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<!DOCTYPE html>
<html lang="en">
<head>
<meta name="author" content="Yuqi Tan">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
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<title>Yuqi Tan</title>
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<body>
<div id="mainMenuWrapper">
<div id="mainMenu">
<a id="menu0" href="#about" class="menuItem menuSelected">About</a>
<a id="menu1" href="#research" class="menuItem">Research</a>
<a id="menu2" href="#teaching" class="menuItem">Teaching</a>
<a id="menu3" href="#interests" class="menuItem">Interests</a>
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<div class="section" id="about">
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<h1>Yuqi Tan</h1>
I am a computational biologist with rigorous training in both statistical learning and cell molecular biology. My research goal is to design machine learning methods that will drive new biomedical discoveries, such as improving stem cell engineering protocols, discovering novel cell types from single-cell measurements, and inferring developmental trajectories during in vitro reprogramming. I plan to lead a research team to understand the high-dimensional spatial arrangement of cell types and how relationships are disrupted in disease by harnessing the power of single-cell multi-omics technologies and volumetric imaging. In pursuing these research goals, I am dedicated to creating an inclusive and open environment and mentoring a diverse team of young scientists to achieve their research vision.
<p> </p>
<p> <b> Academic training </b> <br> Postdoctoral Fellow in <a href = "https://www.nolanlab.org/members/" class="external-link"> the Nolan lab </a> @ Stanford University <br> PhD 2021 in <a href = "https://www.cahanlab.org" class="external-link"> the Cahan lab </a> @ JHU 2021 <br> BSc(Hons) @CUHK 2014 </p>
<a href = "https://scholar.google.com/citations?user=zNOpmasAAAAJ&hl=en" class="external-link">Google Scholar.</a>
<!-- <p>I will be presenting singleCellNet at <a href="https://www.eventscribe.com/2019/ISSCR/agenda.asp?startdate=6/29/2019&enddate=6/29/2019&BCFO=M&tn=&cpf2=&cus2=&pta=&h=Sat,%20Jun%2029&pfp=FullSchedule" class = "external-link"> ISSCR 2019 consession IVE </a> (14:24 - 14:35pm, Jun29, Room 408B).</p>
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<div class="section" id="research">
<h1>Publications & Conferences</h1>
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<h2> Papers </h2>
<h3> <b> Machine Learning Algorithm Development and Spatial-omics </b> </h3>
<ul class="publicationList">
<li> Becker, Nassar, Espinosa, Stelzer, Fayaerts, Berson, Bidoki, Chang, Saarunya, Culos, De Francesco, Fallahzadeh, Liu, Kim, Marić, Mataraso, Payrovnaziri, Phongpreecha, Ravindra, Stanley, Shome, <b>Tan</b>, Thuraiappah, Xenochristou, Xue, Shaw, Stevenson, Angst, Gaudilliere, Aghaeepour. <i><a href = "https://www.nature.com/articles/s43588-023-00429-y" class="external-link"> Large scale correlation network construction for unraveling the coordination of complex biological systems.</a> </i> Nature Computational Science 2023. </li>
<li> Brbic*, Cao*, Hickey*, <b>Tan</b>, Snyder, Nolan, and Leskovec. <i><a href = "https://www.nature.com/articles/s41592-022-01651-8" class="external-link"> Annotation of Spatially Resolved Single-cell Data with STELLAR. </a> </i> Nat Methods. Oct 2022. </li>
<li> Liu, Li, Zhang, van Sambeek, Appleton, Chiang, Ng, Khoshakhlagh, Chen, Garcia-Corral, Wu, Huang, <b>Tan</b>, Chao, Aach, Tam, Lim, Raychaudhuri, and Church. <i><a href = "www.biorxiv.org/content/10.1101/2022.06.03.494617v1.full.pdf" class="external-link">Iterative transcription factor screening enables rapid generation of microglia-like cells from human iPSC.</a> </i> BioRxiv 2022. </li>
<li> Becker, Fayaerts, Stelzer, Berson, Chang, Clark, Marić, Culos, De Francesco, Espinosa, Kim, Maric, Mataraso, Payrovnaziri, Phongpreecha, Ravindra, Stanley, Shome, <b>Tan</b>, Thuraiappah, Xue, Shaw, Stevenson, Angst, Gaudilliere, Aghaeepour. CoDi: Profiling functional disruption in biological systems. Submitted 2022. </li>
