jef.works

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JEFworks Lab - Welcome to the JEFworks Lab

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

SEO Keywords

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heterogeneity data lab bioinformatics jean fan spatial analysis spatially transcriptomics

Consistenza Keywords

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

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