Yuqi Tan

I am a computational biologist specializing in spatial multi-omics, integrating expertise in machine learning with a deep understanding of molecular and cellular biology. My work focuses on developing scalable machine learning models and streamlined computational frameworks to tackle complex biological questions, such as improving stem cell engineering, identifying novel cell types, finding spatial biomarkers for cancer immunotherapy response, and discovering spatial mechanisms in neurological disease. I will lead a research team develop streamlined, scalable machine learning models and apply them to explore the spatial organization of cell types in healthy aging and diseases, leveraging spatial multi-omics and 3D pathology. Through direct mentoring nine students, designing/teaching three custom courses, and contributing to three global health projects, I remain committed to fostering a diverse, equitable, and inclusive scientific environment that empowers future researchers.

Academic training
Postdoctoral Fellow in the Nolan lab @ Stanford University
PhD 2021 in the Cahan lab @ JHU 2021
BSc(Hons) @CUHK 2014

Google Scholar.

Papers

Machine Learning Algorithm Development and Spatial-omics

• Tan*, Kempchen*, Becker*, Haist, Feyaerts, Xiao, Su, Rech, Hickey, and Nolan. SPACEc: A Streamlined, Interactive Python Workflow for Multiplexed Image Processing and Analysis. Under Review in Nat Comm. Jan 2025.
• Xiao*, Su*, Tan*, Deng, Li, Ma, Kim, Bai, Liu, Rosoklija, Sissoko, Wu, Santiago, Dwork, Hen, Mann, Fan$, Leong$, Boldrini$. Spatially resolved multi-omic profiling of human hippocampus reveals region-specific alterations in major depressive disorder. Under Review in Cell. Mar 2024.
• Becker, Nassar, Espinosa, Stelzer, Fayaerts, Berson, Bidoki, Chang, Saarunya, Culos, De Francesco, Fallahzadeh, Liu, Kim, Marić, Mataraso, Payrovnaziri, Phongpreecha, Ravindra, Stanley, Shome, Tan, Thuraiappah, Xenochristou, Xue, Shaw, Stevenson, Angst, Gaudilliere, Aghaeepour. Large scale correlation network construction for unraveling the coordination of complex biological systems. Nature Computational Science 2023.
• Brbic*, Cao*, Hickey*, Tan, Snyder, Nolan, and Leskovec. Annotation of Spatially Resolved Single-cell Data with STELLAR. Nat Methods. Oct 2022.
• Liu, Li, Zhang, van Sambeek, Appleton, Chiang, Ng, Khoshakhlagh, Chen, Garcia-Corral, Wu, Huang, Tan, Chao, Aach, Tam, Lim, Raychaudhuri, and Church. Iterative transcription factor screening enables rapid generation of microglia-like cells from human iPSC. BioRxiv 2022.
• Becker, Fayaerts, Stelzer, Berson, Chang, Clark, Marić, Culos, De Francesco, Espinosa, Kim, Maric, Mataraso, Payrovnaziri, Phongpreecha, Ravindra, Stanley, Shome, Tan, Thuraiappah, Xue, Shaw, Stevenson, Angst, Gaudilliere, Aghaeepour. CoDi: Profiling functional disruption in biological systems. Submitted 2022.
• Becker, Dai, Chang, Fayaerts, Stelzer, Zhang, Berson, Clark, De Francesco, Espinosa, Kim, Marić, Mataraso, Payrovnaziri, Phongpreecha, Ravindra, Shome, Tan, Thuraiappah, Xue, Mayo, Quaintance, Laborde, King, Gotlib, Wong, Angst, Shaw, Stevenson, Gaudilliere, Aghaeepour. Revealing the impact of lifestyle stressors on the risk of adverse pregnancy outcomes with multitask machine learning. Front Pediatr. Nov 2022.

Machine Learning and Computational Stem Cell Engineering

• Tan, and Cahan SingleCellNet: a computational tool to classify single cell RNA-Seq data across platforms and across species. Cell System 2019
• Bian, Cheng, Su, Tan, Kim, Wang, Yoo, Blackshaw and Cahan. Signaling and transcriptional networks governing late synovial joint development. BioRxiv. Jan 2021
• Tan, Spangler, Farid, Peng, and Cahan. Quantitative comparison of in vitro and in vivo embryogenesis at a single cell resolution. May 2021
• Velazquez J, LeGraw R, Moghadam F, Tan Y, Kibourne J, Hislop J, Liu S, Cats D, Chuva de Sousa Lopes S, Plasier C, Cahan P, Kiani S, Ebrahimkhani Mo Synthetic Maturation of Multilineage Human Liver Organoids via Genetically Guided Engineering Cell Sytem 2020
• Chen M, ... ,Cahan P, Tan Y ... Schlaeger TM Transcriptome Dynamics of Hematopoietic Stem Cell Formation Revealed Using a Combinatorial Runx1 and Ly6a Reporter System Stem Cell Reports 2020
• Radley AH, Schwab RM, Tan Y, Kim J, Lo EKW, Cahan P Assessing engineered cells using CellNet and RNA-Seq. Nat Protoc. 2017 12:1089-1102
• Kumar P, Tan Y, Cahan P Understanding development and stem cells using single cell-based analyses of gene expression. Development. 2017 144: 17- 32.

