jef.works

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JEFworks Lab - Welcome to the JEFworks Lab

 Genereret Maj 02 2026 01:05 AM

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JEFworks Lab - Welcome to the JEFworks Lab

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

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

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Egenskab Indhold
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

Overskrifter

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]
  • [H1]
  • [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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Anker Type Juice
Our Mission Intern Sender Juice
Meet the Team Intern Sender Juice
Lab Resources Intern Sender Juice
Publications Intern Sender Juice
Software Intern Sender Juice
Courses Intern Sender Juice
Talks Intern Sender Juice
Join Intern Sender Juice
Contact Intern Sender Juice
Blog Intern Sender Juice
Center for Computational Biology Ekstern Sender Juice
Department of Biomedical Engineering Ekstern Sender Juice
Meet our team! Intern Sender 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 Intern Sender 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 Intern Sender 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 Intern Sender 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 Intern Sender 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 Intern Sender Juice
Spatial Transcriptomics As Rasterized Image Tensors (STARIT) characterizes cell states with subcellular molecular heterogeneity Intern Sender Juice
STcompare - comparative spatial transcriptomics data analysis of structurally matched tissues to characterize differentially spatially patterned genes Intern Sender Juice
Impact of Data Quality on Deep Learning Prediction of Spatial Transcriptomics from Histology Images Intern Sender Juice
Spatiotemporal transcriptomic analysis during cold ischemic injury to the murine kidney reveals compartment-specific changes Intern Sender Juice
Evidence of off-target probe binding in the 10x Genomics Xenium v1 Human Breast Gene Expression Panel compromises accuracy of spatial transcriptomic profiling Intern Sender Juice
Prof. Fan teaches first year BME PhD students about the limitations of summary statistics and the importance of visualizing your data! Intern Sender Juice
Dr. Fan and Caleb give invited talks at the Broad Institute Models, Inference, and Algorithms seminar series. Intern Sender Juice
Prof. Fan teaches Genomic Data Visualization again this semester! JEFworks Lab members give guest lectures in the Genomic Data Visualizations class. Intern Sender Juice
Vivien and Kalen presents their work at the WSE/DOM retreat. Thanks to Liz and Rafael for the photos. Intern Sender Juice
Dr. Fan gives an invited talk at the Center for Bioinformatics and Quantitative Biology at University of Illinois at Chicago. Intern Sender Juice
Vibe coding with SEraster and STcompare to compare spatial transcriptomics technologies Intern Sender Juice
RNA velocity in situ infers gene expression dynamics using spatial transcriptomics data Intern Sender Juice
Analyzing ICE Arrest Data - Part 2 Intern Sender Juice
Analyzing ICE Detention Data from 2021 to 2025 Intern Sender Juice
Creative Commons Attribution 4.0 International License Ekstern Sender Juice

SEO Nøgleord

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analysis spatial heterogeneity jean lab bioinformatics spatially fan data transcriptomics

Nøgleords balance

Nøgleord Indhold Titel Nøgleord Beskrivelse Overskrifter
fan 15
data 14
spatial 12
jean 10
transcriptomics 9

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