We are a bioinformatics research lab in the Department of Biomedical Engineering at Johns Hopkins University. We are also a part of the Center for Computational Biology and Department of Computer Science.
We develop methods for analyzing single cell multi-omic sequencing and imaging data.
While heterogeneity within cellular systems has long been widely recognized, only recently have technological advances enabled measurements to be made on a single cell level. We develop machine learning and other statistical approaches as open-source computational software to analyze such high-throughput single-cell resolution multi-omic and imaging data in order to identify and characterize varying aspects of heterogeneity (transcriptomic, epigenomic, spatial/contextual) and their interplay.
- Jean Fan^, Kamil Slowkikowski, Fan Zhang. Single-cell transcriptomics in cancer - computational challenges and opportunities. Nature Experimental and Molecular Medicine. Sept 15, 2020, doi.org:10.1038/s12276-020-0422-0
- Chenglong Xia*, Jean Fan*, George Emanuel*, Junjie Hao, and Xiaowei Zhuang. Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression. PNAS. 2019. doi:10.1073/pnas.1912459116
- Jean Fan, Neeraj Salathia, Rui Liu, Gwendolyn E Kaeser, Yun C Yung, et al. Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis. Nature Methods. 2016. doi: 10.1038/nmeth.3734
We apply these methods to better understand the impact of cellular heterogeneity on cancer pathogenesis and prognosis.
Advancements in high-throughput sequencing and imaging technologies have uncovered tremendous genetic, epigenetic, transcriptional, and spatial heterogeneity in various cancers but their impact on clinical outcomes is not well understood. We establish close collaborations with clinical collaborators to develop and apply bioinformatics methods that contribute to a more complete understanding of how cellular heterogeneity impacts tumor progression, therapeutic resistance, and ultimately clinical prognosis. We are particularly interested in pediatric gliomas.
- Jean Fan*, Hae-Ock Lee*, Soohyun Lee, Da-eun Ryu, Semin Lee, et al. Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq. Genome Research. 2018. doi:10.1101/gr.228080.117
- Lili Wang*, Jean Fan*, Joshua M. Francis, George Georghiou, Sarah Hergert, et al. Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia. Genome Research. 2017. doi:10.1101/gr.217331.116
- Lili Wang*, Angela N. Brooks*, Jean Fan*, Youzhong Wan*, Rutendo Gambe, et al. Transcriptomic characterization of SF3B1 mutation reveals its pleiotropic effects in chronic lymphocytic leukemia. Cancer Cell. Nov 3, 2016. doi: 10.1016/j.ccell.2016.10.005
- Spatial organization of the transcriptome in individual neurons on 08 December 2020
- Single-cell transcriptomics in cancer - computational challenges and opportunities on 15 September 2020
- Fast, sensitive and accurate integration of single-cell data with Harmony on 19 November 2019
- Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression on 09 September 2019
- A Murine Model of Chronic Lymphocytic Leukemia Based on B Cell-Restricted Expression of Sf3b1 Mutation and Atm Deletion on 11 February 2019
- Happy holidays from the JEFworks Lab! on 18 December 2020
- Check out our preprint led by Guiping Wang on atlasing the spatial organization of RNAs inside individual cultured neurons using MERFISH on 08 December 2020
- Dr. Fan gives an invited seminar and spends the day virtually with the Biochemistry and Molecular Biology Department at JHSPH on 07 December 2020
- We welcome Feiyang Huang to the lab as an undergraduate research intern. Welcome Feiyang! on 13 November 2020
- Catherine Lo successfully completes her lab internship and will be writing up her research results for the Regeneron Science Talent Search competition. Best of luck Catherine! on 09 November 2020
Latest Blog Posts
- Animating the Cell Cycle on 28 December 2020
- Using R To Find The Missing Faculty on 30 November 2020
- Using scVelo in R using Reticulate on 25 August 2020
- A Guide to Responding to Scientific Peer Review on 17 June 2020
- Quickly Creating Pseudobulks on 06 April 2020
- A Guide to Scientific Peer Review on 23 March 2020
- Ten PhD Transition Tips for the Biological Sciences on 23 January 2020
- RNA Velocity Analysis (In Situ) - Tutorial and Tips on 14 January 2020
- How to write an abstract on 24 September 2019
- Figure style faux pas on 19 July 2019