<li> Becker, Dai, Chang, Fayaerts, Stelzer, Zhang, Berson, Clark, De Francesco, Espinosa, Kim, Marić, Mataraso, Payrovnaziri, Phongpreecha, Ravindra, Shome, <b>Tan</b>, Thuraiappah, Xue, Mayo, Quaintance, Laborde, King, Gotlib, Wong, Angst, Shaw, Stevenson, Gaudilliere, Aghaeepour. <i><a href = "https://www.frontiersin.org/articles/10.3389/fped.2022.933266/full" class="external-link"> Revealing the impact of lifestyle stressors on the risk of adverse pregnancy outcomes with multitask machine learning. </a> </i> Front Pediatr. Nov 2022. </li>
<h3> <b>Machine Learning and Computational Stem Cell Engineering </b></h3>
<li><b>Tan</b>, and Cahan <i><a href="https://doi.org/10.1016/j.cels.2019.06.004" class="external-link">SingleCellNet: a computational tool to classify single cell RNA-Seq data across platforms and across species.</a> </i> Cell System 2019 </li>
<li> Bian, Cheng, Su, <b>Tan</b>, Kim, Wang, Yoo, Blackshaw and Cahan. <i><a href = "www.biorxiv.org/content/10.1101/2021.08.25.457383v1.full.pdf" class="external-link"> Signaling and transcriptional networks governing late synovial joint development. </a> </i> BioRxiv. Jan 2021 </li>
<li> <b>Tan</b>, Spangler, Farid, Peng, and Cahan. <i><a href="https://www.biorxiv.org/content/10.1101/2021.05.07.443179v1" class="external-link">Quantitative comparison of in vitro and in vivo embryogenesis at a single cell resolution.</a> </i> May 2021 </li>
<li> Velazquez J, LeGraw R, Moghadam F, <b>Tan Y</b>, Kibourne J, Hislop J, Liu S, Cats D, Chuva de Sousa Lopes S, Plasier C, Cahan P, Kiani S, Ebrahimkhani Mo<i><a href = "https://doi.org/10.1016/j.cels.2020.11.002", class="external-link"> Synthetic Maturation of Multilineage Human Liver Organoids via Genetically Guided Engineering </a></i> Cell Sytem 2020 </li>
<li> Chen M, ... ,Cahan P, <b>Tan Y</b> ... Schlaeger TM <i><a href = "https://doi.org/10.1016/j.stemcr.2020.03.020", class="external-link"> Transcriptome Dynamics of Hematopoietic Stem Cell Formation Revealed Using a Combinatorial Runx1 and Ly6a Reporter System </a></i> Stem Cell Reports 2020 </li>
<li>Radley AH, Schwab RM, <b>Tan Y</b>, Kim J, Lo EKW, Cahan P <i>Assessing engineered cells using CellNet and RNA-Seq.</i> Nat Protoc. 2017 12:1089-1102</li>
<li>Kumar P, <b>Tan Y</b>, Cahan P <i><a href = "https://dev.biologists.org/content/144/1/17" class="external-link"> Understanding development and stem cells using single cell-based analyses of gene expression.</a></i> Development. 2017 144: 17- 32.</li>
<h3> <b> Cancer Immunotherapies </b></h3>
<li> Haist*, Stege*, Rogall, <b>Tan</b>, Wasielewski, Klespe, Meier, Mohr, Kähler, Wichenthal, Schadenfdorf, Ugurel, Lodde, Zimmer, …, Grabbe and Loquai. <i><a href = "https://jitc.bmj.com/content/11/9/e007630" class="external-link"> Treatment management for BRAF-mutant melanoma patients with tumor recurrence upon adjuvant therapy: A multicenter study from the prospective skin cancer registry ADOREG. </a> </i> Journal for Immuno Therapy of Cancer. 2023 Aug. </li>
<li> Hickey, Haist, Horowitz, Caraccio, <b>Tan</b>, Rech, Baertsch, Rovira Clave, Zhu, Vasquez, Barlow, Agmon, Goltsev, Sunwoo, Covert, and Nolan. T Cell Mediated Curation and Restructuring of Tumor Tissue Coordinates an Effective Immune Response. Cell Reports. Accepted 2023 Nov. </li>
<h3> <b> Signaling dynamics and Neuroscience </b> </h3>
<li>Cui Y, Zhao Q, Xie HT, Wong WS, Wang X, Gao C, Ding Y, <b>Tan Y</b>, Ueda T, Zhang Y, Jiang L <i><a href = "http://www.plantphysiol.org/content/173/1/206" class="external-link"> MON1/CCZ1-mediated Rab7 activation regulates tapetal PCD and pollen development in Arabidopsis.</a></i> Plant Physiol. 2017 Jan;173(1):206-218</li>
<li>Mayers JR, Hu T, Wang C, Cárdenas JJ, <b>Tan Y</b>, Pan J, Bednarek SY. <i><a href = "http://www.plantcell.org/content/29/10/2610" class="external-link"> SCD1 and SCD2 Form a Complex that Functions with the Exocyst and RabE1 in Exocytosis and Cytokinesis. </a></i> Plant Cell 00409.2017</li>
<li>James EJ, Gu J, Ramirez-Vizcarrondo CM, Hasan M, Truszkowski TL, <b>Tan Y</b> Oupravanh PM, Khakhalin AS, Aizenman CD <i><a href = "http://www.jneurosci.org/content/35/7/3218.long" class="external-link"> Valproate-induced neurodevelopmental deficits in Xenopus laevis tadpoles.</a></i> J Neurosci. 2015 Feb 18;35(7):3218-29.</li>
<h2>Conferences</h2>
<h3> <b> Oral presentation </b></h3>
<li>Tan, Yale University, Biomedical Engineering Department (2023, New Haven, CT) [Invited talk]: A Spatial Biologist's Guide to Decode Multiplexed Image Analysis.</li>
