzalez-Cavazos_2023b.pdf" data-tooltip="PDF" data-style="bare" aria-label="PDF"> <i class="icon fa-solid fa-newspaper"></i> <span>PDF</span> </a> </div> </div> </div> </div> </div> <div class="citation-container"> <div class="citation"> <a href="https://doi.org/gtrg2c" class="citation-image" aria-label="BioThings Explorer: a query engine for a federated knowledge graph of biomedical APIs"> <img src="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11015316/bin/btad570f1.jpg" alt="BioThings Explorer: a query engine for a federated knowledge graph of biomedical APIs" loading="lazy" onerror="this.src = '/images/fallback.svg'; this.onerror = null;"> </a> <div class="citation-text"> <a href="https://doi.org/gtrg2c" class="citation-title"> BioThings Explorer: a query engine for a federated knowledge graph of biomedical APIs </a> <div class="citation-authors" data-tooltip="Jackson Callaghan, Colleen H Xu, Jiwen Xin, Marco Alvarado Cano, Anders Riutta, Eric Zhou, Rohan Juneja, Yao Yao, Madhumita Narayan, Kristina Hanspers, Ayushi Agrawal, Alexander R Pico, Chunlei Wu, Andrew I Su " tabindex="0"> Jackson Callaghan, Colleen H Xu, Jiwen Xin, Marco Alvarado Cano, Anders Riutta, …, Kristina Hanspers, Ayushi Agrawal, Alexander R Pico, Chunlei Wu, Andrew I Su </div> <div class="citation-details"> <span class="citation-publisher">Bioinformatics</span> · <span class="citation-date">01 Sep 2023</span> · <span class="citation-id">doi:10.1093/bioinformatics/btad570</span> · <span class="citation-pmid"> PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/37707514">37707514</a> </span> · <span class="citation-pmcid"> PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11015316">PMC11015316</a> </span> </div> <div class="citation-buttons"> <div class="button-wrapper"> <a class="button" href="/pdf/Callaghan_2023.pdf" data-tooltip="PDF" data-style="bare" aria-label="PDF"> <i class="icon fa-solid fa-newspaper"></i> <span>PDF</span> </a> </div> </div> </div> </div> </div> <div class="citation-container"> <div class="citation"> <a href="https://doi.org/gtr8pn" class="citation-image" aria-label="Association study between drug prescriptions and Alzheimer’s disease claims in a commercial insurance database"> <img src="https://media.springernature.com/full/springer-static/image/art%3A10.1186%2Fs13195-023-01255-0/MediaObjects/13195_2023_1255_Fig3_HTML.png?as=webp" alt="Association study between drug prescriptions and Alzheimer’s disease claims in a commercial insurance database" loading="lazy" onerror="this.src = '/images/fallback.svg'; this.onerror = null;"> </a> <div class="citation-text"> <a href="https://doi.org/gtr8pn" class="citation-title"> Association study between drug prescriptions and Alzheimer’s disease claims in a commercial insurance database </a> <div class="citation-authors" tabindex="0"> Eric Hu, Tong Shu Li, Nathan E. Wineinger, Andrew I. Su </div> <div class="citation-details"> <span class="citation-publisher">Alzheimer's Research & Therapy</span> · <span class="citation-date">24 Jun 2023</span> · <span class="citation-id">doi:10.1186/s13195-023-01255-0</span> · <span class="citation-pmid"> PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/37355615">37355615</a> </span> · <span class="citation-pmcid"> PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10290352">PMC10290352</a> </span> </div> <div class="citation-buttons"> <div class="button-wrapper"> <a class="button" href="/pdf/Hu_2023.pdf" data-tooltip="PDF" data-style="bare" aria-label="PDF"> <i class="icon fa-solid fa-newspaper"></i> <span>PDF</span> </a> </div> </div> </div> </div> </div> <div class="citation-container"> <div class="citation"> <a href="https://doi.org/gtrg2d" class="citation-image" aria-label="Drug Repurposing using consilience of Knowledge Graph Completion methods"> <img src="https://www.biorxiv.org/content/biorxiv/early/2023/12/20/2023.05.12.540594/F1.large.jpg" alt="Drug Repurposing using consilience of Knowledge Graph Completion