jef.works

Website beoordeling jef.works

JEFworks Lab - Welcome to the JEFworks Lab

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

SEO Keywords

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analysis jean lab data bioinformatics heterogeneity fan spatial transcriptomics spatially

Keywords Consistentie

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

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