<li>Tan, Columbia University, Biomedical Engineering Department (2023, New York City, NY) [Invited talk]: A Spatial Biologist's Guide to Decode Multiplexed Image Analysis.</li>
<li>Tan, Hong Kong Laureate Forum (2023, Hong Kong) [Selected presentation]: Identify structural and cellular drivers of DCIS progression.</li>
<li>Tan, Cancer Grand Challenges Future Leaders Conference 2022 (2022, Barcelona Spain) [Selected presentation]: Universal Cancer Knowledge Encyclopedia. </li>
<li>Tan, Artificial Intelligence in Medicine (2022, Germany) [Selected presentation]: Annotation of Spatially Resolved Single-cell Data with STELLAR.</li>
<li>Tan, East China Normal University (2021, Shanghai, China) [Invited presentation]: Machine-learning tools on multi-omics analysis.</li>
<h3> <b> Poster presentation </b></h3>
<li> Tan, Hickey, Horowitz, and Nolan, Single Cell Genomics Gordon Conference (2022, Switzerland) </li>
<li> Tan, Artificial Intelligence in Medicine (2022, Germany) </li>
<li>Tan and Cahan. <i>Poster presentation at International Society for Stem Cell Research Annual Meeting</i> (2020,Virtual)</li>
<li> Tan. <i> Selected talk at Biochemistry and Cellular Molecular Biology Annual Retreat</i> (2019, Cambridge, Maryland) </li>
<li>Tan. <i> Selected talk at International Society for Stem Cell Research Annual Meeting</i> (2019, Los Angeles)</li>
<li>Tan. <i> Invited talk at Cell Molecular Biology Symposium</i> (2018, Hong Kong)</li>
<li>Tan and Cahan. <i>Poster presentation at International Society for Stem Cell Research Annual Meeting</i> (2017,Boston)</li>
</ul>
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<a href="code/images/research.jpg" title="singleCellNet">
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<div class="section" id="teaching">
<h1>Teaching</h1>
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<td>Pedagogy</td>
<td>
Teaching Academy: Preparing for Future Faculty program (trainee) 2016-2018 <br> Institute for Educational Excellence Summer Teaching camp (trainee) 2017 </td>
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<td>Teaching assistant</td>
<td>Practical Genomics Workshop 2018-2019<br> Computational Biology and Bioinformatics 2017-2019 <br> Computational Stem Cell Biology 2018 </td>
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<tr>
<td>Teaching </td>
<td> Introduction to Biological Molecules (Guest lecturer) 2018 @JHU <br> Biomedical Engineering: Topics in Stem Cell Biology 2019 @JHU <br> Neuroscience: A single cell story 2020 @JHU <br> Computational Stem Cell Biology (Guest lecturer) 2020@JHU <br> Computational Stem Cell Biology (Guest lecturer) 2021 @JHU <br> Single-cell Spatial-omics: with Applications to Stem Cell Engineering and Cancer Immunotherapy 2022 @Stanford <br> Single Cell Biology @Yale University (Guest lecturer) 2023 @Yale </td>
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<a href="code/images/pcr.png" title="homemade pcr meme">
<img src="code/images/pcr.png">
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<div class="section" id="interests">
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<h1>Interests<h1>
<h3>Other areas where I lavish my curiosity and abundant energy</h3>
<ul>
<li>I am a <a href = "http://uhs.jhu.edu/wellness/programs-and-events/fitness-series/" class = "external-link"> certified yoga instructor </a>. </li>
<li>I love ballroom dancing and salsa, I have also dabbled a bit into swing and argentine tango. </li>
<li>I am a avid amature <a href = "http://patterson.audubon.org/" class = "external-link"> bird watcher </a> and I enjoy bird photography.</li>
<li>I am a adventurous foodie and self-proclaimed (!!) good chef. </li>
<li>I love traveling and reading. </li>
<li>I take <a href = "https://www.bigimprov.org/" class = "external-link"> improvisation lessons </a> here and there. </li>
</ul>
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<a href="http://www.gocomics.com/sarahs-scribbles/2014/1/17" title="Sarah's Scribbles" class="external-link">
<img src="code/images/books.gif">
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<figure class="logo">
<a href="https://www.nolanlab.org/">
<img src="http://med.stanford.edu/identity/logo/_jcr_content/main/panel_builder/panel_0/panel_builder_0/panel_1/download_1/file.res/Stanford_Medicine_H-web.png">
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