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.
- Lyla Atta, Arpan Sahoo, Jean Fan^. VeloViz: RNA-velocity informed embeddings for visualizing cellular trajectories. BioRxiv. 2021. doi: 10.1101/2021.01.28.425293
- Brendan F Miller, Dhananjay Bambah-Mukku, Catherine Dulac, Xiaowei Zhuang, Jean Fan^. Characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities. Genome Research. 2021. doi:10.1101/gr.271288.120
- 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
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^, 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
- 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
- Interactions between cancer cells and immune cells drive transitions to mesenchymal-like states in glioblastoma on 03 June 2021
- Characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities on 25 May 2021
- VeloViz - RNA-velocity informed embeddings for visualizing cellular trajectories on 29 January 2021
- 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
- The JEFworks lab receives support from the NSF CAREER awards. on 08 June 2021
- Dr. Fan gives an invited seminar at the USC Biostatistics Division. on 20 May 2021
- Brendan presents his work at the JHU Genomics Collective meeting. on 19 May 2021
- Dr. Fan gives an invited talk to the Pfizer Single Cell working group. on 26 April 2021
- Lyla presents her work at the Broad Single Cell Working Group. on 20 April 2021
Latest Blog Posts
- Randomly Generating Music with R on 19 April 2021
- 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