methods" loading="lazy" onerror="this.src = '/images/fallback.svg'; this.onerror = null;"> </a> <div class="citation-text"> <a href="https://doi.org/gtrg2d" class="citation-title"> Drug Repurposing using consilience of Knowledge Graph Completion methods </a> <div class="citation-authors" tabindex="0"> Roger Tu, Meghamala Sinha, Carolina González, Eric Hu, Shehzaad Dhuliawala, Andrew McCallum, Andrew I. Su </div> <div class="citation-details"> <span class="citation-publisher">Cold Spring Harbor Laboratory</span> · <span class="citation-date">14 May 2023</span> · <span class="citation-id">doi:10.1101/2023.05.12.540594</span> · <span class="citation-pmid"> PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/39149283">39149283</a> </span> · <span class="citation-pmcid"> PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11326126">PMC11326126</a> </span> </div> <div class="citation-buttons"> <div class="button-wrapper"> <a class="button" href="/pdf/Tu_2023.pdf" data-tooltip="PDF" data-style="bare" aria-label="PDF"> <i class="icon fa-solid fa-newspaper"></i> <span>PDF</span> </a> </div> </div> </div> </div> </div> <div class="citation-container"> <div class="citation"> <a href="https://doi.org/gr9ccd" class="citation-image" aria-label="Schema Playground: a tool for authoring, extending, and using metadata schemas to improve FAIRness of biomedical data"> <img src="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10116472/bin/12859_2023_5258_Fig1_HTML.jpg" alt="Schema Playground: a tool for authoring, extending, and using metadata schemas to improve FAIRness of biomedical data" loading="lazy" onerror="this.src = '/images/fallback.svg'; this.onerror = null;"> </a> <div class="citation-text"> <a href="https://doi.org/gr9ccd" class="citation-title"> Schema Playground: a tool for authoring, extending, and using metadata schemas to improve FAIRness of biomedical data </a> <div class="citation-authors" tabindex="0"> Marco A. Cano, Ginger Tsueng, Xinghua Zhou, Jiwen Xin, Laura D. Hughes, Julia L. Mullen, Andrew I. Su, Chunlei Wu </div> <div class="citation-details"> <span class="citation-publisher">BMC Bioinformatics</span> · <span class="citation-date">20 Apr 2023</span> · <span class="citation-id">doi:10.1186/s12859-023-05258-4</span> · <span class="citation-pmid"> PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/37081398">37081398</a> </span> · <span class="citation-pmcid"> PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10116472">PMC10116472</a> </span> </div> <div class="citation-buttons"> <div class="button-wrapper"> <a class="button" href="/pdf/Cano_2023.pdf" data-tooltip="PDF" data-style="bare" aria-label="PDF"> <i class="icon fa-solid fa-newspaper"></i> <span>PDF</span> </a> </div> </div> </div> </div> </div> <div class="citation-container"> <div class="citation"> <a href="https://doi.org/gr9gvs" class="citation-image" aria-label="Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations"> <img src="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10399614/bin/nihms-1918406-f0001.jpg" alt="Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations" loading="lazy" onerror="this.src = '/images/fallback.svg'; this.onerror = null;"> </a> <div class="citation-text"> <a href="https://doi.org/gr9gvs" class="citation-title"> Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations </a> <div class="citation-authors" data-tooltip="Karthik Gangavarapu, Alaa Abdel Latif, Julia L. Mullen, Manar Alkuzweny, Emory Hufbauer, Ginger Tsueng, Emily Haag, Mark Zeller, Christine M. Aceves, Karina Zaiets, Marco Cano, Xinghua Zhou, Zhongchao Qian, Rachel Sattler, Nathaniel L. Matteson, Joshua I. Levy, Raphael T. C. Lee, Lucas Freitas, Sebastian Maurer-Stroh, Marc A. Suchard, Chunlei Wu, Andrew I. Su, Kristian G. Andersen, Laura D. Hughes " tabindex="0"> Karthik Gangavarapu, Alaa Abdel Latif, Julia L. Mullen, Manar Alkuzweny, Emory Hufbauer, …, Marc A. Suchard, Chunlei Wu, Andrew I. Su, Kristian G. Andersen, Laura