Yuqi Tan

I obtained my PhD in Computational biology from the Johns Hopkins University, School of Medicine. During my PhD at the Cahan Lab, I have developed SingleCellNet , a computational tool to classify single cell RNA seq data across platform and across species.

Currently, I am a postdoctoral fellow in Dr. Garry Nolan's lab at Stanford exploring multi-omics integration and 3D tissue imaging.

Here is my CV.

Papers

Machine Learning Algorithm Development and Spatial-omics

• 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.

Computational Stem Cell Engineering

• 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
• Tan, and Cahan SingleCellNet: a computational tool to classify single cell RNA-Seq data across platforms and across species. Cell System 2019
• 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.

Cell & Molecular Biology and Neuroscience

• 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

• 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

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.