jef.works

Website review jef.works

JEFworks Lab - Welcome to the JEFworks Lab

 Generated on May 02 2026 01:05 AM

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The score is 63/100

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Title

JEFworks Lab - Welcome to the JEFworks Lab

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Description

Lab website of Prof. Jean Fan and team work at Johns Hopkins University

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Keywords

bioinformatics, single cell, spatial transcriptomics, spatially resolved transcriptomics, merfish, computational biology, research lab, JHU research opportunities

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Property Content
title Welcome to the JEFworks Lab
locale en_US
description Lab website of Prof. Jean Fan and team work at Johns Hopkins University
url http://jefworks-lab.github.io//
site_name JEFworks Lab
image http://jefworks-lab.github.io//assets/banners/bg.jpg
type website

Headings

H1 H2 H3 H4 H5 H6
4 7 1 0 0 0
  • [H1] Welcome to the JEFworks Lab, where Prof. Jean Fan and team work on statistical analysis approaches and machine learning tools for analyzing big spatially resolved omics data to better understand the molecular and spatial-contextual factors shaping cellular identity and heterogeneity in the context of human health and disease.
  • [H1]
  • [H1]
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  • [H2] We are a bioinformatics research lab in the Center for Computational Biology and the Department of Biomedical Engineering at Johns Hopkins University. Meet our team!
  • [H2] We develop bioinformatics methods for analyzing spatially resolved sequencing and imaging data.
  • [H2] We apply these bioinformatics methods to better understand the role of cellular heterogeneity in disease.
  • [H2] Latest Publications
  • [H2] Latest News
  • [H2] Latest Blog Posts
  • [H2] Latest Lab Fun
  • [H3] Follow us on social media for the latest updates on our blog posts, code tutorials, software tools, and more!

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In-page links

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Anchor Type Juice
Our Mission Internal Passing Juice
Meet the Team Internal Passing Juice
Lab Resources Internal Passing Juice
Publications Internal Passing Juice
Software Internal Passing Juice
Courses Internal Passing Juice
Talks Internal Passing Juice
Join Internal Passing Juice
Contact Internal Passing Juice
Blog Internal Passing Juice
Center for Computational Biology External Passing Juice
Department of Biomedical Engineering External Passing Juice
Meet our team! Internal Passing Juice
Gohta Aihara, Kalen Clifton, Mayling Chen, Zhuoyan Li, Lyla Atta, Brendan F Miller, Rahul Satija, John W Hickey, Jean Fan^. SEraster - a rasterization preprocessing framework for scalable spatial omics data analysis. Bioinformatics. June 20, 2024. doi.org/10.1093/bioinformatics/btae412 Internal Passing Juice
Lyla Atta, Kalen Clifton, Manjari Anant, Gohta Aihara, and Jean Fan^. Gene count normalization in single-cell imaging-based spatially resolved transcriptomics. Genome Biology. June 12, 2024. doi.org/10.1186/s13059-024-03303-w Internal Passing Juice
Kalen Clifton*, Manjari Anant*, Gohta Aihara, Lyla Atta, Osagie K Aimiuwu, Justus M Kebschull, Michael I Miller, Daniel Tward^, Jean Fan^. STalign - alignment of spatial transcriptomics data using diffeomorphic metric mapping. Nature Communications. December 8, 2023. doi.org/10.1038/s41467-023-43915-7 Internal Passing Juice
Brendan F Miller, Feiyang Huang, Lyla Atta, Arpan Sahoo, Jean Fan^. Reference-free cell type deconvolution of pixel-resolution spatially resolved transcriptomics data. Nature Communications. 2022. doi:/10.1038/s41467-022-30033-z Internal Passing Juice
Lyla Atta, Jean Fan^. Computational challenges and opportunities in spatially resolved transcriptomic data analysis. Nature Communications. 2021. doi:10.1038/s41467-021-25557-9 Internal Passing Juice
Spatial Transcriptomics As Rasterized Image Tensors (STARIT) characterizes cell states with subcellular molecular heterogeneity Internal Passing Juice
STcompare - comparative spatial transcriptomics data analysis of structurally matched tissues to characterize differentially spatially patterned genes Internal Passing Juice
Impact of Data Quality on Deep Learning Prediction of Spatial Transcriptomics from Histology Images Internal Passing Juice
Spatiotemporal transcriptomic analysis during cold ischemic injury to the murine kidney reveals compartment-specific changes Internal Passing Juice
Evidence of off-target probe binding in the 10x Genomics Xenium v1 Human Breast Gene Expression Panel compromises accuracy of spatial transcriptomic profiling Internal Passing Juice
Prof. Fan teaches first year BME PhD students about the limitations of summary statistics and the importance of visualizing your data! Internal Passing Juice
Dr. Fan and Caleb give invited talks at the Broad Institute Models, Inference, and Algorithms seminar series. Internal Passing Juice
Prof. Fan teaches Genomic Data Visualization again this semester! JEFworks Lab members give guest lectures in the Genomic Data Visualizations class. Internal Passing Juice
Vivien and Kalen presents their work at the WSE/DOM retreat. Thanks to Liz and Rafael for the photos. Internal Passing Juice
Dr. Fan gives an invited talk at the Center for Bioinformatics and Quantitative Biology at University of Illinois at Chicago. Internal Passing Juice
Vibe coding with SEraster and STcompare to compare spatial transcriptomics technologies Internal Passing Juice
RNA velocity in situ infers gene expression dynamics using spatial transcriptomics data Internal Passing Juice
Analyzing ICE Arrest Data - Part 2 Internal Passing Juice
Analyzing ICE Detention Data from 2021 to 2025 Internal Passing Juice
Creative Commons Attribution 4.0 International License External Passing Juice

SEO Keywords

Keywords Cloud

lab jean bioinformatics fan analysis spatially heterogeneity spatial data transcriptomics

Keywords Consistency

Keyword Content Title Keywords Description Headings
fan 15
data 14
spatial 12
jean 10
transcriptomics 9

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Url

Domain : jef.works

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