Cancer Immunotherapies

• Haist*, Matusiak*, Tan*, Zimmer, Stege, Kempchen, Mischke, Chu, Weidentahler-Barth, Barlow, Rogall, Gonzalez, Vaertsch, Goltsev, Grabbe, Hickey, and Nolan.Merkel-cell polyomavirus-driven Reorganization of the tumor microenvironment orchestrates anti-tumor immunity in Merkel cell carcinoma.Submitted. 2025 Jan
• Haist*, Stege*, Rogall, Tan, Wasielewski, Klespe, Meier, Mohr, Kähler, Wichenthal, Schadenfdorf, Ugurel, Lodde, Zimmer, …, Grabbe and Loquai. Treatment management for BRAF-mutant melanoma patients with tumor recurrence upon adjuvant therapy: A multicenter study from the prospective skin cancer registry ADOREG. Journal for Immuno Therapy of Cancer. 2023 Aug.
• Hickey, Haist, Horowitz, Caraccio, Tan, 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.

Signaling dynamics and Neuroscience

• Tan, Yin, Tan, Ivanov, Plucinska, Ilanges, Herb, Wang, Kosse, Cohen , Lin, Friedman. Leptin Activated Hypothalamic BNC2 Neurons Acutely Suppress Food Intake. Nature. 2024 Oct.
• Cui Y, Zhao Q, Xie HT, Wong WS, Wang X, Gao C, Ding Y, Tan Y, Ueda T, Zhang Y, Jiang L MON1/CCZ1-mediated Rab7 activation regulates tapetal PCD and pollen development in Arabidopsis. Plant Physiol. 2017 Jan;173(1):206-218
• Mayers JR, Hu T, Wang C, Cárdenas JJ, Tan Y, Pan J, Bednarek SY. SCD1 and SCD2 Form a Complex that Functions with the Exocyst and RabE1 in Exocytosis and Cytokinesis. Plant Cell 00409.2017
• James EJ, Gu J, Ramirez-Vizcarrondo CM, Hasan M, Truszkowski TL, Tan Y Oupravanh PM, Khakhalin AS, Aizenman CD Valproate-induced neurodevelopmental deficits in Xenopus laevis tadpoles. J Neurosci. 2015 Feb 18;35(7):3218-29.

Conferences

Oral presentation

• Tan, MultiOmics 2024 (Brisbane, Australia) [Invited]: Make Computational Analysis for Multiplexed Image Easy.
• Tan, EPFL (2024, EPFL, Switzerland) [Invited]: Versatile and Interactive Python Workflow for 2D and 3D Multiplexed Image Analysis.
• Tan, The European Molecular Biology Laboratory (2024, Heidelberg, Germany) [Invited]: Best Practice for Multiplexed Image Analysis.
• Tan, Yale University, Biomedical Engineering Department (2023, New Haven, CT) [Invited talk]: A Spatial Biologist's Guide to Decode Multiplexed Image Analysis.
• Tan, Columbia University, Biomedical Engineering Department (2023, New York City, NY) [Invited talk]: A Spatial Biologist's Guide to Decode Multiplexed Image Analysis.
• Tan, Hong Kong Laureate Forum (2023, Hong Kong) [Selected presentation]: Identify structural and cellular drivers of DCIS progression.
• Tan, Cancer Grand Challenges Future Leaders Conference 2022 (2022, Barcelona Spain) [Selected presentation]: Universal Cancer Knowledge Encyclopedia.
• Tan, Artificial Intelligence in Medicine (2022, Germany) [Selected presentation]: Annotation of Spatially Resolved Single-cell Data with STELLAR.
• Tan, East China Normal University (2021, Shanghai, China) [Invited presentation]: Machine-learning tools on multi-omics analysis.

Poster presentation

• Tan, Hickey, Horowitz, and Nolan, Single Cell Genomics Gordon Conference (2022, Switzerland)
• Tan, Artificial Intelligence in Medicine (2022, Germany)
• Tan and Cahan. Poster presentation at International Society for Stem Cell Research Annual Meeting (2020,Virtual)
• Tan. Selected talk at Biochemistry and Cellular Molecular Biology Annual Retreat (2019, Cambridge, Maryland)
• Tan. Selected talk at International Society for Stem Cell Research Annual Meeting (2019, Los Angeles)
• Tan. Invited talk at Cell Molecular Biology Symposium (2018, Hong Kong)
• Tan and Cahan. Poster presentation at International Society for Stem Cell Research Annual Meeting (2017,Boston)

Pedagogy	Teaching Academy: Preparing for Future Faculty program (trainee) 2016-2018 Institute for Educational Excellence Summer Teaching camp (trainee) 2017
Teaching assistant	Practical Genomics Workshop 2018-2019 Computational Biology and Bioinformatics 2017-2019 Computational Stem Cell Biology 2018
Teaching	Introduction to Biological Molecules (Guest lecturer) 2018 @JHU Biomedical Engineering: Topics in Stem Cell Biology 2019 @JHU Neuroscience: A single cell story 2020 @JHU Computational Stem Cell Biology (Guest lecturer) 2020@JHU Computational Stem Cell Biology (Guest lecturer) 2021 @JHU Single-cell Spatial-omics: with Applications to Stem Cell Engineering and Cancer Immunotherapy 2022 @Stanford Single Cell Biology @Yale University (Guest lecturer) 2023 @Yale Single Cell Biology @Yale University (Guest lecturer) 2023 @Yale Image Processing and Advanced Machine Learning for Cancer Bioinformatics @ University of Michigan (Guest lecturer)

Interests

Other areas where I lavish my curiosity and abundant energy

• I am a certified yoga instructor .
• I love ballroom dancing and salsa, I have also dabbled a bit into swing and argentine tango.
• I am a avid amature bird watcher and I enjoy bird photography.
• I am a adventurous foodie and self-proclaimed (!!) good chef.
• I love traveling and reading.
• I take improvisation lessons here and there.