D. Hughes </div> <div class="citation-details"> <span class="citation-publisher">Nature Methods</span> · <span class="citation-date">23 Feb 2023</span> · <span class="citation-id">doi:10.1038/s41592-023-01769-3</span> · <span class="citation-pmid"> PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/36823332">36823332</a> </span> · <span class="citation-pmcid"> PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10399614">PMC10399614</a> </span> </div> <div class="citation-buttons"> <div class="button-wrapper"> <a class="button" href="/pdf/Gangavarapu_2023.pdf" data-tooltip="PDF" data-style="bare" aria-label="PDF"> <i class="icon fa-solid fa-newspaper"></i> <span>PDF</span> </a> </div> </div> </div> </div> </div> <div class="citation-container"> <div class="citation"> <a href="https://doi.org/gtr8pr" class="citation-image" aria-label="Outbreak.info Research Library: a standardized, searchable platform to discover and explore COVID-19 resources"> <img src="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8820656/bin/nihpp-2022.01.20.477133v5-f0004.jpg" alt="Outbreak.info Research Library: a standardized, searchable platform to discover and explore COVID-19 resources" loading="lazy" onerror="this.src = '/images/fallback.svg'; this.onerror = null;"> </a> <div class="citation-text"> <a href="https://doi.org/gtr8pr" class="citation-title"> Outbreak.info Research Library: a standardized, searchable platform to discover and explore COVID-19 resources </a> <div class="citation-authors" data-tooltip="Ginger Tsueng, Julia L. Mullen, Manar Alkuzweny, Marco Cano, Benjamin Rush, Emily Haag, Jason Lin, Dylan J. Welzel, Xinghua Zhou, Zhongchao Qian, Alaa Abdel Latif, Emory Hufbauer, Mark Zeller, Kristian G. Andersen, Chunlei Wu, Andrew I. Su, Karthik Gangavarapu, Laura D. Hughes " tabindex="0"> Ginger Tsueng, Julia L. Mullen, Manar Alkuzweny, Marco Cano, Benjamin Rush, …, Kristian G. Andersen, Chunlei Wu, Andrew I. Su, Karthik Gangavarapu, Laura D. Hughes </div> <div class="citation-details"> <span class="citation-publisher">Nature Methods</span> · <span class="citation-date">23 Feb 2023</span> · <span class="citation-id">doi:10.1038/s41592-023-01770-w</span> · <span class="citation-pmid"> PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/36823331">36823331</a> </span> · <span class="citation-pmcid"> PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10393269">PMC10393269</a> </span> </div> <div class="citation-buttons"> <div class="button-wrapper"> <a class="button" href="/pdf/Tsueng_2023c.pdf" data-tooltip="PDF" data-style="bare" aria-label="PDF"> <i class="icon fa-solid fa-newspaper"></i> <span>PDF</span> </a> </div> </div> </div> </div> </div> <div class="citation-container"> <div class="citation"> <a href="https://doi.org/gtr8pq" class="citation-image" aria-label="Developing a standardized but extendable framework to increase the findability of infectious disease datasets"> <img src="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9950378/bin/41597_2023_1968_Fig1_HTML.jpg" alt="Developing a standardized but extendable framework to increase the findability of infectious disease datasets" loading="lazy" onerror="this.src = '/images/fallback.svg'; this.onerror = null;"> </a> <div class="citation-text"> <a href="https://doi.org/gtr8pq" class="citation-title"> Developing a standardized but extendable framework to increase the findability of infectious disease datasets </a> <div class="citation-authors" data-tooltip="Ginger Tsueng, Marco A. Alvarado Cano, José Bento, Candice Czech, Mengjia Kang, Lars Pache, Luke V. Rasmussen, Tor C. Savidge, Justin Starren, Qinglong Wu, Jiwen Xin, Michael R. Yeaman, Xinghua Zhou, Andrew I. Su, Chunlei Wu, Liliana Brown, Reed S. Shabman, Laura D. Hughes, Serdar Turkarslan " tabindex="0"> Ginger Tsueng, Marco A. Alvarado Cano, José Bento, Candice Czech, Mengjia Kang, …, Chunlei Wu, Liliana Brown, Reed S. Shabman, Laura D. 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